1
|
Georgopoulos AP, James LM. Association between brain cancer immunogenetic profile and in silico immunogenicities of 11 viruses. Sci Rep 2023; 13:21528. [PMID: 38057480 PMCID: PMC10700375 DOI: 10.1038/s41598-023-48843-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 11/30/2023] [Indexed: 12/08/2023] Open
Abstract
Several viruses including human herpes viruses (HHVs), human polyomavirus JCV, and human papilloma virus (HPV) have been implicated in brain cancer, albeit inconsistently. Since human leukocyte antigen (HLA) is centrally involved in the human immune response to viruses and has been implicated in brain cancer, we evaluated in silico the immunogenicity between 69 Class I HLA alleles with epitopes of proteins of 9 HHVs, JCV, and HPV with respect to a population-based HLA-brain cancer profile. We found that immunogenicity varied widely across HLA alleles with HLA-C alleles exhibiting the highest immunogenicity, and that immunogenicity scores were negatively associated with the population-based HLA-brain cancer profile, particularly for JCV, HHV6A, HHV5, HHV3, HHV8, and HHV7. Consistent with the role of HLA in foreign antigen elimination, the findings suggest that viruses with proteins of high HLA immunogenicity are eliminated more effectively and, consequently, less likely to cause brain cancer; conversely, the absence of highly immunogenic HLA may allow the viral antigens to persist, contributing to cancer.
Collapse
Affiliation(s)
- Apostolos P Georgopoulos
- The HLA Research Group, Brain Sciences Center, Department of Veterans Affairs Health Care System, Minneapolis VAMC, One Veterans Drive, Minneapolis, MN, 55417, USA.
- Department of Neuroscience, University of Minnesota Medical School, Minneapolis, MN, USA.
- Department of Psychiatry, University of Minnesota Medical School, Minneapolis, MN, USA.
- Department of Neurology, University of Minnesota Medical School, Minneapolis, MN, USA.
| | - Lisa M James
- The HLA Research Group, Brain Sciences Center, Department of Veterans Affairs Health Care System, Minneapolis VAMC, One Veterans Drive, Minneapolis, MN, 55417, USA
- Department of Neuroscience, University of Minnesota Medical School, Minneapolis, MN, USA
- Department of Psychiatry, University of Minnesota Medical School, Minneapolis, MN, USA
| |
Collapse
|
2
|
James LM, Georgopoulos AP. Positive Association Between the Immunogenetic Human Leukocyte Antigen (HLA) Profiles of Multiple Sclerosis and Brain Cancer. Neurosci Insights 2023; 18:26331055231214543. [PMID: 38046672 PMCID: PMC10693228 DOI: 10.1177/26331055231214543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 10/31/2023] [Indexed: 12/05/2023] Open
Abstract
Previous research has documented elevated risk of brain cancer in patients with multiple sclerosis (MS). Separately, human leukocyte antigen (HLA) has been implicated in protection or susceptibility for both conditions. The aim of the current study was to assess a possible role of shared immunogenetic influence on risk of MS and brain cancer. We first identified an immunogenetic profile for each condition based on the covariance between the population frequency of 127 high-resolution HLA alleles and the population prevalence of each condition in 14 Continental Western European countries and then evaluated the correspondence between MS and brain cancer immunogenetic profiles. Also, since each individual carries 12 HLA alleles (2 × 6 genes), we estimated HLA protection and susceptibility for MS and brain cancer at the individual level. We found that the immunogenetic profiles of MS and brain cancer were highly correlated overall (P < .001) and across all 6 HLA genes with the strongest association observed for DRB1, followed by DQB1 and HLA-A. These findings of immunogenetic overlap between MS and brain cancer are discussed in light of the role of HLA in the immune system response to viruses and other foreign antigens.
Collapse
Affiliation(s)
- Lisa M James
- Department of Veterans Affairs Health Care System, The HLA Research Group, Brain Sciences Center, Minneapolis, MN, USA
- Department of Neuroscience, University of Minnesota Medical School, Minneapolis, MN, USA
- Department of Psychiatry, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Apostolos P Georgopoulos
- Department of Veterans Affairs Health Care System, The HLA Research Group, Brain Sciences Center, Minneapolis, MN, USA
- Department of Neuroscience, University of Minnesota Medical School, Minneapolis, MN, USA
- Department of Psychiatry, University of Minnesota Medical School, Minneapolis, MN, USA
- Department of Neurology, University of Minnesota Medical School, Minneapolis, MN, USA
| |
Collapse
|
3
|
Dai Z, Zhang N, Zhou R, Zhang H, Zhang L, Wang Z, Zeng W, Luo P, Zhang J, Liu Z, Cheng Q. Identification of a single cell-based signature for predicting prognosis risk and immunotherapy response in patients with glioblastoma. Clin Immunol 2023; 251:109345. [PMID: 37100336 DOI: 10.1016/j.clim.2023.109345] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 11/20/2022] [Accepted: 04/14/2023] [Indexed: 04/28/2023]
Abstract
This study constructed a novel gene pair signature based on bulk and single-cell sequencing samples in relative expression order within the samples. The subsequent analysis included glioma samples from Xiangya Hospital. Gene pair signatures possessed a solid ability to predict the prognosis of glioblastoma and pan-cancer. Samples having different malignant biological hallmarks were distinguished by the algorithm, with the high gene pair score group featuring classic copy number variations, oncogenic mutations, and extensive hypomethylation, mediating poor prognosis. The increased gene pair score group with a poorer prognosis demonstrated significant enrichment in tumor and immune-related signaling pathways while presenting immunological diversity. The remarkable infiltration of M2 macrophages in the high gene pair score group was validated by multiplex immunofluorescence, suggesting that combination therapies targeting adaptive and innate immunity may serve as a therapeutic option. Overall, a gene pair signature applicable to predict prognosis hopefully provides a reference to guide clinical practice.
Collapse
Affiliation(s)
- Ziyu Dai
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410078, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, China
| | - Nan Zhang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410078, China; One-Third Lab, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150088, China
| | - Ran Zhou
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410078, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, China; Division of Neuroscience and Experimental Psychology, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK
| | - Hao Zhang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410078, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, China
| | - Liyang Zhang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410078, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, China; Department of Medicine, The University of Oklahoma Health Sciences Center, OK 73104, USA; Clinical Diagnosis and Therapeutic Center of Glioma, Xiangya Hospital, Central South University, Changsha 410078, China
| | - Zeyu Wang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410078, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, China
| | - Wenjing Zeng
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha 410078, China
| | - Peng Luo
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Jian Zhang
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Zhixiong Liu
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410078, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410078, China.
| | - Quan Cheng
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410078, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410078, China; Clinical Diagnosis and Therapeutic Center of Glioma, Xiangya Hospital, Central South University, Changsha 410078, China.
| |
Collapse
|
4
|
Spatial analysis of the glioblastoma proteome reveals specific molecular signatures and markers of survival. Nat Commun 2022; 13:6665. [PMID: 36333286 PMCID: PMC9636229 DOI: 10.1038/s41467-022-34208-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022] Open
Abstract
Molecular heterogeneity is a key feature of glioblastoma that impedes patient stratification and leads to large discrepancies in mean patient survival. Here, we analyze a cohort of 96 glioblastoma patients with survival ranging from a few months to over 4 years. 46 tumors are analyzed by mass spectrometry-based spatially-resolved proteomics guided by mass spectrometry imaging. Integration of protein expression and clinical information highlights three molecular groups associated with immune, neurogenesis, and tumorigenesis signatures with high intra-tumoral heterogeneity. Furthermore, a set of proteins originating from reference and alternative ORFs is found to be statistically significant based on patient survival times. Among these proteins, a 5-protein signature is associated with survival. The expression of these 5 proteins is validated by immunofluorescence on an additional cohort of 50 patients. Overall, our work characterizes distinct molecular regions within glioblastoma tissues based on protein expression, which may help guide glioblastoma prognosis and improve current glioblastoma classification.
Collapse
|
5
|
Hu T, Wang Y, Wang X, Wang R, Song Y, Zhang L, Han S. Construction and validation of an angiogenesis-related gene expression signature associated with clinical outcome and tumor immune microenvironment in glioma. Front Genet 2022; 13:934683. [PMID: 36035133 PMCID: PMC9403517 DOI: 10.3389/fgene.2022.934683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 07/18/2022] [Indexed: 11/29/2022] Open
Abstract
Background: Glioma is the most prevalent malignant intracranial tumor. Many studies have shown that angiogenesis plays a crucial role in glioma tumorigenesis, metastasis, and prognosis. In this study, we conducted a comprehensive analysis of angiogenesis-related genes (ARGs) in glioma. Methods: RNA-sequencing data of glioma patients were obtained from TCGA and CGGA databases. Via consensus clustering analysis, ARGs in the sequencing data were distinctly classified into two subgroups. We performed univariate Cox regression analysis to determine prognostic differentially expressed ARGs and least absolute shrinkage and selection operator Cox regression to construct a 14-ARG risk signature. The CIBERSORT algorithm was used to explore immune cell infiltration, and the ESTIMATE algorithm was applied to calculate immune and stromal scores. Results: We found that the 14-ARG signature reflected the infiltration characteristics of different immune cells in the tumor immune microenvironment. Additionally, total tumor mutational burden increased significantly in the high-risk group. We combined the 14-ARG signature with patient clinicopathological data to construct a nomogram for predicting 1-, 3-, and 5-year overall survival with good accuracy. The predictive value of the prognostic model was verified in the CGGA cohort. SPP1 was a potential biomarker of glioma risk and was involved in the proliferation, invasion, and angiogenesis of glioma cells. Conclusion: In conclusion, we established and validated a novel ARG risk signature that independently predicted the clinical outcomes of glioma patients and was associated with the tumor immune microenvironment.
Collapse
Affiliation(s)
- Tianhao Hu
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, China
| | - Yutao Wang
- Department of Urology, The First Hospital of China Medical University, Shenyang, China
| | - Xiaoliang Wang
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, China
| | - Run Wang
- Department of Neurosurgery, Huazhong University of Science and Technology Union Shenzhen Hospital, Shenzhen, China
| | - Yifu Song
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, China
| | - Li Zhang
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, China
- *Correspondence: Li Zhang, ; Sheng Han,
| | - Sheng Han
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, China
- *Correspondence: Li Zhang, ; Sheng Han,
| |
Collapse
|
6
|
Ita MI, Wang JH, Toulouse A, Lim C, Fanning N, O’Sullivan M, Nolan Y, Kaar GF, Redmond HP. The utility of plasma circulating cell-free messenger RNA as a biomarker of glioma: a pilot study. Acta Neurochir (Wien) 2022; 164:723-735. [PMID: 34643804 PMCID: PMC8913523 DOI: 10.1007/s00701-021-05014-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 09/28/2021] [Indexed: 11/04/2022]
Abstract
Background Research into the potential utility of plasma-derived circulating cell-free nucleic acids as non-invasive adjuncts to radiological imaging have been occasioned by the invasive nature of brain tumour biopsy. The objective of this study was to determine whether significant differences exist in the plasma transcriptomic profile of glioma patients relative to differences in their tumour characteristics, and also whether any observed differences were representative of synchronously obtained glioma samples and TCGA glioma-derived RNA. Methods Blood samples were collected from twenty glioma patients prior to tumour resection. Plasma ccfmRNAs and glioma-derived RNA were extracted and profiled. Results BCL2L1, GZMB, HLA-A, IRF1, MYD88, TLR2, and TP53 genes were significantly over-expressed in glioma patients (p < 0.001, versus control). GZMB and HLA-A genes were significantly over-expressed in high-grade glioma patients (p < 0.001, versus low-grade glioma patients). Moreover, the fold change of the BCL2L1 gene was observed to be higher in patients with high-grade glioma (p = 0.022, versus low-grade glioma patients). There was positive correlation between the magnitude of fold change of differentially expressed genes in plasma- and glioma-derived RNA (Spearman r = 0.6344, n = 14, p = 0.017), and with the mean FPKM in TCGA glioma-derived RNA samples (Spearman r = 0.4614, n = 19, p < 0.05). There was positive correlation between glioma radiographic tumour burden and the magnitude of fold change of the CSF3 gene (r = 0.9813, n = 20, p < 0.001). Conclusion We identified significant differential expression of genes involved in cancer inflammation and immunity crosstalk among patients with different glioma grades, and there was positive correlation between their transcriptomic profile in plasma and tumour samples, and with TCGA glioma-derived RNA. Supplementary Information The online version contains supplementary material available at 10.1007/s00701-021-05014-8.
Collapse
|
7
|
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
|
8
|
Wang X, Gao M, Ye J, Jiang Q, Yang Q, Zhang C, Wang S, Zhang J, Wang L, Wu J, Zhan H, Hou X, Han D, Zhao S. An Immune Gene-Related Five-lncRNA Signature for to Predict Glioma Prognosis. Front Genet 2020; 11:612037. [PMID: 33391355 PMCID: PMC7772413 DOI: 10.3389/fgene.2020.612037] [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: 09/30/2020] [Accepted: 11/09/2020] [Indexed: 12/19/2022] Open
Abstract
Background The tumor immune microenvironment is closely related to the malignant progression and treatment resistance of glioma. Long non-coding RNA (lncRNA) plays a regulatory role in this process. We investigated the pathological mechanisms within the glioma microenvironment and potential immunotherapy resistance related to lncRNAs. Method We downloaded datasets derived from glioma patients and analyzed them by hierarchical clustering. Next, we analyzed the immune microenvironment of glioma, related gene expression, and patient survival. Coexpressed lncRNAs were analyzed to generate a model of lncRNAs and immune-related genes. We analyzed the model using survival and Cox regression. Then, univariate, multivariate, receiver operating characteristic (ROC), and principle component analysis (PCA) methods were used to verify the accuracy of the model. Finally, GSEA was used to evaluate which functions and pathways were associated with the differential genes. Results Normal brain tissue maintains a low-medium immune state, and gliomas are clearly divided into three groups (low to high immunity). The stromal, immune, and estimate scores increased along with immunity, while tumor purity decreased. Further, human leukocyte antigen (HLA), programmed cell death-1 (PDL1), T cell immunoglobulin and mucin domain 3 (TIM-3), B7-H3, and cytotoxic T lymphocyte-associated antigen-4 (CTLA4) expression increases concomitantly with immune state, and the patient prognosis worsens. Five immune gene-related lncRNAs (AP001007.1, LBX-AS1, MIR155HG, MAPT-AS1, and LINC00515) were screened to construct risk models. We found that risk scores are related to patient prognosis and clinical characteristics, and are positively correlated with PDL1, TIM-3, and B7-H3 expression. These lncRNAs may regulate the tumor immune microenvironment through cytokine-cytokine receptor interactions, complement, and coagulation cascades, and may promote CD8 + T cell, regulatory T cell, M1 macrophage, and infiltrating neutrophils activity in the high-immunity group. In vitro, the abnormal expression of immune-related lncRNAs and the relationship between risk scores and immune-related indicators (PDL1, CTLA4, CD3, CD8, iNOS) were verified by q-PCR and immunohistochemistry (IHC). Conclusion For the first time, we constructed immune gene-related lncRNA risk models. The risk score may be a new biomarker for tumor immune subtypes and provide molecular targets for glioma immunotherapy.
Collapse
Affiliation(s)
- Xinzhuang Wang
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China.,Key Colleges and Universities Laboratory of Neurosurgery in Heilongjiang Province, Harbin, China.,Institute of Neuroscience, Sino-Russian Medical Research Center, Harbin Medical University, Harbin, China
| | - Ming Gao
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China.,Key Colleges and Universities Laboratory of Neurosurgery in Heilongjiang Province, Harbin, China.,Institute of Neuroscience, Sino-Russian Medical Research Center, Harbin Medical University, Harbin, China
| | - Junyi Ye
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China.,Key Colleges and Universities Laboratory of Neurosurgery in Heilongjiang Province, Harbin, China.,Institute of Neuroscience, Sino-Russian Medical Research Center, Harbin Medical University, Harbin, China
| | - Qiuyi Jiang
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China.,Key Colleges and Universities Laboratory of Neurosurgery in Heilongjiang Province, Harbin, China.,Institute of Neuroscience, Sino-Russian Medical Research Center, Harbin Medical University, Harbin, China
| | - Quan Yang
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China.,Key Colleges and Universities Laboratory of Neurosurgery in Heilongjiang Province, Harbin, China.,Institute of Neuroscience, Sino-Russian Medical Research Center, Harbin Medical University, Harbin, China
| | - Cheng Zhang
- North Broward Preparatory School, Coconut Creek, FL, United States
| | - Shengtao Wang
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China.,Key Colleges and Universities Laboratory of Neurosurgery in Heilongjiang Province, Harbin, China.,Institute of Neuroscience, Sino-Russian Medical Research Center, Harbin Medical University, Harbin, China
| | - Jian Zhang
- Department of General Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Ligang Wang
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China.,Key Colleges and Universities Laboratory of Neurosurgery in Heilongjiang Province, Harbin, China.,Institute of Neuroscience, Sino-Russian Medical Research Center, Harbin Medical University, Harbin, China
| | - Jianing Wu
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China.,Key Colleges and Universities Laboratory of Neurosurgery in Heilongjiang Province, Harbin, China.,Institute of Neuroscience, Sino-Russian Medical Research Center, Harbin Medical University, Harbin, China
| | - Hua Zhan
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China.,Key Colleges and Universities Laboratory of Neurosurgery in Heilongjiang Province, Harbin, China.,Institute of Neuroscience, Sino-Russian Medical Research Center, Harbin Medical University, Harbin, China
| | - Xu Hou
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China.,Key Colleges and Universities Laboratory of Neurosurgery in Heilongjiang Province, Harbin, China.,Institute of Neuroscience, Sino-Russian Medical Research Center, Harbin Medical University, Harbin, China
| | - Dayong Han
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China.,Key Colleges and Universities Laboratory of Neurosurgery in Heilongjiang Province, Harbin, China.,Institute of Neuroscience, Sino-Russian Medical Research Center, Harbin Medical University, Harbin, China
| | - Shiguang Zhao
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China.,Key Colleges and Universities Laboratory of Neurosurgery in Heilongjiang Province, Harbin, China.,Institute of Neuroscience, Sino-Russian Medical Research Center, Harbin Medical University, Harbin, China.,Department of Neurosurgery, The Pinghu Hospital of Shenzhen University, Shenzhen, China
| |
Collapse
|
9
|
Xu Y, Li R, Li X, Dong N, Wu D, Hou L, Yin K, Zhao C. An Autophagy-Related Gene Signature Associated With Clinical Prognosis and Immune Microenvironment in Gliomas. Front Oncol 2020; 10:571189. [PMID: 33194668 PMCID: PMC7604433 DOI: 10.3389/fonc.2020.571189] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 09/02/2020] [Indexed: 12/16/2022] Open
Abstract
Glioma is one of the leading causes of death from cancer, and autophagy-related genes (ARGs) play an important role in glioma occurrence, progression, and treatment. In this study, the gene expression profiles and clinical data of glioma patients were obtained from The Cancer Genome Atlas (TCGA) and the Chinese Glioma Genome Atlas (CGGA), respectively. ARGs were obtained from the Human Autophagy Database. We analyzed the expression of the ARGs in glioma and found that 73 ARGs were differentially expressed in tumor and normal tissues. Univariate Cox regression analysis was used to identify prognostic differentially expressed ARGs (PDEARGs). Least absolute shrinkage and selection operator (LASSO) and multivariate Cox regression analyses were performed on the PDEARGs to determine the risk genes; and BRIC5, NFE2L2, GABARAP, IKBKE, BID, MAPK3, FKBP1B, MAPK8IP1, PRKCQ, CX3CL1, NPC1, HSP90AB1, DAPK2, SUPT20H, and PTEN were selected to establish a prognostic risk score model for TCGA and CGGA cohorts. This model accurately stratified patients with different survival outcomes, and the autophagy-related signature was also appraised as being an independent prognostic factor. We also constructed a prognostic nomogram using risk score, age, gender, WHO grade, isocitrate dehydrogenase (IDH) mutation status, and 1p/19q co-deletion status; and the calibration plots showed excellent prognostic performance. Finally, Pearson correlation analysis suggested that the ARG signature also played an essential role in the tumor immune microenvironment. In summary, we constructed and verified a novel autophagy-related signature that was tightly associated with the tumor immune microenvironment and could serve as an independent prognostic biomarker in gliomas.
Collapse
Affiliation(s)
- Yang Xu
- School of Basic Medicine, Qingdao University, Qingdao, China
| | - Renpeng Li
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Xiaoxia Li
- School of Basic Medicine, Qingdao University, Qingdao, China
| | - Naijun Dong
- School of Basic Medicine, Qingdao University, Qingdao, China
| | - Di Wu
- School of Basic Medicine, Qingdao University, Qingdao, China
| | - Lin Hou
- School of Basic Medicine, Qingdao University, Qingdao, China
| | - Kan Yin
- School of Basic Medicine, Qingdao University, Qingdao, China
| | - Chunhua Zhao
- School of Basic Medicine, Qingdao University, Qingdao, China
| |
Collapse
|
10
|
Amiri A, Rasras S, Saki N, Marandi H, Sadegh Pezeshki S. Meningioma and expression of human leukocyte antigen-B5, 7, 8, 27, and 51: Is there any relevance? CLINICAL CANCER INVESTIGATION JOURNAL 2020. [DOI: 10.4103/ccij.ccij_44_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
|
11
|
Cheng SJ, Jiang S, Shi FY, Ding Y, Gao G. Systematic identification and annotation of multiple-variant compound effects at transcription factor binding sites in human genome. J Genet Genomics 2018; 45:373-379. [PMID: 30054217 DOI: 10.1016/j.jgg.2018.05.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Revised: 05/03/2018] [Accepted: 05/25/2018] [Indexed: 12/21/2022]
Abstract
Understanding the functional effects of genetic variants is crucial in modern genomics and genetics. Transcription factor binding sites (TFBSs) are one of the most important cis-regulatory elements. While multiple tools have been developed to assess functional effects of genetic variants at TFBSs, they usually assume that each variant works in isolation and neglect the potential "interference" among multiple variants within the same TFBS. In this study, we presented COPE-TFBS (Context-Oriented Predictor for variant Effect on Transcription Factor Binding Site), a novel method that considers sequence context to accurately predict variant effects on TFBSs. We systematically re-analyzed the sequencing data from both the 1000 Genomes Project and the Genotype-Tissue Expression (GTEx) Project via COPE-TFBS, and identified numbers of novel TFBSs, transformed TFBSs and discordantly annotated TFBSs resulting from multiple variants, further highlighting the necessity of sequence context in accurately annotating genetic variants. COPE-TFBS is freely available for academic use at http://cope.cbi.pku.edu.cn/.
Collapse
Affiliation(s)
- Si-Jin Cheng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Center for Bioinformatics, Peking University, Beijing 100871, China; Beijing Advanced Innovation Center for Genomics, Peking University, Beijing 100871, China
| | - Shuai Jiang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Center for Bioinformatics, Peking University, Beijing 100871, China; Beijing Advanced Innovation Center for Genomics, Peking University, Beijing 100871, China
| | - Fang-Yuan Shi
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Center for Bioinformatics, Peking University, Beijing 100871, China; Beijing Advanced Innovation Center for Genomics, Peking University, Beijing 100871, China
| | - Yang Ding
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Center for Bioinformatics, Peking University, Beijing 100871, China; Beijing Advanced Innovation Center for Genomics, Peking University, Beijing 100871, China
| | - Ge Gao
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Center for Bioinformatics, Peking University, Beijing 100871, China; Beijing Advanced Innovation Center for Genomics, Peking University, Beijing 100871, China.
| |
Collapse
|
12
|
Baldi I, Engelhardt J, Bonnet C, Bauchet L, Berteaud E, Grüber A, Loiseau H. Epidemiology of meningiomas. Neurochirurgie 2018; 64:5-14. [DOI: 10.1016/j.neuchi.2014.05.006] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 05/15/2014] [Accepted: 07/24/2014] [Indexed: 12/15/2022]
|
13
|
Zhang C, de Smith AJ, Smirnov IV, Wiencke JK, Wiemels JL, Witte JS, Walsh KM. Non-additive and epistatic effects of HLA polymorphisms contributing to risk of adult glioma. J Neurooncol 2017; 135:237-244. [PMID: 28721485 DOI: 10.1007/s11060-017-2569-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 07/13/2017] [Indexed: 01/15/2023]
Abstract
Although genome-wide association studies have identified several susceptibility loci for adult glioma, little is known regarding the potential contribution of genetic variation in the human leukocyte antigen (HLA) region to glioma risk. HLA associations have been reported for various malignancies, with many studies investigating selected candidate HLA polymorphisms. However, no systematic analysis has been conducted in glioma patients, and no investigation into potential non-additive effects has been described. We conducted comprehensive genetic analyses of HLA variants among 1746 adult glioma patients and 2312 controls of European-ancestry from the GliomaScan Consortium. Genotype data were generated with the Illumina 660-Quad array, and we imputed HLA alleles using a reference panel of 5225 individuals in the Type 1 Diabetes Genetics Consortium who underwent high-resolution HLA typing via next-generation sequencing. Case-control comparisons were adjusted for population stratification using ancestry-informative principal components. Because alleles in different loci across the HLA region are linked, we created multigene haplotypes consisting of the genes DRB1, DQA1, and DQB1. Although none of the haplotypes were associated with glioma in additive models, inclusion of a dominance term significantly improved the model for multigene haplotype HLA-DRB1*1501-DQA1*0102-DQB1*0602 (P = 0.002). Heterozygous carriers of the haplotype had an increased risk of glioma [odds ratio (OR) 1.23; 95% confidence interval (CI) 1.01-1.49], while homozygous carriers were at decreased risk compared with non-carriers (OR 0.64; 95% CI 0.40-1.01). Our results suggest that the DRB1*1501-DQA1*0102-DQB1*0602 haplotype may contribute to the risk of glioma in a non-additive manner, with the positive dominance effect partly explained by an epistatic interaction with HLA-DRB1*0401-DQA1*0301-DQB1*0301.
Collapse
Affiliation(s)
- Chenan Zhang
- Division of Neuroepidemiology, Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, 94158, USA. .,Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, 94158, USA.
| | - Adam J de Smith
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Ivan V Smirnov
- Division of Neuroepidemiology, Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - John K Wiencke
- Division of Neuroepidemiology, Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Joseph L Wiemels
- Division of Neuroepidemiology, Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, 94158, USA.,Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - John S Witte
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Kyle M Walsh
- Division of Neuroepidemiology, Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, 94158, USA.,Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, 94158, USA.,Division of Neuro-epidemiology, Department of Neurosurgery, Duke University, Durham, NC, 27710, USA
| |
Collapse
|
14
|
Kantorová E, Bittšanský M, Sivák Š, Baranovičová E, Hnilicová P, Nosáľ V, Čierny D, Zeleňák K, Brück W, Kurča E. Anaplastic astrocytoma mimicking progressive multifocal leucoencephalopathy: a case report and review of the overlapping syndromes. BMC Cancer 2017. [PMID: 28629398 PMCID: PMC5477142 DOI: 10.1186/s12885-017-3415-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Background Co-occurrence of multiple sclerosis (MS) and glial tumours (GT) is uncommon although occasionally reported in medical literature. Interpreting the overlapping radiologic and clinical characteristics of glial tumours, MS lesions, and progressive multifocal leukoencephalopathy (PML) can be a significant diagnostic challenge. Case presentation We report a case of anaplastic astrocytoma mimicking PML in a 27-year-old patient with a 15-year history of MS. She was treated with interferon, natalizumab and finally fingolimod due to active MS. Follow-up MRI, blood and cerebrospinal fluid examinations, and biopsy were conducted, but only the latter was able to reveal the cause of progressive worsening of patient’s disease. Conclusions Anaplastic astrocytoma misdiagnosed as PML has not yet been described. We suppose that the astrocytoma could have evolved from a low grade glioma to anaplastic astrocytoma over time, as the tumour developed adjacent to typical MS plaques. The role of the immunomodulatory treatment as well as other immunological factors in the malignant transformation can only be hypothesised. We discuss clinical, laboratory and diagnostic aspects of a malignant GT, MS lesions and PML. The diagnosis of malignant GT must be kept in mind when an atypical lesion develops in a patient with MS.
Collapse
Affiliation(s)
- Ema Kantorová
- Clinic of Neurology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Kollárova 2, 03659, Martin, Slovak Republic.
| | - Michal Bittšanský
- Department of Medical Biochemistry, Jessenius Faculty of Medicine, Comenius University in Bratislava, Kollárova 2, 03659, Martin, Slovak Republic
| | - Štefan Sivák
- Clinic of Neurology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Kollárova 2, 03659, Martin, Slovak Republic
| | - Eva Baranovičová
- Department of Medical Biochemistry, Jessenius Faculty of Medicine, Comenius University in Bratislava, Kollárova 2, 03659, Martin, Slovak Republic
| | - Petra Hnilicová
- Department of Medical Biochemistry, Jessenius Faculty of Medicine, Comenius University in Bratislava, Kollárova 2, 03659, Martin, Slovak Republic
| | - Vladimír Nosáľ
- Clinic of Neurology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Kollárova 2, 03659, Martin, Slovak Republic
| | - Daniel Čierny
- Department of Medical Biochemistry, Jessenius Faculty of Medicine, Comenius University in Bratislava, Kollárova 2, 03659, Martin, Slovak Republic
| | - Kamil Zeleňák
- Clinic of Radiodiagnostics, Jessenius Faculty of Medicine, Comenius University in Bratislava, Kollárova 2, 03659, Martin, Slovak Republic
| | - Wolfgang Brück
- Institut für Neuropathologie Universitätsmedizin Göttingen, Robert-Koch-Str, 40 37075, Göttingen, Germany
| | - Egon Kurča
- Clinic of Neurology, Jessenius Faculty of Medicine, Comenius University in Bratislava, Kollárova 2, 03659, Martin, Slovak Republic
| |
Collapse
|
15
|
Wang L, Wei B, Hu G, Wang L, Bi M, Sun Z, Jin Y. Screening of differentially expressed genes associated with human glioblastoma and functional analysis using a DNA microarray. Mol Med Rep 2015; 12:1991-6. [PMID: 25901754 DOI: 10.3892/mmr.2015.3659] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 03/10/2015] [Indexed: 11/06/2022] Open
Abstract
Glioblastoma multiforme (GBM) is the most malignant type of human glioma, and has a poor prognosis. Screening differentially expressed genes (DEGs) in brain tumor samples and normal brain samples is of importance for identifying GBM and to design specific-targeting drugs. The transcriptional profile of GSE30563, containing three genechips of brain tumor samples and three genechips of normal brain samples, was downloaded from Gene Expression Omnibus to identify the DEGs. The differences in the expression of the DEGs in the two different samples were compared through hierarchical biclustering. The co-expression coefficient of the DEGs was calculated using the information from COXPRESdb, the network of the DEGs was constructed and functional enrichment and pathway analysis were performed. Finally, the transcription factors of important DEGs were predicted. A total of 1,006 DEGs, including 368 upregulated and 638 downregulated DEGs, were identified. A close correlation was demonstrated between six important genes, associated with immune response, HLA-DQB1, HLA-DRB1, HLA-DPA1, HLA-B, HLA-DMA and HLA-DRA, and the immune response. Allograft rejection was selected as the most significant pathway. A total of 17 transcription factors, including nuclear factor (NF)-κB and NF-κB1, and their binding sites containing these six DEGs, were also identified. The DEGs, including major histocompatibility complex (MHC) class II, DQβ1, MHC class II, DRβ1, MHC class IB, MHC class II, DMα, MHC class II, DPα1, MHC class II, DRα, may provide novel targets for the diagnosis and treatment of GBM. The transcription factors of these six genes and their binding sites may also provide evidence and direction for identifying target-specific drugs.
Collapse
Affiliation(s)
- Lina Wang
- Department of Ophthalmology, China‑Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| | - Bo Wei
- Department of Neurosurgery, China‑Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| | - Guozhang Hu
- Department of Emergency Medicine, China‑Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| | - Le Wang
- Department of Ophthalmology, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Miaomiao Bi
- Department of Ophthalmology, China‑Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| | - Zhigang Sun
- Department of Neurosurgery, China‑Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| | - Ying Jin
- Department of Neurology, Institute of Jilin Oilfield General Hospital, Changchun, Jilin 131200, P.R. China
| |
Collapse
|
16
|
Shankarkumar U, Sridharan B. Glioma Indian scenario: Is there a human leucocyte antigen association? J Nat Sci Biol Med 2012; 2:205-8. [PMID: 22346237 PMCID: PMC3276015 DOI: 10.4103/0976-9668.92323] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background: The central nervous system tumors are a rare neoplasm with little knowledge with Human Leukocyte Antigen (HLA) involvement. Primary brain tumors are cancers that originate in brain classified according to their appearance under a microscope as low grade (grade I and II) with diffuse astrocytomas, pliocytic astrocytomas, oligodendrogliomas, gangliogliomas, and mixed gliomas as common subtypes and high grade (grade III and IV). Materials and Methods: HLA associations in common glioma are reported from other parts of the world. The normal cancer treatment is surgery, followed by radiotherapy, and chemotherapy; nowadays immunotherapy is advised. HLA distribution in a Glioma patient was done based on serology and molecular techniques. The immune response gene studies have implicated the HLA allele association in most of the common diseases from India. Considerable variations are noted in HLA association with cancers; hence, we have summarized the HLA involvement in Glioma with respect to the literature. Results: HLA A*030101, A*310102, B*350101, B*4406, Cw*040101, Cw*070101, DRB1*070101, and DRB1*1001. Conclusion: Ethnic diversity and HLA polymorphism precipitate differential immune response genes involved in variable disease manifestations. Therefore, caste-specific HLA allelic specificity needs to be identified, which may help in early identification of the associated HLA allele and establishing clinical practices among glioma patients.
Collapse
Affiliation(s)
- U Shankarkumar
- Human Leukocyte Antigen and Transplantation Department, Department of Medicine National Institute of Immunohaematology, KEM Hospital, Parel, Mumbai, India
| | | |
Collapse
|
17
|
Bassig BA, Inskip PD, Burdette L, Shapiro WR, Selker RG, Fine HA, Loeffler JS, Black PM, Dubrow R, Brenner AV. Selected human leukocyte antigen class II polymorphisms and risk of adult glioma. J Neuroimmunol 2011; 233:185-91. [PMID: 21195488 PMCID: PMC3074044 DOI: 10.1016/j.jneuroim.2010.11.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2010] [Revised: 11/10/2010] [Accepted: 11/15/2010] [Indexed: 10/18/2022]
Abstract
Few studies have examined the relationship between human leukocyte antigen (HLA) polymorphisms and adult glioma, particularly at class II loci. We evaluated the association between selected HLA class II polymorphisms and adult glioma in a large, hospital-based case-control study, using unconditional logistic regression. DQB1 06 (OR=1.67, 95% CI=1.17-2.39) and DRB1 13 (OR=1.69, 95% CI=1.08-2.64) alleles were associated with an increased risk of glioma, while the DQB1 05 allele showed an inverse association (OR=0.63, 95% CI=0.43-0.93). These results, which were of borderline significance once controlled for the false discovery rate, suggest a potential role for the DQB1 06, DQB1 05, and DRB1 13 alleles in glioma susceptibility.
Collapse
Affiliation(s)
- Bryan A. Bassig
- Yale School of Public Health, Yale School of Medicine, 60 College Street, P.O. Box 208034, New Haven, CT 06510, USA
| | - Peter D. Inskip
- Radiation Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, 6120 Executive Blvd. MSC 7242, Bethesda, MD 20892, USA
| | - Laurie Burdette
- Core Genotyping Facility, Advanced Technology Program, SAIC-Frederick Inc., NCI-Frederick, Frederick, MD 21702, USA
| | - William R. Shapiro
- Barrow Neurological Institute, St. Joseph's Hospital and Medical Center, Phoenix, AZ 85013, USA
| | - Robert G. Selker
- Division of Neurosurgery, Western Pennsylvania Hospital, Pittsburgh, PA 15224, USA
| | - Howard A. Fine
- Neuro-Oncology Branch, National Cancer Institute, Bethesda, MD 20892, USA
| | - Jay S. Loeffler
- Department of Radiation Oncology, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | - Robert Dubrow
- Yale School of Public Health, Yale School of Medicine, 60 College Street, P.O. Box 208034, New Haven, CT 06510, USA
| | - Alina V. Brenner
- Radiation Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, 6120 Executive Blvd. MSC 7242, Bethesda, MD 20892, USA
| |
Collapse
|
18
|
HLA-A and breast cancer in West Peninsular Malaysia. Med Oncol 2010; 28:51-6. [PMID: 20069393 DOI: 10.1007/s12032-009-9414-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2009] [Accepted: 12/30/2009] [Indexed: 02/07/2023]
Abstract
Breast cancer is the most common malignancy among females in Malaysia. Attempts have been made to investigate the association between breast cancer and human leukocyte antigen (HLA) types. However, data from those previous studies are highly variable. The aim of this study is to investigate the association between HLA-A types and clinicopathological factors in breast cancer. The frequencies of HLA-A type in 59 female patients with infiltrating ductal of the breast were determined by polymerase chain reaction method. HLA-A2/A30 and A2/A31 haplotype (5.1%; P = 0.045) as well as HLA-A30 (5.1%, P = 0.045) and A31 (6.8%; P = 0.020) allele were significant higher in the patients than controls (0%). HLA-A24 allele was negatively related to lymph node metastasis (r = -0.316; P = 0.021) whereas, A26 (r = -0.430; P = 0.001) and A36 (r = -0.430; P = 0.001) alleles were negatively correlated to distant metastasis in breast cancer. Negative correlations between HLA-A26/A36 (r = -0.430; P = 0.001), A2/A11 (r = -0.276; P = 0.044), A24/A34 (r = -0.430; P = 0.001) haplotypes and distant metastasis were identified. Interestingly, Her2 expression in breast carcinoma was negatively correlated to A11/24 haplotypes (r = -0.294; P = 0.034) but positively correlated to homozygous HLA-A24 (r = 0.396; P = 0.040). In conclusion, HLA-A2, -A30 and A31 were associated with breast cancer.
Collapse
|
19
|
Driggers L, Zhang JG, Newcomb EW, Ge L, Hoa N, Jadus MR. Immunotherapy of pediatric brain tumor patients should include an immunoprevention strategy: a medical hypothesis paper. J Neurooncol 2009; 97:159-69. [PMID: 19802719 PMCID: PMC2837156 DOI: 10.1007/s11060-009-0016-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2009] [Accepted: 09/21/2009] [Indexed: 02/08/2023]
Abstract
Adults diagnosed with Glioblastoma multiforme (GBM) are frequently faced with a 7% chance of surviving 2 years compared with pediatric patients with GBM who have a 26% survival rate. Our recent screen of possible glioma-associated antigen precursor protein (TAPP) profiles displayed from different types of pediatric brain tumors showed that pediatric patients contained a subset of the tumor antigens displayed by adult GBM patients. Adult GBM possess at least 27 tumor antigens that can potentially stimulate T cell immune responses, suggesting that these tumors are quite antigenic. In contrast, pediatric brain tumors only expressed nine tumor antigens with mRNA levels that were equivalent to those displayed by adult GBM. These tumor-associated antigens could be used as possible targets of therapeutic immunization for pediatric brain cancer patients. Children have developing immune systems that peak at puberty. An immune response mounted by these pediatric patients might account for their extended life spans, even though the pediatric brain tumors express far fewer total tumor-associated antigens. Here we present a hypothesis that pediatric brain tumor patients might be the best patients to show that immunotherapy can be used to successfully treat established cancers. We speculate that immunotherapy should include a panel of tumor antigens that might prevent the out-growth of more malignant tumor cells and thereby prevent the brain tumor relapse. Thus, pediatric brain tumor patients might provide an opportunity to prove the concept of immunoprevention.
Collapse
Affiliation(s)
- Lara Driggers
- Pathology and Laboratory Medicine Service, Molecular Medicine Health Care Group, VA Long Beach Healthcare System, Box 113, 5901 E. 7th Street, Long Beach, CA, 90822, USA
| | | | | | | | | | | |
Collapse
|
20
|
Song W, Ruder AM, Hu L, Li Y, Ni R, Shao W, Kaslow RA, Butler M, Tang J. Genetic epidemiology of glioblastoma multiforme: confirmatory and new findings from analyses of human leukocyte antigen alleles and motifs. PLoS One 2009; 4:e7157. [PMID: 19774073 PMCID: PMC2742900 DOI: 10.1371/journal.pone.0007157] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2009] [Accepted: 09/01/2009] [Indexed: 11/19/2022] Open
Abstract
Background Human leukocyte antigen (HLA) class I genes mediate cytotoxic T-lymphocyte responses and natural killer cell function. In a previous study, several HLA-B and HLA-C alleles and haplotypes were positively or negatively associated with the occurrence and prognosis of glioblastoma multiforme (GBM). Methodology/Principal Findings As an extension of the Upper Midwest Health Study, we have performed HLA genotyping for 149 GBM patients and 149 healthy control subjects from a non-metropolitan population consisting almost exclusively of European Americans. Conditional logistic regression models did not reproduce the association of HLA-B*07 or the B*07-Cw*07 haplotype with GBM. Nonetheless, HLA-A*32, which has previously been shown to predispose GBM patients to a favorable prognosis, was negatively associated with occurrence of GBM (odds ratio = 0.41, p = 0.04 by univariate analysis). Other alleles (A*29, A*30, A*31 and A*33) within the A19 serology group to which A*32 belongs showed inconsistent trends. Sequencing-based HLA-A genotyping established that A*3201 was the single A*32 allele underlying the observed association. Additional evaluation of HLA-A promoter and exon 1 sequences did not detect any unexpected single nucleotide polymorphisms that could suggest differential allelic expression. Further analyses restricted to female GBM cases and controls revealed a second association with a specific HLA-B sequence motif corresponding to Bw4-80Ile (odds ratio = 2.71, p = 0.02). Conclusions/Significance HLA-A allelic product encoded by A*3201 is likely to be functionally important to GBM. The novel, sex-specific association will require further confirmation in other representative study populations.
Collapse
Affiliation(s)
- Wei Song
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Avima M. Ruder
- National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Cincinnati, Ohio, United States of America
| | - Liangyuan Hu
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Yufeng Li
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Rong Ni
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Wenshuo Shao
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Richard A. Kaslow
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - MaryAnn Butler
- National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Cincinnati, Ohio, United States of America
| | - Jianming Tang
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- * E-mail:
| |
Collapse
|
21
|
La Torre D, Maugeri R, Angileri FF, Pezzino G, Conti A, Cardali SM, Calisto A, Sciarrone G, Misefari A, Germanò A, Tomasello F. Human leukocyte antigen frequency in human high-grade gliomas: a case-control study in Sicily. Neurosurgery 2009; 64:1082-8; discussion 1088-9. [PMID: 19487887 DOI: 10.1227/01.neu.0000345946.35786.92] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVE Human leukocyte antigens (HLAs) are widely expressed cell surface molecules that present antigenic peptides to T lymphocytes and modulate immune response against inflammatory and malignant diseases. The aim of this study was to compare HLA distribution in patients with newly diagnosed high-grade gliomas (HGGs) and 2 control groups from a restricted geographic area (eastern Sicily). METHODS HLA allele frequency, as determined from peripheral blood of 56 adult patients with HGGs, was compared with that of 2 different control groups: 140 healthy bone marrow donors (group A) and 69 virtually brain tumor-free patients (group B). HLA expression was evaluated using a reverse transcriptase polymerase chain reaction-sequence-specific oligonucleotide probe. RESULTS There was significant expression of HLA-A*11 in patients with HGGs compared with control groups A and B (P < 0.003 and P < 0.018, respectively). Significant expression of HLA genotypes in patients with HGGs was also identified for HLA-DQB1*06 (P = 0.005), HLA-DRB1*14 (P = 0.001), and HLA-DRB3*01 (P = 0.007) compared with control group B. In HGG patients, there was statistically significantly decreased expression, compared with control groups A and B, of HLA-B*07 (P = 0.002 and P = 0.03, respectively) and HLA-C*04 (P = 0.007 and P = 0.016, respectively). There was statistically significant lower expression of HLA-C*05 in the HGG group compared with group B (P < 0.03). CONCLUSION This is the first study to describe the frequency of distribution of HLAs in a population from a restricted geographic area. The findings suggest a possible correlation between HLA allele distribution and the occurrence of newly diagnosed malignant astroglial brain tumors.
Collapse
|
22
|
Abstract
Conventional therapies for glioblastoma multiforme (GBM) fail to target tumor cells exclusively, resulting in non-specific toxicity. Immune targeting of tumor-specific mutations may allow for more precise eradication of neoplastic cells. EGFR variant III (EGFRvIII) is a tumor-specific mutation that is widely expressed in GBM and other neoplasms and its expression enhances tumorigenicity. This in-frame deletion mutation splits a codon, resulting in a novel glycine at the fusion junction producing a tumor-specific epitope target for cellular or humoral immunotherapy. We have previously shown that vaccination with a peptide that spans the EGFRvIII fusion junction (PEPvIII-KLH/CDX-110) is an efficacious immunotherapy in syngeneic murine models. In this review, we summarize our results in GBM patients targeting this mutation in multiple, multi-institutional Phase II immunotherapy trials. These trials demonstrated that a selected population of GBM patients who received vaccines targeting EGFRvIII had an unexpectedly long survival time. Further therapeutic strategies and potential pitfalls of using this approach are discussed.
Collapse
Affiliation(s)
- Amy B Heimberger
- University of Texas MD Anderson Cancer Center, Department of Neurosurgery, Unit 422, Houston, TX 77230-1402, USA.
| | | |
Collapse
|
23
|
Association of HLA-A in autoimmune myasthenia gravis with thymoma. J Neuroimmunol 2009; 210:120-3. [DOI: 10.1016/j.jneuroim.2009.02.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2008] [Revised: 12/23/2008] [Accepted: 02/10/2009] [Indexed: 11/17/2022]
|
24
|
Kurzwelly D, Müller CA, Korfel A, Thiel E, Linnebank M, Weller M, Herrlinger U. Primary CNS lymphoma and HLA class I and II alleles in a German cohort of immunocompetent patients. J Neurooncol 2008; 90:53-5. [DOI: 10.1007/s11060-008-9630-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2008] [Accepted: 06/06/2008] [Indexed: 11/28/2022]
|
25
|
Sanus GZ, Hanimoglu H, Tanriverdi T, Yilmaz E, Ak H, Ulu MO, Kafadar AM, Canbaz B, Kaynar MY. Cerebral cavernomas and human leukocyte antigens: preliminary clinical results. ACTA ACUST UNITED AC 2007; 68:164-6; discussion 167. [PMID: 17662350 DOI: 10.1016/j.surneu.2006.10.054] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2006] [Accepted: 10/10/2006] [Indexed: 11/25/2022]
Abstract
BACKGROUND Although cavernomas are the most common brain vascular malformations, the etiology and risk factor(s) are still not entirely known. Recent publications focusing on the molecular basis suggest that genetic factors may play a role in the development of the brain vascular malformations. We aimed to show HLA typing in brain cavernoma in a group of Turkish patients. METHODS This study compared HLA types of 30 patients who had brain cavernoma with 30 healthy controls. RESULTS The analysis of HLA distribution in the patients, compared with healthy control data, revealed some statistically significant differences, even after the more rigid Bonferoni correction (P(c)). In the patients group, the frequency of following HLA antigens was significantly increased compared with the control group: HLA-A1 (P(c): .005), HLA-A24 (P(c): .02), HLA-A32 (P(c): .01), HLA-B51 (P(c): .00001), HLA-DR1 (P(c): .02), and HLA-DR4 (P(c): .004). CONCLUSION These preliminary data suggest that brain cavernoma susceptibility may be associated with HLA antigens. Further studies should be designed to include a larger population of patients with brain cavernoma in order to expose whether there is association between HLA typing and occurrence of cavernoma more accurately.
Collapse
Affiliation(s)
- Galip Zihni Sanus
- Department of Neurosurgery, Cerrahpasa Medical Faculty, Istanbul University, Istanbul 34301, Turkey
| | | | | | | | | | | | | | | | | |
Collapse
|
26
|
Klingemann H, Rainov NG, Smythe JA, Touitou E. Editorial Board Focus – May 2007. Expert Opin Biol Ther 2007. [DOI: 10.1517/14712598.7.5.573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
27
|
Riemersma SA, Jordanova ES, Haasnoot GW, Drabbels J, Schuuring E, Schreuder GMT, Kluin PM. The Relationship Between HLA Class II Polymorphisms and Somatic Deletions in Testicular B Cell Lymphomas of Dutch Patients. Hum Immunol 2006; 67:303-10. [PMID: 16720210 DOI: 10.1016/j.humimm.2006.03.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2005] [Indexed: 11/21/2022]
Abstract
Several risk factors including immune deficiencies, infections, and autoimmune diseases have been established for non-Hodgkin's lymphoma (NHL). For diffuse large B cell lymphoma (DLBCL), the most common type of lymphoma, no risk factors have been described, which may be due to the intrinsic heterogeneity of this disorder. Previously we reported that, in contrast to nodal DLBCLs, the majority of testicular DLBCLs manifested complete loss of HLA-DR and -DQ expression associated with homozygous deletions of the corresponding genes. To determine the correlation between HLA class II polymorphisms and these lymphomas, we applied DNA typing for HLA-DRB1 and HLA-DQB1 on 50 Dutch patients with testicular and 48 with nodal DLBCL and compared the frequencies with a cohort of healthy Dutch controls. Both the patients with nodal and those with testicular DLBCL manifested significantly higher frequencies of HLA-DRB1*15 than the controls (p < 0.018, odds ratio 2.09 and p < 0.013, odds ratio 2.12, respectively). Moreover, a positive association was seen with HLA-DRB1*12 (p = 0.043, odds ratio 4.17) in the patients with testicular DLBCL, and a negative association was seen with HLA-DRB1*07 (p = 0.022, odds ratio 0.13) in the patients with nodal DLBCL. Homozygous deletions of the HLA-DR/DQ region, evaluated by interphase fluorescence in situ hybridization were seen in 20 of 48 testicular tumors. No preferential loss or retention of a particular HLA-DR or -DQ allele was seen because all alleles were at least once retained or involved in a homozygous deletion.
Collapse
Affiliation(s)
- S A Riemersma
- Laboratorium Pathologie Oost Nederland, Enschede, The Netherlands.
| | | | | | | | | | | | | |
Collapse
|
28
|
Guerini FR, Agliardi C, Zanzottera M, Delbue S, Pagani E, Tinelli C, Boldorini R, Car PG, Veggiani C, Ferrante P. Human leukocyte antigen distribution analysis in North Italian brain Glioma patients: an association with HLA-DRB1*14. J Neurooncol 2005; 77:213-7. [PMID: 16314951 DOI: 10.1007/s11060-005-9032-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2005] [Accepted: 08/16/2005] [Indexed: 11/29/2022]
Abstract
Human leukocyte antigens (HLA) are widely expressed cell surface molecules that present antigenic peptides to T-lymphocytes and modulate the immune response against inflammatory and malignant disease. Frequently, tumoral cells express antigens that are recognized by the immune system. Ineffective immune response could be the result of defects in antigen presentation in those subjects with peculiar HLA alleles, which, owing to mechanisms that are still unknown, are unable to carry out their function. Only a few studies on glioma and HLA association have been performed to date. The aim of our study was to characterize a group of Italian Caucasian patients with glioma, to investigate a possible association between HLA antigens and cerebral glioma tumorigenesis in Italian patients. HLA typing of class I and class II loci was done by molecular typing performed on blood DNA from 36 glioma patients from northern Italy. The data obtained were compared with HLA frequencies taken from the database of northern Italian organ donors.A positive association between HLA-DRB1*14 and the presence of symptomatic cerebral glioma was observed (p = 0.02, odds ratio = 2.48, 95% confidence interval: 1.09-5.45). This is the first Italian report on a case-control data study of HLA distribution conducted on a group of glioma patients and a first step in defining a possible involvement of HLA in susceptibility to brain glioma in the Italian population.
Collapse
Affiliation(s)
- Franca R Guerini
- Laboratory of Molecular Medicine and Biotechnology, Don C. Gnocchi Foundation IRCCS, S. Maria Nascente, Milan, Italy.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
29
|
Tang J, Shao W, Dorak MT, Li Y, Miike R, Lobashevsky E, Wiencke JK, Wrensch M, Kaslow RA, Cobbs CS. Positive and negative associations of human leukocyte antigen variants with the onset and prognosis of adult glioblastoma multiforme. Cancer Epidemiol Biomarkers Prev 2005; 14:2040-4. [PMID: 16103458 DOI: 10.1158/1055-9965.epi-05-0136] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Associations of genetic factors with malignant gliomas have been modest. We examined the relationships of human leukocyte antigen (HLA) and related polymorphisms to glioblastoma multiforme in adult Caucasians (non-Hispanic Whites) from the San Francisco Bay area. For 155 glioblastoma multiforme patients and 157 control subjects closely matched by ethnicity, age, and gender, PCR-based techniques resolved alleles at HLA-A, -B, -C, and -DRB1 loci along with short tandem repeat polymorphisms of MICA exon 5 and TNFb. By multivariable logistic regression, B*13 and the B*07-Cw*07 haplotype were positively associated with glioblastoma multiforme (P=0.01 and <0.001, respectively), whereas Cw*01 was the only variant showing a negative association (P=0.05). Among glioblastoma multiforme patients, progression to death after diagnosis was slower in those with A*32 (relative hazard, 0.45; P<0.01) and faster in those with B*55 (relative hazard, 2.27; P<0.01). Thus, both the occurrence and the prognosis of glioblastoma multiforme could be associated with specific but different HLA genotypes. B*07 and the B*07-Cw*07 haplotype are much more common in Caucasians than other ethnic groups in the U.S., which may partially explain the higher incidence of glioblastoma multiforme in Caucasians.
Collapse
Affiliation(s)
- Jianming Tang
- Department of Medicine, University of Alabama at Birmingham, 1665 University Boulevard, RPHB Room 220A, Birmingham, AL 35294-0022, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|