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Martins S, Coletti R, Lopes MB. Disclosing transcriptomics network-based signatures of glioma heterogeneity using sparse methods. BioData Min 2023; 16:26. [PMID: 37752578 PMCID: PMC10523751 DOI: 10.1186/s13040-023-00341-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 08/13/2023] [Indexed: 09/28/2023] Open
Abstract
Gliomas are primary malignant brain tumors with poor survival and high resistance to available treatments. Improving the molecular understanding of glioma and disclosing novel biomarkers of tumor development and progression could help to find novel targeted therapies for this type of cancer. Public databases such as The Cancer Genome Atlas (TCGA) provide an invaluable source of molecular information on cancer tissues. Machine learning tools show promise in dealing with the high dimension of omics data and extracting relevant information from it. In this work, network inference and clustering methods, namely Joint Graphical lasso and Robust Sparse K-means Clustering, were applied to RNA-sequencing data from TCGA glioma patients to identify shared and distinct gene networks among different types of glioma (glioblastoma, astrocytoma, and oligodendroglioma) and disclose new patient groups and the relevant genes behind groups' separation. The results obtained suggest that astrocytoma and oligodendroglioma have more similarities compared with glioblastoma, highlighting the molecular differences between glioblastoma and the others glioma subtypes. After a comprehensive literature search on the relevant genes pointed our from our analysis, we identified potential candidates for biomarkers of glioma. Further molecular validation of these genes is encouraged to understand their potential role in diagnosis and in the design of novel therapies.
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Affiliation(s)
- Sofia Martins
- NOVA School of Science and Technology, NOVA University of Lisbon, Caparica, 2829-516, Portugal
| | - Roberta Coletti
- Center for Mathematics and Applications (NOVA Math), NOVA School of Science and Technology, Caparica, 2829-516, Portugal.
| | - Marta B Lopes
- NOVA School of Science and Technology, NOVA University of Lisbon, Caparica, 2829-516, Portugal.
- Center for Mathematics and Applications (NOVA Math), NOVA School of Science and Technology, Caparica, 2829-516, Portugal.
- NOVA Laboratory for Computer Science and Informatics (NOVA LINCS), NOVA School of Science and Technology, Caparica, 2829-516, Portugal.
- UNIDEMI, Department of Mechanical and Industrial Engineering, NOVA School of Science and Technology, Caparica, 2829-516, Portugal.
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2
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Cao W, Xiong L, Meng L, Li Z, Hu Z, Lei H, Wu J, Song T, Liu C, Wei R, Shen L, Hong J. Prognostic analysis and nomogram construction for older patients with IDH-wild-type glioblastoma. Heliyon 2023; 9:e18310. [PMID: 37519736 PMCID: PMC10372674 DOI: 10.1016/j.heliyon.2023.e18310] [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: 05/24/2022] [Revised: 07/06/2023] [Accepted: 07/13/2023] [Indexed: 08/01/2023] Open
Abstract
As many countries face an ageing population, the number of older patients with glioblastoma (GB) is increasing. Thus, there is an urgent need for prognostic models to aid in treatment decision-making and life planning. A total of 98 patients with isocitrate dehydrogenase (IDH)-wild-type GB aged ≥65 years were analysed from January 2012 to January 2020. Independent prognostic factors were identified by prognostic analysis. Using the independent prognostic factors for overall survival (OS), a nomogram was constructed by R software to predict the prognosis of older patients with IDH-wild-type GB. The concordance index (C-index) and receiver operating characteristic (ROC) curve were used to assess model discrimination, and the calibration curve was used to assess model calibration. Prognostic analysis showed that the extent of resection (EOR), adjusted Charlson comorbidity index (ACCI), O6-methylguanine-DNA methyltransferase (MGMT) methylation status, postoperative radiotherapy, and postoperative temozolomide (TMZ) chemotherapy were independent prognostic factors for OS. MGMT methylation status and subventricular zone (SVZ) involvement were independent prognostic factors for progression-free survival (PFS). A nomogram was constructed based on EOR, ACCI, MGMT methylation status, postoperative radiotherapy and postoperative TMZ chemotherapy to predict the 6-month, 12-month and 18-month OS of older patients with IDH-wild-type GB. The C-index of the nomogram was 0.72, and the ROC curves showed that the areas under the curve (AUCs) at 6, 12 and 18 months were 0.874, 0.739 and 0.779, respectively. The calibration plots showed that the nomogram was in good agreement with the actual observations in predicting the OS of older patients with IDH-wild-type GB. Older patients with IDH-wild-type GB can benefit from gross total resection (GTR), postoperative radiotherapy and postoperative TMZ chemotherapy. A high ACCI score and MGMT nonmethylation are poor prognostic factors. We constructed a nomogram including the ACCI to facilitate clinical decision-making and follow-up interval selection.
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Affiliation(s)
- Wenjun Cao
- Department of Hematology and Oncology, The First Hospital of Changsha, People's Republic of China
| | - Luqi Xiong
- Department of Oncology, Xiangya Hospital, Central South University, People's Republic of China
| | - Li Meng
- Department of Radiology, Xiangya Hospital, Central South University, People's Republic of China
| | - Zhanzhan Li
- Department of Oncology, Xiangya Hospital, Central South University, People's Republic of China
| | - Zhongliang Hu
- Department of Pathology, Xiangya Hospital, Central South University, People's Republic of China
| | - Huo Lei
- Department of Neurosurgery, Xiangya Hospital, Central South University, People's Republic of China
| | - Jun Wu
- Department of Neurosurgery, Xiangya Hospital, Central South University, People's Republic of China
| | - Tao Song
- Department of Neurosurgery, Xiangya Hospital, Central South University, People's Republic of China
| | - Chao Liu
- Department of Oncology, Xiangya Hospital, Central South University, People's Republic of China
| | - Rui Wei
- Department of Oncology, Xiangya Hospital, Central South University, People's Republic of China
| | - Liangfang Shen
- Department of Oncology, Xiangya Hospital, Central South University, People's Republic of China
| | - Jidong Hong
- Department of Oncology, Xiangya Hospital, Central South University, People's Republic of China
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3
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Wang Y, Li J, Cao Y, Chen W, Xing H, Guo X, Shi Y, Wang Y, Liang T, Ye L, Liu D, Yang T, Wang Y, Ma W. Characteristic analysis and identification of novel molecular biomarkers in elderly glioblastoma patients using the 2021 WHO Classification of Central Nervous System Tumors. Front Neurosci 2023; 17:1165823. [PMID: 37360159 PMCID: PMC10288210 DOI: 10.3389/fnins.2023.1165823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 05/19/2023] [Indexed: 06/28/2023] Open
Abstract
Introduction Elderly glioblastoma (GBM) patients is characterized by high incidence and poor prognosis. Currently, however, there is still a lack of adequate molecular characterization of elderly GBM patients. The fifth edition of the WHO Classification of Central Nervous System Tumors (WHO5) gives a new classification approach for GBM, and the molecular characteristics of elderly GBM patients need to be investigated under this new framework. Methods The clinical and radiological features of patients with different classifications and different ages were compared. Potential prognostic molecular markers in elderly GBM patients under the WHO5 classification were found using Univariate Cox regression and Kaplan-Meier survival analysis. Results A total of 226 patients were included in the study. The prognostic differences between younger and elderly GBM patients were more pronounced under the WHO5 classification. Neurological impairment was more common in elderly patients (p = 0.001), while intracranial hypertension (p = 0.034) and epilepsy (p = 0.038) were more common in younger patients. Elderly patients were more likely to have higher Ki-67(p = 0.013), and in elderly WHO5 GBM patients, KMT5B (p = 0.082), KRAS (p = 0.1) and PPM1D (p = 0.055) were each associated with overall survival (OS). Among them, KRAS and PPM1D were found to be prognostic features unique to WHO5 elderly GBM patients. Conclusion Our study demonstrates that WHO5 classification can better distinguish the prognosis of elderly and younger GBM. Furthermore, KRAS and PPM1D may be potential prognostic predictors in WHO5 elderly GBM patients. The specific mechanism of these two genes in elderly GBM remains to be further studied.
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Affiliation(s)
- Yaning Wang
- Department of Neurosurgery, Center for Malignant Brain Tumors, National Glioma MDT Alliance, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Junlin Li
- Department of Neurosurgery, Center for Malignant Brain Tumors, National Glioma MDT Alliance, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Eight-Year Medical Doctor Program, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yaning Cao
- Department of Neurosurgery, Center for Malignant Brain Tumors, National Glioma MDT Alliance, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Eight-Year Medical Doctor Program, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wenlin Chen
- Department of Neurosurgery, Center for Malignant Brain Tumors, National Glioma MDT Alliance, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hao Xing
- Department of Neurosurgery, Center for Malignant Brain Tumors, National Glioma MDT Alliance, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiaopeng Guo
- Department of Neurosurgery, Center for Malignant Brain Tumors, National Glioma MDT Alliance, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- China Anti-Cancer Association Specialty Committee of Glioma, Beijing, China
| | - Yixin Shi
- Department of Neurosurgery, Center for Malignant Brain Tumors, National Glioma MDT Alliance, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Eight-Year Medical Doctor Program, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuekun Wang
- Department of Neurosurgery, Center for Malignant Brain Tumors, National Glioma MDT Alliance, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Tingyu Liang
- Department of Neurosurgery, Center for Malignant Brain Tumors, National Glioma MDT Alliance, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Liguo Ye
- Department of Neurosurgery, Center for Malignant Brain Tumors, National Glioma MDT Alliance, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Delin Liu
- Department of Neurosurgery, Center for Malignant Brain Tumors, National Glioma MDT Alliance, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Eight-Year Medical Doctor Program, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Tianrui Yang
- Department of Neurosurgery, Center for Malignant Brain Tumors, National Glioma MDT Alliance, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Eight-Year Medical Doctor Program, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yu Wang
- Department of Neurosurgery, Center for Malignant Brain Tumors, National Glioma MDT Alliance, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- China Anti-Cancer Association Specialty Committee of Glioma, Beijing, China
| | - Wenbin Ma
- Department of Neurosurgery, Center for Malignant Brain Tumors, National Glioma MDT Alliance, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- China Anti-Cancer Association Specialty Committee of Glioma, Beijing, China
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4
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Chatsirisupachai K, Lagger C, de Magalhães JP. Age-associated differences in the cancer molecular landscape. Trends Cancer 2022; 8:962-971. [PMID: 35811230 DOI: 10.1016/j.trecan.2022.06.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/11/2022] [Accepted: 06/13/2022] [Indexed: 12/24/2022]
Abstract
Cancer is an age-related disease, as incidence and mortality for most types of cancer increase with age. However, how molecular alterations in tumors differ among patients of different ages remains poorly understood. Recent studies have shed light on the age-associated molecular landscapes in cancer. Here, we summarize the main findings of these current studies, highlighting major differences in the genomic, transcriptomic, epigenetic, and immunological landscapes between cancer in younger and older patients. Importantly, some cancer driver genes are mutated more frequently in younger or older patients. We discuss the potential roles of aging-related processes in shaping these age-related differences in cancer. We further emphasize the remaining unsolved questions that could provide important insights that will have implications in personalized medicine.
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Affiliation(s)
- Kasit Chatsirisupachai
- Integrative Genomics of Ageing Group, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool L7 8TX, UK.
| | - Cyril Lagger
- Integrative Genomics of Ageing Group, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool L7 8TX, UK
| | - João Pedro de Magalhães
- Integrative Genomics of Ageing Group, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool L7 8TX, UK.
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5
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Arakawa Y, Mineharu Y, Uto M, Mizowaki T. Optimal managements of elderly patients with glioblastoma. Jpn J Clin Oncol 2022; 52:833-842. [PMID: 35552425 PMCID: PMC9841411 DOI: 10.1093/jjco/hyac075] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 04/19/2022] [Indexed: 01/21/2023] Open
Abstract
Optimizing the management of elderly patients with glioblastoma is an ongoing task in neuro-oncology. The number of patients with this tumor type is gradually increasing with the aging of the population. Although available data and practice recommendations remain limited, the current strategy is maximal safe surgical resection followed by radiotherapy in combination with temozolomide. However, survival is significantly worse than that in the younger population. Surgical resection provides survival benefit in patients with good performance status. Hypofractionated radiotherapy decreases toxicities while maintaining therapeutic efficacy, thus improving treatment adherence and subsequently leading to better quality of life. The intensity of these treatments should be balanced with patient-specific factors and consideration of quality of life. This review discusses the current optimal management in terms of efficacy and safety, as well as future perspectives.
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Affiliation(s)
- Yoshiki Arakawa
- For reprints and all correspondence: Department of Neurosurgery, Kyoto University Graduate School of Medicine, 54 Kawaharacho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan. E-mail: ; Department of Radiation Oncology and Image-Applied Therapy, Kyoto University Graduate School of Medicine, 54 Kawaharacho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan. E-mail:
| | - Yohei Mineharu
- Department of Neurosurgery, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Megumi Uto
- Department of Radiation Oncology and Image-Applied Therapy, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Takashi Mizowaki
- For reprints and all correspondence: Department of Neurosurgery, Kyoto University Graduate School of Medicine, 54 Kawaharacho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan. E-mail: ; Department of Radiation Oncology and Image-Applied Therapy, Kyoto University Graduate School of Medicine, 54 Kawaharacho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan. E-mail:
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6
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Schwartz KA, Noel M, Nikolai M, Olson LK, Hord NG, Zakem M, Clark J, Elnabtity M, Figueroa B, Chang HT. Long Term Survivals in Aggressive Primary Brain Malignancies Treated With an Adjuvant Ketogenic Diet. Front Nutr 2022; 9:770796. [PMID: 35592625 PMCID: PMC9112915 DOI: 10.3389/fnut.2022.770796] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 02/23/2022] [Indexed: 12/11/2022] Open
Abstract
Aggressive primary brain tumors (APBT) glioblastoma multiforme and grade IV astrocytoma are treated with multimodality treatments that include surgery to remove as much tumor as possible without sacrificing neurological function followed by radiation therapy and chemotherapy usually temozolomide. Survivals in adults are in the range of 8–16 months. The addition of a ketogenic diet (KD) to rodents with transplanted brain tumors increased survival in nine of 11 animals to over 299 days compared to survival in untreated controls of 33 days and radiation only controls of 38 days. We treated humans with APBT with standard of care neurosurgery immediately followed by 6 weeks of an adjuvant ketogenic diet concurrent with radiation therapy and temozolomide. Twice daily measurements of blood ketones and glucose were recorded and the patients' diet was modified toward the goal of maintaining blood ketone levels approaching 3 mM. Of the nine patients who completed the protocol three younger patients age 32, 28, and 22 at enrollment are alive and employed with clinically stable disease and brain images 74, 58, and 52 months since diagnosis. All the six older patients mean age 55 have died with disease progression detected on average 8 months after Dx. In conclusion: 1. It is possible to implement and maintain dietary induced ketosis in patients with APBT; 2. The longer survivals observed in younger patients treated with KD need to be confirmed in larger studies that should be focused on younger patients possibly under age 40.
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Affiliation(s)
- Kenneth A. Schwartz
- Colleges of Human and Osteopathic Medicine, Michigan State University, East Lansing, MI, United States
- Department of Medicine, College of Human Medicine, Michigan State University, East Lansing, MI, United States
- *Correspondence: Kenneth A. Schwartz
| | - Mary Noel
- College of Osteopathic Medicine, Michigan State University, East Lansing, MI, United States
- Department of Family Practice, College of Human Medicine, Michigan State University, East Lansing, MI, United States
| | - Michele Nikolai
- Department of Food Science and Human Nutrition, College of Agriculture and Natural Resources, Michigan State University, East Lansing, MI, United States
| | - Lawrence K. Olson
- Department of Physiology, College of Natural Sciences, Michigan State University, East Lansing, MI, United States
| | - Norman G. Hord
- Department of Nutritional Sciences, Harold Hamm Diabetes Center, College of Allied Health, University of Oklahoma, Oklahoma City, OK, United States
| | - Micheal Zakem
- College of Osteopathic Medicine, Michigan State University, East Lansing, MI, United States
| | - Justin Clark
- College of Human Medicine, Michigan State University, East Lansing, MI, United States
| | - Mohamed Elnabtity
- College of Human Medicine, Michigan State University, East Lansing, MI, United States
| | - Bryan Figueroa
- College of Human Medicine, Michigan State University, East Lansing, MI, United States
| | - Howard T. Chang
- Colleges of Human and Osteopathic Medicine, Michigan State University, East Lansing, MI, United States
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7
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Munquad S, Si T, Mallik S, Das AB, Zhao Z. A Deep Learning-Based Framework for Supporting Clinical Diagnosis of Glioblastoma Subtypes. Front Genet 2022; 13:855420. [PMID: 35419027 PMCID: PMC9000988 DOI: 10.3389/fgene.2022.855420] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 02/17/2022] [Indexed: 12/12/2022] Open
Abstract
Understanding molecular features that facilitate aggressive phenotypes in glioblastoma multiforme (GBM) remains a major clinical challenge. Accurate diagnosis of GBM subtypes, namely classical, proneural, and mesenchymal, and identification of specific molecular features are crucial for clinicians for systematic treatment. We develop a biologically interpretable and highly efficient deep learning framework based on a convolutional neural network for subtype identification. The classifiers were generated from high-throughput data of different molecular levels, i.e., transcriptome and methylome. Furthermore, an integrated subsystem of transcriptome and methylome data was also used to build the biologically relevant model. Our results show that deep learning model outperforms the traditional machine learning algorithms. Furthermore, to evaluate the biological and clinical applicability of the classification, we performed weighted gene correlation network analysis, gene set enrichment, and survival analysis of the feature genes. We identified the genotype-phenotype relationship of GBM subtypes and the subtype-specific predictive biomarkers for potential diagnosis and treatment.
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Affiliation(s)
- Sana Munquad
- Department of Biotechnology, National Institute of Technology Warangal, Warangal, India
| | - Tapas Si
- Department of Computer Science and Engineering, Bankura Unnayani Institute of Engineering, Bankura, India
| | - Saurav Mallik
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Asim Bikas Das
- Department of Biotechnology, National Institute of Technology Warangal, Warangal, India
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, United States.,Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, United States.,Department of Pathology and Laboratory Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, United States
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8
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Bruno F, Pellerino A, Palmiero R, Bertero L, Mantovani C, Garbossa D, Soffietti R, Rudà R. Glioblastoma in the Elderly: Review of Molecular and Therapeutic Aspects. Biomedicines 2022; 10:biomedicines10030644. [PMID: 35327445 PMCID: PMC8945166 DOI: 10.3390/biomedicines10030644] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 03/07/2022] [Accepted: 03/08/2022] [Indexed: 12/22/2022] Open
Abstract
Glioblastoma (GBM) is the most aggressive primary brain tumour. As GBM incidence is associated with age, elderly people represent a consistent subgroup of patients. Elderly people with GBM show dismal prognosis (about 6 months) and limited response to treatments. Age is a negative prognostic factor, which correlates with clinical frailty, poorer tolerability to surgery or adjuvant radio-chemotherapy, and higher occurrence of comorbidities and/or secondary complications. The aim of this paper is to review the clinical and molecular characteristics, current therapeutic options, and prognostic factors of elderly patients with GBM.
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Affiliation(s)
- Francesco Bruno
- Division of Neuro-Oncology, Department of Neuroscience, University and City of Health and Science, 10126 Turin, Italy; (A.P.); (R.P.); (R.S.); (R.R.)
- Correspondence:
| | - Alessia Pellerino
- Division of Neuro-Oncology, Department of Neuroscience, University and City of Health and Science, 10126 Turin, Italy; (A.P.); (R.P.); (R.S.); (R.R.)
| | - Rosa Palmiero
- Division of Neuro-Oncology, Department of Neuroscience, University and City of Health and Science, 10126 Turin, Italy; (A.P.); (R.P.); (R.S.); (R.R.)
| | - Luca Bertero
- Pathology Unit, Department of Medical Sciences, University of Turin, 10126 Turin, Italy;
| | - Cristina Mantovani
- Division of Radiotherapy, Department of Oncology, University and City of Health and Science, 10126 Turin, Italy;
| | - Diego Garbossa
- Division of Neurosurgery, Department of Neuroscience, University and City of Health and Science, 10126 Turin, Italy;
| | - Riccardo Soffietti
- Division of Neuro-Oncology, Department of Neuroscience, University and City of Health and Science, 10126 Turin, Italy; (A.P.); (R.P.); (R.S.); (R.R.)
| | - Roberta Rudà
- Division of Neuro-Oncology, Department of Neuroscience, University and City of Health and Science, 10126 Turin, Italy; (A.P.); (R.P.); (R.S.); (R.R.)
- Department of Neurology, Castelfranco and Treviso Hospitals, 31100 Treviso, Italy
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9
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Radiomic Features Associated with Extent of Resection in Glioma Surgery. ACTA NEUROCHIRURGICA. SUPPLEMENT 2021; 134:341-347. [PMID: 34862558 DOI: 10.1007/978-3-030-85292-4_38] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Radiomics defines a set of techniques for extraction and quantification of digital medical data in an automated and reproducible way. Its goal is to detect features potentially related to a clinical task, like classification, diagnosis, prognosis, and response to treatment, going beyond the intrinsic limits of operator-dependency and qualitative description of conventional radiological evaluation on a mesoscopic scale. In the field of neuro-oncology, researchers have tried to create prognostic models for a better tumor diagnosis, histological and biomolecular classification, prediction of response to treatment, and identification of disease relapse. Concerning glioma surgery, the most significant aid that radiomics can give to surgery is to improve tumor extension detection and identify areas that are more prone to recurrence to increase the extent of tumor resection, thereby ameliorating the patients' prognosis. This chapter aims to review the fundamentals of radiomics models' creation, the latest advance of radiomics in neuro-oncology, and possible radiomic features associated with the extent of resection in the brain gliomas.
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10
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Sun Y, Ou-Yang L, Dai DQ. WMLRR: A Weighted Multi-View Low Rank Representation to Identify Cancer Subtypes From Multiple Types of Omics Data. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021; 18:2891-2897. [PMID: 33656995 DOI: 10.1109/tcbb.2021.3063284] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The identification of cancer subtypes is of great importance for understanding the heterogeneity of tumors and providing patients with more accurate diagnoses and treatments. However, it is still a challenge to effectively integrate multiple omics data to establish cancer subtypes. In this paper, we propose an unsupervised integration method, named weighted multi-view low rank representation (WMLRR), to identify cancer subtypes from multiple types of omics data. Given a group of patients described by multiple omics data matrices, we first learn a unified affinity matrix which encodes the similarities among patients by exploring the sparsity-consistent low-rank representations from the joint decompositions of multiple omics data matrices. Unlike existing subtype identification methods that treat each omics data matrix equally, we assign a weight to each omics data matrix and learn these weights automatically through the optimization process. Finally, we apply spectral clustering on the learned affinity matrix to identify cancer subtypes. Experiment results show that the survival times between our identified cancer subtypes are significantly different, and our predicted survivals are more accurate than other state-of-the-art methods. In addition, some clinical analyses of the diseases also demonstrate the effectiveness of our method in identifying molecular subtypes with biological significance and clinical relevance.
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11
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Gnanavel M, Murugesan A, Konda Mani S, Yli-Harja O, Kandhavelu M. Identifying the miRNA Signature Association with Aging-Related Senescence in Glioblastoma. Int J Mol Sci 2021; 22:ijms22020517. [PMID: 33419230 PMCID: PMC7825621 DOI: 10.3390/ijms22020517] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 12/30/2020] [Accepted: 01/04/2021] [Indexed: 12/13/2022] Open
Abstract
Glioblastoma (GBM) is the most common malignant brain tumor and its malignant phenotypic characteristics are classified as grade IV tumors. Molecular interactions, such as protein–protein, protein–ncRNA, and protein–peptide interactions are crucial to transfer the signaling communications in cellular signaling pathways. Evidences suggest that signaling pathways of stem cells are also activated, which helps the propagation of GBM. Hence, it is important to identify a common signaling pathway that could be visible from multiple GBM gene expression data. microRNA signaling is considered important in GBM signaling, which needs further validation. We performed a high-throughput analysis using micro array expression profiles from 574 samples to explore the role of non-coding RNAs in the disease progression and unique signaling communication in GBM. A series of computational methods involving miRNA expression, gene ontology (GO) based gene enrichment, pathway mapping, and annotation from metabolic pathways databases, and network analysis were used for the analysis. Our study revealed the physiological roles of many known and novel miRNAs in cancer signaling, especially concerning signaling in cancer progression and proliferation. Overall, the results revealed a strong connection with stress induced senescence, significant miRNA targets for cell cycle arrest, and many common signaling pathways to GBM in the network.
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Affiliation(s)
- Mutharasu Gnanavel
- BioMediTech Institute, Faculty of Medicine and Health Technology, Tampere University, ArvoYlpönkatu 34, 33520 Tampere, Finland; (M.G.); (A.M.); (O.Y.-H.)
| | - Akshaya Murugesan
- BioMediTech Institute, Faculty of Medicine and Health Technology, Tampere University, ArvoYlpönkatu 34, 33520 Tampere, Finland; (M.G.); (A.M.); (O.Y.-H.)
- Molecular Signalling Lab, Faculty of Medicine and Health Technology, Tampere University, P.O. Box 553, 33101 Tampere, Finland
- Department of Biotechnology, Lady Doak College, Thallakulam, Madurai 625002, India
| | - Saravanan Konda Mani
- Center for High Performance Computing, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China;
| | - Olli Yli-Harja
- BioMediTech Institute, Faculty of Medicine and Health Technology, Tampere University, ArvoYlpönkatu 34, 33520 Tampere, Finland; (M.G.); (A.M.); (O.Y.-H.)
- Computational Systems Biology Group, Faculty of Medicine and Health Technology, Tampere University, P.O. Box 553, 33101 Tampere, Finland
- Institute for Systems Biology, 1441N 34th Street, Seattle, WA 98109, USA
| | - Meenakshisundaram Kandhavelu
- BioMediTech Institute, Faculty of Medicine and Health Technology, Tampere University, ArvoYlpönkatu 34, 33520 Tampere, Finland; (M.G.); (A.M.); (O.Y.-H.)
- Molecular Signalling Lab, Faculty of Medicine and Health Technology, Tampere University, P.O. Box 553, 33101 Tampere, Finland
- Science Center, Tampere University Hospital, ArvoYlpönkatu 34, 33520 Tampere, Finland
- Correspondence:
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12
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Mo XB, Zhang H, Wang AL, Xu T, Zhang YH. Integrative analysis identifies the association between CASZ1 methylation and ischemic stroke. Neurol Genet 2020; 6:e509. [PMID: 33134510 PMCID: PMC7577558 DOI: 10.1212/nxg.0000000000000509] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 07/27/2020] [Indexed: 01/11/2023]
Abstract
Objective To highlight potential epigenetic risk factors for blood pressure (BP) and ischemic stroke (IS) in loci identified by genome-wide association studies (GWASs). Methods We detected DNA methylation for BP (317,756 individuals from UK Biobank) and IS (521,612 individuals from MEGASTROKE) in Europeans by using the summary data–based mendelian randomization (SMR) method. We selected the most relevant gene to validate the association in 1,207 patients with hypertensive IS and 1,269 controls from the Chinese populations. Results We first identified 173 CpG sites in 90 genes, 337 CpG sites in 142 genes, and 9 CpG sites in 7 genes that were significantly associated with systolic, diastolic BP, and IS, respectively. The methylation level of cg12760995 in CASZ1 was associated with systolic (PSMR = 1.74 × 10−12), diastolic BP (PSMR = 2.48 × 10−10), and IS (odds ratio [OR] = 0.92 [95% confidence interval [CI]: 0.91–0.94]; PSMR = 2.28 × 10−8) in Europeans. The methylation levels of 17 sites in the promoter of CASZ1 were measured in the Chinese individuals, and 10 of them were significantly associated with IS. The higher methylation level of CASZ1 was associated with a lower risk of IS (adjusted OR = 0.97 [95% CI: 0.96–0.99]). CASZ1 seemed to be hypomethylated in hypertensive cases, and the level was negatively correlated with BP. Systolic and diastolic BP mediated approximately 61.2% (p = 3.49 × 10−6) and 45.0% (p = 0.0029) of the association between CASZ1 methylation and IS, respectively. Conclusions This study identified DNA methylations that were associated with BP and IS. CASZ1 was hypomethylated in Chinese patients with hypertensive IS.
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Affiliation(s)
- Xing-Bo Mo
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases (X.-B.M., H.Z., A.-L.W., T.X., Y-.H.Z.); Center for Genetic Epidemiology and Genomics (X.-B.M.); and Department of Epidemiology (X.-B.M., H.Z., A.-L.W., T.X., Y.-H.Z.), School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China
| | - Huan Zhang
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases (X.-B.M., H.Z., A.-L.W., T.X., Y-.H.Z.); Center for Genetic Epidemiology and Genomics (X.-B.M.); and Department of Epidemiology (X.-B.M., H.Z., A.-L.W., T.X., Y.-H.Z.), School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China
| | - Ai-Li Wang
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases (X.-B.M., H.Z., A.-L.W., T.X., Y-.H.Z.); Center for Genetic Epidemiology and Genomics (X.-B.M.); and Department of Epidemiology (X.-B.M., H.Z., A.-L.W., T.X., Y.-H.Z.), School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China
| | - Tan Xu
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases (X.-B.M., H.Z., A.-L.W., T.X., Y-.H.Z.); Center for Genetic Epidemiology and Genomics (X.-B.M.); and Department of Epidemiology (X.-B.M., H.Z., A.-L.W., T.X., Y.-H.Z.), School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China
| | - Yong-Hong Zhang
- Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases (X.-B.M., H.Z., A.-L.W., T.X., Y-.H.Z.); Center for Genetic Epidemiology and Genomics (X.-B.M.); and Department of Epidemiology (X.-B.M., H.Z., A.-L.W., T.X., Y.-H.Z.), School of Public Health, Soochow University, Suzhou, Jiangsu, P. R. China
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13
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Ene CI, Cimino PJ, Fine HA, Holland EC. Incorporating genomic signatures into surgical and medical decision-making for elderly glioblastoma patients. Neurosurg Focus 2020; 49:E11. [PMID: 33002863 DOI: 10.3171/2020.7.focus20418] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 07/17/2020] [Indexed: 11/06/2022]
Abstract
Glioblastoma (GBM) is the most common type of malignant primary brain tumor in adults. It is a uniformly fatal disease (median overall survival 16 months) even with aggressive resection and an adjuvant temozolomide-based chemoradiation regimen. Age remains an independent risk factor for a poor prognosis. Several factors contribute to the dismal outcomes in the elderly population with GBM, including poor baseline health status, differences in underlying genomic alterations, and variability in the surgical and medical management of this subpopulation. The latter arises from a lack of adequate representation of elderly patients in clinical trials, resulting in limited data on the response of this subpopulation to standard treatment. Results from retrospective and some prospective studies have indicated that resection of only contrast-enhancing lesions and administration of hypofractionated radiotherapy in combination with temozolomide are effective strategies for optimizing survival while maintaining baseline quality of life in elderly GBM patients; however, survival remains dismal relative to that in a younger cohort. Here, the authors present historical context for the current strategies used for the multimodal management (surgical and medical) of elderly patients with GBM. Furthermore, they provide insights into elderly GBM patient-specific genomic signatures such as isocitrate dehydrogenase 1/2 (IDH1/2) wildtype status, telomerase reverse transcriptase promoter (TERTp) mutations, and somatic copy number alterations including CDK4/MDM2 coamplification, which are becoming better understood and could be utilized in a clinical trial design and patient stratification to guide the development of more effective adjuvant therapies specifically for elderly GBM patients.
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Affiliation(s)
- Chibawanye I Ene
- 1Department of Neurological Surgery, University of Washington School of Medicine
| | - Patrick J Cimino
- 2Department of Pathology, Division of Neuropathology, University of Washington School of Medicine, Seattle, Washington
| | - Howard A Fine
- 3Meyer Cancer Center, Division of Neuro-Oncology, Department of Neurology, NewYork-Presbyterian Hospital/Weill Cornell Medicine, New York, New York; and
| | - Eric C Holland
- 4Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
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14
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Sakthikumar S, Roy A, Haseeb L, Pettersson ME, Sundström E, Marinescu VD, Lindblad-Toh K, Forsberg-Nilsson K. Whole-genome sequencing of glioblastoma reveals enrichment of non-coding constraint mutations in known and novel genes. Genome Biol 2020; 21:127. [PMID: 32513296 PMCID: PMC7281935 DOI: 10.1186/s13059-020-02035-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 04/30/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Glioblastoma (GBM) has one of the worst 5-year survival rates of all cancers. While genomic studies of the disease have been performed, alterations in the non-coding regulatory regions of GBM have largely remained unexplored. We apply whole-genome sequencing (WGS) to identify non-coding mutations, with regulatory potential in GBM, under the hypothesis that regions of evolutionary constraint are likely to be functional, and somatic mutations are likely more damaging than in unconstrained regions. RESULTS We validate our GBM cohort, finding similar copy number aberrations and mutated genes based on coding mutations as previous studies. Performing analysis on non-coding constraint mutations and their position relative to nearby genes, we find a significant enrichment of non-coding constraint mutations in the neighborhood of 78 genes that have previously been implicated in GBM. Among them, SEMA3C and DYNC1I1 show the highest frequencies of alterations, with multiple mutations overlapping transcription factor binding sites. We find that a non-coding constraint mutation in the SEMA3C promoter reduces the DNA binding capacity of the region. We also identify 1776 other genes enriched for non-coding constraint mutations with likely regulatory potential, providing additional candidate GBM genes. The mutations in the top four genes, DLX5, DLX6, FOXA1, and ISL1, are distributed over promoters, UTRs, and multiple transcription factor binding sites. CONCLUSIONS These results suggest that non-coding constraint mutations could play an essential role in GBM, underscoring the need to connect non-coding genomic variation to biological function and disease pathology.
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Affiliation(s)
- Sharadha Sakthikumar
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, SE-751 23, Uppsala, Sweden
- Broad Institute, Cambridge, MA, 02142, USA
| | - Ananya Roy
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-751 85, Uppsala, Sweden
| | - Lulu Haseeb
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-751 85, Uppsala, Sweden
| | - Mats E Pettersson
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, SE-751 23, Uppsala, Sweden
| | - Elisabeth Sundström
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, SE-751 23, Uppsala, Sweden
| | - Voichita D Marinescu
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, SE-751 23, Uppsala, Sweden
| | - Kerstin Lindblad-Toh
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, SE-751 23, Uppsala, Sweden
- Broad Institute, Cambridge, MA, 02142, USA
| | - Karin Forsberg-Nilsson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-751 85, Uppsala, Sweden.
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15
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Fukai J, Arita H, Umehara T, Yoshioka E, Shofuda T, Kanematsu D, Kodama Y, Mano M, Kinoshita M, Okita Y, Nonaka M, Uda T, Tsuyuguchi N, Sakamoto D, Uematsu Y, Nakao N, Mori K, Kanemura Y. Molecular characteristics and clinical outcomes of elderly patients with IDH-wildtype glioblastomas: comparative study of older and younger cases in Kansai Network cohort. Brain Tumor Pathol 2020; 37:50-59. [PMID: 32361941 DOI: 10.1007/s10014-020-00363-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Accepted: 04/21/2020] [Indexed: 12/13/2022]
Abstract
Aging is a known negative prognostic factor in glioblastomas (GBM). Whether particular genetic backgrounds are a factor in poor outcomes of elderly patients with GBM warrants investigation. We aim to elucidate any differences between older and younger adult patients with IDH-wildtype GBM regarding both molecular characteristics and clinical outcomes. We collected adult cases diagnosed with IDH-wildtype GBM from the Kansai Network. Clinical and pathological characteristics were analyzed retrospectively and compared between older (≥ 70 years) and younger (≤ 50 years) cases. Included were 92 older vs. 33 younger cases. The older group included more patients with preoperative Karnofsky performance status score < 70 and had a shorter survival time than the younger group. MGMT promoter was methylated more frequently in the older group. TERT promoter mutation was more common in the older group. There were significant differences in DNA copy-number alteration profiles between age groups in PTEN deletion and CDK4 amplification/gain. In the older group, no molecular markers were identified, but surgical resection was an independent prognostic factor. Age-specific survival difference was significant in the MGMT methylated and TERT wildtype subgroup. Elderly patients have several potential factors in poor prognosis of glioblastomas. Varying molecular profiles may explain differing rates of survival between generations.
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Affiliation(s)
- Junya Fukai
- Department of Neurological Surgery, Wakayama Medical University School of Medicine, Kimiidera 811-1, Wakayama, 641-0012, Japan. .,Kansai Molecular Diagnosis Network for CNS Tumors, Osaka, 540-0006, Japan.
| | - Hideyuki Arita
- Kansai Molecular Diagnosis Network for CNS Tumors, Osaka, 540-0006, Japan.,Department of Neurosurgery, Takatsuki General Hospital, Takatsuki, Osaka, 569-1192, Japan
| | - Toru Umehara
- Kansai Molecular Diagnosis Network for CNS Tumors, Osaka, 540-0006, Japan.,Department of Neurosurgery, Osaka University Graduate School of Medicine, Osaka, 565-0871, Japan
| | - Ema Yoshioka
- Kansai Molecular Diagnosis Network for CNS Tumors, Osaka, 540-0006, Japan.,Division of Stem Cell Research, Department of Biomedical Research and Innovation, Institute for Clinical Research, National Hospital Organization Osaka National Hospital, Osaka, 540-0006, Japan
| | - Tomoko Shofuda
- Kansai Molecular Diagnosis Network for CNS Tumors, Osaka, 540-0006, Japan.,Division of Stem Cell Research, Department of Biomedical Research and Innovation, Institute for Clinical Research, National Hospital Organization Osaka National Hospital, Osaka, 540-0006, Japan
| | - Daisuke Kanematsu
- Kansai Molecular Diagnosis Network for CNS Tumors, Osaka, 540-0006, Japan.,Division of Regenerative Medicine, Department of Biomedical Research and Innovation, Institute for Clinical Research, National Hospital Organization Osaka National Hospital, Osaka, 540-0006, Japan
| | - Yoshinori Kodama
- Kansai Molecular Diagnosis Network for CNS Tumors, Osaka, 540-0006, Japan.,Department of Diagnostic Pathology, Kobe University Graduate School of Medicine, Kobe, Hyogo, 650-0017, Japan
| | - Masayuki Mano
- Kansai Molecular Diagnosis Network for CNS Tumors, Osaka, 540-0006, Japan.,Department of Central Laboratory and Surgical Pathology, National Hospital Organization Osaka National Hospital, Osaka, 540-0006, Japan
| | - Manabu Kinoshita
- Kansai Molecular Diagnosis Network for CNS Tumors, Osaka, 540-0006, Japan.,Department of Neurosurgery, Osaka University Graduate School of Medicine, Osaka, 565-0871, Japan
| | - Yoshiko Okita
- Kansai Molecular Diagnosis Network for CNS Tumors, Osaka, 540-0006, Japan.,Department of Neurosurgery, Osaka International Cancer Institute, Osaka, 541-8567, Japan.,Department of Neurosurgery, National Hospital Organization Osaka National Hospital, Osaka, 540-0006, Japan
| | - Masahiro Nonaka
- Kansai Molecular Diagnosis Network for CNS Tumors, Osaka, 540-0006, Japan.,Department of Neurosurgery, Kansai Medical University, Hirakata, Osaka, 573-1191, Japan
| | - Takehiro Uda
- Kansai Molecular Diagnosis Network for CNS Tumors, Osaka, 540-0006, Japan.,Department of Neurosurgery, Osaka City University Graduate School of Medicine, Osaka, 545-0051, Japan
| | - Naohiro Tsuyuguchi
- Kansai Molecular Diagnosis Network for CNS Tumors, Osaka, 540-0006, Japan.,Department of Neurosurgery, Osaka City University Graduate School of Medicine, Osaka, 545-0051, Japan.,Department of Neurosurgery, Kindai University Faculty of Medicine, Higashiosaka, Osaka, 589-8511, Japan
| | - Daisuke Sakamoto
- Kansai Molecular Diagnosis Network for CNS Tumors, Osaka, 540-0006, Japan.,Department of Neurosurgery, Hyogo College of Medicine, Nishinomiya, Hyogo, 663-8501, Japan
| | - Yuji Uematsu
- Department of Neurological Surgery, Wakayama Medical University School of Medicine, Kimiidera 811-1, Wakayama, 641-0012, Japan.,Kansai Molecular Diagnosis Network for CNS Tumors, Osaka, 540-0006, Japan
| | - Naoyuki Nakao
- Department of Neurological Surgery, Wakayama Medical University School of Medicine, Kimiidera 811-1, Wakayama, 641-0012, Japan.,Kansai Molecular Diagnosis Network for CNS Tumors, Osaka, 540-0006, Japan
| | - Kanji Mori
- Kansai Molecular Diagnosis Network for CNS Tumors, Osaka, 540-0006, Japan.,Department of Neurosurgery, Kansai Rosai Hospital, Amagasaki, Hyogo, 660-8511, Japan
| | - Yonehiro Kanemura
- Kansai Molecular Diagnosis Network for CNS Tumors, Osaka, 540-0006, Japan.,Division of Regenerative Medicine, Department of Biomedical Research and Innovation, Institute for Clinical Research, National Hospital Organization Osaka National Hospital, Osaka, 540-0006, Japan.,Department of Neurosurgery, National Hospital Organization Osaka National Hospital, Osaka, 540-0006, Japan
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16
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Ren X, Kuan PF. Negative binomial additive model for RNA-Seq data analysis. BMC Bioinformatics 2020; 21:171. [PMID: 32357831 PMCID: PMC7195715 DOI: 10.1186/s12859-020-3506-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 04/20/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND High-throughput sequencing experiments followed by differential expression analysis is a widely used approach for detecting genomic biomarkers. A fundamental step in differential expression analysis is to model the association between gene counts and covariates of interest. Existing models assume linear effect of covariates, which is restrictive and may not be sufficient for certain phenotypes. RESULTS We introduce NBAMSeq, a flexible statistical model based on the generalized additive model and allows for information sharing across genes in variance estimation. Specifically, we model the logarithm of mean gene counts as sums of smooth functions with the smoothing parameters and coefficients estimated simultaneously within a nested iterative method. The variance is estimated by the Bayesian shrinkage approach to fully exploit the information across all genes. CONCLUSIONS Based on extensive simulations and case studies of RNA-Seq data, we show that NBAMSeq offers improved performance in detecting nonlinear effect and maintains equivalent performance in detecting linear effect compared to existing methods. The vignette and source code of NBAMSeq are available at http://bioconductor.org/packages/release/bioc/html/NBAMSeq.html.
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Affiliation(s)
- Xu Ren
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, 11794, NY, USA
| | - Pei-Fen Kuan
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, 11794, NY, USA.
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17
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Zhou J, Wu YC, Xiao BJ, Guo XD, Zheng QX, Wu B. Age-related Changes in the Global DNA Methylation Profile of Oligodendrocyte Progenitor Cells Derived from Rat Spinal Cords. Curr Med Sci 2019; 39:67-74. [PMID: 30868493 DOI: 10.1007/s11596-019-2001-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 12/27/2018] [Indexed: 01/12/2023]
Abstract
Demyelination of axons plays an important role in the pathology of many spinal cord diseases and injuries. Remyelination in demyelinated lesions is primarily performed by oligodendrocyte progenitor cells (OPCs), which generate oligodendrocytes in the developing and mature central nervous system. The efficiency of remyelination decreases with age. Many reports suggest that this decline in remyelination results from impaired OPC recruitment and differentiation during aging. Of the various molecular mechanisms involved in aging, changes in epigenetic modifications have received particular attention. Global DNA methylation is a major epigenetic modification that plays important roles in cellular senescence and organismal aging. Thus, we aimed to evaluate the dynamic changes in the global DNA methylation profiles of OPCs derived from rat spinal cords during the aging process. We separated and cultured OPCs from the spinal cords of neonatal, 4-month-old, and 16-month-old rats and investigated the age-related alterations of genomic DNA methylation levels by using quantitative colorimetric analysis. To determine the potential cause of dynamic changes in global DNA methylation, we further analyzed the activity of DNA methyltransferases (DNMTs) and the expression of DNMT1, DNMT3a, DNMT3b, TET1, TET2, TET3, MBD2, and MeCP2 in the OPCs from each group. Our results showed the genomic DNA methylation level and the activity of DNMTs from OPCs derived from rat spinal cords decreased gradually during aging, and OPCs from 16-month-old rats were characterized by global hypomethylation. During OPC aging, the mRNA and protein expression levels of DNMT3a, DNMT3b, and MeCP2 were significantly elevated; those of DNMT1 were significantly down-regulated; and no significant changes were observed in those for TET1, TET2, TET3, or MBD2. Our results indicated that global DNA hypomethylation in aged OPCs is correlated with DNMT1 downregulation. Together, these data provide important evidence for partly elucidating the mechanism of age-related impaired OPC recruitment and differentiation and assist in the development of new treatments for promoting efficient remyelination.
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Affiliation(s)
- Jing Zhou
- Department of General Surgery, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Yong-Chao Wu
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Bao-Jun Xiao
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Xiao-Dong Guo
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Qi-Xin Zheng
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Bin Wu
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
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18
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Bernal Rubio YL, González-Reymúndez A, Wu KHH, Griguer CE, Steibel JP, de Los Campos G, Doseff A, Gallo K, Vazquez AI. Whole-Genome Multi-omic Study of Survival in Patients with Glioblastoma Multiforme. G3 (BETHESDA, MD.) 2018; 8:3627-3636. [PMID: 30228192 PMCID: PMC6222579 DOI: 10.1534/g3.118.200391] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Accepted: 09/12/2018] [Indexed: 12/22/2022]
Abstract
Glioblastoma multiforme (GBM) has been recognized as the most lethal type of malignant brain tumor. Despite efforts of the medical and research community, patients' survival remains extremely low. Multi-omic profiles (including DNA sequence, methylation and gene expression) provide rich information about the tumor. These profiles are likely to reveal processes that may be predictive of patient survival. However, the integration of multi-omic profiles, which are high dimensional and heterogeneous in nature, poses great challenges. The goal of this work was to develop models for prediction of survival of GBM patients that can integrate clinical information and multi-omic profiles, using multi-layered Bayesian regressions. We apply the methodology to data from GBM patients from The Cancer Genome Atlas (TCGA, n = 501) to evaluate whether integrating multi-omic profiles (SNP-genotypes, methylation, copy number variants and gene expression) with clinical information (demographics as well as treatments) leads to an improved ability to predict patient survival. The proposed Bayesian models were used to estimate the proportion of variance explained by clinical covariates and omics and to evaluate prediction accuracy in cross validation (using the area under the Receiver Operating Characteristic curve, AUC). Among clinical and demographic covariates, age (AUC = 0.664) and the use of temozolomide (AUC = 0.606) were the most predictive of survival. Among omics, methylation (AUC = 0.623) and gene expression (AUC = 0.593) were more predictive than either SNP (AUC = 0.539) or CNV (AUC = 0.547). While there was a clear association between age and methylation, the integration of age, the use of temozolomide, and either gene expression or methylation led to a substantial increase in AUC in cross-validaton (AUC = 0.718). Finally, among the genes whose methylation was higher in aging brains, we observed a higher enrichment of these genes being also differentially methylated in cancer.
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Affiliation(s)
| | | | - Kuan-Han H Wu
- Department of Epidemiology and Biostatistics
- Department of Public Health Sciences, Henry Ford Health System, Detroit, Michigan, 48202
| | - Corinne E Griguer
- Department of Neurosurgery, University of Alabama at Birmingham, Birmingham, Alabama, 35294
| | - Juan P Steibel
- Department of Animal Science and Department of Fisheries and Wildlife
| | - Gustavo de Los Campos
- Department of Epidemiology and Biostatistics
- Institute for Quantitative Health Science and Engineering
- Department of Statistics and Probability
| | - Andrea Doseff
- Department of Physiology
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan, 48823
| | | | - Ana I Vazquez
- Department of Epidemiology and Biostatistics
- Institute for Quantitative Health Science and Engineering
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19
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Abstract
Clinical research in neuro-oncology frequently classifies patients over 60-70 years of age as 'elderly', a designation intended to identify patients with the disease characteristics, psychosocial changes, and susceptibility to treatment toxicities associated with advancing age. The elderly account for a large proportion of patients diagnosed with glioblastoma (GBM), and this population is projected to increase. Their prognosis is inferior to that of GBM patients as a whole, and concerns over treatment toxicity may limit the aggressiveness with which they are treated. Recent clinical studies have assisted with therapeutic decision making in this cohort. Hypofractionated radiation with concurrent and adjuvant temozolomide has been shown to increase survival without worsened quality of life in elderly patients with good functional status. Single modality radiation therapy or temozolomide therapy are frequently used in this population, and while neither has demonstrated superiority, O6-methylguanine-DNA methyltransferase (MGMT) methylation status is predictive of improved survival with temozolomide over radiation therapy. Despite these advances, ambiguity as to how to best define, assess, and treat this population remains. The specific response of elderly patients to emerging therapies, such as immunotherapies, is unclear. Advancing outcomes for elderly patients with GBM requires persistent efforts to include them in translational and clinical research endeavors, and concurrent dedication to the preservation of function and quality of life in this population.
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Affiliation(s)
- Rebecca A Harrison
- Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Unit 0431, Houston, TX, 77030, USA.
| | - John F de Groot
- Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Unit 0431, Houston, TX, 77030, USA
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20
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Mertens J, Reid D, Lau S, Kim Y, Gage FH. Aging in a Dish: iPSC-Derived and Directly Induced Neurons for Studying Brain Aging and Age-Related Neurodegenerative Diseases. Annu Rev Genet 2018; 52:271-293. [PMID: 30208291 DOI: 10.1146/annurev-genet-120417-031534] [Citation(s) in RCA: 182] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Age-associated neurological diseases represent a profound challenge in biomedical research as we are still struggling to understand the interface between the aging process and the manifestation of disease. Various pathologies in the elderly do not directly result from genetic mutations, toxins, or infectious agents but are primarily driven by the many manifestations of biological aging. Therefore, the generation of appropriate model systems to study human aging in the nervous system demands new concepts that lie beyond transgenic and drug-induced models. Although access to viable human brain specimens is limited and induced pluripotent stem cell models face limitations due to reprogramming-associated cellular rejuvenation, the direct conversion of somatic cells into induced neurons allows for the generation of human neurons that capture many aspects of aging. Here, we review advances in exploring age-associated neurodegenerative diseases using human cell reprogramming models, and we discuss general concepts, promises, and limitations of the field.
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Affiliation(s)
- Jerome Mertens
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California 92037, USA; .,Department of Genomics, Stem Cell Biology and Regenerative Medicine, Institute of Molecular Biology, and Center for Molecular Biosciences Innsbruck, University of Innsbruck, A-6020 Innsbruck, Austria
| | - Dylan Reid
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California 92037, USA;
| | - Shong Lau
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California 92037, USA;
| | - Yongsung Kim
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California 92037, USA;
| | - Fred H Gage
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California 92037, USA;
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Fatai AA, Gamieldien J. A 35-gene signature discriminates between rapidly- and slowly-progressing glioblastoma multiforme and predicts survival in known subtypes of the cancer. BMC Cancer 2018; 18:377. [PMID: 29614978 PMCID: PMC5883543 DOI: 10.1186/s12885-018-4103-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 02/06/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Gene expression can be employed for the discovery of prognostic gene or multigene signatures cancer. In this study, we assessed the prognostic value of a 35-gene expression signature selected by pathway and machine learning based methods in adjuvant therapy-linked glioblastoma multiforme (GBM) patients from the Cancer Genome Atlas. METHODS Genes with high expression variance was subjected to pathway enrichment analysis and those having roles in chemoradioresistance pathways were used in expression-based feature selection. A modified Support Vector Machine Recursive Feature Elimination algorithm was employed to select a subset of these genes that discriminated between rapidly-progressing and slowly-progressing patients. RESULTS Survival analysis on TCGA samples not used in feature selection and samples from four GBM subclasses, as well as from an entirely independent study, showed that the 35-gene signature discriminated between the survival groups in all cases (p<0.05) and could accurately predict survival irrespective of the subtype. In a multivariate analysis, the signature predicted progression-free and overall survival independently of other factors considered. CONCLUSION We propose that the performance of the signature makes it an attractive candidate for further studies to assess its utility as a clinical prognostic and predictive biomarker in GBM patients. Additionally, the signature genes may also be useful therapeutic targets to improve both progression-free and overall survival in GBM patients.
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Affiliation(s)
- Azeez A Fatai
- South African Bioinformatics Institute and SAMRC Unit for Bioinformatics Capacity Development, University of the Western Cape, Bellville, 7535, Western Cape, 7530, South Africa
| | - Junaid Gamieldien
- South African Bioinformatics Institute and SAMRC Unit for Bioinformatics Capacity Development, University of the Western Cape, Bellville, 7535, Western Cape, 7530, South Africa.
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22
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OKADA M, MIYAKE K, TAMIYA T. Glioblastoma Treatment in the Elderly. Neurol Med Chir (Tokyo) 2017; 57:667-676. [PMID: 29081442 PMCID: PMC5735230 DOI: 10.2176/nmc.ra.2017-0009] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 07/06/2017] [Indexed: 11/20/2022] Open
Abstract
Although current treatment advances prolong patient survival, treatment for glioblastoma (GBM) in the elderly has become an emerging issue. The definition of "elderly" differs across articles; GBM predominantly occurs at an age ≥65 years, and the prognosis worsens with increasing age. Regarding molecular markers, isocitrate dehydrogenase (IDH) mutations are less common in the elderly with GBM. Meanwhile, O6-methylguanine DNA methyltransferase (MGMT) promoter methylation has been identified in approximately half of patients with GBM. Surgery should be considered as the first-line treatment even for elderly patients, and maximum safe resection is recommended if feasible. Concurrently, radiotherapy is the standard adjuvant therapy. Hypofractionated radiotherapy (e.g., 40 Gy/15 Fr) is suitable for elderly patients. Studies also supported the concurrent use of temozolomide (TMZ) with radiotherapy. In cases wherein elderly patients cannot tolerate chemoradiation, TMZ monotherapy is an effective option when MGMT promoter methylation is verified. Conversely, tumors with MGMT unmethylated promoter may be treated with radiotherapy alone to reduce the possible toxicity of TMZ. Meanwhile, the efficacy of bevacizumab (BEV) in elderly patients remains unclear. Similarly, further studies on the efficacy of carmustine wafers are needed. Based on current knowledge, we propose a treatment diagram for GBM in the elderly.
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Affiliation(s)
- Masaki OKADA
- Department of Neurological Surgery, Kagawa University Faculty of Medicine, Kita-gun, Kagawa, Japan
| | - Keisuke MIYAKE
- Department of Neurological Surgery, Kagawa University Faculty of Medicine, Kita-gun, Kagawa, Japan
| | - Takashi TAMIYA
- Department of Neurological Surgery, Kagawa University Faculty of Medicine, Kita-gun, Kagawa, Japan
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Katoh M, Katoh M. Molecular genetics and targeted therapy of WNT-related human diseases (Review). Int J Mol Med 2017; 40:587-606. [PMID: 28731148 PMCID: PMC5547940 DOI: 10.3892/ijmm.2017.3071] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 07/12/2017] [Indexed: 12/15/2022] Open
Abstract
Canonical WNT signaling through Frizzled and LRP5/6 receptors is transduced to the WNT/β-catenin and WNT/stabilization of proteins (STOP) signaling cascades to regulate cell fate and proliferation, whereas non-canonical WNT signaling through Frizzled or ROR receptors is transduced to the WNT/planar cell polarity (PCP), WNT/G protein-coupled receptor (GPCR) and WNT/receptor tyrosine kinase (RTK) signaling cascades to regulate cytoskeletal dynamics and directional cell movement. WNT/β-catenin signaling cascade crosstalks with RTK/SRK and GPCR-cAMP-PKA signaling cascades to regulate β-catenin phosphorylation and β-catenin-dependent transcription. Germline mutations in WNT signaling molecules cause hereditary colorectal cancer, bone diseases, exudative vitreoretinopathy, intellectual disability syndrome and PCP-related diseases. APC or CTNNB1 mutations in colorectal, endometrial and prostate cancers activate the WNT/β-catenin signaling cascade. RNF43, ZNRF3, RSPO2 or RSPO3 alterations in breast, colorectal, gastric, pancreatic and other cancers activate the WNT/β-catenin, WNT/STOP and other WNT signaling cascades. ROR1 upregulation in B-cell leukemia and solid tumors and ROR2 upregulation in melanoma induce invasion, metastasis and therapeutic resistance through Rho-ROCK, Rac-JNK, PI3K-AKT and YAP signaling activation. WNT signaling in cancer, stromal and immune cells dynamically orchestrate immune evasion and antitumor immunity in a cell context-dependent manner. Porcupine (PORCN), RSPO3, WNT2B, FZD5, FZD10, ROR1, tankyrase and β-catenin are targets of anti-WNT signaling therapy, and ETC-159, LGK974, OMP-18R5 (vantictumab), OMP-54F28 (ipafricept), OMP-131R10 (rosmantuzumab), PRI-724 and UC-961 (cirmtuzumab) are in clinical trials for cancer patients. Different classes of anti-WNT signaling therapeutics are necessary for the treatment of APC/CTNNB1-, RNF43/ZNRF3/RSPO2/RSPO3- and ROR1-types of human cancers. By contrast, Dickkopf-related protein 1 (DKK1), SOST and glycogen synthase kinase 3β (GSK3β) are targets of pro-WNT signaling therapy, and anti-DKK1 (BHQ880 and DKN-01) and anti-SOST (blosozumab, BPS804 and romosozumab) monoclonal antibodies are being tested in clinical trials for cancer patients and osteoporotic post-menopausal women. WNT-targeting therapeutics have also been applied as reagents for in vitro stem-cell processing in the field of regenerative medicine.
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Affiliation(s)
| | - Masaru Katoh
- Department of Omics Network, National Cancer Center, Tokyo 104-0045, Japan
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Schneider H, Lohmann B, Wirsching HG, Hasenbach K, Rushing EJ, Frei K, Pruschy M, Tabatabai G, Weller M. Age-associated and therapy-induced alterations in the cellular microenvironment of experimental gliomas. Oncotarget 2017; 8:87124-87135. [PMID: 29152068 PMCID: PMC5675620 DOI: 10.18632/oncotarget.19894] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 07/16/2017] [Indexed: 01/01/2023] Open
Abstract
The poor prognosis associated with advanced age in patients with glioblastoma remains poorly understood. Glioblastoma in the elderly has been particularly associated with vascular endothelial growth factor (VEGF)-dependent angiogenesis, and early uncontrolled studies suggested that the anti-angiogenic agent bevacizumab (BEV), an antibody to VEGF, might be preferentially active in this patient population. Accordingly, we explored host age-dependent differences in survival and benefit from radiotherapy (RT) or BEV in syngeneic mouse glioma models. Survival was inferior in older mice in the SMA-540 and and less so in SMA-560, but not in the SMA-497 or GL-261 models. Detailed flow cytometric studies revealed increased myeloid and decreased effector T cell population frequencies in SMA-540 tumors of old compared to young mice, but no such difference in the SMA-497 model. Bone marrow transplantation (BMT) from young to old mice had no effect, whereas survival was reduced with BMT from old to young mice. BEV significantly decreased vessel densities in gliomas of old, but not young mice. Accordingly, old, but not young SMA-540 tumor-bearing mice benefited from BEV alone or in combination with RT. End-stage tumors of old BEV- and BEV/RT-treated mice exhibited increased infiltration of T helper and cytotoxic T cells compared to tumors of young mice. The SMA-540 model may provide a valuable tool to evaluate the influence of host age on glioblastoma progression and treatment response. The biological host factors that modulate glioma growth in old as opposed to young mice remain to be identified.
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Affiliation(s)
- Hannah Schneider
- Laboratory of Molecular Neuro-Oncology, Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Birthe Lohmann
- Laboratory of Molecular Neuro-Oncology, Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Hans-Georg Wirsching
- Laboratory of Molecular Neuro-Oncology, Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Kathy Hasenbach
- Laboratory of Molecular Neuro-Oncology, Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Elisabeth J Rushing
- Institute of Neuropathology, University Hospital Zurich, Zurich, Switzerland
| | - Karl Frei
- Center of Neuroscience, University of Zurich, Zurich, Switzerland.,Department of Neurosurgery, University Hospital Zurich, Zurich, Switzerland
| | - Martin Pruschy
- Laboratory for Molecular Radiobiology, Department of Radiation Oncology, University Hospital Zurich, Zurich, Switzerland
| | - Ghazaleh Tabatabai
- Laboratory of Molecular Neuro-Oncology, Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Michael Weller
- Laboratory of Molecular Neuro-Oncology, Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland.,Center of Neuroscience, University of Zurich, Zurich, Switzerland
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Ferreira WAS, Pinheiro DDR, Costa Junior CAD, Rodrigues-Antunes S, Araújo MD, Leão Barros MB, Teixeira ACDS, Faro TAS, Burbano RR, Oliveira EHCD, Harada ML, Borges BDN. An update on the epigenetics of glioblastomas. Epigenomics 2016; 8:1289-305. [PMID: 27585647 DOI: 10.2217/epi-2016-0040] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Glioblastomas, also known as glioblastoma multiforme (GBM), are the most aggressive and malignant type of primary brain tumor in adults, exhibiting notable variability at the histopathological, genetic and epigenetic levels. Recently, epigenetic alterations have emerged as a common hallmark of many tumors, including GBM. Considering that a deeper understanding of the epigenetic modifications that occur in GBM may increase the knowledge regarding the tumorigenesis, progression and recurrence of this disease, in this review we discuss the recent major advances in GBM epigenetics research involving histone modification, glioblastoma stem cells, DNA methylation, noncoding RNAs expression, including their main alterations and the use of epigenetic therapy as a valid option for GBM treatment.
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Affiliation(s)
- Wallax Augusto Silva Ferreira
- Molecular Biology Laboratory, Institute of Biological Sciences, Federal University of Pará (Universidade Federal do Pará-UFPA)-Belém, Pará, Brazil
| | - Danilo do Rosário Pinheiro
- Molecular Biology Laboratory, Institute of Biological Sciences, Federal University of Pará (Universidade Federal do Pará-UFPA)-Belém, Pará, Brazil
| | - Carlos Antonio da Costa Junior
- Molecular Biology Laboratory, Institute of Biological Sciences, Federal University of Pará (Universidade Federal do Pará-UFPA)-Belém, Pará, Brazil
| | - Symara Rodrigues-Antunes
- Molecular Biology Laboratory, Institute of Biological Sciences, Federal University of Pará (Universidade Federal do Pará-UFPA)-Belém, Pará, Brazil
| | - Mariana Diniz Araújo
- Molecular Biology Laboratory, Institute of Biological Sciences, Federal University of Pará (Universidade Federal do Pará-UFPA)-Belém, Pará, Brazil
| | - Mariceli Baia Leão Barros
- Molecular Biology Laboratory, Institute of Biological Sciences, Federal University of Pará (Universidade Federal do Pará-UFPA)-Belém, Pará, Brazil
| | - Adriana Corrêa de Souza Teixeira
- Molecular Biology Laboratory, Institute of Biological Sciences, Federal University of Pará (Universidade Federal do Pará-UFPA)-Belém, Pará, Brazil
| | - Thamirys Aline Silva Faro
- Molecular Biology Laboratory, Institute of Biological Sciences, Federal University of Pará (Universidade Federal do Pará-UFPA)-Belém, Pará, Brazil
| | | | | | - Maria Lúcia Harada
- Molecular Biology Laboratory, Institute of Biological Sciences, Federal University of Pará (Universidade Federal do Pará-UFPA)-Belém, Pará, Brazil
| | - Bárbara do Nascimento Borges
- Molecular Biology Laboratory, Institute of Biological Sciences, Federal University of Pará (Universidade Federal do Pará-UFPA)-Belém, Pará, Brazil
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Abstract
PURPOSE OF REVIEW Genetic, epigenetic, and expression analyses have refined the traditional, histopathology-based classification of diffusely infiltrating gliomas. This review summarizes these trends and implications for elderly patients. RECENT FINDINGS The vast majority of diffusely infiltrating gliomas in elderly patients share an unfavorable molecular phenotype, that is, telomerase reverse transcriptase promoter mutation in the absence of isocitrate dehydrogenase (IDH) mutation and 1p/19q codeletion. Histopathologically, these are mostly astrocytic tumors and treatment is guided by the methylation status of the O6-methylguanine-DNA-methyltransferase (MGMT) promoter. 1p/19q codeletion indicates oligodendroglial histology and benefit from the addition of procarbazine, chlorethyl-cyclohexyl-nitroso-urea/lomustine, and vincristine polychemotherapy to radiotherapy. These tumors are almost exclusively associated with IDH mutations, but their molecular profile is rare in elderly patients. Two large phase III trials, RTOG 0825 and AVAglio, failed to demonstrate an overall survival benefit from antiangiogenic therapy with bevacizumab added to combined chemoradiotherapy (TMZ) in patients with newly diagnosed glioblastoma, but a trend toward improved survival with increasing age can be noted. Ongoing clinical trials in elderly patients with diffusely infiltrating glioma will clarify the role of combined chemoradiotherapy, and of bevacizumab or other antiangiogenic agents as an adjunct to radiotherapy. SUMMARY The choice of first-line therapy in elderly patients with diffusely infiltrating glioma is between postoperative hypofractionated radiotherapy and chemotherapy, guided by MGMT methylation in most patients.
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Saeidimehr S, Ebrahimi A, Saki N, Goodarzi P, Rahim F. MicroRNA-Based Linkage between Aging and Cancer: from Epigenetics View Point. CELL JOURNAL 2016; 18:117-26. [PMID: 27540517 PMCID: PMC4988411 DOI: 10.22074/cellj.2016.4303] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Accepted: 10/01/2015] [Indexed: 02/01/2023]
Abstract
Ageing is a complex process and a broad spectrum of physical, psychological, and
social changes over time. Accompanying diseases and disabilities, which can interfere
with cancer treatment and recovery, occur in old ages. MicroRNAs (miRNAs) are a
set of small non-coding RNAs, which have considerable roles in post-transcriptional
regulation at gene expression level. In this review, we attempted to summarize the current knowledge of miRNAs functions in ageing, with mainly focuses on malignancies
and all underlying genetic, molecular and epigenetics mechanisms. The evidences indicated the complex and dynamic nature of miRNA-based linkage of ageing and cancer
at genomics and epigenomics levels which might be generally crucial for understanding
the mechanisms of age-related cancer and ageing. Recently in the field of cancer and
ageing, scientists claimed that uric acid can be used to regulate reactive oxygen species (ROS), leading to cancer and ageing prevention; these findings highlight the role of
miRNA-based inhibition of the SLC2A9 antioxidant pathway in cancer, as a novel way to
kill malignant cells, while a patient is fighting with cancer.
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Affiliation(s)
| | - Ammar Ebrahimi
- Department of Medical Biotechnology, School of Advanced Medical Technology, Tehran University of Medical Sciences, Tehran, Iran
| | - Najmaldin Saki
- Health Research Institute, Thalassemia and Hemoglobinopathy Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Parisa Goodarzi
- School of Nursing and Midwifery, Iran University of Medical Sciences, Tehran, Iran
| | - Fakher Rahim
- Health Research Institute, Thalassemia and Hemoglobinopathy Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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Wang H, Zheng H, Wang J, Wang C, Wu F. Integrating Omic Data with a Multiplex Network-based Approach for the Identification of Cancer Subtypes. IEEE Trans Nanobioscience 2016; 15:335-342. [PMID: 28113909 DOI: 10.1109/tnb.2016.2556640] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Comprehensive characterization and identification of cancer subtypes have a number of applications and implications in life science and cancer research. Technologies centered on the integration of omics data hold great promise in this endeavor. This paper proposed a multiplex network-based approach for integrative analysis of heterogeneous omics data. It represents a useful alternative network-based solution to the problem and a significant step forward to the methods in which each type of data is treated independently. It has been tested on the identification of the subtypes of glioblastoma multiforme and breast invasive carcinoma from three omics data. The results obtained have shown that it has achieved the performance comparable to state-of-the-art techniques (Normalized Mutual Information > 0.8). In comparison to traditional systems biology tools, the proposed methodology has several significant advantages. It has the ability to correlate and integrate multiple data levels in a holistic manner which may be useful to facilitate our understanding of the pathogenesis of diseases and to capture the heterogeneity of biological processes and the complexity of phenotypes.
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30
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Perez-Janices N, Blanco-Luquin I, Tuñón MT, Barba-Ramos E, Ibáñez B, Zazpe-Cenoz I, Martinez-Aguillo M, Hernandez B, Martínez-Lopez E, Fernández AF, Mercado MR, Cabada T, Escors D, Megias D, Guerrero-Setas D. EPB41L3, TSP-1 and RASSF2 as new clinically relevant prognostic biomarkers in diffuse gliomas. Oncotarget 2016; 6:368-80. [PMID: 25621889 PMCID: PMC4381601 DOI: 10.18632/oncotarget.2745] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 11/12/2014] [Indexed: 12/17/2022] Open
Abstract
Hypermethylation of tumor suppressor genes is one of the hallmarks in the progression of brain tumors. Our objectives were to analyze the presence of the hypermethylation of EPB41L3, RASSF2 and TSP-1 genes in 132 diffuse gliomas (astrocytic and oligodendroglial tumors) and in 10 cases of normal brain, and to establish their association with the patients’ clinicopathological characteristics. Gene hypermethylation was analyzed by methylation-specific-PCR and confirmed by pyrosequencing (for EPB41L3 and TSP-1) and bisulfite-sequencing (for RASSF2). EPB41L3, RASSF2 and TSP-1 genes were hypermethylated only in tumors (29%, 10.6%, and 50%, respectively), confirming their cancer-specific role. Treatment of cells with the DNA-demethylating-agent 5-aza-2′-deoxycytidine restores their transcription, as confirmed by quantitative-reverse-transcription-PCR and immunofluorescence. Immunohistochemistry for EPB41L3, RASSF2 and TSP-1 was performed to analyze protein expression; p53, ki-67, and CD31 expression and 1p/19q co-deletion were considered to better characterize the tumors. EPB41L3 and TSP-1 hypermethylation was associated with worse (p = 0.047) and better (p = 0.037) prognosis, respectively. This observation was confirmed after adjusting the results for age and tumor grade, the role of TSP-1 being most pronounced in oligodendrogliomas (p = 0.001). We conclude that EPB41L3, RASSF2 and TSP-1 genes are involved in the pathogenesis of diffuse gliomas, and that EPB41L3 and TSP-1 hypermethylation are of prognostic significance.
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Affiliation(s)
- N Perez-Janices
- Cancer Epigenetics Group, Navarrabiomed-Fundación Miguel Servet, Navarra, Spain
| | - I Blanco-Luquin
- Cancer Epigenetics Group, Navarrabiomed-Fundación Miguel Servet, Navarra, Spain
| | - M T Tuñón
- Department of Pathology Section A, Complejo Hospitalario de Navarra, Navarra Health Service, Navarra, Spain
| | - E Barba-Ramos
- Department of Pathology Section A, Complejo Hospitalario de Navarra, Navarra Health Service, Navarra, Spain
| | - B Ibáñez
- Navarrabiomed-Fundación Miguel Servet, Navarra, Spain. Red de Evaluación en Servicios Sanitarios y Enfermedades Crónicas (REDISSEC), Navarra, Spain
| | - I Zazpe-Cenoz
- Department of Neurosurgery, Complejo Hospitalario de Navarra, Navarra Health Service, Navarra, Spain
| | - M Martinez-Aguillo
- Department of Medical Oncology, Complejo Hospitalario de Navarra, Navarra Health Service, Navarra, Spain
| | - B Hernandez
- Department of Medical Oncology, Complejo Hospitalario de Navarra, Navarra Health Service, Navarra, Spain
| | - E Martínez-Lopez
- Department of Radiation Oncology, Complejo Hospitalario de Navarra, Navarra Health Service, Navarra, Spain
| | - A F Fernández
- Cancer Epigenetics Laboratory, Instituto Universitario de Oncología del Principado de Asturias (IUOPA), HUCA, Universidad de Oviedo, Asturias, Spain
| | - M R Mercado
- Department of Pathology Section A, Complejo Hospitalario de Navarra, Navarra Health Service, Navarra, Spain
| | - T Cabada
- Department of Radiology, Complejo Hospitalario de Navarra, Navarra Health Service, Navarra, Spain
| | - D Escors
- Navarrabiomed-Fundación Miguel Servet, Navarra, Spain
| | - D Megias
- Confocal Microscopy Core Unit, Spanish National Cancer Research Centre, Madrid, Spain
| | - D Guerrero-Setas
- Cancer Epigenetics Group, Navarrabiomed-Fundación Miguel Servet, Navarra, Spain
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Mohile NA. How I treat glioblastoma in older patients. J Geriatr Oncol 2015; 7:1-6. [PMID: 26725536 DOI: 10.1016/j.jgo.2015.12.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 11/02/2015] [Accepted: 12/04/2015] [Indexed: 11/26/2022]
Abstract
Glioblastoma, a WHO grade IV astrocytoma, is the most common primary malignant brain tumor in adults. It is characterized by molecular heterogeneity and aggressive behavior. Glioblastoma is almost always incurable and most older patients survive less than 6 months. Supportive care with steroids and anti-epileptic drugs is critical to improving and maintain quality of life. Young age, good performance status and methylation of the methyl guanyl methyl transferase promoter are important positive prognostic factors. Several recent clinical trials suggest that there is a subset of the elderly with prolonged survival that is comparable to younger patients. Treatment of glioblastoma in older patients includes maximal safe resection followed by either radiation, chemotherapy or combined modality therapy. Recent advances suggest that some patients can avoid radiation entirely and be treated with chemotherapy alone. Decisions about therapy are individual and based on a patient's performance status, family support and molecular features. Future work needs to better determine the role for comprehensive geriatric assessments in this patient population to better identify patients who may most benefit from aggressive therapies.
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Affiliation(s)
- Nimish A Mohile
- Department of Neurology, University of Rochester Medical Center, 601 Elmwood Avenue, Box 704, Rochester, NY 14642, USA.
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Mertens J, Paquola ACM, Ku M, Hatch E, Böhnke L, Ladjevardi S, McGrath S, Campbell B, Lee H, Herdy JR, Gonçalves JT, Toda T, Kim Y, Winkler J, Yao J, Hetzer MW, Gage FH. Directly Reprogrammed Human Neurons Retain Aging-Associated Transcriptomic Signatures and Reveal Age-Related Nucleocytoplasmic Defects. Cell Stem Cell 2015; 17:705-718. [PMID: 26456686 DOI: 10.1016/j.stem.2015.09.001] [Citation(s) in RCA: 485] [Impact Index Per Article: 53.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 06/18/2015] [Accepted: 09/02/2015] [Indexed: 02/09/2023]
Abstract
Aging is a major risk factor for many human diseases, and in vitro generation of human neurons is an attractive approach for modeling aging-related brain disorders. However, modeling aging in differentiated human neurons has proved challenging. We generated neurons from human donors across a broad range of ages, either by iPSC-based reprogramming and differentiation or by direct conversion into induced neurons (iNs). While iPSCs and derived neurons did not retain aging-associated gene signatures, iNs displayed age-specific transcriptional profiles and revealed age-associated decreases in the nuclear transport receptor RanBP17. We detected an age-dependent loss of nucleocytoplasmic compartmentalization (NCC) in donor fibroblasts and corresponding iNs and found that reduced RanBP17 impaired NCC in young cells, while iPSC rejuvenation restored NCC in aged cells. These results show that iNs retain important aging-related signatures, thus allowing modeling of the aging process in vitro, and they identify impaired NCC as an important factor in human aging.
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Affiliation(s)
- Jerome Mertens
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Apuã C M Paquola
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Manching Ku
- Next Generation Sequencing Core, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Emily Hatch
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Lena Böhnke
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Shauheen Ladjevardi
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Sean McGrath
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Benjamin Campbell
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Hyungjun Lee
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Joseph R Herdy
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - J Tiago Gonçalves
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Tomohisa Toda
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Yongsung Kim
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Jürgen Winkler
- Department of Molecular Neurology, Friedrich-Alexander University Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Jun Yao
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, McGovern Institute for Brain Research, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Martin W Hetzer
- Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Fred H Gage
- Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA.
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Zigmont V, Garrett A, Peng J, Seweryn M, Rempala GA, Harris R, Holloman C, Gundersen TE, Ahlbom A, Feychting M, Johannesen TB, Grimsrud TK, Schwartzbaum J. Association Between Prediagnostic Serum 25-Hydroxyvitamin D Concentration and Glioma. Nutr Cancer 2015; 67:1120-30. [PMID: 26317248 DOI: 10.1080/01635581.2015.1073757] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
There are no previous studies of the association between prediagnostic serum vitamin D concentration and glioma. Vitamin D has immunosuppressive properties; as does glioma. It was, therefore, our hypothesis that elevated vitamin D concentration would increase glioma risk. We conducted a nested case-control study using specimens from the Janus Serum Bank cohort in Norway. Blood donors who were subsequently diagnosed with glioma (n = 592), between 1974 and 2007, were matched to donors without glioma (n = 1112) on date and age at blood collection and sex. We measured 25-hydroxyvitamin D [25(OH)D], an indicator of vitamin D availability, using liquid chromatography coupled with mass spectrometry. Seasonally adjusted odds ratios (ORs) and 95% confidence intervals (95% CIs) were estimated for each control quintile of 25(OH)D using conditional logistic regression. Among men diagnosed with high grade glioma >56, we found a negative trend (P = .04). Men diagnosed ≤ 56 showed a borderline positive trend (P = .08). High levels (>66 nmol/L) of 25(OH)D in men >56 were inversely related to high grade glioma from ≥2 yr before diagnosis (OR = 0.59; 95% CI = 0.38, 0.91) to ≥15 yr before diagnosis (OR = 0.61; 95% CI = 0.38,0.96). Our findings are consistent long before glioma diagnosis and are therefore unlikely to reflect preclinical disease.
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Affiliation(s)
- Victoria Zigmont
- a Comprehensive Cancer Center and Division of Epidemiology, College of Public Health , Ohio State University , Columbus , Ohio , USA
| | - Amy Garrett
- a Comprehensive Cancer Center and Division of Epidemiology, College of Public Health , Ohio State University , Columbus , Ohio , USA
| | - Jin Peng
- b Division of Epidemiology , College of Public Health, Ohio State University , Columbus , Ohio , USA.,c Nationwide Children's Hospital , Columbus , Ohio , USA
| | - Michal Seweryn
- d Division of Biostatistics, College of Public Health and Mathematical Biosciences Institute , Ohio State University , Columbus , Ohio , USA
| | - Grzegorz A Rempala
- d Division of Biostatistics, College of Public Health and Mathematical Biosciences Institute , Ohio State University , Columbus , Ohio , USA
| | - Randall Harris
- a Comprehensive Cancer Center and Division of Epidemiology, College of Public Health , Ohio State University , Columbus , Ohio , USA
| | | | | | - Anders Ahlbom
- g Institute of Environmental Medicine , Division of Epidemiology, Karolinska Institutet , Stockholm , Sweden
| | - Maria Feychting
- g Institute of Environmental Medicine , Division of Epidemiology, Karolinska Institutet , Stockholm , Sweden
| | | | | | - Judith Schwartzbaum
- a Comprehensive Cancer Center and Division of Epidemiology, College of Public Health , Ohio State University , Columbus , Ohio , USA
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Herman A, Gruden K, Blejec A, Podpečan V, Motaln H, Rožman P, Hren M, Zupančič K, Veber M, Verbovšek U, Lah Turnšek T, Porčnik A, Koršič M, Knežević M, Jeras M. Analysis of Glioblastoma Patients' Plasma Revealed the Presence of MicroRNAs with a Prognostic Impact on Survival and Those of Viral Origin. PLoS One 2015; 10:e0125791. [PMID: 25950799 PMCID: PMC4423889 DOI: 10.1371/journal.pone.0125791] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Accepted: 03/25/2015] [Indexed: 12/29/2022] Open
Abstract
Background Glioblastoma multiforme (GBM) is among the most aggressive cancers with a poor prognosis in spite of a plethora of established diagnostic and prognostic biomarkers and treatment modalities. Therefore, the current goal is the detection of novel biomarkers, possibly detectable in the blood of GBM patients that may enable an early diagnosis and are potential therapeutic targets, leading to more efficient interventions. Experimental Procedures MicroRNA profiling of 734 human and human-associated viral miRNAs was performed on blood plasma samples from 16 healthy individuals and 16 patients with GBM, using the nCounter miRNA Expression Assay Kits. Results We identified 19 miRNAs with significantly different plasma levels in GBM patients, compared to the healthy individuals group with the difference limited by a factor of 2. Additionally, 11 viral miRNAs were found differentially expressed in plasma of GBM patients and 24 miRNA levels significantly correlated with the patients’ survival. Moreover, the overlap between the group of candidate miRNAs for diagnostic biomarkers and the group of miRNAs associated with survival, consisted of ten miRNAs, showing both diagnostic and prognostic potential. Among them, hsa miR 592 and hsa miR 514a 3p have not been previously described in GBM and represent novel candidates for selective biomarkers. The possible signalling, induced by the revealed miRNAs is discussed, including those of viral origin, and in particular those related to the impaired immune response in the progression of GBM. Conclusion The GBM burden is reflected in the alteration of the plasma miRNAs pattern, including viral miRNAs, representing the potential for future clinical application. Therefore proposed biomarker candidate miRNAs should be validated in a larger study of an independent cohort of patients.
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Affiliation(s)
- Ana Herman
- Blood Transfusion Centre, Ljubljana, Slovenia
| | - Kristina Gruden
- National Institute of Biology, Ljubljana, Slovenia
- * E-mail: (MJ); (KG)
| | | | - Vid Podpečan
- Department of Knowledge Technologies, Jozef Stefan Institute, Ljubljana, Slovenia
| | | | | | - Matjaž Hren
- BioSistemika, raziskave in razvoj d.o.o., Ljubljana, Slovenia
| | - Klemen Zupančič
- BioSistemika, raziskave in razvoj d.o.o., Ljubljana, Slovenia
| | | | | | - Tamara Lah Turnšek
- National Institute of Biology, Ljubljana, Slovenia
- Faculty of Chemistry and Chemical Engineering, University of Ljubljana, Ljubljana, Slovenia
| | - Andrej Porčnik
- Department of Neurosurgery, Ljubljana University Medical Centre, University of Ljubljana, Ljubljana, Slovenia
| | - Marjan Koršič
- Department of Neurosurgery, Ljubljana University Medical Centre, University of Ljubljana, Ljubljana, Slovenia
| | | | - Matjaž Jeras
- Faculty of Pharmacy, University of Ljubljana, Ljubljana, Slovenia
- Celica d.o.o., Ljubljana, Slovenia
- * E-mail: (MJ); (KG)
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Jabehdar Maralani P, Melhem ER, Wang S, Herskovits EH, Voluck MR, Kim SJ, Learned KO, O’Rourke DM, Mohan S. Association of dynamic susceptibility contrast enhanced MR Perfusion parameters with prognosis in elderly patients with glioblastomas. Eur Radiol 2015; 25:2738-44. [DOI: 10.1007/s00330-015-3640-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2014] [Revised: 12/22/2014] [Accepted: 01/21/2015] [Indexed: 11/25/2022]
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Almenawer SA, Badhiwala JH, Alhazzani W, Greenspoon J, Farrokhyar F, Yarascavitch B, Algird A, Kachur E, Cenic A, Sharieff W, Klurfan P, Gunnarsson T, Ajani O, Reddy K, Singh SK, Murty NK. Biopsy versus partial versus gross total resection in older patients with high-grade glioma: a systematic review and meta-analysis. Neuro Oncol 2015; 17:868-81. [PMID: 25556920 DOI: 10.1093/neuonc/nou349] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 11/29/2014] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Optimal extent of surgical resection (EOR) of high-grade gliomas (HGGs) remains uncertain in the elderly given the unclear benefits and potentially higher rates of mortality and morbidity associated with more extensive degrees of resection. METHODS We undertook a meta-analysis according to a predefined protocol and systematically searched literature databases for reports about HGG EOR. Elderly patients (≥60 y) undergoing biopsy, subtotal resection (STR), and gross total resection (GTR) were compared for the outcome measures of overall survival (OS), postoperative karnofsky performance status (KPS), progression-free survival (PFS), mortality, and morbidity. Treatment effects as pooled estimates, mean differences (MDs), or risk ratios (RRs) with corresponding 95% confidence intervals (CIs) were determined using random effects modeling. RESULTS A total of 12 607 participants from 34 studies met eligibility criteria, including our current cohort of 211 patients. When comparing overall resection (of any extent) with biopsy, in favor of the resection group were OS (MD 3.88 mo, 95% CI: 2.14-5.62, P < .001), postoperative KPS (MD 10.4, 95% CI: 6.58-14.22, P < .001), PFS (MD 2.44 mo, 95% CI: 1.45-3.43, P < .001), mortality (RR = 0.27, 95% CI: 0.12-0.61, P = .002), and morbidity (RR = 0.82, 95% CI: 0.46-1.46, P = .514) . GTR was significantly superior to STR in terms of OS (MD 3.77 mo, 95% CI: 2.26-5.29, P < .001), postoperative KPS (MD 4.91, 95% CI: 0.91-8.92, P = .016), and PFS (MD 2.21 mo, 95% CI: 1.13-3.3, P < .001) with no difference in mortality (RR = 0.53, 95% CI: 0.05-5.71, P = .600) or morbidity (RR = 0.52, 95% CI: 0.18-1.49, P = .223). CONCLUSIONS Our findings suggest an upward improvement in survival time, functional recovery, and tumor recurrence rate associated with increasing extents of safe resection. These benefits did not result in higher rates of mortality or morbidity if considered in conjunction with known established safety measures when managing elderly patients harboring HGGs.
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Affiliation(s)
- Saleh A Almenawer
- Division of Neurosurgery, McMaster University, Hamilton, Ontario, Canada (S.A.A., A.A., E.K., A.C., P.K., T.G., O.A., K.R., S.K.S., N.K.M.); Department of Clinical Epidemiology and Biostatistics, McMaster University, Hamilton, Ontario, Canada (S.A.A., W.A., F.F.); Department of Medicine, McMaster University, Hamilton, Ontario, Canada (W.A.); Department of Oncology, McMaster University, Hamilton, Ontario, Canada (J.G.); Stem Cell and Cancer Research Institute, McMaster University, Hamilton, Ontario, Canada (S.K.S.); Division of Neurosurgery, University of Toronto, Toronto, Ontario, Canada (J.H.B.); Department of Radiation Oncology, Dalhousie University, Halifax, Nova Scotia, Canada (W.S.); Department of Neurological Surgery, University of Texas Southwestern Medical Center, Dallas, Texas (B.Y.)
| | - Jetan H Badhiwala
- Division of Neurosurgery, McMaster University, Hamilton, Ontario, Canada (S.A.A., A.A., E.K., A.C., P.K., T.G., O.A., K.R., S.K.S., N.K.M.); Department of Clinical Epidemiology and Biostatistics, McMaster University, Hamilton, Ontario, Canada (S.A.A., W.A., F.F.); Department of Medicine, McMaster University, Hamilton, Ontario, Canada (W.A.); Department of Oncology, McMaster University, Hamilton, Ontario, Canada (J.G.); Stem Cell and Cancer Research Institute, McMaster University, Hamilton, Ontario, Canada (S.K.S.); Division of Neurosurgery, University of Toronto, Toronto, Ontario, Canada (J.H.B.); Department of Radiation Oncology, Dalhousie University, Halifax, Nova Scotia, Canada (W.S.); Department of Neurological Surgery, University of Texas Southwestern Medical Center, Dallas, Texas (B.Y.)
| | - Waleed Alhazzani
- Division of Neurosurgery, McMaster University, Hamilton, Ontario, Canada (S.A.A., A.A., E.K., A.C., P.K., T.G., O.A., K.R., S.K.S., N.K.M.); Department of Clinical Epidemiology and Biostatistics, McMaster University, Hamilton, Ontario, Canada (S.A.A., W.A., F.F.); Department of Medicine, McMaster University, Hamilton, Ontario, Canada (W.A.); Department of Oncology, McMaster University, Hamilton, Ontario, Canada (J.G.); Stem Cell and Cancer Research Institute, McMaster University, Hamilton, Ontario, Canada (S.K.S.); Division of Neurosurgery, University of Toronto, Toronto, Ontario, Canada (J.H.B.); Department of Radiation Oncology, Dalhousie University, Halifax, Nova Scotia, Canada (W.S.); Department of Neurological Surgery, University of Texas Southwestern Medical Center, Dallas, Texas (B.Y.)
| | - Jeffrey Greenspoon
- Division of Neurosurgery, McMaster University, Hamilton, Ontario, Canada (S.A.A., A.A., E.K., A.C., P.K., T.G., O.A., K.R., S.K.S., N.K.M.); Department of Clinical Epidemiology and Biostatistics, McMaster University, Hamilton, Ontario, Canada (S.A.A., W.A., F.F.); Department of Medicine, McMaster University, Hamilton, Ontario, Canada (W.A.); Department of Oncology, McMaster University, Hamilton, Ontario, Canada (J.G.); Stem Cell and Cancer Research Institute, McMaster University, Hamilton, Ontario, Canada (S.K.S.); Division of Neurosurgery, University of Toronto, Toronto, Ontario, Canada (J.H.B.); Department of Radiation Oncology, Dalhousie University, Halifax, Nova Scotia, Canada (W.S.); Department of Neurological Surgery, University of Texas Southwestern Medical Center, Dallas, Texas (B.Y.)
| | - Forough Farrokhyar
- Division of Neurosurgery, McMaster University, Hamilton, Ontario, Canada (S.A.A., A.A., E.K., A.C., P.K., T.G., O.A., K.R., S.K.S., N.K.M.); Department of Clinical Epidemiology and Biostatistics, McMaster University, Hamilton, Ontario, Canada (S.A.A., W.A., F.F.); Department of Medicine, McMaster University, Hamilton, Ontario, Canada (W.A.); Department of Oncology, McMaster University, Hamilton, Ontario, Canada (J.G.); Stem Cell and Cancer Research Institute, McMaster University, Hamilton, Ontario, Canada (S.K.S.); Division of Neurosurgery, University of Toronto, Toronto, Ontario, Canada (J.H.B.); Department of Radiation Oncology, Dalhousie University, Halifax, Nova Scotia, Canada (W.S.); Department of Neurological Surgery, University of Texas Southwestern Medical Center, Dallas, Texas (B.Y.)
| | - Blake Yarascavitch
- Division of Neurosurgery, McMaster University, Hamilton, Ontario, Canada (S.A.A., A.A., E.K., A.C., P.K., T.G., O.A., K.R., S.K.S., N.K.M.); Department of Clinical Epidemiology and Biostatistics, McMaster University, Hamilton, Ontario, Canada (S.A.A., W.A., F.F.); Department of Medicine, McMaster University, Hamilton, Ontario, Canada (W.A.); Department of Oncology, McMaster University, Hamilton, Ontario, Canada (J.G.); Stem Cell and Cancer Research Institute, McMaster University, Hamilton, Ontario, Canada (S.K.S.); Division of Neurosurgery, University of Toronto, Toronto, Ontario, Canada (J.H.B.); Department of Radiation Oncology, Dalhousie University, Halifax, Nova Scotia, Canada (W.S.); Department of Neurological Surgery, University of Texas Southwestern Medical Center, Dallas, Texas (B.Y.)
| | - Almunder Algird
- Division of Neurosurgery, McMaster University, Hamilton, Ontario, Canada (S.A.A., A.A., E.K., A.C., P.K., T.G., O.A., K.R., S.K.S., N.K.M.); Department of Clinical Epidemiology and Biostatistics, McMaster University, Hamilton, Ontario, Canada (S.A.A., W.A., F.F.); Department of Medicine, McMaster University, Hamilton, Ontario, Canada (W.A.); Department of Oncology, McMaster University, Hamilton, Ontario, Canada (J.G.); Stem Cell and Cancer Research Institute, McMaster University, Hamilton, Ontario, Canada (S.K.S.); Division of Neurosurgery, University of Toronto, Toronto, Ontario, Canada (J.H.B.); Department of Radiation Oncology, Dalhousie University, Halifax, Nova Scotia, Canada (W.S.); Department of Neurological Surgery, University of Texas Southwestern Medical Center, Dallas, Texas (B.Y.)
| | - Edward Kachur
- Division of Neurosurgery, McMaster University, Hamilton, Ontario, Canada (S.A.A., A.A., E.K., A.C., P.K., T.G., O.A., K.R., S.K.S., N.K.M.); Department of Clinical Epidemiology and Biostatistics, McMaster University, Hamilton, Ontario, Canada (S.A.A., W.A., F.F.); Department of Medicine, McMaster University, Hamilton, Ontario, Canada (W.A.); Department of Oncology, McMaster University, Hamilton, Ontario, Canada (J.G.); Stem Cell and Cancer Research Institute, McMaster University, Hamilton, Ontario, Canada (S.K.S.); Division of Neurosurgery, University of Toronto, Toronto, Ontario, Canada (J.H.B.); Department of Radiation Oncology, Dalhousie University, Halifax, Nova Scotia, Canada (W.S.); Department of Neurological Surgery, University of Texas Southwestern Medical Center, Dallas, Texas (B.Y.)
| | - Aleksa Cenic
- Division of Neurosurgery, McMaster University, Hamilton, Ontario, Canada (S.A.A., A.A., E.K., A.C., P.K., T.G., O.A., K.R., S.K.S., N.K.M.); Department of Clinical Epidemiology and Biostatistics, McMaster University, Hamilton, Ontario, Canada (S.A.A., W.A., F.F.); Department of Medicine, McMaster University, Hamilton, Ontario, Canada (W.A.); Department of Oncology, McMaster University, Hamilton, Ontario, Canada (J.G.); Stem Cell and Cancer Research Institute, McMaster University, Hamilton, Ontario, Canada (S.K.S.); Division of Neurosurgery, University of Toronto, Toronto, Ontario, Canada (J.H.B.); Department of Radiation Oncology, Dalhousie University, Halifax, Nova Scotia, Canada (W.S.); Department of Neurological Surgery, University of Texas Southwestern Medical Center, Dallas, Texas (B.Y.)
| | - Waseem Sharieff
- Division of Neurosurgery, McMaster University, Hamilton, Ontario, Canada (S.A.A., A.A., E.K., A.C., P.K., T.G., O.A., K.R., S.K.S., N.K.M.); Department of Clinical Epidemiology and Biostatistics, McMaster University, Hamilton, Ontario, Canada (S.A.A., W.A., F.F.); Department of Medicine, McMaster University, Hamilton, Ontario, Canada (W.A.); Department of Oncology, McMaster University, Hamilton, Ontario, Canada (J.G.); Stem Cell and Cancer Research Institute, McMaster University, Hamilton, Ontario, Canada (S.K.S.); Division of Neurosurgery, University of Toronto, Toronto, Ontario, Canada (J.H.B.); Department of Radiation Oncology, Dalhousie University, Halifax, Nova Scotia, Canada (W.S.); Department of Neurological Surgery, University of Texas Southwestern Medical Center, Dallas, Texas (B.Y.)
| | - Paula Klurfan
- Division of Neurosurgery, McMaster University, Hamilton, Ontario, Canada (S.A.A., A.A., E.K., A.C., P.K., T.G., O.A., K.R., S.K.S., N.K.M.); Department of Clinical Epidemiology and Biostatistics, McMaster University, Hamilton, Ontario, Canada (S.A.A., W.A., F.F.); Department of Medicine, McMaster University, Hamilton, Ontario, Canada (W.A.); Department of Oncology, McMaster University, Hamilton, Ontario, Canada (J.G.); Stem Cell and Cancer Research Institute, McMaster University, Hamilton, Ontario, Canada (S.K.S.); Division of Neurosurgery, University of Toronto, Toronto, Ontario, Canada (J.H.B.); Department of Radiation Oncology, Dalhousie University, Halifax, Nova Scotia, Canada (W.S.); Department of Neurological Surgery, University of Texas Southwestern Medical Center, Dallas, Texas (B.Y.)
| | - Thorsteinn Gunnarsson
- Division of Neurosurgery, McMaster University, Hamilton, Ontario, Canada (S.A.A., A.A., E.K., A.C., P.K., T.G., O.A., K.R., S.K.S., N.K.M.); Department of Clinical Epidemiology and Biostatistics, McMaster University, Hamilton, Ontario, Canada (S.A.A., W.A., F.F.); Department of Medicine, McMaster University, Hamilton, Ontario, Canada (W.A.); Department of Oncology, McMaster University, Hamilton, Ontario, Canada (J.G.); Stem Cell and Cancer Research Institute, McMaster University, Hamilton, Ontario, Canada (S.K.S.); Division of Neurosurgery, University of Toronto, Toronto, Ontario, Canada (J.H.B.); Department of Radiation Oncology, Dalhousie University, Halifax, Nova Scotia, Canada (W.S.); Department of Neurological Surgery, University of Texas Southwestern Medical Center, Dallas, Texas (B.Y.)
| | - Olufemi Ajani
- Division of Neurosurgery, McMaster University, Hamilton, Ontario, Canada (S.A.A., A.A., E.K., A.C., P.K., T.G., O.A., K.R., S.K.S., N.K.M.); Department of Clinical Epidemiology and Biostatistics, McMaster University, Hamilton, Ontario, Canada (S.A.A., W.A., F.F.); Department of Medicine, McMaster University, Hamilton, Ontario, Canada (W.A.); Department of Oncology, McMaster University, Hamilton, Ontario, Canada (J.G.); Stem Cell and Cancer Research Institute, McMaster University, Hamilton, Ontario, Canada (S.K.S.); Division of Neurosurgery, University of Toronto, Toronto, Ontario, Canada (J.H.B.); Department of Radiation Oncology, Dalhousie University, Halifax, Nova Scotia, Canada (W.S.); Department of Neurological Surgery, University of Texas Southwestern Medical Center, Dallas, Texas (B.Y.)
| | - Kesava Reddy
- Division of Neurosurgery, McMaster University, Hamilton, Ontario, Canada (S.A.A., A.A., E.K., A.C., P.K., T.G., O.A., K.R., S.K.S., N.K.M.); Department of Clinical Epidemiology and Biostatistics, McMaster University, Hamilton, Ontario, Canada (S.A.A., W.A., F.F.); Department of Medicine, McMaster University, Hamilton, Ontario, Canada (W.A.); Department of Oncology, McMaster University, Hamilton, Ontario, Canada (J.G.); Stem Cell and Cancer Research Institute, McMaster University, Hamilton, Ontario, Canada (S.K.S.); Division of Neurosurgery, University of Toronto, Toronto, Ontario, Canada (J.H.B.); Department of Radiation Oncology, Dalhousie University, Halifax, Nova Scotia, Canada (W.S.); Department of Neurological Surgery, University of Texas Southwestern Medical Center, Dallas, Texas (B.Y.)
| | - Sheila K Singh
- Division of Neurosurgery, McMaster University, Hamilton, Ontario, Canada (S.A.A., A.A., E.K., A.C., P.K., T.G., O.A., K.R., S.K.S., N.K.M.); Department of Clinical Epidemiology and Biostatistics, McMaster University, Hamilton, Ontario, Canada (S.A.A., W.A., F.F.); Department of Medicine, McMaster University, Hamilton, Ontario, Canada (W.A.); Department of Oncology, McMaster University, Hamilton, Ontario, Canada (J.G.); Stem Cell and Cancer Research Institute, McMaster University, Hamilton, Ontario, Canada (S.K.S.); Division of Neurosurgery, University of Toronto, Toronto, Ontario, Canada (J.H.B.); Department of Radiation Oncology, Dalhousie University, Halifax, Nova Scotia, Canada (W.S.); Department of Neurological Surgery, University of Texas Southwestern Medical Center, Dallas, Texas (B.Y.)
| | - Naresh K Murty
- Division of Neurosurgery, McMaster University, Hamilton, Ontario, Canada (S.A.A., A.A., E.K., A.C., P.K., T.G., O.A., K.R., S.K.S., N.K.M.); Department of Clinical Epidemiology and Biostatistics, McMaster University, Hamilton, Ontario, Canada (S.A.A., W.A., F.F.); Department of Medicine, McMaster University, Hamilton, Ontario, Canada (W.A.); Department of Oncology, McMaster University, Hamilton, Ontario, Canada (J.G.); Stem Cell and Cancer Research Institute, McMaster University, Hamilton, Ontario, Canada (S.K.S.); Division of Neurosurgery, University of Toronto, Toronto, Ontario, Canada (J.H.B.); Department of Radiation Oncology, Dalhousie University, Halifax, Nova Scotia, Canada (W.S.); Department of Neurological Surgery, University of Texas Southwestern Medical Center, Dallas, Texas (B.Y.)
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Henriksen M, Johnsen KB, Andersen HH, Pilgaard L, Duroux M. MicroRNA expression signatures determine prognosis and survival in glioblastoma multiforme--a systematic overview. Mol Neurobiol 2014; 50:896-913. [PMID: 24619503 PMCID: PMC4225053 DOI: 10.1007/s12035-014-8668-y] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 02/25/2014] [Indexed: 12/21/2022]
Abstract
Despite advances in our knowledge about glioblastoma multiforme (GBM) pathology, clinical challenges still lie ahead with respect to treatment in GBM due to high prevalence, poor prognosis, and frequent tumor relapse. The implication of microRNAs (miRNAs) in GBM is a rapidly expanding field of research with the aim to develop more targeted molecular therapies. This review aims to present a comprehensive overview of all the available literature, evaluating miRNA signatures as a function of prognosis and survival in GBM. The results are presented with a focus on studies derived from clinical data in databases and independent tissue cohorts where smaller samples sizes were investigated. Here, miRNA associated to longer survival (protective) and miRNA with shorter survival (risk-associated) have been identified and their signatures based on different prognostic attributes are described. Finally, miRNAs associated with disease progression or survival in several studies are identified and functionally described. These miRNAs may be valuable for future determination of patient prognosis and could possibly serve as targets for miRNA-based therapies, which hold a great potential in the treatment of this severe malignant disease.
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Affiliation(s)
- Michael Henriksen
- Laboratory for Cancer Biology, Institute of Health Science and Technology, Aalborg University, Fredrik Bajers Vej 3B, 9220 Aalborg Ø, Denmark
| | - Kasper Bendix Johnsen
- Laboratory for Cancer Biology, Institute of Health Science and Technology, Aalborg University, Fredrik Bajers Vej 3B, 9220 Aalborg Ø, Denmark
| | - Hjalte Holm Andersen
- Laboratory for Cancer Biology, Institute of Health Science and Technology, Aalborg University, Fredrik Bajers Vej 3B, 9220 Aalborg Ø, Denmark
| | - Linda Pilgaard
- Laboratory for Cancer Biology, Institute of Health Science and Technology, Aalborg University, Fredrik Bajers Vej 3B, 9220 Aalborg Ø, Denmark
| | - Meg Duroux
- Laboratory for Cancer Biology, Institute of Health Science and Technology, Aalborg University, Fredrik Bajers Vej 3B, 9220 Aalborg Ø, Denmark
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Abstract
Although glioblastoma occurs mostly in elderly patients, there is a paucity of trials addressing patients older than 70 years of age. Age, by itself, constitutes an unfavorable prognostic factor, which is probably due to unpropitious genetic features, but also due to iatrogenic defeatism. However, many retrospective studies report a survival benefit achieved by aggressive surgical resection seeking gross total removal of contrast-enhancing tumor according to preoperative MRI. Combined radiochemotherapy with concomitant and adjuvant temozolomide has not been investigated in prospective trials. Numerous retrospective studies and a meta-analysis suggest benefit from combined treatment. Prospective randomized trials only evaluated either temozolomide or radiotherapy. Single-treatment hypofractionated radiotherapy performed superior to conventional fractionation. In patients with methylated MGMT promoter, first-line dose-dense temozolomide facilitates prolonged survival. However, there is no comparison with combined radiochemotherapy as the standard-of-care in adult patients. Comorbidity is more frequent in elderly patients, but does not correlate with preterm termination of temozolomide treatment. This review article compiles data proposing a straightforward glioblastoma treatment, irrespective of age.
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Affiliation(s)
- Florian Stockhammer
- Department of Neurosurgery, Universitätsmedizin Göttingen, Robert-Koch-Straße 40, 37075 Göttingen, Germany
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Micro-environment causes reversible changes in DNA methylation and mRNA expression profiles in patient-derived glioma stem cells. PLoS One 2014; 9:e94045. [PMID: 24728236 PMCID: PMC3984100 DOI: 10.1371/journal.pone.0094045] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Accepted: 03/11/2014] [Indexed: 12/12/2022] Open
Abstract
In vitro and in vivo models are widely used in cancer research. Characterizing the similarities and differences between a patient's tumor and corresponding in vitro and in vivo models is important for understanding the potential clinical relevance of experimental data generated with these models. Towards this aim, we analyzed the genomic aberrations, DNA methylation and transcriptome profiles of five parental tumors and their matched in vitro isolated glioma stem cell (GSC) lines and xenografts generated from these same GSCs using high-resolution platforms. We observed that the methylation and transcriptome profiles of in vitro GSCs were significantly different from their corresponding xenografts, which were actually more similar to their original parental tumors. This points to the potentially critical role of the brain microenvironment in influencing methylation and transcriptional patterns of GSCs. Consistent with this possibility, ex vivo cultured GSCs isolated from xenografts showed a tendency to return to their initial in vitro states even after a short time in culture, supporting a rapid dynamic adaptation to the in vitro microenvironment. These results show that methylation and transcriptome profiles are highly dependent on the microenvironment and growth in orthotopic sites partially reverse the changes caused by in vitro culturing.
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Sturm D, Bender S, Jones DT, Lichter P, Grill J, Becher O, Hawkins C, Majewski J, Jones C, Costello JF, Iavarone A, Aldape K, Brennan CW, Jabado N, Pfister SM. Paediatric and adult glioblastoma: multiform (epi)genomic culprits emerge. Nat Rev Cancer 2014; 14:92-107. [PMID: 24457416 PMCID: PMC4003223 DOI: 10.1038/nrc3655] [Citation(s) in RCA: 397] [Impact Index Per Article: 39.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We have extended our understanding of the molecular biology that underlies adult glioblastoma over many years. By contrast, high-grade gliomas in children and adolescents have remained a relatively under-investigated disease. The latest large-scale genomic and epigenomic profiling studies have yielded an unprecedented abundance of novel data and provided deeper insights into gliomagenesis across all age groups, which has highlighted key distinctions but also some commonalities. As we are on the verge of dissecting glioblastomas into meaningful biological subgroups, this Review summarizes the hallmark genetic alterations that are associated with distinct epigenetic features and patient characteristics in both paediatric and adult disease, and examines the complex interplay between the glioblastoma genome and epigenome.
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Affiliation(s)
- Dominik Sturm
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) Heidelberg, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, and Immunology, Heidelberg University Hospital, Im Neuenheimer Feld 430, D-69120 Heidelberg, Germany
| | - Sebastian Bender
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) Heidelberg, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, and Immunology, Heidelberg University Hospital, Im Neuenheimer Feld 430, D-69120 Heidelberg, Germany
| | - David T.W. Jones
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) Heidelberg, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany
| | - Peter Lichter
- Division of Molecular Genetics, German Cancer Research Center (DKFZ) Heidelberg, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany
| | - Jacques Grill
- Brain Tumor Program, Department of Pediatric and Adolescent Oncology, Gustave Roussy Cancer Institute, Universite Paris Sud, 114 Rue Eduoard Vaillant, 94805 Villejuif, France
| | - Oren Becher
- Division of Pediatric Hematology/Oncology, Duke University Medical Center, DUMC 91001, Durham, NC 27710, USA
| | - Cynthia Hawkins
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, 555 University Avenue, Toronto, ON, M5G 1X8, Canada
| | - Jacek Majewski
- Division of Experimental Medicine and Department of Human Genetics, McGill University and McGill University Health Centre, 2155 Guy Street, Montreal, QC, H3H 2R9, Canada
| | - Chris Jones
- Divisions of Molecular Pathology and Cancer Therapeutics, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey, SM2 5NG, UK
| | - Joseph F. Costello
- Brain Tumor Research Center, Department of Neurosurgery, University of California, 2340 Sutter St., San Francisco, CA 94143, USA
| | - Antonio Iavarone
- Institute for Cancer Genetics and Departments of Pathology and Neurology, Columbia University Medical Center, 1130 St. Nicholas Avenue, New York, NY 10032, USA
| | - Kenneth Aldape
- Department of Neuro-Oncology, University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd. Unit 0085, Houston, TX 77030, USA
| | - Cameron W. Brennan
- Human Oncology & Pathogenesis Program and Department of Neurosurgery, Brain Tumor Center, Memorial Sloan-Kettering Cancer Center, 1275 York Ave, New York, NY 10065, USA
| | - Nada Jabado
- Division of Experimental Medicine and Department of Human Genetics, McGill University and McGill University Health Centre, 2155 Guy Street, Montreal, QC, H3H 2R9, Canada
| | - Stefan M. Pfister
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) Heidelberg, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, and Immunology, Heidelberg University Hospital, Im Neuenheimer Feld 430, D-69120 Heidelberg, Germany
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