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D'Aniello A, Del Bene A, Mottola S, Mazzarella V, Cutolo R, Campagna E, Di Maro S, Messere A. The bright side of chemistry: Exploring synthetic peptide-based anticancer vaccines. J Pept Sci 2024; 30:e3596. [PMID: 38571326 DOI: 10.1002/psc.3596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 04/05/2024]
Abstract
The present review focuses on synthetic peptide-based vaccine strategies in the context of anticancer intervention, paying attention to critical aspects such as peptide epitope selection, adjuvant integration, and nuanced classification of synthetic peptide cancer vaccines. Within this discussion, we delve into the diverse array of synthetic peptide-based anticancer vaccines, each derived from tumor-associated antigens (TAAs), including melanoma antigen recognized by T cells 1 (Melan-A or MART-1), mucin 1 (MUC1), human epidermal growth factor receptor 2 (HER-2), tumor protein 53 (p53), human telomerase reverse transcriptase (hTERT), survivin, folate receptor (FR), cancer-testis antigen 1 (NY-ESO-1), and prostate-specific antigen (PSA). We also describe the synthetic peptide-based vaccines developed for cancers triggered by oncovirus, such as human papillomavirus (HPV), and hepatitis C virus (HCV). Additionally, the potential synergy of peptide-based vaccines with common therapeutics in cancer was considered. The last part of our discussion deals with the realm of the peptide-based vaccines delivery, highlighting its role in translating the most promising candidates into effective clinical strategies. Although this discussion does not cover all the ongoing peptide vaccine investigations, it aims at offering valuable insights into the chemical modifications and the structural complexities of anticancer peptide-based vaccines.
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Affiliation(s)
- Antonia D'Aniello
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania "Luigi Vanvitelli", Caserta, Italy
| | - Alessandra Del Bene
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania "Luigi Vanvitelli", Caserta, Italy
| | - Salvatore Mottola
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania "Luigi Vanvitelli", Caserta, Italy
| | - Vincenzo Mazzarella
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania "Luigi Vanvitelli", Caserta, Italy
| | - Roberto Cutolo
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania "Luigi Vanvitelli", Caserta, Italy
| | - Erica Campagna
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania "Luigi Vanvitelli", Caserta, Italy
| | - Salvatore Di Maro
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania "Luigi Vanvitelli", Caserta, Italy
- Interuniversity Research Centre on Bioactive Peptides (CIRPEB), Naples, Italy
| | - Anna Messere
- Department of Environmental, Biological and Pharmaceutical Science and Technology, University of Campania "Luigi Vanvitelli", Caserta, Italy
- Interuniversity Research Centre on Bioactive Peptides (CIRPEB), Naples, Italy
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2
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Fan Y, Dai T, Zhang D, Guo H, Zhou F, Shi B, Wang S, Ji Z, Wang C, Yao X, Wei Q, Chen N, Xing J, Yang J, Kong C, Huang J, Ye D, Zhou L. PD-L1 expression and its correlation with tumor biomarkers in Chinese urothelial bladder cancer. Sci Rep 2024; 14:16753. [PMID: 39033240 DOI: 10.1038/s41598-024-67508-6] [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: 09/08/2023] [Accepted: 07/11/2024] [Indexed: 07/23/2024] Open
Abstract
Data on prevalence of programmed death ligand-1 (PD-L1) expression and its correlation with tumor biomarkers in Chinese patients with muscle-invasive urothelial bladder cancer (MIUBC) are scarce. We investigated the prevalence of PD-L1 expression, PD-L1 expression in tumor cells (TC) and immune cells (IC), and its correlation with tumor biomarkers (CD8+ T cells and tumor mutation burden [TMB]) in Chinese patients with newly diagnosed MIUBC (NCT03433924). Of 248 patients enrolled, 229 with PD-L1 data available were analysed. High PD-L1 expression (≥ 25% of TC or IC with PD-L1 expression) was observed in 120 (52.4%) patients. 59 cases showed positive staining in ≥ 25% of TC, and 82 cases had positive staining in ≥ 25% of IC. High expression of CD8+ T cell and TMB (> 10 mutations/megabase) was observed in 44.5% and 54.1% patients, respectively. A positive correlation was observed between percentage of TC with membrane PD-L1 positivity and CD8+ T cells (0.34; P < 0.001) and between IC with membrane PD-L1 positivity and CD8+ T cells (0.44; P < 0.001). There is high prevalence of PD-L1 expression in Chinese patients with MIUBC, suggesting that a sizable subset of patients could benefit from immunotherapy. The correlation of PD-L1 expression with tumor biomarkers provide clues for mechanisms underlying the effects of biomarkers for predicting efficacy.
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Affiliation(s)
- Yu Fan
- Department of Urology, Peking University First Hospital, Beijing, 100034, China
| | - Tao Dai
- Department of Urology, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University and Hunan Cancer Hospital, Changsha, 410006, China
| | - Dahong Zhang
- Department of Urology, Zhejiang Provincial People's Hospital, Hangzhou, 310005, Zhejiang, China
| | - Hongqian Guo
- Department of Urology, Drum Tower Hospital, Medical School of Nanjing University, Institute of Urology, Nanjing University, Nanjing, 210000, Jiangsu, China
| | - Fangjian Zhou
- Department of Urology, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Benkang Shi
- Department of Urology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
| | - Shaogang Wang
- Department of Urology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiafang Avenue, Qiaokou, Wuhan, 430000, Hubei, China
| | - Zhigang Ji
- Department of Urology, Peking Union Medical College Hospital, Chinese Academy of Science, Beijing, 100005, China
| | - Chunxi Wang
- Department of Urology, First Hospital of Jilin University, Changchun, 130000, Jilin, China
| | - Xudong Yao
- Department of Urology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, 200040, China
| | - Qiang Wei
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Nanhui Chen
- Department of Urology, Meizhou People's Hospital, Meizhou, 514031, Guangdong, China
| | - Jinchun Xing
- Department of Urology Surgery, The First Affiliated Hospital of Xiamen University, Xiamen, 361003, Fujian, China
| | - Jinjian Yang
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Chuize Kong
- Department of Urology, The First Hospital of China Medical University, Shenyang, 110001, China
| | - Jian Huang
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510000, China
| | - Dingwei Ye
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
| | - Liqun Zhou
- Department of Urology, Peking University First Hospital, Beijing, 100034, China.
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3
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Meng XY, Yang D, Zhang B, Zhang T, Zheng ZC, Zhao Y. Glycolysis-related five-gene signature correlates with prognosis and immune infiltration in gastric cancer. World J Gastrointest Oncol 2024; 16:3097-3117. [DOI: 10.4251/wjgo.v16.i7.3097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/14/2024] [Accepted: 06/13/2024] [Indexed: 07/12/2024] Open
Abstract
BACKGROUND Gastric cancer (GC) is one of the most common malignancies worldwide. Glycolysis has been demonstrated to be pivotal for the carcinogenesis of GC.
AIM To develop a glycolysis-based gene signature for prognostic evaluation in GC patients.
METHODS Differentially expressed genes correlated with glycolysis were identified in stomach adenocarcinoma data (STAD). A risk score was established through a univariate Cox and least absolute shrinkage and selection operator analysis. The model was evaluated using the area under the receiver operating characteristic curves. RNA-sequencing data from high- and low-glycolysis groups of STAD patients were analyzed using Cibersort algorithm and Spearman correlation to analyze the interaction of immune cell infiltration and glycolysis. Multiomics characteristics in different glycolysis status were also analyzed.
RESULTS A five-gene signature comprising syndecan 2, versican, malic enzyme 1, pyruvate carboxylase and SRY-box transcription factor 9 was constructed. Patients were separated to high- or low-glycolysis groups according to risk scores. Overall survival of patients with high glycolysis was poorer. The sensitivity and specificity of the model in prediction of survival of GC patients were also observed by receiver operating characteristic curves. A nomogram including clinicopathological characteristics and the risk score also showed good prediction for 3- and 5-year overall survival. Gene set variation analysis showed that high-glycolysis patients were related to dysregulation of pancreas beta cells and estrogen late pathways, and low-glycolysis patients were related to Myc targets, oxidative phosphorylation, mechanistic target of rapamycin complex 1 signaling and G2M checkpoint pathways. Tumor-infiltrating immune cells and multiomics analysis suggested that the different glycolysis status was significantly correlated with multiple immune cell infiltration. The patients with high glycolysis had lower tumor mutational burden and neoantigen load, higher incidence of microsatellite instability and lower chemosensitivity. High glycolysis status was often found among patients with grade 2/3 cancer or poor prognosis.
CONCLUSION The genetic characteristics revealed by glycolysis could predict the prognosis of GC. High glycolysis significantly affects GC phenotype, but the detailed mechanism needs to be further studied.
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Affiliation(s)
- Xiang-Yu Meng
- Department of Gastric Surgery, Cancer Hospital of China Medical University/Liaoning Cancer Hospital & Institute/The Liaoning Provincial Key Laboratory of Interdisciplinary Research on Gastrointestinal Tumor Combining Medicine with Engineering, Shenyang 110042, Liaoning Province, China
| | - Dong Yang
- Department of Gastric Surgery, Cancer Hospital of China Medical University/Liaoning Cancer Hospital & Institute/The Liaoning Provincial Key Laboratory of Interdisciplinary Research on Gastrointestinal Tumor Combining Medicine with Engineering, Shenyang 110042, Liaoning Province, China
| | - Bao Zhang
- Department of Gastric Surgery, Cancer Hospital of China Medical University/Liaoning Cancer Hospital & Institute/The Liaoning Provincial Key Laboratory of Interdisciplinary Research on Gastrointestinal Tumor Combining Medicine with Engineering, Shenyang 110042, Liaoning Province, China
| | - Tao Zhang
- Department of Gastric Surgery, Cancer Hospital of China Medical University/Liaoning Cancer Hospital & Institute/The Liaoning Provincial Key Laboratory of Interdisciplinary Research on Gastrointestinal Tumor Combining Medicine with Engineering, Shenyang 110042, Liaoning Province, China
| | - Zhi-Chao Zheng
- Department of Gastric Surgery, Cancer Hospital of China Medical University/Liaoning Cancer Hospital & Institute/The Liaoning Provincial Key Laboratory of Interdisciplinary Research on Gastrointestinal Tumor Combining Medicine with Engineering, Shenyang 110042, Liaoning Province, China
| | - Yan Zhao
- Department of Gastric Surgery, Cancer Hospital of China Medical University/Liaoning Cancer Hospital & Institute/The Liaoning Provincial Key Laboratory of Interdisciplinary Research on Gastrointestinal Tumor Combining Medicine with Engineering, Shenyang 110042, Liaoning Province, China
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Liu WS, Chen Z, Lu ZM, Dong JH, Wu JH, Gao J, Deng D, Li M. Multifunctional hydrogels based on photothermal therapy: A prospective platform for the postoperative management of melanoma. J Control Release 2024; 371:406-428. [PMID: 38849093 DOI: 10.1016/j.jconrel.2024.06.001] [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] [Received: 12/20/2023] [Revised: 03/22/2024] [Accepted: 06/01/2024] [Indexed: 06/09/2024]
Abstract
Preventing the recurrence of melanoma after surgery and accelerating wound healing are among the most challenging aspects of melanoma management. Photothermal therapy has been widely used to treat tumors and bacterial infections and promote wound healing. Owing to its efficacy and specificity, it may be used for postoperative management of tumors. However, its use is limited by the uncontrollable distribution of photosensitizers and the likelihood of damage to the surrounding normal tissue. Hydrogels provide a moist environment with strong biocompatibility and adhesion for wound healing owing to their highly hydrophilic three-dimensional network structure. In addition, these materials serve as excellent drug carriers for tumor treatment and wound healing. It is possible to combine the advantages of both of these agents through different loading modalities to provide a powerful platform for the prevention of tumor recurrence and wound healing. This review summarizes the design strategies, research progress and mechanism of action of hydrogels used in photothermal therapy and discusses their role in preventing tumor recurrence and accelerating wound healing. These findings provide valuable insights into the postoperative management of melanoma and may guide the development of promising multifunctional hydrogels for photothermal therapy.
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Affiliation(s)
- Wen-Shang Liu
- Department of Dermatology, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai 200127, People's Republic of China
| | - Zhuo Chen
- Department of Dermatology, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai 200127, People's Republic of China
| | - Zheng-Mao Lu
- Department of Gastrointestinal Surgery, Shanghai Changhai Hospital, Naval Medical University, Shanghai 200433, People's Republic of China
| | - Jin-Hua Dong
- Women and Children Hospital Affiliated to Jiaxing University, 2468 Middle Ring Eastern Road, Jiaxing City, Zhejiang 314000, People's Republic of China
| | - Jin-Hui Wu
- Ophthalmology Department of the Third Affiliated Hospital of Naval Medical University, Shanghai 201805, People's Republic of China.
| | - Jie Gao
- Changhai Clinical Research Unit, The First Affiliated Hospital of Naval Medical University, Shanghai 200433, People's Republic of China; Shanghai Key Laboratory of Nautical Medicine and Translation of Drugs and Medical Devices, Shanghai 200433, People's Republic of China.
| | - Dan Deng
- Department of Dermatology, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai 200127, People's Republic of China.
| | - Meng Li
- Department of Dermatology, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai 200127, People's Republic of China.
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5
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Deguchi Y, Kikutake C, Suyama M. Subtype-specific alternative splicing events in breast cancer identified by large-scale data analysis. Sci Rep 2024; 14:14158. [PMID: 38898123 PMCID: PMC11187070 DOI: 10.1038/s41598-024-65035-y] [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: 03/27/2024] [Accepted: 06/17/2024] [Indexed: 06/21/2024] Open
Abstract
Genome analysis in cancer has focused mainly on elucidating the function and regulatory mechanisms of genes that exhibit differential expression or mutation in cancer samples compared to normal samples. Recently, transcriptome analysis revealed that abnormal splicing events in cancer samples could contribute to cancer pathogenesis. Moreover, splicing variants in cancer reportedly generate diverse cancer antigens. Although abnormal splicing events are expected to be potential targets in cancer immunotherapy, the exploration of such targets and their biological significance in cancer have not been fully understood. In this study, to explore subtype-specific alternative splicing events, we conducted a comprehensive analysis of splicing events for each breast cancer subtype using large-scale splicing data derived from The Cancer Genome Atlas and found subtype-specific alternative splicing patterns. Analyses indicated that genes that produce subtype-specific alternative splicing events are potential novel targets for immunotherapy against breast cancer. The subtype-specific alternative splicing events identified in this study, which were not identified by mutation or differential expression analysis, bring new significance to previously overlooked splicing events.
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Affiliation(s)
- Yui Deguchi
- Division of Bioinformatics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan
| | - Chie Kikutake
- Division of Bioinformatics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan
| | - Mikita Suyama
- Division of Bioinformatics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan.
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6
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Kim S, Han DJ, Lee SY, Moon Y, Kang SJ, Kim TM. A Subset of Microsatellite Unstable Cancer Genomes Prone to Short Insertions over Deletions Is Associated with Elevated Anticancer Immunity. Genes (Basel) 2024; 15:770. [PMID: 38927706 PMCID: PMC11202581 DOI: 10.3390/genes15060770] [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: 05/16/2024] [Revised: 06/10/2024] [Accepted: 06/10/2024] [Indexed: 06/28/2024] Open
Abstract
Deficiencies in DNA mismatch repair (MMRd) leave characteristic footprints of microsatellite instability (MSI) in cancer genomes. We used data from the Cancer Genome Atlas and International Cancer Genome Consortium to conduct a comprehensive analysis of MSI-associated cancers, focusing on indel mutational signatures. We classified MSI-high genomes into two subtypes based on their indel profiles: deletion-dominant (MMRd-del) and insertion-dominant (MMRd-ins). Compared with MMRd-del genomes, MMRd-ins genomes exhibit distinct mutational and transcriptomic features, including a higher prevalence of T>C substitutions and related mutation signatures. Short insertions and deletions in MMRd-ins and MMRd-del genomes target different sets of genes, resulting in distinct indel profiles between the two subtypes. In addition, indels in the MMRd-ins genomes are enriched with subclonal alterations that provide clues about a distinct evolutionary relationship between the MMRd-ins and MMRd-del genomes. Notably, the transcriptome analysis indicated that MMRd-ins cancers upregulate immune-related genes, show a high level of immune cell infiltration, and display an elevated neoantigen burden. The genomic and transcriptomic distinctions between the two types of MMRd genomes highlight the heterogeneity of genetic mechanisms and resulting genomic footprints and transcriptomic changes in cancers, which has potential clinical implications.
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Affiliation(s)
- Sunmin Kim
- Department of Medical Informatics, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea; (S.K.)
- Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
- Department of Biomedicine & Health Sciences, Graduate School, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Dong-Jin Han
- Department of Medical Informatics, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea; (S.K.)
- Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
- Department of Biomedicine & Health Sciences, Graduate School, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Seo-Young Lee
- Department of Medical Informatics, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea; (S.K.)
- Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
- Department of Biomedicine & Health Sciences, Graduate School, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Youngbeen Moon
- Department of Medical Informatics, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea; (S.K.)
- Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
- Department of Biomedicine & Health Sciences, Graduate School, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Su Jung Kang
- Department of Medical Informatics, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea; (S.K.)
- Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
- Department of Biomedicine & Health Sciences, Graduate School, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Tae-Min Kim
- Department of Medical Informatics, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea; (S.K.)
- Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
- Department of Biomedicine & Health Sciences, Graduate School, The Catholic University of Korea, Seoul 06591, Republic of Korea
- CMC Institute for Basic Medical Science, The Catholic Medical Center, The Catholic University of Korea, Seoul 06591, Republic of Korea
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Bowen CM, Demarest K, Vilar E, Shah PD. Novel Cancer Prevention Strategies in Individuals With Hereditary Cancer Syndromes: Focus on BRCA1, BRCA2, and Lynch Syndrome. Am Soc Clin Oncol Educ Book 2024; 44:e433576. [PMID: 38913968 DOI: 10.1200/edbk_433576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Germline pathogenic variants (PVs) in the BRCA1 and BRCA2 genes confer elevated risks of breast, ovarian, and other cancers. Lynch syndrome (LS) is associated with increased risks of multiple cancer types including colorectal and uterine cancers. Current cancer risk mitigation strategies have focused on pharmacologic risk reduction, enhanced surveillance, and preventive surgeries. While these approaches can be effective, they stand to be improved on because of either limited efficacy or undesirable impact on quality of life. The current review summarizes ongoing investigational efforts in cancer risk prevention strategies for patients with germline PVs in BRCA1, BRCA2, or LS-associated genes. These efforts span radiation, surgery, and pharmacology including vaccine strategies. Understanding the molecular events involved in the premalignant to malignant transformation in high-risk individuals may ultimately contribute significantly to novel prevention strategies.
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Affiliation(s)
- Charles M Bowen
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Eduardo Vilar
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Payal D Shah
- Perelman Center for Advanced Medicine, Abramson Cancer Center, Philadelphia, PA
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8
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Strum S, Andersen MH, Svane IM, Siu LL, Weber JS. State-Of-The-Art Advancements on Cancer Vaccines and Biomarkers. Am Soc Clin Oncol Educ Book 2024; 44:e438592. [PMID: 38669611 DOI: 10.1200/edbk_438592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2024]
Abstract
The origins of cancer vaccines date back to the 1800s. Since then, there have been significant efforts to generate vaccines against solid and hematologic malignancies using a variety of platforms. To date, these efforts have generally been met with minimal success. However, in the era of improved methods and technological advancements, supported by compelling preclinical and clinical data, a wave of renewed interest in the field offers the promise of discovering field-changing paradigms in the management of established and resected disease using cancer vaccines. These include novel approaches to personalized neoantigen vaccine development, as well as innovative immune-modulatory vaccines (IMVs) that facilitate activation of antiregulatory T cells to limit immunosuppression caused by regulatory immune cells. This article will introduce some of the limitations that have affected cancer vaccine development over the past several decades, followed by an introduction to the latest advancements in neoantigen vaccine and IMV therapy, and then conclude with a discussion of some of the newest technologies and progress that are occurring across the cancer vaccine space. Cancer vaccines are among the most promising frontiers for breakthrough innovations and strategies poised to make a measurable impact in the ongoing fight against cancer.
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Affiliation(s)
- Scott Strum
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Canada
| | - Mads Hald Andersen
- National Center for Cancer Immune Therapy, Department of Oncology, Copenhagen University Hospital - Herlev and Gentofte, Herlev, Denmark
| | - Inge Marie Svane
- National Center for Cancer Immune Therapy, Department of Oncology, Copenhagen University Hospital - Herlev and Gentofte, Herlev, Denmark
| | - Lillian L Siu
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Canada
| | - Jeffrey S Weber
- Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York, NY
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9
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Lo Greco MC, Marano G, Milazzotto R, Liardo RLE, Finocchiaro I, La Rocca M, Basile A, Foti PV, Palmucci S, David E, Pergolizzi S, Spatola C. The Immunomodulatory Potential of Concurrent High-Dose Radiotherapy and Immune Checkpoint Inhibitor Cemiplimab in Advanced Cutaneous Squamous Cell Carcinoma: Initial Results. J Pers Med 2024; 14:581. [PMID: 38929802 PMCID: PMC11204472 DOI: 10.3390/jpm14060581] [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: 04/15/2024] [Revised: 05/19/2024] [Accepted: 05/28/2024] [Indexed: 06/28/2024] Open
Abstract
In this retrospective case series, we investigate the synergistic effect and the immunomodulatory potential of combination radiotherapy and immunotherapy on 11 patients affected by locally advanced or metastatic cutaneous squamous cell carcinoma (CSCC), treated at our institution between 2020 and 2023. The primary endpoints of this study are objective tumor response, assessed by Immunotherapy Response Evaluation Criteria in Solid Tumors (iRECIST), and time to treatment failure (disease progression). In all patients, surgery was deemed not amenable, due to its potential functional and aesthetic impact. Therefore, upon multidisciplinary agreement, radiotherapy and immunotherapy with cemiplimab were alternatively administered. After 6 months, an early objective tumor response was observed in 9/11 patients, with 17/20 cutaneous lesions (85%) presenting either a complete or partial response. Only 2/11 patients, with a total of 3/20 cutaneous lesions (15%), had stable disease. These benefits persisted at a longer follow-up (21.4 ± 9.7 months), with no patients presenting disease progression. Despite the retrospective nature of this study and small sample size, our experience highlights the ability of concomitant radiotherapy and cemiplimab to promote an early objective response in patients with advanced CSCC. Moreover, in our population, the clinical benefits were also related to a longer progression-free survival, without any safety alert reported.
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Affiliation(s)
- Maria Chiara Lo Greco
- Radiation Oncology Unit, Department of Biomedical, Dental and Morphological and Functional Imaging Sciences, University of Messina, 98122 Messina, Italy; (G.M.); (I.F.); (M.L.R.); (S.P.)
| | - Giorgia Marano
- Radiation Oncology Unit, Department of Biomedical, Dental and Morphological and Functional Imaging Sciences, University of Messina, 98122 Messina, Italy; (G.M.); (I.F.); (M.L.R.); (S.P.)
| | - Roberto Milazzotto
- Radiation Oncology Unit, University Hospital Policlinico “G. Rodolico-San Marco”, 95123 Catania, Italy; (R.M.); (R.L.E.L.); (C.S.)
| | - Rocco Luca Emanuele Liardo
- Radiation Oncology Unit, University Hospital Policlinico “G. Rodolico-San Marco”, 95123 Catania, Italy; (R.M.); (R.L.E.L.); (C.S.)
| | - Irene Finocchiaro
- Radiation Oncology Unit, Department of Biomedical, Dental and Morphological and Functional Imaging Sciences, University of Messina, 98122 Messina, Italy; (G.M.); (I.F.); (M.L.R.); (S.P.)
| | - Madalina La Rocca
- Radiation Oncology Unit, Department of Biomedical, Dental and Morphological and Functional Imaging Sciences, University of Messina, 98122 Messina, Italy; (G.M.); (I.F.); (M.L.R.); (S.P.)
| | - Antonio Basile
- Radiology I Unit, University Hospital Policlinico “G. Rodolico-San Marco”, 95123 Catania, Italy; (A.B.); (P.V.F.); (S.P.); (E.D.)
- Department of Medical Surgical Sciences and Advanced Technologies “G.F. Ingrassia”, University of Catania, 95123 Catania, Italy
| | - Pietro Valerio Foti
- Radiology I Unit, University Hospital Policlinico “G. Rodolico-San Marco”, 95123 Catania, Italy; (A.B.); (P.V.F.); (S.P.); (E.D.)
- Department of Medical Surgical Sciences and Advanced Technologies “G.F. Ingrassia”, University of Catania, 95123 Catania, Italy
| | - Stefano Palmucci
- Radiology I Unit, University Hospital Policlinico “G. Rodolico-San Marco”, 95123 Catania, Italy; (A.B.); (P.V.F.); (S.P.); (E.D.)
- Department of Medical Surgical Sciences and Advanced Technologies “G.F. Ingrassia”, University of Catania, 95123 Catania, Italy
| | - Emanuele David
- Radiology I Unit, University Hospital Policlinico “G. Rodolico-San Marco”, 95123 Catania, Italy; (A.B.); (P.V.F.); (S.P.); (E.D.)
- Department of Medical Surgical Sciences and Advanced Technologies “G.F. Ingrassia”, University of Catania, 95123 Catania, Italy
| | - Stefano Pergolizzi
- Radiation Oncology Unit, Department of Biomedical, Dental and Morphological and Functional Imaging Sciences, University of Messina, 98122 Messina, Italy; (G.M.); (I.F.); (M.L.R.); (S.P.)
| | - Corrado Spatola
- Radiation Oncology Unit, University Hospital Policlinico “G. Rodolico-San Marco”, 95123 Catania, Italy; (R.M.); (R.L.E.L.); (C.S.)
- Department of Medical Surgical Sciences and Advanced Technologies “G.F. Ingrassia”, University of Catania, 95123 Catania, Italy
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10
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Wang AF, Hsueh B, Choi BD, Gerstner ER, Dunn GP. Immunotherapy for Brain Tumors: Where We Have Been, and Where Do We Go From Here? Curr Treat Options Oncol 2024; 25:628-643. [PMID: 38649630 DOI: 10.1007/s11864-024-01200-9] [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: 03/18/2024] [Indexed: 04/25/2024]
Abstract
OPINION STATEMENT Immunotherapy for glioblastoma (GBM) remains an intensive area of investigation. Given the seismic impact of cancer immunotherapy across a range of malignancies, there is optimism that harnessing the power of immunity will influence GBM as well. However, despite several phase 3 studies, there are still no FDA-approved immunotherapies for GBM. Importantly, the field has learned a great deal from the randomized studies to date. Today, we are continuing to better understand the disease-specific features of the microenvironment in GBM-as well as the exploitable antigenic characteristic of the tumor cells themselves-that are informing the next generation of immune-based therapeutic strategies. The coming phase of next-generation immunotherapies is thus poised to bring us closer to treatments that will improve the lives of patients with GBM.
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Affiliation(s)
- Alexander F Wang
- Department of Neurosurgery, Massachusetts General Hospital, 55 Fruit Street, Boston, MA, 02114, USA
| | - Brian Hsueh
- Department of Neurosurgery, Massachusetts General Hospital, 55 Fruit Street, Boston, MA, 02114, USA
| | - Bryan D Choi
- Department of Neurosurgery, Massachusetts General Hospital, 55 Fruit Street, Boston, MA, 02114, USA
- Brain Tumor Immunology and Immunotherapy Program, Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Elizabeth R Gerstner
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Stephen E. and Catherine Pappas Center for Neuro-Oncology, Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Gavin P Dunn
- Department of Neurosurgery, Massachusetts General Hospital, 55 Fruit Street, Boston, MA, 02114, USA.
- Brain Tumor Immunology and Immunotherapy Program, Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
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11
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Bowen CM, Sinha KM, Vilar E. Current Trends in Vaccine Development for Hereditary Colorectal Cancer Syndromes. Clin Colon Rectal Surg 2024; 37:146-156. [PMID: 38606044 PMCID: PMC11006444 DOI: 10.1055/s-0043-1770383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2024]
Abstract
The coming of age for cancer treatment has experienced exponential growth in the last decade with the addition of immunotherapy as the fourth pillar to the fundamentals of cancer treatment-chemotherapy, surgery, and radiation-taking oncology to an astounding new frontier. In this time, rapid developments in computational biology coupled with immunology have led to the exploration of priming the host immune system through vaccination to prevent and treat certain subsets of cancer such as melanoma and hereditary colorectal cancer. By targeting the immune system through tumor-specific antigens-namely, neoantigens (neoAgs)-the future of cancer prevention may lie within arm's reach by employing neoAg vaccines as an immune-preventive modality for hereditary cancer syndromes like Lynch syndrome. In this review, we discuss the history, current trends, utilization, and future direction of neoAg-based vaccines in the setting of hereditary colorectal cancer.
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Affiliation(s)
- Charles M. Bowen
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Krishna M. Sinha
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Eduardo Vilar
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas
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12
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Bao L, Ye Y, Zhang X, Xu X, Wang W, Jiang B. Identification and verification of a PANoptosis-related long noncoding ribonucleic acid signature for predicting the clinical outcomes and immune landscape in lung adenocarcinoma. Heliyon 2024; 10:e29869. [PMID: 38681588 PMCID: PMC11053219 DOI: 10.1016/j.heliyon.2024.e29869] [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: 03/30/2023] [Revised: 03/01/2024] [Accepted: 04/16/2024] [Indexed: 05/01/2024] Open
Abstract
PANoptosis is a type of programmed cell death (PCD) characterised by apoptosis, necroptosis and pyroptosis. Long non-coding ribonucleic acids (lncRNAs) are participating in the malignant behaviour of tumours regulated by PCD. Nevertheless, the function of PANoptosis-associated lncRNAs in lung adenocarcinoma remains to be investigated. In this work, a PANoptosis-related lncRNA signature (PRLSig) was developed based on the least absolute shrinkage and selection operator algorithm. The stability and fitness of PRLSig were confirmed by systematic evaluation of Kaplan-Meier, Cox analysis algorithm, receiver operating characteristic analysis, stratification analysis. In addition, ESTIMATE, single sample gene set enrichment analysis, immune checkpoints and the cancer immunome database confirmed the predictive value of the PRLSig in immune microenvironment and helped to identify populations for which immunotherapy is advantageous. The present research provides novel insights to facilitate risk stratification and optimise personalised treatment for LUAD.
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Affiliation(s)
- Lingling Bao
- Department of Hematology and Oncology, Beilun District People's Hospital, Ningbo, China
| | - Yingquan Ye
- The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Xuede Zhang
- Department of Oncology, Weifang People's Hospital, Weifang, China
| | - Xin Xu
- Department of Hematology and Oncology, Beilun District People's Hospital, Ningbo, China
| | - Wenjuan Wang
- Department of Hematology and Oncology, Beilun District People's Hospital, Ningbo, China
| | - Bitao Jiang
- Department of Hematology and Oncology, Beilun District People's Hospital, Ningbo, China
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13
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Dakal TC, George N, Xu C, Suravajhala P, Kumar A. Predictive and Prognostic Relevance of Tumor-Infiltrating Immune Cells: Tailoring Personalized Treatments against Different Cancer Types. Cancers (Basel) 2024; 16:1626. [PMID: 38730579 PMCID: PMC11082991 DOI: 10.3390/cancers16091626] [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: 03/13/2024] [Revised: 04/12/2024] [Accepted: 04/17/2024] [Indexed: 05/13/2024] Open
Abstract
TIICs are critical components of the TME and are used to estimate prognostic and treatment responses in many malignancies. TIICs in the tumor microenvironment are assessed and quantified by categorizing immune cells into three subtypes: CD66b+ tumor-associated neutrophils (TANs), FoxP3+ regulatory T cells (Tregs), and CD163+ tumor-associated macrophages (TAMs). In addition, many cancers have tumor-infiltrating M1 and M2 macrophages, neutrophils (Neu), CD4+ T cells (T-helper), CD8+ T cells (T-cytotoxic), eosinophils, and mast cells. A variety of clinical treatments have linked tumor immune cell infiltration (ICI) to immunotherapy receptivity and prognosis. To improve the therapeutic effectiveness of immune-modulating drugs in a wider cancer patient population, immune cells and their interactions in the TME must be better understood. This study examines the clinicopathological effects of TIICs in overcoming tumor-mediated immunosuppression to boost antitumor immune responses and improve cancer prognosis. We successfully analyzed the predictive and prognostic usefulness of TIICs alongside TMB and ICI scores to identify cancer's varied immune landscapes. Traditionally, immune cell infiltration was quantified using flow cytometry, immunohistochemistry, gene set enrichment analysis (GSEA), CIBERSORT, ESTIMATE, and other platforms that use integrated immune gene sets from previously published studies. We have also thoroughly examined traditional limitations and newly created unsupervised clustering and deconvolution techniques (SpatialVizScore and ProTICS). These methods predict patient outcomes and treatment responses better. These models may also identify individuals who may benefit more from adjuvant or neoadjuvant treatment. Overall, we think that the significant contribution of TIICs in cancer will greatly benefit postoperative follow-up, therapy, interventions, and informed choices on customized cancer medicines.
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Affiliation(s)
- Tikam Chand Dakal
- Genome and Computational Biology Lab, Department of Biotechnology, Mohanlal Sukhadia University, Udaipur 313001, Rajasthan, India
| | - Nancy George
- Department of Biotechnology, Chandigarh University, Mohali 140413, Punjab, India;
| | - Caiming Xu
- Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of the City of Hope, Monrovia, CA 91010, USA;
| | - Prashanth Suravajhala
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana P.O. 690525, Kerala, India;
| | - Abhishek Kumar
- Manipal Academy of Higher Education (MAHE), Manipal 576104, Karnataka, India
- Institute of Bioinformatics, International Technology Park, Bangalore 560066, Karnataka, India
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14
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He X, Gong G, Chen M, Zhang H, Zhang Y, Richardson JJ, Chan WY, He Y, Guo J. Metal-Phenolic Nanocloaks on Cancer Cells Potentiate STING Pathway Activation for Synergistic Cancer Immunotherapy. Angew Chem Int Ed Engl 2024; 63:e202314501. [PMID: 38302821 DOI: 10.1002/anie.202314501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 12/31/2023] [Accepted: 01/31/2024] [Indexed: 02/03/2024]
Abstract
Due to the presence of natural neoantigens, autologous tumor cells hold great promise as personalized therapeutic vaccines. Yet autologous tumor cell vaccines require multi-step production that frequently leads to the loss of immunoreactive antigens, causing insufficient immune activation and significantly hampering their clinical applications. Herein, we introduce a novel whole-cell cancer vaccine by cloaking cancer cells with lipopolysaccharide-decorated manganese(II)-phenolic networks (MnTA nanocloaks) to evoke tumor-specific immune response for highly efficacious synergistic cancer immunotherapy. The natural polyphenols coordinate with Mn2+ and immediately adhere to the surface of individual cancer cells, thereby forming a nanocloak and encapsulating tumor neoantigens. Subsequent decoration with lipopolysaccharide induces internalization by dendritic cells, where Mn2+ ions are released in the cytosol, further facilitating the activation of the stimulator of the interferon genes (STING) pathway. Highly effective tumor suppression was observed by combining the nanocloaked cancer cell treatment with anti-programmed cell death ligand 1 (anti-PD-L1) antibodies-mediated immune checkpoint blockade therapy. Our work demonstrates a universal yet simple strategy to engineer a cell-based nanobiohybrid system for enhanced cancer immunotherapy.
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Affiliation(s)
- Xianglian He
- BMI Center for Biomass Materials and Nanointerfaces, College of Biomass Science and Engineering, Sichuan University, Chengdu, Sichuan, 610065, China
| | - Guidong Gong
- BMI Center for Biomass Materials and Nanointerfaces, College of Biomass Science and Engineering, Sichuan University, Chengdu, Sichuan, 610065, China
| | - Mei Chen
- BMI Center for Biomass Materials and Nanointerfaces, College of Biomass Science and Engineering, Sichuan University, Chengdu, Sichuan, 610065, China
| | - Haojie Zhang
- BMI Center for Biomass Materials and Nanointerfaces, College of Biomass Science and Engineering, Sichuan University, Chengdu, Sichuan, 610065, China
| | - Yajing Zhang
- BMI Center for Biomass Materials and Nanointerfaces, College of Biomass Science and Engineering, Sichuan University, Chengdu, Sichuan, 610065, China
| | - Joseph J Richardson
- Department of Chemical and Environmental Engineering, RMIT University, Melbourne, Victoria, 3000, Australia
| | - Wood Yee Chan
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Center for Neuromusculoskeletal Restorative Medicine, Hong Kong Science Park, Shatin, New Territories, Hong Kong SAR, China
| | - Yunxiang He
- BMI Center for Biomass Materials and Nanointerfaces, College of Biomass Science and Engineering, Sichuan University, Chengdu, Sichuan, 610065, China
| | - Junling Guo
- BMI Center for Biomass Materials and Nanointerfaces, College of Biomass Science and Engineering, Sichuan University, Chengdu, Sichuan, 610065, China
- Department of Chemical and Biological Engineering, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada
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15
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Liu Y, Yan Q, Zeng Z, Fan C, Xiong W. Advances and prospects of mRNA vaccines in cancer immunotherapy. Biochim Biophys Acta Rev Cancer 2024; 1879:189068. [PMID: 38171406 DOI: 10.1016/j.bbcan.2023.189068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 12/24/2023] [Accepted: 12/27/2023] [Indexed: 01/05/2024]
Abstract
Cancer vaccines, designed to activate the body's own immune system to fight against tumors, are a current trend in cancer treatment and receiving increasing attention. Cancer vaccines mainly include oncolytic virus vaccine, cell vaccine, peptide vaccine and nucleic acid vaccine. Over the course of decades of research, oncolytic virus vaccine T-VEC, cellular vaccine sipuleucel-T, various peptide vaccines, and DNA vaccine against HPV positive cervical cancer have brought encouraging results for cancer therapy, but are losing momentum in development due to their respective shortcomings. In contrast, the advantages of mRNA vaccines such as high safety, ease of production, and unmatched efficacy are on full display. In addition, advances in technology such as pseudouridine modification have cracked down the bottleneck for developing mRNA vaccines including instability, innate immunogenicity, and low efficiency of in vivo delivery. Several cancer mRNA vaccines have achieved promising results in clinical trials, and their usage in conjunction with other immune checkpoint inhibitors (ICIs) has further boosted the efficiency of anti-tumor immune response. We expect a rapid development of mRNA vaccines for cancer immunotherapy in the near future. This review provides a brief overview of the current status of mRNA vaccines, highlights the action mechanism of cancer mRNA vaccines, their recent advances in clinical trials, and prospects for their clinical applications.
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Affiliation(s)
- Yixuan Liu
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China; Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China
| | - Qijia Yan
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha 410078, Hunan, China
| | - Zhaoyang Zeng
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China; Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China
| | - Chunmei Fan
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China; Department of Histology and Embryology, Xiangya School of Medicine, Central South University, Changsha 410013, Hunan Province, China.
| | - Wei Xiong
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China; Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, Hunan, China.
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16
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Miller AM, Koşaloğlu-Yalçın Z, Westernberg L, Montero L, Bahmanof M, Frentzen A, Lanka M, Logandha Ramamoorthy Premlal A, Seumois G, Greenbaum J, Brightman SE, Soria Zavala K, Thota RR, Naradikian MS, Makani SS, Lippman SM, Sette A, Cohen EEW, Peters B, Schoenberger SP. A functional identification platform reveals frequent, spontaneous neoantigen-specific T cell responses in patients with cancer. Sci Transl Med 2024; 16:eabj9905. [PMID: 38416845 DOI: 10.1126/scitranslmed.abj9905] [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: 06/15/2021] [Accepted: 01/29/2024] [Indexed: 03/01/2024]
Abstract
The clinical impact of tumor-specific neoantigens as both immunotherapeutic targets and biomarkers has been impeded by the lack of efficient methods for their identification and validation from routine samples. We have developed a platform that combines bioinformatic analysis of tumor exomes and transcriptional data with functional testing of autologous peripheral blood mononuclear cells (PBMCs) to simultaneously identify and validate neoantigens recognized by naturally primed CD4+ and CD8+ T cell responses across a range of tumor types and mutational burdens. The method features a human leukocyte antigen (HLA)-agnostic bioinformatic algorithm that prioritizes mutations recognized by patient PBMCs at a greater than 40% positive predictive value followed by a short-term in vitro functional assay, which allows interrogation of 50 to 75 expressed mutations from a single 50-ml blood sample. Neoantigens validated by this method include both driver and passenger mutations, and this method identified neoantigens that would not have been otherwise detected using an in silico prediction approach. These findings reveal an efficient approach to systematically validate clinically actionable neoantigens and the T cell receptors that recognize them and demonstrate that patients across a variety of human cancers have a diverse repertoire of neoantigen-specific T cells.
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Affiliation(s)
- Aaron M Miller
- Center for Cancer Immunotherapy, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
- Division of Hematology and Oncology, UCSD Moores Cancer Center, 3855 Health Sciences Drive, La Jolla, CA 92093, USA
| | - Zeynep Koşaloğlu-Yalçın
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Luise Westernberg
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Leslie Montero
- Center for Cancer Immunotherapy, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Milad Bahmanof
- Center for Cancer Immunotherapy, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Angela Frentzen
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Manasa Lanka
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | | | - Gregory Seumois
- Center for Cancer Immunotherapy, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Jason Greenbaum
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Spencer E Brightman
- Center for Cancer Immunotherapy, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Karla Soria Zavala
- Center for Cancer Immunotherapy, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Rukman R Thota
- Center for Cancer Immunotherapy, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Martin S Naradikian
- Center for Cancer Immunotherapy, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Samir S Makani
- Division of Hematology and Oncology, UCSD Moores Cancer Center, 3855 Health Sciences Drive, La Jolla, CA 92093, USA
| | - Scott M Lippman
- Division of Hematology and Oncology, UCSD Moores Cancer Center, 3855 Health Sciences Drive, La Jolla, CA 92093, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Ezra E W Cohen
- Division of Hematology and Oncology, UCSD Moores Cancer Center, 3855 Health Sciences Drive, La Jolla, CA 92093, USA
| | - Bjoern Peters
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
- Department of Medicine, University of California, San Diego (UCSD), La Jolla, CA 92037, USA
| | - Stephen P Schoenberger
- Center for Cancer Immunotherapy, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
- Division of Hematology and Oncology, UCSD Moores Cancer Center, 3855 Health Sciences Drive, La Jolla, CA 92093, USA
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17
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You Y, Yang Q. Glycosylation-related genes mediated prognostic signature contribute to prognostic prediction and treatment options in ovarian cancer: based on bulk and single‑cell RNA sequencing data. BMC Cancer 2024; 24:207. [PMID: 38355446 PMCID: PMC10865697 DOI: 10.1186/s12885-024-11908-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 01/22/2024] [Indexed: 02/16/2024] Open
Abstract
BACKGROUND Ovarian cancer (OC) is a complex disease with significant tumor heterogeneity with the worst prognosis and highest mortality among all gynecological cancers. Glycosylation is a specific post-translational modification that plays an important role in tumor progression, immune escape and metastatic spread. The aim of this work was to identify the major glycosylation-related genes (GRGs) in OC and construct an effective GRGs signature to predict prognosis and immunotherapy. METHODS AUCell algorithm was used to identify glycosylation-related genes (GRGs) based on the scRNA-seq and bulk RNA-seq data. An effective GRGs signature was conducted using COX and LASSO regression algorithm. The texting dataset and clinical sample data were used to assessed the accuracy of GRGs signature. We evaluated the differences in immune cell infiltration, enrichment of immune checkpoints, immunotherapy response, and gene mutation status among different risk groups. Finally, RT-qPCR, Wound-healing assay, Transwell assay were performed to verify the effect of the CYBRD1 on OC. RESULTS A total of 1187 GRGs were obtained and a GRGs signature including 16 genes was established. The OC patients were divided into high- and low- risk group based on the median riskscore and the patients in high-risk group have poor outcome. We also found that the patients in low-risk group have higher immune cell infiltration, enrichment of immune checkpoints and immunotherapy response. The results of laboratory test showed that CYBRD1 can promote the invasion, and migration of OC and is closely related to the poor prognosis of OC patients. CONCLUSIONS Our study established a GRGs signature consisting of 16 genes based on the scRNA-seq and bulk RNA-seq data, which provides a new perspective on the prognosis prediction and treatment strategy for OC.
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Affiliation(s)
- Yue You
- Department of gynaecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Qing Yang
- Department of gynaecology, Shengjing Hospital of China Medical University, Shenyang, China.
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18
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Ye L, Chu X, Ni J, Chu L, Yang X, Zhu Z. NGS-based Tissue-Blood TMB Comparison and Blood-TMB Monitoring in Stage-III Non-Small Cell Lung Cancer Treated with Concurrent Chemoradiotherapy. Cancer Invest 2024; 42:165-175. [PMID: 38390854 DOI: 10.1080/07357907.2024.2316297] [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: 01/30/2022] [Accepted: 02/05/2024] [Indexed: 02/24/2024]
Abstract
In this study, we analyzed the blood-based TMB (b-TMB) and its dynamic changes in patients with locally advanced non-small cell lung cancer (LA-NSCLC) who received concurrent chemoradiotherapy. Baseline tissue and blood TMB from 15 patients showed a strong positive correlation (Pearson correlation = 0.937), and nearly all mutations were markedly reduced in the later course of treatment, indicating a treatment-related response. This study suggests that in patients with LA-NSCLC, b-TMB is a reliable biomarker, and its dynamic monitoring can help distinguish patients who might benefit most from the consolidated immunotherapy.
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Affiliation(s)
- Luxi Ye
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiao Chu
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jianjiao Ni
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Li Chu
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xi Yang
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhengfei Zhu
- Department of Radiation Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Institute of Thoracic Oncology, Fudan University, Shanghai, China
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19
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Gautam N, Ramamoorthi G, Champion N, Han HS, Czerniecki BJ. Reviewing the significance of dendritic cell vaccines in interrupting breast cancer development. Mol Aspects Med 2024; 95:101239. [PMID: 38150884 DOI: 10.1016/j.mam.2023.101239] [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: 06/22/2023] [Revised: 12/06/2023] [Accepted: 12/12/2023] [Indexed: 12/29/2023]
Abstract
Breast cancer is a heterogeneous disease and is the most prevalent cancer in women. According to the U.S breast cancer statistics, about 1 in every 8 women develop an invasive form of breast cancer during their lifetime. Immunotherapy has been a significant advancement in the treatment of cancer with multiple studies reporting favourable patient outcomes by modulating the immune response to cancer cells. Here, we review the significance of dendritic cell vaccines in treating breast cancer patients. We discuss the involvement of dendritic cells and oncodrivers in breast tumorigenesis, highlighting the rationale for targeting oncodrivers and neoantigens using dendritic cell vaccine therapy. We review different dendritic cell subsets and maturation states previously used to develop vaccines and suggest the use of DC vaccines for breast cancer prevention. Further, we highlight that the intratumoral delivery of type 1 dendritic cell vaccines in breast cancer patients activates tumor antigen-specific CD4+ T helper cell type 1 (Th1) cells, promoting an anti-tumorigenic immune response while concurrently blocking pro-tumorigenic responses. In summary, this review provides an overview of the current state of dendritic cell vaccines in breast cancer highlighting the challenges and considerations necessary for an efficient dendritic cell vaccine design in interrupting breast cancer development.
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Affiliation(s)
- Namrata Gautam
- Clinical Science & Immunology Program, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - Ganesan Ramamoorthi
- Clinical Science & Immunology Program, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - Nicholas Champion
- Department of Breast Oncology, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - Hyo S Han
- Department of Breast Oncology, H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | - Brian J Czerniecki
- Clinical Science & Immunology Program, H. Lee Moffitt Cancer Center, Tampa, FL, USA; Department of Breast Oncology, H. Lee Moffitt Cancer Center, Tampa, FL, USA.
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20
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Sakakida T, Ishikawa T, Doi T, Morita R, Kataoka S, Miyake H, Yamaguchi K, Moriguchi M, Sogame Y, Yasuda H, Iwasaku M, Konishi H, Takayama K, Itoh Y. Genomic profile and clinical features of MSI-H and TMB-high pancreatic cancers: real-world data from C-CAT database. J Gastroenterol 2024; 59:145-156. [PMID: 38006445 DOI: 10.1007/s00535-023-02058-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 11/01/2023] [Indexed: 11/27/2023]
Abstract
BACKGROUND Microsatellite instability high (MSI-H) and tumor mutational burden high (TMB-high) pancreatic cancer are rare, and information is lacking. Based on the C-CAT database, we analyzed the clinical and genomic characteristics of patients with these subtypes. METHODS We retrospectively reviewed data on 2206 patients with unresectable pancreatic adenocarcinoma enrolled in C-CAT between July 2019 and January 2022. The clinical features, proportion of genomic variants classified as oncogenic/pathogenic in C-CAT, overall response rate (ORR), disease control rate (DCR), and time to treatment failure (TTF) of chemotherapy as first-line treatment were evaluated. RESULTS Numbers of patients with MSI-H and TMB-high were 7 (0.3%) and 39 (1.8%), respectively. All MSI-H patients were TMB-high. MSI-H and TMB-high patients harbored more mismatch repair genes, such as MSH2, homologous recombination-related genes, such as ATR and BRCA2, and other genes including BRAF, KMT2D, and SMARCA4. None of the 6 MSI-H patients who received chemotherapy achieved a clinical response, including 4 patients treated with gemcitabine plus nab-paclitaxel (GnP) therapy, whose DCR was significantly lower than that of microsatellite stable (MSS) patients (0 vs. 67.0%, respectively, p = 0.01). Among the TMB-high and TMB-low groups, no significant differences were shown in ORR, DCR (17.1 vs. 23.1% and 57.1 vs. 63.1%, respectively), or median TTF (25.9 vs. 28.0 weeks, respectively) of overall first-line chemotherapy. CONCLUSIONS MSI-H and TMB-high pancreatic cancers showed some distinct genomic and clinical features from our real-world data. These results suggest the importance of adapting optimal treatment strategies according to the genomic alterations.
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Affiliation(s)
- Tomoki Sakakida
- Department of Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, 465 Kajiicho, Hirokoji agaru, Kawaramachi Street, Kamigyoku, Kyoto, Kyoto, 602-8566, Japan
- Department of Cancer Genome Medical Center, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Takeshi Ishikawa
- Department of Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, 465 Kajiicho, Hirokoji agaru, Kawaramachi Street, Kamigyoku, Kyoto, Kyoto, 602-8566, Japan.
- Department of Cancer Genome Medical Center, Kyoto Prefectural University of Medicine, Kyoto, Japan.
- Outpatient Oncology Unit, Kyoto Prefectural University of Medicine, Kyoto, Japan.
| | - Toshifumi Doi
- Department of Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, 465 Kajiicho, Hirokoji agaru, Kawaramachi Street, Kamigyoku, Kyoto, Kyoto, 602-8566, Japan
- Department of Cancer Genome Medical Center, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Ryuichi Morita
- Department of Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, 465 Kajiicho, Hirokoji agaru, Kawaramachi Street, Kamigyoku, Kyoto, Kyoto, 602-8566, Japan
- Department of Cancer Genome Medical Center, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Seita Kataoka
- Department of Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, 465 Kajiicho, Hirokoji agaru, Kawaramachi Street, Kamigyoku, Kyoto, Kyoto, 602-8566, Japan
| | - Hayato Miyake
- Department of Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, 465 Kajiicho, Hirokoji agaru, Kawaramachi Street, Kamigyoku, Kyoto, Kyoto, 602-8566, Japan
| | - Kanji Yamaguchi
- Department of Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, 465 Kajiicho, Hirokoji agaru, Kawaramachi Street, Kamigyoku, Kyoto, Kyoto, 602-8566, Japan
| | - Michihisa Moriguchi
- Department of Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, 465 Kajiicho, Hirokoji agaru, Kawaramachi Street, Kamigyoku, Kyoto, Kyoto, 602-8566, Japan
| | - Yoshio Sogame
- Department of Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, 465 Kajiicho, Hirokoji agaru, Kawaramachi Street, Kamigyoku, Kyoto, Kyoto, 602-8566, Japan
| | - Hiroaki Yasuda
- Department of Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, 465 Kajiicho, Hirokoji agaru, Kawaramachi Street, Kamigyoku, Kyoto, Kyoto, 602-8566, Japan
| | - Masahiro Iwasaku
- Department of Cancer Genome Medical Center, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Hideyuki Konishi
- Department of Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, 465 Kajiicho, Hirokoji agaru, Kawaramachi Street, Kamigyoku, Kyoto, Kyoto, 602-8566, Japan
| | - Koichi Takayama
- Department of Cancer Genome Medical Center, Kyoto Prefectural University of Medicine, Kyoto, Japan
- Outpatient Oncology Unit, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yoshito Itoh
- Department of Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, 465 Kajiicho, Hirokoji agaru, Kawaramachi Street, Kamigyoku, Kyoto, Kyoto, 602-8566, Japan
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21
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Wang L, Wan P, Xu Z. A novel PANoptosis-related long non-coding RNA index to predict prognosis, immune microenvironment and personalised treatment in hepatocellular carcinoma. Aging (Albany NY) 2024; 16:2410-2437. [PMID: 38284890 PMCID: PMC10911344 DOI: 10.18632/aging.205488] [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: 12/26/2023] [Indexed: 01/30/2024]
Abstract
BACKGROUND PANoptosis is involved in the interaction of apoptosis, necroptosis and pyroptosis, playing a role in programmed cell death. Moreover, long non-coding RNAs (lncRNAs) regulate the PCD. This work aims to explore the role of PANoptosis-associated lncRNAs in hepatocellular carcinoma (HCC). METHODS Co-expression analysis identified PANoptosis-associated lncRNAs in HCC. Cox and Least Absolute Shrinkage and Selection Operator (LASSO) algorithms were utilised to filter lncRNAs and establish a PANoptosis-related lncRNA index (PANRI). Additionally, Cox, Kaplan-Meier and receiver operating characteristic (ROC) curves were utilised to systematically evaluate the PANRI. Furthermore, Estimation of STromal and Immune cells in MAlignant Tumor tissues using Expression data (ESTIMATE), single sample gene set enrichment analysis (ssGSEA) and immune checkpoints were performed to analyse the potential of the PANRI in differentiating different tumour immune microenvironment (TIME) populations. The consensus clustering algorithm was used to distinguish individuals with HCC having different TIME subtypes. Finally, HCC cell lines HepG2 were utilised for further validation in in vitro experiments. RESULTS The PANRI differentiates patients according to risk. Notably, ESTIMATE and ssGSEA algorithms revealed a high immune infiltration status in high-risk patients. Additionally, consensus clustering divided the patients into three clusters to identify different subtypes of TIME. Moreover, in vitro results showed that siRNA-mediated silencing of AL049840.4 inhibited the viability and migration of HepG2 cells and promoted apoptosis. CONCLUSIONS This is the first PANoptosis-related, lncRNA-based risk index in HCC to assess patient prognosis, TIME and response to immunotherapy. This study offers novel perspectives on the role of PANoptosis-associated lncRNAs in HCC.
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Affiliation(s)
- Liangliang Wang
- Department of Chemoradiotherapy, The Affiliated People’s Hospital of Ningbo University, Ningbo, China
- Chemoradiotherapy Center of Oncology, The Affiliated People’s Hospital of Ningbo University, Ningbo, China
| | - Peng Wan
- Department of Chemoradiotherapy, The Affiliated People’s Hospital of Ningbo University, Ningbo, China
- Chemoradiotherapy Center of Oncology, The Affiliated People’s Hospital of Ningbo University, Ningbo, China
| | - Zhengyang Xu
- Department of Chemoradiotherapy, The Affiliated People’s Hospital of Ningbo University, Ningbo, China
- Chemoradiotherapy Center of Oncology, The Affiliated People’s Hospital of Ningbo University, Ningbo, China
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22
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Keshari S, Shavkunov AS, Miao Q, Saha A, Williams CD, Highsmith AM, Pineda JE, Alspach E, Hu KH, Pauken KE, Chen K, Gubin MM. Neoantigen Cancer Vaccines and Different Immune Checkpoint Therapies Each Utilize Both Converging and Distinct Mechanisms that in Combination Enable Synergistic Therapeutic Efficacy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.20.570816. [PMID: 38187708 PMCID: PMC10769249 DOI: 10.1101/2023.12.20.570816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
The goal of therapeutic cancer vaccines and immune checkpoint therapy (ICT) is to eliminate cancer by expanding and/or sustaining T cells with anti-tumor capabilities. However, whether cancer vaccines and ICT enhance anti-tumor immunity by distinct or overlapping mechanisms remains unclear. Here, we compared effective therapeutic tumor-specific mutant neoantigen (NeoAg) cancer vaccines with anti-CTLA-4 and/or anti-PD-1 ICT in preclinical models. Both NeoAg vaccines and ICT induce expansion of intratumoral NeoAg-specific CD8 T cells, though the degree of expansion and acquisition of effector activity was much more substantial following NeoAg vaccination. Further, we found that NeoAg vaccines are particularly adept at inducing proliferating and stem-like NeoAg-specific CD8 T cells. Single cell T cell receptor (TCR) sequencing revealed that TCR clonotype expansion and diversity of NeoAg-specific CD8 T cells relates to their phenotype and functional state associated with specific immunotherapies employed. Effective NeoAg vaccines and ICT required both CD8 and CD4 T cells. While NeoAg vaccines and anti-PD-1 affected the CD4 T cell compartment, it was to less of an extent than observed with anti-CTLA-4, which notably induced ICOS+Bhlhe40+ Th1-like CD4 T cells and, when combined with anti-PD-1, a small subset of Th2-like CD4 T cells. Although effective NeoAg vaccines or ICT expanded intratumoral M1-like iNOS+ macrophages, NeoAg vaccines expanded rather than suppressed (as observed with ICT) M2-like CX3CR1+CD206+ macrophages, associated with the vaccine adjuvant. Further, combining NeoAg vaccination with ICT induced superior efficacy compared to either therapy in isolation, highlighting the utility of combining these modalities to eliminate cancer.
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Affiliation(s)
- Sunita Keshari
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alexander S. Shavkunov
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Qi Miao
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Akata Saha
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Charmelle D. Williams
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Anna M. Highsmith
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Josué E. Pineda
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Elise Alspach
- Department of Molecular Microbiology and Immunology, Saint Louis University School of Medicine, St. Louis, MO, USA
| | - Kenneth H. Hu
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- The Parker Institute for Cancer Immunotherapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- The James P. Allison Institute, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kristen E. Pauken
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ken Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Matthew M. Gubin
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- The Parker Institute for Cancer Immunotherapy, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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23
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Feng D, Tuo Z, Wang J, Ye L, Li D, Wu R, Wei W, Yang Y, Zhang C. Establishment of novel ferroptosis-related prognostic subtypes correlating with immune dysfunction in prostate cancer patients. Heliyon 2024; 10:e23495. [PMID: 38187257 PMCID: PMC10770465 DOI: 10.1016/j.heliyon.2023.e23495] [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: 07/03/2023] [Revised: 09/19/2023] [Accepted: 12/05/2023] [Indexed: 01/09/2024] Open
Abstract
Background We aimed to identify two new prognostic subtypes and create a predictive index for prostate cancer (PCa) patients based on ferroptosis database. Methods The nonnegative matrix factorization approach was used to identify molecular subtypes. We investigate the differences between cluster 1 and cluster 2 in terms of clinical features, functional pathways, tumour stemness, tumour heterogeneity, gene mutation and tumour immune microenvironment score after identifying the two molecular subtypes. Colony formation assay and flow cytometry assay were performed. Results The stratification of two clusters was closely connected to BCR-free survival using the nonnegative matrix factorization method, which was validated in the other three datasets. Furthermore, multivariate Cox regression analysis revealed that this classification was an independent risk factor for patients with PCa. Ribosome, aminoacyl tRNA production, oxidative phosphorylation, and Parkinson's disease-related pathways were shown to be highly enriched in cluster 1. In comparison to cluster 2, patients in cluster 1 exhibited significantly reduced CD4+ T cells, CD8+ T cells, neutrophils, dendritic cells and tumor immune microenvironment scores. Only HHLA2 was more abundant in cluster 1. Moreover, we found that P4HB downregulation could significantly inhibit the colony formation ability and contributed to cell apoptosis of C4-2B and DU145 cell lines. Conclusions We discovered two new prognostic subtypes associated with immunological dysfunction in PCa patients based on ferroptosis-related genes and found that P4HB downregulation could significantly inhibit the colony formation ability and contributed to cell apoptosis of PCa cell lines.
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Affiliation(s)
- Dechao Feng
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
- Department of Rehabilitation, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, China
| | - Zhouting Tuo
- Department of Urology, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, China
| | - Jie Wang
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Luxia Ye
- Department of Public Research Platform, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, China
| | - Dengxiong Li
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Ruicheng Wu
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Wuran Wei
- Department of Urology, Institute of Urology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yubo Yang
- Department of Urology, Three Gorges Hospital, Chongqing University, Wanzhou, Chongqing, 404000, China
| | - Chi Zhang
- Department of Rehabilitation, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, China
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24
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Gera K, Chauhan A, Castillo P, Rahman M, Mathavan A, Mathavan A, Oganda-Rivas E, Elliott L, Wingard JR, Sayour EJ. Vaccines: a promising therapy for myelodysplastic syndrome. J Hematol Oncol 2024; 17:4. [PMID: 38191498 PMCID: PMC10773074 DOI: 10.1186/s13045-023-01523-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 12/23/2023] [Indexed: 01/10/2024] Open
Abstract
Myelodysplastic neoplasms (MDS) define clonal hematopoietic malignancies characterized by heterogeneous mutational and clinical spectra typically seen in the elderly. Curative treatment entails allogeneic hematopoietic stem cell transplant, which is often not a feasible option due to older age and significant comorbidities. Immunotherapy has the cytotoxic capacity to elicit tumor-specific killing with long-term immunological memory. While a number of platforms have emerged, therapeutic vaccination presents as an appealing strategy for MDS given its promising safety profile and amenability for commercialization. Several preclinical and clinical trials have investigated the efficacy of vaccines in MDS; these include peptide vaccines targeting tumor antigens, whole cell-based vaccines and dendritic cell-based vaccines. These therapeutic vaccines have shown acceptable safety profiles, but consistent clinical responses remain elusive despite robust immunological reactions. Combining vaccines with immunotherapeutic agents holds promise and requires further investigation. Herein, we highlight therapeutic vaccine trials while reviewing challenges and future directions of successful vaccination strategies in MDS.
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Affiliation(s)
- Kriti Gera
- Department of Medicine, University of Florida, Gainesville, FL, USA
| | - Anjali Chauhan
- Department of Neurosurgery, Preston A. Wells, Jr. Center for Brain Tumor Immunotherapy, University of Florida, Gainesville, FL, USA
| | - Paul Castillo
- Division of Hematology and Oncology, Department of Pediatrics, University of Florida, Gainesville, FL, USA
| | - Maryam Rahman
- Department of Neurosurgery, Preston A. Wells, Jr. Center for Brain Tumor Immunotherapy, University of Florida, Gainesville, FL, USA
| | - Akash Mathavan
- Department of Medicine, University of Florida, Gainesville, FL, USA
| | - Akshay Mathavan
- Department of Medicine, University of Florida, Gainesville, FL, USA
| | - Elizabeth Oganda-Rivas
- Department of Neurosurgery, Preston A. Wells, Jr. Center for Brain Tumor Immunotherapy, University of Florida, Gainesville, FL, USA
| | - Leighton Elliott
- Division of Hematology and Oncology, Department of Medicine, University of Florida, Gainesville, FL, USA
| | - John R Wingard
- Division of Hematology and Oncology, Department of Medicine, University of Florida, Gainesville, FL, USA.
| | - Elias J Sayour
- Department of Neurosurgery, Preston A. Wells, Jr. Center for Brain Tumor Immunotherapy, University of Florida, Gainesville, FL, USA.
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Kumar H, Luo R, Wen J, Yang C, Zhou X, Kim P. FusionNeoAntigen: a resource of fusion gene-specific neoantigens. Nucleic Acids Res 2024; 52:D1276-D1288. [PMID: 37870454 PMCID: PMC10767944 DOI: 10.1093/nar/gkad922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 10/02/2023] [Accepted: 10/09/2023] [Indexed: 10/24/2023] Open
Abstract
Among the diverse sources of neoantigens (i.e. single-nucleotide variants (SNVs), insertions or deletions (Indels) and fusion genes), fusion gene-derived neoantigens are generally more immunogenic, have multiple targets per mutation and are more widely distributed across various cancer types. Therefore, fusion gene-derived neoantigens are a potential source of highly immunogenic neoantigens and hold great promise for cancer immunotherapy. However, the lack of fusion protein sequence resources and knowledge prevents this application. We introduce 'FusionNeoAntigen', a dedicated resource for fusion-specific neoantigens, accessible at https://compbio.uth.edu/FusionNeoAntigen. In this resource, we provide fusion gene breakpoint crossing neoantigens focused on ∼43K fusion proteins of ∼16K in-frame fusion genes from FusionGDB2.0. FusionNeoAntigen provides fusion gene information, corresponding fusion protein sequences, fusion breakpoint peptide sequences, fusion gene-derived neoantigen prediction, virtual screening between fusion breakpoint peptides having potential fusion neoantigens and human leucocyte antigens (HLAs), fusion breakpoint RNA/protein sequences for developing vaccines, information on samples with fusion-specific neoantigen, potential CAR-T targetable cell-surface fusion proteins and literature curation. FusionNeoAntigen will help to develop fusion gene-based immunotherapies. We will report all potential fusion-specific neoantigens from all possible open reading frames of ∼120K human fusion genes in future versions.
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Affiliation(s)
- Himansu Kumar
- Department of Bioinformatics and Systems Medicine, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Ruihan Luo
- Department of Bioinformatics and Systems Medicine, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Jianguo Wen
- Department of Bioinformatics and Systems Medicine, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Chengyuan Yang
- School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Xiaobo Zhou
- Department of Bioinformatics and Systems Medicine, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Pora Kim
- Department of Bioinformatics and Systems Medicine, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
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26
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Xue D, Peng H, Li Z, Xu J, Ma H, Dang Y, Li F, Wang G, Sun Q. Comprehensive analysis reveals TSPEAR as a prognostic biomarker in colorectal cancer. J Cancer 2024; 15:809-824. [PMID: 38213725 PMCID: PMC10777046 DOI: 10.7150/jca.90028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 11/27/2023] [Indexed: 01/13/2024] Open
Abstract
Background: Colorectal cancer (CRC) is one of the most common malignant tumors and has high morbidity and mortality rates. Previous studies have shown that TSPEAR mutations are involved in the development and progression of gastric cancer and liver cancer. However, the role of TSPEAR in CRC is still unclear. Methods: In The Cancer Genome Atlas (TCGA) database, 590 CRC patients with complete survival information were analyzed. We assessed TSPEAR expression in a pan-cancer dataset from the TCGA database. Cox regression analysis was performed to evaluate factors associated with prognosis. Enrichment analysis via the R package "clusterProfiler" was used to explore the potential function of TSPEAR. The single-sample GSEA (ssGSEA) method from the R package "GSVA" and the TIMER database were used to investigate the association between the immune infiltration level and TSPEAR expression in CRC. The R package "maftools" was used to explore the association between tumour mutation burden (TMB) and TSPEAR expression in CRC. CCK-8 assays and cell invasion assays were used to detect the effect of TSPEAR and TGIF2 on the biological behavior of CRC cells. Results: Pan-cancer analysis revealed that TSPEAR was upregulated in CRC tissues compared to normal tissues and that high TSPEAR expression was associated with poorer overall survival (OS) (p=0.0053). The expression of TSPEAR increased with increasing TNM stage, T stage, N stage, and M stage. The nomogram constructed with TSPEAR, age, and TNM stage showed better predictive value than TSPEAR, age, or TNM stage alone. Immune cell infiltration analysis revealed that high expression of TSPEAR was associated with lower immune cell infiltration. Tumor mutation burden (TMB) analysis indicated that high expression of TSPEAR was associated with lower TMB (p=0.005), and high TMB was associated with shorter OS (p=0.02). CCK-8 assays and cell invasion assays indicated that in vitro knockdown of TSPEAR inhibited the proliferation, migration, and invasion of CRC cells. In addition, TSPEAR expression may be regulated by the upstream transcription factor TGIF2. Conclusion: TSPEAR expression was higher in CRC tissues than in normal tissues. Its upregulation was significantly associated with a poor prognosis. Additionally, TSPEAR plays a significant role in tumor immunity and the biological behavior of CRC cells. Thus, TSPEAR may become a promising prognostic biomarker and therapeutic target for CRC patients.
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Affiliation(s)
- Dong Xue
- Department of General Surgery, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Hang Peng
- Department of Talent Highland, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Zhenghui Li
- Department of General Surgery, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Jiarui Xu
- Department of General Surgery, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Haiyun Ma
- Department of General Surgery, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Yueyan Dang
- Department of General Surgery, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Fanni Li
- Department of Talent Highland, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Guanghui Wang
- Department of General Surgery, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Qi Sun
- Department of General Surgery, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
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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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28
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Fan T, Zhang M, Yang J, Zhu Z, Cao W, Dong C. Therapeutic cancer vaccines: advancements, challenges, and prospects. Signal Transduct Target Ther 2023; 8:450. [PMID: 38086815 PMCID: PMC10716479 DOI: 10.1038/s41392-023-01674-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 09/08/2023] [Accepted: 09/19/2023] [Indexed: 12/18/2023] Open
Abstract
With the development and regulatory approval of immune checkpoint inhibitors and adoptive cell therapies, cancer immunotherapy has undergone a profound transformation over the past decades. Recently, therapeutic cancer vaccines have shown promise by eliciting de novo T cell responses targeting tumor antigens, including tumor-associated antigens and tumor-specific antigens. The objective was to amplify and diversify the intrinsic repertoire of tumor-specific T cells. However, the complete realization of these capabilities remains an ongoing pursuit. Therefore, we provide an overview of the current landscape of cancer vaccines in this review. The range of antigen selection, antigen delivery systems development the strategic nuances underlying effective antigen presentation have pioneered cancer vaccine design. Furthermore, this review addresses the current status of clinical trials and discusses their strategies, focusing on tumor-specific immunogenicity and anti-tumor efficacy assessment. However, current clinical attempts toward developing cancer vaccines have not yielded breakthrough clinical outcomes due to significant challenges, including tumor immune microenvironment suppression, optimal candidate identification, immune response evaluation, and vaccine manufacturing acceleration. Therefore, the field is poised to overcome hurdles and improve patient outcomes in the future by acknowledging these clinical complexities and persistently striving to surmount inherent constraints.
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Affiliation(s)
- Ting Fan
- Department of Oncology, East Hospital Affiliated to Tongji University, Tongji University School of Medicine, Shanghai, China
| | - Mingna Zhang
- Postgraduate Training Base, Shanghai East Hospital, Jinzhou Medical University, Shanghai, 200120, China
| | - Jingxian Yang
- Department of Oncology, East Hospital Affiliated to Tongji University, Tongji University School of Medicine, Shanghai, China
| | - Zhounan Zhu
- Department of Oncology, East Hospital Affiliated to Tongji University, Tongji University School of Medicine, Shanghai, China
| | - Wanlu Cao
- Department of Oncology, East Hospital Affiliated to Tongji University, Tongji University School of Medicine, Shanghai, China.
| | - Chunyan Dong
- Department of Oncology, East Hospital Affiliated to Tongji University, Tongji University School of Medicine, Shanghai, China.
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Wang Y, Xu J, Lan T, Zhou C, Liu P. The loss of neoantigens is an important reason for immune escape in multiple myeloma patients with high intratumor heterogeneity. Cancer Med 2023; 12:21651-21665. [PMID: 37965778 PMCID: PMC10757111 DOI: 10.1002/cam4.6721] [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: 04/21/2023] [Revised: 07/30/2023] [Accepted: 10/04/2023] [Indexed: 11/16/2023] Open
Abstract
OBJECTIVES Intratumor heterogeneity (ITH) is an important factor for clinical outcomes in patients with multiple myeloma (MM). High ITH has been proven to be a key reason for tumor immune escape and treatment resistance. Neoantigens are thought to be associated with ITH, but the specific correlation and functional basis for this remains unclear. METHODS We study this question through the whole-exome sequencing (WES) data from 43 high ITH newly diagnosed MM patients in our center. Mutant allele tumor heterogeneity (MATH) was conducted to quantify ITH. The cutoff value for high intratumor heterogeneity was determined by comparing MATH of different kinds of tumors. NeoPredPipe was performed to predict neoantigens and binding affinity. RESULTS Compared to other tumors, MM has a relatively low tumor mutation burden but a high ITH. Patients with high MATH had significantly shorter progression-free survival times than those with low MATH (p = 0.001). In high ITH samples, there is a decrease in strong-binding neoantigens (p = 0.019). The loss of strong-binding neoantigens is a key factor for insensitivity to therapy (p = 0.015). Loss of heterozygosity in HLA was not observed. In addition, patients with fewer neoantigens loss had higher rates of disease remission (p = 0.047). CD8 + T cells (p = 0.012) and NK cells (p = 0.011) decreased significantly in patients with high neoantigens loss rate. A prediction model based on neoantigens was built to evaluate the strength of immune escape. CONCLUSION The loss of strong-binding neoantigens explains why tumors with high ITH have a higher degree of immune escape and may be feasible for deciding the clinical treatment of MM.
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Affiliation(s)
- Yue Wang
- Department of Hematology, Zhongshan HospitalFudan UniversityShanghaiChina
| | - Jiadai Xu
- Department of Hematology, Zhongshan HospitalFudan UniversityShanghaiChina
| | - Tianwei Lan
- Department of Hematology, Zhongshan HospitalFudan UniversityShanghaiChina
| | - Chi Zhou
- Department of Hematology, Zhongshan HospitalFudan UniversityShanghaiChina
| | - Peng Liu
- Department of Hematology, Zhongshan HospitalFudan UniversityShanghaiChina
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Yao T, Zhang Z, Li Q, Huang R, Hong Y, Li C, Zhang F, Huang Y, Fang Y, Cao Q, Jin X, Li C, Wang Z, Lin XJ, Li L, Wei W, Wang Z, Shen J. Long-Read Sequencing Reveals Alternative Splicing-Driven, Shared Immunogenic Neoepitopes Regardless of SF3B1 Status in Uveal Melanoma. Cancer Immunol Res 2023; 11:1671-1687. [PMID: 37756564 DOI: 10.1158/2326-6066.cir-23-0083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 07/13/2023] [Accepted: 09/22/2023] [Indexed: 09/29/2023]
Abstract
Tumor-specific neoepitopes are promising targets in cancer immunotherapy. However, the identification of functional tumor-specific neoepitopes remains challenging. In addition to the most common source, single-nucleotide variants (SNV), alternative splicing (AS) represents another rich source of neoepitopes and can be utilized in cancers with low SNVs such as uveal melanoma (UM). UM, the most prevalent adult ocular malignancy, has poor clinical outcomes due to a lack of effective therapies. Recent studies have revealed the promise of harnessing tumor neoepitopes to treat UM. Previous studies have focused on neoepitope targets associated with mutations in splicing factor 3b subunit 1 (SF3B1), a key splicing factor; however, little is known about the neoepitopes that are commonly shared by patients independent of SF3B1 status. To identify the AS-derived neoepitopes regardless of SF3B1 status, we herein used a comprehensive nanopore long-read-sequencing approach to elucidate the landscape of AS and novel isoforms in UM. We also performed high-resolution mass spectrometry to further validate the presence of neoepitope candidates and analyzed their structures using the AlphaFold2 algorithm. We experimentally evaluated the antitumor effects of these neoepitopes and found they induced robust immune responses by stimulating interferon (IFN)γ production and activating T cell-based UM tumor killing. These results provide novel insights into UM-specific neoepitopes independent of SF3B1 and lay the foundation for developing therapies by targeting these actionable neoepitopes.
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Affiliation(s)
- Tengteng Yao
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
| | - Zhe Zhang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
- Institute of Translational Medicine, National Facility for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Qian Li
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
- Institute of Translational Medicine, National Facility for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Rui Huang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
- Institute of Translational Medicine, National Facility for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yanhong Hong
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Lingang Laboratory, Shanghai, China
| | - Chen Li
- High Performance Computing Center, Shanghai Jiao Tong University, Shanghai, China
| | - Feng Zhang
- Department of Histoembryology, Genetics and Developmental Biology, Shanghai Key Laboratory of Reproductive Medicine, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yingying Huang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Lingang Laboratory, Shanghai, China
| | - Yan Fang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
- Institute of Translational Medicine, National Facility for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Qin Cao
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoliang Jin
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
| | - Chunliang Li
- Department of Tumor Cell Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Zefeng Wang
- CAS Key Laboratory of Computational Biology, CAS Shanghai Institute of Nutrition and Health, Shanghai, China
| | - Xinhua James Lin
- High Performance Computing Center, Shanghai Jiao Tong University, Shanghai, China
| | - Lingjie Li
- Department of Histoembryology, Genetics and Developmental Biology, Shanghai Key Laboratory of Reproductive Medicine, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wu Wei
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Lingang Laboratory, Shanghai, China
| | - Zhaoyang Wang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
| | - Jianfeng Shen
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
- Institute of Translational Medicine, National Facility for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
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Ma T, Zhang Y, Zhao M, Wang L, Wang H, Ye Z. A machine learning-based radiomics model for prediction of tumor mutation burden in gastric cancer. Front Genet 2023; 14:1283090. [PMID: 38028587 PMCID: PMC10657897 DOI: 10.3389/fgene.2023.1283090] [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: 08/25/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Purpose: To evaluate the potential of machine learning (ML)-based radiomics approach for predicting tumor mutation burden (TMB) in gastric cancer (GC). Methods: The contrast enhanced CT (CECT) images with corresponding clinical information of 256 GC patients were retrospectively collected. Patients were separated into training set (n = 180) and validation set (n = 76). A total of 3,390 radiomics features were extracted from three phases images of CECT. The least absolute shrinkage and selection operator (LASSO) model was used for feature screening. Seven machine learning (ML) algorithms were employed to find the optimal classifier. The predictive ability of radiomics model (RM) was evaluated with receiver operating characteristic. The correlation between RM and TMB values was evaluated using Spearman's correlation coefficient. The explainability of RM was assessed by the Shapley Additive explanations (SHAP) method. Results: Logistic regression algorithm was chosen for model construction. The RM showed good predictive ability of TMB status with AUCs of 0.89 [95% confidence interval (CI): 0.85-0.94] and 0.86 (95% CI: 0.74-0.98) in the training and validation sets. The correlation analysis revealed a good correlation between RM and TMB levels (correlation coefficient: 0.62, p < 0.001). The RM also showed favorable and stable predictive accuracy within the cutoff value range 6-16 mut/Mb in both sets. Conclusion: The ML-based RM offered a promising image biomarker for predicting TMB status in GC patients.
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Affiliation(s)
- Tingting Ma
- Department of Radiology, Tianjin Cancer Hospital Airport Hospital, Tianjin, China
- Department of Radiology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
- National Clinical Research Center for Cancer, Tianjin, China
- Tianjin’s Clinical Research Center for Cancer, Tianjin, China
- The Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
| | - Yuwei Zhang
- Department of Radiology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
- National Clinical Research Center for Cancer, Tianjin, China
- Tianjin’s Clinical Research Center for Cancer, Tianjin, China
- The Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
| | - Mengran Zhao
- Department of Radiology, Tianjin Cancer Hospital Airport Hospital, Tianjin, China
- Department of Radiology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
- National Clinical Research Center for Cancer, Tianjin, China
- Tianjin’s Clinical Research Center for Cancer, Tianjin, China
- The Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
| | - Lingwei Wang
- Department of Radiology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
- National Clinical Research Center for Cancer, Tianjin, China
- Tianjin’s Clinical Research Center for Cancer, Tianjin, China
- The Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
| | - Hua Wang
- Department of Radiology, Tianjin Cancer Hospital Airport Hospital, Tianjin, China
- Department of Radiology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
- National Clinical Research Center for Cancer, Tianjin, China
- Tianjin’s Clinical Research Center for Cancer, Tianjin, China
- The Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
| | - Zhaoxiang Ye
- Department of Radiology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
- National Clinical Research Center for Cancer, Tianjin, China
- Tianjin’s Clinical Research Center for Cancer, Tianjin, China
- The Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
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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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Wu M, Zhou S. Harnessing tumor immunogenomics: Tumor neoantigens in ovarian cancer and beyond. Biochim Biophys Acta Rev Cancer 2023; 1878:189017. [PMID: 37935309 DOI: 10.1016/j.bbcan.2023.189017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 10/30/2023] [Accepted: 11/01/2023] [Indexed: 11/09/2023]
Abstract
Ovarian cancer is a major cause of death among gynecological cancers due to its highly aggressive nature. Immunotherapy has emerged as a promising avenue for ovarian cancer treatment, offering targeted approaches with reduced off-target effects. With the advent of next-generation sequencing, it has become possible to identify genomic alterations that can serve as potential targets for immunotherapy. Furthermore, immunogenomics research has revealed the importance of genetic alterations in shaping the cancer immune responses. However, the heterogeneity of immunogenicity and the low tumor mutation burden pose challenges for neoantigen-based immunotherapies. Further research is needed to identify neoantigen-specific tumor-infiltrating lymphocytes (TIL) and establish guidelines for patient inclusion criteria in TIL-based therapy. The study of neoantigens and their implications in ovarian cancer immunotherapy holds great promise, and efforts focused on personalized treatment strategies, refined neoantigen selection, and optimized therapeutic combinations will contribute to improving patient outcomes in the future.
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Affiliation(s)
- Mengrui Wu
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, PR China
| | - Shengtao Zhou
- Department of Obstetrics and Gynecology, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, PR China.
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Chen G, Li X, Li R, Wu K, Lei Z, Dai R, Roche K, Wang AZ, Min Y. Chemotherapy-Induced Neoantigen Nanovaccines Enhance Checkpoint Blockade Cancer Immunotherapy. ACS NANO 2023; 17:18818-18831. [PMID: 37750443 DOI: 10.1021/acsnano.3c03274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
Chemotherapeutics have the potential to increase the efficacy of cancer immunotherapies by stimulating the production of damage-associated molecular patterns (DAMPs) and eliciting mutations that result in the production of neoantigens, thereby increasing the immunogenicity of cancerous lesions. However, the dose-limiting toxicity and limited immunogenicity of chemotherapeutics are not sufficient to induce a robust antitumor response. We hypothesized that cancer cells in vitro treated with ultrahigh doses of various chemotherapeutics artificially increased the abundance, variety, and specificity of DAMPs and neoantigens, thereby improving chemoimmunotherapy. The in vitro chemotherapy-induced (IVCI) nanovaccines manufactured from cell lysates comprised multiple neoantigens and DAMPs, thereby exhibiting comprehensive antigenicity and adjuvanticity. Our IVCI nanovaccines exhibited enhanced immune responses in CT26 tumor-bearing mice, with a significant increase in CD4+/CD8+ T cells in tumors in combination with immune checkpoint inhibitors. The concept of IVCI nanovaccines provides an idea for manufacturing and artificial enhancement of immunogenicity vaccines to improve chemoimmunotherapy.
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Affiliation(s)
- Guiyuan Chen
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, China
| | - Xiangxia Li
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, China
| | - Rui Li
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, China
| | - Kecheng Wu
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, China
| | - Zhouhang Lei
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, China
| | - Ruike Dai
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, China
| | - Kyle Roche
- School of Medicine and Health Sciences, The George Washington University, Washington D.C. 20052, United States
| | - Andrew Z Wang
- Department of Radiation Oncology, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390, United States
| | - Yuanzeng Min
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, China
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230026, China
- The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
- CAS Key Lab of Soft Matter Chemistry, University of Science and Technology of China, Hefei 230026, China
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Li W, Zhao Y, Zhang H, Zheng W, Wang R, Gu X. Predictive value of tumor mutational burden for PD-1/PD-L1 inhibitors in NSCLC: A meta-analysis. Medicine (Baltimore) 2023; 102:e34990. [PMID: 37800825 PMCID: PMC10553067 DOI: 10.1097/md.0000000000034990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 08/08/2023] [Indexed: 10/07/2023] Open
Abstract
BACKGROUND To investigate the association between tumor mutational burden (TMB) and the therapeutic effect of Programmed Death 1/Programmed Death Ligand 1 inhibitors in non-small cell lung cancer. METHODS Four electronic databases, PubMed, Embase, Web of Science, and Cochrane Library, were searched on May 10, 2023, and no time limitation was applied. Analyses were performed using STATA17.0. We assessed the methodological quality of each randomized controlled trial using the Newcastle-Ottawa scale. RESULTS After exhaustive database search and rigorous screening, 10 studies were included in the meta-analysis. Our findings indicate that high TMB significantly improves progression-free survival but reduces overall response rate. The overall survival was not significantly different between the high and low TMB groups. No significant publication bias was observed. CONCLUSION High TMB serves as a potential predictive biomarker for improved progression-free survival and reduced overall response rate in patients with non-small cell lung cancer treated with programmed death 1/programmed death ligand 1 inhibitors. However, its predictive value in overall survival requires further investigation.
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Affiliation(s)
- Wenjie Li
- Department of Respiratory and Critical Care Medicine, Xi’an Chest Hospital, Chang’an District, Xi’an, Shanxi, China
| | - Yanjun Zhao
- Department of Respiratory and Critical Care Medicine, Xi’an Chest Hospital, Chang’an District, Xi’an, Shanxi, China
| | - Hongjun Zhang
- Department of Respiratory and Critical Care Medicine, Xi’an Chest Hospital, Chang’an District, Xi’an, Shanxi, China
| | - Wenying Zheng
- Department of Respiratory and Critical Care Medicine, Xi’an Chest Hospital, Chang’an District, Xi’an, Shanxi, China
| | - Ruixuan Wang
- Department of Respiratory and Critical Care Medicine, Xi’an Chest Hospital, Chang’an District, Xi’an, Shanxi, China
| | - Xing Gu
- Department of Respiratory and Critical Care Medicine, Xi’an Chest Hospital, Chang’an District, Xi’an, Shanxi, China
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Jia M, Liang J, Li Z, Qin Y, Li Q, Wang J, Lu X. Screening tumor stage-specific candidate neoantigens in thyroid adenocarcinoma using integrated exome and transcriptome sequencing. Front Immunol 2023; 14:1187160. [PMID: 37854594 PMCID: PMC10579579 DOI: 10.3389/fimmu.2023.1187160] [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: 03/15/2023] [Accepted: 09/11/2023] [Indexed: 10/20/2023] Open
Abstract
Background The incidence of thyroid carcinoma (THCA), the most common endocrine tumor, is continuously increasing worldwide. Although the overall prognosis of THCA is good, patients with distant metastases exhibit a mortality rate of 5-20%. Methods To improve the diagnosis and overall prognosis of patients with thyroid cancer, we screened specific candidate neoantigen genes in early- and late-stage THCA by analyzing the transcriptome and somatic cell mutations in this study. Results The top five early-stage neoantigen-related genes (NRGs) were G protein-coupled receptor 4 [GPR4], chondroitin sulfate proteoglycan 4 [CSPG4], teneurin transmembrane protein 1 [TENM1], protein S 1 [PROS1], and thymidine kinase 1 [TK1], whereas the top five late-stage NRGs were cadherin 6 [CDH6], semaphorin 6B [SEMA6B], dysferlin [DYSF], xenotropic and polytropic retrovirus receptor 1 [XPR1], and ABR activator of RhoGEF and GTPase [ABR]. Subsequently, we used machine learning models to verify their ability to screen NRGs and analyze the correlations among NRGs, immune cell types, and immune checkpoint regulators. The use of candidate antigen genes resulted in a better diagnostic model (the area under the curve [AUC] value of the early-stage group [0.979] was higher than that of the late-stage group [0.959]). Then, a prognostic model was constructed to predict NRG survival, and the 1-, 3- and 5-year AUC values were 0.83, 0.87, and 0.86, respectively, which were closely related to different immune cell types. Comparison of the expression trends and mutation frequencies of NRGs in multiple tumors revealed their potential for the development of broad spectrum therapeutic drugs. Conclusion In conclusion, the candidate NRGs identified in this study could potentially be used as therapeutic targets and diagnostic biomarkers for the development of novel broad spectrum therapeutic agents.
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Affiliation(s)
- Meng Jia
- Department of Thyroid Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jiawen Liang
- Department of Thyroid Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Academy of Medical Science, Zhengzhou University, Zhengzhou, China
| | - Zhuyao Li
- Department of Thyroid Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ye Qin
- Department of Thyroid Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Qianqian Li
- Department of Thyroid Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jianwei Wang
- School of Computer and Artificial Intelligence, Zhengzhou University, Zhengzhou, China
| | - Xiubo Lu
- Department of Thyroid Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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Yan X, Qu F, Zhou Y. Progress of immune checkpoint inhibitors therapy for non-small cell lung cancer with brain metastases. Lung Cancer 2023; 184:107322. [PMID: 37611495 DOI: 10.1016/j.lungcan.2023.107322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 07/22/2023] [Accepted: 08/05/2023] [Indexed: 08/25/2023]
Abstract
About 40% of patients with non-small cell lung cancer (NSCLC) develop brain metastases (BMs) throughout the disease, and the occurrence of BMs is considered to have a fairly high mortality rate. Therefore, the management of brain metastases in NSCLC patients is a clinical challenge. Currently, multidisciplinary diagnosis and treatment methods are often used to achieve effective control of intracranial disease and prolong survival. Immunotherapy (IT) is one of the core therapies for NSCLC. Single or combined IT represented by immune checkpoint inhibitors(ICIs) of programmed death-1(PD-1)/ programmed cell death-ligand 1 (PD-L1) can significantly improve the prognosis of patients with advanced NSCLC.ICIs has been shown to be safe and effective in patients with BMs, although patients with BMs are mostly underrepresented in randomized clinical trials. In this review, we summarized the mechanism of ICIs in the treatment of BMs, and the clinical research and treatment progress of ICIs and their combination with other therapies in patients with BMs s from NSCLC.
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Affiliation(s)
- Xin Yan
- Department of Oncology, Affiliated Dalian Third People's Hospital of Dalian Medical University, 116033, China
| | - Fanjie Qu
- Department of Oncology, Affiliated Dalian Third People's Hospital of Dalian Medical University, 116033, China.
| | - Yi Zhou
- Department of Oncology, Affiliated Dalian Third People's Hospital of Dalian Medical University, 116033, China
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Kou X, He T, Zhang M, Wu X, Li X, Luo R, Wu R, Gou X, Shen M, Wu Q, Gong C. A Multivalent Personalized Vaccine Orchestrating Two-Signal Activation Rebuilds the Bridge Between Innate and Adaptive Antitumor Immunity. SMALL METHODS 2023; 7:e2300019. [PMID: 37386794 DOI: 10.1002/smtd.202300019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 05/20/2023] [Indexed: 07/01/2023]
Abstract
Personalized vaccines capable of circumventing tumor heterogeneity have exhibited compelling prospects. However, their therapeutic benefit is greatly hindered by the limited antigen repertoire and poor response of CD8+ T-cell immunity. Here, a double-signal coregulated cross-linking hydrogel-based vaccine (Bridge-Vax) is engineered to rebuild the bridge between innate and adaptive immunity for activating CD8+ T-cells against full repertoire of tumor antigens. Mechanistically, unlike prominent CD4+ T-cell responses in most cases, administration of Bridge-Vax encapsulated with granulocyte-macrophage colony-stimulating factor concentrates a wave of dendritic cells (DCs), which further promotes DCs activation with costimulatory signal by the self-adjuvanted nature of polysaccharide hydrogel. Simultaneously, synergy with the increased MHC-I epitopes by codelivered simvastatin for cross-presentation enhancement, Bridge-Vax endows DCs with necessary two signals for orchestrating CD8+ T-cell activation. Bridge-Vax elicits potent antigen-specific CD8+ T-cell responses in vivo, which not only shows efficacy in B16-OVA model but confers specific immunological memory to protect against tumor rechallenge. Moreover, personalized multivalent Bridge-Vax tailored by leveraging autologous tumor cell membranes as antigens inhibits postsurgical B16F10 tumor recurrence. Hence, this work provides a facile strategy to rebuild the bridge between innate and adaptive immunity for inducing potent CD8+ T-cell immunity and would be a powerful tool for personalized cancer immunotherapy.
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Affiliation(s)
- Xiaorong Kou
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, P. R. China
| | - Tao He
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, P. R. China
| | - Miaomiao Zhang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, P. R. China
| | - Xinyue Wu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, P. R. China
| | - Xinchao Li
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, P. R. China
| | - Rui Luo
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, P. R. China
| | - Rui Wu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, P. R. China
| | - Xinyu Gou
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, P. R. China
| | - Meiling Shen
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, P. R. China
| | - Qinjie Wu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, P. R. China
| | - Changyang Gong
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, P. R. China
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Liu D, Che X, Wang X, Ma C, Wu G. Tumor Vaccines: Unleashing the Power of the Immune System to Fight Cancer. Pharmaceuticals (Basel) 2023; 16:1384. [PMID: 37895855 PMCID: PMC10610367 DOI: 10.3390/ph16101384] [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: 09/02/2023] [Revised: 09/25/2023] [Accepted: 09/27/2023] [Indexed: 10/29/2023] Open
Abstract
This comprehensive review delves into the rapidly evolving arena of cancer vaccines. Initially, we examine the intricate constitution of the tumor microenvironment (TME), a dynamic factor that significantly influences tumor heterogeneity. Current research trends focusing on harnessing the TME for effective tumor vaccine treatments are also discussed. We then provide a detailed overview of the current state of research concerning tumor immunity and the mechanisms of tumor vaccines, describing the complex immunological processes involved. Furthermore, we conduct an exhaustive analysis of the contemporary research landscape of tumor vaccines, with a particular focus on peptide vaccines, DNA/RNA-based vaccines, viral-vector-based vaccines, dendritic-cell-based vaccines, and whole-cell-based vaccines. We analyze and summarize these categories of tumor vaccines, highlighting their individual advantages, limitations, and the factors influencing their effectiveness. In our survey of each category, we summarize commonly used tumor vaccines, aiming to provide readers with a more comprehensive understanding of the current state of tumor vaccine research. We then delve into an innovative strategy combining cancer vaccines with other therapies. By studying the effects of combining tumor vaccines with immune checkpoint inhibitors, radiotherapy, chemotherapy, targeted therapy, and oncolytic virotherapy, we establish that this approach can enhance overall treatment efficacy and offset the limitations of single-treatment approaches, offering patients more effective treatment options. Following this, we undertake a meticulous analysis of the entire process of personalized cancer vaccines, elucidating the intricate process from design, through research and production, to clinical application, thus helping readers gain a thorough understanding of its complexities. In conclusion, our exploration of tumor vaccines in this review aims to highlight their promising potential in cancer treatment. As research in this field continues to evolve, it undeniably holds immense promise for improving cancer patient outcomes.
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Affiliation(s)
- Dequan Liu
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, China; (D.L.); (X.C.)
| | - Xiangyu Che
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, China; (D.L.); (X.C.)
| | - Xiaoxi Wang
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, China;
| | - Chuanyu Ma
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, China; (D.L.); (X.C.)
| | - Guangzhen Wu
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, China; (D.L.); (X.C.)
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Shim K, Jo H, Jeoung D. Cancer/Testis Antigens as Targets for RNA-Based Anticancer Therapy. Int J Mol Sci 2023; 24:14679. [PMID: 37834126 PMCID: PMC10572814 DOI: 10.3390/ijms241914679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/25/2023] [Accepted: 09/27/2023] [Indexed: 10/15/2023] Open
Abstract
In the last few decades, RNA-based drugs have emerged as a promising candidate in the treatment of various diseases. The introduction of messenger RNA (mRNA) as a vaccine or therapeutic agent enables the production of almost any functional protein/peptide. The key to applying RNA therapy in clinical trials is developing safe and effective delivery systems. Exosomes and lipid nanoparticles (LNPs) have been exploited as promising vehicles for drug delivery. This review discusses the feasibility of exosomes and LNPs as vehicles for mRNA delivery. Cancer/testis antigens (CTAs) show restricted expression in normal tissues and widespread expression in cancer tissues. Many of these CTAs show expression in the sera of patients with cancers. These characteristics of CTAs make them excellent targets for cancer immunotherapy. This review summarizes the roles of CTAs in various life processes and current studies on mRNAs encoding CTAs. Clinical studies present the beneficial effects of mRNAs encoding CTAs in patients with cancers. This review highlight clinical studies employing mRNA-LNPs encoding CTAs.
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Affiliation(s)
| | | | - Dooil Jeoung
- Department of Biochemistry, College of Natural Sciences, Kangwon National University, Chuncheon 24341, Republic of Korea; (K.S.); (H.J.)
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Kästle S, Stechele MR, Richter L, Schinner R, Öcal E, Alunni-Fabbroni M, De Toni E, Corradini S, Seidensticker M, Goldberg SN, Ricke J, Wildgruber M, Kimm MA. Peripheral blood-based cell signature indicates response to interstitial brachytherapy in primary liver cancer. J Cancer Res Clin Oncol 2023; 149:9777-9786. [PMID: 37247078 PMCID: PMC10423129 DOI: 10.1007/s00432-023-04875-z] [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: 04/25/2023] [Accepted: 05/19/2023] [Indexed: 05/30/2023]
Abstract
PURPOSE Biomarkers are essential to implement personalized therapies in cancer treatment options. As primary liver tumors are increasing and treatment is coupled to liver function and activation of systemic cells of the immune system, we investigated blood-based cells for their ability to predict response to local ablative therapy. METHODS We analyzed peripheral blood cells in 20 patients with primary liver cancer at baseline and following brachytherapy. In addition to platelets, leukocytes, lymphocytes, monocytes, neutrophils and most common ratios PLR, LMR, NMR and NLR, we investigated T cell and NKT cell populations of 11 responders and 9 non-responders using flow cytometry. RESULTS We have found a peripheral blood cell signature that differed significantly between responders and non-responders treated with interstitial brachytherapy (IBT). At baseline, non-responders featured higher numbers of platelets, monocytes and neutrophils, a higher platelet-to-lymphocyte ratio and an increase in the NKT cell population with a concurrent reduction in CD16 + NKT cells. Simultaneously, a lower percentage of CD4 + T cells was present in non-responders, as also reflected in a lower CD4/8 ratio. CD45RO + memory cells were lower in both, CD4 + and CD8 + T cell populations whereas PD-1 + T cells were only present in the CD4 + T cell population. CONCLUSION Baseline blood-based cell signature may function as a biomarker to predict response following brachytherapy in primary liver cancer.
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Affiliation(s)
- Sophia Kästle
- Department of Radiology, University Hospital, LMU Munich, Munich, Germany
| | | | - Lisa Richter
- Core Facility Flow Cytometry, Biomedical Center Munich, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Regina Schinner
- Department of Radiology, University Hospital, LMU Munich, Munich, Germany
| | - Elif Öcal
- Department of Radiology, University Hospital, LMU Munich, Munich, Germany
| | | | - Enrico De Toni
- Department of Medicine II, University Hospital, LMU Munich, Munich, Germany
| | - Stefanie Corradini
- Department of Radiation Oncology, University Hospital, LMU Munich, Munich, Germany
| | - Max Seidensticker
- Department of Radiology, University Hospital, LMU Munich, Munich, Germany
| | - S Nahum Goldberg
- Goldyne Savad Institute of Gene Therapy, Hadassah Hebrew University Hospital, Jerusalem, Israel
- Laboratory for Minimally Invasive Tumor Therapies, Department of Radiology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Division of Image-Guided Therapy and Interventional Oncology, Department of Radiology, Hadassah Hebrew University Hospital, Jerusalem, Israel
| | - Jens Ricke
- Department of Radiology, University Hospital, LMU Munich, Munich, Germany
| | - Moritz Wildgruber
- Department of Radiology, University Hospital, LMU Munich, Munich, Germany
| | - Melanie A Kimm
- Department of Radiology, University Hospital, LMU Munich, Munich, Germany.
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Buonaguro L, Tagliamonte M. Peptide-based vaccine for cancer therapies. Front Immunol 2023; 14:1210044. [PMID: 37654484 PMCID: PMC10467431 DOI: 10.3389/fimmu.2023.1210044] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 07/31/2023] [Indexed: 09/02/2023] Open
Abstract
Different strategies based on peptides are available for cancer treatment, in particular to counter-act the progression of tumor growth and disease relapse. In the last decade, in the context of therapeutic strategies against cancer, peptide-based vaccines have been evaluated in different tumor models. The peptides selected for cancer vaccine development can be classified in two main type: tumor-associated antigens (TAAs) and tumor-specific antigens (TSAs), which are captured, internalized, processed and presented by antigen-presenting cells (APCs) to cell-mediated immunity. Peptides loaded onto MHC class I are recognized by a specific TCR of CD8+ T cells, which are activated to exert their cytotoxic activity against tumor cells presenting the same peptide-MHC-I complex. This process is defined as active immunotherapy as the host's immune system is either de novo activated or restimulated to mount an effective, tumor-specific immune reaction that may ultimately lead to tu-mor regression. However, while the preclinical data have frequently shown encouraging results, therapeutic cancer vaccines clinical trials, including those based on peptides have not provided satisfactory data to date. The limited efficacy of peptide-based cancer vaccines is the consequence of several factors, including the identification of specific target tumor antigens, the limited immunogenicity of peptides and the highly immunosuppressive tumor microenvironment (TME). An effective cancer vaccine can be developed only by addressing all such different aspects. The present review describes the state of the art for each of such factors.
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Affiliation(s)
| | - Maria Tagliamonte
- Innovative Immunological Models Unit, Istituto Nazionale Tumori - IRCCS - “Fond G. Pascale”, Naples, Italy
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Kong B, Kim Y, Kim EH, Suk JS, Yang Y. mRNA: A promising platform for cancer immunotherapy. Adv Drug Deliv Rev 2023; 199:114993. [PMID: 37414361 DOI: 10.1016/j.addr.2023.114993] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 06/22/2023] [Accepted: 07/03/2023] [Indexed: 07/08/2023]
Abstract
Messenger RNA (mRNA) is now in the limelight as a powerful tool for treating various human diseases, especially malignant tumors, thanks to the remarkable clinical outcomes of mRNA vaccines using lipid nanoparticle technology during the COVID-19 pandemic. Recent promising preclinical and clinical results that epitomize the advancement in mRNA and nanoformulation-based delivery technologies have highlighted the tremendous potential of mRNA in cancer immunotherapy. mRNAs can be harnessed for cancer immunotherapy in forms of various therapeutic modalities, including cancer vaccines, adoptive T-cell therapies, therapeutic antibodies, and immunomodulatory proteins. This review provides a comprehensive overview of the current state and prospects of mRNA-based therapeutics, including numerous delivery and therapeutic strategies.
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Affiliation(s)
- Byoungjae Kong
- Center for Nanomedicine, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Yelee Kim
- Biomedical Research Division, Korea Institute of Science and Technology (KIST), Seoul, Republic of Korea; Department of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Eun Hye Kim
- Biomedical Research Division, Korea Institute of Science and Technology (KIST), Seoul, Republic of Korea; Department of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Jung Soo Suk
- Center for Nanomedicine, Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.
| | - Yoosoo Yang
- Biomedical Research Division, Korea Institute of Science and Technology (KIST), Seoul, Republic of Korea.
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XU WENHAO, LI HAOMING, HAMEED YASIR, ABDEL-MAKSOUD MOSTAFAA, ALMUTAIRI SAEEDAHMUSAED, MUBARAK AYMAN, AUFY MOHAMMED, ALTURAIKI WAEL, ALSHALANI ABDULAZIZJ, MAHMOUD AYMANM, LI CHEN. Elucidating the clinical and immunological value of m6A regulator-mediated methylation modification patterns in adrenocortical carcinoma. Oncol Res 2023; 31:819-831. [PMID: 37547754 PMCID: PMC10398396 DOI: 10.32604/or.2023.029414] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 04/26/2023] [Indexed: 08/08/2023] Open
Abstract
N6-methyladenosine methylation (m6A) is a common type of epigenetic alteration that prominently affects the prognosis of tumor patients. However, it is unknown how the m6A regulator affects the tumor microenvironment (TME) cell infiltration in adrenocortical carcinoma (ACC) and how it affects the prognosis of ACC patients yet. The m6A alteration patterns of 112 ACC patients were evaluated, furthermore, the association with immune infiltration cell features was investigated. The unsupervised clustering method was applied to typify the m6A alteration patterns of ACC patients. The principal component analysis (PCA) technique was taken to create the m6A score to assess the alteration pattern in specific malignancies. We found two independent patterns of m6A alteration in ACC patients. The TME cell infiltration features were significantly in accordance with phenotypes of tumor immune-inflamed and immune desert in both patterns. The m6Ascore also served as an independent predictive factor in ACC patients. The somatic copy number variation (CNV) and patients prognosis can be predicted by m6A alteration patterns. Moreover, the ACC patients with high m6A scores had better overall survival (OS) and higher efficiency in immune checkpoint blockade therapy. Our work demonstrated the significance of m6A alteration to the ACC patients immunotherapy. The individual m6A alteration patterns analysis might contribute to ACC patients prognosis prediction and immunotherapy choice.
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Affiliation(s)
- WENHAO XU
- Department of Urology, Urological Surgery Research Institute, First Affiliated Hospital, Army Medical University (Third Military Medical University), Chongqing, China
| | - HAOMING LI
- Department of Urology, Affiliated Hospital of Guilin Medical University, Guilin, China
| | - YASIR HAMEED
- Department of Applied Biological Sciences, Tokyo University of Science, Tokyo, Japan
| | - MOSTAFA A. ABDEL-MAKSOUD
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - SAEEDAH MUSAED ALMUTAIRI
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - AYMAN MUBARAK
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - MOHAMMED AUFY
- Department of Pharmaceutical Sciences, Division of Pharmacology and Toxicology, University of Vienna, Vienna, Austria
| | - WAEL ALTURAIKI
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - ABDULAZIZ J. ALSHALANI
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - AYMAN M. MAHMOUD
- Department of Life Sciences, Faculty of Science and Engineering, Manchester Metropolitan University, Manchester, UK
| | - CHEN LI
- Department of Biology, Chemistry, Pharmacy, Free University of Berlin, Berlin, Germany
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Czarnywojtek A, Borowska M, Dyrka K, Van Gool S, Sawicka-Gutaj N, Moskal J, Kościński J, Graczyk P, Hałas T, Lewandowska AM, Czepczyński R, Ruchała M. Glioblastoma Multiforme: The Latest Diagnostics and Treatment Techniques. Pharmacology 2023; 108:423-431. [PMID: 37459849 DOI: 10.1159/000531319] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 05/05/2023] [Indexed: 09/23/2023]
Abstract
BACKGROUND Glioblastoma multiforme (GBM) is a WHO grade 4 glioma and the most common malignant primary brain tumour. Recently, there has been outstanding progress in the treatment of GBM. In addition to the newest form of GBM removal using fluorescence, three-dimensional (3D) imaging, tomoradiotherapy, moderate electro-hyperthermia, and adjuvant temozolomide (post-operative chemotherapy), new developments have been made in the fields of immunology, molecular biology, and virotherapy. An unusual and modern treatment has been created, especially for stage 4 GBM, using the latest therapeutic techniques, including immunotherapy and virotherapy. Modern oncological medicine is producing extraordinary and progressive therapeutic methods. Oncological therapy includes individual analysis of the properties of a tumour and targeted therapy using small-molecule inhibitors. Individualised medicine covers the entire patient (tumour and host) in the context of immunotherapy. An example is individualised multimodal immunotherapy (IMI), which relies on individual immunological tumour-host interactions. In addition, IMI is based on the concept of oncolytic virus-induced immunogenic tumour cell death. SUMMARY In this review, we outline current knowledge of the various available treatment options used in the therapy of GBM including both traditional therapeutic strategy and modern therapies, such as tomotherapy, electro-hyperthermia, and oncolytic virotherapy, which are promising treatment strategies with the potential to improve prognosis in patients with GBM. KEY MESSAGES This newest therapy, immunotherapy combined with virotherapy (oncolytic viruses and cancer vaccines), is displaying encouraging signs for combating GBM. Additionally, the latest 3D imaging is compared to conventional two-dimensional imaging.
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Affiliation(s)
- Agata Czarnywojtek
- Chair and Department of Pharmacology, Poznan University of Medical Sciences, Poznan, Poland
- Department of Endocrinology, Metabolism and Internal Medicine, Poznan University of Medical Sciences, Poznan, Poland
| | - Magdalena Borowska
- Chair and Department of Pharmacology, Poznan University of Medical Sciences, Poznan, Poland
| | - Kamil Dyrka
- Department of Pediatric Endocrinology and Rheumatology, Institute of Pediatrics, Poznan University of Medical Sciences, Poznan, Poland
| | | | - Nadia Sawicka-Gutaj
- Department of Endocrinology, Metabolism and Internal Medicine, Poznan University of Medical Sciences, Poznan, Poland
| | - Jakub Moskal
- Department of Neurosurgery, Poznan University of Medical Sciences, Poznan, Poland
| | - Jeremi Kościński
- Department of Neurosurgery, Poznan University of Medical Sciences, Poznan, Poland
| | - Patryk Graczyk
- Chair and Department of Pharmacology, Poznan University of Medical Sciences, Poznan, Poland
| | - Tomasz Hałas
- Chair and Department of Pharmacology, Poznan University of Medical Sciences, Poznan, Poland
| | | | - Rafał Czepczyński
- Department of Endocrinology, Metabolism and Internal Medicine, Poznan University of Medical Sciences, Poznan, Poland
| | - Marek Ruchała
- Department of Endocrinology, Metabolism and Internal Medicine, Poznan University of Medical Sciences, Poznan, Poland
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Wolf MM, Rathmell WK, de Cubas AA. Immunogenicity in renal cell carcinoma: shifting focus to alternative sources of tumour-specific antigens. Nat Rev Nephrol 2023; 19:440-450. [PMID: 36973495 PMCID: PMC10801831 DOI: 10.1038/s41581-023-00700-5] [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] [Accepted: 02/27/2023] [Indexed: 03/29/2023]
Abstract
Renal cell carcinoma (RCC) comprises a group of malignancies arising from the kidney with unique tumour-specific antigen (TSA) signatures that can trigger cytotoxic immunity. Two classes of TSAs are now considered potential drivers of immunogenicity in RCC: small-scale insertions and deletions (INDELs) that result in coding frameshift mutations, and activation of human endogenous retroviruses. The presence of neoantigen-specific T cells is a hallmark of solid tumours with a high mutagenic burden, which typically have abundant TSAs owing to non-synonymous single nucleotide variations within the genome. However, RCC exhibits high cytotoxic T cell reactivity despite only having an intermediate non-synonymous single nucleotide variation mutational burden. Instead, RCC tumours have a high pan-cancer proportion of INDEL frameshift mutations, and coding frameshift INDELs are associated with high immunogenicity. Moreover, cytotoxic T cells in RCC subtypes seem to recognize tumour-specific endogenous retrovirus epitopes, whose presence is associated with clinical responses to immune checkpoint blockade therapy. Here, we review the distinct molecular landscapes in RCC that promote immunogenic responses, discuss clinical opportunities for discovery of biomarkers that can inform therapeutic immune checkpoint blockade strategies, and identify gaps in knowledge for future investigations.
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Affiliation(s)
- Melissa M Wolf
- Department of Medicine, Program in Cancer Biology, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - W Kimryn Rathmell
- Department of Medicine, Program in Cancer Biology, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA.
| | - Aguirre A de Cubas
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, SC, USA.
- Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, USA.
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Lv X, Wang W, Liu X, Liu Y, Guo L, Wang C. Low expression of acyl-CoA thioesterase 13 is associated with poor prognosis in ovarian serous cystadenocarcinoma. Front Genet 2023; 14:1213022. [PMID: 37424730 PMCID: PMC10323136 DOI: 10.3389/fgene.2023.1213022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 06/14/2023] [Indexed: 07/11/2023] Open
Abstract
Objective: Acyl-CoA thioesterase 13 (ACOT13) encodes a member of the thioesterase superfamily. It has not been reported in ovarian cancer. This research aimed at evaluating the expression and prognostic value of ACOT13 in ovarian serous cystadenocarcinoma (OSC). Methods: We extracted and analyzed TCGA, GEPIA, THPA, GTEx, miRWalk, and GDSC databases to investigate the potential carcinogenic mechanism of ACOT13 in OSC, including the correlation of ACOT13 with prognosis, immune checkpoint, tumor mutational burden (TMB), and 50% inhibition concentration (IC50) score. The incidence of endpoint events was compared with Kaplan-Meier survival analysis. Independent prognostic factors for OSC were evaluated with univariate and multivariate Cox regression analyses, and a nomogram was established. Results: The expression of ACOT13 was increased in OSC and correlated with tumor stage, with higher expression in stages I and II than in stages III and IV. Besides, it was observed that low expression of ACOT13 is correlated with poor overall survival (OS), progression-free survival (PFS), and disease-specific survival (DSS) in patients with OSC. There was a positive correlation between ACOT13 expression and immune checkpoint sialic acid-binding Ig-like lectin (SIGLEC) 15 and TMB. Patients with low ACOT13 expression had higher cisplatin IC50 scores. Conclusion: ACOT13 is an independent prognostic factor and a promising clinical target for OSC. In the future, the carcinogenic mechanism and clinical application value of ACOT13 in ovarian cancer need to be further studied.
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Affiliation(s)
- Xiaofeng Lv
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Weijiao Wang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoyu Liu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuhuan Liu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lili Guo
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Changyu Wang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Hu X, Guo J, Shi J, Li D, Li X, Zhao W. A 20-gene mutation signature predicts the efficacy of immune checkpoint inhibitor therapy in advanced non-small cell lung cancer patients. BMC Pulm Med 2023; 23:223. [PMID: 37349743 DOI: 10.1186/s12890-023-02512-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 06/07/2023] [Indexed: 06/24/2023] Open
Abstract
BACKGROUND There is an unmet need to identify novel predictive biomarkers that enable more accurate identification of individuals who can benefit from immune checkpoint inhibitor (ICI) therapy. The US FDA recently approved tumor mutational burden (TMB) score of ≥ 10 mut/Mb as a threshold for pembrolizumab treatment of solid tumors. Our study aimed to test the hypothesis that specific gene mutation signature may predict the efficacy of ICI therapy more precisely than high TMB (≥ 10). METHODS We selected 20 candidate genes that may predict for the efficacy of ICI therapy by the analysis of data from a published cohort of 350 advanced non-small cell lung cancer (NSCLC) patients. Then, we compared the influences of various gene mutation signatures on the efficacy of ICI treatment. They were also compared with PD-L1 and TMB. The Kaplan-Meier method was utilized to evaluate the prognosis univariates, while selected univariates were adopted to develop a systematic nomogram. RESULTS A high mutation signature, where three or more of the 20 selected genes were mutated, was associated with the significant benefits of ICI therapy. Specifically, patients with high mutation signature were confirmed to have better prognosis for ICI treatment, compared with those with wild type (the median PFS: 7.17 vs. 2.90 months, p = 0.0004, HR = 0.47 (95% [CI]:0.32-0.68); the median OS: unreached vs. 9 months, p = 1.8E-8, HR = 0.17 (95% [CI]:0.11-0.25)). Moreover, those patients with the high mutation signature achieved significant ICI treatment benefits, while there was no difference of OS and PFS between patients without the signature but TMB-H (≥ 10) and those without the signature and low TMB(< 10). Finally, we constructed a novel nomogram to evaluate the efficacy of ICI therapy. CONCLUSION A high mutational signature with 3 or more of the 20-gene panel could provide more accurate predictions for the outcomes of ICI therapy than TMB ≥ 10 in NSCLC patients.
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Affiliation(s)
- Xilin Hu
- Department of Thoracic Surgery, The First Affiliated Hospital of Ningbo University, 315010, Ningbo, China
| | - Jing Guo
- Department of Thoracic Surgery, The First Affiliated Hospital of Ningbo University, 315010, Ningbo, China
| | - Jianguang Shi
- Department of Thoracic Surgery, The First Affiliated Hospital of Ningbo University, 315010, Ningbo, China
| | - Da Li
- Department of Thoracic Surgery, The First Affiliated Hospital of Ningbo University, 315010, Ningbo, China
| | - Xinjian Li
- Department of Thoracic Surgery, The First Affiliated Hospital of Ningbo University, 315010, Ningbo, China
| | - Weijun Zhao
- Department of Thoracic Surgery, The First Affiliated Hospital of Ningbo University, 315010, Ningbo, China.
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Geng T, Zheng M, Wang Y, Reseland JE, Samara A. An artificial intelligence prediction model based on extracellular matrix proteins for the prognostic prediction and immunotherapeutic evaluation of ovarian serous adenocarcinoma. Front Mol Biosci 2023; 10:1200354. [PMID: 37388244 PMCID: PMC10301747 DOI: 10.3389/fmolb.2023.1200354] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 05/31/2023] [Indexed: 07/01/2023] Open
Abstract
Background: Ovarian Serous Adenocarcinoma is a malignant tumor originating from epithelial cells and one of the most common causes of death from gynecological cancers. The objective of this study was to develop a prediction model based on extracellular matrix proteins, using artificial intelligence techniques. The model aimed to aid healthcare professionals to predict the overall survival of patients with ovarian cancer (OC) and determine the efficacy of immunotherapy. Methods: The Cancer Genome Atlas Ovarian Cancer (TCGA-OV) data collection was used as the study dataset, whereas the TCGA-Pancancer dataset was used for validation. The prognostic importance of 1068 known extracellular matrix proteins for OC were determined by the Random Forest algorithm and the Lasso algorithm establishing the ECM risk score. Based on the gene expression data, the differences in mRNA abundance, tumour mutation burden (TMB) and tumour microenvironment (TME) between the high- and low-risk groups were assessed. Results: Combining multiple artificial intelligence algorithms we were able to identify 15 key extracellular matrix genes, namely, AMBN, CXCL11, PI3, CSPG5, TGFBI, TLL1, HMCN2, ESM1, IL12A, MMP17, CLEC5A, FREM2, ANGPTL4, PRSS1, FGF23, and confirm the validity of this ECM risk score for overall survival prediction. Several other parameters were identified as independent prognostic factors for OC by multivariate COX analysis. The analysis showed that thyroglobulin (TG) targeted immunotherapy was more effective in the high ECM risk score group, while the low ECM risk score group was more sensitive to the RYR2 gene-related immunotherapy. Additionally, the patients with low ECM risk scores had higher immune checkpoint gene expression and immunophenoscore levels and responded better to immunotherapy. Conclusion: The ECM risk score is an accurate tool to assess the patient's sensitivity to immunotherapy and forecast OC prognosis.
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Affiliation(s)
- Tianxiang Geng
- Department of Biomaterials, FUTURE, Center for Functional Tissue Reconstruction, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Mengxue Zheng
- Laboratory of Reproductive Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Yongfeng Wang
- Department of Obstetrics and Gynecology, Seventh People’s Hospital of Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Janne Elin Reseland
- Department of Biomaterials, FUTURE, Center for Functional Tissue Reconstruction, Faculty of Dentistry, University of Oslo, Oslo, Norway
| | - Athina Samara
- Department of Biomaterials, FUTURE, Center for Functional Tissue Reconstruction, Faculty of Dentistry, University of Oslo, Oslo, Norway
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Zhang Y, Zhou J, Li H, Liu Y, Li J. Prediction of risk and clinical outcome of cuproptosis in lung squamous carcinoma. BMC Pulm Med 2023; 23:205. [PMID: 37308925 PMCID: PMC10258956 DOI: 10.1186/s12890-023-02490-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 05/23/2023] [Indexed: 06/14/2023] Open
Abstract
BACKGROUND Lung squamous cell carcinoma (LUSC) is an important subtype of non-small cell lung cancer. Its special clinicopathological features and molecular background determine the limitations of its treatment. A recent study published on Science defined a newly regulatory cell death (RCD) form - cuproptosis. Which manifested as an excessive intracellular copper accumulation, mitochondrial respiration-dependent, protein acylation-mediated cell death. Different from apoptosis, pyroptosis, necroptosis, ferroptosis and other forms of regulatory cell death (RCD). The imbalance of copper homeostasis in vivo will trigger cytotoxicity and further affect the occurrence and progression of tumors. Our study is the first to predict the prognosis and immune landscape of cuproptosis-related genes (CRGs) in LUSC. METHODS The RNA-seq profiles and clinical data of LUSC patients were downloaded from TCGA and GEO databases and then combined into a novel cohort. R language packages are used to analyze and process the data, and CRGs related to the prognosis of LUSC were screened according to the differentially expressed genes (DEGs). After analyzed the tumor mutation burden (TMB), copy number variation (CNV) and CRGs interaction network. Based on CRGs and DEGs, cluster analysis was used to classify LUSC patients twice. The selected key genes were used to construct a CRGs prognostic model to further analyze the correlation between LUSC immune cell infiltration and immunity. Through the risk score and clinical factors, a more accurate nomogram was further constructed. Finally, the drug sensitivity of CRGs in LUSC was analyzed. RESULTS Patients with LUSC were divided into different cuproptosis subtypes and gene clusters, showing different levels of immune infiltration. The risk score showed that the high-risk group had higher tumor microenvironment score, lower tumor mutation load frequency and worse prognosis than the low-risk group. In addition, the high-risk group was more sensitive to vinorelbine, cisplatin, paclitaxel, doxorubicin, etoposide and other drugs. CONCLUSIONS Through bioinformatics analysis, we successfully constructed a prognostic risk assessment model based on CRGs, which can not only accurately predict the prognosis of LUSC patients, but also evaluate the patient 's immune infiltration status and sensitivity to chemotherapy drugs. This model shows satisfactory predictive results and provides a reference for subsequent tumor immunotherapy.
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Affiliation(s)
| | - Jia Zhou
- Ningxia Hui Autonomous Region People's Hospital, Yinchuan, Ningxi, China
| | - Hong Li
- Department of Surgical Oncology, General Hospital of Ningxia Medical University, Yinchuan, Ningxia, China
| | - Yaobang Liu
- Department of Surgical Oncology, General Hospital of Ningxia Medical University, Yinchuan, Ningxia, China
| | - Jinping Li
- Department of Surgical Oncology, General Hospital of Ningxia Medical University, Yinchuan, Ningxia, China.
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