51
|
Raufaste-Cazavieille V, Santiago R, Droit A. Multi-omics analysis: Paving the path toward achieving precision medicine in cancer treatment and immuno-oncology. Front Mol Biosci 2022; 9:962743. [PMID: 36304921 PMCID: PMC9595279 DOI: 10.3389/fmolb.2022.962743] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 09/21/2022] [Indexed: 11/13/2022] Open
Abstract
The acceleration of large-scale sequencing and the progress in high-throughput computational analyses, defined as omics, was a hallmark for the comprehension of the biological processes in human health and diseases. In cancerology, the omics approach, initiated by genomics and transcriptomics studies, has revealed an incredible complexity with unsuspected molecular diversity within a same tumor type as well as spatial and temporal heterogeneity of tumors. The integration of multiple biological layers of omics studies brought oncology to a new paradigm, from tumor site classification to pan-cancer molecular classification, offering new therapeutic opportunities for precision medicine. In this review, we will provide a comprehensive overview of the latest innovations for multi-omics integration in oncology and summarize the largest multi-omics dataset available for adult and pediatric cancers. We will present multi-omics techniques for characterizing cancer biology and show how multi-omics data can be combined with clinical data for the identification of prognostic and treatment-specific biomarkers, opening the way to personalized therapy. To conclude, we will detail the newest strategies for dissecting the tumor immune environment and host–tumor interaction. We will explore the advances in immunomics and microbiomics for biomarker identification to guide therapeutic decision in immuno-oncology.
Collapse
Affiliation(s)
| | - Raoul Santiago
- CHU de Québec Research Center, Université Laval, Québec, QC, Canada
- Division of Pediatric Hematology-Oncology, Centre Hospitalier Universitaire de L’Université Laval, Charles Bruneau Cancer Center, Québec, QC, Canada
- *Correspondence: Raoul Santiago, ; Arnaud Droit,
| | - Arnaud Droit
- CHU de Québec Research Center, Université Laval, Québec, QC, Canada
- *Correspondence: Raoul Santiago, ; Arnaud Droit,
| |
Collapse
|
52
|
Ye Y, Jiang H, Wu Y, Wang G, Huang Y, Sun W, Zhang M. Role of ARRB1 in prognosis and immunotherapy: A Pan-Cancer analysis. Front Mol Biosci 2022; 9:1001225. [PMID: 36213111 PMCID: PMC9538973 DOI: 10.3389/fmolb.2022.1001225] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 09/12/2022] [Indexed: 11/13/2022] Open
Abstract
Background: β-arrestin1 (ARRB1), was originally identified as a multifunctional adaptor protein. Although ARRB1 has recently been shown to also play an important role in tumor growth, metastasis, inflammation, and immunity, its relationship with distinct tumor types and the tumor immune microenvironment remains unclear.Methods: We analyzed the ARRB1 expression profile and clinical characteristics in 33 cancer types using datasets from The Cancer Genome Atlas (TCGA) database. Clinical parameters such as patient survival, tumor stage, age, and gender were used to assess the prognostic value of ARRB1. The Human Protein Atlas (HPA) database was used to explore ARRB1 protein expression data. ESTIMATE and CIBERSORT algorithms were performed to assess immune infiltration. Furthermore, putative correlations between ARRB1 and tumor-infiltrating immune cells, the signatures of T-cell subtypes, immunomodulators, the tumor mutation burden (TMB), Programmed cell death ligand 1 (PD-L1), and microsatellite instability (MSI) were also explored. Gene functional enrichment was determined using GSEA. GSE40435 and GSE13213 cohorts were used to validate the correlation of ARRB1 with KIRC and LUAD clinicopathological parameters. Finally, the relationship between ARRB1 and immunotherapeutic responses was assessed using three independent immunotherapy cohorts, namely, GSE67501, GSE168204, and IMvigor210.Results: We found that ARRB1 expression levels were lower in 17 tumor tissues than in the corresponding normal tissues. We further found that ARRB1 expression was significantly correlated with tumor stage in BRCA, ESCA, KIRC, TGCT, and THCA, while in some tumors, particularly KIRC and LUAD, ARRB1 expression was associated with better prognosis. ARRB1 expression was also positively correlated with the stromal score or the immune score in some tumors. Regarding immune cell infiltration, ARRB1 expression in DLBC was positively correlated with M1 macrophage content and negatively correlated with B-cell infiltration. Additionally, there was a broad correlation between ARRB1 expression and three classes of immunomodulators. Furthermore, high ARRB1 expression levels were significantly correlated with some tumor immune-related pathways. Finally, ARRB1 expression was significantly associated with MSI, PD-L1, and TMB in some tumors and with the efficacy of immune checkpoint inhibitors (ICIs) in melanoma.Conclusion: ARRB1 has prognostic value in malignant tumors, especially in KIRC and LUAD. At the same time, ARRB1 was closely correlated with the tumor immune microenvironment and indicators of immunotherapy efficacy, indicating its great potential as a reliable marker for predicting the efficacy of immunotherapy.
Collapse
Affiliation(s)
- Yingquan Ye
- Oncology Department of Integrated Traditional Chinese and Western Medicine, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- The Traditional and Western Medicine (TCM)-Integrated Cancer Center of Anhui Medical University, Hefei, China
| | - Haili Jiang
- Oncology Department of Integrated Traditional Chinese and Western Medicine, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- The Traditional and Western Medicine (TCM)-Integrated Cancer Center of Anhui Medical University, Hefei, China
| | - Yue Wu
- Oncology Department of Integrated Traditional Chinese and Western Medicine, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- The Traditional and Western Medicine (TCM)-Integrated Cancer Center of Anhui Medical University, Hefei, China
| | - Gaoxiang Wang
- Oncology Department of Integrated Traditional Chinese and Western Medicine, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- The Traditional and Western Medicine (TCM)-Integrated Cancer Center of Anhui Medical University, Hefei, China
| | - Yi Huang
- Oncology Department of Integrated Traditional Chinese and Western Medicine, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- The Traditional and Western Medicine (TCM)-Integrated Cancer Center of Anhui Medical University, Hefei, China
| | - Weijie Sun
- Department of Infectious Diseases, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- *Correspondence: Weijie Sun, ; Mei Zhang,
| | - Mei Zhang
- Oncology Department of Integrated Traditional Chinese and Western Medicine, The First Affiliated Hospital of Anhui Medical University, Hefei, China
- The Traditional and Western Medicine (TCM)-Integrated Cancer Center of Anhui Medical University, Hefei, China
- *Correspondence: Weijie Sun, ; Mei Zhang,
| |
Collapse
|
53
|
Slotta-Huspenina J, Schwamborn K, Steiger K, Simon R, Kirchhoff FP, Büchler JW, Fiedler J, Retz M, Nawroth R, Ritschel C, Gschwend JE, Horn T. MHC I Expression Predicts Response to Checkpoint Inhibitors in Metastatic Urothelial Carcinoma but Lacks Prognostic Value in Localized Disease. Bladder Cancer 2022; 8:269-276. [PMID: 38993685 PMCID: PMC11181837 DOI: 10.3233/blc-211604] [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: 09/11/2021] [Accepted: 03/12/2022] [Indexed: 11/15/2022]
Abstract
BACKGROUND Loss of MHC I expression is a tumoral escape mechanism, part of the process of immunoediting. MHC expression patterns and their prognostic and predictive value have not been studied in urothelial carcinoma of the bladder (UC) so far. OBJECTIVE To correlate the expression of MHC I and MHC II with prognosis after curative treatment, response to chemotherapy and checkpoint inhibition. PATIENTS AND METHODS We analyzed different patient cohorts for their expression of MHC I(HLA-A/B/C) and II (HLA-DR/DP/DQ) and examined potential correlations with prognosis and response to cisplatin-based chemotherapy or PD-1/PD-L1 directed immunotherapy. RESULTS AND LIMITATIONS Overall, MHC expression was analyzed in 246 patients, and complete MHC I loss was seen in 29.7% of patients. In 35% of patients aberrant tumoral expression of MHC II was observed. In a homogeneous cohort of 149 patients with cystectomy with curative intent there were no significant differences in survival between the MHC expression groups. MHC I+ and MHC II+ patients had higher infiltration densities with CD8+ T effector cells.An analysis of 77 additional patients (cohort II) with neoadjuvant chemotherapy revealed no associations of MHC status with response defined as < pT2 pN0 in the cystectomy specimen. Lastly, we analyzed 26 patients with metastatic disease treated with PD-1/PD-L1 directed immunotherapy (cohort III, best response: 11 PD, 5 SD, 10 OR) and observed responses exclusively in MHC I+ patients (10/19 patients, 52.6). All four MHC I+ /MHC II+ /PD-L1+ patients had a progression-free interval of at least 12 months. CONCLUSIONS Tumoral MHC I expression is frequently lost in UC. We found no association with prognosis or response to cisplatin-based chemotherapy but response to checkpoint inhibitors was limited to MHC I+ patients.
Collapse
Affiliation(s)
| | | | - Katja Steiger
- Institute of Pathology, Technical University of Munich, Munich, Germany
| | - Ricarda Simon
- Department of Urology, Klinikum Rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Florian Paul Kirchhoff
- Department of Urology, Klinikum Rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Jakob Wolf Büchler
- Department of Urology, Klinikum Rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Julia Fiedler
- Department of Urology, Klinikum Rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Margitta Retz
- Department of Urology, Klinikum Rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Roman Nawroth
- Department of Urology, Klinikum Rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Christoph Ritschel
- Department of Urology, Klinikum Rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Jürgen Erich Gschwend
- Department of Urology, Klinikum Rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Thomas Horn
- Department of Urology, Klinikum Rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| |
Collapse
|
54
|
Chen L, He C, Zhou M, Long J, Li L. Research Progress on the Mechanisms of Polysaccharides against Gastric Cancer. Molecules 2022; 27:5828. [PMID: 36144560 PMCID: PMC9501385 DOI: 10.3390/molecules27185828] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 09/05/2022] [Accepted: 09/06/2022] [Indexed: 12/24/2022] Open
Abstract
Gastric cancer is a common type of cancer that poses a serious threat to human health. Polysaccharides are important functional phytochemicals, and research shows that polysaccharides have good anti-gastric cancer effects. We collated all relevant literature published from 2000 to 2020 and found that more than 60 natural polysaccharides demonstrate anti-gastric cancer activity. At the present, the sources of these polysaccharides include fungi, algae, tea, Astragalus membranaceus, Caulis Dendrobii, and other foods and Chinese herbal medicines. By regulating various signaling pathways, including the PI3K/AKT, MAPK, Fas/FasL, Wnt/β-catenin, IGF-IR, and TGF-β signaling pathways, polysaccharides induce gastric cancer cell apoptosis, cause cell cycle arrest, and inhibit migration and invasion. In addition, polysaccharides can enhance the immune system and killing activity of immune cells in gastric cancer patients and rats. This comprehensive review covers the extraction, purification, structural characterization, and mechanism of plant and fungal polysaccharides against gastric cancer. We hope this review is helpful for researchers to design, research, and develop plant and fungal polysaccharides.
Collapse
Affiliation(s)
- Liping Chen
- School of Food and Bioengineering, Xihua University, Chengdu 610039, China
| | - Chunrong He
- School of Food and Bioengineering, Xihua University, Chengdu 610039, China
| | - Min Zhou
- School of Food and Bioengineering, Xihua University, Chengdu 610039, China
| | - Jiaying Long
- Key Laboratory of Drug Targeting and Drug Delivery Systems, Ministry of Education, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Ling Li
- School of Food and Bioengineering, Xihua University, Chengdu 610039, China
| |
Collapse
|
55
|
Ritter A, Kreis NN, Hoock SC, Solbach C, Louwen F, Yuan J. Adipose Tissue-Derived Mesenchymal Stromal/Stem Cells, Obesity and the Tumor Microenvironment of Breast Cancer. Cancers (Basel) 2022; 14:3908. [PMID: 36010901 PMCID: PMC9405791 DOI: 10.3390/cancers14163908] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/01/2022] [Accepted: 08/09/2022] [Indexed: 11/16/2022] Open
Abstract
Breast cancer is the most frequently diagnosed cancer and a common cause of cancer-related death in women. It is well recognized that obesity is associated with an enhanced risk of more aggressive breast cancer as well as reduced patient survival. Adipose tissue is the major microenvironment of breast cancer. Obesity changes the composition, structure, and function of adipose tissue, which is associated with inflammation and metabolic dysfunction. Interestingly, adipose tissue is rich in ASCs/MSCs, and obesity alters the properties and functions of these cells. As a key component of the mammary stroma, ASCs play essential roles in the breast cancer microenvironment. The crosstalk between ASCs and breast cancer cells is multilateral and can occur both directly through cell-cell contact and indirectly via the secretome released by ASC/MSC, which is considered to be the main effector of their supportive, angiogenic, and immunomodulatory functions. In this narrative review, we aim to address the impact of obesity on ASCs/MSCs, summarize the current knowledge regarding the potential pathological roles of ASCs/MSCs in the development of breast cancer, discuss related molecular mechanisms, underline the possible clinical significance, and highlight related research perspectives. In particular, we underscore the roles of ASCs/MSCs in breast cancer cell progression, including proliferation and survival, angiogenesis, migration and invasion, the epithelial-mesenchymal transition, cancer stem cell development, immune evasion, therapy resistance, and the potential impact of breast cancer cells on ASCS/MSCs by educating them to become cancer-associated fibroblasts. We conclude that ASCs/MSCs, especially obese ASCs/MSCs, may be key players in the breast cancer microenvironment. Targeting these cells may provide a new path of effective breast cancer treatment.
Collapse
Affiliation(s)
- Andreas Ritter
- Obstetrics and Prenatal Medicine, Gynecology and Obstetrics, University Hospital Frankfurt, J. W. Goethe-University, Theodor-Stern-Kai 7, D-60590 Frankfurt, Germany
| | | | | | | | | | - Juping Yuan
- Obstetrics and Prenatal Medicine, Gynecology and Obstetrics, University Hospital Frankfurt, J. W. Goethe-University, Theodor-Stern-Kai 7, D-60590 Frankfurt, Germany
| |
Collapse
|
56
|
Zhang D, Li Q, Chen X, Nie X, Xue F, Xu W, Luan Y. An Injectable Hydrogel to Modulate T Cells for Cancer Immunotherapy. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2202663. [PMID: 35843879 DOI: 10.1002/smll.202202663] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/20/2022] [Indexed: 06/15/2023]
Abstract
T cell exhaustion caused by mitochondrial dysfunction is the major obstacle of T cells-based cancer immunotherapy. Besides exhausted T cells, the insufficient major histocompatibility complex class I (MHC I) on tumor cells leads to inefficient T cell recognition of tumor cells, compromising therapeutic efficacy. Therapeutic platform to regulate T cell exhaustion and MHC I expression for boosting T cells-based cancer immunotherapy has not been realized up to date. Herein, an injectable hydrogel is designed to simultaneously tune T cell exhaustion and MHC I expression for amplified cancer immunotherapy. The hydrogel is in situ constructed in tumor site by utilizing oxidized sodium alginate-modified tumor cell membrane vesicle (O-TMV) as a gelator, where axitinib is encapsulated in the lipid bilayer of O-TMV while 4-1BB antibody and proprotein convertase subtilisin/kexin type 9 inhibitor PF-06446846 nanoparticles are present in the cavities of hydrogel. After immune response trigged by O-TMV antigen, the 4-1BB antibody-promoted T cell mitochondrial biogenesis and the axitinib-lowered hypoxia synergistically reverse T cell exhaustion while the PF-06446846-amplified MHC I expression facilitates T cell recognition of tumor cells, demonstrating a powerful immunotherapeutic efficacy. This strategy on reprograming T cell exhaustion and improving T cell potency offers new concept for T cells-based cancer immunotherapy.
Collapse
Affiliation(s)
- Di Zhang
- NMPA Key Laboratory for Technology Research and Evaluation of Drug Products, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Wenhua Road, Jinan, 250012, China
| | - Qian Li
- NMPA Key Laboratory for Technology Research and Evaluation of Drug Products, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Wenhua Road, Jinan, 250012, China
| | - Xiangwu Chen
- NMPA Key Laboratory for Technology Research and Evaluation of Drug Products, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Wenhua Road, Jinan, 250012, China
| | - Xinxin Nie
- NMPA Key Laboratory for Technology Research and Evaluation of Drug Products, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Wenhua Road, Jinan, 250012, China
| | - Fumin Xue
- School of Pharmaceutical Sciences, Shandong Analysis and Test Center, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250014, China
| | - Wei Xu
- Shandong Provincial Qianfoshan Hospital, the First Hospital Affiliated with Shandong First Medical University, Jinan, 250014, China
| | - Yuxia Luan
- NMPA Key Laboratory for Technology Research and Evaluation of Drug Products, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Wenhua Road, Jinan, 250012, China
| |
Collapse
|
57
|
Song P, Li W, Guo L, Ying J, Gao S, He J. Identification and Validation of a Novel Signature Based on NK Cell Marker Genes to Predict Prognosis and Immunotherapy Response in Lung Adenocarcinoma by Integrated Analysis of Single-Cell and Bulk RNA-Sequencing. Front Immunol 2022; 13:850745. [PMID: 35757748 PMCID: PMC9231585 DOI: 10.3389/fimmu.2022.850745] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 04/12/2022] [Indexed: 12/11/2022] Open
Abstract
Natural killer (NK) cells, the effectors of the innate immune system, have a remarkable influence on cancer prognosis and immunotherapy. In this study, a total of 1,816 samples from nine independent cohorts in public datasets were enrolled. We first conducted a comprehensive analysis of single-cell RNA-sequencing data of lung adenocarcinoma (LUAD) from the Gene Expression Omnibus (GEO) database and determined 189 NK cell marker genes. Subsequently, we developed a seven-gene prognostic signature based on NK cell marker genes in the TCGA LUAD cohort, which stratified patients into high-risk and low-risk groups. The predictive power of the signature was well verified in different clinical subgroups and GEO cohorts. With a multivariate analysis, the signature was identified as an independent prognostic factor. Low-risk patients had higher immune cell infiltration states, especially CD8+ T cells and follicular helper T cells. There existed a negative association between inflammatory activities and risk score, and the richness and diversity of the T-cell receptor (TCR) repertoire was higher in the low-risk groups. Importantly, analysis of an independent immunotherapy cohort (IMvigor210) revealed that low-risk patients had better immunotherapy responses and prognosis than high-risk patients. Collectively, our study developed a novel signature based on NK cell marker genes, which had a potent capability to predict the prognosis and immunotherapy response of LUAD patients.
Collapse
Affiliation(s)
- Peng Song
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wenbin Li
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lei Guo
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jianming Ying
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shugeng Gao
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jie He
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| |
Collapse
|
58
|
Jiang L, Tang J, Guo F, Guo Y. Prediction of Major Histocompatibility Complex Binding with Bilateral and Variable Long Short Term Memory Networks. BIOLOGY 2022; 11:biology11060848. [PMID: 35741369 PMCID: PMC9220200 DOI: 10.3390/biology11060848] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/25/2022] [Accepted: 05/27/2022] [Indexed: 11/18/2022]
Abstract
Simple Summary Major histocompatibility complex molecules are of significant biological and clinical importance due to their utility in immunotherapy. The prediction of potential MHC binding peptides can estimate a T-cell immune response. The variable length of existing MHC binding peptides creates difficulty for MHC binding prediction algorithms. Thus, we utilized a bilateral and variable long-short term memory neural network to address this specific problem and developed a novel MHC binding prediction tool. Abstract As an important part of immune surveillance, major histocompatibility complex (MHC) is a set of proteins that recognize foreign molecules. Computational prediction methods for MHC binding peptides have been developed. However, existing methods share the limitation of fixed peptide sequence length, which necessitates the training of models by peptide length or prediction with a length reduction technique. Using a bidirectional long short-term memory neural network, we constructed BVMHC, an MHC class I and II binding prediction tool that is independent of peptide length. The performance of BVMHC was compared to seven MHC class I prediction tools and three MHC class II prediction tools using eight performance criteria independently. BVMHC attained the best performance in three of the eight criteria for MHC class I, and the best performance in four of the eight criteria for MHC class II, including accuracy and AUC. Furthermore, models for non-human species were also trained using the same strategy and made available for applications in mice, chimpanzees, macaques, and rats. BVMHC is composed of a series of peptide length independent MHC class I and II binding predictors. Models from this study have been implemented in an online web portal for easy access and use.
Collapse
Affiliation(s)
- Limin Jiang
- Comprehensive Cancer Center, Department of Internal Medicine, University of New Mexico, Albuquerque, NM 87131, USA;
| | - Jijun Tang
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China;
| | - Fei Guo
- School of Computer Science and Technology, College of Intelligence and Computing, Tianjin University, Tianjin 300350, China
- Correspondence: (F.G.); (Y.G.)
| | - Yan Guo
- Comprehensive Cancer Center, Department of Internal Medicine, University of New Mexico, Albuquerque, NM 87131, USA;
- Correspondence: (F.G.); (Y.G.)
| |
Collapse
|
59
|
Rodriguez GM, Galpin KJ, Cook DP, Yakubovich E, Maranda V, Macdonald EA, Wilson-Sanchez J, Thomas AL, Burdette JE, Vanderhyden BC. The Tumor Immune Profile of Murine Ovarian Cancer Models: An Essential Tool For Ovarian Cancer Immunotherapy Research. CANCER RESEARCH COMMUNICATIONS 2022; 2:417-433. [PMID: 36311166 PMCID: PMC9616009 DOI: 10.1158/2767-9764.crc-22-0017] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 03/07/2022] [Accepted: 05/18/2022] [Indexed: 06/16/2023]
Abstract
Epithelial ovarian cancer (EOC) is the most lethal gynecologic cancer with an imperative need for new treatments. Immunotherapy has had marked success in some cancer types; however, clinical trials studying the efficacy of immune checkpoint inhibitors for the treatment of EOC benefited less than 15% of patients. Given that EOC develops from multiple tissues in the reproductive system and metastasizes widely throughout the peritoneal cavity, responses to immunotherapy are likely hindered by heterogeneous tumor microenvironments (TME) containing a variety of immune profiles. To fully characterize and compare syngeneic model systems that may reflect this diversity, we determined the immunogenicity of six ovarian tumor models in vivo, the T and myeloid profile of orthotopic tumors and the immune composition and cytokine profile of ascites, by single-cell RNA sequencing, flow cytometry and IHC. The selected models reflect the different cellular origins of EOC (ovarian and fallopian tube epithelium) and harbor mutations relevant to human disease, including Tp53 mutation, PTEN suppression, and constitutive KRAS activation. ID8-p53-/- and ID8-C3 tumors were most highly infiltrated by T cells, whereas STOSE and MOE-PTEN/KRAS tumors were primarily infiltrated by tumor associated macrophages and were unique in MHC class I and II expression. MOE-PTEN/KRAS tumors were capable of forming T cell clusters. This panel of well-defined murine EOC models reflects some of the heterogeneity found in human disease and can serve as a valuable resource for studies that aim to test immunotherapies, explore the mechanisms of immune response to therapy, and guide selection of treatments for patient populations.
Collapse
Affiliation(s)
- Galaxia M. Rodriguez
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Kristianne J.C. Galpin
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - David P. Cook
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Edward Yakubovich
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Vincent Maranda
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Elizabeth A. Macdonald
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Juliette Wilson-Sanchez
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Anjali L. Thomas
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Joanna E. Burdette
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois
| | - Barbara C. Vanderhyden
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
- Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Ontario, Canada
| |
Collapse
|
60
|
Emery A, Moore S, Turner JE, Campbell JP. Reframing How Physical Activity Reduces The Incidence of Clinically-Diagnosed Cancers: Appraising Exercise-Induced Immuno-Modulation As An Integral Mechanism. Front Oncol 2022; 12:788113. [PMID: 35359426 PMCID: PMC8964011 DOI: 10.3389/fonc.2022.788113] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 01/14/2022] [Indexed: 12/13/2022] Open
Abstract
Undertaking a high volume of physical activity is associated with reduced risk of a broad range of clinically diagnosed cancers. These findings, which imply that physical activity induces physiological changes that avert or suppress neoplastic activity, are supported by preclinical intervention studies in rodents demonstrating that structured regular exercise commonly represses tumour growth. In Part 1 of this review, we summarise epidemiology and preclinical evidence linking physical activity or regular structured exercise with reduced cancer risk or tumour growth. Despite abundant evidence that physical activity commonly exerts anti-cancer effects, the mechanism(s)-of-action responsible for these beneficial outcomes is undefined and remains subject to ongoing speculation. In Part 2, we outline why altered immune regulation from physical activity - specifically to T cells - is likely an integral mechanism. We do this by first explaining how physical activity appears to modulate the cancer immunoediting process. In doing so, we highlight that augmented elimination of immunogenic cancer cells predominantly leads to the containment of cancers in a 'precancerous' or 'covert' equilibrium state, thus reducing the incidence of clinically diagnosed cancers among physically active individuals. In seeking to understand how physical activity might augment T cell function to avert cancer outgrowth, in Part 3 we appraise how physical activity affects the determinants of a successful T cell response against immunogenic cancer cells. Using the cancer immunogram as a basis for this evaluation, we assess the effects of physical activity on: (i) general T cell status in blood, (ii) T cell infiltration to tissues, (iii) presence of immune checkpoints associated with T cell exhaustion and anergy, (iv) presence of inflammatory inhibitors of T cells and (v) presence of metabolic inhibitors of T cells. The extent to which physical activity alters these determinants to reduce the risk of clinically diagnosed cancers - and whether physical activity changes these determinants in an interconnected or unrelated manner - is unresolved. Accordingly, we analyse how physical activity might alter each determinant, and we show how these changes may interconnect to explain how physical activity alters T cell regulation to prevent cancer outgrowth.
Collapse
Affiliation(s)
- Annabelle Emery
- Department for Health, University of Bath, Bath, United Kingdom
| | - Sally Moore
- Department of Haematology, Royal United Hospitals Bath NHS Foundation Trust, Bath, United Kingdom
| | - James E Turner
- Department for Health, University of Bath, Bath, United Kingdom
| | - John P Campbell
- Department for Health, University of Bath, Bath, United Kingdom
| |
Collapse
|
61
|
Bunting MD, Vyas M, Requesens M, Langenbucher A, Schiferle EB, Manguso RT, Lawrence MS, Demehri S. Extracellular matrix proteins regulate NK cell function in peripheral tissues. SCIENCE ADVANCES 2022; 8:eabk3327. [PMID: 35294229 PMCID: PMC8926340 DOI: 10.1126/sciadv.abk3327] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Natural killer (NK) cells reject major histocompatibility complex class I (MHC-I)-deficient bone marrow through direct cytotoxicity but not solid organ transplants devoid of MHC-I. Here, we demonstrate an immediate switch in NK cell function upon exit from the circulation, characterized by a shift from direct cytotoxicity to chemokine/cytokine production. In the skin transplant paradigm, combining an NK cell-specific activating ligand, m157, with missing self MHC-I resulted in complete graft rejection, which was dependent on NK cells as potential helpers and T cells as effectors. Extracellular matrix proteins, collagen I, collagen III, and elastin, blocked NK cell cytotoxicity and promoted their chemokine/cytokine production. NK cell cytotoxicity against MHC-I-deficient melanoma in the skin was markedly increased by blocking tumor collagen deposition. MHC-I down-regulation occurred in solid human cancers but not leukemias, which could be directly targeted by circulating cytotoxic NK cells. Our findings uncover a fundamental mechanism that restricts direct NK cell cytotoxicity in peripheral tissues.
Collapse
Affiliation(s)
- Mark D. Bunting
- Center for Cancer Immunology and Cutaneous Biology Research Center, Department of Dermatology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Maulik Vyas
- Center for Cancer Immunology and Cutaneous Biology Research Center, Department of Dermatology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Marta Requesens
- Center for Cancer Immunology and Cutaneous Biology Research Center, Department of Dermatology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Adam Langenbucher
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Erik B. Schiferle
- Center for Cancer Immunology and Cutaneous Biology Research Center, Department of Dermatology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Robert T. Manguso
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Michael S. Lawrence
- Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Shadmehr Demehri
- Center for Cancer Immunology and Cutaneous Biology Research Center, Department of Dermatology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
- Corresponding author.
| |
Collapse
|
62
|
Fanfone D, Wu Z, Mammi J, Berthenet K, Neves D, Weber K, Halaburkova A, Virard F, Bunel F, Jamard C, Hernandez-Vargas H, Tait SWG, Hennino A, Ichim G. Confined migration promotes cancer metastasis through resistance to anoikis and increased invasiveness. eLife 2022; 11:e73150. [PMID: 35256052 PMCID: PMC8903834 DOI: 10.7554/elife.73150] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 02/15/2022] [Indexed: 12/12/2022] Open
Abstract
Mechanical stress is known to fuel several hallmarks of cancer, ranging from genome instability to uncontrolled proliferation or invasion. Cancer cells are constantly challenged by mechanical stresses not only in the primary tumour but also during metastasis. However, this latter has seldom been studied with regards to mechanobiology, in particular resistance to anoikis, a cell death programme triggered by loss of cell adhesion. Here, we show in vitro that migrating breast cancer cells develop resistance to anoikis following their passage through microporous membranes mimicking confined migration (CM), a mechanical constriction that cancer cells encounter during metastasis. This CM-induced resistance was mediated by Inhibitory of Apoptosis Proteins, and sensitivity to anoikis could be restored after their inhibition using second mitochondria-derived activator of caspase (SMAC) mimetics. Anoikis-resistant mechanically stressed cancer cells displayed enhanced cell motility and evasion from natural killer cell-mediated immune surveillance, as well as a marked advantage to form lung metastatic lesions in mice. Our findings reveal that CM increases the metastatic potential of breast cancer cells.
Collapse
Affiliation(s)
- Deborah Fanfone
- Cancer Research Center of Lyon (CRCL), INSERM 1052, CNRSLyonFrance
- Cancer Cell Death Laboratory, part of LabEx DEVweCAN, Université de LyonLyonFrance
| | - Zhichong Wu
- Cancer Research Center of Lyon (CRCL), INSERM 1052, CNRSLyonFrance
- Université Lyon 1, VilleurbanneVilleurbanneFrance
- Centre Léon BérardLyonFrance
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Jade Mammi
- Cancer Research Center of Lyon (CRCL), INSERM 1052, CNRSLyonFrance
- Cancer Cell Death Laboratory, part of LabEx DEVweCAN, Université de LyonLyonFrance
| | - Kevin Berthenet
- Cancer Research Center of Lyon (CRCL), INSERM 1052, CNRSLyonFrance
- Cancer Cell Death Laboratory, part of LabEx DEVweCAN, Université de LyonLyonFrance
- Centre Léon BérardLyonFrance
| | | | - Kathrin Weber
- Cancer Research Center of Lyon (CRCL), INSERM 1052, CNRSLyonFrance
- Cancer Cell Death Laboratory, part of LabEx DEVweCAN, Université de LyonLyonFrance
| | - Andrea Halaburkova
- Cancer Research Center of Lyon (CRCL), INSERM 1052, CNRSLyonFrance
- Cancer Cell Death Laboratory, part of LabEx DEVweCAN, Université de LyonLyonFrance
| | - François Virard
- Cancer Research Center of Lyon (CRCL), INSERM 1052, CNRSLyonFrance
- Université Claude Bernard Lyon 1, Faculté d’Odontologie, Hospices Civils de LyonLyonFrance
| | - Félix Bunel
- ENS de Lyon, Université Claude Bernard Lyon 1, CNRS, Laboratoire de PhysiqueLyonFrance
| | - Catherine Jamard
- Cancer Research Center of Lyon (CRCL), INSERM 1052, CNRSLyonFrance
- Cancer Cell Death Laboratory, part of LabEx DEVweCAN, Université de LyonLyonFrance
| | - Hector Hernandez-Vargas
- Cancer Research Center of Lyon (CRCL), INSERM 1052, CNRSLyonFrance
- Centre Léon BérardLyonFrance
- Université Claude Bernard Lyon 1LyonFrance
| | - Stephen WG Tait
- Cancer Research UK Beatson InstituteGlasgowUnited Kingdom
- Institute of Cancer Sciences, University of GlasgowGlasgowUnited Kingdom
| | - Ana Hennino
- Cancer Research Center of Lyon (CRCL), INSERM 1052, CNRSLyonFrance
- Université Lyon 1, VilleurbanneVilleurbanneFrance
- Centre Léon BérardLyonFrance
| | - Gabriel Ichim
- Cancer Research Center of Lyon (CRCL), INSERM 1052, CNRSLyonFrance
- Cancer Cell Death Laboratory, part of LabEx DEVweCAN, Université de LyonLyonFrance
| |
Collapse
|
63
|
Fei F, Rong L, Jiang N, Wayne AS, Xie J. Targeting HLA-DR loss in hematologic malignancies with an inhibitory chimeric antigen receptor. Mol Ther 2022; 30:1215-1226. [PMID: 34801727 PMCID: PMC8899520 DOI: 10.1016/j.ymthe.2021.11.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 08/19/2021] [Accepted: 11/16/2021] [Indexed: 02/08/2023] Open
Abstract
Chimeric antigen receptor natural killer (CAR-NK) cells have remarkable cytotoxicity against hematologic malignancies; however, they may also attack normal cells sharing the target antigen. Since human leukocyte antigen DR (HLA-DR) is reportedly lost or downregulated in a substantial proportion of hematologic malignancies, presumably a mechanism to escape immune surveillance, we hypothesize that the anti-cancer specificity of CAR-NK cells can be enhanced by activating them against cancer antigens while inhibiting them against HLA-DR. Here, we report the development of an anti-HLA-DR inhibitory CAR (iCAR) that can effectively suppress NK cell activation against HLA-DR-expressing cells. We show that dual CAR-NK cells, which co-express the anti-CD19 or CD33 activating CAR and the anti-HLA-DR iCAR, can preferentially target HLA-DR-negative cells over HLA-DR-positive cells in vitro. We find that the HLA-DR-mediated inhibition is positively correlated with both iCAR and HLA-DR densities. We also find that HLA-DR-expressing surrounding cells do not affect the target selectivity of dual CAR-NK cells. Finally, we confirm that HLA-DR-positive cells are resistant to dual CAR-NK cell-mediated killing in a xenograft mouse model. Our approach holds great promise for enhancing CAR-NK and CAR-T cell specificity against malignancies with HLA-DR loss.
Collapse
Affiliation(s)
- Fan Fei
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA 90089, USA
| | - Liang Rong
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA 90089, USA
| | - Nan Jiang
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA 90089, USA
| | - Alan S. Wayne
- Cancer and Blood Disease Institute, Division of Hematology-Oncology, Children's Hospital Los Angeles, Los Angeles, CA 90027, USA,Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Jianming Xie
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA 90089, USA; Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA.
| |
Collapse
|
64
|
Discovering the Triad between Nav1.5, Breast Cancer, and the Immune System: A Fundamental Review and Future Perspectives. Biomolecules 2022; 12:biom12020310. [PMID: 35204811 PMCID: PMC8869595 DOI: 10.3390/biom12020310] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 02/12/2022] [Accepted: 02/13/2022] [Indexed: 02/05/2023] Open
Abstract
Nav1.5 is one of the nine voltage-gated sodium channel-alpha subunit (VGSC-α) family members. The Nav1.5 channel typically carries an inward sodium ion current that depolarises the membrane potential during the upstroke of the cardiac action potential. The neonatal isoform of Nav1.5, nNav1.5, is produced via VGSC-α alternative splicing. nNav1.5 is known to potentiate breast cancer metastasis. Despite their well-known biological functions, the immunological perspectives of these channels are poorly explored. The current review has attempted to summarise the triad between Nav1.5 (nNav1.5), breast cancer, and the immune system. To date, there is no such review available that encompasses these three components as most reviews focus on the molecular and pharmacological prospects of Nav1.5. This review is divided into three major subsections: (1) the review highlights the roles of Nav1.5 and nNav1.5 in potentiating the progression of breast cancer, (2) focuses on the general connection between breast cancer and the immune system, and finally (3) the review emphasises the involvements of Nav1.5 and nNav1.5 in the functionality of the immune system and the immunogenicity. Compared to the other subsections, section three is pretty unexploited; it would be interesting to study this subsection as it completes the triad.
Collapse
|
65
|
CW. Wong K, Johnson D, Hui EP, CT. Lam R, BY. Ma B, TC. Chan A. Opportunities and Challenges in Combining Immunotherapy and Radiotherapy in Head and Neck Cancers. Cancer Treat Rev 2022; 105:102361. [DOI: 10.1016/j.ctrv.2022.102361] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 02/10/2022] [Accepted: 02/12/2022] [Indexed: 02/06/2023]
|
66
|
Cancer immunoediting hypothesis: history, clinical implications and controversies. Cent Eur J Immunol 2022; 47:168-174. [PMID: 36751395 PMCID: PMC9894085 DOI: 10.5114/ceji.2022.117376] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/18/2022] [Indexed: 11/17/2022] Open
Abstract
The main function of the immune system is to protect against infectious pathogens and to ensure tissue homeostasis. The latter function includes preventing autoimmune reactions, tolerizing cells to nonpathogenic environmental microorganisms, and eliminating apoptotic/damaged, transformed, or neoplastic cells. The process of carcinogenesis and tumor development and the role of the immune system in inhibiting progression of cancer have been the subject of intense research since the end of the 20th century and resulted in formulation of the cancer immunoediting hypothesis. The hypothesis postulates three steps in oncogenesis: 1) elimination - corresponding to immunosurveillance, 2) equilibrium in which the growth of transformed or neoplastic cells is efficiently controlled by immune effector mechanisms, and 3) escape in which cancer progresses due to an ineffective antitumor response. In parallel, a new field of science - immune-oncology - has arisen. Attempts are also being made to quantify intra-tumoral and peritumoral T cell infiltrations and to define optimal immunological parameters for prognostic/predictive purposes in several types of cancer. The knowledge of relationships between the tumor and the immune system has been and is practically exploited therapeutically in the clinic to treat cancer. Immunotherapy is a standard or supplementary treatment in various types of cancer.
Collapse
|
67
|
Xie X, Lv J, Zhu W, Tian C, Li J, Liu J, Zhou H, Sun C, Hu Z, Li X. The combination therapy of oncolytic HSV-1 armed with anti-PD-1 antibody and IL-12 enhances anti-tumor efficacy. Transl Oncol 2022; 15:101287. [PMID: 34808461 PMCID: PMC8607272 DOI: 10.1016/j.tranon.2021.101287] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 11/15/2021] [Indexed: 11/21/2022] Open
Abstract
Cancer immunotherapy is a new therapeutic strategy for cancer treatment that targets tumors by improving or restoring immune system function. Therapies targeting immune checkpoint molecules have exerted potent anti-tumor effects and prolonged the overall survival rate of patients. However, only a small number of patients benefit from the treatment. Oncolytic viruses exert anti-tumor effects by regulating the tumor microenvironment and affecting multiple steps of tumor immune circulation. In this study, we engineered two oncolytic viruses that express mouse anti-PD-1 antibody (VT1093M) or mouse IL-12 (VT1092M). We found that both oncolytic viruses showed significant anti-tumor effects in a murine CT26 colon adenocarcinoma model. Importantly, the intratumoral combined injection with VT1092M and VT1093M inhibited growth of the primary tumor, prevented growth of the contralateral untreated tumor, produced a vaccine-like response, activated antigen-specific T cell responses and prolonged the overall survival rate of mice. These results indicate that combination therapy with the engineered oncolytic virus may represent a potent immunotherapy strategy for cancer patients, especially those resistant to PD-1/PD-L1 blockade therapy.
Collapse
Affiliation(s)
- Xin Xie
- School of Pharmacy, Yantai University, Yantai Shandong 264005, China
| | - Jingwen Lv
- School of Pharmacy, Yantai University, Yantai Shandong 264005, China
| | - Wei Zhu
- School of Pharmacy, Yantai University, Yantai Shandong 264005, China
| | - Chao Tian
- Beijing WellGene Company, Ltd, Beijing 100085, China
| | - Jingfeng Li
- School of Pharmacy, Yantai University, Yantai Shandong 264005, China; Beijing WellGene Company, Ltd, Beijing 100085, China
| | - Jiajia Liu
- Beijing WellGene Company, Ltd, Beijing 100085, China
| | - Hua Zhou
- Beijing WellGene Company, Ltd, Beijing 100085, China
| | - Chunyang Sun
- Beijing WellGene Company, Ltd, Beijing 100085, China
| | - Zongfeng Hu
- School of Pharmacy, Yantai University, Yantai Shandong 264005, China
| | - Xiaopeng Li
- School of Pharmacy, Yantai University, Yantai Shandong 264005, China; Beijing WellGene Company, Ltd, Beijing 100085, China.
| |
Collapse
|
68
|
Hu S, Zhang W, Ye J, Zhang Y, Zhang D, Peng J, Yu D, Xu J, Wei Y. DNA methylation of ARHGAP30 is negatively associated with ARHGAP30 expression in lung adenocarcinoma, which reduces tumor immunity and is detrimental to patient survival. Aging (Albany NY) 2021; 13:25799-25845. [PMID: 34910688 PMCID: PMC8751594 DOI: 10.18632/aging.203762] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 11/22/2021] [Indexed: 12/24/2022]
Abstract
Rho-GTPase activating protein 30 (ARHGAP30) can enhance the intrinsic hydrolysis of GTP and regulates Rho-GTPase negatively. The relationship between ARHGAP30 expression and lung adenocarcinoma is unclear. Therefore, the present study aimed to assess the differences in expression of ARHGAP30 between lung adenocarcinoma tissues and normal tissues and the relationship between DNA methylation and ARHGAP30 expression in lung adenocarcinoma. To determine the role of ARHGAP30 expression in the prognosis and survival of patients with lung adenocarcinoma, gene set enrichment analysis of ARHGAP30 was performed, comprising analyses of Kyoto Encyclopedia of Genes and Genomes pathways, Panther pathways, Reactome pathways, Wikipathways, Gene Ontology, Kinase Target Network, Transcription Factor Network, and a protein-protein interaction network. The association of ARHGAP30 expression with tumor-infiltrating lymphocytes, immunostimulators, major histocompatibility complex molecules, chemokines, and chemokine receptors in lung adenocarcinoma tissues was also analyzed. DNA methylation of ARHGAP30 correlated negatively with ARHGAP30 expression. Patients with lung adenocarcinoma with high DNA methylation of ARHGAP30 had poor prognosis. The prognosis of patients with lung adenocarcinoma with low ARHGAP30 expression was also poor. ARHGAP30 expression in lung adenocarcinoma correlated positively, whereas methylation of ARHGAP30 correlated negatively, with levels of tumor infiltrating lymphocytes. Gene set enrichment analysis revealed that many pathways associated with ARHGAP30 should be studied to improve the diagnosis, treatment, and prognosis of lung adenocarcinoma. We speculated that DNA methylation of ARHGAP30 suppresses ARHGAP30 expression, which reduces tumor immunity, leading to poor prognosis for patients with lung adenocarcinoma.
Collapse
Affiliation(s)
- Sheng Hu
- Department of Thoracic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Wenxiong Zhang
- Department of Thoracic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jiayue Ye
- Department of Thoracic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Yang Zhang
- Department of Thoracic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Deyuan Zhang
- Department of Thoracic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jinhua Peng
- Department of Thoracic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Dongliang Yu
- Department of Thoracic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jianjun Xu
- Department of Thoracic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Yiping Wei
- Department of Thoracic Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| |
Collapse
|
69
|
Choi SS, Choi H, Baek IC, Park SA, Park JS, Kim TG, Jeun SS, Ahn S. HLA polymorphisms and risk of glioblastoma in Koreans. PLoS One 2021; 16:e0260618. [PMID: 34882724 PMCID: PMC8659341 DOI: 10.1371/journal.pone.0260618] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 11/13/2021] [Indexed: 11/18/2022] Open
Abstract
Purpose Immune responses for cancer cells can be altered according to genetic variation of human leukocyte antigen (HLA). Association of HLA polymorphism with risk of various cancer types is well known. However, the association between HLA and glioblastoma (GBM) remains uncertain. We sought to evaluate the association of HLA polymorphism with risk of GBM development in Koreans. Materials and methods A case-control study was performed to identify the odds ratios (OR) of HLA class I and II genes for GBM. The control group consisted of 142 healthy Korean volunteers, and the GBM group was 80 patients with newly diagnosed GBM at our institution. HLA class I (-A, -B, and–C) and class II (-DR, -DQ, and–DP) genotyping was performed by high-resolution polymerase chain reaction (PCR)-sequence-based typing (PCR-SBT) methods. Results There were significantly decreased frequencies of HLA-A*26:02 (OR 0.22 CI 0.05–0.98), HLA-C*08:01 (OR 0.29 CI 0.10–0.87), and HLA-DRB1*08:03 (OR 0.32 CI 0.11–0.98), while there was significantly increased frequency of HLA-C*04:01 (OR 2.29 CI 1.05–4.97). In analysis of haplotypes, the frequency of DRB1*14:05-DQB1*05:03 was significantly decreased (OR 0.22 CI 0.05–0.98). Conclusion This study suggests that genetic variations of HLA may affect GBM development in Koreans. Further investigations with larger sample sizes are needed to delineate any potential role of the HLA polymorphisms in the pathogenesis of GBM development.
Collapse
Affiliation(s)
- Sang-Soo Choi
- Department of Neurosurgery, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Haeyoun Choi
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - In-Cheol Baek
- Catholic Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Soon A. Park
- Department of Biomedicine and Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Jae-Sung Park
- Department of Neurosurgery, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Tai-Gyu Kim
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, South Korea
- Department of Biomedicine and Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Sin-Soo Jeun
- Department of Neurosurgery, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Stephen Ahn
- Department of Neurosurgery, Seoul St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Seoul, South Korea
- * E-mail:
| |
Collapse
|
70
|
Chavez-Dominguez R, Perez-Medina M, Aguilar-Cazares D, Galicia-Velasco M, Meneses-Flores M, Islas-Vazquez L, Camarena A, Lopez-Gonzalez JS. Old and New Players of Inflammation and Their Relationship With Cancer Development. Front Oncol 2021; 11:722999. [PMID: 34881173 PMCID: PMC8645998 DOI: 10.3389/fonc.2021.722999] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 11/04/2021] [Indexed: 12/18/2022] Open
Abstract
Pathogens or genotoxic agents continuously affect the human body. Acute inflammatory reaction induced by a non-sterile or sterile environment is triggered for the efficient elimination of insults that caused the damage. According to the insult, pathogen-associated molecular patterns, damage-associated molecular patterns, and homeostasis-altering molecular processes are released to facilitate the arrival of tissue resident and circulating cells to the injured zone to promote harmful agent elimination and tissue regeneration. However, when inflammation is maintained, a chronic phenomenon is induced, in which phagocytic cells release toxic molecules damaging the harmful agent and the surrounding healthy tissues, thereby inducing DNA lesions. In this regard, chronic inflammation has been recognized as a risk factor of cancer development by increasing the genomic instability of transformed cells and by creating an environment containing proliferation signals. Based on the cancer immunoediting concept, a rigorous and regulated inflammation process triggers participation of innate and adaptive immune responses for efficient elimination of transformed cells. When immune response does not eliminate all transformed cells, an equilibrium phase is induced. Therefore, excessive inflammation amplifies local damage caused by the continuous arrival of inflammatory/immune cells. To regulate the overstimulation of inflammatory/immune cells, a network of mechanisms that inhibit or block the cell overactivity must be activated. Transformed cells may take advantage of this process to proliferate and gradually grow until they become preponderant over the immune cells, preserving, increasing, or creating a microenvironment to evade the host immune response. In this microenvironment, tumor cells resist the attack of the effector immune cells or instruct them to sustain tumor growth and development until its clinical consequences. With tumor development, evolving, complex, and overlapping microenvironments are arising. Therefore, a deeper knowledge of cytokine, immune, and tumor cell interactions and their role in the intricated process will impact the combination of current or forthcoming therapies.
Collapse
Affiliation(s)
- Rodolfo Chavez-Dominguez
- Departamento de Enfermedades Cronico-Degenerativas, Instituto Nacional de Enfermedades Respiratorias "Ismael Cosio Villegas", Mexico City, Mexico.,Posgrado en Ciencias Biologicas, Universidad Nacional Autonoma de Mexico, Mexico City, Mexico
| | - Mario Perez-Medina
- Departamento de Enfermedades Cronico-Degenerativas, Instituto Nacional de Enfermedades Respiratorias "Ismael Cosio Villegas", Mexico City, Mexico.,Laboratorio de Quimioterapia Experimental, Departamento de Bioquímica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Dolores Aguilar-Cazares
- Departamento de Enfermedades Cronico-Degenerativas, Instituto Nacional de Enfermedades Respiratorias "Ismael Cosio Villegas", Mexico City, Mexico
| | - Miriam Galicia-Velasco
- Departamento de Enfermedades Cronico-Degenerativas, Instituto Nacional de Enfermedades Respiratorias "Ismael Cosio Villegas", Mexico City, Mexico
| | - Manuel Meneses-Flores
- Departamento de Patología, Instituto Nacional de Enfermedades Respiratorias "Ismael Cosio Villegas", Mexico City, Mexico
| | - Lorenzo Islas-Vazquez
- Departamento de Enfermedades Cronico-Degenerativas, Instituto Nacional de Enfermedades Respiratorias "Ismael Cosio Villegas", Mexico City, Mexico
| | - Angel Camarena
- Laboratorio de Human Leukocyte Antigen (HLA), Instituto Nacional de Enfermedades Respiratorias "Ismael Cosio Villegas", Mexico City, Mexico
| | - Jose S Lopez-Gonzalez
- Departamento de Enfermedades Cronico-Degenerativas, Instituto Nacional de Enfermedades Respiratorias "Ismael Cosio Villegas", Mexico City, Mexico
| |
Collapse
|
71
|
Immune Regulatory Processes of the Tumor Microenvironment under Malignant Conditions. Int J Mol Sci 2021; 22:ijms222413311. [PMID: 34948104 PMCID: PMC8706102 DOI: 10.3390/ijms222413311] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 12/03/2021] [Accepted: 12/05/2021] [Indexed: 02/07/2023] Open
Abstract
The tumor microenvironment (TME) is a critical regulator of tumor growth, progression, and metastasis. Since immune cells represent a large fraction of the TME, they play a key role in mediating pro- and anti-tumor immune responses. Immune escape, which suppresses anti-tumor immunity, enables tumor cells to maintain their proliferation and growth. Numerous mechanisms, which have been intensively studied in recent years, are involved in this process and based on these findings, novel immunotherapies have been successfully developed. Here, we review the composition of the TME and the mechanisms by which immune evasive processes are regulated. In detail, we describe membrane-bound and soluble factors, their regulation, and their impact on immune cell activation in the TME. Furthermore, we give an overview of the tumor/antigen presentation and how it is influenced under malignant conditions. Finally, we summarize novel TME-targeting agents, which are already in clinical trials for different tumor entities.
Collapse
|
72
|
Liu Y, Pang Z, Zhao X, Zeng Y, Shen H, Du J. Prognostic model of AU-rich genes predicting the prognosis of lung adenocarcinoma. PeerJ 2021; 9:e12275. [PMID: 34707942 PMCID: PMC8504460 DOI: 10.7717/peerj.12275] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 09/19/2021] [Indexed: 12/15/2022] Open
Abstract
Background AU-rich elements (ARE) are vital cis-acting short sequences in the 3’UTR affecting mRNA stability and translation. The deregulation of ARE-mediated pathways can contribute to tumorigenesis and development. Consequently, ARE-genes are promising to predict prognosis of lung adenocarcinoma (LUAD) patients. Methods Differentially expressed ARE-genes between LUAD and adjacent tissues in TCGA were investigated by Wilcoxon test. LASSO and Cox regression analyses were performed to identify a prognostic genetic signature. The genetic signature was combined with clinicopathological features to establish a prognostic model. LUAD patients were divided into high- and low-risk groups by the model. Kaplan–Meier curve, Harrell’s concordance index (C-index), calibration curves and decision curve analyses (DCA) were used to assess the model. Function enrichment analysis, immunity and tumor mutation analyses were performed to further explore the underlying molecular mechanisms. GEO data were used for external validation. Results Twelve prognostic genes were identified. The gene riskScore, age and stage were independent prognostic factors. The high-risk group had worse overall survival and was less sensitive to chemotherapy and radiotherapy (P < 0.01). C-index and calibration curves showed good performance on survival prediction in both TCGA (1, 3, 5-year ROC: 0.788, 0.776, 0.766) and the GSE13213 validation cohort (1, 3, 5-year ROC: 0.781, 0.811, 0.734). DCA showed the model had notable clinical net benefit. Furthermore, the high-risk group were enriched in cell cycle, DNA damage response, multiple oncological pathways and associated with higher PD-L1 expression, M1 macrophage infiltration. There was no significant difference in tumor mutation burden (TMB) between high- and low-risk groups. Conclusion ARE-genes can reliably predict prognosis of LUAD and may become new therapeutic targets for LUAD.
Collapse
Affiliation(s)
- Yong Liu
- Institute of Oncology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong Province, China
| | - Zhaofei Pang
- Institute of Oncology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong Province, China.,Institute of Oncology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong Province, China.,Department of Oncology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong Province, China
| | - Xiaogang Zhao
- Department of Thoracic Surgery, The Second Hospital of Shandong University, Jinan, Shandong Province, China
| | - Yukai Zeng
- Institute of Oncology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong Province, China
| | - Hongchang Shen
- Department of Oncology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong Province, China
| | - Jiajun Du
- Institute of Oncology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong Province, China.,Institute of Oncology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong Province, China.,Department of Thoracic Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong Province, China
| |
Collapse
|
73
|
Lin Y, Pan X, Zhao L, Yang C, Zhang Z, Wang B, Gao Z, Jiang K, Ye Y, Wang S, Shen Z. Immune cell infiltration signatures identified molecular subtypes and underlying mechanisms in gastric cancer. NPJ Genom Med 2021; 6:83. [PMID: 34635662 PMCID: PMC8505616 DOI: 10.1038/s41525-021-00249-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 09/23/2021] [Indexed: 12/14/2022] Open
Abstract
Increasing evidence has clarified that the tumor microenvironment (TME) is closely related to the prognosis and therapeutic efficacy of cancer. However, there is no reliable TME evaluation system used to accurately predict the prognosis of and therapeutic efficacy in gastric cancer. We evaluated the immune microenvironment score (IMS) of 1422 gastric cancer samples based on 51 immune cell signatures. We explored the relationship between the IMS and prognosis, immune cell infiltration, cancer subtype, and potential immune escape mechanisms. The results show that activation of the stroma and decreased levels of immune infiltration were associated with a low IMS. A high IMS was characterized by Epstein–Barr virus infection, increased mutation load, microsatellite instability, and immune cell infiltration. A high IMS was also related to high expression of immune checkpoint molecules (PD-1/PD-L1). Finally, patients with a high IMS had a better response to PD-1/PD-L1 inhibitors and may be more suitable for immune checkpoint inhibitors (area under the curve = 0.81). In addition, a low IMS may be converted into the immune-infiltrating subtype after romidepsin treatment. Stratification based on the IMS may enable gastric cancer patients to benefit more from immunotherapy and help identify new cancer treatment strategies.
Collapse
Affiliation(s)
- Yilin Lin
- Department of Gastroenterological Surgery, Peking University People's Hospital, Beijing, 100044, PR China.,Laboratory of Surgical Oncology, Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Peking University People's Hospital, Beijing, 100044, PR China
| | - Xiaoxian Pan
- Department of Radiotherapy, First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, 350004, PR China
| | - Long Zhao
- Department of Gastroenterological Surgery, Peking University People's Hospital, Beijing, 100044, PR China.,Laboratory of Surgical Oncology, Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Peking University People's Hospital, Beijing, 100044, PR China
| | - Changjiang Yang
- Department of Gastroenterological Surgery, Peking University People's Hospital, Beijing, 100044, PR China.,Laboratory of Surgical Oncology, Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Peking University People's Hospital, Beijing, 100044, PR China
| | - Zhen Zhang
- Department of Gastroenterological Surgery, Peking University People's Hospital, Beijing, 100044, PR China.,Laboratory of Surgical Oncology, Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Peking University People's Hospital, Beijing, 100044, PR China
| | - Bo Wang
- Department of Gastroenterological Surgery, Peking University People's Hospital, Beijing, 100044, PR China.,Laboratory of Surgical Oncology, Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Peking University People's Hospital, Beijing, 100044, PR China
| | - Zhidong Gao
- Department of Gastroenterological Surgery, Peking University People's Hospital, Beijing, 100044, PR China.,Laboratory of Surgical Oncology, Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Peking University People's Hospital, Beijing, 100044, PR China
| | - Kewei Jiang
- Department of Gastroenterological Surgery, Peking University People's Hospital, Beijing, 100044, PR China.,Laboratory of Surgical Oncology, Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Peking University People's Hospital, Beijing, 100044, PR China
| | - Yingjiang Ye
- Department of Gastroenterological Surgery, Peking University People's Hospital, Beijing, 100044, PR China.,Laboratory of Surgical Oncology, Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Peking University People's Hospital, Beijing, 100044, PR China
| | - Shan Wang
- Department of Gastroenterological Surgery, Peking University People's Hospital, Beijing, 100044, PR China.,Laboratory of Surgical Oncology, Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Peking University People's Hospital, Beijing, 100044, PR China
| | - Zhanlong Shen
- Department of Gastroenterological Surgery, Peking University People's Hospital, Beijing, 100044, PR China. .,Laboratory of Surgical Oncology, Beijing Key Laboratory of Colorectal Cancer Diagnosis and Treatment Research, Peking University People's Hospital, Beijing, 100044, PR China.
| |
Collapse
|
74
|
Zheng M, Hu Y, Gou R, Li S, Nie X, Li X, Lin B. Development of a seven-gene tumor immune microenvironment prognostic signature for high-risk grade III endometrial cancer. MOLECULAR THERAPY-ONCOLYTICS 2021; 22:294-306. [PMID: 34553020 PMCID: PMC8426172 DOI: 10.1016/j.omto.2021.07.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 07/02/2021] [Indexed: 02/06/2023]
Abstract
Uterine corpus endometrial carcinoma locally infiltrates numerous immune cells and other tumor immune microenvironment components. These cells are involved in malignant tumor growth and proliferation and the process of resistance toward immunotherapies. Here, we aimed to develop a tumor immune microenvironment-related prognostic signature for high-risk grade III endometrial carcinoma based on The Cancer Genome Atlas. The signature was systematically correlated with immune infiltration characteristics of the tumor microenvironment. The seven-gene Riskscore signature was robust and performed well in training, testing, and Gene Expression Omnibus-independent cohorts. A nomogram comprising the gene signature accurately predicted patient prognosis, with our model performing better than other endometrial cancer-related signatures. Analysis of the IMvigor210 immunotherapy cohort revealed that subgroups with a low Riskscore had a better prognosis than subgroups with a high Riskscore. Subgroups with a low Riskscore exhibited immune cell infiltration and inflammatory profiles, whereas subgroups with a high Riskscore experienced progressive disease. The receiver operating characteristic curve indicated that risk score, neoantigen, and tumor mutation burden models together accurately predicted treatment response. Taken together, we developed a tumor microenvironment-based seven-gene prognostic stratification system to predict the prognosis of patients with high-risk endometrial cancer and guide more effective immunotherapy strategies.
Collapse
Affiliation(s)
- Mingjun Zheng
- Department of Gynecology and Obstetrics, Shengjing Hospital of China Medical University, Liaoning 110004, China.,Key Laboratory of Maternal-Fetal Medicine of Liaoning Province, Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, China.,Department of Obstetrics and Gynecology, University Hospital, LMU Munich, Maistrasse 11, 80337 Munich, Germany
| | - Yuexin Hu
- Department of Gynecology and Obstetrics, Shengjing Hospital of China Medical University, Liaoning 110004, China.,Key Laboratory of Maternal-Fetal Medicine of Liaoning Province, Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, China
| | - Rui Gou
- Department of Gynecology and Obstetrics, Shengjing Hospital of China Medical University, Liaoning 110004, China.,Key Laboratory of Maternal-Fetal Medicine of Liaoning Province, Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, China
| | - Siting Li
- Department of Gynecology and Obstetrics, Shengjing Hospital of China Medical University, Liaoning 110004, China.,Key Laboratory of Maternal-Fetal Medicine of Liaoning Province, Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, China
| | - Xin Nie
- Department of Gynecology and Obstetrics, Shengjing Hospital of China Medical University, Liaoning 110004, China.,Key Laboratory of Maternal-Fetal Medicine of Liaoning Province, Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, China
| | - Xiao Li
- Department of Gynecology and Obstetrics, Shengjing Hospital of China Medical University, Liaoning 110004, China.,Key Laboratory of Maternal-Fetal Medicine of Liaoning Province, Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, China
| | - Bei Lin
- Department of Gynecology and Obstetrics, Shengjing Hospital of China Medical University, Liaoning 110004, China.,Key Laboratory of Maternal-Fetal Medicine of Liaoning Province, Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, China
| |
Collapse
|
75
|
Wang YY, Shi LY, Xu MH, Jing Y, Sun CC, Yang JH, Wang RN, Sheng NN, Zhang CF, Zhang L, Zhu ZT, Wang QJ. A pan-cancer analysis of the expression of gasdermin genes in tumors and their relationship with the immune microenvironment. Transl Cancer Res 2021; 10:4125-4147. [PMID: 35116710 PMCID: PMC8797575 DOI: 10.21037/tcr-21-1635] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/14/2021] [Indexed: 12/11/2022]
Abstract
BACKGROUND Gasdermins (GSDMs) are a class of proteins related to pyrolysis and in humans, consist of GSDMA, GSDMB, GSDMC, GSDMD, DFNA5, and DFNB59. The inflammatory factors and cell contents released during pyrolysis can recruit immune cells and change the microenvironment. However, to date, there is a paucity of studies examining the relationship between GSDMs and the immune microenvironment in tumors. Therefore, this current report analyzed the expression of GSDM genes in tumors and their relationship with the immune microenvironment. METHODS Apply GSCALite and GEPIA2 online analysis tools to analyze the gene expression levels and the Single nucleotide variant (SNV), copy number variation (CNV), and methylation characteristics of GSDM genes respectively. Use R software or TISIDB online analysis tool to carry out the correlation analysis required in the article. Furthermore, Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were conducted to examine the role of these GSDM genes in various cancers. RESULTS The results demonstrated that CNV can cause an increase in GSDM gene expression, and methylation can inhibit GSDM gene expression. The elevated expression of GSDMA, GSDMB, GSDMC, GSDMD, and DFNA5 in some or most tumors was often accompanied by elevated immune scores, increased immune cell infiltration, and high expression of major histocompatibility complex (MHC) molecules, chemokines and their receptors, and immune checkpoint-related genes. However, DFNB59 was often negatively correlated with these indicators in tumors. GSDMD was the most highly expressed GSDM protein in various normal tissues and tumors, and showed the strongest correlation with immune microenvironment-related genes. Moreover, the methylation of GSDMD was accompanied by low immune cell infiltration, low expression of MHC molecule-related genes, low expression of chemokines and receptor-related genes, and low expression of immune checkpoint-related genes. CONCLUSIONS Therefore, the expression of GSDM-related genes is associated with the tumor immune microenvironment. The GSDM genes, especially GSDMD, may be used as therapeutic targets to predict or change the tumor microenvironment and as biomarkers to predict the therapeutic efficacy of immune checkpoint inhibitors.
Collapse
Affiliation(s)
- Yuan-Yuan Wang
- Department of Clinical Trial, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, China
| | - Lin-Yang Shi
- Department of Oncology, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, China
| | - Ming-Hao Xu
- Department of Clinical Trial, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, China
| | - Yu Jing
- Department of Clinical Trial, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, China
| | - Cui-Cui Sun
- Department of Clinical Trial, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, China
| | - Jia-Hui Yang
- Department of Oncology, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, China
| | - Ruo-Nan Wang
- Department of Oncology, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, China
| | - Ning-Ning Sheng
- Department of Oncology, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, China
| | - Ca-Fa Zhang
- Department of Oncology, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, China
| | - Li Zhang
- Department of Clinical Trial, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, China
| | - Zhi-Tu Zhu
- Department of Clinical Trial, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, China
| | - Qing-Jun Wang
- Department of Clinical Trial, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, China
| |
Collapse
|
76
|
Hazini A, Fisher K, Seymour L. Deregulation of HLA-I in cancer and its central importance for immunotherapy. J Immunother Cancer 2021; 9:e002899. [PMID: 34353849 PMCID: PMC8344275 DOI: 10.1136/jitc-2021-002899] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/21/2021] [Indexed: 12/28/2022] Open
Abstract
It is now well accepted that many tumors undergo a process of clonal selection which means that tumor antigens arising at various stages of tumor progression are likely to be represented in just a subset of tumor cells. This process is thought to be driven by constant immunosurveillance which applies selective pressure by eliminating tumor cells expressing antigens that are recognized by T cells. It is becoming increasingly clear that the same selective pressure may also select for tumor cells that evade immune detection by acquiring deficiencies in their human leucocyte antigen (HLA) presentation pathways, allowing important tumor antigens to persist within cells undetected by the immune system. Deficiencies in antigen presentation pathway can arise by a variety of mechanisms, including genetic and epigenetic changes, and functional antigen presentation is a hard phenomenon to assess using our standard analytical techniques. Nevertheless, it is likely to have profound clinical significance and could well define whether an individual patient will respond to a particular type of therapy or not. In this review we consider the mechanisms by which HLA function may be lost in clinical disease, we assess the implications for current immunotherapy approaches using checkpoint inhibitors and examine the prognostic impact of HLA loss demonstrated in clinical trials so far. Finally, we propose strategies that might be explored for possible patient stratification.
Collapse
Affiliation(s)
- Ahmet Hazini
- Department of Oncology, University of Oxford, Oxford, Oxfordshire, UK
| | - Kerry Fisher
- Department of Oncology, University of Oxford, Oxford, Oxfordshire, UK
| | - Len Seymour
- Department of Oncology, University of Oxford, Oxford, Oxfordshire, UK
| |
Collapse
|
77
|
Murtadha AH, Azahar IIM, Sharudin NA, Has ATC, Mokhtar NF. Influence of nNav1.5 on MHC class I expression in breast cancer. J Biosci 2021. [DOI: 10.1007/s12038-021-00196-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
78
|
Huang W, Xue S, Zhang Y, Liu F, Wang J. Two cases of acute lymphoid leukemia patients with loss of heterozygosity in HLA region before transplantation. HLA 2021; 98:207-212. [PMID: 34288574 DOI: 10.1111/tan.14372] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/22/2021] [Accepted: 07/12/2021] [Indexed: 11/30/2022]
Abstract
Leukemia is a complex disease in which mutations and other genomic and epigenomic abnormalities play a role in both its initiation and progression. Acute lymphoid leukemia (ALL) patients with loss of heterozygosity (LOH) in the HLA region before transplantation have been described rarely. In this report, we described two ALL cases with LOH encompassing the HLA, wholly or partly. HLA molecular typing was performed on peripheral blood (PB) and somatic cell. Simultaneously, we performed whole-exome sequencing. Typing results on PB samples collected during blast crisis demonstrated complete or partial homozygosity at the -A, -B, -C, -DR, and -DQ loci. Two somatic samples demonstrated heterozygosity at all loci. LOH at the HLA gene locus may significantly influence the donor search, resulting in misidentification of homozygous donors. We recommend confirming the patients' HLA typing with hematological malignancies when homozygosity is detected at any locus by using somatic samples or alternatively from PB when remission is achieved.
Collapse
Affiliation(s)
- Wenqiu Huang
- Department of Hematology, Aerospace Center Hospital, Beijing, China
| | - Song Xue
- Department of Hematology, Aerospace Center Hospital, Beijing, China
| | - Yongping Zhang
- Department of Hematology, Aerospace Center Hospital, Beijing, China
| | - Fuhong Liu
- Department of Hematology, Aerospace Center Hospital, Beijing, China
| | - Jingbo Wang
- Department of Hematology, Aerospace Center Hospital, Beijing, China
| |
Collapse
|
79
|
Long J, Wang D, Yang X, Wang A, Lin Y, Zheng M, Zhang H, Sang X, Wang H, Hu K, Zhao H. Identification of NOTCH4 mutation as a response biomarker for immune checkpoint inhibitor therapy. BMC Med 2021; 19:154. [PMID: 34284787 PMCID: PMC8293505 DOI: 10.1186/s12916-021-02031-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 06/10/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Immune checkpoint inhibitor (ICI) therapy elicits durable antitumor responses in patients with many types of cancer. Genomic mutations may be used to predict the clinical benefits of ICI therapy. NOTCH homolog-4 (NOTCH4) is frequently mutated in several cancer types, but its role in immunotherapy is still unclear. Our study is the first to study the association between NOTCH4 mutation and the response to ICI therapy. METHODS We tested the predictive value of NOTCH4 mutation in the discovery cohort, which included non-small cell lung cancer, melanoma, head and neck squamous cell carcinoma, esophagogastric cancer, and bladder cancer patients, and validated it in the validation cohort, which included non-small cell lung cancer, melanoma, renal cell carcinoma, colorectal cancer, esophagogastric cancer, glioma, bladder cancer, head and neck cancer, cancer of unknown primary, and breast cancer patients. Then, the relationships between NOTCH4 mutation and intrinsic and extrinsic immune response mechanisms were studied with multiomics data. RESULTS We collected an ICI-treated cohort (n = 662) and found that patients with NOTCH4 mutation had better clinical benefits in terms of objective response rate (ORR: 42.9% vs 25.9%, P = 0.007), durable clinical benefit (DCB: 54.0% vs 38.1%, P = 0.021), progression-free survival (PFS, hazard ratio [HR] = 0.558, P < 0.001), and overall survival (OS, HR = 0.568, P = 0.006). In addition, we validated the prognostic value of NOTCH4 mutation in an independent ICI-treated cohort (n = 1423). Based on multiomics data, we found that NOTCH4 mutation is significantly associated with enhanced immunogenicity, including a high tumor mutational burden, the expression of costimulatory molecules, and activation of the antigen-processing machinery, and NOTCH4 mutation positively correlates activated antitumor immunity, including infiltration of diverse immune cells and various immune marker sets. CONCLUSIONS Our findings indicated that NOTCH4 mutation serves as a novel biomarker correlated with a better response to ICI therapy.
Collapse
Affiliation(s)
- Junyu Long
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Dongxu Wang
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xu Yang
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Anqiang Wang
- Department of Gastrointestinal Surgery, Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education, Peking University Cancer Hospital & Institute, Beijing, China
| | - Yu Lin
- Shenzhen Withsum Technology Limited, Shenzhen, China
| | - Mingjun Zheng
- Department of Obstetrics and Gynecology, University Hospital, LMU Munich, Maistrasse 11, 80337, Munich, Germany
| | - Haohai Zhang
- Liver Center and The Transplant Institute, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Xinting Sang
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Hanping Wang
- Division of Pulmonary and Critical Care Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
| | - Ke Hu
- Department of Radiation Oncology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, China.
| | - Haitao Zhao
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
| |
Collapse
|
80
|
Fang Y, Huang S, Han L, Wang S, Xiong B. Comprehensive Analysis of Peritoneal Metastasis Sequencing Data to Identify LINC00924 as a Prognostic Biomarker in Gastric Cancer. Cancer Manag Res 2021; 13:5599-5611. [PMID: 34285580 PMCID: PMC8285530 DOI: 10.2147/cmar.s318704] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 06/29/2021] [Indexed: 12/31/2022] Open
Abstract
Background Gastric cancer peritoneal metastasis has high mortality. At present, there is no effective way to cure the patients diagnosed with gastric cancer peritoneal metastasis due to its indistinct molecular mechanism. Therefore, to understand the pathogenesis and help for further target therapy, we conduct comprehensive analysis of peritoneal metastasis by bioinformatics in gastric cancer. Methods Microarray sequencing was used to find differential mRNAs and long non-coding RNAs (lncRNAs) expression between primary foci and peritoneal metastases lesion in gastric cancer. RT-qPCR was used to verify the expression levels of lncRNAs in gastric cancer cells after co-culture with adipocytes. TCGA, Cytoscape, lnCAR, cBioPoratal and R packages (ggrisk, survival, survminer, timeROC, forestplot, immunedeconv, ggplot2, pheatmap and ggpubr) were applied in this work. Results Adipocytes co-culture model was used to mimic the peritoneal microenvironment and found that LINC01151 (NR_126348), FAM27B (NR_027422) and LINC00924 (NR_027133) were up-regulated in co-culture group. Increased LINC00924 expression was significantly associated with reduced overall survival and up-regulated percentage abundance of tumor-infiltrating CD8+ T, B, macrophage and NK immune cells; moreover, immune checkpoint blockers (ICBs) had a worse effect on the LINC00924 high expression group. Furthermore, through univariate and multivariate Cox regression analysis, we found that LINC00924-related PEX5L in CNC network was an independent prognostic factor in gastric cancer progression. Conclusion LINC00924 expression was associated with poor survival, immune infiltrations and worse response to ICBs. LINC00924 might be immunotherapeutic targets of advanced gastric cancer.
Collapse
Affiliation(s)
- Yan Fang
- Department of Gastrointestinal Surgery & Department of Gastric and Colorectal Surgical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, People's Republic of China.,Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital of Wuhan university, Wuhan, 430071, People's Republic of China.,Hubei Cancer Clinical Study Center, Zhongnan Hospital of Wuhan university, Wuhan, 430071, People's Republic of China.,Department of Obstetrics and Gynecology, Guangzhou Women and Children's Medical Center, Guangzhou, 510620, People's Republic of China
| | - Sihao Huang
- Department of Gastrointestinal Surgery & Department of Gastric and Colorectal Surgical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, People's Republic of China.,Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital of Wuhan university, Wuhan, 430071, People's Republic of China.,Hubei Cancer Clinical Study Center, Zhongnan Hospital of Wuhan university, Wuhan, 430071, People's Republic of China
| | - Lei Han
- Department of Gastrointestinal Surgery & Department of Gastric and Colorectal Surgical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, People's Republic of China.,Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital of Wuhan university, Wuhan, 430071, People's Republic of China.,Hubei Cancer Clinical Study Center, Zhongnan Hospital of Wuhan university, Wuhan, 430071, People's Republic of China
| | - Shuyi Wang
- Department of Gastrointestinal Surgery & Department of Gastric and Colorectal Surgical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, People's Republic of China.,Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital of Wuhan university, Wuhan, 430071, People's Republic of China.,Hubei Cancer Clinical Study Center, Zhongnan Hospital of Wuhan university, Wuhan, 430071, People's Republic of China
| | - Bin Xiong
- Department of Gastrointestinal Surgery & Department of Gastric and Colorectal Surgical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, People's Republic of China.,Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital of Wuhan university, Wuhan, 430071, People's Republic of China.,Hubei Cancer Clinical Study Center, Zhongnan Hospital of Wuhan university, Wuhan, 430071, People's Republic of China
| |
Collapse
|
81
|
Shklovskaya E, Rizos H. MHC Class I Deficiency in Solid Tumors and Therapeutic Strategies to Overcome It. Int J Mol Sci 2021; 22:ijms22136741. [PMID: 34201655 PMCID: PMC8268865 DOI: 10.3390/ijms22136741] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 06/18/2021] [Accepted: 06/21/2021] [Indexed: 12/21/2022] Open
Abstract
It is now well accepted that the immune system can control cancer growth. However, tumors escape immune-mediated control through multiple mechanisms and the downregulation or loss of major histocompatibility class (MHC)-I molecules is a common immune escape mechanism in many cancers. MHC-I molecules present antigenic peptides to cytotoxic T cells, and MHC-I loss can render tumor cells invisible to the immune system. In this review, we examine the dysregulation of MHC-I expression in cancer, explore the nature of MHC-I-bound antigenic peptides recognized by immune cells, and discuss therapeutic strategies that can be used to overcome MHC-I deficiency in solid tumors, with a focus on the role of natural killer (NK) cells and CD4 T cells.
Collapse
|
82
|
Jiang L, Yu H, Li J, Tang J, Guo Y, Guo F. Predicting MHC class I binder: existing approaches and a novel recurrent neural network solution. Brief Bioinform 2021; 22:6299205. [PMID: 34131696 DOI: 10.1093/bib/bbab216] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 05/14/2021] [Accepted: 05/17/2021] [Indexed: 01/04/2023] Open
Abstract
Major histocompatibility complex (MHC) possesses important research value in the treatment of complex human diseases. A plethora of computational tools has been developed to predict MHC class I binders. Here, we comprehensively reviewed 27 up-to-date MHC I binding prediction tools developed over the last decade, thoroughly evaluating feature representation methods, prediction algorithms and model training strategies on a benchmark dataset from Immune Epitope Database. A common limitation was identified during the review that all existing tools can only handle a fixed peptide sequence length. To overcome this limitation, we developed a bilateral and variable long short-term memory (BVLSTM)-based approach, named BVLSTM-MHC. It is the first variable-length MHC class I binding predictor. In comparison to the 10 mainstream prediction tools on an independent validation dataset, BVLSTM-MHC achieved the best performance in six out of eight evaluated metrics. A web server based on the BVLSTM-MHC model was developed to enable accurate and efficient MHC class I binder prediction in human, mouse, macaque and chimpanzee.
Collapse
Affiliation(s)
- Limin Jiang
- Comprehensive cancer center, Department of Internal Medicine, University of New Mexico, Albuquerque, NM, USA
| | - Hui Yu
- Comprehensive cancer center, Department of Internal Medicine, University of New Mexico, Albuquerque, NM, USA
| | - Jiawei Li
- School of Computer Science and Technology, College of Intelligence and Computing, Tianjin University, Tianjin, China
| | - Jijun Tang
- Department of Computer Science, University of South Carolina, SC, USA.,Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yan Guo
- Comprehensive cancer center, Department of Internal Medicine, University of New Mexico, Albuquerque, NM, USA
| | - Fei Guo
- School of Computer Science and Engineering, Central South University, Changsha, China
| |
Collapse
|
83
|
Abstract
In this review, Shen and Kang provide an overview of the tumor-intrinsic and microenvironment- and treatment-induced stresses that tumor cells encounter in the metastatic cascade and the molecular pathways they develop to relieve these stresses. Metastasis is the ultimate “survival of the fittest” test for cancer cells, as only a small fraction of disseminated tumor cells can overcome the numerous hurdles they encounter during the transition from the site of origin to a distinctly different distant organ in the face of immune and therapeutic attacks and various other stresses. During cancer progression, tumor cells develop a variety of mechanisms to cope with the stresses they encounter, and acquire the ability to form metastases. Restraining these stress-releasing pathways could serve as potentially effective strategies to prevent or reduce metastasis and improve the survival of cancer patients. Here, we provide an overview of the tumor-intrinsic, microenvironment- and treatment-induced stresses that tumor cells encounter in the metastatic cascade and the molecular pathways they develop to relieve these stresses. We also summarize the preclinical and clinical studies that evaluate the potential therapeutic benefit of targeting these stress-relieving pathways.
Collapse
Affiliation(s)
- Minhong Shen
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
| | - Yibin Kang
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
| |
Collapse
|
84
|
Zhang Z, Su J, Li L, Du W. Identification of Precise Therapeutic Targets and Characteristic Prognostic Genes Based on Immune Gene Characteristics in Uveal Melanoma. Front Cell Dev Biol 2021; 9:666462. [PMID: 34124047 PMCID: PMC8187912 DOI: 10.3389/fcell.2021.666462] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 03/04/2021] [Indexed: 11/13/2022] Open
Abstract
The tumor microenvironment is an important factor for the immunotherapy of tumor patients. The sequenced transcriptome data can be used to describe the tumor microenvironment and various immune subtypes. We exploited published data on patients with uveal melanoma (UVM) to identify immune subtypes. Based on the immune-related gene sets of 80 patients with UVM in the TCGA database, we used consensus clustering to identify two immune subgroups. In the two immune subtypes, we analyzed clinical characteristics and immune infiltration. Class1 has low immune infiltration, contains memory B cells, Th2 cells, Th17 cells, eosinophils, natural killer cells, and has a better prognosis. Class2 has higher immune infiltration. CD8+ T cells, Th1 cells, MDSCs, and Dendritic cells are enriched in class2, which has strong cytolytic activity, high expression of immune checkpoint genes, and poor outcome. Moreover, we have developed and verified an immune characteristic model that can predict the prognosis of patients well. Through this model, we screened prostaglandin-endoperoxide synthase 2 (PTGS2) as the therapeutic target of UVM. Treatment of choroidal melanoma cell line (OCM1) cells with celecoxib (an inhibitor of PTGS2) effectively inhibits cell growth, proliferation, and promotes apoptosis. Our results show the immunological heterogeneity of UVM patients and also provide an ideal therapeutic target for the future treatment design of patients.
Collapse
Affiliation(s)
| | | | - Li Li
- State Key Laboratory of Medical Molecular Biology, Department of Cell Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
| | - Wenjing Du
- State Key Laboratory of Medical Molecular Biology, Department of Cell Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing, China
| |
Collapse
|
85
|
Brouwer NJ, Verdijk RM, Heegaard S, Marinkovic M, Esmaeli B, Jager MJ. Conjunctival melanoma: New insights in tumour genetics and immunology, leading to new therapeutic options. Prog Retin Eye Res 2021; 86:100971. [PMID: 34015548 DOI: 10.1016/j.preteyeres.2021.100971] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 04/18/2021] [Accepted: 04/19/2021] [Indexed: 12/14/2022]
Abstract
Recent developments in oncology have led to a better molecular and cellular understanding of cancer, and the introduction of novel therapies. Conjunctival melanoma (CoM) is a rare but potentially devastating disease. A better understanding of CoM, leading to the development of novel therapies, is urgently needed. CoM is characterized by mutations that have also been identified in cutaneous melanoma, e.g. in BRAF, NRAS and TERT. These mutations are distinct from the mutations found in uveal melanoma (UM), affecting genes such as GNAQ, GNA11, and BAP1. Targeted therapies that are successful in cutaneous melanoma may therefore be useful in CoM. A recent breakthrough in the treatment of patients with metastatic cutaneous melanoma was the development of immunotherapy. While immunotherapy is currently sparsely effective in intraocular tumours such as UM, the similarities between CoM and cutaneous melanoma (including in their immunological tumour micro environment) provide hope for the application of immunotherapy in CoM, and preliminary clinical data are indeed emerging to support this use. This review aims to provide a comprehensive overview of the current knowledge regarding CoM, with a focus on the genetic and immunologic understanding. We elaborate on the distinct position of CoM in contrast to other types of melanoma, and explain how new insights in the pathophysiology of this disease guide the development of new, personalized, treatments.
Collapse
Affiliation(s)
- Niels J Brouwer
- Department of Ophthalmology, Leiden University Medical Center, Leiden, the Netherlands.
| | - Robert M Verdijk
- Department of Ophthalmology, Leiden University Medical Center, Leiden, the Netherlands; Department of Pathology, Leiden University Medica Center, Leiden, the Netherlands; Department of Pathology, Erasmus University Medical Center, Rotterdam, the Netherlands.
| | - Steffen Heegaard
- Department of Ophthalmology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark; Department of Pathology, Eye Pathology Section, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark.
| | - Marina Marinkovic
- Department of Ophthalmology, Leiden University Medical Center, Leiden, the Netherlands.
| | - Bita Esmaeli
- Department of Plastic Surgery, Orbital Oncology and Ophthalmic Plastic Surgery, M.D. Anderson Cancer Center, Houston, TX, USA.
| | - Martine J Jager
- Department of Ophthalmology, Leiden University Medical Center, Leiden, the Netherlands.
| |
Collapse
|
86
|
Acute Myeloid Leukemia: Is It T Time? Cancers (Basel) 2021; 13:cancers13102385. [PMID: 34069204 PMCID: PMC8156992 DOI: 10.3390/cancers13102385] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 04/30/2021] [Accepted: 05/10/2021] [Indexed: 12/24/2022] Open
Abstract
Acute myeloid leukemia (AML) is a heterogeneous disease driven by impaired differentiation of hematopoietic primitive cells toward myeloid lineages (monocytes, granulocytes, red blood cells, platelets), leading to expansion and accumulation of "stem" and/or "progenitor"-like or differentiated leukemic cells in the bone marrow and blood. AML progression alters the bone marrow microenvironment and inhibits hematopoiesis' proper functioning, causing sustained cytopenia and immunodeficiency. This review describes how the AML microenvironment influences lymphoid lineages, particularly T lymphocytes that originate from the thymus and orchestrate adaptive immune response. We focus on the elderly population, which is mainly affected by this pathology. We discuss how a permissive AML microenvironment can alter and even worsen the thymic function, T cells' peripheral homeostasis, phenotype, and functions. Based on the recent findings on the mechanisms supporting that AML induces quantitative and qualitative changes in T cells, we suggest and summarize current immunotherapeutic strategies and challenges to overcome these anomalies to improve the anti-leukemic immune response and the clinical outcome of patients.
Collapse
|
87
|
Algarra I, Garrido F, Garcia-Lora AM. MHC heterogeneity and response of metastases to immunotherapy. Cancer Metastasis Rev 2021; 40:501-517. [PMID: 33860434 DOI: 10.1007/s10555-021-09964-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 04/06/2021] [Indexed: 01/05/2023]
Abstract
In recent years, immunotherapy has proven to be an effective treatment against cancer. Cytotoxic T lymphocytes perform an important role in this anti-tumor immune response, recognizing cancer cells as foreign, through the presentation of tumor antigens by MHC class I molecules. However, tumors and metastases develop escape mechanisms for evading this immunosurveillance and may lose the expression of these polymorphic molecules to become invisible to cytotoxic T lymphocytes. In other situations, they may maintain MHC class I expression and promote immunosuppression of cytotoxic T lymphocytes. Therefore, the analysis of the expression of MHC class I molecules in tumors and metastases is important to elucidate these escape mechanisms. Moreover, it is necessary to determine the molecular mechanisms involved in these alterations to reverse them and recover the expression of MHC class I molecules on tumor cells. This review discusses the role and regulation of MHC class I expression in tumor progression. We focus on altered MHC class I phenotypes present in tumors and metastases, as well as the molecular mechanisms responsible for MHC-I alterations, emphasizing the mechanisms of recovery of the MHC class I molecules expression on cancer cells. The individualized study of the HLA class I phenotype of the tumor and the metastases of each patient will allow choosing the most appropriate immunotherapy treatment based on a personalized medicine.
Collapse
Affiliation(s)
- Ignacio Algarra
- Departamento de Ciencias de la Salud, Universidad de Jaén, Jaén, Spain
| | - Federico Garrido
- Servicio de Análisis Clínicos e Inmunología, UGC Laboratorio Clínico, Hospital Universitario Virgen de las Nieves, Av. de las Fuerzas Armadas 2, 18014, Granada, Spain.,Instituto de Investigación Biosanitaria ibs.Granada, Granada, Spain.,Departamento de Bioquímica, Biología Molecular e Inmunología III, Universidad de Granada, Granada, Spain
| | - Angel M Garcia-Lora
- Servicio de Análisis Clínicos e Inmunología, UGC Laboratorio Clínico, Hospital Universitario Virgen de las Nieves, Av. de las Fuerzas Armadas 2, 18014, Granada, Spain. .,Instituto de Investigación Biosanitaria ibs.Granada, Granada, Spain. .,Unidad de Biobanco, Hospital Universitario Virgen de las Nieves, Granada, Spain.
| |
Collapse
|
88
|
Dhatchinamoorthy K, Colbert JD, Rock KL. Cancer Immune Evasion Through Loss of MHC Class I Antigen Presentation. Front Immunol 2021; 12:636568. [PMID: 33767702 PMCID: PMC7986854 DOI: 10.3389/fimmu.2021.636568] [Citation(s) in RCA: 412] [Impact Index Per Article: 137.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 02/05/2021] [Indexed: 02/03/2023] Open
Abstract
Major histocompatibility class I (MHC I) molecules bind peptides derived from a cell's expressed genes and then transport and display this antigenic information on the cell surface. This allows CD8 T cells to identify pathological cells that are synthesizing abnormal proteins, such as cancers that are expressing mutated proteins. In order for many cancers to arise and progress, they need to evolve mechanisms to avoid elimination by CD8 T cells. MHC I molecules are not essential for cell survival and therefore one mechanism by which cancers can evade immune control is by losing MHC I antigen presentation machinery (APM). Not only will this impair the ability of natural immune responses to control cancers, but also frustrate immunotherapies that work by re-invigorating anti-tumor CD8 T cells, such as checkpoint blockade. Here we review the evidence that loss of MHC I antigen presentation is a frequent occurrence in many cancers. We discuss new insights into some common underlying mechanisms through which some cancers inactivate the MHC I pathway and consider some possible strategies to overcome this limitation in ways that could restore immune control of tumors and improve immunotherapy.
Collapse
|
89
|
Song D, Liu H, Wu J, Gao X, Hao J, Fan D. Insights into the role of ERp57 in cancer. J Cancer 2021; 12:2456-2464. [PMID: 33758622 PMCID: PMC7974888 DOI: 10.7150/jca.48707] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 02/04/2021] [Indexed: 12/28/2022] Open
Abstract
Endoplasmic reticulum resident protein 57 (ERp57) has a molecular weight of 57 kDa, belongs to the protein disulfide-isomerase (PDI) family, and is primarily located in the endoplasmic reticulum (ER). ERp57 functions in the quality control of nascent synthesized glycoproteins, participates in major histocompatibility complex (MHC) class I molecule assembly, regulates immune responses, maintains immunogenic cell death (ICD), regulates the unfolded protein response (UPR), functions as a 1,25-dihydroxy vitamin D3 (1,25(OH)2D3) receptor, regulates the NF-κB and STAT3 pathways, and participates in DNA repair processes and cytoskeletal remodeling. Recent studies have reported ERp57 overexpression in various human cancers, and altered expression and aberrant functionality of ERp57 are associated with cancer growth and progression and changes in the chemosensitivity of cancers. ERp57 may become a potential biomarker and therapeutic target to combat cancer development and chemoresistance. Here, we summarize the available knowledge of the role of ERp57 in cancer and the underlying mechanisms.
Collapse
Affiliation(s)
- Danyang Song
- Department of Gastroenterology, Beijing Chaoyang Hospital, Capital Medical University, Beijing 100020, China
| | - Hao Liu
- State key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases and Xijing Hospital of Digestive Diseases, Air Force Military Medical University, Xi'an 710032, China
| | - Jian Wu
- State key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases and Xijing Hospital of Digestive Diseases, Air Force Military Medical University, Xi'an 710032, China
| | - Xiaoliang Gao
- State key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases and Xijing Hospital of Digestive Diseases, Air Force Military Medical University, Xi'an 710032, China
| | - Jianyu Hao
- Department of Gastroenterology, Beijing Chaoyang Hospital, Capital Medical University, Beijing 100020, China
| | - Daiming Fan
- Department of Gastroenterology, Beijing Chaoyang Hospital, Capital Medical University, Beijing 100020, China
- State key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases and Xijing Hospital of Digestive Diseases, Air Force Military Medical University, Xi'an 710032, China
| |
Collapse
|
90
|
HLA class I loss in colorectal cancer: implications for immune escape and immunotherapy. Cell Mol Immunol 2021; 18:556-565. [PMID: 33473191 PMCID: PMC8027055 DOI: 10.1038/s41423-021-00634-7] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 12/23/2020] [Indexed: 01/30/2023] Open
Abstract
T cell-mediated immune therapies have emerged as a promising treatment modality in different malignancies including colorectal cancer (CRC). However, only a fraction of patients currently respond to treatment. Understanding the lack of responses and finding biomarkers with predictive value is of great importance. There is evidence that CRC is a heterogeneous disease and several classification systems have been proposed that are based on genomic instability, immune cell infiltration, stromal content and molecular subtypes of gene expression. Human leukocyte antigen class I (HLA-I) plays a pivotal role in presenting processed antigens to T lymphocytes, including tumour antigens. These molecules are frequently lost in different types of cancers, including CRC, resulting in tumour immune escape from cytotoxic T lymphocytes during the natural history of cancer development. The aim of this review is to (i) summarize the prevalence and molecular mechanisms behind HLA-I loss in CRC, (ii) discuss HLA-I expression/loss in the context of the newly identified CRC molecular subtypes, (iii) analyze the HLA-I phenotypes of CRC metastases disseminated via blood or the lymphatic system, (iv) discuss strategies to recover/circumvent HLA-I expression/loss and finally (v) review the role of HLA class II (HLA-II) in CRC prognosis.
Collapse
|
91
|
Abstract
Changes in glycosylation on proteins or lipids are one of the hallmarks of tumorigenesis. In many cases, it is still not understood how glycan information is translated into biological function. In this review, we discuss at the example of specific cancer-related glycoproteins how their endocytic uptake into eukaryotic cells is tuned by carbohydrate modifications. For this, we not only focus on overall uptake rates, but also illustrate how different uptake processes-dependent or not on the conventional clathrin machinery-are used under given glycosylation conditions. Furthermore, we discuss the role of certain sugar-binding proteins, termed galectins, to tune glycoprotein uptake by inducing their crosslinking into lattices, or by co-clustering them with glycolipids into raft-type membrane nanodomains from which the so-called clathrin-independent carriers (CLICs) are formed for glycoprotein internalization into cells. The latter process has been termed glycolipid-lectin (GL-Lect) hypothesis, which operates in a complementary manner to the clathrin pathway and galectin lattices.
Collapse
Affiliation(s)
- Ludger Johannes
- Cellular and Chemical Biology Unit, INSERM U1143, CNRS UMR3666, Institut Curie, PSL Research University, 26 rue d'Ulm, 75248, Paris Cedex 05, France.
| | - Anne Billet
- Cellular and Chemical Biology Unit, INSERM U1143, CNRS UMR3666, Institut Curie, PSL Research University, 26 rue d'Ulm, 75248, Paris Cedex 05, France.,Université de Paris, F-75005, Paris, France
| |
Collapse
|
92
|
Mpakali A, Stratikos E. The Role of Antigen Processing and Presentation in Cancer and the Efficacy of Immune Checkpoint Inhibitor Immunotherapy. Cancers (Basel) 2021; 13:E134. [PMID: 33406696 PMCID: PMC7796214 DOI: 10.3390/cancers13010134] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 12/28/2020] [Accepted: 12/30/2020] [Indexed: 02/07/2023] Open
Abstract
Recent clinical successes of cancer immunotherapy using immune checkpoint inhibitors (ICIs) are rapidly changing the landscape of cancer treatment. Regardless of initial impressive clinical results though, the therapeutic benefit of ICIs appears to be limited to a subset of patients and tumor types. Recent analyses have revealed that the potency of ICI therapies depends on the efficient presentation of tumor-specific antigens by cancer cells and professional antigen presenting cells. Here, we review current knowledge on the role of antigen presentation in cancer. We focus on intracellular antigen processing and presentation by Major Histocompatibility class I (MHCI) molecules and how it can affect cancer immune evasion. Finally, we discuss the pharmacological tractability of manipulating intracellular antigen processing as a complementary approach to enhance tumor immunogenicity and the effectiveness of ICI immunotherapy.
Collapse
Affiliation(s)
- Anastasia Mpakali
- National Centre for Scientific Research Demokritos, Agia Paraskevi, 15341 Athens, Greece
| | - Efstratios Stratikos
- National Centre for Scientific Research Demokritos, Agia Paraskevi, 15341 Athens, Greece
- Laboratory of Biochemistry, Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zographou, 15784 Athens, Greece
| |
Collapse
|
93
|
Mi K, Chen F, Qian Z, Chen J, Lv D, Zhang C, Xu Y, Wang H, Zhang Y, Jiang Y, Shang D. Characterizing heterogeneity of non-small cell lung tumour microenvironment to identify signature prognostic genes. J Cell Mol Med 2020; 24:14608-14618. [PMID: 33184998 PMCID: PMC7754023 DOI: 10.1111/jcmm.16092] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 10/27/2020] [Accepted: 10/28/2020] [Indexed: 12/24/2022] Open
Abstract
Growing evidence has highlighted the immune response as an important feature of carcinogenesis and therapeutic efficacy in non‐small cell lung cancer (NSCLC). This study focused on the characterization of immune infiltration profiling in patients with NSCLC and its correlation with survival outcome. All TCGA samples were divided into three heterogeneous clusters based on immune cell profiles: cluster 1 ('low infiltration' cluster), cluster 2 ('heterogeneous infiltration' cluster) and cluster 3 ('high infiltration' cluster). The immune cells were responsible for a significantly favourable prognosis for the 'high infiltration' community. Cluster 1 had the lowest cytotoxic activity, tumour‐infiltrating lymphocytes and interferon‐gamma (IFN‐γ), as well as immune checkpoint molecules expressions. In addition, MHC‐I and immune co‐stimulator were also found to have lower cluster 1 expressions, indicating a possible immune escape mechanism. A total of 43 differentially expressed genes (DEGs) that overlapped among the groups were determined based on three clusters. Finally, based on a univariate Cox regression model, prognostic immune‐related genes were identified and combined to construct a risk score model able to predict overall survival (OS) rates in the validation datasets.
Collapse
Affiliation(s)
- Kai Mi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Fuhui Chen
- Department of Respiratory, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Zhipeng Qian
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Jing Chen
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Dongxu Lv
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Chunlong Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yanjun Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Hongguang Wang
- School of Civil Engineering, Northeast Forestry University, Harbin, China.,Key Laboratory of Bio-based Material Science and Technology (Ministry of Education), School of Material Science and Engineering, Northeast Forestry University, Harbin, China
| | - Yuepeng Zhang
- Department of Respiratory, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yanan Jiang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.,Department of Pharmacology (State-Province Key Laboratories of Biomedicine- Pharmaceutics of China, Key Laboratory of Cardiovascular Research, Ministry of Education), College of Pharmacy, Harbin Medical University, Harbin, China.,Translational Medicine Research and Cooperation Center of Northern China, Heilongjiang Academy of Medical Sciences, Harbin, China
| | - Desi Shang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| |
Collapse
|
94
|
Shaffer BC, Hsu KC. Selection of allogeneic hematopoietic cell transplant donors to optimize natural killer cell alloreactivity. Semin Hematol 2020; 57:167-174. [PMID: 33256909 DOI: 10.1053/j.seminhematol.2020.10.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 10/08/2020] [Accepted: 10/22/2020] [Indexed: 12/26/2022]
Abstract
Natural killer (NK) cells are potent mediators of the graft versus leukemia phenomenon critical to the success of allogeneic hematopoietic cell transplantation. Central to calibrating NK effector function via their interaction with class I human leukocyte antigens are the numerous inhibitory killer Ig-like receptors (KIR). The KIR receptors are encoded by a family of polymorphic genes, whose expression is largely stochastic and uninfluenced by human leukocyte antigens genotype. These features provide the opportunity to select hematopoietic cell donors with favorable KIR genotypes that confer enhanced protection from relapse via NK-mediated graft versus leukemia. Over the last 2 decades, a large body of work has emerged examining the use of KIR genotyping to stratify potential donors based on anticipated NK alloreactivity. Overall, these results support KIR-based donor selection for patients undergoing allogeneic hematopoietic cell transplantation for a diagnosis of acute myelogenous leukemia. Despite this, the underlying factors that control NK cell responsiveness are not completely understood, and opportunities remain to refine donor selection using NK cell receptor genotyping. In this review, we will summarize the relevant findings with respect to KIR genotyping as a selection parameter for allogeneic hematopoietic cell donors and address practical considerations with respect to KIR-based selection of donors for patients with myeloid neoplasia.
Collapse
Affiliation(s)
- Brian C Shaffer
- Adult Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY; Department of Medicine, Weill Cornell School of Medicine, New York, NY
| | - Katharine C Hsu
- Adult Bone Marrow Transplant Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY; Department of Medicine, Weill Cornell School of Medicine, New York, NY; Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY.
| |
Collapse
|
95
|
Sabbatino F, Liguori L, Polcaro G, Salvato I, Caramori G, Salzano FA, Casolaro V, Stellato C, Dal Col J, Pepe S. Role of Human Leukocyte Antigen System as A Predictive Biomarker for Checkpoint-Based Immunotherapy in Cancer Patients. Int J Mol Sci 2020; 21:ijms21197295. [PMID: 33023239 PMCID: PMC7582904 DOI: 10.3390/ijms21197295] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/26/2020] [Accepted: 09/29/2020] [Indexed: 12/11/2022] Open
Abstract
Recent advances in cancer immunotherapy have clearly shown that checkpoint-based immunotherapy is effective in a small subgroup of cancer patients. However, no effective predictive biomarker has been identified so far. The major histocompatibility complex, better known in humans as human leukocyte antigen (HLA), is a very polymorphic gene complex consisting of more than 200 genes. It has a crucial role in activating an appropriate host immune response against pathogens and tumor cells by discriminating self and non-self peptides. Several lines of evidence have shown that down-regulation of expression of HLA class I antigen derived peptide complexes by cancer cells is a mechanism of tumor immune escape and is often associated to poor prognosis in cancer patients. In addition, it has also been shown that HLA class I and II antigen expression, as well as defects in the antigen processing machinery complex, may predict tumor responses in cancer immunotherapy. Nevertheless, the role of HLA in predicting tumor responses to checkpoint-based immunotherapy is still debated. In this review, firstly, we will describe the structure and function of the HLA system. Secondly, we will summarize the HLA defects and their clinical significance in cancer patients. Thirdly, we will review the potential role of the HLA as a predictive biomarker for checkpoint-based immunotherapy in cancer patients. Lastly, we will discuss the potential strategies that may restore HLA function to implement novel therapeutic strategies in cancer patients.
Collapse
Affiliation(s)
- Francesco Sabbatino
- Department of Medicine, Surgery and Dentistry ’Scuola Medica Salernitana’, University of Salerno, 84081 Baronissi, Salerno, Italy; (F.S.); (G.P.); (I.S.); (F.A.S.); (V.C.); (C.S.); (S.P.)
- Oncology Unit, AOU San Giovanni di Dio e Ruggi D’Aragona, 84131 Salerno, Italy
| | - Luigi Liguori
- Department of Clinical Medicine and Surgery, University of Naples “Federico II”, 80131 Naples, Italy;
| | - Giovanna Polcaro
- Department of Medicine, Surgery and Dentistry ’Scuola Medica Salernitana’, University of Salerno, 84081 Baronissi, Salerno, Italy; (F.S.); (G.P.); (I.S.); (F.A.S.); (V.C.); (C.S.); (S.P.)
| | - Ilaria Salvato
- Department of Medicine, Surgery and Dentistry ’Scuola Medica Salernitana’, University of Salerno, 84081 Baronissi, Salerno, Italy; (F.S.); (G.P.); (I.S.); (F.A.S.); (V.C.); (C.S.); (S.P.)
- Pulmonary Unit, Department of Biomedical Sciences, Dentistry, Morphological and Functional Imaging (BIOMORF), University of Messina, 98125 Messina, Italy;
| | - Gaetano Caramori
- Pulmonary Unit, Department of Biomedical Sciences, Dentistry, Morphological and Functional Imaging (BIOMORF), University of Messina, 98125 Messina, Italy;
| | - Francesco A. Salzano
- Department of Medicine, Surgery and Dentistry ’Scuola Medica Salernitana’, University of Salerno, 84081 Baronissi, Salerno, Italy; (F.S.); (G.P.); (I.S.); (F.A.S.); (V.C.); (C.S.); (S.P.)
| | - Vincenzo Casolaro
- Department of Medicine, Surgery and Dentistry ’Scuola Medica Salernitana’, University of Salerno, 84081 Baronissi, Salerno, Italy; (F.S.); (G.P.); (I.S.); (F.A.S.); (V.C.); (C.S.); (S.P.)
| | - Cristiana Stellato
- Department of Medicine, Surgery and Dentistry ’Scuola Medica Salernitana’, University of Salerno, 84081 Baronissi, Salerno, Italy; (F.S.); (G.P.); (I.S.); (F.A.S.); (V.C.); (C.S.); (S.P.)
| | - Jessica Dal Col
- Department of Medicine, Surgery and Dentistry ’Scuola Medica Salernitana’, University of Salerno, 84081 Baronissi, Salerno, Italy; (F.S.); (G.P.); (I.S.); (F.A.S.); (V.C.); (C.S.); (S.P.)
- Correspondence: ; Tel.: +39-08996-5210
| | - Stefano Pepe
- Department of Medicine, Surgery and Dentistry ’Scuola Medica Salernitana’, University of Salerno, 84081 Baronissi, Salerno, Italy; (F.S.); (G.P.); (I.S.); (F.A.S.); (V.C.); (C.S.); (S.P.)
- Oncology Unit, AOU San Giovanni di Dio e Ruggi D’Aragona, 84131 Salerno, Italy
| |
Collapse
|
96
|
Wu W, Chen Y, Huang L, Li W, Tao C, Shen H. Point mutation screening of tumor neoantigens and peptide-induced specific cytotoxic T lymphocytes using The Cancer Genome Atlas database. Oncol Lett 2020; 20:123. [PMID: 32934692 PMCID: PMC7471748 DOI: 10.3892/ol.2020.11986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 05/18/2020] [Indexed: 12/30/2022] Open
Abstract
The aim of the present study was to use The Cancer Genome Atlas (TCGA) database to identify tumor neoantigens, combined with a bioinformatics analysis to design and analyze antigen epitope peptides. Epitopes were screened using immunogenicity tests to identify the ideal epitope peptides to target tumor neoantigens, which can specifically activate the immune response of T cells. The high-frequency mutation loci (top 10) of colorectal, lung and liver cancer genes were screened using TCGA database. The antigenic epitope peptides with high affinity for major histocompatibility complex molecules were selected and synthesized using computer prediction algorithms, and were subsequently detected using flow cytometry. The cytotoxicity of specific cytotoxic T lymphocytes (CTLs) on peptide-loaded T2 cells was initially verified using interferon IFN-γ detection and a calcein-acetoxymethyl (Cal-AM) release assay. Tumor cell lines expressing point mutations in KRAS, TP53 and CTNNB1 genes were constructed respectively, and the cytotoxicity of peptide-induced specific CTLs on wild-type and mutant tumor cells was verified using a Cal-AM release assay and carboxyfluorescein succinimidyl ester-propidium iodide staining. The high-frequency gene mutation loci of KRAS proto-oncogene (KRAS) G12V, tumor protein p53 (TP53) R158L and catenin β1 (CTNNB1) K335I were identified in TCGA database. A total of 3 groups of wild-type and mutant peptides were screened using a peptide prediction algorithm. The CTNNB1 group had a strong affinity for the human leukocyte antigen-A2 molecule, as determined using flow cytometry. The IFN-γ secretion of specific CTLs in the CTNNB1 group was the highest, followed by the TP53 and the KRAS groups. The killing rate of mutant peptide-induced specific CTLs on peptide-loaded T2 cells in the CTNNB1 group was higher compared with that observed in the other groups. The killing rate of specific CTLs induced by mutant peptides present on tumor cells was higher compared with that induced by wild-type peptides. However, when compared with the TP53 and KRAS groups, specific CTLs induced by mutant peptides in the CTNNB1 group had more potent cytotoxicity towards mutant and wild-type tumor cells. In conclusion, point mutant tumor neoantigens screened in the three groups improved the cytotoxicity of specific T cells, and the mutant peptides in the CTNNB1 group were more prominent, indicating that they may activate the cellular immune response more readily.
Collapse
Affiliation(s)
- Wanwen Wu
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong 510006, P.R. China
| | - Ying Chen
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong 510006, P.R. China
| | - Lan Huang
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong 510006, P.R. China
| | - Wenjian Li
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong 510006, P.R. China
| | - Changli Tao
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong 510006, P.R. China
| | - Han Shen
- Guangdong Province Key Laboratory for Biotechnology Drug Candidates, School of Life Sciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, Guangdong 510006, P.R. China
| |
Collapse
|
97
|
Lazaridou MF, Massa C, Handke D, Mueller A, Friedrich M, Subbarayan K, Tretbar S, Dummer R, Koelblinger P, Seliger B. Identification of microRNAs Targeting the Transporter Associated with Antigen Processing TAP1 in Melanoma. J Clin Med 2020; 9:jcm9092690. [PMID: 32825219 PMCID: PMC7563967 DOI: 10.3390/jcm9092690] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/12/2020] [Accepted: 08/14/2020] [Indexed: 12/15/2022] Open
Abstract
The underlying molecular mechanisms of the aberrant expression of components of the HLA class I antigen processing and presentation machinery (APM) in tumors leading to evasion from T cell-mediated immune surveillance could be due to posttranscriptional regulation mediated by microRNAs (miRs). So far, some miRs controlling the expression of different APM components have been identified. Using in silico analysis and an miR enrichment protocol in combination with small RNA sequencing, miR-26b-5p and miR-21-3p were postulated to target the 3′ untranslated region (UTR) of the peptide transporter TAP1, which was confirmed by high free binding energy and dual luciferase reporter assays. Overexpression of miR-26b-5p and miR-21-3p in melanoma cells downregulated the TAP1 protein and reduced expression of HLA class I cell surface antigens, which could be reverted by miR inhibitors. Moreover, miR-26b-5p overexpression induced a decreased T cell recognition. Furthermore, an inverse expression of miR-26b-5p and miR-21-3p with TAP1 was found in primary melanoma lesions, which was linked with the frequency of CD8+ T cell infiltration. Thus, miR-26-5p and miR-21-3p are involved in the HLA class I-mediated immune escape and might be used as biomarkers or therapeutic targets for HLA class Ilow melanoma cells.
Collapse
Affiliation(s)
- Maria-Filothei Lazaridou
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Magdeburger Str. 2, 06112 Halle, Germany; (M.-F.L.); (C.M.); (D.H.); (A.M.); (M.F.); (K.S.); (S.T.)
| | - Chiara Massa
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Magdeburger Str. 2, 06112 Halle, Germany; (M.-F.L.); (C.M.); (D.H.); (A.M.); (M.F.); (K.S.); (S.T.)
| | - Diana Handke
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Magdeburger Str. 2, 06112 Halle, Germany; (M.-F.L.); (C.M.); (D.H.); (A.M.); (M.F.); (K.S.); (S.T.)
| | - Anja Mueller
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Magdeburger Str. 2, 06112 Halle, Germany; (M.-F.L.); (C.M.); (D.H.); (A.M.); (M.F.); (K.S.); (S.T.)
| | - Michael Friedrich
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Magdeburger Str. 2, 06112 Halle, Germany; (M.-F.L.); (C.M.); (D.H.); (A.M.); (M.F.); (K.S.); (S.T.)
| | - Karthikeyan Subbarayan
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Magdeburger Str. 2, 06112 Halle, Germany; (M.-F.L.); (C.M.); (D.H.); (A.M.); (M.F.); (K.S.); (S.T.)
| | - Sandy Tretbar
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Magdeburger Str. 2, 06112 Halle, Germany; (M.-F.L.); (C.M.); (D.H.); (A.M.); (M.F.); (K.S.); (S.T.)
| | - Reinhard Dummer
- Institute of Dermatology, University Hospital Zürich, 8091 Zürich, Switzerland;
| | - Peter Koelblinger
- Department of Dermatology and Allergology, University Hospital Salzburg, 5020 Salzburg, Austria;
| | - Barbara Seliger
- Institute of Medical Immunology, Martin Luther University Halle-Wittenberg, Magdeburger Str. 2, 06112 Halle, Germany; (M.-F.L.); (C.M.); (D.H.); (A.M.); (M.F.); (K.S.); (S.T.)
- Correspondence: ; Tel.: +49-(0)-345-557-4054
| |
Collapse
|
98
|
Xu HH, Yan WH, Lin A. The Role of HLA-G in Human Papillomavirus Infections and Cervical Carcinogenesis. Front Immunol 2020; 11:1349. [PMID: 32670296 PMCID: PMC7330167 DOI: 10.3389/fimmu.2020.01349] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 05/27/2020] [Indexed: 12/24/2022] Open
Abstract
Human leukocyte antigen (HLA)-G, a non-classical HLA-class I molecule, has a low polymorphism frequency, restricted tissue distribution and immunoinhibitory property. HLA-G expression in tumor cells and cells chronically infected with virus may enable them to escape from host immune surveillance. It is well-known that the HLA-G molecule is a novel biomarker and potential therapeutic target that is relevant in various types of cancers, but its role in cervical cancer has not been fully explored. In this review, we aim to summarize and discuss the immunologic role of the HLA-G molecule in the context of HPV infections and the process of cervical cancer carcinogenesis. A better understanding of the potential impact of HLA-G on the clinical course of persistent HPV infections, cervical epithelial cell transformation, tumor growth, recurrence and metastasis is needed to identify a novel diagnostic/prognostic biomarker for cervical cancer, which is critical for cervical cancer risk screening. In addition, it is also necessary to identify HLA-G-driven immune mechanisms involved in the interactions between host and virus to explore novel immunotherapy strategies that target HLA-G/immunoglobulin-like transcript (ILT) immune checkpoints.
Collapse
Affiliation(s)
- Hui-Hui Xu
- Medical Research Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, China
| | - Wei-Hua Yan
- Medical Research Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, China
| | - Aifen Lin
- Biological Resource Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, China
| |
Collapse
|
99
|
Magnadóttir B, Uysal-Onganer P, Kraev I, Svansson V, Skírnisson K, Lange S. Deiminated proteins and extracellular vesicles as novel biomarkers in pinnipeds: Grey seal (Halichoerus gryptus) and harbour seal (Phoca vitulina). Biochimie 2020; 171-172:79-90. [PMID: 32105816 DOI: 10.1016/j.biochi.2020.02.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 02/21/2020] [Indexed: 12/16/2022]
Abstract
Peptidylarginine deiminases (PADs) are phylogenetically conserved calcium-dependent enzymes which post-translationally convert arginine into citrulline in target proteins in an irreversible manner, leading to functional and structural changes in target proteins. Protein deimination can cause the generation of neo-epitopes, affect gene regulation and also allow for protein moonlighting and therefore facilitate multifaceted functions of the same protein. PADs are furthermore a key regulator of cellular release of extracellular vesicle (EVs), which are found in most body fluids and participate in cellular communication via transfer of cargo proteins and genetic material. In this study, post-translationally deiminated proteins and EVs were assessed in sera of two seal species, grey seal and harbour seal. We report a poly-dispersed population of serum-EVs, which were positive for phylogenetically conserved EV-specific markers and characterised by transmission electron microscopy. A number of deiminated proteins critical for immune and metabolic functions were identified in the seal sera and varied somewhat between the two species under study, while some targets were in common. EV profiles of the seal sera further revealed that key microRNAs for inflammation, immunity and hypoxia also vary between the two species. Protein deimination and EVs profiles may be useful biomarkers for assessing health status of sea mammals, which face environmental challenges, including opportunistic infection, pollution and shifting habitat due to global warming.
Collapse
Affiliation(s)
- Bergljót Magnadóttir
- Institute for Experimental Pathology, University of Iceland, Keldur V. Vesturlandsveg, 112 Reykjavik, Iceland.
| | - Pinar Uysal-Onganer
- Cancer Research Group, School of Life Sciences, University of Westminster, London, W1W 6UW, UK.
| | - Igor Kraev
- Electron Microscopy Suite, Faculty of Science, Technology, Engineering and Mathematics, Open University, Milton Keynes, MK7 6AA, UK.
| | - Vilhjálmur Svansson
- Institute for Experimental Pathology, University of Iceland, Keldur V. Vesturlandsveg, 112 Reykjavik, Iceland.
| | - Karl Skírnisson
- Institute for Experimental Pathology, University of Iceland, Keldur V. Vesturlandsveg, 112 Reykjavik, Iceland.
| | - Sigrun Lange
- Tissue Architecture and Regeneration Research Group, School of Life Sciences, University of Westminster, London, W1W 6UW, UK.
| |
Collapse
|