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Zheng J, Li X, Masci AM, Kahn H, Huffman A, Asfaw E, Pan Y, Guo J, He V, Song J, Seleznev AI, Lin AY, He Y. Empowering standardization of cancer vaccines through ontology: enhanced modeling and data analysis. J Biomed Semantics 2024; 15:12. [PMID: 38890666 PMCID: PMC11186274 DOI: 10.1186/s13326-024-00312-3] [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: 04/02/2024] [Accepted: 05/21/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND The exploration of cancer vaccines has yielded a multitude of studies, resulting in a diverse collection of information. The heterogeneity of cancer vaccine data significantly impedes effective integration and analysis. While CanVaxKB serves as a pioneering database for over 670 manually annotated cancer vaccines, it is important to distinguish that a database, on its own, does not offer the structured relationships and standardized definitions found in an ontology. Recognizing this, we expanded the Vaccine Ontology (VO) to include those cancer vaccines present in CanVaxKB that were not initially covered, enhancing VO's capacity to systematically define and interrelate cancer vaccines. RESULTS An ontology design pattern (ODP) was first developed and applied to semantically represent various cancer vaccines, capturing their associated entities and relations. By applying the ODP, we generated a cancer vaccine template in a tabular format and converted it into the RDF/OWL format for generation of cancer vaccine terms in the VO. '12MP vaccine' was used as an example of cancer vaccines to demonstrate the application of the ODP. VO also reuses reference ontology terms to represent entities such as cancer diseases and vaccine hosts. Description Logic (DL) and SPARQL query scripts were developed and used to query for cancer vaccines based on different vaccine's features and to demonstrate the versatility of the VO representation. Additionally, ontological modeling was applied to illustrate cancer vaccine related concepts and studies for in-depth cancer vaccine analysis. A cancer vaccine-specific VO view, referred to as "CVO," was generated, and it contains 928 classes including 704 cancer vaccines. The CVO OWL file is publicly available on: http://purl.obolibrary.org/obo/vo/cvo.owl , for sharing and applications. CONCLUSION To facilitate the standardization, integration, and analysis of cancer vaccine data, we expanded the Vaccine Ontology (VO) to systematically model and represent cancer vaccines. We also developed a pipeline to automate the inclusion of cancer vaccines and associated terms in the VO. This not only enriches the data's standardization and integration, but also leverages ontological modeling to deepen the analysis of cancer vaccine information, maximizing benefits for researchers and clinicians. AVAILABILITY The VO-cancer GitHub website is: https://github.com/vaccineontology/VO/tree/master/CVO .
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Affiliation(s)
- Jie Zheng
- Unit for Laboratory Animal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Xingxian Li
- College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Anna Maria Masci
- Data Impact and Governance, Technology Data and Innovation, University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Hayleigh Kahn
- College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Anthony Huffman
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Eliyas Asfaw
- University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Yuanyi Pan
- Unit for Laboratory Animal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jinjing Guo
- Unit for Laboratory Animal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Virginia He
- The College of Brown University, Brown University, Providence, RI, 02912, USA
| | - Justin Song
- College of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Andrey I Seleznev
- Dietrich School of Arts and Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Asiyah Yu Lin
- Axle Research and Technology, Rockville, MD, 20852, USA
| | - Yongqun He
- Unit for Laboratory Animal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA.
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
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Wisdom AJ, Barker CA, Chang JY, Demaria S, Formenti S, Grassberger C, Gregucci F, Hoppe BS, Kirsch DG, Marciscano AE, Mayadev J, Mouw KW, Palta M, Wu CC, Jabbour SK, Schoenfeld JD. The Next Chapter in Immunotherapy and Radiation Combination Therapy: Cancer-Specific Perspectives. Int J Radiat Oncol Biol Phys 2024; 118:1404-1421. [PMID: 38184173 DOI: 10.1016/j.ijrobp.2023.12.046] [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: 12/11/2023] [Revised: 12/20/2023] [Accepted: 12/30/2023] [Indexed: 01/08/2024]
Abstract
Immunotherapeutic agents have revolutionized cancer treatment over the past decade. However, most patients fail to respond to immunotherapy alone. A growing body of preclinical studies highlights the potential for synergy between radiation therapy and immunotherapy, but the outcomes of clinical studies have been mixed. This review summarizes the current state of immunotherapy and radiation combination therapy across cancers, highlighting existing challenges and promising areas for future investigation.
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Affiliation(s)
- Amy J Wisdom
- Harvard Radiation Oncology Program, Boston, Massachusetts
| | - Christopher A Barker
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Joe Y Chang
- Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sandra Demaria
- Department of Radiation Oncology, Weill Cornell Medicine, New York, New York
| | - Silvia Formenti
- Department of Radiation Oncology, Weill Cornell Medicine, New York, New York
| | - Clemens Grassberger
- Department of Radiation Oncology, University of Washington, Fred Hutch Cancer Center, Seattle, Washington
| | - Fabiana Gregucci
- Department of Radiation Oncology, Weill Cornell Medicine, New York, New York
| | - Bradford S Hoppe
- Department of Radiation Oncology, Mayo Clinic, Jacksonville, Florida
| | - David G Kirsch
- Department of Radiation Oncology, University of Toronto, Radiation Medicine Program, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Ariel E Marciscano
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, Massachusetts
| | - Jyoti Mayadev
- Department of Radiation Oncology, UC San Diego School of Medicine, San Diego, California
| | - Kent W Mouw
- Department of Radiation Oncology, Brigham and Women's Hospital/Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Manisha Palta
- Department of Radiation Oncology, Duke Cancer Center, Durham, North Carolina
| | - Cheng-Chia Wu
- Department of Radiation Oncology, Columbia University Irving Medical Center, New York, New York
| | - Salma K Jabbour
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey.
| | - Jonathan D Schoenfeld
- Department of Radiation Oncology, Brigham and Women's Hospital/Dana-Farber Cancer Institute, Boston, Massachusetts.
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Heras-Murillo I, Adán-Barrientos I, Galán M, Wculek SK, Sancho D. Dendritic cells as orchestrators of anticancer immunity and immunotherapy. Nat Rev Clin Oncol 2024; 21:257-277. [PMID: 38326563 DOI: 10.1038/s41571-024-00859-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/09/2024] [Indexed: 02/09/2024]
Abstract
Dendritic cells (DCs) are a heterogeneous group of antigen-presenting innate immune cells that regulate adaptive immunity, including against cancer. Therefore, understanding the precise activities of DCs in tumours and patients with cancer is important. The classification of DC subsets has historically been based on ontogeny; however, single-cell analyses are now additionally revealing a diversity of functional states of DCs in cancer. DCs can promote the activation of potent antitumour T cells and immune responses via numerous mechanisms, although they can also be hijacked by tumour-mediated factors to contribute to immune tolerance and cancer progression. Consequently, DC activities are often key determinants of the efficacy of immunotherapies, including immune-checkpoint inhibitors. Potentiating the antitumour functions of DCs or using them as tools to orchestrate short-term and long-term anticancer immunity has immense but as-yet underexploited therapeutic potential. In this Review, we outline the nature and emerging complexity of DC states as well as their functions in regulating adaptive immunity across different cancer types. We also describe how DCs are required for the success of current immunotherapies and explore the inherent potential of targeting DCs for cancer therapy. We focus on novel insights on DCs derived from patients with different cancers, single-cell studies of DCs and their relevance to therapeutic strategies.
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Affiliation(s)
- Ignacio Heras-Murillo
- Immunobiology Laboratory, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Irene Adán-Barrientos
- Immunobiology Laboratory, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Miguel Galán
- Immunobiology Laboratory, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Stefanie K Wculek
- Innate Immune Biology Laboratory, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
| | - David Sancho
- Immunobiology Laboratory, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain.
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Salvato I, Marchini A. Immunotherapeutic Strategies for the Treatment of Glioblastoma: Current Challenges and Future Perspectives. Cancers (Basel) 2024; 16:1276. [PMID: 38610954 PMCID: PMC11010873 DOI: 10.3390/cancers16071276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 03/14/2024] [Accepted: 03/21/2024] [Indexed: 04/14/2024] Open
Abstract
Despite decades of research and the best up-to-date treatments, grade 4 Glioblastoma (GBM) remains uniformly fatal with a patient median overall survival of less than 2 years. Recent advances in immunotherapy have reignited interest in utilizing immunological approaches to fight cancer. However, current immunotherapies have so far not met the anticipated expectations, achieving modest results in their journey from bench to bedside for the treatment of GBM. Understanding the intrinsic features of GBM is of crucial importance for the development of effective antitumoral strategies to improve patient life expectancy and conditions. In this review, we provide a comprehensive overview of the distinctive characteristics of GBM that significantly influence current conventional therapies and immune-based approaches. Moreover, we present an overview of the immunotherapeutic strategies currently undergoing clinical evaluation for GBM treatment, with a specific emphasis on those advancing to phase 3 clinical studies. These encompass immune checkpoint inhibitors, adoptive T cell therapies, vaccination strategies (i.e., RNA-, DNA-, and peptide-based vaccines), and virus-based approaches. Finally, we explore novel innovative strategies and future prospects in the field of immunotherapy for GBM.
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Affiliation(s)
- Ilaria Salvato
- NORLUX Neuro-Oncology Laboratory, Department of Cancer Research, Luxembourg Institute of Health (LIH), L-1210 Luxembourg, Luxembourg;
- Laboratory of Oncolytic Virus Immuno-Therapeutics (LOVIT), Department of Cancer Research, Luxembourg Institute of Health (LIH), L-1210 Luxembourg, Luxembourg
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine (FSTM), University of Luxembourg, L-4367 Belvaux, Luxembourg
| | - Antonio Marchini
- Laboratory of Oncolytic Virus Immuno-Therapeutics (LOVIT), Department of Cancer Research, Luxembourg Institute of Health (LIH), L-1210 Luxembourg, Luxembourg
- Laboratory of Oncolytic Virus Immuno-Therapeutics, German Cancer Research Center, 69120 Heidelberg, Germany
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Di Nunno V, Aprile M, Bartolini S, Gatto L, Tosoni A, Ranieri L, De Biase D, Asioli S, Franceschi E. The Biological and Clinical Role of the Telomerase Reverse Transcriptase Gene in Glioblastoma: A Potential Therapeutic Target? Cells 2023; 13:44. [PMID: 38201248 PMCID: PMC10778438 DOI: 10.3390/cells13010044] [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: 10/25/2023] [Revised: 12/15/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024] Open
Abstract
Glioblastoma IDH-wildtype represents the most lethal and frequent primary tumor of the central nervous system. Thanks to important scientific efforts, we can now investigate its deep genomic assessment, elucidating mutated genes and altered biological mechanisms in addition to its clinical aggressiveness. The telomerase reverse transcriptase gene (TERT) is the most frequently altered gene in solid tumors, including brain tumors and GBM IDH-wildtype. In particular, it can be observed in approximately 80-90% of GBM IDH-wildtype cases. Its clonal distribution on almost all cancer cells makes this gene an optimal target. However, the research of effective TERT inhibitors is complicated by several biological and clinical obstacles which can be only partially surmounted. Very recently, novel immunological approaches leading to TERT inhibition have been investigated, offering the potential to develop an effective target for this altered protein. Here, we perform a narrative review investigating the biological role of TERT alterations on glioblastoma and the principal obstacles associated with TERT inhibitions in this population. Moreover, we discuss possible combination treatment strategies to overcome these limitations.
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Affiliation(s)
- Vincenzo Di Nunno
- Nervous System Medical Oncology Department, IRCCS Istituto delle Scienze Neurologiche di Bologna, 40139 Bologna, Italy (E.F.)
| | - Marta Aprile
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138 Bologna, Italy
| | - Stefania Bartolini
- Nervous System Medical Oncology Department, IRCCS Istituto delle Scienze Neurologiche di Bologna, 40139 Bologna, Italy (E.F.)
| | - Lidia Gatto
- Department of Oncology, Azienda Unità Sanitaria Locale (AUSL) Bologna, 40139 Bologna, Italy
| | - Alicia Tosoni
- Nervous System Medical Oncology Department, IRCCS Istituto delle Scienze Neurologiche di Bologna, 40139 Bologna, Italy (E.F.)
| | - Lucia Ranieri
- Nervous System Medical Oncology Department, IRCCS Istituto delle Scienze Neurologiche di Bologna, 40139 Bologna, Italy (E.F.)
| | - Dario De Biase
- Solid Tumor Molecular Pathology Laboratory, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy
- Department of Pharmacy and Biotechnology (FaBit), University of Bologna, 40126 Bologna, Italy
| | - Sofia Asioli
- IRCCS Istituto delle Scienze Neurologiche di Bologna, 40139 Bologna, Italy
- Department of Biomedical and Neuromotor Sciences (DIBINEM), Surgical Pathology Section, Alma Mater Studiorum, University of Bologna, 40126 Bologna, Italy
| | - Enrico Franceschi
- Nervous System Medical Oncology Department, IRCCS Istituto delle Scienze Neurologiche di Bologna, 40139 Bologna, Italy (E.F.)
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