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Xin K, Wei X, Shao J, Chen F, Liu Q, Liu B. Establishment of a novel tumor neoantigen prediction tool for personalized vaccine design. Hum Vaccin Immunother 2024; 20:2300881. [PMID: 38214336 DOI: 10.1080/21645515.2023.2300881] [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: 09/06/2023] [Accepted: 12/28/2023] [Indexed: 01/13/2024] Open
Abstract
The personalized neoantigen nanovaccine (PNVAC) platform for patients with gastric cancer we established previously exhibited promising anti-tumor immunoreaction. However, limited by the ability of traditional neoantigen prediction tools, a portion of epitopes failed to induce specific immune response. In order to filter out more neoantigens to optimize our PNVAC platform, we develop a novel neoantigen prediction model, NUCC. This prediction tool trained through a deep learning approach exhibits better neoantigen prediction performance than other prediction tools, not only in two independent epitope datasets, but also in a totally new epitope dataset we construct from scratch, including 25 patients with advance gastric cancer and 150 candidate mutant peptides, 13 of which prove to be neoantigen by immunogenicity test in vitro. Our work lay the foundation for the improvement of our PNVAC platform for gastric cancer in the future.
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Affiliation(s)
- Kai Xin
- Department of Oncology, Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Nanjing, Jiangsu Province, China
| | - Xiao Wei
- Department of Pathology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, Jiangsu Province, China
| | - Jie Shao
- Department of Oncology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, Jiangsu Province, China
| | - Fangjun Chen
- Department of Oncology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, Jiangsu Province, China
| | - Qin Liu
- Department of Oncology, Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Nanjing, Jiangsu Province, China
- Department of Oncology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, Jiangsu Province, China
| | - Baorui Liu
- Department of Oncology, Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Nanjing, Jiangsu Province, China
- Department of Oncology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, Jiangsu Province, China
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2
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Aparicio B, Theunissen P, Hervas-Stubbs S, Fortes P, Sarobe P. Relevance of mutation-derived neoantigens and non-classical antigens for anticancer therapies. Hum Vaccin Immunother 2024; 20:2303799. [PMID: 38346926 PMCID: PMC10863374 DOI: 10.1080/21645515.2024.2303799] [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: 09/29/2023] [Accepted: 01/06/2024] [Indexed: 02/15/2024] Open
Abstract
Efficacy of cancer immunotherapies relies on correct recognition of tumor antigens by lymphocytes, eliciting thus functional responses capable of eliminating tumor cells. Therefore, important efforts have been carried out in antigen identification, with the aim of understanding mechanisms of response to immunotherapy and to design safer and more efficient strategies. In addition to classical tumor-associated antigens identified during the last decades, implementation of next-generation sequencing methodologies is enabling the identification of neoantigens (neoAgs) arising from mutations, leading to the development of new neoAg-directed therapies. Moreover, there are numerous non-classical tumor antigens originated from other sources and identified by new methodologies. Here, we review the relevance of neoAgs in different immunotherapies and the results obtained by applying neoAg-based strategies. In addition, the different types of non-classical tumor antigens and the best approaches for their identification are described. This will help to increase the spectrum of targetable molecules useful in cancer immunotherapies.
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Affiliation(s)
- Belen Aparicio
- Program of Immunology and Immunotherapy, Center for Applied Medical Research (CIMA) University of Navarra, Pamplona, Spain
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
- Navarra Institute for Health Research (IDISNA), Pamplona, Spain
- CIBERehd, Pamplona, Spain
| | - Patrick Theunissen
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
- Navarra Institute for Health Research (IDISNA), Pamplona, Spain
- CIBERehd, Pamplona, Spain
- DNA and RNA Medicine Division, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
| | - Sandra Hervas-Stubbs
- Program of Immunology and Immunotherapy, Center for Applied Medical Research (CIMA) University of Navarra, Pamplona, Spain
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
- Navarra Institute for Health Research (IDISNA), Pamplona, Spain
- CIBERehd, Pamplona, Spain
| | - Puri Fortes
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
- Navarra Institute for Health Research (IDISNA), Pamplona, Spain
- CIBERehd, Pamplona, Spain
- DNA and RNA Medicine Division, Center for Applied Medical Research (CIMA), University of Navarra, Pamplona, Spain
- Spanish Network for Advanced Therapies (TERAV ISCIII), Spain
| | - Pablo Sarobe
- Program of Immunology and Immunotherapy, Center for Applied Medical Research (CIMA) University of Navarra, Pamplona, Spain
- Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain
- Navarra Institute for Health Research (IDISNA), Pamplona, Spain
- CIBERehd, Pamplona, Spain
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3
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Ramirez CA, Becker-Hapak M, Singhal K, Russler-Germain DA, Frenkel F, Barnell EK, McClain ED, Desai S, Schappe T, Onyeador OC, Kudryashova O, Belousov V, Bagaev A, Ocheredko E, Kiwala S, Hundal J, Skidmore ZL, Watkins MP, Mooney TB, Walker JR, Krysiak K, Gomez F, Fronick CC, Fulton RS, Schreiber RD, Mehta-Shah N, Cashen AF, Kahl BS, Ataullakhanov R, Bartlett NL, Griffith M, Griffith OL, Fehniger TA. Neoantigen landscape supports feasibility of personalized cancer vaccine for follicular lymphoma. Blood Adv 2024; 8:4035-4049. [PMID: 38713894 PMCID: PMC11339042 DOI: 10.1182/bloodadvances.2022007792] [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: 04/07/2022] [Revised: 04/18/2024] [Accepted: 04/23/2024] [Indexed: 05/09/2024] Open
Abstract
ABSTRACT Personalized cancer vaccines designed to target neoantigens represent a promising new treatment paradigm in oncology. In contrast to classical idiotype vaccines, we hypothesized that "polyvalent" vaccines could be engineered for the personalized treatment of follicular lymphoma (FL) using neoantigen discovery by combined whole-exome sequencing (WES) and RNA sequencing (RNA-seq). Fifty-eight tumor samples from 57 patients with FL underwent WES and RNA-seq. Somatic and B-cell clonotype neoantigens were predicted and filtered to identify high-quality neoantigens. B-cell clonality was determined by the alignment of B-cell receptor (BCR) CDR3 regions from RNA-seq data, grouping at the protein level, and comparison with the BCR repertoire from healthy individuals using RNA-seq data. An average of 52 somatic mutations per patient (range, 2-172) were identified, and ≥2 (median, 15) high-quality neoantigens were predicted for 56 of 58 FL samples. The predicted neoantigen peptides were composed of missense mutations (77%), indels (9%), gene fusions (3%), and BCR sequences (11%). Building off of these preclinical analyses, we initiated a pilot clinical trial using personalized neoantigen vaccination combined with PD-1 blockade in patients with relapsed or refractory FL (#NCT03121677). Synthetic long peptide vaccines targeting predicted high-quality neoantigens were successfully synthesized for and administered to all 4 patients enrolled. Initial results demonstrate feasibility, safety, and potential immunologic and clinical responses. Our study suggests that a genomics-driven personalized cancer vaccine strategy is feasible for patients with FL, and this may overcome prior challenges in the field. This trial was registered at www.ClinicalTrials.gov as #NCT03121677.
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Affiliation(s)
- Cody A. Ramirez
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
| | | | - Kartik Singhal
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
| | - David A. Russler-Germain
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO
| | | | - Erica K. Barnell
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
| | - Ethan D. McClain
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Sweta Desai
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Timothy Schappe
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | | | | | | | | | | | - Susanna Kiwala
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
| | - Jasreet Hundal
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
| | - Zachary L. Skidmore
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
| | - Marcus P. Watkins
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Thomas B. Mooney
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
| | - Jason R. Walker
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
| | - Kilannin Krysiak
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Felicia Gomez
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Catrina C. Fronick
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
| | - Robert S. Fulton
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
| | - Robert D. Schreiber
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Neha Mehta-Shah
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO
| | - Amanda F. Cashen
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO
| | - Brad S. Kahl
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO
| | | | - Nancy L. Bartlett
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO
| | - Malachi Griffith
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO
- Department of Genetics, Washington University School of Medicine, St. Louis, MO
| | - Obi L. Griffith
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO
- Department of Genetics, Washington University School of Medicine, St. Louis, MO
| | - Todd A. Fehniger
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO
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4
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Johanns TM, Garfinkle EA, Miller KE, Livingstone AJ, Roberts KF, Rao Venkata LP, Dowling JL, Chicoine MR, Dacey RG, Zipfel GJ, Kim AH, Mardis ER, Dunn GP. Integrating Multisector Molecular Characterization into Personalized Peptide Vaccine Design for Patients with Newly Diagnosed Glioblastoma. Clin Cancer Res 2024; 30:2729-2742. [PMID: 38639919 PMCID: PMC11215407 DOI: 10.1158/1078-0432.ccr-23-3077] [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: 10/16/2023] [Revised: 01/18/2024] [Accepted: 04/15/2024] [Indexed: 04/20/2024]
Abstract
PURPOSE Outcomes for patients with glioblastoma (GBM) remain poor despite multimodality treatment with surgery, radiation, and chemotherapy. There are few immunotherapy options due to the lack of tumor immunogenicity. Several clinical trials have reported promising results with cancer vaccines. To date, studies have used data from a single tumor site to identify targetable antigens, but this approach limits the antigen pool and is antithetical to the heterogeneity of GBM. We have implemented multisector sequencing to increase the pool of neoantigens across the GBM genomic landscape that can be incorporated into personalized peptide vaccines called NeoVax. PATIENTS AND METHODS In this study, we report the findings of four patients enrolled onto the NeoVax clinical trial (NCT0342209). RESULTS Immune reactivity to NeoVax neoantigens was assessed in peripheral blood mononuclear cells pre- and post-NeoVax for patients 1 to 3 using IFNγ-ELISPOT assay. A statistically significant increase in IFNγ producing T cells at the post-NeoVax time point for several neoantigens was observed. Furthermore, a post-NeoVax tumor biopsy was obtained from patient 3 and, upon evaluation, revealed evidence of infiltrating, clonally expanded T cells. CONCLUSIONS Collectively, our findings suggest that NeoVax stimulated the expansion of neoantigen-specific effector T cells and provide encouraging results to aid in the development of future neoantigen vaccine-based clinical trials in patients with GBM. Herein, we demonstrate the feasibility of incorporating multisector sampling in cancer vaccine design and provide information on the clinical applicability of clonality, distribution, and immunogenicity of the neoantigen landscape in patients with GBM.
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Affiliation(s)
- Tanner M. Johanns
- Division of Medical Oncology, Washington University School of Medicine, St. Louis, Missouri.
- Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, Missouri.
- The Brain Tumor Center at Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri.
| | - Elizabeth A.R. Garfinkle
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio.
| | - Katherine E. Miller
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio.
| | | | - Kaleigh F. Roberts
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri.
| | - Lakshmi P. Rao Venkata
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio.
| | - Joshua L. Dowling
- The Brain Tumor Center at Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri.
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, Missouri.
| | - Michael R. Chicoine
- Department of Neurosurgery, University of Missouri in Columbia, Columbia, Missouri.
| | - Ralph G. Dacey
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, Missouri.
| | - Gregory J. Zipfel
- The Brain Tumor Center at Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri.
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, Missouri.
| | - Albert H. Kim
- The Brain Tumor Center at Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri.
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, Missouri.
| | - Elaine R. Mardis
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio.
- Department of Pediatrics, Ohio State University College of Medicine, Columbus, Ohio.
| | - Gavin P. Dunn
- Department of Neurosurgery, Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts.
- Brain Tumor Immunology and Immunotherapy Program, Department of Neurosurgery, Harvard Medical School, Massachusetts General Hospital, Boston, Massachusetts.
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5
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Sueangoen N, Thuwajit P, Yenchitsomanus PT, Thuwajit C. Public neoantigens in breast cancer immunotherapy (Review). Int J Mol Med 2024; 54:65. [PMID: 38904202 PMCID: PMC11188978 DOI: 10.3892/ijmm.2024.5388] [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: 01/17/2024] [Accepted: 05/15/2024] [Indexed: 06/22/2024] Open
Abstract
Among women globally, breast cancer is the most prevalent cancer and the leading cause of cancer‑related death. Interestingly, though genetic mutations contribute to the disease, <15% of women diagnosed with breast cancer have a family history of the disease, suggesting a prevalence of sporadic genetic mutations in breast cancer development. In the rapidly rising field of cancer genomics, neoantigen‑based immunotherapy has come to the fore. The investigation of novel proteins arising from unique somatic mutations or neoantigens have opened a new pathway for both individualized and public cancer treatments. Because they are shared among individuals with similar genetic changes, public neoantigens provide an opportunity for 'off‑the‑shelf' anticancer therapies, potentially extending the benefits to a wider patient group. The present review aimed to highlight the role of shared or public neoantigens as therapeutic targets for patients with breast cancer, emphasizing common hotspot mutations of certain genes identified in breast cancer. The clinical utilization of public neoantigen‑based therapies for breast cancer treatment were also discussed.
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Affiliation(s)
- Natthaporn Sueangoen
- Research Center, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Peti Thuwajit
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Pa-Thai Yenchitsomanus
- Siriraj Center of Research Excellence for Cancer Immunotherapy (SiCORE-CIT), Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
- Division of Molecular Medicine, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Chanitra Thuwajit
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
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6
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Xia H, Hoang M, Schmidt E, Kiwala S, McMichael J, Skidmore ZL, Fisk B, Song JJ, Hundal J, Mooney T, Walker JR, Peter Goedegebuure S, Miller CA, Gillanders WE, Griffith OL, Griffith M. pVACview: an interactive visualization tool for efficient neoantigen prioritization and selection. ARXIV 2024:arXiv:2406.06985v1. [PMID: 38947921 PMCID: PMC11213132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Background Neoantigen targeting therapies including personalized vaccines have shown promise in the treatment of cancers, particularly when used in combination with checkpoint blockade therapy. At least 100 clinical trials involving these therapies are underway globally. Accurate identification and prioritization of neoantigens is highly relevant to designing these trials, predicting treatment response, and understanding mechanisms of resistance. With the advent of massively parallel DNA and RNA sequencing technologies, it is now possible to computationally predict neoantigens based on patient-specific variant information. However, numerous factors must be considered when prioritizing neoantigens for use in personalized therapies. Complexities such as alternative transcript annotations, various binding, presentation and immunogenicity prediction algorithms, and variable peptide lengths/registers all potentially impact the neoantigen selection process. There has been a rapid development of computational tools that attempt to account for these complexities. While these tools generate numerous algorithmic predictions for neoantigen characterization, results from these pipelines are difficult to navigate and require extensive knowledge of the underlying tools for accurate interpretation. This often leads to over-simplification of pipeline outputs to make them tractable, for example limiting prediction to a single RNA isoform or only summarizing the top ranked of many possible peptide candidates. In addition to variant detection, gene expression and predicted peptide binding affinities, recent studies have also demonstrated the importance of mutation location, allele-specific anchor locations, and variation of T-cell response to long versus short peptides. Due to the intricate nature and number of salient neoantigen features, presenting all relevant information to facilitate candidate selection for downstream applications is a difficult challenge that current tools fail to address. Results We have created pVACview, the first interactive tool designed to aid in the prioritization and selection of neoantigen candidates for personalized neoantigen therapies including cancer vaccines. pVACview has a user-friendly and intuitive interface where users can upload, explore, select and export their neoantigen candidates. The tool allows users to visualize candidates across three different levels, including variant, transcript and peptide information. Conclusions pVACview will allow researchers to analyze and prioritize neoantigen candidates with greater efficiency and accuracy in basic and translational settings The application is available as part of the pVACtools pipeline at pvactools.org and as an online server at pvacview.org.
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Affiliation(s)
- Huiming Xia
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - My Hoang
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Evelyn Schmidt
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Susanna Kiwala
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Joshua McMichael
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Zachary L Skidmore
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Bryan Fisk
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Jonathan J Song
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Jasreet Hundal
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Thomas Mooney
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Jason R Walker
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - S Peter Goedegebuure
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Christopher A Miller
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | - William E Gillanders
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Obi L Griffith
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Malachi Griffith
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
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7
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Chaudhry Z, Boyadzhyan A, Sasaninia K, Rai V. Targeting Neoantigens in Cancer: Possibilities and Opportunities in Breast Cancer. Antibodies (Basel) 2024; 13:46. [PMID: 38920970 PMCID: PMC11200483 DOI: 10.3390/antib13020046] [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: 05/13/2024] [Revised: 06/05/2024] [Accepted: 06/06/2024] [Indexed: 06/27/2024] Open
Abstract
As one of the most prevalent forms of cancer worldwide, breast cancer has garnered significant attention within the clinical research setting. While traditional treatment employs a multidisciplinary approach including a variety of therapies such as chemotherapy, hormone therapy, and even surgery, researchers have since directed their attention to the budding role of neoantigens. Neoantigens are defined as tumor-specific antigens that result from a multitude of genetic alterations, the most prevalent of which is the single nucleotide variant. As a result of their foreign nature, neoantigens elicit immune responses upon presentation by Major Histocompatibility Complexes I and II followed by recognition by T cell receptors. Previously, researchers have been able to utilize these immunogenic properties and manufacture neoantigen-specific T-cells and neoantigen vaccines. Within the context of breast cancer, biomarkers such as tumor protein 53 (TP53), Survivin, Partner and Localizer of BRCA2 (PALB2), and protein tyrosine phosphatase receptor T (PTPRT) display exceeding potential to serve as neoantigens. However, despite their seemingly limitless potential, neoantigens must overcome various obstacles if they are to be fairly distributed to patients. For instance, a prolonged period between the identification of a neoantigen and the dispersal of treatment poses a serious risk within the context of breast cancer. Regardless of these current obstacles, it appears highly promising that future research into neoantigens will make an everlasting impact on the health outcomes within the realm of breast cancer. The purpose of this literature review is to comprehensively discuss the etiology of various forms of breast cancer and current treatment modalities followed by the significance of neoantigens in cancer therapeutics and their application to breast cancer. Further, we have discussed the limitations, future directions, and the role of transcriptomics in neoantigen identification and personalized medicine. The concepts discussed in the original and review articles were included in this review article.
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Affiliation(s)
| | | | | | - Vikrant Rai
- Department of Translational Research, College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA 91766, USA; (Z.C.); (A.B.); (K.S.)
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8
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Martin MV, Aguilar-Rosas S, Franke K, Pieterse M, Langelaar JV, Schreurs R, Bijlsma MF, Besselink MG, Koster J, Timens W, Khasraw M, Ashley DM, Keir ST, Ottensmeier CH, King EV, Verheij J, Waasdorp C, Valk PJM, Engels SAG, Oostenbach E, van Dinter JT, Hofman DA, Mok JY, van Esch WJE, Wilmink H, Monkhorst K, Verheul HMW, Poel D, Hiltermann TJN, Kempen LCLTV, Groen HJM, Aerts JGJV, Heesch SV, Löwenberg B, Plasterk R, Kloosterman WP. The Neo-Open Reading Frame Peptides That Comprise the Tumor Framome Are a Rich Source of Neoantigens for Cancer Immunotherapy. Cancer Immunol Res 2024; 12:759-778. [PMID: 38573707 DOI: 10.1158/2326-6066.cir-23-0158] [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: 02/21/2023] [Revised: 09/22/2023] [Accepted: 03/27/2024] [Indexed: 04/05/2024]
Abstract
Identification of immunogenic cancer neoantigens as targets for therapy is challenging. Here, we integrate the whole-genome and long-read transcript sequencing of cancers to identify the collection of neo-open reading frame peptides (NOP) expressed in tumors. We termed this collection of NOPs the tumor framome. NOPs represent tumor-specific peptides that are different from wild-type proteins and may be strongly immunogenic. We describe a class of hidden NOPs that derive from structural genomic variants involving an upstream protein coding gene driving expression and translation of noncoding regions of the genome downstream of a rearrangement breakpoint, i.e., where no gene annotation or evidence for transcription exists. The entire collection of NOPs represents a vast number of possible neoantigens particularly in tumors with many structural genomic variants and a low number of missense mutations. We show that NOPs are immunogenic and epitopes derived from NOPs can bind to MHC class I molecules. Finally, we provide evidence for the presence of memory T cells specific for hidden NOPs in peripheral blood from a patient with lung cancer. This work highlights NOPs as a major source of possible neoantigens for personalized cancer immunotherapy and provides a rationale for analyzing the complete cancer genome and transcriptome as a basis for the detection of NOPs.
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Affiliation(s)
| | | | - Katka Franke
- CureVac Netherlands B.V., Amsterdam, the Netherlands
| | - Mark Pieterse
- CureVac Netherlands B.V., Amsterdam, the Netherlands
| | | | | | - Maarten F Bijlsma
- Amsterdam UMC location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory for Experimental Oncology and Radiobiology, Amsterdam, the Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, the Netherlands
| | - Marc G Besselink
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, the Netherlands
- Amsterdam UMC, location University of Amsterdam, Department of Surgery, Amsterdam, the Netherlands
| | - Jan Koster
- Amsterdam UMC location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory for Experimental Oncology and Radiobiology, Amsterdam, the Netherlands
| | - Wim Timens
- Department of Pathology and Medical Biology, University of Groningen, University, Medical Center Groningen, the Netherlands
| | - Mustafa Khasraw
- Duke University Medical Center, Duke University, Durham, North Carolina
| | - David M Ashley
- Preston Robert Tisch Brain Tumor Center, Department of Neurosurgery, Duke University, Durham, North Carolina
| | - Stephen T Keir
- Duke University Medical Center, Duke University, Durham, North Carolina
| | - Christian H Ottensmeier
- Liverpool Head and Neck Centre, Institute of Systems, Molecular and Integrative Biology, University of Liverpool and Clatterbridge Cancer Center NHS Foundation Trust, Liverpool, UK
| | - Emma V King
- Department of Otorhinolaryngology, Head and Neck Surgery, Poole Hospital, Poole, UK
| | - Joanne Verheij
- Amsterdam UMC, location University of Amsterdam, Department of Pathology, Amsterdam, the Netherlands
| | - Cynthia Waasdorp
- Amsterdam UMC location University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory for Experimental Oncology and Radiobiology, Amsterdam, the Netherlands
| | - Peter J M Valk
- Department of Hematology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Sem A G Engels
- The Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Ellen Oostenbach
- The Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Jip T van Dinter
- The Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Damon A Hofman
- The Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Juk Yee Mok
- Sanquin Reagents, Sanquin, Amsterdam, the Netherlands
| | | | - Hanneke Wilmink
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, the Netherlands
- Amsterdam UMC, location University of Amsterdam, Department of Medical Oncology, Amsterdam, the Netherlands
| | - Kim Monkhorst
- Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Henk M W Verheul
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Dennis Poel
- Department of Medical Oncology, Radboud University Medical Center, Nijmegen, the, Netherlands
| | - T Jeroen N Hiltermann
- Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, the Netherlands
| | - Léon C L T van Kempen
- Department of Pathology and Medical Biology, University of Groningen, University, Medical Center Groningen, the Netherlands
- University of Antwerp, Antwerp University Hospital, Edegem, Belgium
| | - Harry J M Groen
- Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, the Netherlands
| | | | | | - Bob Löwenberg
- CureVac Netherlands B.V., Amsterdam, the Netherlands
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9
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Bulashevska A, Nacsa Z, Lang F, Braun M, Machyna M, Diken M, Childs L, König R. Artificial intelligence and neoantigens: paving the path for precision cancer immunotherapy. Front Immunol 2024; 15:1394003. [PMID: 38868767 PMCID: PMC11167095 DOI: 10.3389/fimmu.2024.1394003] [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: 02/29/2024] [Accepted: 05/13/2024] [Indexed: 06/14/2024] Open
Abstract
Cancer immunotherapy has witnessed rapid advancement in recent years, with a particular focus on neoantigens as promising targets for personalized treatments. The convergence of immunogenomics, bioinformatics, and artificial intelligence (AI) has propelled the development of innovative neoantigen discovery tools and pipelines. These tools have revolutionized our ability to identify tumor-specific antigens, providing the foundation for precision cancer immunotherapy. AI-driven algorithms can process extensive amounts of data, identify patterns, and make predictions that were once challenging to achieve. However, the integration of AI comes with its own set of challenges, leaving space for further research. With particular focus on the computational approaches, in this article we have explored the current landscape of neoantigen prediction, the fundamental concepts behind, the challenges and their potential solutions providing a comprehensive overview of this rapidly evolving field.
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Affiliation(s)
- Alla Bulashevska
- Host-Pathogen-Interactions, Paul-Ehrlich-Institut, Langen, Germany
| | - Zsófia Nacsa
- Host-Pathogen-Interactions, Paul-Ehrlich-Institut, Langen, Germany
| | - Franziska Lang
- TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg University gGmbH, Mainz, Germany
| | - Markus Braun
- Host-Pathogen-Interactions, Paul-Ehrlich-Institut, Langen, Germany
| | - Martin Machyna
- Host-Pathogen-Interactions, Paul-Ehrlich-Institut, Langen, Germany
| | - Mustafa Diken
- TRON - Translational Oncology at the University Medical Center of the Johannes Gutenberg University gGmbH, Mainz, Germany
| | - Liam Childs
- Host-Pathogen-Interactions, Paul-Ehrlich-Institut, Langen, Germany
| | - Renate König
- Host-Pathogen-Interactions, Paul-Ehrlich-Institut, Langen, Germany
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10
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Mösch A, Grazioli F, Machart P, Malone B. NeoAgDT: optimization of personal neoantigen vaccine composition by digital twin simulation of a cancer cell population. Bioinformatics 2024; 40:btae205. [PMID: 38614133 PMCID: PMC11076149 DOI: 10.1093/bioinformatics/btae205] [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: 07/07/2023] [Revised: 03/28/2024] [Accepted: 04/11/2024] [Indexed: 04/15/2024] Open
Abstract
MOTIVATION Neoantigen vaccines make use of tumor-specific mutations to enable the patient's immune system to recognize and eliminate cancer. Selecting vaccine elements, however, is a complex task which needs to take into account not only the underlying antigen presentation pathway but also tumor heterogeneity. RESULTS Here, we present NeoAgDT, a two-step approach consisting of: (i) simulating individual cancer cells to create a digital twin of the patient's tumor cell population and (ii) optimizing the vaccine composition by integer linear programming based on this digital twin. NeoAgDT shows improved selection of experimentally validated neoantigens over ranking-based approaches in a study of seven patients. AVAILABILITY AND IMPLEMENTATION The NeoAgDT code is published on Github: https://github.com/nec-research/neoagdt.
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Affiliation(s)
- Anja Mösch
- Biomedical AI Group, NEC Laboratories Europe GmbH, Heidelberg 69115, Germany
| | - Filippo Grazioli
- Biomedical AI Group, NEC Laboratories Europe GmbH, Heidelberg 69115, Germany
| | - Pierre Machart
- Biomedical AI Group, NEC Laboratories Europe GmbH, Heidelberg 69115, Germany
| | - Brandon Malone
- Biomedical AI Group, NEC Laboratories Europe GmbH, Heidelberg 69115, Germany
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11
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Desai N, Chavda V, Singh TRR, Thorat ND, Vora LK. Cancer Nanovaccines: Nanomaterials and Clinical Perspectives. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2401631. [PMID: 38693099 DOI: 10.1002/smll.202401631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 03/30/2024] [Indexed: 05/03/2024]
Abstract
Cancer nanovaccines represent a promising frontier in cancer immunotherapy, utilizing nanotechnology to augment traditional vaccine efficacy. This review comprehensively examines the current state-of-the-art in cancer nanovaccine development, elucidating innovative strategies and technologies employed in their design. It explores both preclinical and clinical advancements, emphasizing key studies demonstrating their potential to elicit robust anti-tumor immune responses. The study encompasses various facets, including integrating biomaterial-based nanocarriers for antigen delivery, adjuvant selection, and the impact of nanoscale properties on vaccine performance. Detailed insights into the complex interplay between the tumor microenvironment and nanovaccine responses are provided, highlighting challenges and opportunities in optimizing therapeutic outcomes. Additionally, the study presents a thorough analysis of ongoing clinical trials, presenting a snapshot of the current clinical landscape. By curating the latest scientific findings and clinical developments, this study aims to serve as a comprehensive resource for researchers and clinicians engaged in advancing cancer immunotherapy. Integrating nanotechnology into vaccine design holds immense promise for revolutionizing cancer treatment paradigms, and this review provides a timely update on the evolving landscape of cancer nanovaccines.
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Affiliation(s)
- Nimeet Desai
- Department of Biomedical Engineering, Indian Institute of Technology Hyderabad, Kandi, Telangana, 502285, India
| | - Vivek Chavda
- Department of Pharmaceutics and Pharmaceutical Technology, L M College of Pharmacy, Ahmedabad, 380009, India
| | | | - Nanasaheb D Thorat
- Limerick Digital Cancer Research Centre (LDCRC), University of Limerick, Castletroy, Limerick, V94T9PX, Ireland
- Department of Physics, Bernal Institute, Castletroy, Limerick, V94T9PX, Ireland
- Nuffield Department of Women's & Reproductive Health, Medical Science Division, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, UK
| | - Lalitkumar K Vora
- School of Pharmacy, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7BL, UK
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12
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Goldberg J, Qiao N, Guerriero JL, Gross B, Meneksedag Y, Lu YF, Philips AV, Rahman T, Meric-Bernstam F, Roszik J, Chen K, Jeselsohn R, Tolaney SM, Peoples GE, Alatrash G, Mittendorf EA. Estrogen Receptor Mutations as Novel Targets for Immunotherapy in Metastatic Estrogen Receptor-positive Breast Cancer. CANCER RESEARCH COMMUNICATIONS 2024; 4:496-504. [PMID: 38335301 PMCID: PMC10883292 DOI: 10.1158/2767-9764.crc-23-0244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 12/12/2023] [Accepted: 02/07/2024] [Indexed: 02/12/2024]
Abstract
Estrogen receptor-positive (ER+) breast cancer is not considered immunogenic and, to date, has been proven resistant to immunotherapy. Endocrine therapy remains the cornerstone of treatment for ER+ breast cancers. However, constitutively activating mutations in the estrogen receptor alpha (ESR1) gene can emerge during treatment, rendering tumors resistant to endocrine therapy. Although these mutations represent a pathway of resistance, they also represent a potential source of neoepitopes that can be targeted by immunotherapy. In this study, we investigated ESR1 mutations as novel targets for breast cancer immunotherapy. Using machine learning algorithms, we identified ESR1-derived peptides predicted to form stable complexes with HLA-A*0201. We then validated the binding affinity and stability of the top predicted peptides through in vitro binding and dissociation assays and showed that these peptides bind HLA-A*0201 with high affinity and stability. Using tetramer assays, we confirmed the presence and expansion potential of antigen-specific CTLs from healthy female donors. Finally, using in vitro cytotoxicity assays, we showed the lysis of peptide-pulsed targets and breast cancer cells expressing common ESR1 mutations by expanded antigen-specific CTLs. Ultimately, we identified five peptides derived from the three most common ESR1 mutations (D538G, Y537S, and E380Q) and their associated wild-type peptides, which were the most immunogenic. Overall, these data confirm the immunogenicity of epitopes derived from ESR1 and highlight the potential of these peptides to be targeted by novel immunotherapy strategies. SIGNIFICANCE Estrogen receptor (ESR1) mutations have emerged as a key factor in endocrine therapy resistance. We identified and validated five novel, immunogenic ESR1-derived peptides that could be targeted through vaccine-based immunotherapy.
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Affiliation(s)
- Jonathan Goldberg
- Division of Breast Surgery, Department of Surgery, Brigham and Women's Hospital, Boston, Massachusetts
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, Massachusetts
| | - Na Qiao
- Department of Hematopoietic Biology & Malignancy, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jennifer L Guerriero
- Division of Breast Surgery, Department of Surgery, Brigham and Women's Hospital, Boston, Massachusetts
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Brett Gross
- Division of Breast Surgery, Department of Surgery, Brigham and Women's Hospital, Boston, Massachusetts
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, Massachusetts
| | | | - Yoshimi F Lu
- McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas
| | - Anne V Philips
- Department of Hematopoietic Biology & Malignancy, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Tasnim Rahman
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, Massachusetts
| | - Funda Meric-Bernstam
- Department of Investigational Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jason Roszik
- Department of Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ken Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rinath Jeselsohn
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Sara M Tolaney
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | - Gheath Alatrash
- Department of Hematopoietic Biology & Malignancy, University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Stem Cell Transplant and Cellular Therapy, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Elizabeth A Mittendorf
- Division of Breast Surgery, Department of Surgery, Brigham and Women's Hospital, Boston, Massachusetts
- Breast Oncology Program, Dana-Farber Brigham Cancer Center, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
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13
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Sueangoen N, Grove H, Chuangchot N, Prasopsiri J, Rungrotmongkol T, Sanachai K, Darai N, Thongchot S, Suriyaphol P, Sa-Nguanraksa D, Thuwajit P, Yenchitsomanus PT, Thuwajit C. Stimulating T cell responses against patient-derived breast cancer cells with neoantigen peptide-loaded peripheral blood mononuclear cells. Cancer Immunol Immunother 2024; 73:43. [PMID: 38349410 PMCID: PMC10864427 DOI: 10.1007/s00262-024-03627-3] [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: 10/20/2023] [Accepted: 01/06/2024] [Indexed: 02/15/2024]
Abstract
Breast cancer stands as a formidable global health challenge for women. While neoantigens exhibit efficacy in activating T cells specific to cancer and instigating anti-tumor immune responses, the accuracy of neoantigen prediction remains suboptimal. In this study, we identified neoantigens from the patient-derived breast cancer cells, PC-B-142CA and PC-B-148CA cells, utilizing whole-genome and RNA sequencing. The pVAC-Seq pipeline was employed, with minor modification incorporating criteria (1) binding affinity of mutant (MT) peptide with HLA (IC50 MT) ≤ 500 nm in 3 of 5 algorithms and (2) IC50 wild type (WT)/MT > 1. Sequencing results unveiled 2513 and 3490 somatic mutations, and 646 and 652 non-synonymous mutations in PC-B-142CA and PC-B-148CA, respectively. We selected the top 3 neoantigens to perform molecular dynamic simulation and synthesized 9-12 amino acid neoantigen peptides, which were then pulsed onto healthy donor peripheral blood mononuclear cells (PBMCs). Results demonstrated that T cells activated by ADGRL1E274K, PARP1E619K, and SEC14L2R43Q peptides identified from PC-B-142CA exhibited significantly increased production of interferon-gamma (IFN-γ), while PARP1E619K and SEC14L2R43Q peptides induced the expression of CD107a on T cells. The % tumor cell lysis was notably enhanced by T cells activated with MT peptides across all three healthy donors. Moreover, ALKBH6V83M and GAAI823T peptides from PC-B-148CA remarkably stimulated IFN-γ- and CD107a-positive T cells, displaying high cell-killing activity against target cancer cells. In summary, our findings underscore the successful identification of neoantigens with anti-tumor T cell functions and highlight the potential of personalized neoantigens as a promising avenue for breast cancer treatment.
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Grants
- R016341038 The Research and Innovation Grant, the National Research Council of Thailand, Ministry of Higher Education, Science, Research and Innovation
- R016341038 The Research and Innovation Grant, the National Research Council of Thailand, Ministry of Higher Education, Science, Research and Innovation
- R016334002 Siriraj Research Grant, Faculty of Medicine Siriraj Hospital, Mahidol University
- R016334002 Siriraj Research Grant, Faculty of Medicine Siriraj Hospital, Mahidol University
- Mahidol University
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Affiliation(s)
- Natthaporn Sueangoen
- Graduate Program in Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Harald Grove
- Division of Bioinformatics and Data Management for Research, Research Group and Research Network Division, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Nisa Chuangchot
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Siriraj Center of Research Excellence for Cancer Immunotherapy (SiCORE-CIT), Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Jaturawitt Prasopsiri
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Thanyada Rungrotmongkol
- Center of Excellence in Biocatalyst and Sustainable Biotechnology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, Thailand
| | - Kamonpan Sanachai
- Department of Biochemistry, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
| | - Nitchakan Darai
- ASEAN Institute for Health Development, Mahidol University, Nakon Pathom, Thailand
| | - Suyanee Thongchot
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Siriraj Center of Research Excellence for Cancer Immunotherapy (SiCORE-CIT), Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Prapat Suriyaphol
- Division of Bioinformatics and Data Management for Research, Research Group and Research Network Division, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Doonyapat Sa-Nguanraksa
- Division of Head Neck and Breast Surgery, Department of Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Peti Thuwajit
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Pa-Thai Yenchitsomanus
- Siriraj Center of Research Excellence for Cancer Immunotherapy (SiCORE-CIT), Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Chanitra Thuwajit
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.
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14
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Atkins TK, Solanki A, Vasmatzis G, Cornette J, Riedel M. Evaluating NetMHCpan performance on non-European HLA alleles not present in training data. Front Immunol 2024; 14:1288105. [PMID: 38292493 PMCID: PMC10825027 DOI: 10.3389/fimmu.2023.1288105] [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: 09/03/2023] [Accepted: 12/21/2023] [Indexed: 02/01/2024] Open
Abstract
Bias in neural network model training datasets has been observed to decrease prediction accuracy for groups underrepresented in training data. Thus, investigating the composition of training datasets used in machine learning models with healthcare applications is vital to ensure equity. Two such machine learning models are NetMHCpan-4.1 and NetMHCIIpan-4.0, used to predict antigen binding scores to major histocompatibility complex class I and II molecules, respectively. As antigen presentation is a critical step in mounting the adaptive immune response, previous work has used these or similar predictions models in a broad array of applications, from explaining asymptomatic viral infection to cancer neoantigen prediction. However, these models have also been shown to be biased toward hydrophobic peptides, suggesting the network could also contain other sources of bias. Here, we report the composition of the networks' training datasets are heavily biased toward European Caucasian individuals and against Asian and Pacific Islander individuals. We test the ability of NetMHCpan-4.1 and NetMHCpan-4.0 to distinguish true binders from randomly generated peptides on alleles not included in the training datasets. Unexpectedly, we fail to find evidence that the disparities in training data lead to a meaningful difference in prediction quality for alleles not present in the training data. We attempt to explain this result by mapping the HLA sequence space to determine the sequence diversity of the training dataset. Furthermore, we link the residues which have the greatest impact on NetMHCpan predictions to structural features for three alleles (HLA-A*34:01, HLA-C*04:03, HLA-DRB1*12:02).
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Affiliation(s)
- Thomas Karl Atkins
- Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN, United States
| | - Arnav Solanki
- Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN, United States
| | - George Vasmatzis
- Biomarker Discovery Group, Mayo Clinic, Center for Individualized Medicine, Rochester, MN, United States
| | - James Cornette
- Department of Mathematics, Iowa State University, Ames, IA, United States
| | - Marc Riedel
- Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, MN, United States
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15
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Ricker CA, Meli K, Van Allen EM. Historical perspective and future directions: computational science in immuno-oncology. J Immunother Cancer 2024; 12:e008306. [PMID: 38191244 PMCID: PMC10826578 DOI: 10.1136/jitc-2023-008306] [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] [Accepted: 12/07/2023] [Indexed: 01/10/2024] Open
Abstract
Immuno-oncology holds promise for transforming patient care having achieved durable clinical response rates across a variety of advanced and metastatic cancers. Despite these achievements, only a minority of patients respond to immunotherapy, underscoring the importance of elucidating molecular mechanisms responsible for response and resistance to inform the development and selection of treatments. Breakthroughs in molecular sequencing technologies have led to the generation of an immense amount of genomic and transcriptomic sequencing data that can be mined to uncover complex tumor-immune interactions using computational tools. In this review, we discuss existing and emerging computational methods that contextualize the composition and functional state of the tumor microenvironment, infer the reactivity and clonal dynamics from reconstructed immune cell receptor repertoires, and predict the antigenic landscape for immune cell recognition. We further describe the advantage of multi-omics analyses for capturing multidimensional relationships and artificial intelligence techniques for integrating omics data with histopathological and radiological images to encapsulate patterns of treatment response and tumor-immune biology. Finally, we discuss key challenges impeding their widespread use and clinical application and conclude with future perspectives. We are hopeful that this review will both serve as a guide for prospective researchers seeking to use existing tools for scientific discoveries and inspire the optimization or development of novel tools to enhance precision, ultimately expediting advancements in immunotherapy that improve patient survival and quality of life.
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Affiliation(s)
- Cora A Ricker
- Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Kevin Meli
- Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
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16
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Li X, You J, Hong L, Liu W, Guo P, Hao X. Neoantigen cancer vaccines: a new star on the horizon. Cancer Biol Med 2023; 21:j.issn.2095-3941.2023.0395. [PMID: 38164734 PMCID: PMC11033713 DOI: 10.20892/j.issn.2095-3941.2023.0395] [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: 10/27/2023] [Accepted: 11/22/2023] [Indexed: 01/03/2024] Open
Abstract
Immunotherapy represents a promising strategy for cancer treatment that utilizes immune cells or drugs to activate the patient's own immune system and eliminate cancer cells. One of the most exciting advances within this field is the targeting of neoantigens, which are peptides derived from non-synonymous somatic mutations that are found exclusively within cancer cells and absent in normal cells. Although neoantigen-based therapeutic vaccines have not received approval for standard cancer treatment, early clinical trials have yielded encouraging outcomes as standalone monotherapy or when combined with checkpoint inhibitors. Progress made in high-throughput sequencing and bioinformatics have greatly facilitated the precise and efficient identification of neoantigens. Consequently, personalized neoantigen-based vaccines tailored to each patient have been developed that are capable of eliciting a robust and long-lasting immune response which effectively eliminates tumors and prevents recurrences. This review provides a concise overview consolidating the latest clinical advances in neoantigen-based therapeutic vaccines, and also discusses challenges and future perspectives for this innovative approach, particularly emphasizing the potential of neoantigen-based therapeutic vaccines to enhance clinical efficacy against advanced solid tumors.
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Affiliation(s)
- Xiaoling Li
- Cell Biotechnology Laboratory, Tianjin Cancer Hospital Airport Hospital, Tianjin 300308, China
- National Clinical Research Center for Cancer, Tianjin 300060, China
- Haihe Laboratory of Synthetic Biology, Tianjin 300090, China
| | - Jian You
- Department of Thoracic Oncology, Tianjin Cancer Hospital Airport Hospital, Tianjin 300308, China
- Department of Thoracic Oncology Surgery, Tianjin Medical University Cancer Institute & Hospital, Tianjin 300060, China
| | - Liping Hong
- Cell Biotechnology Laboratory, Tianjin Cancer Hospital Airport Hospital, Tianjin 300308, China
- National Clinical Research Center for Cancer, Tianjin 300060, China
- Haihe Laboratory of Synthetic Biology, Tianjin 300090, China
| | - Weijiang Liu
- Cell Biotechnology Laboratory, Tianjin Cancer Hospital Airport Hospital, Tianjin 300308, China
- National Clinical Research Center for Cancer, Tianjin 300060, China
- Haihe Laboratory of Synthetic Biology, Tianjin 300090, China
| | - Peng Guo
- Cell Biotechnology Laboratory, Tianjin Cancer Hospital Airport Hospital, Tianjin 300308, China
- National Clinical Research Center for Cancer, Tianjin 300060, China
- Haihe Laboratory of Synthetic Biology, Tianjin 300090, China
| | - Xishan Hao
- Cell Biotechnology Laboratory, Tianjin Cancer Hospital Airport Hospital, Tianjin 300308, China
- National Clinical Research Center for Cancer, Tianjin 300060, China
- Haihe Laboratory of Synthetic Biology, Tianjin 300090, China
- Tianjin Medical University Cancer Institute & Hospital, Tianjin 300060, China
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17
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London CA, Gardner H, Zhao S, Knapp DW, Utturkar SM, Duval DL, Chambers MR, Ostrander E, Trent JM, Kuffel G. Leading the pack: Best practices in comparative canine cancer genomics to inform human oncology. Vet Comp Oncol 2023; 21:565-577. [PMID: 37778398 DOI: 10.1111/vco.12935] [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: 05/10/2023] [Revised: 08/17/2023] [Accepted: 08/18/2023] [Indexed: 10/03/2023]
Abstract
Pet dogs develop spontaneous cancers at a rate estimated to be five times higher than that of humans, providing a unique opportunity to study disease biology and evaluate novel therapeutic strategies in a model system that possesses an intact immune system and mirrors key aspects of human cancer biology. Despite decades of interest, effective utilization of pet dog cancers has been hindered by a limited repertoire of necessary cellular and molecular reagents for both in vitro and in vivo studies, as well as a dearth of information regarding the genomic landscape of these cancers. Recently, many of these critical gaps have been addressed through the generation of a highly annotated canine reference genome, the creation of several tools necessary for multi-omic analysis of canine tumours, and the development of a centralized repository for key genomic and associated clinical information from canine cancer patients, the Integrated Canine Data Commons. Together, these advances have catalysed multidisciplinary efforts designed to integrate the study of pet dog cancers more effectively into the translational continuum, with the ultimate goal of improving human outcomes. The current review summarizes this recent progress and provides a guide to resources and tools available for comparative study of pet dog cancers.
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Affiliation(s)
- Cheryl A London
- Cummings School of Veterinary Medicine, Tufts University, North Grafton, Massachusetts, USA
| | - Heather Gardner
- Cummings School of Veterinary Medicine, Tufts University, North Grafton, Massachusetts, USA
| | - Shaying Zhao
- University of Georgia Cancer Center, University of Georgia, Athens, Georgia, USA
| | - Deborah W Knapp
- College of Veterinary Medicine, Purdue University, West Lafayette, Indiana, USA
| | - Sagar M Utturkar
- Purdue Institute for Cancer Research, Purdue University, West Lafayette, Indiana, USA
| | - Dawn L Duval
- College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, USA
| | | | - Elaine Ostrander
- Cancer Genetics and Comparative Genomics Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Jeffrey M Trent
- Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - Gina Kuffel
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
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18
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Meng W, Schreiber RD, Lichti CF. Recent advances in immunopeptidomic-based tumor neoantigen discovery. Adv Immunol 2023; 160:1-36. [PMID: 38042584 DOI: 10.1016/bs.ai.2023.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2023]
Abstract
The role of aberrantly expressed proteins in tumors in driving immune-mediated control of cancer has been well documented for more than five decades. Today, we know that both aberrantly expressed normal proteins as well as mutant proteins (neoantigens) can function as tumor antigens in both humans and mice. Next-generation sequencing (NGS) and high-resolution mass spectrometry (MS) technologies have made significant advances since the early 2010s, enabling detection of rare but clinically relevant neoantigens recognized by T cells. MS profiling of tumor-specific immunopeptidomes remains the most direct method to identify mutant peptides bound to cellular MHC. However, the need for use of large numbers of cells or significant amounts of tumor tissue to achieve neoantigen detection has historically limited the application of MS. Newer, more sensitive MS technologies have recently demonstrated the capacities to detect neoantigens from fewer cells. Here, we highlight recent advancements in immunopeptidomics-based characterization of tumor-specific neoantigens. Various tumor antigen categories and neoantigen identification approaches are also discussed. Furthermore, we summarize recent reports that achieved successful tumor neoantigen detection by MS using a variety of starting materials, MS acquisition modes, and novel ion mobility devices.
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Affiliation(s)
- Wei Meng
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, United States; The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, Saint Louis, MO, United States
| | - Robert D Schreiber
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, United States; The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, Saint Louis, MO, United States.
| | - Cheryl F Lichti
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, MO, United States; The Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, Saint Louis, MO, United States.
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19
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Zhu Y, Li X, Chen T, Wang J, Zhou Y, Mu X, Du Y, Wang J, Tang J, Liu J. Personalised neoantigen-based therapy in colorectal cancer. Clin Transl Med 2023; 13:e1461. [PMID: 37921274 PMCID: PMC10623652 DOI: 10.1002/ctm2.1461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 10/06/2023] [Accepted: 10/13/2023] [Indexed: 11/04/2023] Open
Abstract
Colorectal cancer (CRC) has become one of the most common tumours with high morbidity, mortality and distinctive evolution mechanism. The neoantigens arising from the somatic mutations have become considerable treatment targets in the management of CRC. As cancer-specific aberrant peptides, neoantigens can trigger the robust host immune response and exert anti-tumour effects while minimising the emergence of adverse events commonly associated with alternative therapeutic regimens. In this review, we summarised the mechanism, generation, identification and prognostic significance of neoantigens, as well as therapeutic strategies challenges of neoantigen-based therapy in CRC. The evidence suggests that the establishment of personalised neoantigen-based therapy holds great promise as an effective treatment approach for patients with CRC.
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Affiliation(s)
- Ya‐Juan Zhu
- Department of Biotherapy and Cancer CenterState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
| | - Xiong Li
- Department of GastroenterologyThe Second Affiliated Hospital of Xi'an Jiaotong UniversityXi'anChina
| | - Ting‐Ting Chen
- The Second Clinical Medical College of Lanzhou UniversityLanzhouChina
| | - Jia‐Xiang Wang
- Department of Renal Cancer and MelanomaPeking University Cancer Hospital & InstituteBeijingChina
| | - Yi‐Xin Zhou
- Department of Biotherapy and Cancer CenterState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
| | - Xiao‐Li Mu
- Department of Biotherapy and Cancer CenterState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
| | - Yang Du
- Department of Biotherapy and Cancer CenterState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
| | - Jia‐Ling Wang
- Department of Biotherapy and Cancer CenterState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
| | - Jie Tang
- Clinical Trial CenterWest China HospitalSichuan UniversityChengduChina
| | - Ji‐Yan Liu
- Department of Biotherapy and Cancer CenterState Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengduChina
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20
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Wang YS, Kumari M, Chen GH, Hong MH, Yuan JPY, Tsai JL, Wu HC. mRNA-based vaccines and therapeutics: an in-depth survey of current and upcoming clinical applications. J Biomed Sci 2023; 30:84. [PMID: 37805495 PMCID: PMC10559634 DOI: 10.1186/s12929-023-00977-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 09/29/2023] [Indexed: 10/09/2023] Open
Abstract
mRNA-based drugs have tremendous potential as clinical treatments, however, a major challenge in realizing this drug class will promise to develop methods for safely delivering the bioactive agents with high efficiency and without activating the immune system. With regard to mRNA vaccines, researchers have modified the mRNA structure to enhance its stability and promote systemic tolerance of antigenic presentation in non-inflammatory contexts. Still, delivery of naked modified mRNAs is inefficient and results in low levels of antigen protein production. As such, lipid nanoparticles have been utilized to improve delivery and protect the mRNA cargo from extracellular degradation. This advance was a major milestone in the development of mRNA vaccines and dispelled skepticism about the potential of this technology to yield clinically approved medicines. Following the resounding success of mRNA vaccines for COVID-19, many other mRNA-based drugs have been proposed for the treatment of a variety of diseases. This review begins with a discussion of mRNA modifications and delivery vehicles, as well as the factors that influence administration routes. Then, we summarize the potential applications of mRNA-based drugs and discuss further key points pertaining to preclinical and clinical development of mRNA drugs targeting a wide range of diseases. Finally, we discuss the latest market trends and future applications of mRNA-based drugs.
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Affiliation(s)
- Yu-Shiuan Wang
- Institute of Cellular and Organismic Biology, Academia Sinica, No. 128, Academia Road, Section 2, Nankang, Taipei, 11529, Taiwan
| | - Monika Kumari
- Institute of Cellular and Organismic Biology, Academia Sinica, No. 128, Academia Road, Section 2, Nankang, Taipei, 11529, Taiwan
| | - Guan-Hong Chen
- Biomedical Translation Research Center (BioTReC), Academia Sinica, Taipei, 11571, Taiwan
| | - Ming-Hsiang Hong
- Biomedical Translation Research Center (BioTReC), Academia Sinica, Taipei, 11571, Taiwan
| | - Joyce Pei-Yi Yuan
- Biomedical Translation Research Center (BioTReC), Academia Sinica, Taipei, 11571, Taiwan
| | - Jui-Ling Tsai
- Institute of Cellular and Organismic Biology, Academia Sinica, No. 128, Academia Road, Section 2, Nankang, Taipei, 11529, Taiwan
| | - Han-Chung Wu
- Institute of Cellular and Organismic Biology, Academia Sinica, No. 128, Academia Road, Section 2, Nankang, Taipei, 11529, Taiwan.
- Biomedical Translation Research Center (BioTReC), Academia Sinica, Taipei, 11571, Taiwan.
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21
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FAN H, GE X, ZHOU X, LI Y, WANG A, HU Y. [Research Progress of Lung Cancer Vaccines]. ZHONGGUO FEI AI ZA ZHI = CHINESE JOURNAL OF LUNG CANCER 2023; 26:692-700. [PMID: 37985155 PMCID: PMC10600751 DOI: 10.3779/j.issn.1009-3419.2023.106.19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Indexed: 11/22/2023]
Abstract
With the development of medical technology, tumor vaccines as a novel precise immunotherapy approach have gradually received attention in clinical applications. Against the backdrop of the global corona virus disease 2019 (COVID-19) outbreak, vaccine technology has further advanced. Depending on the types of antigens, tumor vaccines can be divided into whole-cell vaccines, peptide vaccines, messenger ribonucleic acid (mRNA) vaccines, recombinant virus vaccines, etc. Although some tumor vaccines have been marketed and achieved certain therapeutic effects, the results of tumor vaccines in clinical trials have been unsatisfactory in the past period. With the maturation of next-generation sequencing (NGS) technology and the continuous development of bioinformatics, dynamic monitoring of the entire process of tumor subpopulation development has become a reality, which has laid a solid foundation for personalized, neoantigen-centered therapeutic tumor vaccines. This article reviews the recent developments of tumor vaccines of different types, starts with lung cancer and summarizes the achievements of tumor vaccines in clinical applications, and provides an outlook for the future development of antigen-centered tumor vaccines.
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22
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Pu T, Peddle A, Zhu J, Tejpar S, Verbandt S. Neoantigen identification: Technological advances and challenges. Methods Cell Biol 2023; 183:265-302. [PMID: 38548414 DOI: 10.1016/bs.mcb.2023.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/02/2024]
Abstract
Neoantigens have emerged as promising targets for cutting-edge immunotherapies, such as cancer vaccines and adoptive cell therapy. These neoantigens are unique to tumors and arise exclusively from somatic mutations or non-genomic aberrations in tumor proteins. They encompass a wide range of alterations, including genomic mutations, post-transcriptomic variants, and viral oncoproteins. With the advancements in technology, the identification of immunogenic neoantigens has seen rapid progress, raising new opportunities for enhancing their clinical significance. Prediction of neoantigens necessitates the acquisition of high-quality samples and sequencing data, followed by mutation calling. Subsequently, the pipeline involves integrating various tools that can predict the expression, processing, binding, and recognition potential of neoantigens. However, the continuous improvement of computational tools is constrained by the availability of datasets which contain validated immunogenic neoantigens. This review article aims to provide a comprehensive summary of the current knowledge as well as limitations in neoantigen prediction and validation. Additionally, it delves into the origin and biological role of neoantigens, offering a deeper understanding of their significance in the field of cancer immunotherapy. This article thus seeks to contribute to the ongoing efforts to harness neoantigens as powerful weapons in the fight against cancer.
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Affiliation(s)
- Ting Pu
- Digestive Oncology Unit, KULeuven, Leuven, Belgium
| | | | - Jingjing Zhu
- de Duve Institute, Université catholique de Louvain, Brussels, Belgium
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23
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Boll LM, Perera-Bel J, Rodriguez-Vida A, Arpí O, Rovira A, Juanpere N, Vázquez Montes de Oca S, Hernández-Llodrà S, Lloreta J, Albà MM, Bellmunt J. The impact of mutational clonality in predicting the response to immune checkpoint inhibitors in advanced urothelial cancer. Sci Rep 2023; 13:15287. [PMID: 37714872 PMCID: PMC10504302 DOI: 10.1038/s41598-023-42495-2] [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: 04/05/2023] [Accepted: 09/11/2023] [Indexed: 09/17/2023] Open
Abstract
Immune checkpoint inhibitors (ICI) have revolutionized cancer treatment and can result in complete remissions even at advanced stages of the disease. However, only a small fraction of patients respond to the treatment. To better understand which factors drive clinical benefit, we have generated whole exome and RNA sequencing data from 27 advanced urothelial carcinoma patients treated with anti-PD-(L)1 monoclonal antibodies. We assessed the influence on the response of non-synonymous mutations (tumor mutational burden or TMB), clonal and subclonal mutations, neoantigen load and various gene expression markers. We found that although TMB is significantly associated with response, this effect can be mostly explained by clonal mutations, present in all cancer cells. This trend was validated in an additional cohort. Additionally, we found that responders with few clonal mutations had abnormally high levels of T and B cell immune markers, suggesting that a high immune cell infiltration signature could be a better predictive biomarker for this subset of patients. Our results support the idea that highly clonal cancers are more likely to respond to ICI and suggest that non-additive effects of different signatures should be considered for predictive models.
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Affiliation(s)
| | | | - Alejo Rodriguez-Vida
- Hospital del Mar Research Institute, Barcelona, Spain
- Medical Oncology Department, Hospital del Mar, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Oncología (CIBERONC-ISCIII), Barcelona, Spain
| | - Oriol Arpí
- Hospital del Mar Research Institute, Barcelona, Spain
| | - Ana Rovira
- Hospital del Mar Research Institute, Barcelona, Spain
- Medical Oncology Department, Hospital del Mar, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Oncología (CIBERONC-ISCIII), Barcelona, Spain
| | | | | | | | - Josep Lloreta
- Hospital del Mar Research Institute, Barcelona, Spain
- Department of Medicine and Life Science, Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - M Mar Albà
- Hospital del Mar Research Institute, Barcelona, Spain.
- Catalan Institute for Research and Advanced Studies (ICREA), Barcelona, Spain.
| | - Joaquim Bellmunt
- Hospital del Mar Research Institute, Barcelona, Spain.
- Dana Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
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24
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Godazandeh K, Van Olmen L, Van Oudenhove L, Lefever S, Bogaert C, Fant B. Methods behind neoantigen prediction for personalized anticancer vaccines. Methods Cell Biol 2023; 183:161-186. [PMID: 38548411 DOI: 10.1016/bs.mcb.2023.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/02/2024]
Abstract
Next to conventional cancer therapies, immunotherapies such as immune checkpoint inhibitors have broadened the cancer treatment landscape over the past decades. Recent advances in next generation sequencing and bioinformatics technologies have made it possible to identify a patient's own immunogenic neoantigens. These cancer neoantigens serve as important targets for personalized immunotherapy which has the benefit of being more active and effective in targeting cancer cells. This paper is a step-by-step guide discussing the different analyses and challenges encountered during in-silico neoantigen prediction. The protocol describes all the tools and steps required for the identification of immunogenic neoantigens.
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25
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Nguyen BQT, Tran TPD, Nguyen HT, Nguyen TN, Pham TMQ, Nguyen HTP, Tran DH, Nguyen V, Tran TS, Pham TVN, Le MT, Phan MD, Giang H, Nguyen HN, Tran LS. Improvement in neoantigen prediction via integration of RNA sequencing data for variant calling. Front Immunol 2023; 14:1251603. [PMID: 37731488 PMCID: PMC10507271 DOI: 10.3389/fimmu.2023.1251603] [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: 07/02/2023] [Accepted: 08/17/2023] [Indexed: 09/22/2023] Open
Abstract
Introduction Neoantigen-based immunotherapy has emerged as a promising strategy for improving the life expectancy of cancer patients. This therapeutic approach heavily relies on accurate identification of cancer mutations using DNA sequencing (DNAseq) data. However, current workflows tend to provide a large number of neoantigen candidates, of which only a limited number elicit efficient and immunogenic T-cell responses suitable for downstream clinical evaluation. To overcome this limitation and increase the number of high-quality immunogenic neoantigens, we propose integrating RNA sequencing (RNAseq) data into the mutation identification step in the neoantigen prediction workflow. Methods In this study, we characterize the mutation profiles identified from DNAseq and/or RNAseq data in tumor tissues of 25 patients with colorectal cancer (CRC). Immunogenicity was then validated by ELISpot assay using long synthesis peptides (sLP). Results We detected only 22.4% of variants shared between the two methods. In contrast, RNAseq-derived variants displayed unique features of affinity and immunogenicity. We further established that neoantigen candidates identified by RNAseq data significantly increased the number of highly immunogenic neoantigens (confirmed by ELISpot) that would otherwise be overlooked if relying solely on DNAseq data. Discussion This integrative approach holds great potential for improving the selection of neoantigens for personalized cancer immunotherapy, ultimately leading to enhanced treatment outcomes and improved survival rates for cancer patients.
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Affiliation(s)
| | | | - Huu Thinh Nguyen
- University Medical Center Ho Chi Minh City, Ho Chi Minh, Vietnam
| | | | | | | | - Duc Huy Tran
- University Medical Center Ho Chi Minh City, Ho Chi Minh, Vietnam
| | - Vy Nguyen
- Medical Genetics Institute, Ho Chi Minh, Vietnam
| | - Thanh Sang Tran
- University Medical Center Ho Chi Minh City, Ho Chi Minh, Vietnam
| | | | - Minh-Triet Le
- University Medical Center Ho Chi Minh City, Ho Chi Minh, Vietnam
| | | | - Hoa Giang
- Medical Genetics Institute, Ho Chi Minh, Vietnam
| | | | - Le Son Tran
- Medical Genetics Institute, Ho Chi Minh, Vietnam
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26
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Ros J, Baraibar I, Saoudi N, Rodriguez M, Salvà F, Tabernero J, Élez E. Immunotherapy for Colorectal Cancer with High Microsatellite Instability: The Ongoing Search for Biomarkers. Cancers (Basel) 2023; 15:4245. [PMID: 37686520 PMCID: PMC10486610 DOI: 10.3390/cancers15174245] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 09/10/2023] Open
Abstract
Microsatellite instability (MSI) is a biological condition associated with inflamed tumors, high tumor mutational burden (TMB), and responses to immune checkpoint inhibitors. In colorectal cancer (CRC), MSI tumors are found in 5% of patients in the metastatic setting and 15% in early-stage disease. Following the impressive clinical activity of immune checkpoint inhibitors in the metastatic setting, associated with deep and long-lasting responses, the development of immune checkpoint inhibitors has expanded to early-stage disease. Several phase II trials have demonstrated a high rate of pathological complete responses, with some patients even spared from surgery. However, in both settings, not all patients respond and some responses are short, emphasizing the importance of the ongoing search for accurate biomarkers. While various biomarkers of response have been evaluated in the context of MSI CRC, including B2M and JAK1/2 mutations, TMB, WNT pathway mutations, and Lynch syndrome, with mixed results, liver metastases have been associated with a lack of activity in such strategies. To improve patient selection and treatment outcomes, further research is required to identify additional biomarkers and refine existing ones. This will allow for the development of personalized treatment approaches and the integration of novel therapeutic strategies for MSI CRC patients with liver metastases.
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Affiliation(s)
- Javier Ros
- Medical Oncology Department, Vall d’Hebron University Hospital, 08035 Barcelona, Spain; (J.R.); (I.B.); (N.S.); (M.R.); (F.S.); (J.T.)
- Vall d’Hebron Institute of Oncology, 08035 Barcelona, Spain
| | - Iosune Baraibar
- Medical Oncology Department, Vall d’Hebron University Hospital, 08035 Barcelona, Spain; (J.R.); (I.B.); (N.S.); (M.R.); (F.S.); (J.T.)
- Vall d’Hebron Institute of Oncology, 08035 Barcelona, Spain
| | - Nadia Saoudi
- Medical Oncology Department, Vall d’Hebron University Hospital, 08035 Barcelona, Spain; (J.R.); (I.B.); (N.S.); (M.R.); (F.S.); (J.T.)
- Vall d’Hebron Institute of Oncology, 08035 Barcelona, Spain
| | - Marta Rodriguez
- Medical Oncology Department, Vall d’Hebron University Hospital, 08035 Barcelona, Spain; (J.R.); (I.B.); (N.S.); (M.R.); (F.S.); (J.T.)
- Vall d’Hebron Institute of Oncology, 08035 Barcelona, Spain
| | - Francesc Salvà
- Medical Oncology Department, Vall d’Hebron University Hospital, 08035 Barcelona, Spain; (J.R.); (I.B.); (N.S.); (M.R.); (F.S.); (J.T.)
- Vall d’Hebron Institute of Oncology, 08035 Barcelona, Spain
| | - Josep Tabernero
- Medical Oncology Department, Vall d’Hebron University Hospital, 08035 Barcelona, Spain; (J.R.); (I.B.); (N.S.); (M.R.); (F.S.); (J.T.)
- Vall d’Hebron Institute of Oncology, 08035 Barcelona, Spain
| | - Elena Élez
- Medical Oncology Department, Vall d’Hebron University Hospital, 08035 Barcelona, Spain; (J.R.); (I.B.); (N.S.); (M.R.); (F.S.); (J.T.)
- Vall d’Hebron Institute of Oncology, 08035 Barcelona, Spain
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27
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Schindler NR, Braun DA. Antigenic targets in clear cell renal cell carcinoma. KIDNEY CANCER 2023; 7:81-91. [PMID: 38014393 PMCID: PMC10475986 DOI: 10.3233/kca-230006] [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: 05/16/2023] [Accepted: 07/11/2023] [Indexed: 11/29/2023]
Abstract
Immune checkpoint inhibitors (ICIs) have transformed the management of advanced renal cell carcinoma (RCC), but most patients still do not receive a long-term benefit from these therapies, and many experience off-target, immune-related adverse effects. RCC is also different from many other ICI-responsive tumors, as it has only a modest mutation burden, and total neoantigen load does not correlate with ICI response. In order to improve the efficacy and safety of immunotherapies for RCC, it is therefore critical to identify the antigens that are targeted in effective anti-tumor immunity. In this review, we describe the potential classes of target antigens, and provide examples of previous and ongoing efforts to investigate and target antigens in RCC, with a focus on clear cell histology. Ultimately, we believe that a concerted antigen discovery effort in RCC will enable an improved understanding of response and resistance to current therapies, and lay a foundation for the future development of "precision" antigen-directed immunotherapies.
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Affiliation(s)
- Nicholas R. Schindler
- Section of Medical Oncology, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
- Center of Molecular and Cellular Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - David A. Braun
- Section of Medical Oncology, Department of Internal Medicine, Yale School of Medicine, New Haven, CT, USA
- Center of Molecular and Cellular Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
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28
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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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29
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Bao L, Zhu P, Mou Y, Song Y, Qin Y. Targeting LSD1 in tumor immunotherapy: rationale, challenges and potential. Front Immunol 2023; 14:1214675. [PMID: 37483603 PMCID: PMC10360200 DOI: 10.3389/fimmu.2023.1214675] [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: 04/30/2023] [Accepted: 06/23/2023] [Indexed: 07/25/2023] Open
Abstract
Lysine-specific demethylase 1 (LSD1) is an enzyme that removes lysine methylation marks from nucleosome histone tails and plays an important role in cancer initiation, progression, metastasis, and recurrence. Recent research shows that LSD1 regulates tumor cells and immune cells through multiple upstream and downstream pathways, enabling tumor cells to adapt to the tumor microenvironment (TME). As a potential anti-tumor treatment strategy, immunotherapy has developed rapidly in the past few years. However, most patients have a low response rate to available immune checkpoint inhibitors (ICIs), including anti-PD-(L)1 therapy and CAR-T cell therapy, due to a broad array of immunosuppressive mechanisms. Notably, inhibition of LSD1 turns "cold tumors" into "hot tumors" and subsequently enhances tumor cell sensitivity to ICIs. This review focuses on recent advances in LSD1 and tumor immunity and discusses a potential therapeutic strategy for combining LSD1 inhibition with immunotherapy.
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Affiliation(s)
- Lei Bao
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, China
- College of Basic Medical Science, China Three Gorges University, Yichang, China
| | - Ping Zhu
- Department of Nephrology, The First College of Clinical Medical Science, China Three Gorges University, Yichang, China
- Institute of Infection and Inflammation, China Three Gorges University, Yichang, China
| | - Yuan Mou
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, China
- College of Basic Medical Science, China Three Gorges University, Yichang, China
| | - Yinhong Song
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, China
- College of Basic Medical Science, China Three Gorges University, Yichang, China
- Institute of Infection and Inflammation, China Three Gorges University, Yichang, China
| | - Ye Qin
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, China
- College of Basic Medical Science, China Three Gorges University, Yichang, China
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30
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Amaya-Ramirez D, Martinez-Enriquez LC, Parra-López C. Usefulness of Docking and Molecular Dynamics in Selecting Tumor Neoantigens to Design Personalized Cancer Vaccines: A Proof of Concept. Vaccines (Basel) 2023; 11:1174. [PMID: 37514989 PMCID: PMC10386133 DOI: 10.3390/vaccines11071174] [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: 03/17/2023] [Revised: 04/24/2023] [Accepted: 04/27/2023] [Indexed: 07/30/2023] Open
Abstract
Personalized cancer vaccines based on neoantigens are a new and promising treatment for cancer; however, there are still multiple unresolved challenges to using this type of immunotherapy. Among these, the effective identification of immunogenic neoantigens stands out, since the in silico tools used generate a significant portion of false positives. Inclusion of molecular simulation techniques can refine the results these tools produce. In this work, we explored docking and molecular dynamics to study the association between the stability of peptide-HLA complexes and their immunogenicity, using as a proof of concept two HLA-A2-restricted neoantigens that were already evaluated in vitro. The results obtained were in accordance with the in vitro immunogenicity, since the immunogenic neoantigen ASTN1 remained bound at both ends to the HLA-A2 molecule. Additionally, molecular dynamic simulation suggests that position 1 of the peptide has a more relevant role in stabilizing the N-terminus than previously proposed. Likewise, the mutations may have a "delocalized" effect on the peptide-HLA interaction, which means that the mutated amino acid influences the intensity of the interactions of distant amino acids of the peptide with the HLA. These findings allow us to propose the inclusion of molecular simulation techniques to improve the identification of neoantigens for cancer vaccines.
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Affiliation(s)
| | - Laura Camila Martinez-Enriquez
- Grupo de Inmunología y Medicina Traslacional, Departamento de Microbiología, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá 111321, Colombia
| | - Carlos Parra-López
- Grupo de Inmunología y Medicina Traslacional, Departamento de Microbiología, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá 111321, Colombia
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Xia H, McMichael J, Becker-Hapak M, Onyeador OC, Buchli R, McClain E, Pence P, Supabphol S, Richters MM, Basu A, Ramirez CA, Puig-Saus C, Cotto KC, Freshour SL, Hundal J, Kiwala S, Goedegebuure SP, Johanns TM, Dunn GP, Ribas A, Miller CA, Gillanders WE, Fehniger TA, Griffith OL, Griffith M. Computational prediction of MHC anchor locations guides neoantigen identification and prioritization. Sci Immunol 2023; 8:eabg2200. [PMID: 37027480 PMCID: PMC10450883 DOI: 10.1126/sciimmunol.abg2200] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 03/16/2023] [Indexed: 04/09/2023]
Abstract
Neoantigens are tumor-specific peptide sequences resulting from sources such as somatic DNA mutations. Upon loading onto major histocompatibility complex (MHC) molecules, they can trigger recognition by T cells. Accurate neoantigen identification is thus critical for both designing cancer vaccines and predicting response to immunotherapies. Neoantigen identification and prioritization relies on correctly predicting whether the presenting peptide sequence can successfully induce an immune response. Because most somatic mutations are single-nucleotide variants, changes between wild-type and mutated peptides are typically subtle and require cautious interpretation. A potentially underappreciated variable in neoantigen prediction pipelines is the mutation position within the peptide relative to its anchor positions for the patient's specific MHC molecules. Whereas a subset of peptide positions are presented to the T cell receptor for recognition, others are responsible for anchoring to the MHC, making these positional considerations critical for predicting T cell responses. We computationally predicted anchor positions for different peptide lengths for 328 common HLA alleles and identified unique anchoring patterns among them. Analysis of 923 tumor samples shows that 6 to 38% of neoantigen candidates are potentially misclassified and can be rescued using allele-specific knowledge of anchor positions. A subset of anchor results were orthogonally validated using protein crystallography structures. Representative anchor trends were experimentally validated using peptide-MHC stability assays and competition binding assays. By incorporating our anchor prediction results into neoantigen prediction pipelines, we hope to formalize, streamline, and improve the identification process for relevant clinical studies.
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Affiliation(s)
- Huiming Xia
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Joshua McMichael
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Michelle Becker-Hapak
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Onyinyechi C. Onyeador
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Rico Buchli
- Pure Protein LLC, Oklahoma City, OK 73104, USA
| | - Ethan McClain
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Patrick Pence
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Suangson Supabphol
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
- The Center of Excellence in Systems Biology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Megan M. Richters
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Anamika Basu
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Cody A. Ramirez
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Cristina Puig-Saus
- Division of Hematology/Oncology, Department of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Jonsson Comprehensive Cancer Center, Los Angeles, CA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | - Kelsy C. Cotto
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Sharon L. Freshour
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Jasreet Hundal
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - Susanna Kiwala
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
| | - S. Peter Goedegebuure
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Tanner M. Johanns
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Gavin P. Dunn
- Department of Neurosurgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Antoni Ribas
- Division of Hematology/Oncology, Department of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Jonsson Comprehensive Cancer Center, Los Angeles, CA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | - Christopher A. Miller
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | - William E. Gillanders
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Todd A. Fehniger
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Obi L. Griffith
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Malachi Griffith
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
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Xu Y, Nowsheen S, Deng M. DNA Repair Deficiency Regulates Immunity Response in Cancers: Molecular Mechanism and Approaches for Combining Immunotherapy. Cancers (Basel) 2023; 15:cancers15051619. [PMID: 36900418 PMCID: PMC10000854 DOI: 10.3390/cancers15051619] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/26/2023] [Accepted: 03/04/2023] [Indexed: 03/09/2023] Open
Abstract
Defects in DNA repair pathways can lead to genomic instability in multiple tumor types, which contributes to tumor immunogenicity. Inhibition of DNA damage response (DDR) has been reported to increase tumor susceptibility to anticancer immunotherapy. However, the interplay between DDR and the immune signaling pathways remains unclear. In this review, we will discuss how a deficiency in DDR affects anti-tumor immunity, highlighting the cGAS-STING axis as an important link. We will also review the clinical trials that combine DDR inhibition and immune-oncology treatments. A better understanding of these pathways will help exploit cancer immunotherapy and DDR pathways to improve treatment outcomes for various cancers.
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Affiliation(s)
- Yi Xu
- State Key Laboratory of Molecular Oncology and Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Somaira Nowsheen
- Department of Dermatology, University of California San Diego, San Diego, CA 92122, USA
- Correspondence: (S.N.); (M.D.)
| | - Min Deng
- State Key Laboratory of Molecular Oncology and Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
- Correspondence: (S.N.); (M.D.)
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Current Trends in Neoantigen-Based Cancer Vaccines. Pharmaceuticals (Basel) 2023; 16:ph16030392. [PMID: 36986491 PMCID: PMC10056833 DOI: 10.3390/ph16030392] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 02/18/2023] [Accepted: 02/24/2023] [Indexed: 03/08/2023] Open
Abstract
Cancer immunotherapies are treatments that use drugs or cells to activate patients’ own immune systems against cancer cells. Among them, cancer vaccines have recently been rapidly developed. Based on tumor-specific antigens referred to as neoantigens, these vaccines can be in various forms such as messenger (m)RNA and synthetic peptides to activate cytotoxic T cells and act with or without dendritic cells. Growing evidence suggests that neoantigen-based cancer vaccines possess a very promising future, yet the processes of immune recognition and activation to relay identification of a neoantigen through the histocompatibility complex (MHC) and T-cell receptor (TCR) remain unclear. Here, we describe features of neoantigens and the biological process of validating neoantigens, along with a discussion of recent progress in the scientific development and clinical applications of neoantigen-based cancer vaccines.
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Li T, Li Y, Zhu X, He Y, Wu Y, Ying T, Xie Z. Artificial intelligence in cancer immunotherapy: Applications in neoantigen recognition, antibody design and immunotherapy response prediction. Semin Cancer Biol 2023; 91:50-69. [PMID: 36870459 DOI: 10.1016/j.semcancer.2023.02.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 02/13/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023]
Abstract
Cancer immunotherapy is a method of controlling and eliminating tumors by reactivating the body's cancer-immunity cycle and restoring its antitumor immune response. The increased availability of data, combined with advancements in high-performance computing and innovative artificial intelligence (AI) technology, has resulted in a rise in the use of AI in oncology research. State-of-the-art AI models for functional classification and prediction in immunotherapy research are increasingly used to support laboratory-based experiments. This review offers a glimpse of the current AI applications in immunotherapy, including neoantigen recognition, antibody design, and prediction of immunotherapy response. Advancing in this direction will result in more robust predictive models for developing better targets, drugs, and treatments, and these advancements will eventually make their way into the clinical setting, pushing AI forward in the field of precision oncology.
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Affiliation(s)
- Tong Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Yupeng Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Xiaoyi Zhu
- MOE/NHC Key Laboratory of Medical Molecular Virology, Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China; Shanghai Engineering Research Center for Synthetic Immunology, Shanghai, China
| | - Yao He
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Yanling Wu
- MOE/NHC Key Laboratory of Medical Molecular Virology, Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China; Shanghai Engineering Research Center for Synthetic Immunology, Shanghai, China
| | - Tianlei Ying
- MOE/NHC Key Laboratory of Medical Molecular Virology, Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China; Shanghai Engineering Research Center for Synthetic Immunology, Shanghai, China.
| | - Zhi Xie
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China; Center for Precision Medicine, Sun Yat-sen University, Guangzhou, China.
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Wu Y, Feng L. Biomaterials-assisted construction of neoantigen vaccines for personalized cancer immunotherapy. Expert Opin Drug Deliv 2023; 20:323-333. [PMID: 36634017 DOI: 10.1080/17425247.2023.2168640] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
INTRODUCTION Cancer vaccine represents a promising strategy toward personalized immunotherapy, and its therapeutic potency highly relies on the specificity of tumor antigens. Among these extensively studied tumor antigens, neoantigens, a type of short synthetic peptides derived from random somatic mutations, have been shown to be able to elicit tumor-specific antitumor immune response for tumor suppression. However, challenges remain in the efficient and safe delivery of neoantigens to antigen-presenting cells inside lymph nodes for eliciting potent and sustained antitumor immune responses. The rapid advance of biomaterials including various nanomaterials, injectable hydrogels, and macroscopic scaffolds has been found to hold great promises to facilitate the construction of efficient cancer vaccines attributing to their high loading and controllable release capacities. AREAS COVERED In this review, we will summarize and discuss the recent advances in the utilization of different types of biomaterials to construct neoantigen-based cancer vaccines, followed by a simple perspective on the future development of such biomaterial-assisted cancer neoantigen vaccination and personalized immunotherapy. EXPERT OPINION These latest progresses in biomaterial-assisted cancer vaccinations have shown great promises in boosting substantially potentiated tumor-specific antitumor immunity to suppress tumor growth, thus preventing tumor metastasis and recurrence.
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Affiliation(s)
- Yumin Wu
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou, PR China
| | - Liangzhu Feng
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Soochow University, Suzhou, PR China
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D'Alise AM, Scarselli E. Getting personal in metastatic melanoma: neoantigen-based vaccines as a new therapeutic strategy. Curr Opin Oncol 2023; 35:94-99. [PMID: 36721894 PMCID: PMC9894148 DOI: 10.1097/cco.0000000000000923] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
PURPOSE OF REVIEW Cancer vaccines are facing renewed interest, thanks to the progress recently achieved in the immunotherapy field, including the success of immune checkpoint inhibitors (CPIs). The advances in understanding the CPI mode of action revealed a central role of neoantigens for the outcome of such treatments. Neoantigens became the preferred antigens for cancer vaccines and have been evaluated in several clinical trials. Here, we review the recent results from neoantigen-based vaccines in melanoma patients and discuss avenues for improvement. RECENT FINDINGS The importance of neoantigens for tumor control comes from the positive correlation between tumor mutational burden (TMB) and response to CPI. Preclinical studies have proved the effectiveness of neoantigen vaccines in models, expediting their clinical testing. Tumor mutations are not shared in most tumor types including melanoma, mandating the need of a personalized approach. Several clinical studies have shown the safety, feasibility, immunogenicity and preliminary evidence of antitumor activity of personalized vaccination. Currently, new trials have been started aiming to both confirm clinical activity and combining vaccines with other immunotherapies for improved efficacy. SUMMARY Personalized vaccines hold the promise for highly mutated and immunogenic cancers, including melanoma. Continuous efforts are underway to increase their likelihood of success.
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Puig-Saus C, Sennino B, Peng S, Wang CL, Pan Z, Yuen B, Purandare B, An D, Quach BB, Nguyen D, Xia H, Jilani S, Shao K, McHugh C, Greer J, Peabody P, Nayak S, Hoover J, Said S, Jacoby K, Dalmas O, Foy SP, Conroy A, Yi MC, Shieh C, Lu W, Heeringa K, Ma Y, Chizari S, Pilling MJ, Ting M, Tunuguntla R, Sandoval S, Moot R, Hunter T, Zhao S, Saco JD, Perez-Garcilazo I, Medina E, Vega-Crespo A, Baselga-Carretero I, Abril-Rodriguez G, Cherry G, Wong DJ, Hundal J, Chmielowski B, Speiser DE, Bethune MT, Bao XR, Gros A, Griffith OL, Griffith M, Heath JR, Franzusoff A, Mandl SJ, Ribas A. Neoantigen-targeted CD8 + T cell responses with PD-1 blockade therapy. Nature 2023; 615:697-704. [PMID: 36890230 PMCID: PMC10441586 DOI: 10.1038/s41586-023-05787-1] [Citation(s) in RCA: 55] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 02/02/2023] [Indexed: 03/10/2023]
Abstract
Neoantigens are peptides derived from non-synonymous mutations presented by human leukocyte antigens (HLAs), which are recognized by antitumour T cells1-14. The large HLA allele diversity and limiting clinical samples have restricted the study of the landscape of neoantigen-targeted T cell responses in patients over their treatment course. Here we applied recently developed technologies15-17 to capture neoantigen-specific T cells from blood and tumours from patients with metastatic melanoma with or without response to anti-programmed death receptor 1 (PD-1) immunotherapy. We generated personalized libraries of neoantigen-HLA capture reagents to single-cell isolate the T cells and clone their T cell receptors (neoTCRs). Multiple T cells with different neoTCR sequences (T cell clonotypes) recognized a limited number of mutations in samples from seven patients with long-lasting clinical responses. These neoTCR clonotypes were recurrently detected over time in the blood and tumour. Samples from four patients with no response to anti-PD-1 also demonstrated neoantigen-specific T cell responses in the blood and tumour to a restricted number of mutations with lower TCR polyclonality and were not recurrently detected in sequential samples. Reconstitution of the neoTCRs in donor T cells using non-viral CRISPR-Cas9 gene editing demonstrated specific recognition and cytotoxicity to patient-matched melanoma cell lines. Thus, effective anti-PD-1 immunotherapy is associated with the presence of polyclonal CD8+ T cells in the tumour and blood specific for a limited number of immunodominant mutations, which are recurrently recognized over time.
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Affiliation(s)
- Cristina Puig-Saus
- Division of Hematology-Oncology, Department of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA, USA.
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA.
- Broad Stem Cell Research Center, UCLA, Los Angeles, CA, USA.
| | | | | | | | | | | | | | - Duo An
- PACT Pharma, San Francisco, CA, USA
| | | | | | - Huiming Xia
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | - Sameeha Jilani
- Division of Hematology-Oncology, Department of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Yan Ma
- PACT Pharma, San Francisco, CA, USA
| | | | | | | | | | | | | | | | - Sidi Zhao
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | - Justin D Saco
- Division of Hematology-Oncology, Department of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Ivan Perez-Garcilazo
- Division of Hematology-Oncology, Department of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Egmidio Medina
- Division of Hematology-Oncology, Department of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Agustin Vega-Crespo
- Division of Hematology-Oncology, Department of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Ignacio Baselga-Carretero
- Division of Hematology-Oncology, Department of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Gabriel Abril-Rodriguez
- Division of Hematology-Oncology, Department of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | - Grace Cherry
- Division of Hematology-Oncology, Department of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Deborah J Wong
- Division of Hematology-Oncology, Department of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Jasreet Hundal
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | - Bartosz Chmielowski
- Division of Hematology-Oncology, Department of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA, USA
| | - Daniel E Speiser
- Department of Oncology, University of Lausanne, Lausanne, Switzerland
| | | | | | - Alena Gros
- Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Obi L Griffith
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | - Malachi Griffith
- McDonnell Genome Institute, Washington University School of Medicine, St Louis, MO, USA
| | | | | | | | - Antoni Ribas
- Division of Hematology-Oncology, Department of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, CA, USA.
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA.
- Broad Stem Cell Research Center, UCLA, Los Angeles, CA, USA.
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Feng Y, Hess PR, Tompkins SM, Hildebrand WH, Zhao S. A Kmer-based paired-end read de novo assembler and genotyper for canine MHC class I genotyping. iScience 2023; 26:105996. [PMID: 36798440 PMCID: PMC9926114 DOI: 10.1016/j.isci.2023.105996] [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: 08/05/2022] [Revised: 11/28/2022] [Accepted: 01/11/2023] [Indexed: 01/18/2023] Open
Abstract
The major histocompatibility complex class I (MHC-I) genes are highly polymorphic. MHC-I genotyping is required for determining the peptide epitopes available to an individual's T-cell repertoire. Current genotyping software tools do not work for the dog, due to very limited known canine alleles. To address this, we developed a Kmer-based paired-end read (KPR) de novo assembler and genotyper, which assemble paired-end RNA-seq reads from MHC-I regions into contigs, and then genotype each contig and estimate its expression level. KPR tools outperform other popular software examined in typing new alleles. We used KPR tools to successfully genotype152 dogs from a published dataset. The study discovers 33 putative new alleles, finds dominant alleles in 4 dog breeds, and builds allele diversity and expression landscapes among the 152 dogs. Our software meets a significant need in biomedical research.
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Affiliation(s)
- Yuan Feng
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Paul R. Hess
- Department of Clinical Sciences, North Carolina State University, College of Veterinary Medicine, Raleigh, NC 27607, USA
| | - Stephen M. Tompkins
- Center for Vaccines and Immunology, University of Georgia, UGA, Athens, GA 30602, USA
| | - William H. Hildebrand
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Shaying Zhao
- Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA,Corresponding author
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Cai Y, Chen R, Gao S, Li W, Liu Y, Su G, Song M, Jiang M, Jiang C, Zhang X. Artificial intelligence applied in neoantigen identification facilitates personalized cancer immunotherapy. Front Oncol 2023; 12:1054231. [PMID: 36698417 PMCID: PMC9868469 DOI: 10.3389/fonc.2022.1054231] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 12/16/2022] [Indexed: 01/10/2023] Open
Abstract
The field of cancer neoantigen investigation has developed swiftly in the past decade. Predicting novel and true neoantigens derived from large multi-omics data became difficult but critical challenges. The rise of Artificial Intelligence (AI) or Machine Learning (ML) in biomedicine application has brought benefits to strengthen the current computational pipeline for neoantigen prediction. ML algorithms offer powerful tools to recognize the multidimensional nature of the omics data and therefore extract the key neoantigen features enabling a successful discovery of new neoantigens. The present review aims to outline the significant technology progress of machine learning approaches, especially the newly deep learning tools and pipelines, that were recently applied in neoantigen prediction. In this review article, we summarize the current state-of-the-art tools developed to predict neoantigens. The standard workflow includes calling genetic variants in paired tumor and blood samples, and rating the binding affinity between mutated peptide, MHC (I and II) and T cell receptor (TCR), followed by characterizing the immunogenicity of tumor epitopes. More specifically, we highlight the outstanding feature extraction tools and multi-layer neural network architectures in typical ML models. It is noted that more integrated neoantigen-predicting pipelines are constructed with hybrid or combined ML algorithms instead of conventional machine learning models. In addition, the trends and challenges in further optimizing and integrating the existing pipelines are discussed.
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Affiliation(s)
- Yu Cai
- School of Medicine, Northwest University, Xi’an, Shaanxi, China
| | - Rui Chen
- School of Medicine, Northwest University, Xi’an, Shaanxi, China
| | - Shenghan Gao
- School of Medicine, Northwest University, Xi’an, Shaanxi, China
| | - Wenqing Li
- School of Medicine, Northwest University, Xi’an, Shaanxi, China
| | - Yuru Liu
- School of Medicine, Northwest University, Xi’an, Shaanxi, China
| | - Guodong Su
- School of Medicine, Northwest University, Xi’an, Shaanxi, China
| | - Mingming Song
- School of Medicine, Northwest University, Xi’an, Shaanxi, China
| | - Mengju Jiang
- School of Medicine, Northwest University, Xi’an, Shaanxi, China
| | - Chao Jiang
- Department of Neurology, The Second Affiliated Hospital of Xi’an Medical University, Xi’an, Shaanxi, China,*Correspondence: Chao Jiang, ; Xi Zhang,
| | - Xi Zhang
- School of Medicine, Northwest University, Xi’an, Shaanxi, China,*Correspondence: Chao Jiang, ; Xi Zhang,
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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: 176] [Impact Index Per Article: 176.0] [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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Malaina I, Martínez L, Montoya JM, Alonso S, Boyano MD, Asumendi A, Izu R, Sanchez-Diez A, Cancho-Galan G, M. de la Fuente I. A Universal Antigen-Ranking Method to Design Personalized Vaccines Targeting Neoantigens against Melanoma. LIFE (BASEL, SWITZERLAND) 2023; 13:life13010155. [PMID: 36676104 PMCID: PMC9867041 DOI: 10.3390/life13010155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 01/02/2023] [Accepted: 01/03/2023] [Indexed: 01/06/2023]
Abstract
Background: The main purpose of this article is to introduce a universal mathematics-aided vaccine design method against malignant melanoma based on neoantigens. The universal method can be adapted to the mutanome of each patient so that a specific candidate vaccine can be tailored for the corresponding patient. Methods: We extracted the 1134 most frequent mutations in melanoma, and we associated each of them to a vector with 10 components estimated with different bioinformatics tools, for which we found an aggregated value according to a set of weights, and then we ordered them in decreasing order of the scores. Results: We prepared a universal table of the most frequent mutations in melanoma ordered in decreasing order of viability to be used as candidate vaccines, so that the selection of a set of appropriate peptides for each particular patient can be easily and quickly implemented according to their specific mutanome and transcription profile. Conclusions: We have shown that the techniques that are commonly used for the design of personalized anti-tumor vaccines against malignant melanoma can be adapted for the design of universal rankings of neoantigens that originate personalized vaccines when the mutanome and transcription profile of specific patients is considered, with the consequent savings in time and money, shortening the design and production time.
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Affiliation(s)
- Iker Malaina
- Department of Mathematics, University of the Basque Country UPV/EHU, 48940 Bizkaia, Spain
- Correspondence:
| | - Luis Martínez
- Department of Mathematics, University of the Basque Country UPV/EHU, 48940 Bizkaia, Spain
| | - Juan Manuel Montoya
- Department of Mathematics, University of the Basque Country UPV/EHU, 48940 Bizkaia, Spain
- Faculty of Basic Sciences, University of Pamplona, Pamplona 6800, Colombia
| | - Santos Alonso
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country UPV/EHU, 48940 Bizkaia, Spain
| | - María Dolores Boyano
- Department of Cell Biology and Histology, University of the Basque Country UPV/EHU, 48940 Bizkaia, Spain
- Biocruces Bizkaia Health Research Institute, 48903 Bizkaia, Spain
| | - Aintzane Asumendi
- Department of Cell Biology and Histology, University of the Basque Country UPV/EHU, 48940 Bizkaia, Spain
- Biocruces Bizkaia Health Research Institute, 48903 Bizkaia, Spain
| | - Rosa Izu
- Biocruces Bizkaia Health Research Institute, 48903 Bizkaia, Spain
- Department of Dermatology, Basurto University Hospital, 48013 Bizkaia, Spain
| | - Ana Sanchez-Diez
- Biocruces Bizkaia Health Research Institute, 48903 Bizkaia, Spain
- Department of Dermatology, Basurto University Hospital, 48013 Bizkaia, Spain
| | - Goikoane Cancho-Galan
- Biocruces Bizkaia Health Research Institute, 48903 Bizkaia, Spain
- Department of Pathology, Basurto University Hospital, 48013 Bizkaia, Spain
| | - Ildefonso M. de la Fuente
- Department of Mathematics, University of the Basque Country UPV/EHU, 48940 Bizkaia, Spain
- CEBAS-CSIC Institute, Department of Nutrition, 30100 Murcia, Spain
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Chan AP, Choi Y, Rangan A, Zhang G, Podder A, Berens M, Sharma S, Pirrotte P, Byron S, Duggan D, Schork NJ. Interrogating the Human Diplome: Computational Methods, Emerging Applications, and Challenges. Methods Mol Biol 2023; 2590:1-30. [PMID: 36335489 DOI: 10.1007/978-1-0716-2819-5_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Human DNA sequencing protocols have revolutionized human biology, biomedical science, and clinical practice, but still have very important limitations. One limitation is that most protocols do not separate or assemble (i.e., "phase") the nucleotide content of each of the maternally and paternally derived chromosomal homologs making up the 22 autosomal pairs and the chromosomal pair making up the pseudo-autosomal region of the sex chromosomes. This has led to a dearth of studies and a consequent underappreciation of many phenomena of fundamental importance to basic and clinical genomic science. We discuss a few protocols for obtaining phase information as well as their limitations, including those that could be used in tumor phasing settings. We then describe a number of biological and clinical phenomena that require phase information. These include phenomena that require precise knowledge of the nucleotide sequence in a chromosomal segment from germline or somatic cells, such as DNA binding events, and insight into unique cis vs. trans-acting functionally impactful variant combinations-for example, variants implicated in a phenotype governed by compound heterozygosity. In addition, we also comment on the need for reliable and consensus-based diploid-context computational workflows for variant identification as well as the need for laboratory-based functional verification strategies for validating cis vs. trans effects of variant combinations. We also briefly describe available resources, example studies, as well as areas of further research, and ultimately argue that the science behind the study of human diploidy, referred to as "diplomics," which will be enabled by nucleotide-level resolution of phased genomes, is a logical next step in the analysis of human genome biology.
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Affiliation(s)
- Agnes P Chan
- The Translational Genomics Research Institute (TGen), part of the City of Hope National Medical Center, Phoenix, AZ, USA
| | - Yongwook Choi
- The Translational Genomics Research Institute (TGen), part of the City of Hope National Medical Center, Phoenix, AZ, USA
| | - Aditya Rangan
- Courant Institute of Mathematical Sciences at New York University, New York, NY, USA
| | - Guangfa Zhang
- The Translational Genomics Research Institute (TGen), part of the City of Hope National Medical Center, Phoenix, AZ, USA
| | - Avijit Podder
- The Translational Genomics Research Institute (TGen), part of the City of Hope National Medical Center, Phoenix, AZ, USA
| | - Michael Berens
- The Translational Genomics Research Institute (TGen), part of the City of Hope National Medical Center, Phoenix, AZ, USA
- The City of Hope National Medical Center, Duarte, CA, USA
| | - Sunil Sharma
- The Translational Genomics Research Institute (TGen), part of the City of Hope National Medical Center, Phoenix, AZ, USA
- The City of Hope National Medical Center, Duarte, CA, USA
| | - Patrick Pirrotte
- The Translational Genomics Research Institute (TGen), part of the City of Hope National Medical Center, Phoenix, AZ, USA
- The City of Hope National Medical Center, Duarte, CA, USA
| | - Sara Byron
- The Translational Genomics Research Institute (TGen), part of the City of Hope National Medical Center, Phoenix, AZ, USA
- The City of Hope National Medical Center, Duarte, CA, USA
| | - Dave Duggan
- The Translational Genomics Research Institute (TGen), part of the City of Hope National Medical Center, Phoenix, AZ, USA
- The City of Hope National Medical Center, Duarte, CA, USA
| | - Nicholas J Schork
- The Translational Genomics Research Institute (TGen), part of the City of Hope National Medical Center, Phoenix, AZ, USA.
- The City of Hope National Medical Center, Duarte, CA, USA.
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Artificial intelligence for prediction of response to cancer immunotherapy. Semin Cancer Biol 2022; 87:137-147. [PMID: 36372326 DOI: 10.1016/j.semcancer.2022.11.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 11/02/2022] [Accepted: 11/08/2022] [Indexed: 11/13/2022]
Abstract
Artificial intelligence (AI) indicates the application of machines to imitate intelligent behaviors for solving complex tasks with minimal human intervention, including machine learning and deep learning. The use of AI in medicine improves health-care systems in multiple areas such as diagnostic confirmation, risk stratification, analysis, prognosis prediction, treatment surveillance, and virtual health support, which has considerable potential to revolutionize and reshape medicine. In terms of immunotherapy, AI has been applied to unlock underlying immune signatures to associate with responses to immunotherapy indirectly as well as predict responses to immunotherapy responses directly. The AI-based analysis of high-throughput sequences and medical images can provide useful information for management of cancer immunotherapy considering the excellent abilities in selecting appropriate subjects, improving therapeutic regimens, and predicting individualized prognosis. In present review, we aim to evaluate a broad framework about AI-based computational approaches for prediction of response to cancer immunotherapy on both indirect and direct manners. Furthermore, we summarize our perspectives about challenges and opportunities of further AI applications on cancer immunotherapy relating to clinical practicability.
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44
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Neoantigen discovery and applications in glioblastoma: An immunotherapy perspective. Cancer Lett 2022; 550:215945. [DOI: 10.1016/j.canlet.2022.215945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/27/2022] [Accepted: 10/03/2022] [Indexed: 11/21/2022]
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45
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Thuesen NH, Klausen MS, Gopalakrishnan S, Trolle T, Renaud G. Benchmarking freely available HLA typing algorithms across varying genes, coverages and typing resolutions. Front Immunol 2022; 13:987655. [PMID: 36426357 PMCID: PMC9679531 DOI: 10.3389/fimmu.2022.987655] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 10/10/2022] [Indexed: 11/02/2023] Open
Abstract
Identifying the specific human leukocyte antigen (HLA) allele combination of an individual is crucial in organ donation, risk assessment of autoimmune and infectious diseases and cancer immunotherapy. However, due to the high genetic polymorphism in this region, HLA typing requires specialized methods. We investigated the performance of five next-generation sequencing (NGS) based HLA typing tools with a non-restricted license namely HLA*LA, Optitype, HISAT-genotype, Kourami and STC-Seq. This evaluation was done for the five HLA loci, HLA-A, -B, -C, -DRB1 and -DQB1 using whole-exome sequencing (WES) samples from 829 individuals. The robustness of the tools to lower depth of coverage (DOC) was evaluated by subsampling and HLA typing 230 WES samples at DOC ranging from 1X to 100X. The HLA typing accuracy was measured across four typing resolutions. Among these, we present two clinically-relevant typing resolutions (P group and pseudo-sequence), which specifically focus on the peptide binding region. On average, across the five HLA loci examined, HLA*LA was found to have the highest typing accuracy. For the individual loci, HLA-A, -B and -C, Optitype's typing accuracy was the highest and HLA*LA had the highest typing accuracy for HLA-DRB1 and -DQB1. The tools' robustness to lower DOC data varied widely and further depended on the specific HLA locus. For all Class I loci, Optitype had a typing accuracy above 95% (according to the modification of the amino acids in the functionally relevant portion of the HLA molecule) at 50X, but increasing the DOC beyond even 100X could still improve the typing accuracy of HISAT-genotype, Kourami, and STC-seq across all five HLA loci as well as HLA*LA's typing accuracy for HLA-DQB1. HLA typing is also used in studies of ancient DNA (aDNA), which is often based on sequencing data with lower quality and DOC. Interestingly, we found that Optitype's typing accuracy is not notably impaired by short read length or by DNA damage, which is typical of aDNA, as long as the DOC is sufficiently high.
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Affiliation(s)
- Nikolas Hallberg Thuesen
- Evaxion Biotech, Copenhagen, Denmark
- Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, Lyngby, Denmark
| | | | - Shyam Gopalakrishnan
- Section for Hologenomics, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Gabriel Renaud
- Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, Lyngby, Denmark
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46
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Shukla GS, Pero SC, Mei L, Sun YJ, Krag DN. Targeting of palpable B16-F10 melanoma tumors with polyclonal antibodies on white blood cells. J Immunol Methods 2022; 510:113362. [PMID: 36174735 DOI: 10.1016/j.jim.2022.113362] [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: 09/27/2021] [Revised: 09/15/2022] [Accepted: 09/22/2022] [Indexed: 12/31/2022]
Abstract
BACKGROUND Antibodies and other recognition molecules direct cancer cell death by multiple types of immune cells. Therapy directed at only one target typically results in tumor regrowth because of tumor heterogeneity. Our goal is to direct therapy to multiple targets simultaneously. Our previous studies showed that multiple antibodies targeting mutated tumor proteins inhibited tumor growth when injected subcutaneously near the time of cancer cell implantation. METHODS A cocktail of rabbit antibodies against B16-F10 cell surface related mutated proteins were generated. Implanted B16-F10 cells were allowed to grow to palpable size before treatment. Antibodies were administered using different routes of exposure. Free antibody was compared to antibody armed on mouse splenic white blood cells (WBCs). Binding of the antibody cocktail was determined for mouse and human WBCs. RESULTS The antibody cocktail inhibited tumor growth and prolonged survival when administered as free antibody or armed on WBCs. The antibody cocktail armed on WBCs achieved similar tumor inhibition as free antibody but at a dose 1000-fold less. Armed WBCs achieved tumor inhibition by intravenous and subcutaneous administration. The antibody cocktail bound well to human WBCs and saturation dose was defined. Binding was stable under simulated in vivo condition in human plasma at 37 °C. CONCLUSIONS Antibodies targeting multiple tumor mutated proteins inhibited tumor growth and prolonged survival. Effective antibody dose was reduced 1000-fold by arming WBCs. Rabbit antibodies saturated human WBCs using <1 mg per billion cells. A phase I trial in cancer patients using this strategy has been approved by the FDA.
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Affiliation(s)
- Girja S Shukla
- Department of Surgery, University of Vermont Cancer Center, University of Vermont Larner College of Medicine, Burlington, VT, USA.
| | - Stephanie C Pero
- Department of Surgery, University of Vermont Cancer Center, University of Vermont Larner College of Medicine, Burlington, VT, USA.
| | - Linda Mei
- Department of Surgery, University of Vermont Cancer Center, University of Vermont Larner College of Medicine, Burlington, VT, USA.
| | - Yu-Jing Sun
- Department of Surgery, University of Vermont Cancer Center, University of Vermont Larner College of Medicine, Burlington, VT, USA.
| | - David N Krag
- Department of Surgery, University of Vermont Cancer Center, University of Vermont Larner College of Medicine, Burlington, VT, USA.
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Zeng C, Zhou Y, Ye W, Fang Z, Wang K. Exploration and validation of hub genes in lung adenocarcinoma based on bioinformatics analysis. Transl Cancer Res 2022; 11:3814-3826. [PMID: 36388051 PMCID: PMC9641136 DOI: 10.21037/tcr-22-2225] [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: 08/29/2022] [Accepted: 10/12/2022] [Indexed: 11/22/2022]
Abstract
BACKGROUND Genomic abnormality is a crucial factor for lung cancer development. This study used bioinformatics analysis to explore the hub genes involved in lung adenocarcinoma. METHODS The GeneCards, Comparative Toxicogenomics Database (CTD), and DISEASES databases were used to screen the genes associated with lung adenocarcinoma. The hub genes were then identified using WebGestalt. The Cancer Genome Atlas (TCGA), UALCAN, and the Human Protein Atlas (HPA) were used to validate the expression of hub genes. The predictive effects of hub genes on the risk of lung adenocarcinoma were evaluated using receiver operating characteristic (ROC) curve analysis. The Tumor-Immune System Interaction Database (TISIDB) was used to estimate the correlation between hub genes and immune infiltration. RESULTS A total of 21 genes were defined as common genes associated with lung adenocarcinoma, and from these, AKT1, CD44, and CDKN2A were identified as hub genes. Significant differences in the hub gene mRNA and protein expression were observed between lung adenocarcinoma samples and normal samples derived from the TCGA and UALCAN databases. The area under the ROC curve (AUC) for AKT1, CD44, and CDKN2A in predicting lung adenocarcinoma risk was 0.847, 0.880, and 0.805, respectively, with sensitivity of 89.8%, 93.2%, and 94.9%, respectively. TISIDB analysis indicated that AKT1, CD44, and CDKN2A expression had a strong relationship with immune infiltration in lung adenocarcinoma. CONCLUSIONS These hub genes, AKT1, CD44, and CDKN2A, may represent tumor biomarkers that may contribute to the understanding, diagnosis, and treatment of lung adenocarcinoma.
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Affiliation(s)
- Changyi Zeng
- Department of Preventive Medicine, Medical College, Hubei University of Arts and Science, Xiangyang, China;,Research Centre for Evidence-Based and Translational Medicine, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, China
| | - You Zhou
- Department of Preventive Medicine, Medical College, Hubei University of Arts and Science, Xiangyang, China
| | - Wanqing Ye
- Department of Preventive Medicine, Medical College, Hubei University of Arts and Science, Xiangyang, China
| | - Zihan Fang
- Department of Preventive Medicine, Medical College, Hubei University of Arts and Science, Xiangyang, China
| | - Ke Wang
- Department of Preventive Medicine, Medical College, Hubei University of Arts and Science, Xiangyang, China;,Research Centre for Evidence-Based and Translational Medicine, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang, China
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48
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Research progress of neoantigens in gynecologic cancers. Int Immunopharmacol 2022; 112:109236. [PMID: 36113318 DOI: 10.1016/j.intimp.2022.109236] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 09/01/2022] [Accepted: 09/04/2022] [Indexed: 11/24/2022]
Abstract
The incidence and mortality of gynecological cancers have increased over the past decade. In the absence of effective treatment strategies, many advanced patients develop resistance to conventional therapies and have poor prognosis. Neoantigens have emerged as a novel tumor-specific antigen (TSA) that arises from genomic mutations in tumor cells. With higher immunogenicity than tumor-associated antigens (TAA), they have no risk of developing autoimmune response, leading them an attractive candidate for tumor therapeutic vaccines. With the development of next-generation sequencing (NGS) technology, the identification of neoantigens has been gradually improved, and the scope of application of neoantigen vaccines has continued to expand. Combined with other therapies such as immune-checkpoint inhibitors (ICIs) or adoptive cell therapy (ACT), the application of neoantigen in gynecological cancers has extended to clinical practice. Here, we reviewed the preclinical and clinical studies of neoantigens in gynecological cancers.
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49
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Sources of Cancer Neoantigens beyond Single-Nucleotide Variants. Int J Mol Sci 2022; 23:ijms231710131. [PMID: 36077528 PMCID: PMC9455963 DOI: 10.3390/ijms231710131] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 09/01/2022] [Accepted: 09/02/2022] [Indexed: 11/17/2022] Open
Abstract
The success of checkpoint blockade therapy against cancer has unequivocally shown that cancer cells can be effectively recognized by the immune system and eliminated. However, the identity of the cancer antigens that elicit protective immunity remains to be fully explored. Over the last decade, most of the focus has been on somatic mutations derived from non-synonymous single-nucleotide variants (SNVs) and small insertion/deletion mutations (indels) that accumulate during cancer progression. Mutated peptides can be presented on MHC molecules and give rise to novel antigens or neoantigens, which have been shown to induce potent anti-tumor immune responses. A limitation with SNV-neoantigens is that they are patient-specific and their accurate prediction is critical for the development of effective immunotherapies. In addition, cancer types with low mutation burden may not display sufficient high-quality [SNV/small indels] neoantigens to alone stimulate effective T cell responses. Accumulating evidence suggests the existence of alternative sources of cancer neoantigens, such as gene fusions, alternative splicing variants, post-translational modifications, and transposable elements, which may be attractive novel targets for immunotherapy. In this review, we describe the recent technological advances in the identification of these novel sources of neoantigens, the experimental evidence for their presentation on MHC molecules and their immunogenicity, as well as the current clinical development stage of immunotherapy targeting these neoantigens.
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50
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Jobanputra V, Wrzeszczynski KO, Buttner R, Caldas C, Cuppen E, Grimmond S, Haferlach T, Mullighan C, Schuh A, Elemento O. Clinical interpretation of whole-genome and whole-transcriptome sequencing for precision oncology. Semin Cancer Biol 2022; 84:23-31. [PMID: 34256129 DOI: 10.1016/j.semcancer.2021.07.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 07/01/2021] [Accepted: 07/07/2021] [Indexed: 02/08/2023]
Abstract
Whole-genome sequencing either alone or in combination with whole-transcriptome sequencing has started to be used to analyze clinical tumor samples to improve diagnosis, provide risk stratification, and select patient-specific therapies. Compared with current genomic testing strategies, largely focused on small number of genes tested individually or targeted panels, whole-genome and transcriptome sequencing (WGTS) provides novel opportunities to identify and report a potentially much larger number of actionable alterations with diagnostic, prognostic, and/or predictive impact. Such alterations include point mutations, indels, copy- number aberrations and structural variants, but also germline variants, fusion genes, noncoding alterations and mutational signatures. Nevertheless, these comprehensive tests are accompanied by many challenges ranging from the extent and diversity of sequence alterations detected by these methods to the complexity and limited existing standardization in interpreting them. We describe the challenges of WGTS interpretation and the opportunities with comprehensive genomic testing.
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Affiliation(s)
- Vaidehi Jobanputra
- New York Genome Center, 101 Avenue of the Americas, New York, NY 100132, United States; Columbia University Medical Center, 650 W 168th St, New York, NY 10032, United States.
| | | | | | - Carlos Caldas
- Cancer Research UK Cambridge Institute and Department of Oncology, University of Cambridge, United Kingdom
| | - Edwin Cuppen
- Hartwig Medical Foundation, Amsterdam, Netherlands; Center for Molecular Medicine and Oncode Institute, University Medical Center, Utrecht, Netherlands
| | - Sean Grimmond
- Centre for Cancer Research, University of Melbourne, Melbourne, Australia
| | | | - Charles Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, United States
| | - Anna Schuh
- NIHR Oxford Biomedical Research Centre and Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Olivier Elemento
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, United States; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, United States.
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