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Duan L, He Y, Guo W, Du Y, Yin S, Yang S, Dong G, Li W, Chen F. Machine learning-based pathomics signature of histology slides as a novel prognostic indicator in primary central nervous system lymphoma. J Neurooncol 2024; 168:283-298. [PMID: 38557926 PMCID: PMC11147825 DOI: 10.1007/s11060-024-04665-8] [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: 02/20/2024] [Accepted: 03/26/2024] [Indexed: 04/04/2024]
Abstract
PURPOSE To develop and validate a pathomics signature for predicting the outcomes of Primary Central Nervous System Lymphoma (PCNSL). METHODS In this study, 132 whole-slide images (WSIs) of 114 patients with PCNSL were enrolled. Quantitative features of hematoxylin and eosin (H&E) stained slides were extracted using CellProfiler. A pathomics signature was established and validated. Cox regression analysis, receiver operating characteristic (ROC) curves, Calibration, decision curve analysis (DCA), and net reclassification improvement (NRI) were performed to assess the significance and performance. RESULTS In total, 802 features were extracted using a fully automated pipeline. Six machine-learning classifiers demonstrated high accuracy in distinguishing malignant neoplasms. The pathomics signature remained a significant factor of overall survival (OS) and progression-free survival (PFS) in the training cohort (OS: HR 7.423, p < 0.001; PFS: HR 2.143, p = 0.022) and independent validation cohort (OS: HR 4.204, p = 0.017; PFS: HR 3.243, p = 0.005). A significantly lower response rate to initial treatment was found in high Path-score group (19/35, 54.29%) as compared to patients in the low Path-score group (16/70, 22.86%; p < 0.001). The DCA and NRI analyses confirmed that the nomogram showed incremental performance compared with existing models. The ROC curve demonstrated a relatively sensitive and specific profile for the nomogram (1-, 2-, and 3-year AUC = 0.862, 0.932, and 0.927, respectively). CONCLUSION As a novel, non-invasive, and convenient approach, the newly developed pathomics signature is a powerful predictor of OS and PFS in PCNSL and might be a potential predictive indicator for therapeutic response.
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Affiliation(s)
- Ling Duan
- Department of Neuro-Oncology, Cancer Center, Beijing Tiantan Hospital, Capital Medical University, No.119 West Nansihuan Road, Beijing, 100070, China
| | - Yongqi He
- Department of Neuro-Oncology, Cancer Center, Beijing Tiantan Hospital, Capital Medical University, No.119 West Nansihuan Road, Beijing, 100070, China
| | - Wenhui Guo
- Department of Neuro-Oncology, Cancer Center, Beijing Tiantan Hospital, Capital Medical University, No.119 West Nansihuan Road, Beijing, 100070, China
| | - Yanru Du
- Department of Pathology, Beijing Tiantan Hospital, Capital Medical University, No.119 West Nansihuan Road, Beijing, 100070, China
| | - Shuo Yin
- Department of Neuro-Oncology, Cancer Center, Beijing Tiantan Hospital, Capital Medical University, No.119 West Nansihuan Road, Beijing, 100070, China
| | - Shoubo Yang
- Department of Neuro-Oncology, Cancer Center, Beijing Tiantan Hospital, Capital Medical University, No.119 West Nansihuan Road, Beijing, 100070, China
| | - Gehong Dong
- Department of Pathology, Beijing Tiantan Hospital, Capital Medical University, No.119 West Nansihuan Road, Beijing, 100070, China.
| | - Wenbin Li
- Department of Neuro-Oncology, Cancer Center, Beijing Tiantan Hospital, Capital Medical University, No.119 West Nansihuan Road, Beijing, 100070, China.
| | - Feng Chen
- Department of Neuro-Oncology, Cancer Center, Beijing Tiantan Hospital, Capital Medical University, No.119 West Nansihuan Road, Beijing, 100070, China.
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Zeremski V, Adolph L, Beer S, Berisha M, Jacobs B, Kahl C, Koenecke C, Kropf S, Panse J, Petersen J, Schmidt-Hieber M, Schneider J, Vucinic V, Walter J, Weigert O, Witte HM, Mougiakakos D. Relevance of different prognostic scores in primary CNS lymphoma in the era of intensified treatment regimens: A retrospective, multicenter analysis of 174 patients. Eur J Haematol 2024; 112:641-649. [PMID: 38164819 DOI: 10.1111/ejh.14159] [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: 11/06/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 01/03/2024]
Abstract
OBJECTIVES Treatment intensification (including consolidative high-dose chemotherapy with autologous stem cell transplantation [HDT-ASCT]) significantly improved outcome in primary central nervous system lymphoma (PCNSL) patients. METHODS We conducted a multicenter, retrospective analysis of newly diagnosed PCNSL patients, treated with intensified treatment regimens. The following scores were evaluated in terms of overall survival (OS) and progression-free survival (PFS): Memorial Sloan-Kettering Cancer Center (MSKCC), International Extranodal Lymphoma Study Group (IELSG), and three-factor (3F) prognostic score. Further, all scores were comparatively investigated for model quality and concordance. RESULTS Altogether, 174 PCNSL patients were included. One hundred and five patients (60.3%) underwent HDT-ASCT. Two-year OS and 2-year PFS for the entire population were 73.3% and 48.5%, respectively. The MSKCC (p = .003) and 3F score (p < .001), but not the IELSG score (p = .06), had the discriminatory power to identify different risk groups for OS. In regard to concordance, the 3F score (C-index [0.71]) outperformed both the MSKCC (C-index [0.64]) and IELSG (C-index [0.53]) score. Moreover, the superiority of the 3F score was shown for PFS, successfully stratifying patients in three risk groups, which also resulted in the highest C-index (0.66). CONCLUSION The comparative analysis of established PCNSL risk scores affirm the clinical utility of the 3F score stratifying the widest prognostic spectrum among PCNSL patients treated with intensified treatment approaches.
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Affiliation(s)
- Vanja Zeremski
- Department of Hematology and Oncology, Medical Faculty, Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - Louisa Adolph
- Department of Internal Medicine III, Ludwig-Maximilians-University Hospital, Munich, Germany
| | - Sina Beer
- Department of Hematology and Oncology, University Hospital Tuebingen, Tuebingen, Germany
| | - Mirjeta Berisha
- Department of Hematology and Oncology, Medical Faculty, Otto von Guericke University Magdeburg, Magdeburg, Germany
- Department of Internal Medicine 5, Hematology and Clinical Oncology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), University Hospital Erlangen, Erlangen, Germany
| | - Benedikt Jacobs
- Department of Internal Medicine 5, Hematology and Clinical Oncology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), University Hospital Erlangen, Erlangen, Germany
| | - Christoph Kahl
- Department of Hematology, Oncology and Palliative Care, Klinikum Magdeburg, Magdeburg, Germany
- Department of Hematology, Oncology, and Palliative Care, University Medical Center, University of Rostock, Rostock, Germany
| | - Christian Koenecke
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - Siegfried Kropf
- Department of Biometry and Medical Informatics, Medical Faculty, Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - Jens Panse
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty, RWTH Aachen University, Aachen, Germany
- Center for Integrated Oncology (CIO), Aachen, Bonn, Cologne, Düsseldorf (ABCD), Aachen, Germany
| | - Judith Petersen
- Department of Hematology, Cell Therapy, Hemostaseology and Infectious Diseases, Leipzig University Medical Center, Leipzig, Germany
| | - Martin Schmidt-Hieber
- Clinic of Hematology, Oncology, Pneumology and Nephrology, Carl-Thiem-Hospital Cottbus, Cottbus, Germany
| | - Jessica Schneider
- Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation, Hannover Medical School, Hannover, Germany
| | - Vladan Vucinic
- Department of Hematology, Cell Therapy, Hemostaseology and Infectious Diseases, Leipzig University Medical Center, Leipzig, Germany
| | - Jeanette Walter
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty, RWTH Aachen University, Aachen, Germany
- Center for Integrated Oncology (CIO), Aachen, Bonn, Cologne, Düsseldorf (ABCD), Aachen, Germany
| | - Oliver Weigert
- Department of Internal Medicine III, Ludwig-Maximilians-University Hospital, Munich, Germany
| | - Hanno M Witte
- Department of Hematology and Oncology, Federal Armed Hospital Ulm, Ulm, Germany
| | - Dimitrios Mougiakakos
- Department of Hematology and Oncology, Medical Faculty, Otto von Guericke University Magdeburg, Magdeburg, Germany
- Department of Internal Medicine 5, Hematology and Clinical Oncology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), University Hospital Erlangen, Erlangen, Germany
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Identification of a novel autophagy-related prognostic signature and small molecule drugs for glioblastoma by bioinformatics. BMC Med Genomics 2022; 15:111. [PMID: 35550147 PMCID: PMC9097333 DOI: 10.1186/s12920-022-01261-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 04/25/2022] [Indexed: 12/22/2022] Open
Abstract
OBJECTIVE To explore the autophagy-related prognostic signature (ARPs) via data mining in gene expression profiles for glioblastoma (GBM). METHODS Using the Cancer Genome Atlas (TCGA) database, we obtained 156 GBM samples and 5 adjacent normal samples, and denoted them as discovery cohort. Univariate Cox regression analysis was used to screen autophagy genes that related to GBM prognosis. Then, the least absolute shrinkage and selection operator Cox regression model was used to construct an autophagy-based ARPs, which was validated in an external cohort containing 80 GBM samples. The patients in the above-mentioned cohorts were divided into low-risk group and high-risk group according to the median prognostic risk score, and the diagnostic performance of the model was assessed by receiver operating characteristic curve analyses. The gene ontology and Kyoto encyclopedia of genes and genomes pathway enrichment analyses were performed between the high-risk and low-risk patients. Additionally, the genetic features of ARPs, such as genetic variation profiles, correlations with tumor-infiltrating lymphocytes (TILs), and potential drug sensitivity, were further assessed in the TCGA-GBM data set. RESULTS A signature of ARPs including NDUFB9, BAK1, SUPT3H, GAPDH, CDKN1B, CHMP6, and EGFR were detected and validated. We identified a autophagy-related prognosis 7-gene signature correlated survival prognosis, immune infiltration, level of cytokines, and cytokine receptor in tumor microenvironment. Furthermore, the signature was tested in several pathways related to disorders of tumor microenvironment, as well as cancer-related pathways. Additionally, a range of small molecular drugs, shown to have a potential therapeutic effect on GBM. CONCLUSIONS We constructed an autophagy-based 7-gene signature, which could serve as an independent prognostic indicator for cases of GBM and sheds light on the role of autophagy as a potential therapeutic target in GBM.
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Takashima Y, Kawaguchi A, Fukai J, Iwadate Y, Kajiwara K, Hondoh H, Yamanaka R. Survival prediction based on the gene expression associated with cancer morphology and microenvironment in primary central nervous system lymphoma. PLoS One 2021; 16:e0251272. [PMID: 34166375 PMCID: PMC8224980 DOI: 10.1371/journal.pone.0251272] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 04/23/2021] [Indexed: 11/18/2022] Open
Abstract
Dysregulation of cell morphology and cell-cell interaction results in cancer cell growth, migration, invasion, and metastasis. Besides, a balance between the extracellular matrix (ECM) and matrix metalloprotease (MMP) is required for cancer cell morphology and angiogenesis. Here, we determined gene signatures associated with the morphology and microenvironment of primary central nervous system lymphoma (PCNSL) to enable prognosis prediction. Next-generation sequencing (NGS) on 31 PCNSL samples revealed gene signatures as follows: ACTA2, ACTR10, CAPG, CORO1C, KRT17, and PALLD in cytoskeleton, CDH5, CLSTN1, ITGA10, ITGAX, ITGB7, ITGA8, FAT4, ITGAE, CDH10, ITGAM, ITGB6, and CDH18 in adhesion, COL8A2, FBN1, LAMB3, and LAMA2 in ECM, ADAM22, ADAM28, MMP11, and MMP24 in MMP. Prognosis prediction formulas with the gene expression values and the Cox regression model clearly divided survival curves of the subgroups in each status. Furthermore, collagen genes contributed to gene network formation in glasso, suggesting that the ECM balance controls the PCNSL microenvironment. Finally, the comprehensive balance of morphology and microenvironment enabled prognosis prediction by a combinatorial expression of 8 representative genes, including KRT17, CDH10, CDH18, COL8A2, ADAM22, ADAM28, MMP11, and MMP24. Besides, these genes could also diagnose PCNSL cell types with MTX resistances in vitro. These results would not only facilitate the understanding of biology of PCNSL but also consider targeting pathways for anti-cancer treatment in personalized precision medicine in PCNSL.
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Affiliation(s)
- Yasuo Takashima
- Osaka Iseikai Clinic for Cancer Therapy, Iseikai Holonics Group, Osaka, Japan
- Laboratory of Molecular Target Therapy for Cancer, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Atsushi Kawaguchi
- Faculty of Medicine, Center for Comprehensive Community Medicine, Saga University, Saga, Japan
| | - Junya Fukai
- Department of Neurological Surgery, Wakayama Medical University School of Medicine, Wakayama, Japan
| | - Yasuo Iwadate
- Department of Neurosurgery, Graduate School of Medical Sciences, Chiba University, Chiba, Japan
| | - Koji Kajiwara
- Department of Neurosurgery, Graduate School of Medical Sciences, Yamaguchi University, Ube, Yamaguchi, Japan
| | - Hiroaki Hondoh
- Department of Neurosurgery, Toyama Prefectural Central Hospital, Toyama, Japan
| | - Ryuya Yamanaka
- Osaka Iseikai Clinic for Cancer Therapy, Iseikai Holonics Group, Osaka, Japan
- Laboratory of Molecular Target Therapy for Cancer, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
- * E-mail:
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Chen H, Li H, Wang L, Li Y, Yang C. A 5-gene DNA methylation signature is a promising prognostic biomarker for early-stage cervical cancer. J OBSTET GYNAECOL 2021; 42:327-332. [PMID: 34082663 DOI: 10.1080/01443615.2021.1907563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The demographic information and overall survival (OS) of patients with cervical cancer (CC) (pathological stage: IA-IIA) were extracted from the TCGA database. A univariate and multivariate Cox proportional hazard model was performed to identify methylation markers significantly associated with the OS of patients in the training dataset. Then such a prognostic classifier was tested on the validation set and all subgroups. The Kaplan-Meier analysis and ROC analysis were performed to detect the ability to discriminate between patients with different risks and different OS. A DNA methylation signature which contained five genes was found to be significantly associated with the OS of CC patients by the Cox regression analysis in the training dataset. Such a signature could efficiently distinguish the patients into two risk groups with significantly different OS in both datasets. The receiver operating characteristic (ROC) analysis showed it had high sensitivity and specificity. Moreover, such a prognostic model also could be effectively applied to different subgroups, including groups of different ages, tumour sizes, histologic types, etc. A 5-DNA methylation signature identified by this study may act as a novel prognostic indicator for early-stage CC, and it may be helpful for the timely diagnosis and intervention of CC at pathological stages IA-IIA.Impact StatementWhat is already known on this subject? Cervical cancer (CC) is one of the most common gynaecological malignant tumours.What the results of this study add? This study constructed a risk model based on a 5-DNA methylation signature for early-stage CC patients' survival prediction.What the implications are of these findings for clinical practice and/or further research? Methylated markers have the potential to discriminate patients of different risks and different OS. Our results may shed new light on the early diagnosis and intervention, and potential therapeutic targets for CC patients at pathological stages IA-IIA.
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Affiliation(s)
- Hongxia Chen
- Department of Pathophysiology, School of Basic Medicine, Hubei University of Science and Technology, Xianning, China
| | - Hongying Li
- Maternal and Child Health Hospital of Hubei Province, Hongshan District, Wuhan, Hubei, China.,Hubei Province Key Laboratory of Occupational Hazard Identification and Control, Wuhan University of Science and Technology, Wuhan, Hubei, China
| | - Lei Wang
- School of Laboratory Medicine, Hubei University of Chinese Medicine, Wuhan, China
| | - Yaxiong Li
- Information Center of Hubei University of Science and Technology, Xianning, China
| | - ChunYan Yang
- Department of Public Health Management, School of Basic Medicine, Hubei University of Science and Technology, Xianning, China
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Jelicic J, Stauffer Larsen T, Bukumiric Z, Juul-Jensen K, Andjelic B. Prognostic models in primary central nervous system lymphoma patients: A systematic review. Crit Rev Oncol Hematol 2021; 161:103341. [PMID: 33865995 DOI: 10.1016/j.critrevonc.2021.103341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 03/16/2021] [Accepted: 03/31/2021] [Indexed: 11/16/2022] Open
Abstract
Over the last decade, several prognostic models have been proposed for primary central nervous system lymphoma (PCNSL), but consensus on the optimal model for these patients is absent or lacking. This study aims to review available prognostic models for PCNSL and discuss their prognostic features. A comprehensive literature search performed in Pubmed/Embase identified ten studies with a variable number of analysed patients (range 32-3453), which proposed 12 prognostic models. Age and performance status were the most important prognostic factors in PCNSL and an integral part of the majority of the proposed models. However, there is no universally accepted prognostic model for PCNSL owning to a number of limitations such as a small number of patients, limited samples obtained for genetic analysis, retrospective nature of studies, single centre studies, and lack of validation. Future multicentre studies are necessary to determine the optimal prognostic model for PCNSL by combining different prognostic markers of significance.
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Affiliation(s)
- Jelena Jelicic
- Department of Haematology, Odense University Hospital, Odense, Denmark
| | - Thomas Stauffer Larsen
- Department of Haematology, Odense University Hospital, Odense, Denmark; Department of Clinical Research, University of Southern Denmark, Odense, Denmark.
| | - Zoran Bukumiric
- Department of Statistics, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Karen Juul-Jensen
- Department of Haematology, Odense University Hospital, Odense, Denmark
| | - Bosko Andjelic
- Department of Haematology, Blackpool Victoria Hospital, Lancashire Haematology Centre, Blackpool, United Kingdom
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Alame M, Cornillot E, Cacheux V, Rigau V, Costes-Martineau V, Lacheretz-Szablewski V, Colinge J. The immune contexture of primary central nervous system diffuse large B cell lymphoma associates with patient survival and specific cell signaling. Am J Cancer Res 2021; 11:3565-3579. [PMID: 33664848 PMCID: PMC7914352 DOI: 10.7150/thno.54343] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 11/19/2020] [Indexed: 12/24/2022] Open
Abstract
Rationale: Primary central nervous system diffuse large B-cell lymphoma (PCNSL) is a rare and aggressive entity that resides in an immune-privileged site. The tumor microenvironment (TME) and the disruption of the immune surveillance influence lymphoma pathogenesis and immunotherapy resistance. Despite growing knowledge on heterogeneous therapeutic responses, no comprehensive description of the PCNSL TME is available. We hence investigated the immune subtypes of PCNSL and their association with molecular signaling and survival. Methods: Analysis of PCNSL transcriptomes (sequencing, n = 20; microarrays, n = 34). Integrated correlation analysis and signaling pathway topology enabled us to infer intercellular interactions. Immunohistopathology and digital imaging were used to validate bioinformatic results. Results: Transcriptomics revealed three immune subtypes: immune-rich, poor, and intermediate. The immune-rich subtype was associated to better survival and characterized by hyper-activation of STAT3 signaling and inflammatory signaling, e.g., IFNγ and TNF-α, resembling the hot subtype described in primary testicular lymphoma and solid cancer. WNT/β-catenin, HIPPO, and NOTCH signaling were hyper-activated in the immune-poor subtype. HLA down-modulation was clearly associated with a low or intermediate immune infiltration and the absence of T-cell activation. Moreover, HLA class I down-regulation was also correlated with worse survival with implications on immune-intermediate PCNSL that frequently feature reduced HLA expression. A ligand-receptor intercellular network revealed high expression of two immune checkpoints, i.e., CTLA-4/CD86 and TIM-3/LAGLS9. TIM-3 and galectin-9 proteins were clearly upregulated in PCNSL. Conclusion: Altogether, our study reveals that patient stratification according to immune subtypes, HLA status, and immune checkpoint molecule quantification should be considered prior to immune checkpoint inhibitor therapy. Moreover, TIM-3 protein should be considered an axis for future therapeutic development.
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Lv J, Guo Y, Yan L, Lu Y, Liu D, Niu J. Development and validation of a five-lncRNA signature with prognostic value in colon cancer. J Cell Biochem 2020; 121:3780-3793. [PMID: 31680309 DOI: 10.1002/jcb.29518] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 10/08/2019] [Indexed: 01/24/2023]
Abstract
Dysregulation of long noncoding RNAs (lncRNAs) has been found in a large number of human cancers, including colon cancer. Therefore, the implementation of potential lncRNAs biomarkers with prognostic prediction value are very much essential. GSE39582 data set was downloaded from database of Gene Expression Omnibus. Re-annotation analysis of lncRNA expression profiles was performed by NetAffx annotation files. Univariate and multivariate Cox proportional analyses helped select prognostic lncRNAs. Algorithm of random survival forest-variable hunting (RSF-VH) together with stepwise multivariate Cox proportional analysis were performed to establish lncRNA signature. The log-rank test was carried out to analyze and compare the Kaplan-Meier survival curves of patients' overall survival (OS). Receiver operating characteristic (ROC) analysis was used for comparing the survival prediction regarding its specificity and sensitivity based on lncRNA risk score, followed by calculating the values of area under the curve (AUC). The single-sample GSEA (ssGSEA) analysis was used to describe biological functions associated with this signature. Finally, to determine the robustness of this model, we used the validation sets including GSE17536 and The Cancer Genome Atlas data set. After re-annotation analysis of lncRNAs, a total of 14 lncRNA probes were obtained by univariate and multivariate Cox proportional analysis. Then, the RSF-VH algorithm and stepwise multivariate Cox analysis helped to build a five-lncRNA prognostic signature for colon cancer. The patients in group with high risk showed an obviously shorter survival time compared with patients in group with low risk with AUC of 0.75. In addition, the five-lncRNA signature can be used to independently predict the survival of patients with colon cancer. The ssGSEA analysis revealed that pathways such as extracellular matrix-receptor interaction was activated with an increase in risk score. These findings determined the strong power of prognostic prediction value of this five-lncRNA signature for colon cancer.
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Affiliation(s)
- Ji Lv
- Department of Surgery, The First Hospital of Qinhuangdao, Qinhuangdao, China
| | - Ying Guo
- Department of Obstetrics and Gynecology, Maternity and Child Health Hospital of Qinhuangdao, Qinhuangdao, Hebei, China
| | - Lili Yan
- Department of Surgery, The First Hospital of Qinhuangdao, Qinhuangdao, China
| | - Yang Lu
- Department of Surgery, The First Hospital of Qinhuangdao, Qinhuangdao, China
| | - Dongfeng Liu
- Department of Surgery, The First Hospital of Qinhuangdao, Qinhuangdao, China
| | - Jia Niu
- Department of Surgery, The First Hospital of Qinhuangdao, Qinhuangdao, China
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GSEA-assisted gene signatures valid for combinations of prognostic markers in PCNSL. Sci Rep 2020; 10:8435. [PMID: 32439996 PMCID: PMC7242340 DOI: 10.1038/s41598-020-65463-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 05/05/2020] [Indexed: 02/07/2023] Open
Abstract
Primary central nervous system lymphoma (PCNSL) is a brain malignant non-Hodgkin’s B-cell lymphoma. The standard treatments are high-dose methotrexate (MTX)-based chemotherapies and deferred whole brain radiotherapy. However, MTX resistance-dependent global expression and signaling pathway changes and their relationship with prognoses have not yet been elucidated. Here, we conducted a global expression analysis with next-generation sequencing and gene set enrichment analysis (GSEA) in MTX-resistant PCNSL cell lines (HKBML-MTX and TK-MTX) and PCNSL tissues. In rank scores, genes listed in HKBML-MTX and TK-MTX were enriched in PCNSL with poor prognoses. In fold changes, a part of differentially-expressed genes in PCNSL tissues were also detected in HKBML-MTX and TK-MTX cells; FOXD2-AS1 and MMP19 were commonly expressed in both HKBML-MTX and TK-MTX, FABP5 and CD70 were HKBML-MTX-specifically expressed, and CLCN2, HOXB9, INE1, and LRP5L were TK-MTX-specifically expressed, which may provide a combination of prognostic markers on MTX-sensitivities in PCNSL. Additionally, PCNSL subgroups, divided with hierarchical clustering and Kaplan-Meier methods, included twenty commonly expressed genes in both HKBML-MTX and TK-MTX, ten HKBML-MTX-specifically expressed genes, and two TK-MTX-specifically expressed genes. These results suggest that the GSEA-assisted gene signatures can provide a combination for prognostic markers in recurrent PCNSL with MTX resistances.
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Cai S, Yu X, Gu Z, Yang Q, Wen B, Sheng J, Guan R. A 10-gene prognostic methylation signature for stage I-III cervical cancer. Arch Gynecol Obstet 2020; 301:1275-1287. [PMID: 32274635 DOI: 10.1007/s00404-020-05524-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 03/28/2020] [Indexed: 12/14/2022]
Abstract
PURPOSE Cervical cancer (CC) patients usually have poor prognosis. The present study aims to find a DNA methylation signature for predicting survival of CC patients. METHODS We selected CC patients at pathological stage I-III with corresponding information on radiotherapy and overall survival (OS) from TCGA. Differential expression and methylation analysis was done between patients with and without radiotherapy. We selected feature genes using recursive feature elimination algorithm to build a support vector machine classifier. DNA methylation biomarkers predictive of prognosis were identified using a LASSO Cox-Proportional Hazards model to construct a prognostic scoring model. The classifier and the prognostic model were tested on the training set and the validation set. Nomogram combining risk score and prognostic clinical factors were used. RESULTS We obtained 497 differentially expressed genes (DEGs) and 865 differentially methylated genes (DMGs). Fifteen feature genes were selected from the 292 common genes between the DEGs and the DMGs to construct a classification model for radiotherapy. A DNA methylation signature including 10 genes was identified and used to establish a prognostic scoring model. The 10-gene methylation signature could effectively separate patients into two risk groups with markedly different OS time. Predictive capability of the methylation signature was successfully confirmed on the validation set. A nomogram comprised of risk score, radiotherapy, and recurrence was applied, with calibration plots displaying good concordance between predicted and actual OS. The DEGs were involved in 12 KEGG pathways most of which were correlated with metastasis and proliferation of various cancers, such as pathways in cancer, basal cell carcinoma, transcriptional misregulation in cancer and ECM-receptor interaction. CONCLUSION We Identified a 10-gene methylation signature for risk stratification of CC patients at pathological stages I-III, and ten methylation biomarkers might be novel therapeutic targets for CC.
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Affiliation(s)
- Shengyun Cai
- Department of Obstetrics and Gynecology, Changhai Hospital, Second Military Medical University, NO.168, Changhai Road, Shanghai, 200433, People's Republic of China
| | - Xiaomin Yu
- Department of Obstetrics and Gynecology, Changhai Hospital, Second Military Medical University, NO.168, Changhai Road, Shanghai, 200433, People's Republic of China
| | - Zhongyi Gu
- Department of Obstetrics and Gynecology, Changhai Hospital, Second Military Medical University, NO.168, Changhai Road, Shanghai, 200433, People's Republic of China
| | - Qingqing Yang
- Department of Obstetrics and Gynecology, Changhai Hospital, Second Military Medical University, NO.168, Changhai Road, Shanghai, 200433, People's Republic of China
| | - Biwei Wen
- Department of Obstetrics and Gynecology, Changhai Hospital, Second Military Medical University, NO.168, Changhai Road, Shanghai, 200433, People's Republic of China
| | - Jizi Sheng
- Department of Obstetrics and Gynecology, Changhai Hospital, Second Military Medical University, NO.168, Changhai Road, Shanghai, 200433, People's Republic of China
| | - Rui Guan
- Department of Obstetrics and Gynecology, Changhai Hospital, Second Military Medical University, NO.168, Changhai Road, Shanghai, 200433, People's Republic of China.
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11
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Takashima Y, Kawaguchi A, Iwadate Y, Hondoh H, Fukai J, Kajiwara K, Hayano A, Yamanaka R. miR-101, miR-548b, miR-554, and miR-1202 are reliable prognosis predictors of the miRNAs associated with cancer immunity in primary central nervous system lymphoma. PLoS One 2020; 15:e0229577. [PMID: 32101576 PMCID: PMC7043771 DOI: 10.1371/journal.pone.0229577] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 02/11/2020] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs (miRNAs) inhibit protein function by silencing the translation of target mRNAs. However, in primary central nervous system lymphoma (PCNSL), the expression and functions of miRNAs are inadequately known. Here, we examined the expression of 847 miRNAs in 40 PCNSL patients with a microarray and investigated for the miRNA predictors associated with cancer immunity-related genes such as T helper cell type 1/2 (Th-1/Th-2) and regulatory T cell (T-reg) status, and stimulatory and inhibitory checkpoint genes, for prognosis prediction in PCNSL. The aim of this study is to find promising prognosis markers based on the miRNA expression in PCNSL. We detected 334 miRNAs related to 66 cancer immunity-related genes in the microarray profiling. Variable importance measured by the random survival forest analysis and Cox proportional hazards regression model elucidated that 11 miRNAs successfully constitute the survival formulae dividing the Kaplan-Meier curve of the respective PCNSL subgroups. On the other hand, univariate analysis shortlisted 23 miRNAs for overall survival times, with four miRNAs clearly dividing the survival curves-miR-101/548b/554/1202. These miRNAs regulated Th-1/Th-2 status, T-reg cell status, and immune checkpoints. The miRNAs were also associated with gene ontology terms as Ras/MAP-kinase, ubiquitin ligase, PRC2 and acetylation, CDK, and phosphorylation, and several diseases including acquired immunodeficiency syndrome, glioma, and those related to blood and hippocampus with statistical significance. In conclusion, the results demonstrated that the four miRNAs comprising miR-101/548b/554/1202 associated with cancer immunity can be a useful prognostic marker in PCNSL and would help us understand target pathways for PCNSL treatments.
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Affiliation(s)
- Yasuo Takashima
- Laboratory of Molecular Target Therapy for Cancer, Graduate School for Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Atsushi Kawaguchi
- Center for Comprehensive Community Medicine, Faculty of Medicine, Saga University, Saga, Japan
| | - Yasuo Iwadate
- Department of Neurosurgery, Graduate School of Medical Sciences, Chiba University, Chiba, Japan
| | - Hiroaki Hondoh
- Departments of Neurosurgery, Toyama Prefectural Central Hospital, Toyama, Japan
| | - Junya Fukai
- Department of Neurological Surgery, Wakayama Medical University School of Medicine, Wakayama, Japan
| | - Koji Kajiwara
- Department of Neurosurgery, Graduate School of Medical Sciences, Yamaguchi University, Ube, Yamaguchi, Japan
| | - Azusa Hayano
- Laboratory of Molecular Target Therapy for Cancer, Graduate School for Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Ryuya Yamanaka
- Laboratory of Molecular Target Therapy for Cancer, Graduate School for Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
- * E-mail:
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12
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Takashima Y, Kawaguchi A, Yamanaka R. Promising Prognosis Marker Candidates on the Status of Epithelial-Mesenchymal Transition and Glioma Stem Cells in Glioblastoma. Cells 2019; 8:cells8111312. [PMID: 31653034 PMCID: PMC6912254 DOI: 10.3390/cells8111312] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 10/21/2019] [Accepted: 10/22/2019] [Indexed: 12/20/2022] Open
Abstract
Multivariable analyses of global expression profiling are valid indicators of the prognosis of various diseases including brain cancers. To identify the candidates for markers of prognosis of glioblastoma, we performed multivariable analyses on the status of epithelial (EPI)-mesenchymal (MES) transition (EMT), glioma (GLI) stem cells (GSCs), molecular target therapy (MTT), and potential glioma biomarkers (PGBs) using the expression data and clinical information from patients. Random forest survival and Cox proportional hazards regression analyses indicated significant variable values for DSG3, CLDN1, CDH11, FN1, HDAC3/7, PTEN, L1CAM, OLIG2, TIMP4, IGFBP2, and GFAP. The analyses also comprised prognosis prediction formulae that could distinguish between the survival curves of the glioblastoma patients. In addition to the genes mentioned above, HDAC1, FLT1, EGFR, MGMT, PGF, STAT3, SIRT1, and GADD45A constituted complex genetic interaction networks. The calculated status scores obtained by principal component analysis indicated that GLI genes covered the status of EPI, GSC, and MTT-related genes. Moreover, survival tree analyses indicated that MEShigh, MEShighGLIlow, GSChighGLIlow, MEShighMTTlow, and PGBhigh showed poor prognoses and MESmiddle, GSClow, and PGBlow showed good prognoses, suggesting that enhanced EMT and GSC are associated with poor survival and that lower expression of EPI markers and the pre-stages of EMT are relatively less malignant in glioblastoma. These results demonstrate that the assessment of EMT and GSC enables the prediction of the prognosis of glioblastoma that would help develop novel therapeutics and de novo marker candidates for the prognoses of glioblastoma.
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Affiliation(s)
- Yasuo Takashima
- Laboratory of Molecular Target Therapy for Cancer, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan.
| | - Atsushi Kawaguchi
- Center for Comprehensive Community Medicine, Faculty of Medicine, Saga University, Saga 849-8501, Japan.
| | - Ryuya Yamanaka
- Laboratory of Molecular Target Therapy for Cancer, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan.
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13
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Differential expression of individual transcript variants of PD-1 and PD-L2 genes on Th-1/Th-2 status is guaranteed for prognosis prediction in PCNSL. Sci Rep 2019; 9:10004. [PMID: 31292525 PMCID: PMC6620277 DOI: 10.1038/s41598-019-46473-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 07/01/2019] [Indexed: 12/22/2022] Open
Abstract
In current molecular medicine, next-generation sequencing (NGS) for transcript variant detection and multivariable analyses are valid methods for evaluating gene expression, cancer mechanisms, and prognoses of patients. We conducted RNA-sequencing on samples from patients with primary central nervous system lymphoma (PCNSL) using NGS and performed multivariable analysis on gene expression data and correlations focused on Th-1/Th-2 helper T cell balance and immune checkpoint to identify diagnosis/prognosis markers and cancer immune pathways in PCNSL. We selected 84 transcript variants to limit the analysis range for Th-1/Th-2 balance and stimulatory and inhibitory checkpoints in 31 PCNSLs. Of these, 21 highly-expressed transcript variants were composed of the formulas for prognoses based on Th-1/Th-2 status and checkpoint activities. Using formulas, Th-1low, Th-2high, and stimulatory checkpointhigh resulted in poor prognoses. Further, Th-1highTh-2low was associated with good prognoses. On the other hand, CD40-001high and CD70-001high as stimulatory genes, and LAG3-001high, PDCD1 (PD-1)-001/002/003high, and PDCD1LG2 (PD-L2)-201low as inhibitory genes were associated with poor prognoses. Interestingly, Th-1highTh-2low and Th-1lowTh-2high were correlated with stimulatory checkpointlow as CD70-001low and inhibitory checkpointlow as HAVCR2 (TIM-3)-001low and PDCD1LG2-001/201low, respectively. Focused on the inhibitory checkpoint, specific variants of CD274 (PD-L1)-001 and PDCD1-002 served severe hazard ratios. In particular, PDCD1-002high by a cut off score was associated with poor prognoses, in addition to PDCD1-001/003high, PDCD1LG2-201low, and LAG3-001high. These results mainly suggest that expression of transcript variants of PDCD1 and PDCD1LG2 on the Th-1/Th-2 balance enable prognostic prediction in PCNSL. This study provides insights for development of molecular target therapies and identification of diagnosis/prognosis markers in PCNSL.
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14
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Takashima Y, Kawaguchi A, Hayano A, Yamanaka R. CD276 and the gene signature composed of GATA3 and LGALS3 enable prognosis prediction of glioblastoma multiforme. PLoS One 2019; 14:e0216825. [PMID: 31075138 PMCID: PMC6510475 DOI: 10.1371/journal.pone.0216825] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 04/29/2019] [Indexed: 01/04/2023] Open
Abstract
Glioma is the most common type of primary brain tumor, accounting for 40% of malignant brain tumors. Although a single gene may not be a marker, an expression profiling and multivariate analyses for cancer immunotherapy must estimate survival of patients. In this study, we conducted expression profiling of immunotherapy-related genes, including those in Th1/2 helper T and regulatory T cells, and stimulatory and inhibitory checkpoint molecules associated with survival prediction in 571 patients with malignant and aggressive form of gliomas, glioblastoma multiforme (GBM). Expression profiling and Random forests analysis of 21 immunosuppressive genes and Kaplan-Meier analysis in 158 patients in the training data set suggested that CD276, also known as B7-H3, could be a single gene marker candidate. Furthermore, prognosis prediction formulas, composed of Th2 cell-related GATA transcription factor 3 (GATA3) and immunosuppressive galactose-specific lectin 3 (LGALS3), based on 67 immunotherapy-related genes showed poor survival with high scores in training data set, which was also validated in another 413 patients in the test data set. The CD276 expression helped distinguish survival curves in the test data set. In addition, inhibitory checkpoint genes, including T cell immunoreceptor with Ig and ITIM domains, V-set domain containing T cell activation inhibitor 1, T-cell immunoglobulin and mucin-domain containing 3, and tumor necrosis factor receptor superfamily 14, showed potential as secondary marker candidates. These results suggest that CD276 expression and the gene signature composed of GATA3 and LGALS3 are effective for prognosis in GBM and will help us understanding target pathways for immunotherapy in GBM.
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Affiliation(s)
- Yasuo Takashima
- Laboratory of Molecular Target Therapy for Cancer, Graduate School for Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Atsushi Kawaguchi
- Center for Comprehensive Community Medicine, Faculty of Medicine, Saga University, Saga, Japan
| | - Azusa Hayano
- Laboratory of Molecular Target Therapy for Cancer, Graduate School for Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Ryuya Yamanaka
- Laboratory of Molecular Target Therapy for Cancer, Graduate School for Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
- * E-mail:
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15
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Takashima Y, Kawaguchi A, Iwadate Y, Hondoh H, Fukai J, Kajiwara K, Hayano A, Yamanaka R. MicroRNA signature constituted of miR-30d, miR-93, and miR-181b is a promising prognostic marker in primary central nervous system lymphoma. PLoS One 2019; 14:e0210400. [PMID: 30615673 PMCID: PMC6322780 DOI: 10.1371/journal.pone.0210400] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 12/15/2018] [Indexed: 02/06/2023] Open
Abstract
MicroRNAs (miRNAs) are small RNA molecules that inhibit gene function by suppressing translation of target genes. However, in primary central nervous system lymphoma (PCNSL), the biological significance of miRNAs is largely unknown, although some miRNAs are known to be prognosis markers. Here, we analyzed 847 miRNAs expressed in 27 PCNSL specimens using microarray profiling and surveyed miRNA signature for prognostic prediction. Of these, 16 miRNAs were expressed in 27 PCNSL specimens at a frequency of 48%. Their variable importance measured by Random forest model revealed miR-192, miR-486, miR-28, miR-52, miR-181b, miR-194, miR-197, miR-93, miR-708, and let-7g as having positive effects; miR-29b-2*, miR-126, and miR-182 as having negative effects; and miR-18a*, miR-425, and miR-30d as neutral. After principal component analysis, the prediction formula for prognosis, consisting of the expression values of the above-mentioned miRNAs, clearly divided Kaplan-Meier survival curves by the calculated Z-score (HR = 6.4566, P = 0.0067). The 16 miRNAs were enriched by gene ontology terms including angiogenesis, cell migration and proliferation, and apoptosis, in addition to signaling pathways including TGF-β/SMAD, Notch, TNF, and MAPKinase. Their target genes included BCL2-related genes, HMGA2 oncogene, and LIN28B cancer stem cell marker. Furthermore, three miRNAs including miR-181b, miR-30d, and miR-93, selected from the 16 miRNAs, also showed comparable results for survival (HR = 8.9342, P = 0.0007), suggestive of a miRNA signature for prognostic prediction in PCNSL. These results indicate that this miRNA signature is useful for prognostic prediction in PCNSL and would help us understand target pathways for therapies in PCNSL.
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Affiliation(s)
- Yasuo Takashima
- Laboratory of Molecular Target Therapy for Cancer, Graduate School for Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Atsushi Kawaguchi
- Center for Comprehensive Community Medicine, Faculty of Medicine, Saga University, Saga, Japan
| | - Yasuo Iwadate
- Department of Neurosurgery, Graduate School of Medical Sciences, Chiba University, Chiba, Japan
| | - Hiroaki Hondoh
- Departments of Neurosurgery, Toyama Prefectural Central Hospital, Toyama, Japan
| | - Junya Fukai
- Department of Neurological Surgery, Wakayama Medical University School of Medicine, Wakayama, Japan
| | - Koji Kajiwara
- Department of Neurosurgery, Graduate School of Medical Sciences, Yamaguchi University, Ube, Yamaguchi, Japan
| | - Azusa Hayano
- Laboratory of Molecular Target Therapy for Cancer, Graduate School for Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Ryuya Yamanaka
- Laboratory of Molecular Target Therapy for Cancer, Graduate School for Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
- * E-mail:
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16
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An Y, Bi F, You Y, Liu X, Yang Q. Development of a Novel Autophagy-related Prognostic Signature for Serous Ovarian Cancer. J Cancer 2018; 9:4058-4071. [PMID: 30410611 PMCID: PMC6218776 DOI: 10.7150/jca.25587] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Accepted: 07/23/2018] [Indexed: 12/19/2022] Open
Abstract
Purpose: Considerable evidence suggests that autophagy plays a crucial role in the biological processes of ovarian cancer. The aim of this study was to develop a novel autophagy-related prognostic signature for serous ovarian cancer. Methods: A univariate Cox proportional regression model was used to analyze mRNA microarray and clinical data in The Cancer Genome Atlas (TCGA) for the purpose of selecting autophagy-related prognostic genes. A multivariate Cox proportional regression model and the survival analysis were used to develop an eight-gene prognostic signature. The multivariate Cox and stratification analysis suggested that this signature was an independent prognostic factor for serous ovarian cancer patients. Bioinformatics functions were investigated by a principal components analysis and gene set enrichment analysis (GSEA). Finally, the correlation between the prognostic signature and gene mutation status was further analyzed in serous ovarian cancer, and especially with regard to the mutation status of BRCA1 and BRCA2 (BRCA1/2) genes. Results: Distinctly different autophagy-related gene expression profiles were identified in normal ovarian tissues and serous ovarian cancer tissues. We profiled an autophagy-related gene set and identified eight genes with significant prognostic values for serous ovarian cancer. Subsequently, an autophagy-related ovarian cancer risk signature was constructed, and patients at a high-risk or low-risk for poor prognosis were identified based on their signature. High-risk patients had significantly shorter overall survival (OS) and disease-free survival (DFS) times than low-risk patients. GSEA results suggested an enhanced intensity of autophagy regulation in high-risk patients when compared with low-risk patients. When studied as an independent prognostic factor for serous ovarian cancer, the significant prognostic value of this signature could be seen in the stratified cohorts. For clinical use, we developed a nomogram that included the prognostic classifier and seven clinical risk factors. Additionally, we identified the 10 most frequently mutated genes found in serous ovarian cancer patients, and analyzed them for their differences in high-risk and low-risk patients. Among 293 patients, 62 had BRCA1/2 gene mutations, and this result was significantly correlated with the autophagy-related prognostic signature. Conclusions: Our findings suggest that the eight-gene autophagy-related signature could serve as an independent prognostic indicator for cases of serous ovarian cancer.
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Affiliation(s)
- Yuanyuan An
- Department of Gynecology and Obstetrics, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Fangfang Bi
- Department of Gynecology and Obstetrics, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Yue You
- Department of Gynecology and Obstetrics, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Xinhui Liu
- Department of Gynecology and Obstetrics, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
| | - Qing Yang
- Department of Gynecology and Obstetrics, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, P.R. China
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17
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Dong C, Cui D, Liu G, Xu H, Peng X, Duan J, Liu L. Cancer stem cell associated eight gene-based signature predicts clinical outcomes of colorectal cancer. Oncol Lett 2018; 17:442-449. [PMID: 30655785 DOI: 10.3892/ol.2018.9533] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 07/20/2017] [Indexed: 12/21/2022] Open
Abstract
Previous studies have suggested that cancer stem cells serve crucial functions in tumorigenesis, metastasis and therapy failure. Stem cell signaling transduction pathways are frequently dysregulated in cancer and associated with tumorigenesis, metastasis and the cell cycle, which are necessary for cancer proliferation. However, cancer stem cell-associated gene signatures have not been established for predicting patient outcomes in colorectal cancer. Using a gene-mining approach, the present study performed mRNA expression profiling in large colorectal cancer cohorts from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) database, including a TCGA colorectal cancer cohort (n=383) and three independent validation series GSE39582 (n=582), GSE17536 (n=177) and GSE17537 (n=55). The present study identified that an eight-gene signature in cancer stem cell signaling was associated with the overall survival and disease/recurrence-free survival of patients with colorectal. On the basis of this signature, patients in the TCGA training sets were divided into high-risk and low-risk subgroups with a significantly different overall survival rate (hazard ratio, 2.38; P=0.0005). The prognostic value of this signature was confirmed using three independent GEO colorectal cancer sets. Identifying this prognostic stem cell signaling signature may provide an efficient classification tool for clinical prognosis evaluation, and facilitate cancer stem cell-targeted therapy.
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Affiliation(s)
- Chuanpeng Dong
- Institute of Biomedical Sciences, Fudan University, Shanghai 200032, P.R. China
| | - Danni Cui
- Institute of Biomedical Sciences, Fudan University, Shanghai 200032, P.R. China
| | - Gang Liu
- Institute of Biomedical Sciences, Fudan University, Shanghai 200032, P.R. China
| | - Huilin Xu
- Institute of Biomedical Sciences, Fudan University, Shanghai 200032, P.R. China
| | - Xueqing Peng
- Institute of Biomedical Sciences, Fudan University, Shanghai 200032, P.R. China
| | - Juan Duan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian 350004, P.R. China.,Translational Medicine Institute, Fujian Medical University, Fuzhou, Fujian 350004, P.R. China
| | - Lei Liu
- Institute of Biomedical Sciences, Fudan University, Shanghai 200032, P.R. China
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18
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Miyasato Y, Takashima Y, Takeya H, Yano H, Hayano A, Nakagawa T, Makino K, Takeya M, Yamanaka R, Komohara Y. The expression of PD-1 ligands and IDO1 by macrophage/microglia in primary central nervous system lymphoma. J Clin Exp Hematop 2018; 58:95-101. [PMID: 29998979 DOI: 10.3960/jslrt.18001] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Recent progress in anti-tumor immunotherapy has focused on the significance of the tumor microenvironment in tumor progression and resistance to chemo/radio-therapy. Myeloid cells such as macrophages are predominant stromal components in hematological malignancies. In the present study, we investigated the regulation of programmed death-1 (PD-1) ligand expression in primary central nervous system lymphoma (PCNSL) using PCNSL cell lines and human monocyte-derived macrophages. TK PCNSL cell line-derived soluble factors induced overexpression of PD-1 ligands, indoleamine 2,3-dioxygenase (IDO1), and several other cytokines in macrophages. The expression of PD-1 ligands was dependent on the activation of signal transducer and activator of transcription 3. PD-L1 and IDO1 were overexpressed by macrophage/microglia in PCNSL tissues, and gene expression profiling indicated that IDO1 expression was positively correlated with the expression of macrophage and lymphocyte markers. Macrophage-derived factors did not influence the proliferation or chemo-sensitivity of cell lines. These data suggest that the expression of immunosuppressive molecules, including PD-1 ligands and IDO1, by macrophage/microglia may be involved in immune evasion of lymphoma cells.
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19
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Abstract
Objective: Primary central nervous system lymphoma (PCNSL) is a specific type of non-Hodgkin lymphoma with poor prognosis. The rare incidence of this disease and difficulty to obtain sufficient tissue material impede deep research into PCNSL. However, application of modern molecular techniques makes it possible to find biological characteristics exclusive to PCNSL. Therefore, we systematically reviewed the latest research progress on biological characteristics and pathogenesis of PCNSL. Data Sources: The data analyzed in this review were from the articles listed in PubMed database. Study Selection: Articles focusing on the biology of PCNSL at the cytogenetic or molecular level were reviewed, including clinical, basic research, and review articles. Results: With respect to histopathology, perivascular growth pattern and reactive perivascular T-cell infiltration are regarded as typical histopathological manifestations of tumor cells in PCNSL. Moreover, tumor cells of PCNSL predominantly express an activated B-cell-like phenotype, including CD10− BCL-6+ MUM1+, CD10− BCL-6− MUM1+, and CD10− BCL-6− MUM1−. On the molecular level, some molecular and genetic alterations may contribute to malignant transformation, including mutations of proto-oncogenes and tumor suppressor genes, gains and losses of genetic material, as well as aberrant activation of some important signaling pathways, such as nuclear factor-κB and JAK/STAT pathway. Conclusions: The integrated molecular mechanisms involved in pathogenesis of PCNSL are not well understood. The important biomarkers indicating prognosis are not identified. Multicenter studies should be carried out to elucidate pathogenesis of PCNSL to find novel and effective therapeutic strategies.
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Affiliation(s)
- Xue-Liang Yang
- Department of Hematology, Beijing Tiantan Hospital, Capital Medical University, Beijing 100050, China
| | - Yuan-Bo Liu
- Department of Hematology, Beijing Tiantan Hospital, Capital Medical University, Beijing 100050, China
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20
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Takashima Y, Kawaguchi A, Kanayama T, Hayano A, Yamanaka R. Correlation between lower balance of Th2 helper T-cells and expression of PD-L1/PD-1 axis genes enables prognostic prediction in patients with glioblastoma. Oncotarget 2018; 9:19065-19078. [PMID: 29721184 PMCID: PMC5922378 DOI: 10.18632/oncotarget.24897] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 03/06/2018] [Indexed: 12/18/2022] Open
Abstract
Common cancer treatments include radiation therapy, chemotherapy including molecular targeted drugs and anticancer drugs, and surgical treatment. Recent studies have focused on investigating the mechanisms by which immune cells attack cancer cells and produce immune tolerance-suppressing cytokines, as well as on their potential application in cancer immunotherapy. We conducted expression profiling of CD274 (PD-L1), GATA3, IFNG, IL12R, IL12RB2, IL4, PDCD1 (PD-1), PDCD1LG2 (PD-L2), and TBX21 (T-bet) using data of 158 glioblastoma multiforme (GBM) patients with clinical information available at The Cancer Genome Atlas. Principal component analysis of the expression profiling data was used to derive an equation for evaluating the status of Th1 and Th2 cells. GBM specimens were divided based on the median of the Th scores. The results revealed that Th1HighTh2Low and Th1LowTh2Low statuses indicated better prognosis than Th1HighTh2High, and were evaluated based on the downregulation of PD-L1, PD-L2, and PD-1. Furthermore, Th2Low divided based on the threshold, as well as CD274Low and PDCD1Low, were associated with good prognosis. In the Th2Low subgroup, 14 genes were identified as potential prognostic markers. Of these, SLC11A1Low, TNFRSF1BLow, and LTBRLow also indicated good prognosis. These results suggest that low Th2 balance and low activity of the PD-L1/PD-1 axis predict good prognosis in GBM. The set of genes identified in the present study could reliably predict survival in GBM patients and serve as useful molecular markers. Furthermore, this set of genes could prove to be novel targets for cancer immunotherapy.
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Affiliation(s)
- Yasuo Takashima
- Laboratory of Molecular Target Therapy for Cancer, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan
| | - Atsushi Kawaguchi
- Center for Comprehensive Community Medicine, Faculty of Medicine, Saga University, Saga 849-8501, Japan
| | - Tomohiko Kanayama
- Laboratory of Molecular Target Therapy for Cancer, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan
| | - Azusa Hayano
- Laboratory of Molecular Target Therapy for Cancer, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan
| | - Ryuya Yamanaka
- Laboratory of Molecular Target Therapy for Cancer, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan
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21
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Zhan X, Dong C, Liu G, Li Y, Liu L. Panel of seven long noncoding RNA as a candidate prognostic biomarker for ovarian cancer. Onco Targets Ther 2017; 10:2805-2813. [PMID: 28620265 PMCID: PMC5466362 DOI: 10.2147/ott.s128797] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Ovarian cancer is one of the most common and lethal gynecological malignancies. The diagnosis of ovarian cancer is often at an advanced stage. Accumulated evidence suggests that long noncoding RNAs (lncRNAs) play important roles during ovarian tumorigenesis. In this study, using the lncRNA-mining approach, we analyzed lncRNA expression profiles of 493 ovarian cancer patients from Gene Expression Omnibus datasets, and identified a signature group of seven lncRNAs (BC037530, AK021924, AK094536, AK094536, BC062365, BC004123 and BC007937) associated with patient survival in the training dataset GSE9891. We also formulated a risk score model to divide patients into low-risk and high-risk groups based on the expression of these seven lncRNAs. We further validated the predictive power of our risk score model in two other datasets, GSE26193 and GSE63885. Our analysis showed that the seven-lncRNA signature can serve as an independent predictor apart from Federation of Gynecology and Obstetrics (FIGO) stage and patient age. Further investigation revealed the seven-lncRNA signature correlated with few critical signaling pathways involved in cancer. Combined, all these findings strongly support that the seven-lncRNA signature can serve as a strong prognosis biomarker.
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Affiliation(s)
- Xiaohui Zhan
- Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai.,University of Chinese Academy of Sciences, Beijing
| | - Chuanpeng Dong
- Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai
| | - Gang Liu
- Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai
| | - Yixue Li
- Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai.,University of Chinese Academy of Sciences, Beijing.,Shanghai Center for Bioinformation Technology, Shanghai Industrial Technology Institute, Shanghai, People's Republic of China
| | - Lei Liu
- Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai
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22
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Zheng S, Zheng D, Dong C, Jiang J, Xie J, Sun Y, Chen H. Development of a novel prognostic signature of long non-coding RNAs in lung adenocarcinoma. J Cancer Res Clin Oncol 2017; 143:1649-1657. [PMID: 28409273 DOI: 10.1007/s00432-017-2411-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 03/29/2017] [Indexed: 12/30/2022]
Abstract
OBJECTIVES Increasing evidence suggests that long non-coding RNAs (lncRNAs) may play a crucial role in many biological processes in a variety of cancers and serve as the basis for many clinical applications including prognostic biomarkers and potential therapeutic targets. The aim of this study is to develop a prognostic lncRNA signature with RNA-seq data in lung adenocarcinomas. METHODS LncRNA expression profiles and clinical data of lung adenocarcinoma patients from The Cancer Genome Atlas (TCGA) were analyzed. Univariate Cox proportional regression model was used to identify prognostic lncRNAs, and then multivariate Cox proportional regression model was used to develop a prognostic signature. Survivals were compared using log-rank test, and the biological implications of prognostic lncRNAs were analyzed using the KEGG pathway functional enrichment analysis. RESULTS We identified eight lncRNAs which had prognostic association with p value <0.01 in a TCGA lung adenocarcinoma cohort of 478 patients. Then a novel prognostic signature with the eight lncRNAs was developed using Cox regression model. Signature high-risk cases had worse overall survival (OS, median 85.97 vs. 38.34 months, p < 0.001) and disease-free survival (DFS, median 44.02 vs. 26.58 months, p = 0.007) than low-risk cases. Multivariate Cox regression analysis suggested that the eight-lncRNA signature was independent of clinical and pathological factors. KEGG pathway functional enrichment analysis indicated potential functional roles of the eight prognostic lncRNAs in tumorigenesis. CONCLUSIONS Our findings suggest that the eight-lncRNA signature might provide an effective independent prognostic model for the prediction of lung adenocarcinoma patients.
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Affiliation(s)
- Shanbo Zheng
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai, 200032, People's Republic of China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Difan Zheng
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai, 200032, People's Republic of China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Chuanpeng Dong
- Institute of Biomedical Sciences, Fudan University, Shanghai, China
| | - Jiahua Jiang
- Department of Translational Medicine, Shanghai Hengrui Pharmaceuticals Co. Ltd., Shanghai, China
| | - Juntao Xie
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai, 200032, People's Republic of China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yihua Sun
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai, 200032, People's Republic of China. .,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Haiquan Chen
- Department of Thoracic Surgery, Fudan University Shanghai Cancer Center, 270 Dong-An Road, Shanghai, 200032, People's Republic of China. .,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
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23
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A potential panel of four-long noncoding RNA signature in prostate cancer predicts biochemical recurrence-free survival and disease-free survival. Int Urol Nephrol 2017; 49:825-835. [DOI: 10.1007/s11255-017-1536-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 01/31/2017] [Indexed: 12/28/2022]
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24
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Kishimoto W, Nishikori M, Arima H, Miyoshi H, Sasaki Y, Kitawaki T, Shirakawa K, Kato T, Imaizumi Y, Ishikawa T, Ohno H, Haga H, Ohshima K, Takaori-Kondo A. Expression of Tim-1 in primary CNS lymphoma. Cancer Med 2016; 5:3235-3245. [PMID: 27709813 PMCID: PMC5119979 DOI: 10.1002/cam4.930] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 09/07/2016] [Accepted: 09/07/2016] [Indexed: 11/16/2022] Open
Abstract
Primary central nervous system lymphoma (PCNSL) is a distinct subtype of extranodal lymphoma with aggressive clinical course and poor outcome. As increased IL‐10/IL‐6 ratio is recognized in the cerebrospinal fluid (CSF) of PCNSL patients, we hypothesized that PCNSL might originate from a population of B cells with high IL‐10‐producing capacity, an equivalent of “regulatory B cells” in mice. We intended in this study to clarify whether Tim‐1, a molecule known as a marker for regulatory B cells in mice, is expressed in PCNSL. By immunohistochemical analysis, Tim‐1 was shown to be positive in as high as 54.2% of PCNSL (26 of 58 samples), while it was positive in 19.1% of systemic diffuse large B‐cell lymphoma (DLBCL) samples (17 of 89 samples; P < 0.001). Tim‐1 expression positively correlated with IL‐10 expression in PCNSL (Cramer's V = 0.55, P < 0.001), and forced expression of Tim‐1 in a PCNSL cell line resulted in increased IL‐10 secretion, suggesting that Tim‐1 is functionally linked with IL‐10 production in PCNSL. Moreover, soluble Tim‐1 was detectable in the CSF of PCNSL patients, and was suggested to parallel disease activity. In summary, PCNSL is characterized by frequent Tim‐1 expression, and its soluble form in CSF may become a useful biomarker for PCNSL.
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Affiliation(s)
- Wataru Kishimoto
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Momoko Nishikori
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiroshi Arima
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiroaki Miyoshi
- Department of Pathology, Kurume University School of Medicine, Asahimachi, Kurume, Fukuoka, Japan
| | - Yuya Sasaki
- Department of Pathology, Kurume University School of Medicine, Asahimachi, Kurume, Fukuoka, Japan
| | - Toshio Kitawaki
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kotaro Shirakawa
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takeharu Kato
- Department of Hematology, Nagasaki University Hospital, Sakamoto, Nagasaki, Japan
| | - Yoshitaka Imaizumi
- Department of Hematology, Nagasaki University Hospital, Sakamoto, Nagasaki, Japan
| | - Takayuki Ishikawa
- Department of Hematology, Kobe City Medical Center General Hospital, Kobe, Hyogo, Japan
| | - Hitoshi Ohno
- Department of Hematology, Tenri Hospital, Mishima-cho, Tenri, Nara, Japan
| | - Hironori Haga
- Department of Pathology, Kyoto University Hospital, Kyoto, Japan
| | - Koichi Ohshima
- Department of Pathology, Kurume University School of Medicine, Asahimachi, Kurume, Fukuoka, Japan
| | - Akifumi Takaori-Kondo
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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25
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Zhu X, Tian X, Yu C, Shen C, Yan T, Hong J, Wang Z, Fang JY, Chen H. A long non-coding RNA signature to improve prognosis prediction of gastric cancer. Mol Cancer 2016; 15:60. [PMID: 27647437 PMCID: PMC5029104 DOI: 10.1186/s12943-016-0544-0] [Citation(s) in RCA: 139] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 09/07/2016] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Increasing evidence suggests long non-coding RNAs (lncRNAs) are frequently aberrantly expressed in cancers, however, few related lncRNA signatures have been established for prediction of cancer prognosis. We aimed at developing alncRNA signature to improve prognosis prediction of gastric cancer (GC). METHODS Using a lncRNA-mining approach, we performed lncRNA expression profiling in large GC cohorts from Gene Expression Ominus (GEO), including GSE62254 data set (N = 300) and GSE15459 data set (N = 192). We established a set of 24-lncRNAs that were significantly associated with the disease free survival (DFS) in the test series. RESULTS Based on this 24-lncRNA signature, the test series patients could be classified into high-risk or low-risk subgroup with significantly different DFS (HR = 1.19, 95 % CI = 1.13-1.25, P < 0.0001). The prognostic value of this 24-lncRNA signature was confirmed in the internal validation series and another external validation series, respectively. Further analysis revealed that the prognostic value of this signature was independent of lymph node ratio (LNR) and postoperative chemotherapy. Gene set enrichment analysis (GSEA) indicated that high risk score group was associated with several cancer recurrence and metastasis associated pathways. CONCLUSIONS The identification of the prognostic lncRNAs indicates the potential roles of lncRNAs in GC biogenesis. Our results may provide an efficient classification tool for clinical prognosis evaluation of GC.
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Affiliation(s)
- Xiaoqiang Zhu
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai Institute of Digestive Disease, 145 Middle Shandong Road, Shanghai, 200001 China
| | - Xianglong Tian
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai Institute of Digestive Disease, 145 Middle Shandong Road, Shanghai, 200001 China
| | - Chenyang Yu
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai Institute of Digestive Disease, 145 Middle Shandong Road, Shanghai, 200001 China
| | - Chaoqin Shen
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai Institute of Digestive Disease, 145 Middle Shandong Road, Shanghai, 200001 China
| | - Tingting Yan
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai Institute of Digestive Disease, 145 Middle Shandong Road, Shanghai, 200001 China
| | - Jie Hong
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai Institute of Digestive Disease, 145 Middle Shandong Road, Shanghai, 200001 China
| | - Zheng Wang
- Department of gastrointestinal surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127 China
| | - Jing-Yuan Fang
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai Institute of Digestive Disease, 145 Middle Shandong Road, Shanghai, 200001 China
| | - Haoyan Chen
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai Institute of Digestive Disease, 145 Middle Shandong Road, Shanghai, 200001 China
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26
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Park H, Niida A, Miyano S, Imoto S. Sparse Overlapping Group Lasso for Integrative Multi-Omics Analysis. J Comput Biol 2015; 22:73-84. [PMID: 25629319 DOI: 10.1089/cmb.2014.0197] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
- Heewon Park
- Human Genome Center, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan
| | - Atushi Niida
- Human Genome Center, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan
| | - Satoru Miyano
- Human Genome Center, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan
| | - Seiya Imoto
- Human Genome Center, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan
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27
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Meng J, Li P, Zhang Q, Yang Z, Fu S. A four-long non-coding RNA signature in predicting breast cancer survival. J Exp Clin Cancer Res 2014; 33:84. [PMID: 25288503 PMCID: PMC4198622 DOI: 10.1186/s13046-014-0084-7] [Citation(s) in RCA: 130] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2014] [Accepted: 09/24/2014] [Indexed: 11/12/2022] Open
Abstract
Background Many long non-coding RNAs(lncRNAs) have been found to be a good marker for several tumors. Using lncRNA-mining approach, we aimed to identify lncRNA expression signature that can predict breast cancer patient survival. Methods We performed LncRNA expression profiling in 887 breast cancer patients from Gene Expression Omnibus (GEO) datasets. The association between lncRNA signature and clinical survival was analyzed using the training set(n = 327, from GSE 20685). The validation for the association was performed in another three independent testing sets(252 from GSE21653, 204 from GSE12276, and 104 from GSE42568). Results A set of four lncRNA genes (U79277, AK024118, BC040204, AK000974) have been identified by the random survival forest algorithm. Using a risk score based on the expression signature of these lncRNAs, we separated the patients into low-risk and high-risk groups with significantly different survival times in the training set. This signature was validated in the other three cohorts. Further study revealed that the four-lncRNA expression signature was independent of age and subtype. Gene Set Enrichment Analysis (GSEA) suggested that gene sets were involved in several cancer metastasis related pathways. Conclusions These findings indicate that lncRNAs may be implicated in breast cancer pathogenesis. The four-lncRNA signature may have clinical implications in the selection of high-risk patients for adjuvant therapy. Electronic supplementary material The online version of this article (doi:10.1186/s13046-014-0084-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jin Meng
- Department of Radiation Oncology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, 600 Yi Shan Rd, Shanghai, 200233, China.
| | - Ping Li
- Department of Radiation Oncology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, 600 Yi Shan Rd, Shanghai, 200233, China.
| | - Qing Zhang
- Radiation Oncology Center, Fudan University Shanghai Cancer Center (FUSCC), 399 LingLing Rd, Xu Hui District, Shanghai, 200032, China. .,Radiation Oncology Department, Shanghai Proton and Heavy Ion Center (SPHIC), 4365 Kang Xin Rd, Pudong New District, Shanghai, 201321, China.
| | - Zhangru Yang
- Department of Radiation Oncology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, 600 Yi Shan Rd, Shanghai, 200233, China.
| | - Shen Fu
- Radiation Oncology Center, Fudan University Shanghai Cancer Center (FUSCC), 399 LingLing Rd, Xu Hui District, Shanghai, 200032, China. .,Radiation Oncology Department, Shanghai Proton and Heavy Ion Center (SPHIC), 4365 Kang Xin Rd, Pudong New District, Shanghai, 201321, China.
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28
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Non-deep-seated primary CNS lymphoma: therapeutic responses and a molecular signature. J Neurooncol 2014; 117:261-8. [DOI: 10.1007/s11060-014-1379-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 01/19/2014] [Indexed: 10/25/2022]
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29
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Kawaguchi A, Yajima N, Tsuchiya N, Homma J, Sano M, Natsumeda M, Takahashi H, Fujii Y, Kakuma T, Yamanaka R. Gene expression signature-based prognostic risk score in patients with glioblastoma. Cancer Sci 2013; 104:1205-10. [PMID: 23745793 DOI: 10.1111/cas.12214] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Revised: 05/22/2013] [Accepted: 05/29/2013] [Indexed: 12/20/2022] Open
Abstract
The present study aimed to identify genes associated with patient survival to improve our understanding of the underlying biology of gliomas. We investigated whether the expression of genes selected using random survival forests models could be used to define glioma subgroups more objectively than standard pathology. The RNA from 32 non-treated grade 4 gliomas were analyzed using the GeneChip Human Genome U133 Plus 2.0 Expression array (which contains approximately 47 000 genes). Twenty-five genes whose expressions were strongly and consistently related to patient survival were identified. The prognosis prediction score of these genes was most significant among several variables and survival analyses. The prognosis prediction score of three genes and age classifiers also revealed a strong prognostic value among grade 4 gliomas. These results were validated in an independent samples set (n = 488). Our method was effective for objectively classifying grade 4 gliomas and was a more accurate prognosis predictor than histological grading.
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Affiliation(s)
- Atsushi Kawaguchi
- Biostatistic Center, Kurume University School of Medicine, Kurume, Japan
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