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Ye D, Zhou S, Dai X, Xu H, Tang Q, Huang H, Bi F. Targeting the MHC-I endosomal-lysosomal trafficking pathway in cancer: From mechanism to immunotherapy. Biochim Biophys Acta Rev Cancer 2024; 1879:189161. [PMID: 39096977 DOI: 10.1016/j.bbcan.2024.189161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 07/21/2024] [Accepted: 07/23/2024] [Indexed: 08/05/2024]
Abstract
Immune checkpoint blockade (ICB) therapy has achieved broad applicability and durable clinical responses across cancer types. However, the overall response rate remains suboptimal because some patients do not respond or develop drug resistance. The low infiltration of CD8+ cytotoxic T cells (CTLs) in the tumor microenvironment due to insufficient antigen presentation is closely related to the innate resistance to ICB. The duration and spatial distribution of major histocompatibility complex class I (MHC-I) expression on the cell surface is critical for the efficient presentation of endogenous tumor antigens and subsequent recognition and clearance by CTLs. Tumor cells reduce the surface expression of MHC-I via multiple mechanisms to impair antigen presentation pathways and evade immunity and/or develop resistance to ICB therapy. As an increasing number of studies have focused on membrane MHC-I trafficking and degradation in tumor cells, which may impact the effectiveness of tumor immunotherapy. It is necessary to summarize the mechanism regulating membrane MHC-I translocation into the cytoplasm and degradation via the lysosome. We reviewed recent advances in the understanding of endosomal-lysosomal MHC-I transport and highlighted the means exploited by tumor cells to evade detection and clearance by CTLs. We also summarized new therapeutic strategies targeting these pathways to enhance classical ICB treatment and provide new avenues for optimizing cancer immunotherapy.
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Affiliation(s)
- Di Ye
- Division of Abdominal Cancer, Department of Medical Oncology, Cancer Center and Laboratory of Molecular Targeted Therapy in Oncology, West China Hospital, Sichuan University, Chengdu, Sichuan Province 610041, China
| | - Shuang Zhou
- Division of Abdominal Cancer, Department of Medical Oncology, Cancer Center and Laboratory of Molecular Targeted Therapy in Oncology, West China Hospital, Sichuan University, Chengdu, Sichuan Province 610041, China
| | - Xinyu Dai
- Division of Abdominal Cancer, Department of Medical Oncology, Cancer Center and Laboratory of Molecular Targeted Therapy in Oncology, West China Hospital, Sichuan University, Chengdu, Sichuan Province 610041, China
| | - Huanji Xu
- Division of Abdominal Cancer, Department of Medical Oncology, Cancer Center and Laboratory of Molecular Targeted Therapy in Oncology, West China Hospital, Sichuan University, Chengdu, Sichuan Province 610041, China
| | - Qiulin Tang
- Division of Abdominal Cancer, Department of Medical Oncology, Cancer Center and Laboratory of Molecular Targeted Therapy in Oncology, West China Hospital, Sichuan University, Chengdu, Sichuan Province 610041, China
| | - Huixi Huang
- Division of Abdominal Cancer, Department of Medical Oncology, Cancer Center and Laboratory of Molecular Targeted Therapy in Oncology, West China Hospital, Sichuan University, Chengdu, Sichuan Province 610041, China
| | - Feng Bi
- Division of Abdominal Cancer, Department of Medical Oncology, Cancer Center and Laboratory of Molecular Targeted Therapy in Oncology, West China Hospital, Sichuan University, Chengdu, Sichuan Province 610041, China.
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2
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Efe G, Rustgi AK, Prives C. p53 at the crossroads of tumor immunity. NATURE CANCER 2024; 5:983-995. [PMID: 39009816 DOI: 10.1038/s43018-024-00796-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 06/03/2024] [Indexed: 07/17/2024]
Abstract
The p53 tumor suppressor protein has a plethora of cell-intrinsic functions and consequences that impact diverse cell types and tissues. Recent studies are beginning to unravel how wild-type and mutant p53 work in distinct ways to modulate tumor immunity. This sets up a disequilibrium between tumor immunosurveillance and escape therefrom. The ability to exploit this emerging knowledge for translational approaches may shape immunotherapy and targeted therapeutics in the future, especially in combinatorial settings.
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Affiliation(s)
- Gizem Efe
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA
- Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | - Anil K Rustgi
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA.
- Vagelos College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA.
- Division of Digestive and Liver Diseases, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA.
| | - Carol Prives
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY, USA.
- Department of Biological Sciences, Columbia University, New York, NY, USA.
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3
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Xian W, Asad M, Wu S, Bai Z, Li F, Lu J, Zu G, Brintnell E, Chen H, Mao Y, Zhou G, Liao B, Wu J, Wang E, You L. Distinct immune escape and microenvironment between RG-like and pri-OPC-like glioma revealed by single-cell RNA-seq analysis. Front Med 2024; 18:147-168. [PMID: 37955814 DOI: 10.1007/s11684-023-1017-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 06/24/2023] [Indexed: 11/14/2023]
Abstract
The association of neurogenesis and gliogenesis with glioma remains unclear. By conducting single-cell RNA-seq analyses on 26 gliomas, we reported their classification into primitive oligodendrocyte precursor cell (pri-OPC)-like and radial glia (RG)-like tumors and validated it in a public cohort and TCGA glioma. The RG-like tumors exhibited wild-type isocitrate dehydrogenase and tended to carry EGFR mutations, and the pri-OPC-like ones were prone to carrying TP53 mutations. Tumor subclones only in pri-OPC-like tumors showed substantially down-regulated MHC-I genes, suggesting their distinct immune evasion programs. Furthermore, the two subgroups appeared to extensively modulate glioma-infiltrating lymphocytes in distinct manners. Some specific genes not expressed in normal immune cells were found in glioma-infiltrating lymphocytes. For example, glial/glioma stem cell markers OLIG1/PTPRZ1 and B cell-specific receptors IGLC2/IGKC were expressed in pri-OPC-like and RG-like glioma-infiltrating lymphocytes, respectively. Their expression was positively correlated with those of immune checkpoint genes (e.g., LGALS33) and poor survivals as validated by the increased expression of LGALS3 upon IGKC overexpression in Jurkat cells. This finding indicated a potential inhibitory role in tumor-infiltrating lymphocytes and could provide a new way of cancer immune evasion.
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Affiliation(s)
- Weiwei Xian
- Department of Human Anatomy & Histoembryology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Mohammad Asad
- Cumming School of Medicine, University of Calgary, Calgary, Alberta, T2N 4N1, Canada
| | - Shuai Wu
- Glioma Surgery Division, Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Zhixin Bai
- Department of Human Anatomy & Histoembryology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Fengjiao Li
- Department of Human Anatomy & Histoembryology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Junfeng Lu
- Glioma Surgery Division, Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Gaoyu Zu
- Department of Human Anatomy & Histoembryology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Erin Brintnell
- Cumming School of Medicine, University of Calgary, Calgary, Alberta, T2N 4N1, Canada
| | - Hong Chen
- Department of Pathology, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Ying Mao
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Guomin Zhou
- Department of Human Anatomy & Histoembryology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
- Shanghai Key Laboratory of Medical Imaging Computing and Computer Assisted Intervention, Fudan University, Shanghai, 200040, China
| | - Bo Liao
- School of Mathematics and Statistics, Hainan Normal University, Haikou, 570100, China
| | - Jinsong Wu
- Glioma Surgery Division, Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, 200040, China.
| | - Edwin Wang
- Cumming School of Medicine, University of Calgary, Calgary, Alberta, T2N 4N1, Canada.
| | - Linya You
- Department of Human Anatomy & Histoembryology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China.
- Shanghai Key Laboratory of Medical Imaging Computing and Computer Assisted Intervention, Fudan University, Shanghai, 200040, China.
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4
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A novel defined risk signature of endoplasmic reticulum stress-related genes for predicting the prognosis and immune infiltration status of ovarian cancer. J Zhejiang Univ Sci B 2023; 24:64-77. [PMID: 36632751 PMCID: PMC9837372 DOI: 10.1631/jzus.b2200272] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Endoplasmic reticulum (ER) stress, as an emerging hallmark feature of cancer, has a considerable impact on cell proliferation, metastasis, invasion, and chemotherapy resistance. Ovarian cancer (OvCa) is one of the leading causes of cancer-related mortality across the world due to the late stage of disease at diagnosis. Studies have explored the influence of ER stress on OvCa in recent years, while the predictive role of ER stress-related genes in OvCa prognosis remains unexplored. Here, we enrolled 552 cases of ER stress-related genes involved in OvCa from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) cohorts for the screening of prognosis-related genes. The least absolute shrinkage and selection operator (LASSO) regression was applied to establish an ER stress-related risk signature based on the TCGA cohort. A seven-gene signature revealed a favorable predictive efficacy for the TCGA, International Cancer Genome Consortium (ICGC), and another GEO cohort (P<0.001, P<0.001, and P=0.04, respectively). Moreover, functional annotation indicated that this signature was enriched in cellular response and senescence, cytokines interaction, as well as multiple immune-associated terms. The immune infiltration profiles further delineated an immunologic unresponsive status in the high-risk group. In conclusion, ER stress-related genes are vital factors predicting the prognosis of OvCa, and possess great application potential in the clinic.
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Dhall A, Patiyal S, Raghava GPS. HLAncPred: a method for predicting promiscuous non-classical HLA binding sites. Brief Bioinform 2022; 23:6587168. [PMID: 35580839 DOI: 10.1093/bib/bbac192] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 03/23/2022] [Accepted: 04/27/2022] [Indexed: 12/25/2022] Open
Abstract
Human leukocyte antigens (HLA) regulate various innate and adaptive immune responses and play a crucial immunomodulatory role. Recent studies revealed that non-classical HLA-(HLA-E & HLA-G) based immunotherapies have many advantages over traditional HLA-based immunotherapy, particularly against cancer and COVID-19 infection. In the last two decades, several methods have been developed to predict the binders of classical HLA alleles. In contrast, limited attempts have been made to develop methods for predicting non-classical HLA binding peptides, due to the scarcity of sufficient experimental data. Of note, in order to facilitate the scientific community, we have developed an artificial intelligence-based method for predicting binders of class-Ib HLA alleles. All the models were trained and tested on experimentally validated data obtained from the recent release of IEDB. The machine learning models achieved more than 0.98 AUC for HLA-G alleles on validation dataset. Similarly, our models achieved the highest AUC of 0.96 and 0.94 on the validation dataset for HLA-E*01:01 and HLA-E*01:03, respectively. We have summarized the models developed in the past for non-classical HLA and validated the performance with the models developed in this study. Moreover, to facilitate the community, we have utilized our tool for predicting the potential non-classical HLA binding peptides in the spike protein of different variants of virus causing COVID-19, including Omicron (B.1.1.529). One of the major challenges in the field of immunotherapy is to identify the promiscuous binders or antigenic regions that can bind to a large number of HLA alleles. To predict the promiscuous binders for the non-classical HLA alleles, we developed a web server HLAncPred (https://webs.iiitd.edu.in/raghava/hlancpred) and standalone package.
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Affiliation(s)
- Anjali Dhall
- Department of Computational Biology, Indraprastha Institute of Information Technology, Okhla Phase 3, New Delhi-110020, India
| | - Sumeet Patiyal
- Department of Computational Biology, Indraprastha Institute of Information Technology, Okhla Phase 3, New Delhi-110020, India
| | - Gajendra P S Raghava
- Department of Computational Biology, Indraprastha Institute of Information Technology, Okhla Phase 3, New Delhi-110020, India
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6
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Feng J. The p53 Pathway Related Genes Predict the Prognosis of Colon Cancer. Int J Gen Med 2022; 15:169-177. [PMID: 35023955 PMCID: PMC8747760 DOI: 10.2147/ijgm.s346280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 12/22/2021] [Indexed: 12/14/2022] Open
Abstract
Background Colon cancer is a common gastrointestinal malignancy. This study aimed to explore the relationship between p53 pathway-related genes and prognosis of colon cancer. Methods The mRNA datasets of colon cancer and adjacent tissues were downloaded from The Cancer Genome Atlas (TCGA) database, and the differential expression of genes in two groups was analyzed. Then, P53 pathway-related genes were intersected with differentially expressed genes (DEGs) to obtain P53 pathway-related differentially expressed genes. Then, overall survival (OS), disease-specific survival (DSS), and progression-free survival (PFS) in clusters were compared by consistent cluster analysis. Univariate and multivariate Cox regression analysis of DEGs was performed to obtain survival-related DEGs. Risk scores were calculated for each sample based on survival-related DEGs, and patients were divided into high/low risk scores. Prognostic differences, tumor immune cell infiltration levels, and immune pathway activation status were compared between the two groups. Results We identified 28 DEGs and two clusters. There are significant differences in PFS between the two clusters (P=0.011), and no significant difference between OS and DSS. We obtained 3 DEGs (CDKN2A, BAK1, BTG1) that were significantly related to PFS, and CDKN2A was considered an independent prognostic factor. PFS showed statistically significant difference between high/low risk score groups (P=0.015). There were significant differences in immune cell infiltration level and immune pathway activity between two groups. Conclusion The p53 pathway-related genes are significantly related to PFS in colon cancer patients and play an important role in regulating the tumor immune microenvironment.
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Affiliation(s)
- Jinggao Feng
- Department of Gastrointestinal and Anorectal Surgery, The Central Hospital of Yongzhou, Yongzhou City, Hunan Province, 425100, People's Republic of China
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7
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Zhang X, Sabio E, Krishna C, Ma X, Wang J, Jiang H, Havel JJ, Chan TA. Qa-1 b Modulates Resistance to Anti-PD-1 Immune Checkpoint Blockade in Tumors with Defects in Antigen Processing. Mol Cancer Res 2021; 19:1076-1084. [PMID: 33674442 PMCID: PMC8178214 DOI: 10.1158/1541-7786.mcr-20-0652] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 01/29/2021] [Accepted: 02/26/2021] [Indexed: 11/16/2022]
Abstract
Immune checkpoint blockade (ICB) has improved cancer care, but ICB is only effective in some patients. The molecular mechanisms that influence ICB therapy response are not completely understood. The non-classical MHC class I molecule HLA-E and its mouse ortholog, Qa-1b, present a limited set of peptides in a TAP1-dependent manner to the NKG2A/CD94 heterodimer to transduce an inhibitory signal to natural killer (NK) and CD8+ T cells. However, deficiency of TAP1 allows Qa-1b to present an alternative peptidome to Qa-1b-restricted T-cell receptors of cytotoxic T cells. In this study, we used CRISPR-Cas9 to study the relationship between TAP1, Qa-1b, and response to anti-PD1 therapy. We hypothesized that immunotherapy response in TAP1-deficient tumors would be influenced by Qa-1b. Strikingly, using a syngeneic orthotopic mouse model, we found that although TAP1-deficient tumors were resistant to anti-PD1 treatment, anti-PD1 response was significantly enhanced in tumors lacking both TAP1 and Qa-1b. This increased sensitivity is partially dependent on NK cells. TAP1-deficient tumors were associated with an increase of intratumoral regulatory T cells (Treg) and neutrophils, whereas tumors lacking both TAP1 and Qa-1b exhibited an increased CD8+ T-cell to Treg ratio. These data suggest that direct inhibition of Qa-1b may alter the immune microenvironment to reverse resistance to anti-PD1 therapy, particularly in the context of antigen-processing defects. IMPLICATIONS: This study reveals important functional crosstalk between classical TAP-dependent MHC complexes and Qa-1b/HLA-E, particularly in tumors with impaired antigen-processing machinery. This can dramatically influence immunotherapy efficacy.
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MESH Headings
- ATP Binding Cassette Transporter, Subfamily B, Member 2/genetics
- ATP Binding Cassette Transporter, Subfamily B, Member 2/immunology
- ATP Binding Cassette Transporter, Subfamily B, Member 2/metabolism
- Animals
- Antigen Presentation/drug effects
- Antigen Presentation/genetics
- Antigen Presentation/immunology
- Cell Line, Tumor
- Forkhead Transcription Factors/immunology
- Forkhead Transcription Factors/metabolism
- Gene Knockout Techniques
- Histocompatibility Antigens Class I/genetics
- Histocompatibility Antigens Class I/immunology
- Histocompatibility Antigens Class I/metabolism
- Humans
- Immune Checkpoint Inhibitors/pharmacology
- Killer Cells, Natural/drug effects
- Killer Cells, Natural/immunology
- Killer Cells, Natural/metabolism
- Lymphocyte Depletion/methods
- Mice, Inbred C57BL
- Neoplasms/genetics
- Neoplasms/immunology
- Neoplasms/therapy
- T-Lymphocytes, Regulatory/drug effects
- T-Lymphocytes, Regulatory/immunology
- T-Lymphocytes, Regulatory/metabolism
- Tumor Burden/drug effects
- Tumor Burden/genetics
- Tumor Burden/immunology
- Tumor Microenvironment/drug effects
- Tumor Microenvironment/genetics
- Tumor Microenvironment/immunology
- Mice
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Affiliation(s)
- Xiao Zhang
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, New York
- Xiangya Medical School, Central South University, Changsha, China
- Center for Immunotherapy and Precision Immuno-Oncology, Cleveland Clinic, Cleveland, Ohio
| | - Erich Sabio
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Chirag Krishna
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, New York
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Xiaoxiao Ma
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, New York
- Center for Immunotherapy and Precision Immuno-Oncology, Cleveland Clinic, Cleveland, Ohio
| | - Jingming Wang
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Hui Jiang
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jonathan J Havel
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York.
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Timothy A Chan
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York.
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, New York
- Center for Immunotherapy and Precision Immuno-Oncology, Cleveland Clinic, Cleveland, Ohio
- Computational and Systems Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
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Lau WM, Subramaniam M, Goh HH, Lim YM. Temporal gene expression profiling of maslinic acid-treated Raji cells. Mol Omics 2021; 17:252-259. [PMID: 33346776 DOI: 10.1039/d0mo00168f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Maslinic acid is a novel phytochemical reported to target multiple signaling pathways. A complete gene expression profile was therefore constructed to illustrate the anti-tumourigenesis effects of maslinic acid in Raji cells across five time-points. Microarray analysis was used to identify genes that were differentially expressed in maslinic acid treated Raji cells at 0, 4, 8, 12, 24 and 48 h. Extracted RNA was hybridized using the AffymetrixGeneChip to obtain expression profiles. A total of 109 genes were found to be significantly expressed over a period of 48 hours. By 12 hours, maslinic acid regulates the majority of genes involved in the cell cycle, p53 and NF-κB signaling pathways. At the same time, XAF1, APAF1, SESN3, and TP53BP2 were evidently up-regulated, while oncogenes, FAIM, CD27, and RRM2B, were down-regulated by at least 2-fold. In conclusion, maslinic acid shows an hourly progression of gene expression in Raji cells.
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Affiliation(s)
- Wai Meng Lau
- Centre for Cancer Research, Faculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, PT21144, Jalan Sungai Long, Bandar Sungai Long, 43000 Kajang, Selangor, Malaysia.
| | - Menaga Subramaniam
- Centre for Cancer Research, Faculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, PT21144, Jalan Sungai Long, Bandar Sungai Long, 43000 Kajang, Selangor, Malaysia.
| | - Hoe Han Goh
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, UKM Bangi, Bangi, Malaysia
| | - Yang Mooi Lim
- Centre for Cancer Research, Faculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, PT21144, Jalan Sungai Long, Bandar Sungai Long, 43000 Kajang, Selangor, Malaysia. and Department of Pre-Clinical Science, Faculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, Lot PT21144, Jalan Sungai Long, Bandar Sungai Long, 43000 Kajang, Selangor, Malaysia
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9
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Dhall A, Patiyal S, Kaur H, Bhalla S, Arora C, Raghava GPS. Computing Skin Cutaneous Melanoma Outcome From the HLA-Alleles and Clinical Characteristics. Front Genet 2020; 11:221. [PMID: 32273881 PMCID: PMC7113398 DOI: 10.3389/fgene.2020.00221] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 02/25/2020] [Indexed: 12/16/2022] Open
Abstract
Human leukocyte antigen (HLA) are essential components of the immune system that stimulate immune cells to provide protection and defense against cancer. Thousands of HLA alleles have been reported in the literature, but only a specific set of HLA alleles are present in an individual. The capability of the immune system to recognize cancer-associated mutations depends on the presence of a particular set of alleles, which elicit an immune response to fight against cancer. Therefore, the occurrence of specific HLA alleles affects the survival outcome of cancer patients. In the current study, prediction models were developed, using 401 cutaneous melanoma patients, to predict the overall survival (OS) of patients using their clinical data and HLA alleles. We observed that the presence of certain favorable superalleles like HLA-B∗55 (HR = 0.15, 95% CI 0.034-0.67), HLA-A∗01 (HR = 0.5, 95% CI 0.3-0.8), is responsible for the improved OS. In contrast, the presence of certain unfavorable superalleles such as HLA-B∗50 (HR = 2.76, 95% CI 1.284-5.941), HLA-DRB1∗12 (HR = 3.44, 95% CI 1.64-7.2) is responsible for the poor survival. We developed prediction models using key 14 HLA superalleles, demographic, and clinical characteristics for predicting high-risk cutaneous melanoma patients and achieved HR = 4.52 (95% CI 3.088-6.609, p-value = 8.01E-15). Eventually, we also provide a web-based service to the community for predicting the risk status in cutaneous melanoma patients (https://webs.iiitd.edu.in/raghava/skcmhrp/).
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Affiliation(s)
- Anjali Dhall
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India
| | - Sumeet Patiyal
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India
| | - Harpreet Kaur
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India
- Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Sherry Bhalla
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India
| | - Chakit Arora
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India
| | - Gajendra P. S. Raghava
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India
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10
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Abstract
The importance of cancer-cell-autonomous functions of the tumour suppressor p53 (encoded by TP53) has been established in many studies, but it is now clear that the p53 status of the cancer cell also has a profound impact on the immune response. Loss or mutation of p53 in cancers can affect the recruitment and activity of myeloid and T cells, allowing immune evasion and promoting cancer progression. p53 can also function in immune cells, resulting in various outcomes that can impede or support tumour development. Understanding the role of p53 in tumour and immune cells will help in the development of therapeutic approaches that can harness the differential p53 status of cancers compared with most normal tissue.
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Affiliation(s)
- Julianna Blagih
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Michael D Buck
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Karen H Vousden
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
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11
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Santana-Codina N, Carretero R, Sanz-Pamplona R, Cabrera T, Guney E, Oliva B, Clezardin P, Olarte OE, Loza-Alvarez P, Méndez-Lucas A, Perales JC, Sierra A. A transcriptome-proteome integrated network identifies endoplasmic reticulum thiol oxidoreductase (ERp57) as a hub that mediates bone metastasis. Mol Cell Proteomics 2013; 12:2111-25. [PMID: 23625662 DOI: 10.1074/mcp.m112.022772] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Bone metastasis is the most common distant relapse in breast cancer. The identification of key proteins involved in the osteotropic phenotype would represent a major step toward the development of new prognostic markers and therapeutic improvements. The aim of this study was to characterize functional phenotypes that favor bone metastasis in human breast cancer. We used the human breast cancer cell line MDA-MB-231 and its osteotropic BO2 subclone to identify crucial proteins in bone metastatic growth. We identified 31 proteins, 15 underexpressed and 16 overexpressed, in BO2 cells compared with parental cells. We employed a network-modeling approach in which these 31 candidate proteins were prioritized with respect to their potential in metastasis formation, based on the topology of the protein-protein interaction network and differential expression. The protein-protein interaction network provided a framework to study the functional relationships between biological molecules by attributing functions to genes whose functions had not been characterized. The combination of expression profiles and protein interactions revealed an endoplasmic reticulum-thiol oxidoreductase, ERp57, functioning as a hub that retained four down-regulated nodes involved in antigen presentation associated with the human major histocompatibility complex class I molecules, including HLA-A, HLA-B, HLA-E, and HLA-F. Further analysis of the interaction network revealed an inverse correlation between ERp57 and vimentin, which influences cytoskeleton reorganization. Moreover, knockdown of ERp57 in BO2 cells confirmed its bone organ-specific prometastatic role. Altogether, ERp57 appears as a multifunctional chaperone that can regulate diverse biological processes to maintain the homeostasis of breast cancer cells and promote the development of bone metastasis.
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Affiliation(s)
- Naiara Santana-Codina
- Biological Clues of the Invasive and Metastatic Phenotype Group, Bellvitge Biomedical Research Institute IDIBELL, L'Hospitalet de Llobregat, Barcelona E-08908, Spain
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12
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Garrido C, Paco L, Romero I, Berruguilla E, Stefansky J, Collado A, Algarra I, Garrido F, Garcia-Lora AM. MHC class I molecules act as tumor suppressor genes regulating the cell cycle gene expression, invasion and intrinsic tumorigenicity of melanoma cells. Carcinogenesis 2012; 33:687-93. [PMID: 22219178 DOI: 10.1093/carcin/bgr318] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The alteration of MHC class I (MHC-I) expression is a frequent event during cancer progression, allowing tumor cells to evade the immune system. We report that the loss of one major histocompatibility complex haplotype in human melanoma cells not only allowed them to evade immunosurveillance but also increased their intrinsic oncogenic potential. A second successive defect in MHC-I expression, MHC-I total downregulation, gave rise to melanoma cells that were more oncogenic per se in vivo and showed a higher proliferation rate and greater migratory and invasive potential in vitro. All these processes were reversed by restoring MHC-I expression via human leukocite antigen-A2 gene transfection. MHC-I cell surface expression was inversely correlated with intrinsic oncogenic potential. Modifications in the expression of various cell cycle genes were correlated with changes in MHC-I expression; the most important differences among the melanoma cell lines were in the transcriptional level of AP2-alpha, cyclin A1 and p21WAF1/CIP1. According to these results, altered MHC-I expression in malignant cells can directly increase their intrinsic oncogenic and invasive potential and modulate the expression of cell cycle genes. These findings suggest that human leukocite antigen class I molecules may act directly as tumor suppressor genes in melanoma.
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Affiliation(s)
- Cristina Garrido
- Departamento de Bioquímica, Biología Molecular e Inmunología III, Universidad de Granada, 18012 Granada, Spain
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13
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Abstract
The early steps in the biogenesis of secreted and membrane proteins occur in the lumen of the endoplasmic reticulum (ER), where resident proteins that make up the ER machinery assist in their folding, maturation, and complex assembly. Variation in the load of ER client proteins and in the function of the organelle's aforementioned machinery for coping with that load can lead to an imbalance between the two that is referred to as ER stress. This triggers a cellular response, mediated by highly conserved signaling pathways that collectively restore equilibrium to the protein-folding environment in the organelle by increasing the expression of genes that enhance nearly all aspects of ER function, and by transiently repressing the biosynthesis of new client proteins. Evidence accrued over the past 10 years suggests that ER stress and response to it influence the fate of mutant proteins that fold inefficiently, impact on the functionality of cells and tissues that cope with unusual loads of ER client proteins, and intersect with signaling pathways that influence inflammation and cancer biology. Here, we review some of the basic workings of unfolded protein response and relate them to processes that are of potential relevance to pulmonary disease.
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14
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Garrido C, Algarra I, Maleno I, Stefanski J, Collado A, Garrido F, Garcia-Lora AM. Alterations of HLA class I expression in human melanoma xenografts in immunodeficient mice occur frequently and are associated with higher tumorigenicity. Cancer Immunol Immunother 2010; 59:13-26. [PMID: 19430787 PMCID: PMC11031073 DOI: 10.1007/s00262-009-0716-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2008] [Accepted: 04/16/2009] [Indexed: 11/25/2022]
Abstract
Animal models are widely used to study the biological behavior of human tumors in vivo. Murine immunodeficient models are used to test novel human anti-tumor therapies, and humanized mice are employed to study immunotherapeutic protocols. We find that human melanoma cell lines lose HLA class I surface expression after growth in immunodeficient mice and that this phenomenon occurs frequently and is reproducible. This HLA loss is due to a coordinated down-regulation of APM and HLA heavy chain expression at the transcriptional level. It is produced by epigenetic modifications and can be reversed by treatment with histone deacetylase inhibitors or IFN-gamma. These HLA alterations only appear during in vivo growth and not during successive in vitro passages. Interestingly, these new tumor variants with HLA class I loss show higher tumorigenicity per se and may represent a more advanced state of the original tumor. Lack of MHC class I expression on tumor cells represents a frequent escape mechanism from the immune response. Our results indicate that tumor variants with alterations in MHC can also appear in vivo after the immunoescape phase in the absence of anti-tumor immune response. Our findings suggest that any studied parameter, i.e., HLA expression, of malignant cells in xenograft models, has to be evaluated before and after growth in immunodeficient mice, in order to design more appropriate immunotherapy and chemotherapy treatments against tumor cells growing in vivo.
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Affiliation(s)
- Cristina Garrido
- Servicio de Análisis Clínicos e Inmunologia, Hospital Universitario Virgen de las Nieves, Av. Fuerzas Armadas 2, 18014 Granada, Spain
- Departamento de Bioquimica y Biologia Molecular III e Inmunologia, Universidad de Granada, Granada, Spain
| | - Ignacio Algarra
- Departamento Ciencias de La Salud, Universidad de Jaén, 23014 Jaén, Spain
| | - Isabel Maleno
- Servicio de Análisis Clínicos e Inmunologia, Hospital Universitario Virgen de las Nieves, Av. Fuerzas Armadas 2, 18014 Granada, Spain
| | - Julia Stefanski
- Servicio de Análisis Clínicos e Inmunologia, Hospital Universitario Virgen de las Nieves, Av. Fuerzas Armadas 2, 18014 Granada, Spain
| | - Antonia Collado
- Unidad de Investigación, Hospital Universitario Virgen de las Nieves, 18014 Granada, Spain
| | - Federico Garrido
- Servicio de Análisis Clínicos e Inmunologia, Hospital Universitario Virgen de las Nieves, Av. Fuerzas Armadas 2, 18014 Granada, Spain
- Departamento de Bioquimica y Biologia Molecular III e Inmunologia, Universidad de Granada, Granada, Spain
| | - Angel M. Garcia-Lora
- Servicio de Análisis Clínicos e Inmunologia, Hospital Universitario Virgen de las Nieves, Av. Fuerzas Armadas 2, 18014 Granada, Spain
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15
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Rowe M, Kelly GL, Bell AI, Rickinson AB. Burkitt's lymphoma: the Rosetta Stone deciphering Epstein-Barr virus biology. Semin Cancer Biol 2009; 19:377-88. [PMID: 19619657 PMCID: PMC3764430 DOI: 10.1016/j.semcancer.2009.07.004] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2009] [Accepted: 07/10/2009] [Indexed: 02/07/2023]
Abstract
Epstein-Barr virus was originally identified in the tumour cells of a Burkitt's lymphoma, and was the first virus to be associated with the pathogenesis of a human cancer. Studies on the relationship of EBV with Burkitt's lymphoma have revealed important general principles that are relevant to other virus-associated cancers. In addition, the impact of such studies on the knowledge of EBV biology has been enormous. Here, we review some of the key historical observations arising from studies on Burkitt's lymphoma that have informed our understanding of EBV, and we summarise the current hypotheses regarding the role of EBV in the pathogenesis of Burkitt's lymphoma.
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Affiliation(s)
- Martin Rowe
- Institute for Cancer Studies, School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
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16
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Mendez R, Aptsiauri N, Del Campo A, Maleno I, Cabrera T, Ruiz-Cabello F, Garrido F, Garcia-Lora A. HLA and melanoma: multiple alterations in HLA class I and II expression in human melanoma cell lines from ESTDAB cell bank. Cancer Immunol Immunother 2009; 58:1507-15. [PMID: 19340423 PMCID: PMC11030131 DOI: 10.1007/s00262-009-0701-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2008] [Accepted: 03/14/2009] [Indexed: 10/20/2022]
Abstract
Altered HLA class I and class II cell surface expression has been reported in many types of malignancy and represents one of the major mechanism by which tumour cells escape from T lymphocytes. In this report, we review the results obtained from the study of constitutive and IFN-gamma-induced expression of HLA class I and II molecules in 91 human melanoma cell lines from the European Searchable Tumour Cell Line Database, and compare them with published data on HLA expression in other types of cancer. Various types of alterations in HLA class I cell surface expression were found in a high percentage (67%) of the studied cell lines. These alterations range from total to selective HLA class I loss and are associated with beta2-microglobulin gene mutations, transcriptional downregulation of HLA class I genes and antigen processing machinery components, or with the loss of heterozygosity in chromosome 6. The most frequently observed phenotype is selective downregulation of HLA-B locus, reversible after treatment with IFN-gamma. The expression of constitutive- or IFN-gamma induced-surface expression of at least one HLA class II locus is positive in 71.5% of the analysed cell lines. Four different HLA class II expression phenotypes were defined, and a positive correlation between the expression of class I and II molecules is discussed. More detailed information on the HLA expression patterns and others immunological characteristics of these melanoma cell lines can be found on the following website http://www.ebi.ac.uk/ipd/estdab .
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Affiliation(s)
- Rosa Mendez
- Departamento de Análisis Clínicos, Hospital Universitario Virgen de las Nieves, Avd. Fuerzas Armadas 2, 18014 Granada, Spain
| | - Natalia Aptsiauri
- Departamento de Análisis Clínicos, Hospital Universitario Virgen de las Nieves, Avd. Fuerzas Armadas 2, 18014 Granada, Spain
| | - Ana Del Campo
- Departamento de Análisis Clínicos, Hospital Universitario Virgen de las Nieves, Avd. Fuerzas Armadas 2, 18014 Granada, Spain
| | - Isabel Maleno
- Departamento de Análisis Clínicos, Hospital Universitario Virgen de las Nieves, Avd. Fuerzas Armadas 2, 18014 Granada, Spain
| | - Teresa Cabrera
- Departamento de Análisis Clínicos, Hospital Universitario Virgen de las Nieves, Avd. Fuerzas Armadas 2, 18014 Granada, Spain
- Departamento de Bioquímica, Biologia Molecular e Inmunología III, Universidad de Granada, Granada, Spain
| | - Francisco Ruiz-Cabello
- Departamento de Análisis Clínicos, Hospital Universitario Virgen de las Nieves, Avd. Fuerzas Armadas 2, 18014 Granada, Spain
- Departamento de Bioquímica, Biologia Molecular e Inmunología III, Universidad de Granada, Granada, Spain
| | - Federico Garrido
- Departamento de Análisis Clínicos, Hospital Universitario Virgen de las Nieves, Avd. Fuerzas Armadas 2, 18014 Granada, Spain
- Departamento de Bioquímica, Biologia Molecular e Inmunología III, Universidad de Granada, Granada, Spain
| | - Angel Garcia-Lora
- Departamento de Análisis Clínicos, Hospital Universitario Virgen de las Nieves, Avd. Fuerzas Armadas 2, 18014 Granada, Spain
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