1
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Dailey GP, Rabiola CA, Lei G, Wei J, Yang XY, Wang T, Liu CX, Gajda M, Hobeika AC, Summers A, Marek RD, Morse MA, Lyerly HK, Crosby EJ, Hartman ZC. Vaccines targeting ESR1 activating mutations elicit anti-tumor immune responses and suppress estrogen signaling in therapy resistant ER+ breast cancer. Hum Vaccin Immunother 2024; 20:2309693. [PMID: 38330990 PMCID: PMC10857653 DOI: 10.1080/21645515.2024.2309693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 01/19/2024] [Indexed: 02/10/2024] Open
Abstract
ER+ breast cancers (BC) are characterized by the elevated expression and signaling of estrogen receptor alpha (ESR1), which renders them sensitive to anti-endocrine therapy. While these therapies are clinically effective, prolonged treatment inevitably results in therapeutic resistance, which can occur through the emergence of gain-of-function mutations in ESR1. The central importance of ESR1 and development of mutated forms of ESR1 suggest that vaccines targeting these proteins could potentially be effective in preventing or treating endocrine resistance. To explore the potential of this approach, we developed several recombinant vaccines encoding different mutant forms of ESR1 (ESR1mut) and validated their ability to elicit ESR1-specific T cell responses. We then developed novel ESR1mut-expressing murine mammary cancer models to test the anti-tumor potential of ESR1mut vaccines. We found that these vaccines could suppress tumor growth, ESR1mut expression and estrogen signaling in vivo. To illustrate the applicability of these findings, we utilize HPLC to demonstrate the presentation of ESR1 and ESR1mut peptides on human ER+ BC cell MHC complexes. We then show the presence of human T cells reactive to ESR1mut epitopes in an ER+ BC patient. These findings support the development of ESR1mut vaccines, which we are testing in a Phase I clinical trial.
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Affiliation(s)
- Gabrielle P. Dailey
- Department of Surgery, Division of Surgical Sciences, Duke University, Durham, NC, USA
| | | | - Gangjun Lei
- Department of Surgery, Division of Surgical Sciences, Duke University, Durham, NC, USA
| | - Junping Wei
- Department of Surgery, Division of Surgical Sciences, Duke University, Durham, NC, USA
| | - Xiao-Yi Yang
- Department of Surgery, Division of Surgical Sciences, Duke University, Durham, NC, USA
| | - Tao Wang
- Department of Surgery, Division of Surgical Sciences, Duke University, Durham, NC, USA
| | - Cong-Xiao Liu
- Department of Surgery, Division of Surgical Sciences, Duke University, Durham, NC, USA
| | - Melissa Gajda
- Department of Surgery, Division of Surgical Sciences, Duke University, Durham, NC, USA
| | - Amy C. Hobeika
- Department of Surgery, Division of Surgical Sciences, Duke University, Durham, NC, USA
| | - Amanda Summers
- Department of Surgery, Division of Surgical Sciences, Duke University, Durham, NC, USA
| | - Robert D. Marek
- Department of Surgery, Division of Surgical Sciences, Duke University, Durham, NC, USA
| | | | - Herbert K. Lyerly
- Department of Surgery, Division of Surgical Sciences, Duke University, Durham, NC, USA
- Department of Pathology, Duke University, Durham, NC, USA
- Department of Integrative Immunobiology, Duke University, Durham, NC, USA
| | - Erika J. Crosby
- Department of Surgery, Division of Surgical Sciences, Duke University, Durham, NC, USA
- Department of Integrative Immunobiology, Duke University, Durham, NC, USA
| | - Zachary C. Hartman
- Department of Surgery, Division of Surgical Sciences, Duke University, Durham, NC, USA
- Department of Pathology, Duke University, Durham, NC, USA
- Department of Integrative Immunobiology, Duke University, Durham, NC, USA
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2
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Flender D, Vilenne F, Adams C, Boonen K, Valkenborg D, Baggerman G. Exploring the dynamic landscape of immunopeptidomics: Unravelling posttranslational modifications and navigating bioinformatics terrain. MASS SPECTROMETRY REVIEWS 2024. [PMID: 39152539 DOI: 10.1002/mas.21905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 07/30/2024] [Accepted: 08/01/2024] [Indexed: 08/19/2024]
Abstract
Immunopeptidomics is becoming an increasingly important field of study. The capability to identify immunopeptides with pivotal roles in the human immune system is essential to shift the current curative medicine towards personalized medicine. Throughout the years, the field has matured, giving insight into the current pitfalls. Nowadays, it is commonly accepted that generalizing shotgun proteomics workflows is malpractice because immunopeptidomics faces numerous challenges. While many of these difficulties have been addressed, the road towards the ideal workflow remains complicated. Although the presence of Posttranslational modifications (PTMs) in the immunopeptidome has been demonstrated, their identification remains highly challenging despite their significance for immunotherapies. The large number of unpredictable modifications in the immunopeptidome plays a pivotal role in the functionality and these challenges. This review provides a comprehensive overview of the current advancements in immunopeptidomics. We delve into the challenges associated with identifying PTMs within the immunopeptidome, aiming to address the current state of the field.
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Affiliation(s)
- Daniel Flender
- Centre for Proteomics, University of Antwerp, Antwerpen, Belgium
- Health Unit, VITO, Mol, Belgium
| | - Frédérique Vilenne
- Health Unit, VITO, Mol, Belgium
- Data Science Institute, University of Hasselt, Hasselt, Belgium
| | - Charlotte Adams
- Department of Computer Science, University of Antwerp, Antwerp, Belgium
| | - Kurt Boonen
- Centre for Proteomics, University of Antwerp, Antwerpen, Belgium
- ImmuneSpec, Niel, Belgium
| | - Dirk Valkenborg
- Data Science Institute, University of Hasselt, Hasselt, Belgium
| | - Geert Baggerman
- Department of Computer Science, University of Antwerp, Antwerp, Belgium
- ImmuneSpec, Niel, Belgium
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3
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Mog BJ, Marcou N, DiNapoli SR, Pearlman AH, Nichakawade TD, Hwang MS, Douglass J, Hsiue EHC, Glavaris S, Wright KM, Konig MF, Paul S, Wyhs N, Ge J, Miller MS, Azurmendi P, Watson E, Pardoll DM, Gabelli SB, Bettegowda C, Papadopoulos N, Kinzler KW, Vogelstein B, Zhou S. Preclinical studies show that Co-STARs combine the advantages of chimeric antigen and T cell receptors for the treatment of tumors with low antigen densities. Sci Transl Med 2024; 16:eadg7123. [PMID: 38985855 DOI: 10.1126/scitranslmed.adg7123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 04/01/2024] [Accepted: 06/13/2024] [Indexed: 07/12/2024]
Abstract
Two types of engineered T cells have been successfully used to treat patients with cancer, one with an antigen recognition domain derived from antibodies [chimeric antigen receptors (CARs)] and the other derived from T cell receptors (TCRs). CARs use high-affinity antigen-binding domains and costimulatory domains to induce T cell activation but can only react against target cells with relatively high amounts of antigen. TCRs have a much lower affinity for their antigens but can react against target cells displaying only a few antigen molecules. Here, we describe a new type of receptor, called a Co-STAR (for costimulatory synthetic TCR and antigen receptor), that combines aspects of both CARs and TCRs. In Co-STARs, the antigen-recognizing components of TCRs are replaced by high-affinity antibody fragments, and costimulation is provided by two modules that drive NF-κB signaling (MyD88 and CD40). Using a TCR-mimic antibody fragment that targets a recurrent p53 neoantigen presented in a common human leukocyte antigen (HLA) allele, we demonstrate that T cells equipped with Co-STARs can kill cancer cells bearing low densities of antigen better than T cells engineered with conventional CARs and patient-derived TCRs in vitro. In mouse models, we show that Co-STARs mediate more robust T cell expansion and more durable tumor regressions than TCRs similarly modified with MyD88 and CD40 costimulation. Our data suggest that Co-STARs may have utility for other peptide-HLA antigens in cancer and other targets where antigen density may limit the efficacy of engineered T cells.
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Affiliation(s)
- Brian J Mog
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Nikita Marcou
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Sarah R DiNapoli
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Alexander H Pearlman
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Tushar D Nichakawade
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Institute for NanoBioTechnology, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Michael S Hwang
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Jacqueline Douglass
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Emily Han-Chung Hsiue
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Stephanie Glavaris
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Katharine M Wright
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287, USA
| | - Maximilian F Konig
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Division of Rheumatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21224, USA
| | - Suman Paul
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Nicolas Wyhs
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Jiaxin Ge
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Michelle S Miller
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287, USA
| | - P Azurmendi
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287, USA
| | - Evangeline Watson
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Drew M Pardoll
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287, USA
| | - Sandra B Gabelli
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Chetan Bettegowda
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Nickolas Papadopoulos
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Kenneth W Kinzler
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287, USA
| | - Bert Vogelstein
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Shibin Zhou
- Ludwig Center, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Lustgarten Pancreatic Cancer Research Laboratory, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Bloomberg~Kimmel Institute for Cancer Immunotherapy, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287, USA
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4
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Vitale S, Calapà F, Colonna F, Luongo F, Biffoni M, De Maria R, Fiori ME. Advancements in 3D In Vitro Models for Colorectal Cancer. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2405084. [PMID: 38962943 DOI: 10.1002/advs.202405084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Indexed: 07/05/2024]
Abstract
The process of drug discovery and pre-clinical testing is currently inefficient, expensive, and time-consuming. Most importantly, the success rate is unsatisfactory, as only a small percentage of tested drugs are made available to oncological patients. This is largely due to the lack of reliable models that accurately predict drug efficacy and safety. Even animal models often fail to replicate human-specific pathologies and human body's complexity. These factors, along with ethical concerns regarding animal use, urge the development of suitable human-relevant, translational in vitro models.
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Affiliation(s)
- Sara Vitale
- Department of Oncology and Molecular Medicine (OMM), Istituto Superiore di Sanità, Viale Regina Elena 299, Rome, 00161, Italy
| | - Federica Calapà
- Dipartimento di Medicina e Chirurgia traslazionale, Università Cattolica del Sacro Cuore, Largo F. Vito 1, Rome, Italy
| | - Francesca Colonna
- Department of Oncology and Molecular Medicine (OMM), Istituto Superiore di Sanità, Viale Regina Elena 299, Rome, 00161, Italy
| | - Francesca Luongo
- Dipartimento di Medicina e Chirurgia traslazionale, Università Cattolica del Sacro Cuore, Largo F. Vito 1, Rome, Italy
| | - Mauro Biffoni
- Department of Oncology and Molecular Medicine (OMM), Istituto Superiore di Sanità, Viale Regina Elena 299, Rome, 00161, Italy
| | - Ruggero De Maria
- Dipartimento di Medicina e Chirurgia traslazionale, Università Cattolica del Sacro Cuore, Largo F. Vito 1, Rome, Italy
- Fondazione Policlinico Universitario "A. Gemelli" - IRCCS, Largo F. Vito 1, Rome, Italy
| | - Micol E Fiori
- Department of Oncology and Molecular Medicine (OMM), Istituto Superiore di Sanità, Viale Regina Elena 299, Rome, 00161, Italy
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5
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Du P, Fan R, Zhang N, Wu C, Zhang Y. Advances in Integrated Multi-omics Analysis for Drug-Target Identification. Biomolecules 2024; 14:692. [PMID: 38927095 PMCID: PMC11201992 DOI: 10.3390/biom14060692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Revised: 06/08/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024] Open
Abstract
As an essential component of modern drug discovery, the role of drug-target identification is growing increasingly prominent. Additionally, single-omics technologies have been widely utilized in the process of discovering drug targets. However, it is difficult for any single-omics level to clearly expound the causal connection between drugs and how they give rise to the emergence of complex phenotypes. With the progress of large-scale sequencing and the development of high-throughput technologies, the tendency in drug-target identification has shifted towards integrated multi-omics techniques, gradually replacing traditional single-omics techniques. Herein, this review centers on the recent advancements in the domain of integrated multi-omics techniques for target identification, highlights the common multi-omics analysis strategies, briefly summarizes the selection of multi-omics analysis tools, and explores the challenges of existing multi-omics analyses, as well as the applications of multi-omics technology in drug-target identification.
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Affiliation(s)
- Peiling Du
- School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China; (P.D.); (R.F.); (N.Z.); (C.W.)
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, China
| | - Rui Fan
- School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China; (P.D.); (R.F.); (N.Z.); (C.W.)
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, China
| | - Nana Zhang
- School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China; (P.D.); (R.F.); (N.Z.); (C.W.)
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, China
| | - Chenyuan Wu
- School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China; (P.D.); (R.F.); (N.Z.); (C.W.)
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, China
| | - Yingqian Zhang
- School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China; (P.D.); (R.F.); (N.Z.); (C.W.)
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, China
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6
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Little JS, Kampouri E, Friedman DZ, McCarty T, Thompson GR, Kontoyiannis DP, Vazquez J, Baddley JW, Hammond SP. The Burden of Invasive Fungal Disease Following Chimeric Antigen Receptor T-Cell Therapy and Strategies for Prevention. Open Forum Infect Dis 2024; 11:ofae133. [PMID: 38887472 PMCID: PMC11181190 DOI: 10.1093/ofid/ofae133] [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: 12/01/2023] [Accepted: 03/05/2024] [Indexed: 06/20/2024] Open
Abstract
Chimeric antigen receptor (CAR) T-cell therapy is a novel immunotherapy approved for the treatment of hematologic malignancies. This therapy leads to a variety of immunologic deficits that could place patients at risk for invasive fungal disease (IFD). Studies assessing IFD in this setting are limited by inconsistent definitions and heterogeneity in prophylaxis use, although the incidence of IFD after CAR T-cell therapy, particularly for lymphoma and myeloma, appears to be low. This review evaluates the incidence of IFD after CAR T-cell therapy, and discusses optimal approaches to prevention, highlighting areas that require further study as well as future applications of cellular therapy that may impact IFD risk. As the use of CAR T-cell therapy continues to expand for hematologic malignancies, solid tumors, and most recently to include non-oncologic diseases, understanding the risk for IFD in this uniquely immunosuppressed population is imperative to prevent morbidity and mortality.
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Affiliation(s)
- Jessica S Little
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- Division of Infectious Diseases, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Eleftheria Kampouri
- Infectious Diseases Service, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Daniel Z Friedman
- Section of Infectious Diseases and Global Health, The University of Chicago, Chicago, Illinois, USA
| | - Todd McCarty
- Division of Infectious Diseases, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - George R Thompson
- Division of Infectious Diseases, University of California-Davis, Sacramento, California, USA
| | - Dimitrios P Kontoyiannis
- Department of Infectious Diseases, Infection Control and Employee Health, The University of Texas, M.D. Anderson Cancer Center, Houston, Texas, USA
| | - Jose Vazquez
- Division of Infectious Diseases, Medical College of Georgia/Augusta University, Augusta, Georgia, USA
| | - John W Baddley
- Division of Infectious Diseases, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Sarah P Hammond
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Medical Oncology, Massachusetts General Hospital Cancer Center, Boston, Massachusetts, USA
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7
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Kim SH, Lee BR, Kim SM, Kim S, Kim MS, Kim J, Lee I, Kim HS, Nam GH, Kim IS, Song K, Choi Y, Lee DS, Park WY. The identification of effective tumor-suppressing neoantigens using a tumor-reactive TIL TCR-pMHC ternary complex. Exp Mol Med 2024; 56:1461-1471. [PMID: 38866910 PMCID: PMC11263684 DOI: 10.1038/s12276-024-01259-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 03/14/2024] [Indexed: 06/14/2024] Open
Abstract
Neoantigens are ideal targets for cancer immunotherapy because they are expressed de novo in tumor tissue but not in healthy tissue and are therefore recognized as foreign by the immune system. Advances in next-generation sequencing and bioinformatics technologies have enabled the quick identification and prediction of tumor-specific neoantigens; however, only a small fraction of predicted neoantigens are immunogenic. To improve the predictability of immunogenic neoantigens, we developed the in silico neoantigen prediction workflows VACINUSpMHC and VACINUSTCR: VACINUSpMHC incorporates physical binding between peptides and MHCs (pMHCs), and VACINUSTCR integrates T cell reactivity to the pMHC complex through deep learning-based pairing with T cell receptors (TCRs) of putative tumor-reactive CD8 tumor-infiltrating lymphocytes (TILs). We then validated our neoantigen prediction workflows both in vitro and in vivo in patients with hepatocellular carcinoma (HCC) and in a B16F10 mouse melanoma model. The predictive abilities of VACINUSpMHC and VACINUSTCR were confirmed in a validation cohort of 8 patients with HCC. Of a total of 118 neoantigen candidates predicted by VACINUSpMHC, 48 peptides were ultimately selected using VACINUSTCR. In vitro validation revealed that among the 48 predicted neoantigen candidates, 13 peptides were immunogenic. Assessment of the antitumor efficacy of the candidate neoepitopes using a VACINUSTCR in vivo mouse model suggested that vaccination with the predicted neoepitopes induced neoantigen-specific T cell responses and enabled the trafficking of neoantigen-specific CD8 + T cell clones into the tumor tissue, leading to tumor suppression. This study showed that the prediction of immunogenic neoantigens can be improved by integrating a tumor-reactive TIL TCR-pMHC ternary complex.
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MESH Headings
- Antigens, Neoplasm/immunology
- Animals
- Humans
- Lymphocytes, Tumor-Infiltrating/immunology
- Lymphocytes, Tumor-Infiltrating/metabolism
- Mice
- Receptors, Antigen, T-Cell/immunology
- Receptors, Antigen, T-Cell/metabolism
- Cell Line, Tumor
- Melanoma, Experimental/immunology
- Melanoma, Experimental/therapy
- Major Histocompatibility Complex/immunology
- Liver Neoplasms/immunology
- Liver Neoplasms/therapy
- Carcinoma, Hepatocellular/immunology
- Carcinoma, Hepatocellular/therapy
- CD8-Positive T-Lymphocytes/immunology
- Female
- Immunotherapy/methods
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Affiliation(s)
| | | | | | | | | | - Jaehyun Kim
- Department of Research and Development, SHIFTBIO Inc., Seoul, 02751, Korea
| | - Inkyu Lee
- Department of Research and Development, SHIFTBIO Inc., Seoul, 02751, Korea
- KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul, 02841, Korea
| | | | - Gi-Hoon Nam
- Department of Research and Development, SHIFTBIO Inc., Seoul, 02751, Korea
- Department of Biochemistry and Molecular Biology, Korea University College of Medicine, Seoul, 02841, Korea
| | - In-San Kim
- KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul, 02841, Korea
- Chemical & Biological Integrative Research Center, Biomedical Research Division, Korea Institute of Science and Technology (KIST), Seoul, 02792, Korea
| | | | - Yoonjoo Choi
- Combinatorial Tumor Immunotherapy MRC, Chonnam National University Medical School, Hwasun-gun, Jeollanam-do, 58128, Korea.
| | - Dong-Sup Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Korea.
| | - Woong-Yang Park
- Geninus Inc., Seoul, 05836, Korea.
- Department of Health Science and Technology, Samsung Advanced Institute of Health Science and Technology, Sungkyunkwan University, Seoul, Korea.
- Samsung Genome Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.
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8
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Wu Y, Yu S, de Lázaro I. Advances in lipid nanoparticle mRNA therapeutics beyond COVID-19 vaccines. NANOSCALE 2024; 16:6820-6836. [PMID: 38502114 DOI: 10.1039/d4nr00019f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
The remarkable success of two lipid nanoparticle-mRNA vaccines against coronavirus disease (COVID-19) has placed the therapeutic and prophylactic potential of messenger RNA (mRNA) in the spotlight. It has also drawn attention to the indispensable role of lipid nanoparticles in enabling the effects of this nucleic acid. To date, lipid nanoparticles are the most clinically advanced non-viral platforms for mRNA delivery. This is thanks to their favorable safety profile and efficiency in protecting the nucleic acid from degradation and allowing its cellular uptake and cytoplasmic release upon endosomal escape. Moreover, the development of lipid nanoparticle-mRNA therapeutics was already a very active area of research even before the COVID-19 pandemic, which has likely only begun to bear its fruits. In this Review, we first discuss key aspects of the development of lipid nanoparticles as mRNA carriers. We then highlight promising preclinical and clinical studies involving lipid nanoparticle-mRNA formulations against infectious diseases and cancer, and to enable protein replacement or supplementation and genome editing. Finally, we elaborate on the challenges in advancing lipid nanoparticle-mRNA technology to widespread therapeutic use.
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Affiliation(s)
- Yeung Wu
- Department of Biomedical Engineering, NYU Tandon School of Engineering, New York University, USA.
| | - Sinuo Yu
- Department of Biomedical Engineering, NYU Tandon School of Engineering, New York University, USA.
| | - Irene de Lázaro
- Department of Biomedical Engineering, NYU Tandon School of Engineering, New York University, USA.
- Cardiovascular Research Center, Division of Cardiology, Department of Medicine, NYU Grossman School of Medicine, New York University, USA
- Harvard John A. Paulson School of Engineering and Applied Science, Harvard University, USA
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9
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Fang CH, Cheng WF, Cheng YF, Lan KL, Lee JM. Characterization of tumoricidal activities mediated by a novel immune cell regimen composing interferon-producing killer dendritic cells and tumor-specific cytotoxic T lymphocytes. BMC Cancer 2024; 24:395. [PMID: 38549061 PMCID: PMC10979599 DOI: 10.1186/s12885-024-12101-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 03/09/2024] [Indexed: 04/01/2024] Open
Abstract
BACKGROUND Although immune cell therapy has long been used for treating solid cancer, its efficacy remains limited. Interferon (IFN)-producing killer dendritic cells (IKDCs) exhibit cytotoxicity and present antigens to relevant cells; thus, they can selectively induce tumor-associated antigen (TAA)-specific CD8 T cells and may be useful in cancer treatment. Various protocols have been used to amplify human IKDCs from peripheral sources, but the complexity of the process has prevented their widespread clinical application. Additionally, the induction of TAA-specific CD8 T cells through the adoptive transfer of IKDCs to immunocompromised patients with cancer may be insufficient. Therefore, we developed a method for generating an immune cell-based regimen, Phyduxon-T, comprising a human IKDC counterpart (Phyduxon) and expanded TAA-specific CD8 T cells. METHODS Peripheral blood mononuclear cells from ovarian cancer patients were cultured with human interleukin (hIL)-15, hIL-12, and hIL-18 to generate Phyduxon-T. Then, its phenotype, cytotoxicity, and antigen-presenting function were evaluated through flow cytometry using specific monoclonal antibodies. RESULTS Phyduxon exhibited the characteristics of both natural killer and dendritic cells. This regimen also exhibited cytotoxicity against primary ovarian cancer cells and presented TAAs, thereby inducing TAA-specific CD8 T cells, as evidenced by the expression of 4-1BB and IFN-γ. Notably, the Phyduxon-T manufacturing protocol effectively expanded IFN-γ-producing 4-1BB+ TAA-specific CD8 T cells from peripheral sources; these cells exhibited cytotoxic activities against ovarian cancer cells. CONCLUSIONS Phyduxon-T, which is a combination of natural killer cells, dendritic cells, and TAA-specific CD8 T cells, may enhance the efficacy of cancer immunotherapy.
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Affiliation(s)
- Chih-Hao Fang
- Biomedical Industry Ph.D. Program, College of Life Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan
- FullHope Biomedical Co.,Ltd, 10F., No. 10, Ln. 609, Sec. 5, Chongxin Rd., Sanchong Dist., New Taipei City, 241405, Taiwan
| | - Wen-Fang Cheng
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
- Department of Obstetrics and Gynecology, College of Medicine, National Taiwan University, Taipei, Taiwan
- Graduate Institute of Oncology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Ya-Fang Cheng
- FullHope Biomedical Co.,Ltd, 10F., No. 10, Ln. 609, Sec. 5, Chongxin Rd., Sanchong Dist., New Taipei City, 241405, Taiwan
| | - Keng-Li Lan
- Department of Heavy Particles & Radiation Oncology, Taipei Veterans General Hospital, Taipei, Taiwan.
- Institute of Traditional Medicine, School of Medicine, National Yang Ming Chiao Tung University, No. 155, Sec. 2, Linong St. Beitou Dist., Taipei City, 112304, Taiwan.
| | - Jan-Mou Lee
- FullHope Biomedical Co.,Ltd, 10F., No. 10, Ln. 609, Sec. 5, Chongxin Rd., Sanchong Dist., New Taipei City, 241405, Taiwan.
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10
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Kirk AM, Crawford JC, Chou CH, Guy C, Pandey K, Kozlik T, Shah RK, Chung S, Nguyen P, Zhang X, Wang J, Bell M, Mettelman RC, Allen EK, Pogorelyy MV, Kim H, Minervina AA, Awad W, Bajracharya R, White T, Long D, Gordon B, Morrison M, Glazer ES, Murphy AJ, Jiang Y, Fitzpatrick EA, Yarchoan M, Sethupathy P, Croft NP, Purcell AW, Federico SM, Stewart E, Gottschalk S, Zamora AE, DeRenzo C, Strome SE, Thomas PG. DNAJB1-PRKACA fusion neoantigens elicit rare endogenous T cell responses that potentiate cell therapy for fibrolamellar carcinoma. Cell Rep Med 2024; 5:101469. [PMID: 38508137 PMCID: PMC10983114 DOI: 10.1016/j.xcrm.2024.101469] [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: 08/23/2023] [Revised: 11/29/2023] [Accepted: 02/20/2024] [Indexed: 03/22/2024]
Abstract
Fibrolamellar carcinoma (FLC) is a liver tumor with a high mortality burden and few treatment options. A promising therapeutic vulnerability in FLC is its driver mutation, a conserved DNAJB1-PRKACA gene fusion that could be an ideal target neoantigen for immunotherapy. In this study, we aim to define endogenous CD8 T cell responses to this fusion in FLC patients and evaluate fusion-specific T cell receptors (TCRs) for use in cellular immunotherapies. We observe that fusion-specific CD8 T cells are rare and that FLC patient TCR repertoires lack large clusters of related TCR sequences characteristic of potent antigen-specific responses, potentially explaining why endogenous immune responses are insufficient to clear FLC tumors. Nevertheless, we define two functional fusion-specific TCRs, one of which has strong anti-tumor activity in vivo. Together, our results provide insights into the fragmented nature of neoantigen-specific repertoires in humans and indicate routes for clinical development of successful immunotherapies for FLC.
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Affiliation(s)
- Allison M Kirk
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Jeremy Chase Crawford
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Ching-Heng Chou
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Cliff Guy
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Kirti Pandey
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Melbourne, VIC 3800, Australia
| | - Tanya Kozlik
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Ravi K Shah
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Shanzou Chung
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Melbourne, VIC 3800, Australia
| | - Phuong Nguyen
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Xiaoyu Zhang
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Jin Wang
- Department of Microbiology, Immunology, and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Matthew Bell
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Robert C Mettelman
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - E Kaitlynn Allen
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Mikhail V Pogorelyy
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Hyunjin Kim
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Anastasia A Minervina
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Walid Awad
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Resha Bajracharya
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Toni White
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Donald Long
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14850, USA
| | - Brittney Gordon
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Michelle Morrison
- Center for Cancer Research, College of Medicine, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Evan S Glazer
- Center for Cancer Research, College of Medicine, The University of Tennessee Health Science Center, Memphis, TN 38163, USA; Department of Surgery, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Andrew J Murphy
- Department of Surgery, The University of Tennessee Health Science Center, Memphis, TN 38163, USA; Department of Surgery, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Yixing Jiang
- Department of Medical Oncology, Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Elizabeth A Fitzpatrick
- Department of Microbiology, Immunology, and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Mark Yarchoan
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Praveen Sethupathy
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14850, USA
| | - Nathan P Croft
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Melbourne, VIC 3800, Australia
| | - Anthony W Purcell
- Department of Biochemistry and Molecular Biology and Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Melbourne, VIC 3800, Australia
| | - Sara M Federico
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Elizabeth Stewart
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Stephen Gottschalk
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Anthony E Zamora
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Christopher DeRenzo
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Scott E Strome
- College of Medicine, The University of Tennessee Health Science Center, Memphis, TN 38163, USA.
| | - Paul G Thomas
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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11
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Xiang N, Zhang K, Zhao Y, Xu C, Zhang X, Meng S. Characterization of antigen presentation capability for neoantigen-based products using targeted LC-MS/MS method. J Pharm Biomed Anal 2024; 240:115886. [PMID: 38184916 DOI: 10.1016/j.jpba.2023.115886] [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: 09/27/2023] [Revised: 11/15/2023] [Accepted: 11/26/2023] [Indexed: 01/09/2024]
Abstract
The generation of an immune response in neoantigen-based products relies on antigen presentation, which is closely analyzed by bioassays for T-cell functions such as tetramer or cytokine release. Mass spectrometry (MS) has the potential to directly assess the antigen-presenting capability of antigen-presenting cells (APCs), offering advantages such as speed, multi-target analysis, robustness, and ease of transferability. However, it has not been used for quality control of these products due to challenges in sensitivity, including the number of cells and peptide diversity. In this study, we describe the development and validation of an improved targeted LC-MS/MS method with high sensitivity for characterizing antigen presentation, which could be applied in the quality control of neoantigen-based products. The parameters for the extraction were carefully optimized by different short peptides. Highly sensitive targeted triple quadrupole mass spectrometry combined with ultra-high performance liquid chromatography (UHPLC) was employed using a selective ion monitoring mode (Multiple Reaction Monitoring, MRM). Besides, we successfully implemented robust quality control peptides to ensure the reliability and consistency of this method, which proved invaluable for different APCs. With reference to the guidelines from ICH Q2 (R2), M10, as well as considering the specific attributes of the product itself, we validated the method for selectivity, specificity, sensitivity, limit of detection (LOD), recovery rate, matrix effect, repeatability, and application in dendritic cells (DCs) associated with neoantigen-based products. The validation process yields satisfactory results. Combining this approach with T cell assays will comprehensively assess cell product quality attributes from physicochemical and biological perspectives.
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Affiliation(s)
- Nan Xiang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; The Cell Collection and Research Center, National Institutes for Food and Drug Control, No. 31 Huatuo St., Daxing District, Beijing, China
| | - Kehua Zhang
- The Cell Collection and Research Center, National Institutes for Food and Drug Control, No. 31 Huatuo St., Daxing District, Beijing, China
| | - Yinghua Zhao
- SCIEX China, 5F, Building 1, No. 24 Jiuxianqiao Middle Road, Chaoyang District, Beijing, China
| | - Chongfeng Xu
- The Cell Collection and Research Center, National Institutes for Food and Drug Control, No. 31 Huatuo St., Daxing District, Beijing, China
| | - Xiuqing Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Shufang Meng
- The Cell Collection and Research Center, National Institutes for Food and Drug Control, No. 31 Huatuo St., Daxing District, Beijing, China.
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12
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Wang F, Zhang Z, Mao M, Yang Y, Xu P, Lu S. COSMIC-based mutation database enhances identification efficiency of HLA-I immunopeptidome. J Transl Med 2024; 22:144. [PMID: 38336780 PMCID: PMC10858511 DOI: 10.1186/s12967-023-04821-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 12/20/2023] [Indexed: 02/12/2024] Open
Abstract
BACKGROUND Neoantigens have emerged as a promising area of focus in tumor immunotherapy, with several established strategies aiming to enhance their identification. Human leukocyte antigen class I molecules (HLA-I), which present intracellular immunopeptides to T cells, provide an ideal source for identifying neoantigens. However, solely relying on a mutation database generated through commonly used whole exome sequencing (WES) for the identification of HLA-I immunopeptides, may result in potential neoantigens being missed due to limitations in sequencing depth and sample quality. METHOD In this study, we constructed and evaluated an extended database for neoantigen identification, based on COSMIC mutation database. This study utilized mass spectrometry-based proteogenomic profiling to identify the HLA-I immunopeptidome enriched from HepG2 cell. HepG2 WES-based and the COSMIC-based mutation database were generated and utilized to identify HepG2-specific mutant immunopeptides. RESULT The results demonstrated that COSMIC-based database identified 5 immunopeptides compared to only 1 mutant peptide identified by HepG2 WES-based database, indicating its effectiveness in identifying mutant immunopeptides. Furthermore, HLA-I affinity of the mutant immunopeptides was evaluated through NetMHCpan and peptide-docking modeling to validate their binding to HLA-I molecules, demonstrating the potential of mutant peptides identified by the COSMIC-based database as neoantigens. CONCLUSION Utilizing the COSMIC-based mutation database is a more efficient strategy for identifying mutant peptides from HLA-I immunopeptidome without significantly increasing the false positive rate. HepG2 specific WES-based database may exclude certain mutant peptides due to WES sequencing depth or sample heterogeneity. The COSMIC-based database can effectively uncover potential neoantigens within the HLA-I immunopeptidomes.
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Affiliation(s)
- Fangzhou Wang
- Medical School of Chinese People's Liberation Army (PLA), Faculty of Hepato-Pancreato-Biliary Surgery, Chinese PLA General Hospital, Institute of Hepatobiliary Surgery of Chinese PLA, Key Laboratory of Digital Hepatobiliary Surgery PLA, 28 Fuxing Road, Haidian District, Beijing, 100853, China
| | - Zhenpeng Zhang
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Research Unit of Proteomics and Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Proteome Research Center, Institute of Lifeomics, 38 Life Science Park Road, Changping District, Beijing, 102206, China
| | - Mingsong Mao
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Research Unit of Proteomics and Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Proteome Research Center, Institute of Lifeomics, 38 Life Science Park Road, Changping District, Beijing, 102206, China
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Yudai Yang
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Research Unit of Proteomics and Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Proteome Research Center, Institute of Lifeomics, 38 Life Science Park Road, Changping District, Beijing, 102206, China
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Ping Xu
- State Key Laboratory of Proteomics, National Center for Protein Sciences (Beijing), Research Unit of Proteomics and Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Proteome Research Center, Institute of Lifeomics, 38 Life Science Park Road, Changping District, Beijing, 102206, China.
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China.
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
- School of Medicine, Guizhou University, Guiyang, China.
| | - Shichun Lu
- Medical School of Chinese People's Liberation Army (PLA), Faculty of Hepato-Pancreato-Biliary Surgery, Chinese PLA General Hospital, Institute of Hepatobiliary Surgery of Chinese PLA, Key Laboratory of Digital Hepatobiliary Surgery PLA, 28 Fuxing Road, Haidian District, Beijing, 100853, China.
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13
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Wang S, Mu X, Wang X, Chen L, Lu C, Song L. Peripheral Blood CD8 + CD28 + T Cells as an Independent Predictor of Treatment Response and Survival After Concurrent Chemoradiotherapy in Pediatric High-Grade Glioma Patients. Clin Med Insights Oncol 2024; 18:11795549241227421. [PMID: 38322666 PMCID: PMC10845990 DOI: 10.1177/11795549241227421] [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: 05/11/2023] [Accepted: 01/01/2024] [Indexed: 02/08/2024] Open
Abstract
Backgroud The tumor immune microenvironment influences the efficiency of concurrent chemoradiotherapy (CCRT) in high-grade glioma (HGG). This study investigated peripheral blood T lymphocyte subsets as clinical indicators of therapeutic response and prognosis in pediatric high-grade glioma (pHGG). Methods This retrospective study included 77 patients with postoperative pHGG who were treated concurrently with temozolomide and external beam radiotherapy between January 1, 2012, and December 31, 2018. The median follow-up was 26 (range: 5-106) months. Peripheral venous blood samples were collected before and after CCRT. The proportions of peripheral blood T lymphocytes and their association with treatment outcome and survival were determined. Results Sixty-four (83.1%) patients achieved complete remission, partial remission, and stable disease, and 13 (16.9%) patients had progressive disease. Higher CD3+ T cell, CD4+ T cell, and CD8+ CD28+ T cell ratios were predictive of better response, while a higher CD8+ CD28- T cell ratio was predictive of poorer response. Binary logistic regression analysis showed that the CD8+ CD28+ T cell ratio was a significant independent predictor of CCRT response (odds ratio [OR] = 53.521, 95% confidence interval [CI] = 4.294-667.119, P = .002). Univariate and multivariate analysis of prognostic factors associated with survival showed that the CD8+ CD28+ T lymphocyte ratio was a significant independent predictor of progression-free survival (hazard ratio [HR] = 1.80, 95% CI = 1.06-3.08, P = .03), but none of the subsets were significantly associated with overall survival. Conclusion Peripheral blood T lymphocytes have potential as predictors of CCRT response and prognosis in pHGG.
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Affiliation(s)
- Shuo Wang
- Department of Medical Oncology, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Xiaofeng Mu
- Department of Radiotherapy, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Xiaoli Wang
- Department of Medical Oncology, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Li Chen
- Department of Radiotherapy, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Changyu Lu
- Department of Neurosurgery, Peking University International Hospital, Beijing, China
| | - Linan Song
- Department of Radiotherapy, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
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14
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Gu Z, Wu Q, Shang B, Zhang K, Zhang W. Organoid co-culture models of the tumor microenvironment promote precision medicine. CANCER INNOVATION 2024; 3:e101. [PMID: 38948532 PMCID: PMC11212345 DOI: 10.1002/cai2.101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 09/11/2023] [Accepted: 09/13/2023] [Indexed: 07/02/2024]
Abstract
In recent years, the three-dimensional (3D) culture system has emerged as a promising preclinical model for tumor research owing to its ability to replicate the tissue structure and molecular characteristics of solid tumors in vivo. This system offers several advantages, including high throughput, efficiency, and retention of tumor heterogeneity. Traditional Matrigel-submerged organoid cultures primarily support the long-term proliferation of epithelial cells. One solution for the exploration of the tumor microenvironment is a reconstitution approach involving the introduction of exogenous cell types, either in dual, triple or even multiple combinations. Another solution is a holistic approach including patient-derived tumor fragments, air-liquid interface, suspension 3D culture, and microfluidic tumor-on-chip models. Organoid co-culture models have also gained popularity for studying the tumor microenvironment, evaluating tumor immunotherapy, identifying predictive biomarkers, screening for effective drugs, and modeling infections. By leveraging these 3D culture systems, it is hoped to advance the clinical application of therapeutic approaches and improve patient outcomes.
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Affiliation(s)
- Zhaoru Gu
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center, National Clinical Research Center for Cancer, Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Quanyou Wu
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center, National Clinical Research Center for Cancer, Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Bingqing Shang
- Department of Urology, National Cancer Center, National Clinical Research Center for Cancer, Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Kaitai Zhang
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center, National Clinical Research Center for Cancer, Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Wen Zhang
- Department of Immunology, National Cancer Center, National Clinical Research Center for Cancer, Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
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15
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Katopodi T, Petanidis S, Anestakis D, Charalampidis C, Chatziprodromidou I, Floros G, Eskitzis P, Zarogoulidis P, Koulouris C, Sevva C, Papadopoulos K, Dagher M, Karakousis VA, Varsamis N, Theodorou V, Mystakidou CM, Vlassopoulos K, Kosmidis S, Katsios NI, Farmakis K, Kosmidis C. Tumor cell metabolic reprogramming and hypoxic immunosuppression: driving carcinogenesis to metastatic colonization. Front Immunol 2024; 14:1325360. [PMID: 38292487 PMCID: PMC10824957 DOI: 10.3389/fimmu.2023.1325360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Accepted: 12/27/2023] [Indexed: 02/01/2024] Open
Abstract
A significant factor in the antitumor immune response is the increased metabolic reprogramming of immunological and malignant cells. Increasing data points to the fact that cancer metabolism affects not just cancer signaling, which is essential for maintaining carcinogenesis and survival, but also the expression of immune cells and immune-related factors such as lactate, PGE2, arginine, IDO, which regulate the antitumor immune signaling mechanism. In reality, this energetic interaction between the immune system and the tumor results in metabolic competition in the tumor ecosystem, limiting the amount of nutrients available and causing microenvironmental acidosis, which impairs the ability of immune cells to operate. More intriguingly, different types of immune cells use metabolic reprogramming to keep the body and self in a state of homeostasis. The process of immune cell proliferation, differentiation, and performance of effector functions, which is crucial to the immune response, are currently being linked to metabolic reprogramming. Here, we cover the regulation of the antitumor immune response by metabolic reprogramming in cancer cells and immune cells as well as potential strategies for metabolic pathway targeting in the context of anticancer immunotherapy. We also discuss prospective immunotherapy-metabolic intervention combinations that might be utilized to maximize the effectiveness of current immunotherapy regimes.
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Affiliation(s)
- Theodora Katopodi
- Department of Medicine, Laboratory of Medical Biology and Genetics, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Savvas Petanidis
- Department of Medicine, Laboratory of Medical Biology and Genetics, Aristotle University of Thessaloniki, Thessaloniki, Greece
- Department of Pulmonology, I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Doxakis Anestakis
- Department of Anatomy, Medical School, University of Cyprus, Nicosia, Cyprus
| | | | | | - George Floros
- Department of Electrical and Computer Engineering, University of Thessaly, Volos, Greece
| | | | - Paul Zarogoulidis
- Third Department of Surgery, “AHEPA” University Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Charilaos Koulouris
- Third Department of Surgery, “AHEPA” University Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Christina Sevva
- Third Department of Surgery, “AHEPA” University Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Konstantinos Papadopoulos
- Third Department of Surgery, “AHEPA” University Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Marios Dagher
- Third Department of Surgery, “AHEPA” University Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | | | - Nikolaos Varsamis
- Department of Surgery, Interbalkan Medical Center, Thessaloniki, Greece
| | - Vasiliki Theodorou
- Department of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Chrysi Maria Mystakidou
- Department of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Konstantinos Vlassopoulos
- Department of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Stylianos Kosmidis
- Department of Medicine, Medical University of Plovdiv, Plovdiv, Bulgaria
| | | | - Konstantinos Farmakis
- Pediatric Surgery Clinic, General Hospital of Thessaloniki “G. Gennimatas”, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Christoforos Kosmidis
- Third Department of Surgery, “AHEPA” University Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
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16
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Zhang S, Song D, Yu W, Li J, Wang X, Li Y, Zhao Z, Xue Q, Zhao J, Li JP, Guo Z. Combining cisplatin and a STING agonist into one molecule for metalloimmunotherapy of cancer. Natl Sci Rev 2024; 11:nwae020. [PMID: 38332843 PMCID: PMC10852989 DOI: 10.1093/nsr/nwae020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 11/06/2023] [Accepted: 12/04/2023] [Indexed: 02/10/2024] Open
Abstract
Mounting evidence suggests that strategies combining DNA-damaging agents and stimulator of interferon genes (STING) agonists are promising cancer therapeutic regimens because they can amplify STING activation and remodel the immunosuppressive tumor microenvironment. However, a single molecular entity comprising both agents has not yet been developed. Herein, we designed two PtIV-MSA-2 conjugates (I and II) containing the DNA-damaging chemotherapeutic drug cisplatin and the innate immune-activating STING agonist MSA-2; these conjugates showed great potential as multispecific small-molecule drugs against pancreatic cancer. Mechanistic studies revealed that conjugate I upregulated the expression of transcripts associated with innate immunity and metabolism in cancer cells, significantly differing from cisplatin and MSA-2. An analysis of the tumor microenvironment demonstrated that conjugate I could enhance the infiltration of natural killer (NK) cells into tumors and promote the activation of T cells, NK cells and dendritic cells in tumor tissues. These findings indicated that conjugate I, which was created by incorporating a Pt chemotherapeutic drug and STING agonist into one molecule, is a promising and potent anticancer drug candidate, opening new avenues for small-molecule-based cancer metalloimmunotherapy.
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Affiliation(s)
- Shuren Zhang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Dongfan Song
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Wenhao Yu
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Ji Li
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Xiaoyu Wang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Yachao Li
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Zihan Zhao
- Department of Urology, Affiliated Drum Tower Hospital, Medical School, Nanjing University, Nanjing 210023, China
| | - Qi Xue
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Jing Zhao
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
- Nanchuang (Jiangsu) Institute of Chemistry and Health, Nanjing 210023, China
| | - Jie P Li
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Zijian Guo
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
- Nanchuang (Jiangsu) Institute of Chemistry and Health, Nanjing 210023, China
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17
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Faghfuri E. Recent advances in personalized cancer immunotherapy with immune checkpoint inhibitors, T cells and vaccines. Per Med 2024; 21:45-57. [PMID: 38088165 DOI: 10.2217/pme-2023-0054] [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: 01/06/2024]
Abstract
The results of genomic and molecular profiling of cancer patients can be effectively applied to immunotherapy agents, including immune checkpoint inhibitors, to select the most appropriate treatment. In addition, accurate prediction of neoantigens facilitates the development of individualized cancer vaccines and T-cell therapy. This review summarizes the biomarker(s) predicting responses to immune checkpoint inhibitors and focuses on current strategies to identify and isolate neoantigen-reactive T cells as well as the clinical development of neoantigen-based therapeutics. The results suggest that maximal T-cell stimulation and expansion can be achieved with combination therapies that enhance antigen-presenting cells' function and optimal T-cell priming in lymph nodes.
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Affiliation(s)
- Elnaz Faghfuri
- Digestive Disease Research Center, Ardabil University of Medical Sciences, Ardabil, 5613658115, Iran
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18
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Addala V, Newell F, Pearson JV, Redwood A, Robinson BW, Creaney J, Waddell N. Computational immunogenomic approaches to predict response to cancer immunotherapies. Nat Rev Clin Oncol 2024; 21:28-46. [PMID: 37907723 DOI: 10.1038/s41571-023-00830-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/03/2023] [Indexed: 11/02/2023]
Abstract
Cancer immunogenomics is an emerging field that bridges genomics and immunology. The establishment of large-scale genomic collaborative efforts along with the development of new single-cell transcriptomic techniques and multi-omics approaches have enabled characterization of the mutational and transcriptional profiles of many cancer types and helped to identify clinically actionable alterations as well as predictive and prognostic biomarkers. Researchers have developed computational approaches and machine learning algorithms to accurately obtain clinically useful information from genomic and transcriptomic sequencing data from bulk tissue or single cells and explore tumours and their microenvironment. The rapid growth in sequencing and computational approaches has resulted in the unmet need to understand their true potential and limitations in enabling improvements in the management of patients with cancer who are receiving immunotherapies. In this Review, we describe the computational approaches currently available to analyse bulk tissue and single-cell sequencing data from cancer, stromal and immune cells, as well as how best to select the most appropriate tool to address various clinical questions and, ultimately, improve patient outcomes.
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Affiliation(s)
- Venkateswar Addala
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia.
| | - Felicity Newell
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - John V Pearson
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Alec Redwood
- National Centre for Asbestos Related Diseases, University of Western Australia, Perth, Western Australia, Australia
- Institute of Respiratory Health, Perth, Western Australia, Australia
- School of Biomedical Science, University of Western Australia, Perth, Western Australia, Australia
| | - Bruce W Robinson
- National Centre for Asbestos Related Diseases, University of Western Australia, Perth, Western Australia, Australia
- Institute of Respiratory Health, Perth, Western Australia, Australia
- Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Perth, Western Australia, Australia
- Medical School, University of Western Australia, Perth, Western Australia, Australia
| | - Jenette Creaney
- National Centre for Asbestos Related Diseases, University of Western Australia, Perth, Western Australia, Australia
- Institute of Respiratory Health, Perth, Western Australia, Australia
- School of Biomedical Science, University of Western Australia, Perth, Western Australia, Australia
- Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Perth, Western Australia, Australia
| | - Nicola Waddell
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.
- Faculty of Medicine, The University of Queensland, Brisbane, Queensland, Australia.
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19
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Wang L, Zhou Y, Cui H, Zhuang X, Cheng C, Weng Y, Liu H, Wang S, Pan X, Cui Y, Zhang W. IGH repertoire analysis at scale: deciphering the complexity of B cell infiltration and migration in esophageal squamous cell carcinoma. Cancer Gene Ther 2024; 31:131-147. [PMID: 37985722 DOI: 10.1038/s41417-023-00689-w] [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: 08/01/2023] [Revised: 10/10/2023] [Accepted: 11/02/2023] [Indexed: 11/22/2023]
Abstract
Tumor-infiltrating B-lineage cells have become predictors of prognosis and immunotherapy responses in various cancers. However, limited knowledge about their infiltration and migration patterns has hindered the understanding of their anti-tumor functions. Here, we examined the immunoglobulin heavy chain (IGH) repertoires in 496 multi-regional tumor, 107 normal tissue, and 48 metastatic lymph node samples obtained from 107 patients with esophageal squamous cell carcinoma (ESCC). Our study revealed higher IgG-type B-lineage cells infiltration in tumors than in healthy tissue, which was associated with improved patient outcomes. Genes such as ACTN1, COL6A5, and pathways like focal adhesion, which shapes the physical structure of tumors, could affect B-lineage cell infiltration. Notably, the IGH sequence was used as an identity-tag to monitor B cell migration, and their infiltration schema within the tumor were depicted based on our multi-regional tumor specimens. This analysis revealed an escalation in B cell clones overlapped between metastatic lymph nodes and tumors. Therefore, the Lymph Node Activation Index was defined, which could predict the outcomes of patients with lymph node metastasis. This research introduces a novel framework for probing B cell infiltration and migration within the tumor microenvironment using large-scale transcriptome data, while simultaneously providing fresh perspectives on B cell immunology within ESCC.
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Affiliation(s)
- Longlong Wang
- Cancer Institute, Department of Oncology, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology (PKU-HKUST) Medical Center, Shenzhen, Guangdong, 518035, China
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518028, China
| | - Yong Zhou
- Cancer Institute, Department of Oncology, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology (PKU-HKUST) Medical Center, Shenzhen, Guangdong, 518035, China
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518028, China
| | - Heyang Cui
- Cancer Institute, Department of Oncology, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology (PKU-HKUST) Medical Center, Shenzhen, Guangdong, 518035, China
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518028, China
| | - Xuehan Zhuang
- Cancer Institute, Department of Oncology, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology (PKU-HKUST) Medical Center, Shenzhen, Guangdong, 518035, China
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518028, China
| | - Chen Cheng
- Cancer Institute, Department of Oncology, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology (PKU-HKUST) Medical Center, Shenzhen, Guangdong, 518035, China
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518028, China
| | - Yongjia Weng
- Cancer Institute, Department of Oncology, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology (PKU-HKUST) Medical Center, Shenzhen, Guangdong, 518035, China
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518028, China
| | - Huijuan Liu
- Key Laboratory of Cellular Physiology of the Ministry of Education, Department of Pathology, Shanxi Medical University, Taiyuan, Shanxi, 030001, China
| | - Shubin Wang
- Cancer Institute, Department of Oncology, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology (PKU-HKUST) Medical Center, Shenzhen, Guangdong, 518035, China
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518028, China
| | - Xinghua Pan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, 510515, China.
| | - Yongping Cui
- Cancer Institute, Department of Oncology, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology (PKU-HKUST) Medical Center, Shenzhen, Guangdong, 518035, China.
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518028, China.
- Key Laboratory of Cellular Physiology of the Ministry of Education, Department of Pathology, Shanxi Medical University, Taiyuan, Shanxi, 030001, China.
| | - Weimin Zhang
- Cancer Institute, Department of Oncology, Peking University Shenzhen Hospital, Shenzhen Peking University-the Hong Kong University of Science and Technology (PKU-HKUST) Medical Center, Shenzhen, Guangdong, 518035, China.
- Institute of Cancer Research, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518028, China.
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, 100142, China.
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20
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Hung SI, Chu MT, Hou MM, Lee YS, Yang CK, Chu SY, Liu FY, Hsu HC, Pao SC, Teng YC, Chen CB, Chao A, Chung WH, Chang JWC, Lai CH. Personalized neoantigen-based T cell therapy triggers cytotoxic lymphocytes expressing polyclonal TCR against metastatic ovarian cancer. Biomed Pharmacother 2023; 169:115928. [PMID: 38011788 DOI: 10.1016/j.biopha.2023.115928] [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: 08/26/2023] [Revised: 11/17/2023] [Accepted: 11/20/2023] [Indexed: 11/29/2023] Open
Abstract
Neoantigen-reactive cytotoxic T lymphocytes play a vital role in precise cancer cell elimination. In this study, we demonstrate the effectiveness of personalized neoantigen-based T cell therapy in inducing tumor regression in two patients suffering from heavily-burdened metastatic ovarian cancer. Our approach involved the development of a robust pipeline for ex vivo expansion of neoantigen-reactive T lymphocytes. Neoantigen peptides were designed and synthesized based on the somatic mutations of the tumors and their predicted HLA binding affinities. These peptides were then presented to T lymphocytes through co-culture with neoantigen-loaded dendritic cells for ex vivo expansion. Subsequent to cell therapy, both patients exhibited significant reductions in tumor marker levels and experienced substantial tumor regression. One patient achieved repeated cancer regression through infusions of T cell products generated from newly identified neoantigens. Transcriptomic analyses revealed a remarkable increase in neoantigen-reactive cytotoxic lymphocytes in the peripheral blood of the patients following cell therapy. These cytotoxic T lymphocytes expressed polyclonal T cell receptors (TCR) against neoantigens, along with abundant cytotoxic proteins and pro-inflammatory cytokines. The efficacy of neoantigen targeting was significantly associated with the immunogenicity and TCR polyclonality. Notably, the neoantigen-specific TCR clonotypes persisted in the peripheral blood after cell therapy. Our findings indicate that personalized neoantigen-based T cell therapy triggers cytotoxic lymphocytes expressing polyclonal TCR against ovarian cancer, suggesting its promising potential in cancer immunotherapy.
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Affiliation(s)
- Shuen-Iu Hung
- Cancer Vaccine & Immune Cell Therapy Core Lab, Department of Medical Research, Chang Gung Memorial Hospital, Linkou Branch, No. 5. Fuxing Street, Taoyuan 333, Taiwan; Institute of Pharmacology, College of Medicine, National Yang Ming Chiao Tung University, No.155, Section 2, Linong Street, Taipei 112, Taiwan.
| | - Mu-Tzu Chu
- Cancer Vaccine & Immune Cell Therapy Core Lab, Department of Medical Research, Chang Gung Memorial Hospital, Linkou Branch, No. 5. Fuxing Street, Taoyuan 333, Taiwan.
| | - Ming-Mo Hou
- Division of Hematology-Oncology, Chang Gung Memorial Hospital, Linkou Branch, No. 5. Fuxing Street, Taoyuan 333, Taiwan; College of Medicine, Chang Gung University, No. 5, De-Ming Road., Taoyuan 333, Taiwan.
| | - Yun-Shien Lee
- Genomic Medicine Research Core Laboratory, Chang Gung Memorial Hospital, Linkou Branch, No. 5. Fuxing Street, Guishan, Taoyuan 333, Taiwan; Department of Biotechnology, Ming-Chuan University, Taoyuan 333, Taiwan.
| | - Chan-Keng Yang
- Division of Hematology-Oncology, Chang Gung Memorial Hospital, Linkou Branch, No. 5. Fuxing Street, Taoyuan 333, Taiwan; College of Medicine, Chang Gung University, No. 5, De-Ming Road., Taoyuan 333, Taiwan.
| | - Sung-Yu Chu
- Department of Medical Imaging and Intervention, Chang Gung Memorial Hospital, Linkou Branch, No. 5. Fuxing Street, Taoyuan 333, Taiwan.
| | - Feng-Yuan Liu
- College of Medicine, Chang Gung University, No. 5, De-Ming Road., Taoyuan 333, Taiwan; Department of Nuclear Medicine and Molecular Imaging Center, Chang Gung Memorial Hospital, Linkou Branch, No. 5. Fuxing Street, Taoyuan 333, Taiwan; Gynecologic Cancer Research Center, Chang Gung Memorial Hospital, Linkou Branch, No. 5. Fuxing Street, Taoyuan 333, Taiwan; School of Medicine, National Tsing Hua University, No.101, Section 2, Kuang-Fu Road, Hsinchu 300, Taiwan.
| | - Hung-Chih Hsu
- Division of Hematology-Oncology, Chang Gung Memorial Hospital, Linkou Branch, No. 5. Fuxing Street, Taoyuan 333, Taiwan; College of Medicine, Chang Gung University, No. 5, De-Ming Road., Taoyuan 333, Taiwan.
| | - Shih-Cheng Pao
- Cancer Vaccine & Immune Cell Therapy Core Lab, Department of Medical Research, Chang Gung Memorial Hospital, Linkou Branch, No. 5. Fuxing Street, Taoyuan 333, Taiwan; Institute of Pharmacology, College of Medicine, National Yang Ming Chiao Tung University, No.155, Section 2, Linong Street, Taipei 112, Taiwan.
| | - Yu-Chuan Teng
- Genomic Medicine Research Core Laboratory, Chang Gung Memorial Hospital, Linkou Branch, No. 5. Fuxing Street, Guishan, Taoyuan 333, Taiwan.
| | - Chun-Bing Chen
- College of Medicine, Chang Gung University, No. 5, De-Ming Road., Taoyuan 333, Taiwan; Department of Dermatology, Drug Hypersensitivity Clinical and Research Center, Chang Gung Memorial Hospital, Linkou Branch, No. 5. Fuxing Street, Taoyuan 333, Taiwan.
| | - Angel Chao
- College of Medicine, Chang Gung University, No. 5, De-Ming Road., Taoyuan 333, Taiwan; Gynecologic Cancer Research Center, Chang Gung Memorial Hospital, Linkou Branch, No. 5. Fuxing Street, Taoyuan 333, Taiwan; Department of Obstetrics and Gynecology, Chang Gung Memorial Hospital, Linkou Branch, No. 5. Fuxing Street, Taoyuan 333, Taiwan.
| | - Wen-Hung Chung
- Cancer Vaccine & Immune Cell Therapy Core Lab, Department of Medical Research, Chang Gung Memorial Hospital, Linkou Branch, No. 5. Fuxing Street, Taoyuan 333, Taiwan; College of Medicine, Chang Gung University, No. 5, De-Ming Road., Taoyuan 333, Taiwan; Department of Dermatology, Drug Hypersensitivity Clinical and Research Center, Chang Gung Memorial Hospital, Linkou Branch, No. 5. Fuxing Street, Taoyuan 333, Taiwan; Whole-Genome Research Core Laboratory of Human Diseases, Chang Gung Memorial Hospital, Keelung Branch, No. 222, Maijin Road., Keelung 204, Taiwan.
| | - John Wen-Cheng Chang
- Division of Hematology-Oncology, Chang Gung Memorial Hospital, Linkou Branch, No. 5. Fuxing Street, Taoyuan 333, Taiwan; College of Medicine, Chang Gung University, No. 5, De-Ming Road., Taoyuan 333, Taiwan.
| | - Chyong-Huey Lai
- College of Medicine, Chang Gung University, No. 5, De-Ming Road., Taoyuan 333, Taiwan; Gynecologic Cancer Research Center, Chang Gung Memorial Hospital, Linkou Branch, No. 5. Fuxing Street, Taoyuan 333, Taiwan; Department of Obstetrics and Gynecology, Chang Gung Memorial Hospital, Linkou Branch, No. 5. Fuxing Street, Taoyuan 333, Taiwan.
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21
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McShan AC, Flores-Solis D, Sun Y, Garfinkle SE, Toor JS, Young MC, Sgourakis NG. Conformational plasticity of RAS Q61 family of neoepitopes results in distinct features for targeted recognition. Nat Commun 2023; 14:8204. [PMID: 38081856 PMCID: PMC10713829 DOI: 10.1038/s41467-023-43654-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 11/15/2023] [Indexed: 12/18/2023] Open
Abstract
The conformational landscapes of peptide/human leucocyte antigen (pHLA) protein complexes encompassing tumor neoantigens provide a rationale for target selection towards autologous T cell, vaccine, and antibody-based therapeutic modalities. Here, using complementary biophysical and computational methods, we characterize recurrent RAS55-64 Q61 neoepitopes presented by the common HLA-A*01:01 allotype. We integrate sparse NMR restraints with Rosetta docking to determine the solution structure of NRASQ61K/HLA-A*01:01, which enables modeling of other common RAS55-64 neoepitopes. Hydrogen/deuterium exchange mass spectrometry experiments alongside molecular dynamics simulations reveal differences in solvent accessibility and conformational plasticity across a panel of common Q61 neoepitopes that are relevant for recognition by immunoreceptors. Finally, we predict binding and provide structural models of NRASQ61K antigens spanning the entire HLA allelic landscape, together with in vitro validation for HLA-A*01:191, HLA-B*15:01, and HLA-C*08:02. Our work provides a basis to delineate the solution surface features and immunogenicity of clinically relevant neoepitope/HLA targets for cancer therapy.
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Affiliation(s)
- Andrew C McShan
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- School of Chemistry & Biochemistry, Georgia Institute of Technology, 901 Atlantic Dr NW, Atlanta, GA, 30318, USA
| | - David Flores-Solis
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, 95064, USA
- German Center for Neurodegenerative Diseases (DZNE), Von-Siebold Straße 3A, 37075, Göttingen, Germany
| | - Yi Sun
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Samuel E Garfinkle
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Jugmohit S Toor
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, 95064, USA
- Immunology Research Program, Henry Ford Cancer Institute, Henry Ford Health, Detroit, MI, 48202, USA
| | - Michael C Young
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Nikolaos G Sgourakis
- Center for Computational and Genomic Medicine, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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22
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Chehelgerdi M, Behdarvand Dehkordi F, Chehelgerdi M, Kabiri H, Salehian-Dehkordi H, Abdolvand M, Salmanizadeh S, Rashidi M, Niazmand A, Ahmadi S, Feizbakhshan S, Kabiri S, Vatandoost N, Ranjbarnejad T. Exploring the promising potential of induced pluripotent stem cells in cancer research and therapy. Mol Cancer 2023; 22:189. [PMID: 38017433 PMCID: PMC10683363 DOI: 10.1186/s12943-023-01873-0] [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: 07/04/2023] [Accepted: 09/27/2023] [Indexed: 11/30/2023] Open
Abstract
The advent of iPSCs has brought about a significant transformation in stem cell research, opening up promising avenues for advancing cancer treatment. The formation of cancer is a multifaceted process influenced by genetic, epigenetic, and environmental factors. iPSCs offer a distinctive platform for investigating the origin of cancer, paving the way for novel approaches to cancer treatment, drug testing, and tailored medical interventions. This review article will provide an overview of the science behind iPSCs, the current limitations and challenges in iPSC-based cancer therapy, the ethical and social implications, and the comparative analysis with other stem cell types for cancer treatment. The article will also discuss the applications of iPSCs in tumorigenesis, the future of iPSCs in tumorigenesis research, and highlight successful case studies utilizing iPSCs in tumorigenesis research. The conclusion will summarize the advancements made in iPSC-based tumorigenesis research and the importance of continued investment in iPSC research to unlock the full potential of these cells.
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Affiliation(s)
- Matin Chehelgerdi
- Novin Genome (NG) Lab, Research and Development Center for Biotechnology, Shahrekord, Iran
- Young Researchers and Elite Club, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Fereshteh Behdarvand Dehkordi
- Novin Genome (NG) Lab, Research and Development Center for Biotechnology, Shahrekord, Iran
- Young Researchers and Elite Club, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Mohammad Chehelgerdi
- Novin Genome (NG) Lab, Research and Development Center for Biotechnology, Shahrekord, Iran.
- Young Researchers and Elite Club, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran.
| | - Hamidreza Kabiri
- Novin Genome (NG) Lab, Research and Development Center for Biotechnology, Shahrekord, Iran
- Young Researchers and Elite Club, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | | | - Mohammad Abdolvand
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Science, Isfahan, Iran
| | - Sharareh Salmanizadeh
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Hezar-Jereeb Street, Isfahan, 81746-73441, Iran
| | - Mohsen Rashidi
- Department Pharmacology, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
- The Health of Plant and Livestock Products Research Center, Mazandaran University of Medical Sciences, Sari, Iran
| | - Anoosha Niazmand
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Science, Isfahan, Iran
| | - Saba Ahmadi
- Department of Molecular and Medical Genetics, Tbilisi State Medical University, Tbilisi, Georgia
| | - Sara Feizbakhshan
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Science, Isfahan, Iran
| | - Saber Kabiri
- Novin Genome (NG) Lab, Research and Development Center for Biotechnology, Shahrekord, Iran
- Young Researchers and Elite Club, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Nasimeh Vatandoost
- Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Non-Communicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Tayebeh Ranjbarnejad
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Science, Isfahan, Iran
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23
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Chen G, Kong D, Lin Y. Neo-Antigen-Reactive T Cells Immunotherapy for Colorectal Cancer: A More Personalized Cancer Therapy Approach. GLOBAL CHALLENGES (HOBOKEN, NJ) 2023; 7:2200186. [PMID: 37970536 PMCID: PMC10632666 DOI: 10.1002/gch2.202200186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 05/09/2023] [Indexed: 11/17/2023]
Abstract
Colorectal cancer (CRC) is the second most common malignancy in women and the third most frequent cancer in men. Evidence has revealed that the survival of patients with metastatic CRC is very low, between one and three years. Neoantigens are known proteins encoded by mutations in tumor cells. It is theorized that recognizing neoantigens by T cells leads to T cell activation and further antitumor responses. Neoantigen-reactive T cells (NRTs) are designed against the mentioned neoantigens expressed by tumor cells. NRTs selectively kill tumor cells without damage to non-cancerous cells. Identifying patient-specific and high immunogen neoantigens is important in NRT immunotherapy of patients with CRC. However, the main challenges are the side effects and preparation of NRTs, as well as the effectiveness of these cells in vivo. This review summarized the properties of neoantigens as well as the preparation and therapeutic outcomes of NRTs for the treatment of CRC.
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Affiliation(s)
- Guan‐Liang Chen
- Department of Gastroenterology SurgeryAffiliated Hospital of Shaoxing UniversityShaoxing312000China
| | - De‐Xia Kong
- Center for General Practice MedicineDepartment of GastroenterologyZhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical CollegeNo. 158 Shangtang RoadHangzhouZhejiang310014China
| | - Yan Lin
- Center for General Practice MedicineDepartment of GastroenterologyZhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical CollegeNo. 158 Shangtang RoadHangzhouZhejiang310014China
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24
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Monzo HJ, Kalander K, Hyytiäinen MM, Elbasani E, Wall J, Moyano-Galceran L, Tanjore Ramanathan J, Jukonen J, Laakkonen P, Ristimäki A, Carlson JW, Lehti K, Salehi S, Puolakkainen P, Haglund C, Seppänen H, Leppä S, Ojala PM. Efficacy and Safety of Glycosphingolipid SSEA-4 Targeting CAR-T Cells in an Ovarian Carcinoma Model. Mol Cancer Ther 2023; 22:1319-1331. [PMID: 37486980 DOI: 10.1158/1535-7163.mct-23-0008] [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: 01/09/2023] [Revised: 05/04/2023] [Accepted: 07/21/2023] [Indexed: 07/26/2023]
Abstract
Chimeric antigen receptor (CAR) T-cell immunotherapies for solid tumors face critical challenges such as heterogeneous antigen expression. We characterized stage-specific embryonic antigen-4 (SSEA-4) cell-surface glycolipid as a target for CAR T-cell therapy. SSEA-4 is mainly expressed during embryogenesis but is also found in several cancer types making it an attractive tumor-associated antigen. Anti-SSEA-4 CAR-T cells were generated and assessed preclinically in vitro and in vivo for antitumor response and safety. SSEA-4 CAR-T cells effectively eliminated SSEA-4-positive cells in all the tested cancer cell lines, whereas SSEA-4-negative cells lines were not targeted. In vivo efficacy and safety studies using NSG mice and the high-grade serous ovarian cancer cell line OVCAR4 demonstrated a remarkable and specific antitumor response at all the CAR T-cell doses used. At high T-cell doses, CAR T cell-treated mice showed signs of health deterioration after a follow-up period. However, the severity of toxicity was reduced with a delayed onset when lower CAR T-cell doses were used. Our data demonstrate the efficacy of anti-SSEA-4 CAR T-cell therapy; however, safety strategies, such as dose-limiting and/or equipping CAR-T cells with combinatorial antigen recognition should be implemented for its potential clinical translation.
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Affiliation(s)
- Hector J Monzo
- Translational Cancer Medicine Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Kerttu Kalander
- Translational Cancer Medicine Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Applied Tumor Genomics Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Marko M Hyytiäinen
- Translational Cancer Medicine Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Endrit Elbasani
- Translational Cancer Medicine Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Johanna Wall
- Applied Tumor Genomics Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Lidia Moyano-Galceran
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | | | - Joonas Jukonen
- Translational Cancer Medicine Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Pirjo Laakkonen
- Translational Cancer Medicine Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Laboratory Animal Center, Helsinki Institute of Life Science-HiLIFE, University of Helsinki, Helsinki, Finland
| | - Ari Ristimäki
- Applied Tumor Genomics Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Pathology, University of Helsinki and Helsinki University Hospital, Helsinli, Finland
| | - Joseph W Carlson
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden. Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Kaisa Lehti
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Department of Biomedical Laboratory Science, Norwegian University of Science and Technology, Trondheim, Norway
| | - Sahar Salehi
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Department of Pelvic Cancer, Theme Cancer, Karolinska University Hospital, Stockholm, Sweden
| | - Pauli Puolakkainen
- Translational Cancer Medicine Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Caj Haglund
- Translational Cancer Medicine Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Surgery, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Hanna Seppänen
- Translational Cancer Medicine Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Sirpa Leppä
- Applied Tumor Genomics Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Oncology, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Päivi M Ojala
- Translational Cancer Medicine Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
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25
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Liang C, He J, Zhao X, Hong J, Ma X, Mao M, Nie W, Wu G, Dong Y, Xu W, Huang L, Xie HY. Monitoring the Cascade of Tumor-specific Immune Response in vivo via Chemoenzymatic Proximity Labeling. Angew Chem Int Ed Engl 2023; 62:e202304838. [PMID: 37650228 DOI: 10.1002/anie.202304838] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 06/25/2023] [Accepted: 08/30/2023] [Indexed: 09/01/2023]
Abstract
Monitoring the highly dynamic and complex immune response remains a great challenge owing to the lack of reliable and specific approaches. Here, we develop a strategy to monitor the cascade of tumor immune response through the cooperation of pore-forming alginate gel with chemoenzymatic proximity-labeling. A macroporous gel containing tumor-associated antigens, adjuvants, and pro-inflammatory cytokines is utilized to recruit endogenous DCs and enhance their maturation in vivo. The mature DCs are then modified with GDP-fucose-fucosyltransferase (GDP-Fuc-Fuct) via the self-catalysis of fucosyltransferase (Fuct). Following the migration of the obtained Fuct-DCs to the draining lymph nodes (dLNs), the molecular recognition mediated interaction of DCs and T cells leads to the successful decoration of T cells with GDP-Fuc-azide through the Fuct catalyzed proximity-labeling. Therefore, the activated tumor-specific T cells in dLNs and tumors can be identified through bioorthogonal labeling, opening up a new avenue for studying the immune mechanism of tumors in situ.
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Affiliation(s)
- Chao Liang
- School of Life Science, Beijing Institute of Technology, Beijing, 100081, P. R. China
| | - Jiaqi He
- School of Life Science, Beijing Institute of Technology, Beijing, 100081, P. R. China
| | - Xin Zhao
- School of Material Science & Engineering, Beijing Institute of Technology, Beijing, 100081, P. R. China
| | - Jie Hong
- School of Life Science, Beijing Institute of Technology, Beijing, 100081, P. R. China
| | - Xianbin Ma
- School of Medical Technology, Beijing Institute of Technology, Beijing, 100081, P. R. China
| | - Mingchuan Mao
- School of Life Science, Beijing Institute of Technology, Beijing, 100081, P. R. China
| | - Weidong Nie
- School of Life Science, Beijing Institute of Technology, Beijing, 100081, P. R. China
| | - Guanghao Wu
- School of Life Science, Beijing Institute of Technology, Beijing, 100081, P. R. China
| | - Yuping Dong
- School of Material Science & Engineering, Beijing Institute of Technology, Beijing, 100081, P. R. China
| | - Wei Xu
- School of Life Science, Beijing Institute of Technology, Beijing, 100081, P. R. China
| | - Lili Huang
- School of Medical Technology, Beijing Institute of Technology, Beijing, 100081, P. R. China
| | - Hai-Yan Xie
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Chemical Biology Center, Peking University, Beijing, 100191, P. R. China
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26
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Kwok DW, Stevers NO, Nejo T, Chen LH, Etxeberria I, Jung J, Okada K, Cove MC, Lakshmanachetty S, Gallus M, Barpanda A, Hong C, Chan GKL, Wu SH, Ramos E, Yamamichi A, Liu J, Watchmaker P, Ogino H, Saijo A, Du A, Grishanina N, Woo J, Diaz A, Chang SM, Phillips JJ, Wiita AP, Klebanoff CA, Costello JF, Okada H. Tumor-wide RNA splicing aberrations generate immunogenic public neoantigens. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.19.563178. [PMID: 37904942 PMCID: PMC10614978 DOI: 10.1101/2023.10.19.563178] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2023]
Abstract
T-cell-mediated immunotherapies are limited by the extent to which cancer-specific antigens are homogenously expressed throughout a tumor. We reasoned that recurrent splicing aberrations in cancer represent a potential source of tumor-wide and public neoantigens, and to test this possibility, we developed a novel pipeline for identifying neojunctions expressed uniformly within a tumor across diverse cancer types. Our analyses revealed multiple neojunctions that recur across patients and either exhibited intratumor heterogeneity or, in some cases, were tumor-wide. We identified CD8+ T-cell clones specific for neoantigens derived from tumor-wide and conserved neojunctions in GNAS and RPL22 , respectively. TCR-engineered CD8 + T-cells targeting these mutations conferred neoantigen-specific tumor cell eradication. Furthermore, we revealed that cancer-specific dysregulation in splicing factor expression leads to recurrent neojunction expression. Together, these data reveal that a subset of neojunctions are both intratumorally conserved and public, providing the molecular basis for novel T-cell-based immunotherapies that address intratumoral heterogeneity.
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27
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Huang M, Xia Y, Li K, Shao F, Feng Z, Li T, Azin M, Demehri S. Carcinogen exposure enhances cancer immunogenicity by blocking the development of an immunosuppressive tumor microenvironment. J Clin Invest 2023; 133:e166494. [PMID: 37843274 PMCID: PMC10575722 DOI: 10.1172/jci166494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 08/15/2023] [Indexed: 10/17/2023] Open
Abstract
Carcinogen exposure is strongly associated with enhanced cancer immunogenicity. Increased tumor mutational burden and resulting neoantigen generation have been proposed to link carcinogen exposure and cancer immunogenicity. However, the neoantigen-independent immunological impact of carcinogen exposure on cancer is unknown. Here, we demonstrate that chemical carcinogen-exposed cancer cells fail to establish an immunosuppressive tumor microenvironment (TME), resulting in their T cell-mediated rejection in vivo. A chemical carcinogen-treated breast cancer cell clone that lacked any additional coding region mutations (i.e., neoantigen) was rejected in mice in a T cell-dependent manner. Strikingly, the coinjection of carcinogen- and control-treated cancer cells prevented this rejection, suggesting that the loss of immunosuppressive TME was the dominant cause of rejection. Reduced M-CSF expression by carcinogen-treated cancer cells significantly suppressed tumor-associated macrophages (TAMs) and resulted in the loss of an immunosuppressive TME. Single-cell analysis of human lung cancers revealed a significant reduction in the immunosuppressive TAMs in former smokers compared with individuals who had never smoked. These findings demonstrate that carcinogen exposure impairs the development of an immunosuppressive TME and indicate a novel link between carcinogens and cancer immunogenicity.
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Affiliation(s)
- Mei Huang
- Center for Cancer Immunology and Cutaneous Biology Research Center, Department of Dermatology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Yun Xia
- Center for Cancer Immunology and Cutaneous Biology Research Center, Department of Dermatology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Kaiwen Li
- Center for Cancer Immunology and Cutaneous Biology Research Center, Department of Dermatology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Feng Shao
- Department of General Surgery, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Zhaoyi Feng
- Center for Cancer Immunology and Cutaneous Biology Research Center, Department of Dermatology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Tiancheng Li
- Center for Cancer Immunology and Cutaneous Biology Research Center, Department of Dermatology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Marjan Azin
- Center for Cancer Immunology and Cutaneous Biology Research Center, Department of Dermatology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Shadmehr Demehri
- Center for Cancer Immunology and Cutaneous Biology Research Center, Department of Dermatology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
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28
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Jaton F. Groundwork for AI: Enforcing a benchmark for neoantigen prediction in personalized cancer immunotherapy. SOCIAL STUDIES OF SCIENCE 2023; 53:787-810. [PMID: 37650579 PMCID: PMC10543129 DOI: 10.1177/03063127231192857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
This article expands on recent studies of machine learning or artificial intelligence (AI) algorithms that crucially depend on benchmark datasets, often called 'ground truths.' These ground-truth datasets gather input-data and output-targets, thereby establishing what can be retrieved computationally and evaluated statistically. I explore the case of the Tumor nEoantigen SeLection Alliance (TESLA), a consortium-based ground-truthing project in personalized cancer immunotherapy, where the 'truth' of the targets-immunogenic neoantigens-to be retrieved by the would-be AI algorithms depended on a broad technoscientific network whose setting up implied important organizational and material infrastructures. The study shows that instead of grounding an undisputable 'truth', the TESLA endeavor ended up establishing a contestable reference, the biology of neoantigens and how to measure their immunogenicity having slightly evolved alongside this four-year project. However, even if this controversy played down the scope of the TESLA ground truth, it did not discredit the whole undertaking. The magnitude of the technoscientific efforts that the TESLA project set into motion and the needs it ultimately succeeded in filling for the scientific and industrial community counterbalanced its metrological uncertainties, effectively instituting its contestable representation of 'true' neoantigens within the field of personalized cancer immunotherapy (at least temporarily). More generally, this case study indicates that the enforcement of ground truths, and what it leaves out, is a necessary condition to enable AI technologies in personalized medicine.
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Affiliation(s)
- Florian Jaton
- Graduate Institute of International and Development Studies, Geneva, Switzerland
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29
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Du S, Yan J, Xue Y, Zhong Y, Dong Y. Adoptive cell therapy for cancer treatment. EXPLORATION (BEIJING, CHINA) 2023; 3:20210058. [PMID: 37933232 PMCID: PMC10624386 DOI: 10.1002/exp.20210058] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 05/17/2023] [Indexed: 11/08/2023]
Abstract
Adoptive cell therapy (ACT) is a rapidly growing anti-cancer strategy that has shown promise in treating various cancer types. The concept of ACT involves activating patients' own immune cells ex vivo and then transferring them back to the patients to recognize and eliminate cancer cells. Currently, the commonly used ACT includes tumor-infiltrating lymphocytes (TILs), genetically engineered immune cells, and dendritic cells (DCs) vaccines. With the advancement of cell culture and genetic engineering techniques, ACT has been used in clinics to treat malignant hematological diseases and many new ACT-based regimens are in different stages of clinical trials. Here, representative ACT approaches are introduced and the opportunities and challenges for clinical translation of ACT are discussed.
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Affiliation(s)
- Shi Du
- Division of Pharmaceutics and PharmacologyCollege of PharmacyOhio State UniversityColumbusUSA
- Icahn Genomics InstitutePrecision Immunology InstituteDepartment of Oncological SciencesTisch Cancer InstituteFriedman Brain InstituteIcahn School of Medicine at Mount SinaiNew YorkUSA
| | - Jingyue Yan
- Division of Pharmaceutics and PharmacologyCollege of PharmacyOhio State UniversityColumbusUSA
- Icahn Genomics InstitutePrecision Immunology InstituteDepartment of Oncological SciencesTisch Cancer InstituteFriedman Brain InstituteIcahn School of Medicine at Mount SinaiNew YorkUSA
| | - Yonger Xue
- Division of Pharmaceutics and PharmacologyCollege of PharmacyOhio State UniversityColumbusUSA
- Icahn Genomics InstitutePrecision Immunology InstituteDepartment of Oncological SciencesTisch Cancer InstituteFriedman Brain InstituteIcahn School of Medicine at Mount SinaiNew YorkUSA
| | - Yichen Zhong
- Division of Pharmaceutics and PharmacologyCollege of PharmacyOhio State UniversityColumbusUSA
- Icahn Genomics InstitutePrecision Immunology InstituteDepartment of Oncological SciencesTisch Cancer InstituteFriedman Brain InstituteIcahn School of Medicine at Mount SinaiNew YorkUSA
| | - Yizhou Dong
- Division of Pharmaceutics and PharmacologyCollege of PharmacyOhio State UniversityColumbusUSA
- Icahn Genomics InstitutePrecision Immunology InstituteDepartment of Oncological SciencesTisch Cancer InstituteFriedman Brain InstituteIcahn School of Medicine at Mount SinaiNew YorkUSA
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30
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Sharma D, Xuan Leong K, Palhares D, Czarnota GJ. Radiation combined with ultrasound and microbubbles: A potential novel strategy for cancer treatment. Z Med Phys 2023; 33:407-426. [PMID: 37586962 PMCID: PMC10517408 DOI: 10.1016/j.zemedi.2023.04.007] [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: 01/11/2023] [Revised: 03/31/2023] [Accepted: 04/11/2023] [Indexed: 08/18/2023]
Abstract
Cancer is one of the leading causes of death worldwide. Several emerging technologies are helping to battle cancer. Cancer therapies have been effective at killing cancer cells, but a large portion of patients still die to this disease every year. As such, more aggressive treatments of primary cancers are employed and have been shown to be capable of saving a greater number of lives. Recent research advances the field of cancer therapy by employing the use of physical methods to alter tumor biology. It uses microbubbles to enhance radiation effect by damaging tumor vasculature followed by tumor cell death. The technique can specifically target tumor volumes by conforming ultrasound fields capable of microbubbles stimulation and localizing it to avoid vascular damage in surrounding tissues. Thus, this new application of ultrasound-stimulated microbubbles (USMB) can be utilized as a novel approach to cancer therapy by inducing vascular disruption resulting in tumor cell death. Using USMB alongside radiation has showed to augment the anti-vascular effect of radiation, resulting in enhanced tumor response. Recent work with nanobubbles has shown vascular permeation into intracellular space, extending the use of this new treatment method to potentially further improve the therapeutic effect of the ultrasound-based therapy. The significant enhancement of localized tumor cell kill means that radiation-based treatments can be made more potent with lower doses of radiation. This technique can manifest a greater impact on radiation oncology practice by increasing treatment effectiveness significantly while reducing normal tissue toxicity. This review article summarizes the past and recent advances in USMB enhancement of radiation treatments. The review mainly focuses on preclinical findings but also highlights some clinical findings that use USMB as a therapeutic modality in cancer therapy.
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Affiliation(s)
- Deepa Sharma
- Physical Sciences, Sunnybrook Research Institute, Toronto, Ontario, Canada; Department of Radiation Oncology, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada; Departments of Radiation Oncology, and Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Kai Xuan Leong
- Physical Sciences, Sunnybrook Research Institute, Toronto, Ontario, Canada
| | - Daniel Palhares
- Physical Sciences, Sunnybrook Research Institute, Toronto, Ontario, Canada; Department of Radiation Oncology, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada; Departments of Radiation Oncology, and Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Gregory J Czarnota
- Physical Sciences, Sunnybrook Research Institute, Toronto, Ontario, Canada; Department of Radiation Oncology, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada; Departments of Radiation Oncology, and Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
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31
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Chehelgerdi M, Chehelgerdi M. The use of RNA-based treatments in the field of cancer immunotherapy. Mol Cancer 2023; 22:106. [PMID: 37420174 PMCID: PMC10401791 DOI: 10.1186/s12943-023-01807-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 06/13/2023] [Indexed: 07/09/2023] Open
Abstract
Over the past several decades, mRNA vaccines have evolved from a theoretical concept to a clinical reality. These vaccines offer several advantages over traditional vaccine techniques, including their high potency, rapid development, low-cost manufacturing, and safe administration. However, until recently, concerns over the instability and inefficient distribution of mRNA in vivo have limited their utility. Fortunately, recent technological advancements have mostly resolved these concerns, resulting in the development of numerous mRNA vaccination platforms for infectious diseases and various types of cancer. These platforms have shown promising outcomes in both animal models and humans. This study highlights the potential of mRNA vaccines as a promising alternative approach to conventional vaccine techniques and cancer treatment. This review article aims to provide a thorough and detailed examination of mRNA vaccines, including their mechanisms of action and potential applications in cancer immunotherapy. Additionally, the article will analyze the current state of mRNA vaccine technology and highlight future directions for the development and implementation of this promising vaccine platform as a mainstream therapeutic option. The review will also discuss potential challenges and limitations of mRNA vaccines, such as their stability and in vivo distribution, and suggest ways to overcome these issues. By providing a comprehensive overview and critical analysis of mRNA vaccines, this review aims to contribute to the advancement of this innovative approach to cancer treatment.
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Affiliation(s)
- Mohammad Chehelgerdi
- Novin Genome (NG) Lab, Research and Development Center for Biotechnology, Shahrekord, Iran.
- Young Researchers and Elite Club, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran.
| | - Matin Chehelgerdi
- Novin Genome (NG) Lab, Research and Development Center for Biotechnology, Shahrekord, Iran
- Young Researchers and Elite Club, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
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32
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Das A, Ghose A, Naicker K, Sanchez E, Chargari C, Rassy E, Boussios S. Advances in adoptive T-cell therapy for metastatic melanoma. Curr Res Transl Med 2023; 71:103404. [PMID: 37478776 DOI: 10.1016/j.retram.2023.103404] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 05/30/2023] [Accepted: 07/06/2023] [Indexed: 07/23/2023]
Abstract
Adoptive T cell therapy (ACT) is a fast developing, niche area of immunotherapy (IO), which is revolutionising the therapeutic landscape of solid tumour oncology, especially metastatic melanoma (MM). Identifying tumour antigens (TAs) as potential targets, the ACT response is mediated by either Tumour Infiltrating Lymphocytes (TILs) or genetically modified T cells with specific receptors - T cell receptors (TCRs) or chimeric antigen receptors (CARs) or more prospectively, natural killer (NK) cells. Clinical trials involving ACT in MM from 2006 to present have shown promising results. Yet it is not without its drawbacks which include significant auto-immune toxicity and need for pre-conditioning lymphodepletion. Although immune-modulation is underway using various combination therapies in the hope of enhancing efficacy and reducing toxicity. Our review article explores the role of ACT in MM, including the various modalities - their safety, efficacy, risks and their development in the trial and the real world setting.
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Affiliation(s)
- Aparimita Das
- Department of Medical Oncology, Medway NHS Foundation Trust, Windmill Road, ME7 5NY, Gillingham, Kent, United Kingdom; Faculty of Allied Health Sciences, Chettinad Academy of Research and Education, Chennai, India
| | - Aruni Ghose
- Department of Medical Oncology, Medway NHS Foundation Trust, Windmill Road, ME7 5NY, Gillingham, Kent, United Kingdom; Department of Medical Oncology, Barts Cancer Centre, St. Bartholomew's Hospital, Barts Health NHS Trust, London, United Kingdom; Department of Medical Oncology, Mount Vernon Cancer Centre, East and North Hertfordshire NHS Trust, London, United Kingdom
| | - Kevin Naicker
- Department of Medical Oncology, Medway NHS Foundation Trust, Windmill Road, ME7 5NY, Gillingham, Kent, United Kingdom
| | - Elisabet Sanchez
- Department of Medical Oncology, Medway NHS Foundation Trust, Windmill Road, ME7 5NY, Gillingham, Kent, United Kingdom
| | - Cyrus Chargari
- Department of Radiation Oncology, Pitié Salpêtrière University Hospital, Paris, France
| | - Elie Rassy
- Department of Medical Oncology, Gustave Roussy Institut, 94805, Villejuif, France
| | - Stergios Boussios
- Department of Medical Oncology, Medway NHS Foundation Trust, Windmill Road, ME7 5NY, Gillingham, Kent, United Kingdom; Kent and Medway Medical School, University of Kent, Canterbury, United Kingdom; Faculty of Life Sciences & Medicine, School of Cancer & Pharmaceutical Sciences, King's College London, SE1 9RT, London, United Kingdom; AELIA Organization, 9th Km Thessaloniki, Thermi 57001, Thessaloniki, Greece.
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33
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Lybaert L, Thielemans K, Feldman SA, van der Burg SH, Bogaert C, Ott PA. Neoantigen-directed therapeutics in the clinic: where are we? Trends Cancer 2023; 9:503-519. [PMID: 37055237 PMCID: PMC10414146 DOI: 10.1016/j.trecan.2023.02.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 02/17/2023] [Accepted: 02/22/2023] [Indexed: 04/15/2023]
Abstract
In the past decade, immune checkpoint inhibitors (ICIs) and chimeric antigen receptor (CAR) T cell therapy have brought immunotherapy to the forefront of cancer treatment; however, only subsets of patients benefit from current approaches. Neoantigen-driven therapeutics specifically redirect the immune system of the patient to enable or reinduce its ability to recognize and eliminate cancer cells. The tumor specificity of this strategy spares healthy and normal cells from being attacked. Consistent with this concept, initial clinical trials have demonstrated the feasibility, safety, and immunogenicity of neoantigen-directed personalized vaccines. We review neoantigen-driven therapy strategies as well as their promise and clinical successes to date.
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Affiliation(s)
| | | | - Steven A Feldman
- Center for Cancer Cell Therapy, Stanford University School of Medicine, Stanford, CA, USA
| | - Sjoerd H van der Burg
- Medical Oncology, Oncode Institute, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Patrick A Ott
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
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34
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Mao L, Ma P, Luo X, Cheng H, Wang Z, Ye E, Loh XJ, Wu YL, Li Z. Stimuli-Responsive Polymeric Nanovaccines Toward Next-Generation Immunotherapy. ACS NANO 2023. [PMID: 37207347 DOI: 10.1021/acsnano.3c02273] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The development of nanovaccines that employ polymeric delivery carriers has garnered substantial interest in therapeutic treatment of cancer and a variety of infectious diseases due to their superior biocompatibility, lower toxicity and reduced immunogenicity. Particularly, stimuli-responsive polymeric nanocarriers show great promise for delivering antigens and adjuvants to targeted immune cells, preventing antigen degradation and clearance, and increasing the uptake of specific antigen-presenting cells, thereby sustaining adaptive immune responses and improving immunotherapy for certain diseases. In this review, the most recent advances in the utilization of stimulus-responsive polymer-based nanovaccines for immunotherapeutic applications are presented. These sophisticated polymeric nanovaccines with diverse functions, aimed at therapeutic administration for disease prevention and immunotherapy, are further classified into several active domains, including pH, temperature, redox, light and ultrasound-sensitive intelligent nanodelivery systems. Finally, the potential strategies for the future design of multifunctional next-generation polymeric nanovaccines by integrating materials science with biological interface are proposed.
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Affiliation(s)
- Liuzhou Mao
- Fujian Provincial Key Laboratory of Innovative Drug Target Research and State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China
| | - Panqin Ma
- Fujian Provincial Key Laboratory of Innovative Drug Target Research and State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China
| | - Xi Luo
- BE/Phase I Clinical Center, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361000, China
| | - Hongwei Cheng
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics and Center for Molecular Imaging and Translational Medicine, School of Public Health, Xiamen University, Xiamen 361102, China
| | - Zhanxiang Wang
- BE/Phase I Clinical Center, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361000, China
| | - Enyi Ye
- Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis #08-03, Singapore 138634, Republic of Singapore
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 1 Pesek Road, Jurong Island, Singapore 627833, Republic of Singapore
| | - Xian Jun Loh
- Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis #08-03, Singapore 138634, Republic of Singapore
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 1 Pesek Road, Jurong Island, Singapore 627833, Republic of Singapore
| | - Yun-Long Wu
- Fujian Provincial Key Laboratory of Innovative Drug Target Research and State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, China
| | - Zibiao Li
- Institute of Materials Research and Engineering (IMRE), Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, Innovis #08-03, Singapore 138634, Republic of Singapore
- Institute of Sustainability for Chemicals, Energy and Environment (ISCE2), Agency for Science, Technology and Research (A*STAR), 1 Pesek Road, Jurong Island, Singapore 627833, Republic of Singapore
- Department of Materials Science and Engineering, National University of Singapore, 9 Engineering Drive 1, Singapore 117576, Republic of Singapore
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35
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Lv X, Mao Z, Sun X, Liu B. Intratumoral Heterogeneity in Lung Cancer. Cancers (Basel) 2023; 15:2709. [PMID: 37345046 DOI: 10.3390/cancers15102709] [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: 04/19/2023] [Revised: 05/07/2023] [Accepted: 05/09/2023] [Indexed: 06/23/2023] Open
Abstract
The diagnosis and treatment of lung cancer (LC) is always a challenge. The difficulty in the decision of therapeutic schedule and diagnosis is directly related to intratumoral heterogeneity (ITH) in the progression of LC. It has been proven that most tumors emerge and evolve under the pressure of their living microenvironment, which involves genetic, immunological, metabolic, and therapeutic components. While most research on ITH revealed multiple mechanisms and characteristic, a systemic exposition of ITH in LC is still hard to find. In this review, we describe how ITH in LC develops from the perspective of space and time. We discuss elaborate details and affection of every aspect of ITH in LC and the relationship between them. Based on ITH in LC, we describe a more accurate multidisciplinary therapeutic strategy on LC and provide the newest opinion on the potential approach of LC therapy.
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Affiliation(s)
- Xiaodi Lv
- Department of Integrative Medicine, Huashan Hospital, Fudan University, Shanghai 200437, China
| | - Zixian Mao
- Pujiang Community Health Center of Minhang District of Shanghai, Shanghai 201114, China
| | - Xianjun Sun
- Department of Integrative Medicine, Huashan Hospital, Fudan University, Shanghai 200437, China
- Institutes of Integrative Medicine, Fudan University, Shanghai 200437, China
| | - Baojun Liu
- Department of Integrative Medicine, Huashan Hospital, Fudan University, Shanghai 200437, China
- Institutes of Integrative Medicine, Fudan University, Shanghai 200437, China
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36
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Oreper D, Klaeger S, Jhunjhunwala S, Delamarre L. The peptide woods are lovely, dark and deep: Hunting for novel cancer antigens. Semin Immunol 2023; 67:101758. [PMID: 37027981 DOI: 10.1016/j.smim.2023.101758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 03/22/2023] [Accepted: 03/22/2023] [Indexed: 04/08/2023]
Abstract
Harnessing the patient's immune system to control a tumor is a proven avenue for cancer therapy. T cell therapies as well as therapeutic vaccines, which target specific antigens of interest, are being explored as treatments in conjunction with immune checkpoint blockade. For these therapies, selecting the best suited antigens is crucial. Most of the focus has thus far been on neoantigens that arise from tumor-specific somatic mutations. Although there is clear evidence that T-cell responses against mutated neoantigens are protective, the large majority of these mutations are not immunogenic. In addition, most somatic mutations are unique to each individual patient and their targeting requires the development of individualized approaches. Therefore, novel antigen types are needed to broaden the scope of such treatments. We review high throughput approaches for discovering novel tumor antigens and some of the key challenges associated with their detection, and discuss considerations when selecting tumor antigens to target in the clinic.
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Affiliation(s)
- Daniel Oreper
- Genentech, 1 DNA way, South San Francisco, 94080 CA, USA.
| | - Susan Klaeger
- Genentech, 1 DNA way, South San Francisco, 94080 CA, USA.
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37
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Yang J, Chen Y, Jing Y, Green MR, Han L. Advancing CAR T cell therapy through the use of multidimensional omics data. Nat Rev Clin Oncol 2023; 20:211-228. [PMID: 36721024 DOI: 10.1038/s41571-023-00729-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/09/2023] [Indexed: 02/01/2023]
Abstract
Despite the notable success of chimeric antigen receptor (CAR) T cell therapies in the treatment of certain haematological malignancies, challenges remain in optimizing CAR designs and cell products, improving response rates, extending the durability of remissions, reducing toxicity and broadening the utility of this therapeutic modality to other cancer types. Data from multidimensional omics analyses, including genomics, epigenomics, transcriptomics, T cell receptor-repertoire profiling, proteomics, metabolomics and/or microbiomics, provide unique opportunities to dissect the complex and dynamic multifactorial phenotypes, processes and responses of CAR T cells as well as to discover novel tumour targets and pathways of resistance. In this Review, we summarize the multidimensional cellular and molecular profiling technologies that have been used to advance our mechanistic understanding of CAR T cell therapies. In addition, we discuss current applications and potential strategies leveraging multi-omics data to identify optimal target antigens and other molecular features that could be exploited to enhance the antitumour activity and minimize the toxicity of CAR T cell therapy. Indeed, fully utilizing multi-omics data will provide new insights into the biology of CAR T cell therapy, further accelerate the development of products with improved efficacy and safety profiles, and enable clinicians to better predict and monitor patient responses.
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Affiliation(s)
- Jingwen Yang
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
| | - Yamei Chen
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA
| | - Ying Jing
- Department of Biochemistry and Molecular Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, USA
| | - Michael R Green
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Leng Han
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, USA.
- Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, TX, USA.
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38
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Wang D, He F, Yu Y, Xu D. Immunology: Meta-learning for T cell-receptor binding specificity and beyond. NAT MACH INTELL 2023; 5:337-339. [PMID: 38260002 PMCID: PMC10803063 DOI: 10.1038/s42256-023-00641-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
Abstract
Predicting whether T-cell receptors bind to specific peptides is a challenging problem as the majority of binding examples in the training data involves only a few peptides. A new approach employs meta-learning to improve predictions for binding to peptides for which no or little binding data exists.
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Affiliation(s)
- Duolin Wang
- Department of Electrical Engineering and Computer Science, Bond Life Sciences Center, University of Missouri, Columbia, Missouri, United States
| | - Fei He
- Department of Electrical Engineering and Computer Science, Bond Life Sciences Center, University of Missouri, Columbia, Missouri, United States
| | - Yang Yu
- Department of Electrical Engineering and Computer Science, Bond Life Sciences Center, University of Missouri, Columbia, Missouri, United States
| | - Dong Xu
- Department of Electrical Engineering and Computer Science, Bond Life Sciences Center, University of Missouri, Columbia, Missouri, United States
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39
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Peng X, Lei Y, Feng P, Jia L, Ma J, Zhao D, Zeng J. Characterizing the interaction conformation between T-cell receptors and epitopes with deep learning. NAT MACH INTELL 2023. [DOI: 10.1038/s42256-023-00634-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
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40
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Ritter A, Koirala N, Wieland A, Kaumaya PTP, Mitchell DL. Therapeutic Cancer Vaccines for the Management of Recurrent and Metastatic Head and Neck Cancer: A Review. JAMA Otolaryngol Head Neck Surg 2023; 149:168-176. [PMID: 36580281 DOI: 10.1001/jamaoto.2022.4264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Importance Squamous cell carcinoma of the head and neck (HNSCC) is prevalent globally and in the US. Management, particularly after disease recurrence, can be challenging, and exploring additional treatment modalities, such as therapeutic cancer vaccines, may offer an opportunity to improve outcomes in this setting. Observations This review provides an overview of the clinical efficacy of different treatment modalities that are currently available for the treatment of recurrent and metastatic HNSCC, including checkpoint inhibitors and targeted therapies, with a detailed summary of the numerous T-cell vaccines that have been studied in the setting of HNSCC, as well as a detailed summary of B-cell therapeutic vaccines being investigated for various malignant tumors. Conclusions and Relevance The findings of this review suggest that several therapeutic T-cell and B-cell vaccines, which have been recently developed and evaluated in a clinical setting, offer a promising treatment modality with the potential to improve outcomes for patients with recurrent and metastatic HNSCC.
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Affiliation(s)
- Alex Ritter
- Department of Radiation Oncology, College of Medicine, The Ohio State University Wexner Medical Center, The James Cancer Hospital and Solove Research Institute, Columbus
| | - Nischal Koirala
- Department of Radiation Oncology, College of Medicine, The Ohio State University Wexner Medical Center, The James Cancer Hospital and Solove Research Institute, Columbus
| | - Andreas Wieland
- Department of Otolaryngology, College of Medicine, The Ohio State University Wexner Medical Center, The James Cancer Hospital and Solove Research Institute, Columbus.,Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University Wexner Medical Center, The James Cancer Hospital and Solove Research Institute, Columbus.,Pelotonia Institute for Immuno-Oncology, College of Medicine, The Ohio State University Wexner Medical Center, The James Cancer Hospital and Solove Research Institute, Columbus
| | - Pravin T P Kaumaya
- Department of Obstetrics and Gynecology, College of Medicine, The Ohio State University Wexner Medical Center, The James Cancer Hospital and Solove Research Institute, Columbus
| | - Darrion L Mitchell
- Department of Radiation Oncology, College of Medicine, The Ohio State University Wexner Medical Center, The James Cancer Hospital and Solove Research Institute, Columbus
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Biri-Kovács B, Bánóczi Z, Tummalapally A, Szabó I. Peptide Vaccines in Melanoma: Chemical Approaches towards Improved Immunotherapeutic Efficacy. Pharmaceutics 2023; 15:pharmaceutics15020452. [PMID: 36839774 PMCID: PMC9963291 DOI: 10.3390/pharmaceutics15020452] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/22/2023] [Accepted: 01/25/2023] [Indexed: 01/31/2023] Open
Abstract
Cancer of the skin is by far the most common of all cancers. Although the incidence of melanoma is relatively low among skin cancers, it can account for a high number of skin cancer deaths. Since the start of deeper insight into the mechanisms of melanoma tumorigenesis and their strong interaction with the immune system, the development of new therapeutical strategies has been continuously rising. The high number of melanoma cell mutations provides a diverse set of antigens that the immune system can recognize and use to distinguish tumor cells from normal cells. Peptide-based synthetic anti-tumor vaccines are based on tumor antigens that elicit an immune response due to antigen-presenting cells (APCs). Although targeting APCs with peptide antigens is the most important assumption for vaccine development, peptide antigens alone are poorly immunogenic. The immunogenicity of peptide antigens can be improved not only by synthetic modifications but also by the assistance of adjuvants and/or delivery systems. The current review summarizes the different chemical approaches for the development of effective peptide-based vaccines for the immunotherapeutic treatment of advanced melanoma.
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Affiliation(s)
- Beáta Biri-Kovács
- ELKH-ELTE Research Group of Peptide Chemistry, 1117 Budapest, Hungary
| | - Zoltán Bánóczi
- ELKH-ELTE Research Group of Peptide Chemistry, 1117 Budapest, Hungary
- Institute of Chemistry, Eötvös Loránd University, 1117 Budapest, Hungary
| | | | - Ildikó Szabó
- ELKH-ELTE Research Group of Peptide Chemistry, 1117 Budapest, Hungary
- Institute of Chemistry, Eötvös Loránd University, 1117 Budapest, Hungary
- MTA-TTK Lendület “Momentum” Peptide-Based Vaccines Research Group, Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, 1117 Budapest, Hungary
- Correspondence: ; Tel.: +36-13722500
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42
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mRNA-From COVID-19 Treatment to Cancer Immunotherapy. Biomedicines 2023; 11:biomedicines11020308. [PMID: 36830845 PMCID: PMC9953480 DOI: 10.3390/biomedicines11020308] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/05/2023] [Accepted: 01/09/2023] [Indexed: 01/24/2023] Open
Abstract
This review provides an overview covering mRNA from its use in the COVID-19 pandemic to cancer immunotherapy, starting from the selection of appropriate antigens, tumor-associated and tumor-specific antigens, neoantigens, the basics of optimizing the mRNA molecule in terms of stability, efficacy, and tolerability, choosing the best formulation and the optimal route of administration, to summarizing current clinical trials of mRNA vaccines in tumor therapy.
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43
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Neoantigens: promising targets for cancer therapy. Signal Transduct Target Ther 2023; 8:9. [PMID: 36604431 PMCID: PMC9816309 DOI: 10.1038/s41392-022-01270-x] [Citation(s) in RCA: 164] [Impact Index Per Article: 164.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/14/2022] [Accepted: 11/27/2022] [Indexed: 01/07/2023] Open
Abstract
Recent advances in neoantigen research have accelerated the development and regulatory approval of tumor immunotherapies, including cancer vaccines, adoptive cell therapy and antibody-based therapies, especially for solid tumors. Neoantigens are newly formed antigens generated by tumor cells as a result of various tumor-specific alterations, such as genomic mutation, dysregulated RNA splicing, disordered post-translational modification, and integrated viral open reading frames. Neoantigens are recognized as non-self and trigger an immune response that is not subject to central and peripheral tolerance. The quick identification and prediction of tumor-specific neoantigens have been made possible by the advanced development of next-generation sequencing and bioinformatic technologies. Compared to tumor-associated antigens, the highly immunogenic and tumor-specific neoantigens provide emerging targets for personalized cancer immunotherapies, and serve as prospective predictors for tumor survival prognosis and immune checkpoint blockade responses. The development of cancer therapies will be aided by understanding the mechanism underlying neoantigen-induced anti-tumor immune response and by streamlining the process of neoantigen-based immunotherapies. This review provides an overview on the identification and characterization of neoantigens and outlines the clinical applications of prospective immunotherapeutic strategies based on neoantigens. We also explore their current status, inherent challenges, and clinical translation potential.
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44
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Blazeska N, Kosaloglu-Yalcin Z, Vita R, Peters B, Sette A. IEDB and CEDAR: Two Sibling Databases to Serve the Global Scientific Community. Methods Mol Biol 2023; 2673:133-149. [PMID: 37258911 PMCID: PMC11008223 DOI: 10.1007/978-1-0716-3239-0_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] [Indexed: 06/02/2023]
Abstract
Various methodologies have been utilized to analyze epitope-specific responses in the context of non-self-antigens, such as those associated with infectious diseases and allergies, and in the context of self-antigens, such as those associated with transplantation, autoimmunity, and cancer. Further to this, epitope-specific data, and its associated immunological context, are crucial to training and developing predictive algorithms and pipelines for the development of specific vaccines and diagnostics. In this chapter, we describe the methodology utilized to derive two sibling resources, the Immune Epitope Database (IEDB) and Cancer Epitope Database and Analysis Resource (CEDAR), to specifically host this data, and make them freely available to the scientific community.
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Affiliation(s)
- Nina Blazeska
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Zeynep Kosaloglu-Yalcin
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Randi Vita
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Bjoern Peters
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA.
- Department of Medicine, University of California San Diego, La Jolla, CA, USA.
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45
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Zheng G, Lu Y, Yang Z, Chen H, Liang Q, Zhu Q, Li Y, Xiao X, He Z, Zhu Y, Li B, Huang L, Dong N, Hu S, Pan Y, Zhang C, Zhu C. Immune desert in MMR-deficient tumors predicts poor responsiveness of immune checkpoint inhibition. Front Immunol 2023; 14:1142862. [PMID: 37187745 PMCID: PMC10175608 DOI: 10.3389/fimmu.2023.1142862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 04/10/2023] [Indexed: 05/17/2023] Open
Abstract
Background Although many efforts have been devoted to identify biomarkers to predict the responsiveness of immune checkpoint inhibitors, including expression of programmed death-ligand 1 (PD-L1) and major histocompatibility complex (MHC) I, microsatellite instability (MSI), mismatch repair (MMR) defect, tumor mutation burden (TMB), tertiary lymphoid structures (TLSs), and several transcriptional signatures, the sensitivity of these indicators remains to be further improved. Materials and methods Here, we integrated T-cell spatial distribution and intratumor transcriptional signals in predicting the response to immune checkpoint therapy in MMR-deficient tumors including tumors of Lynch syndrome (LS). Results In both cohorts, MMR-deficient tumors displayed personalized tumor immune signatures, including inflamed, immune excluded, and immune desert, which were not only individual-specific but also organ-specific. Furthermore, the immune desert tumor exhibited a more malignant phenotype characterized by low differentiation adenocarcinoma, larger tumor sizes, and higher metastasis rate. Moreover, the tumor immune signatures associated with distinct populations of infiltrating immune cells were comparable to TLSs and more sensitive than transcriptional signature gene expression profiles (GEPs) in immunotherapy prediction. Surprisingly, the tumor immune signatures might arise from the somatic mutations. Notably, patients with MMR deficiency had benefited from the typing of immune signatures and later immune checkpoint inhibition. Conclusion Our findings suggest that compared to PD-L1 expression, MMR, TMB, and GEPs, characterization of the tumor immune signatures in MMR-deficient tumors improves the efficiency of predicting the responsiveness of immune checkpoint inhibition.
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Affiliation(s)
- Guoxing Zheng
- The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong, China
- Guangdong Provincial Key Laboratory of Digestive Cancer Research, Shenzhen, Guangdong, China
- *Correspondence: Guoxing Zheng, ; Chengming Zhu,
| | - Yingsi Lu
- The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Zheng Yang
- The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong, China
- Guangdong Provincial Key Laboratory of Digestive Cancer Research, Shenzhen, Guangdong, China
| | - Hong Chen
- The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Qian Liang
- The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Qingqing Zhu
- The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Yan Li
- The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Xing Xiao
- The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Zhuzhen He
- The Obstetrics, Shenzhen Amcare Maternity Hospital, Shenzhen, Guangdong, China
| | - Yifan Zhu
- The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Bo Li
- The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong, China
- Guangdong Provincial Key Laboratory of Digestive Cancer Research, Shenzhen, Guangdong, China
| | - Leilei Huang
- The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Nan Dong
- The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Shuang Hu
- The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Yihang Pan
- The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong, China
- Guangdong Provincial Key Laboratory of Digestive Cancer Research, Shenzhen, Guangdong, China
| | - Changhua Zhang
- The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong, China
- Guangdong Provincial Key Laboratory of Digestive Cancer Research, Shenzhen, Guangdong, China
| | - Chengming Zhu
- The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, Guangdong, China
- Guangdong Provincial Key Laboratory of Digestive Cancer Research, Shenzhen, Guangdong, China
- *Correspondence: Guoxing Zheng, ; Chengming Zhu,
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46
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Su Y, Yuan C, Shi M. Editorial: Screening and verification of new targets for CAR-T immunotherapy in cancer. Front Immunol 2023; 14:1189773. [PMID: 37114061 PMCID: PMC10126677 DOI: 10.3389/fimmu.2023.1189773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 04/03/2023] [Indexed: 04/29/2023] Open
Affiliation(s)
- Yang Su
- Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China
- Center of Clinical Oncology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Chen Yuan
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, United States
| | - Ming Shi
- Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China
- Center of Clinical Oncology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Xuzhou Medical University, Xuzhou, Jiangsu, China
- *Correspondence: Ming Shi,
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Wu J, Zhou Z. TSNAD and TSNAdb: The Useful Toolkit for Clinical Application of Tumor-Specific Neoantigens. Methods Mol Biol 2023; 2673:167-174. [PMID: 37258913 DOI: 10.1007/978-1-0716-3239-0_11] [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
Tumor-specific neoantigens play important roles in tumor immunotherapy. How to predict neoantigens accurately and efficiently has attracted much attention. TSNAD is the first one-stop neoantigen prediction tool from next-generation sequencing data, and TSNAdb provides both predicted and validated neoantigens based on pan-cancer immunogenomics analyses. In this chapter, we describe the usage of TSNAD and TSNAdb for the clinical application of neoantigens. The latest version of TSNAD is available at https://pgx.zju.edu.cn/tsnad , and the latest version of TSNAdb is available at https://pgx.zju.edu.cn/tsnadb .
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Affiliation(s)
- Jingcheng Wu
- Innovative Institute for Artificial Intelligence in Medicine and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Zhan Zhou
- Innovative Institute for Artificial Intelligence in Medicine and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China.
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48
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Kazemi MH, Sadri M, Najafi A, Rahimi A, Baghernejadan Z, Khorramdelazad H, Falak R. Tumor-infiltrating lymphocytes for treatment of solid tumors: It takes two to tango? Front Immunol 2022; 13:1018962. [PMID: 36389779 PMCID: PMC9651159 DOI: 10.3389/fimmu.2022.1018962] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 10/14/2022] [Indexed: 07/30/2023] Open
Abstract
Tumor-infiltrating lymphocytes (TILs), frontline soldiers of the adaptive immune system, are recruited into the tumor site to fight against tumors. However, their small number and reduced activity limit their ability to overcome the tumor. Enhancement of TILs number and activity against tumors has been of interest for a long time. A lack of knowledge about the tumor microenvironment (TME) has limited success in primary TIL therapies. Although the advent of engineered T cells has revolutionized the immunotherapy methods of hematologic cancers, the heterogeneity of solid tumors warrants the application of TILs with a wide range of specificity. Recent advances in understanding TME, immune exhaustion, and immune checkpoints have paved the way for TIL therapy regimens. Nowadays, TIL therapy has regained attention as a safe personalized immunotherapy, and currently, several clinical trials are evaluating the efficacy of TIL therapy in patients who have failed conventional immunotherapies. Gaining favorable outcomes following TIL therapy of patients with metastatic melanoma, cervical cancer, ovarian cancer, and breast cancer has raised hope in patients with refractory solid tumors, too. Nevertheless, TIL therapy procedures face several challenges, such as high cost, timely expansion, and technical challenges in selecting and activating the cells. Herein, we reviewed the recent advances in the TIL therapy of solid tumors and discussed the challenges and perspectives.
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Affiliation(s)
- Mohammad Hossein Kazemi
- Department of Immunology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
- Immunology Research Center, Institute of Immunology and Infectious Diseases, Iran University of Medical Sciences, Tehran, Iran
| | - Maryam Sadri
- Department of Immunology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
- Immunology Research Center, Institute of Immunology and Infectious Diseases, Iran University of Medical Sciences, Tehran, Iran
| | - Alireza Najafi
- Department of Immunology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
- Immunology Research Center, Institute of Immunology and Infectious Diseases, Iran University of Medical Sciences, Tehran, Iran
| | - Ali Rahimi
- Department of Immunology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
- Immunology Research Center, Institute of Immunology and Infectious Diseases, Iran University of Medical Sciences, Tehran, Iran
| | - Zeinab Baghernejadan
- Department of Immunology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
- Immunology Research Center, Institute of Immunology and Infectious Diseases, Iran University of Medical Sciences, Tehran, Iran
| | - Hossein Khorramdelazad
- Department of Immunology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Reza Falak
- Department of Immunology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
- Immunology Research Center, Institute of Immunology and Infectious Diseases, Iran University of Medical Sciences, Tehran, Iran
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Furuya G, Katoh H, Atsumi S, Hashimoto I, Komura D, Hatanaka R, Senga S, Hayashi S, Akita S, Matsumura H, Miura A, Mita H, Nakakido M, Nagatoishi S, Sugiyama A, Suzuki R, Konishi H, Yamamoto A, Abe H, Hiraoka N, Aoki K, Kato Y, Seto Y, Yoshimura C, Miyadera K, Tsumoto K, Ushiku T, Ishikawa S. Nucleic acid-triggered tumoral immunity propagates pH-selective therapeutic antibodies through tumor-driven epitope spreading. Cancer Sci 2022; 114:321-338. [PMID: 36136061 PMCID: PMC9807517 DOI: 10.1111/cas.15596] [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: 08/11/2022] [Revised: 09/09/2022] [Accepted: 09/12/2022] [Indexed: 01/07/2023] Open
Abstract
Important roles of humoral tumor immunity are often pointed out; however, precise profiles of dominant antigens and developmental mechanisms remain elusive. We systematically investigated the humoral antigens of dominant intratumor immunoglobulin clones found in human cancers. We found that approximately half of the corresponding antigens were restricted to strongly and densely negatively charged polymers, resulting in simultaneous reactivities of the antibodies to both densely sulfated glycosaminoglycans (dsGAGs) and nucleic acids (NAs). These anti-dsGAG/NA antibodies matured and expanded via intratumoral immunological driving force of innate immunity via NAs. These human cancer-derived antibodies exhibited acidic pH-selective affinity across both antigens and showed specific reactivity to diverse spectrums of human tumor cells. The antibody-drug conjugate exerted therapeutic effects against multiple cancers in vivo by targeting cell surface dsGAG antigens. This study reveals that intratumoral immunological reactions propagate tumor-oriented immunoglobulin clones and demonstrates a new therapeutic modality for the universal treatment of human malignancies.
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Affiliation(s)
- Genta Furuya
- Department of Preventive medicine, Graduate School of MedicineThe University of TokyoTokyoJapan
| | - Hiroto Katoh
- Department of Preventive medicine, Graduate School of MedicineThe University of TokyoTokyoJapan
| | - Shinichiro Atsumi
- Department of Preventive medicine, Graduate School of MedicineThe University of TokyoTokyoJapan
| | - Itaru Hashimoto
- Department of Preventive medicine, Graduate School of MedicineThe University of TokyoTokyoJapan
| | - Daisuke Komura
- Department of Preventive medicine, Graduate School of MedicineThe University of TokyoTokyoJapan
| | - Ryo Hatanaka
- Discovery and Preclinical Research DivisionTaiho Pharmaceutical Co., Ltd.IbarakiJapan
| | - Shogo Senga
- Discovery and Preclinical Research DivisionTaiho Pharmaceutical Co., Ltd.IbarakiJapan
| | - Shuto Hayashi
- Department of Preventive medicine, Graduate School of MedicineThe University of TokyoTokyoJapan
| | - Shoji Akita
- Discovery and Preclinical Research DivisionTaiho Pharmaceutical Co., Ltd.IbarakiJapan
| | - Hirofumi Matsumura
- Discovery and Preclinical Research DivisionTaiho Pharmaceutical Co., Ltd.IbarakiJapan
| | - Akihiro Miura
- Discovery and Preclinical Research DivisionTaiho Pharmaceutical Co., Ltd.IbarakiJapan
| | - Hideaki Mita
- Department of Preventive medicine, Graduate School of MedicineThe University of TokyoTokyoJapan
| | - Makoto Nakakido
- Laboratory of Medical Proteomics, Institute of Medical ScienceThe University of TokyoTokyoJapan
| | - Satoru Nagatoishi
- Laboratory of Medical Proteomics, Institute of Medical ScienceThe University of TokyoTokyoJapan
| | - Akira Sugiyama
- Laboratory of Systems Biology and MedicineResearch Center for Advanced Science and Technology, The University of TokyoTokyoJapan
| | - Ryohei Suzuki
- Department of Preventive medicine, Graduate School of MedicineThe University of TokyoTokyoJapan
| | - Hiroki Konishi
- Department of Preventive medicine, Graduate School of MedicineThe University of TokyoTokyoJapan
| | - Asami Yamamoto
- Department of Preventive medicine, Graduate School of MedicineThe University of TokyoTokyoJapan
| | - Hiroyuki Abe
- Department of Pathology, Graduate School of MedicineThe University of TokyoTokyoJapan
| | - Nobuyoshi Hiraoka
- Department of Analytical PathologyNational Cancer Center Research InstituteTokyoJapan
| | - Kazunori Aoki
- Division of Molecular and Cellular MedicineNational Cancer Center Research InstituteTokyoJapan
| | - Yasumasa Kato
- Department of Oral Function and Molecular BiologyOhu University School of DentistryFukushimaJapan
| | - Yasuyuki Seto
- Department of Gastrointestinal SurgeryGraduate School of Medicine, The University of TokyoTokyoJapan
| | - Chihoko Yoshimura
- Discovery and Preclinical Research DivisionTaiho Pharmaceutical Co., Ltd.IbarakiJapan
| | - Kazutaka Miyadera
- Discovery and Preclinical Research DivisionTaiho Pharmaceutical Co., Ltd.IbarakiJapan
| | - Kouhei Tsumoto
- Laboratory of Medical Proteomics, Institute of Medical ScienceThe University of TokyoTokyoJapan
| | - Tetsuo Ushiku
- Department of Pathology, Graduate School of MedicineThe University of TokyoTokyoJapan
| | - Shumpei Ishikawa
- Department of Preventive medicine, Graduate School of MedicineThe University of TokyoTokyoJapan
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Zhang H, Ye L, Yu X, Jin K, Wu W. Neoadjuvant therapy alters the immune microenvironment in pancreatic cancer. Front Immunol 2022; 13:956984. [PMID: 36225934 PMCID: PMC9548645 DOI: 10.3389/fimmu.2022.956984] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 09/08/2022] [Indexed: 11/13/2022] Open
Abstract
Pancreatic cancer has an exclusive inhibitory tumor microenvironment characterized by a dense mechanical barrier, profound infiltration of immunosuppressive cells, and a lack of penetration of effector T cells, which constitute an important cause for recurrence and metastasis, resistance to chemotherapy, and insensitivity to immunotherapy. Neoadjuvant therapy has been widely used in clinical practice due to its many benefits, including the ability to improve the R0 resection rate, eliminate tumor cell micrometastases, and identify highly malignant tumors that may not benefit from surgery. In this review, we summarize multiple aspects of the effect of neoadjuvant therapy on the immune microenvironment of pancreatic cancer, discuss possible mechanisms by which these changes occur, and generalize the theoretical basis of neoadjuvant chemoradiotherapy combined with immunotherapy, providing support for the development of more effective combination therapeutic strategies to induce potent immune responses to tumors.
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Affiliation(s)
- Huiru Zhang
- Department of Pancreatic Surgery, Shanghai Cancer Centre, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Pancreatic Cancer Institute, Fudan University, Shanghai, China
- Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Longyun Ye
- Department of Pancreatic Surgery, Shanghai Cancer Centre, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Pancreatic Cancer Institute, Fudan University, Shanghai, China
- Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Xianjun Yu
- Department of Pancreatic Surgery, Shanghai Cancer Centre, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Pancreatic Cancer Institute, Fudan University, Shanghai, China
- Pancreatic Cancer Institute, Fudan University, Shanghai, China
- *Correspondence: Weiding Wu, ; Kaizhou Jin, ; Xianjun Yu,
| | - Kaizhou Jin
- Department of Pancreatic Surgery, Shanghai Cancer Centre, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Pancreatic Cancer Institute, Fudan University, Shanghai, China
- Pancreatic Cancer Institute, Fudan University, Shanghai, China
- *Correspondence: Weiding Wu, ; Kaizhou Jin, ; Xianjun Yu,
| | - Weiding Wu
- Department of Pancreatic Surgery, Shanghai Cancer Centre, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Pancreatic Cancer Institute, Fudan University, Shanghai, China
- Pancreatic Cancer Institute, Fudan University, Shanghai, China
- *Correspondence: Weiding Wu, ; Kaizhou Jin, ; Xianjun Yu,
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