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Liu X, Wang W, Zhang X, Liang J, Feng D, Li Y, Xue M, Ling B. Metabolism pathway-based subtyping in endometrial cancer: An integrated study by multi-omics analysis and machine learning algorithms. Mol Ther Nucleic Acids 2024; 35:102155. [PMID: 38495844 PMCID: PMC10943971 DOI: 10.1016/j.omtn.2024.102155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 02/14/2024] [Indexed: 03/19/2024]
Abstract
Endometrial cancer (EC), the second most common malignancy in the female reproductive system, has garnered increasing attention for its genomic heterogeneity, but understanding of its metabolic characteristics is still poor. We explored metabolic dysfunctions in EC through a comprehensive multi-omics analysis (RNA-seq datasets from The Cancer Genome Atlas [TCGA], Cancer Cell Line Encyclopedia [CCLE], and GEO datasets; the Clinical Proteomic Tumor Analysis Consortium [CPTAC] proteomics; CCLE metabolomics) to develop useful molecular targets for precision therapy. Unsupervised consensus clustering was performed to categorize EC patients into three metabolism-pathway-based subgroups (MPSs). These MPS subgroups had distinct clinical prognoses, transcriptomic and genomic alterations, immune microenvironment landscape, and unique patterns of chemotherapy sensitivity. Moreover, the MPS2 subgroup had a better response to immunotherapy. Finally, three machine learning algorithms (LASSO, random forest, and stepwise multivariate Cox regression) were used for developing a prognostic metagene signature based on metabolic molecules. Thus, a 13-hub gene-based classifier was constructed to predict patients' MPS subtypes, offering a more accessible and practical approach. This metabolism-based classification system can enhance prognostic predictions and guide clinical strategies for immunotherapy and metabolism-targeted therapy in EC.
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Affiliation(s)
- Xiaodie Liu
- Department of Obstetrics and Gynecology, China-Japan Friendship Hospital (Institute of Clinical Medical Sciences), Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100029, China
- Department of Obstetrics and Gynecology, Shandong Provincial Hospital, Jinan 250000, China
| | - Wenhui Wang
- Department of Obstetrics and Gynecology, China-Japan Friendship Hospital, Beijing 100029, China
| | - Xiaolei Zhang
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, No. 107 Wenhua West Road, Jinan, Shandong 250012, China
| | - Jing Liang
- Department of Obstetrics and Gynecology, China-Japan Friendship Hospital, Beijing 100029, China
| | - Dingqing Feng
- Department of Obstetrics and Gynecology, China-Japan Friendship Hospital, Beijing 100029, China
| | - Yuebo Li
- Department of Obstetrics and Gynecology, China-Japan Friendship Hospital (Institute of Clinical Medical Sciences), Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100029, China
| | - Ming Xue
- Department of Obstetrics and Gynecology, China-Japan Friendship Hospital (Institute of Clinical Medical Sciences), Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100029, China
| | - Bin Ling
- Department of Obstetrics and Gynecology, China-Japan Friendship Hospital (Institute of Clinical Medical Sciences), Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100029, China
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Das A, Gaikwad U, Krishnan G, Rajendran A, Patil S, Subramaniam P, Krishna U, Wakde MG, Chilukuri S, Jalali R. Successful Implementation of Image-Guided Pencil-Beam Scanning Proton Therapy in Medulloblastomas. Diagnostics (Basel) 2023; 13:3378. [PMID: 37958274 PMCID: PMC10647744 DOI: 10.3390/diagnostics13213378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 10/27/2023] [Accepted: 11/01/2023] [Indexed: 11/15/2023] Open
Abstract
Medulloblastoma is the most common malignant brain tumour in children, while much rarer in adults. Although the prognosis and outcomes have greatly improved in the era of modern multidisciplinary management, long-term treatment-induced toxicities are common. Craniospinal irradiation followed by a boost to the primary and metastatic tumour sites forms the backbone of treatment. Proton therapy has been endorsed over conventional photon-based radiotherapy due to its superior dosimetric advantages and subsequently lower incidence and severity of toxicities. We report here our experience from South-East Asia's first proton therapy centre of treating 40 patients with medulloblastoma (38 children and adolescents, 2 adults) who received image-guided, intensity-modulated proton therapy with pencil-beam scanning between 2019 and 2023, with a focus on dosimetry, acute toxicities, and early survival outcomes. All patients could complete the planned course of proton therapy, with mostly mild acute toxicities that were manageable on an outpatient basis. Haematological toxicity was not dose-limiting and did not prolong the overall treatment time. Preliminary data on early outcomes including overall survival and disease-free survival are encouraging, although a longer follow-up and data on long-term toxicities are needed.
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Affiliation(s)
- Anindita Das
- Neuro-Oncology Cancer Management Team, Department of Radiation Oncology, Apollo Proton Cancer Centre, Chennai 600041, India; (A.D.)
| | - Utpal Gaikwad
- Neuro-Oncology Cancer Management Team, Department of Radiation Oncology, Apollo Proton Cancer Centre, Chennai 600041, India; (A.D.)
| | - Ganapathy Krishnan
- Department of Medical Physics, Apollo Proton Cancer Centre, Chennai 600041, India
| | - Adhithyan Rajendran
- Department of Diagnostic and Intervention Radiology, Apollo Proton Cancer Centre, Chennai 600041, India
| | - Sushama Patil
- Department of Pathology, Apollo Proton Cancer Centre, Chennai 600041, India
| | - Preethi Subramaniam
- Neuro-Oncology Cancer Management Team, Department of Radiation Oncology, Apollo Proton Cancer Centre, Chennai 600041, India; (A.D.)
| | - Uday Krishna
- Neuro-Oncology Cancer Management Team, Department of Radiation Oncology, Apollo Proton Cancer Centre, Chennai 600041, India; (A.D.)
| | - Manoj G. Wakde
- Neuro-Oncology Cancer Management Team, Department of Radiation Oncology, Apollo Proton Cancer Centre, Chennai 600041, India; (A.D.)
| | - Srinivas Chilukuri
- Paediatric Oncology Cancer Management Team, Department of Radiation Oncology, Apollo Proton Cancer Centre, Chennai 600041, India
| | - Rakesh Jalali
- Neuro-Oncology Cancer Management Team, Department of Radiation Oncology, Apollo Proton Cancer Centre, Chennai 600041, India; (A.D.)
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Ismail M, Craig S, Ahmed R, de Blank P, Tiwari P. Opportunities and Advances in Radiomics and Radiogenomics for Pediatric Medulloblastoma Tumors. Diagnostics (Basel) 2023; 13:2727. [PMID: 37685265 PMCID: PMC10487205 DOI: 10.3390/diagnostics13172727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/19/2023] [Accepted: 08/21/2023] [Indexed: 09/10/2023] Open
Abstract
Recent advances in artificial intelligence have greatly impacted the field of medical imaging and vastly improved the development of computational algorithms for data analysis. In the field of pediatric neuro-oncology, radiomics, the process of obtaining high-dimensional data from radiographic images, has been recently utilized in applications including survival prognostication, molecular classification, and tumor type classification. Similarly, radiogenomics, or the integration of radiomic and genomic data, has allowed for building comprehensive computational models to better understand disease etiology. While there exist excellent review articles on radiomics and radiogenomic pipelines and their applications in adult solid tumors, in this review article, we specifically review these computational approaches in the context of pediatric medulloblastoma tumors. Based on our systematic literature research via PubMed and Google Scholar, we provide a detailed summary of a total of 15 articles that have utilized radiomic and radiogenomic analysis for survival prognostication, tumor segmentation, and molecular subgroup classification in the context of pediatric medulloblastoma. Lastly, we shed light on the current challenges with the existing approaches as well as future directions and opportunities with using these computational radiomic and radiogenomic approaches for pediatric medulloblastoma tumors.
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Affiliation(s)
- Marwa Ismail
- Department of Radiology, University of Wisconsin-Madison, Madison, WI 53706, USA; (S.C.); (P.T.)
| | - Stephen Craig
- Department of Radiology, University of Wisconsin-Madison, Madison, WI 53706, USA; (S.C.); (P.T.)
| | - Raheel Ahmed
- Department of Neurosurgery, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53706, USA;
| | - Peter de Blank
- Department of Pediatrics, College of Medicine, University of Cincinnati, Cincinnati, OH 45267, USA;
| | - Pallavi Tiwari
- Department of Radiology, University of Wisconsin-Madison, Madison, WI 53706, USA; (S.C.); (P.T.)
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
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Yu R, Huang X, Lin J, Lin S, Shen G, Chen W. Bioinformatics analysis based on DNA methylation data identified in lung adenocarcinoma subgroups with different immune characteristics and clinical outcomes. J Thorac Dis 2023; 15:2184-2197. [PMID: 37197548 PMCID: PMC10183559 DOI: 10.21037/jtd-23-494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 04/23/2023] [Indexed: 05/19/2023]
Abstract
Background DNA methylation can be used to predict clinical outcomes and improve the classification of tumors. The present study aimed to develop a new lung adenocarcinoma (LUAD) classification system according to the immune cell gene-related methylation sites and to reveal the survival outcomes, clinical characteristics, immune cell infiltration, stem cell characteristics, and genomic variations of each molecular subgroup. Methods The DNA methylation sites of LUAD samples collected from The Cancer Genome Atlas (TCGA) database were analyzed, and the prognosis-related differential methylation sites (DMS) were screened. Consistent clustering of the samples was conducted using ConsensusClusterPlus, and the classification results were verified by principal component analysis (PCA). The survival and clinical results, immune cell infiltration, stemness, DNA mutation, and copy number variation (CNV) of each molecular subgroup were analyzed. Results A total of 40 DMS were obtained by difference and univariate COX analyses, and the TCGA LUAD samples were divided into three subgroups: cluster 1 (C1), cluster 2 (C2), and cluster 3 (C3). Among these subgroups, the overall survival (OS) of C3 was significantly higher than that of C1 and C2. Compared with C1 and C3, C2 had the lowest innate immune cell and adaptive immune cell infiltration scores; the lowest stromal score, immune score, and iconic immune checkpoint expression; and the highest expression of messenger RNA (mRNA) expression-based stemness indices (mRNAsi), DNA methylation-based stemness index (mDNAsi), and tumor mutational burden (TMB). Conclusions In this study, we proposed a LUAD typing system based on DMS, which was closely related to the survival, clinical features, immune characteristics, and genomic variations of LUAD, and may contribute to the development of personalized therapy for new specific subtypes.
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Affiliation(s)
- Ruilin Yu
- Department of Respiratory Medicine, People’s Hospital of Longhua, The Affiliated Hospital of Southern Medical University, Shenzhen, China
| | - Xiaoming Huang
- Department of Respiratory Medicine, People’s Hospital of Longhua, The Affiliated Hospital of Southern Medical University, Shenzhen, China
| | - Junqi Lin
- Department of Respiratory Medicine, People’s Hospital of Longhua, The Affiliated Hospital of Southern Medical University, Shenzhen, China
| | - Shaoming Lin
- Department of Respiratory Medicine, People’s Hospital of Longhua, The Affiliated Hospital of Southern Medical University, Shenzhen, China
| | - Guanle Shen
- Department of Respiratory Medicine, People’s Hospital of Longhua, The Affiliated Hospital of Southern Medical University, Shenzhen, China
| | - Wenbiao Chen
- Department of Respiratory Medicine, People’s Hospital of Longhua, The Affiliated Hospital of Southern Medical University, Shenzhen, China
- Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, The First Affiliated Hospital of Southern University of Science and Technology, The Second Clinical Medical College of Jinan University, Shenzhen People’s Hospital, Shenzhen, China
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Ye LF, Weng JY, Wu LD. Integrated genomic analysis defines molecular subgroups in dilated cardiomyopathy and identifies novel biomarkers based on machine learning methods. Front Genet 2023; 14:1050696. [PMID: 36824437 PMCID: PMC9941670 DOI: 10.3389/fgene.2023.1050696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 01/20/2023] [Indexed: 02/09/2023] Open
Abstract
Aim: As the most common cardiomyopathy, dilated cardiomyopathy (DCM) often leads to progressive heart failure and sudden cardiac death. This study was designed to investigate the molecular subgroups of DCM. Methods: Three datasets of DCM were downloaded from GEO database (GSE17800, GSE79962 and GSE3585). After log2-transformation and background correction with "limma" package in R software, the three datasets were merged into a metadata cohort. The consensus clustering was conducted by the "Consensus Cluster Plus" package to uncover the molecular subgroups of DCM. Moreover, clinical characteristics of different molecular subgroups were compared in detail. We also adopted Weighted gene co-expression network analysis (WGCNA) analysis based on subgroup-specific signatures of gene expression profiles to further explore the specific gene modules of each molecular subgroup and its biological function. Two machine learning methods of LASSO regression algorithm and SVM-RFE algorithm was used to screen out the genetic biomarkers, of which the discriminative ability of molecular subgroups was evaluated by receiver operating characteristic (ROC) curve. Results: Based on the gene expression profiles, heart tissue samples from patients with DCM were clustered into three molecular subgroups. No statistical difference was found in age, body mass index (BMI) and left ventricular internal diameter at end-diastole (LVIDD) among three molecular subgroups. However, the results of left ventricular ejection fraction (LVEF) statistics showed that patients from subgroup 2 had a worse condition than the other group. We found that some of the gene modules (pink, black and grey) in WGCNA analysis were significantly related to cardiac function, and each molecular subgroup had its specific gene modules functions in modulating occurrence and progression of DCM. LASSO regression algorithm and SVM-RFE algorithm was used to further screen out genetic biomarkers of molecular subgroup 2, including TCEAL4, ISG15, RWDD1, ALG5, MRPL20, JTB and LITAF. The results of ROC curves showed that all of the genetic biomarkers had favorable discriminative effectiveness. Conclusion: Patients from different molecular subgroups have their unique gene expression patterns and different clinical characteristics. More personalized treatment under the guidance of gene expression patterns should be realized.
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Affiliation(s)
- Ling-Fang Ye
- Changzhi People’s Hospital, Changzhi, Shanxi, China
| | - Jia-Yi Weng
- Department of Cardiology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University,Suzhou, China,*Correspondence: Li-Da Wu, ; Jia-Yi Weng,
| | - Li-Da Wu
- Nanjing Medical University, Nanjing, China,*Correspondence: Li-Da Wu, ; Jia-Yi Weng,
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Erratum: Novel MRI deformation-heterogeneity radiomic features are associated with molecular subgroups and overall survival in pediatric medulloblastoma: Preliminary findings from a multi-institutional study. Front Oncol 2023; 13:1163188. [PMID: 36890823 PMCID: PMC9986554 DOI: 10.3389/fonc.2023.1163188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 02/10/2023] [Indexed: 02/22/2023] Open
Abstract
[This corrects the article DOI: 10.3389/fonc.2022.915143.].
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Akhoundova D, Hussung S, Sivakumar S, Töpfer A, Rechsteiner M, Kahraman A, Arnold F, Angst F, Britschgi C, Zoche M, Moch H, Weber A, Sokol E, Fritsch RM. ROS1 genomic rearrangements are rare actionable drivers in microsatellite stable colorectal cancer. Int J Cancer 2022; 151:2161-2171. [PMID: 36053834 PMCID: PMC9804412 DOI: 10.1002/ijc.34257] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 07/05/2022] [Accepted: 07/14/2022] [Indexed: 01/05/2023]
Abstract
c-Ros oncogene 1, receptor tyrosine kinase (ROS1) genomic rearrangements have been reported previously in rare cases of colorectal cancer (CRC), yet little is known about the frequency, molecular characteristics, and therapeutic vulnerabilities of ROS1-driven CRC. We analyzed a clinical dataset of 40 589 patients with CRC for ROS1 genomic rearrangements and their associated genomic characteristics (Foundation Medicine, Inc [FMI]). We moreover report the disease course and treatment response of an index patient with ROS1-rearranged metastatic CRC. ROS1 genomic rearrangements were identified in 34 (0.08%) CRC samples. GOPC-ROS1 was the most common ROS1 fusion identified (11 samples), followed by TTC28-ROS1 (3 samples). Four novel 5' gene partners of ROS1 were identified (MCM9, SRPK1, EPHA6, P4HA1). Contrary to previous reports on fusion-positive CRC, ROS1-rearrangements were found exclusively in microsatellite stable (MSS) CRCs. KRAS mutations were significantly less abundant in ROS1-rearranged vs ROS1 wild type cases. The index patient presented with chemotherapy-refractory metastatic right-sided colon cancer harboring GOPC-ROS1. Molecularly targeted treatment with crizotinib induced a rapid and sustained partial response. After 15 months on crizotinib disseminated tumor progression occurred and KRAS Q61H emerged in tissue and liquid biopsies. ROS1 rearrangements define a small, yet therapeutically actionable molecular subgroup of MSS CRC. In summary, the high prevalence of GOPC-ROS1 and noncanonical ROS1 fusions pose diagnostic challenges. We advocate NGS-based comprehensive molecular profiling of MSS CRCs that are wild type for RAS and BRAF and patient enrollment in precision trials.
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Affiliation(s)
- Dilara Akhoundova
- Department of Medical Oncology and HematologyUniversity Hospital of ZurichZurichSwitzerland
| | - Saskia Hussung
- Department of Medical Oncology and HematologyUniversity Hospital of ZurichZurichSwitzerland
| | - Smruthy Sivakumar
- Cancer Genomics ResearchFoundation Medicine, IncCambridgeMassachusettsUSA
| | - Antonia Töpfer
- Department of Pathology and Molecular PathologyUniversity Hospital of ZurichZurichSwitzerland
| | - Markus Rechsteiner
- Department of Pathology and Molecular PathologyUniversity Hospital of ZurichZurichSwitzerland
| | - Abdullah Kahraman
- Department of Pathology and Molecular PathologyUniversity Hospital of ZurichZurichSwitzerland
| | - Fabian Arnold
- Department of Pathology and Molecular PathologyUniversity Hospital of ZurichZurichSwitzerland
| | - Florian Angst
- Institute of Diagnostic and Interventional RadiologyUniversity Hospital of ZurichZurichSwitzerland
| | - Christian Britschgi
- Department of Medical Oncology and HematologyUniversity Hospital of ZurichZurichSwitzerland
| | - Martin Zoche
- Department of Pathology and Molecular PathologyUniversity Hospital of ZurichZurichSwitzerland
| | - Holger Moch
- Department of Pathology and Molecular PathologyUniversity Hospital of ZurichZurichSwitzerland
| | - Achim Weber
- Department of Pathology and Molecular PathologyUniversity Hospital of ZurichZurichSwitzerland
| | - Ethan Sokol
- Cancer Genomics ResearchFoundation Medicine, IncCambridgeMassachusettsUSA
| | - Ralph M. Fritsch
- Department of Medical Oncology and HematologyUniversity Hospital of ZurichZurichSwitzerland
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8
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Yang Z, Wang G, Luo N, Tsang CK, Huang L. Consensus clustering of gene expression profiles in peripheral blood of acute ischemic stroke patients. Front Neurol 2022; 13:937501. [PMID: 35989931 PMCID: PMC9388856 DOI: 10.3389/fneur.2022.937501] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/11/2022] [Indexed: 11/13/2022] Open
Abstract
Acute ischemic stroke (AIS) is a primary cause of mortality and morbidity worldwide. Currently, no clinically approved immune intervention is available for AIS treatment, partly due to the lack of relevant patient classification based on the peripheral immunity status of patients with AIS. In this study, we adopted the consensus clustering approach to classify patients with AIS into molecular subgroups based on the transcriptomic profiles of peripheral blood, and we identified three distinct AIS molecular subgroups and 8 modules in each subgroup by the weighted gene co-expression network analysis. Remarkably, the pre-ranked gene set enrichment analysis revealed that the co-expression modules with subgroup I-specific signature genes significantly overlapped with the differentially expressed genes in AIS patients with hemorrhagic transformation (HT). With respect to subgroup II, exclusively male patients with decreased proteasome activity were identified. Intriguingly, the majority of subgroup III was composed of female patients who showed a comparatively lower level of AIS-induced immunosuppression (AIIS). In addition, we discovered a non-linear relationship between female age and subgroup-specific gene expression, suggesting a gender- and age-dependent alteration of peripheral immunity. Taken together, our novel AIS classification approach could facilitate immunomodulatory therapies, including the administration of gender-specific therapeutics, and attenuation of the risk of HT and AIIS after ischemic stroke.
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Affiliation(s)
- Zhiyong Yang
- Clinical Neuroscience Institute, The First Affiliated Hospital of Jinan University, Guangzhou, China.,Department of Neurology, The First Clinical Medical School of Jinan University, Guangzhou, China
| | - Guanghui Wang
- Clinical Neuroscience Institute, The First Affiliated Hospital of Jinan University, Guangzhou, China.,Department of Neurology, The First Clinical Medical School of Jinan University, Guangzhou, China
| | - Nan Luo
- Clinical Neuroscience Institute, The First Affiliated Hospital of Jinan University, Guangzhou, China.,Department of Neurology, The First Clinical Medical School of Jinan University, Guangzhou, China
| | - Chi Kwan Tsang
- Clinical Neuroscience Institute, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Li'an Huang
- Clinical Neuroscience Institute, The First Affiliated Hospital of Jinan University, Guangzhou, China.,Department of Neurology, The First Clinical Medical School of Jinan University, Guangzhou, China
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Raspollini MR, Comperat EM, Lopez-Beltran A, Montironi R, Cimadamore A, Tsuzuki T, Netto GJ. News in the classification of WHO 2022 bladder tumors. Pathologica 2022; 115:32-40. [PMID: 36704871 DOI: 10.32074/1591-951x-838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 12/12/2022] [Indexed: 01/27/2023] Open
Abstract
The fifth-edition of World Health Organization (WHO) Classification of Tumors series for urinary and male genital tract tumors has been published, six years later the fourth-edition. In these years, new treatment approaches have been implemented and new molecular data on urological cancers are known. Morphology remains the groundwork for taxonomy of the urinary tract tumors. However, a molecular approach to classification of urothelial carcinomas and the management of selected neoplasms with new therapeutic modalities such as immunotherapy are emerging. More data are needed for the application of these advances in routine pathology practice and patient management. The 2022 World Health Organization (WHO) Classification of Tumors of the Urinary System and Male Genital Organs represents an update in classification on urinary tract tumors. It also offers new insights with regards to the grading of heterogeneous non-invasive urothelial neoplasms, the definition of inverted neoplasms, the grading of invasive urothelial carcinomas, the diversity of morphological appearance of urothelial carcinomas, the definition of precursor lesions and the lineage of differentiation of the tumors.
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Affiliation(s)
- Maria Rosaria Raspollini
- Histopathology and Molecular Diagnostics, University Hospital Careggi, Florence, Florence, Italy
| | - Eva M Comperat
- Department of Pathology, Medical University of Vienna, General Hospital of Vienna, Wien, AT, Austria
| | | | - Rodolfo Montironi
- Molecular Medicine and Cell Therapy Foundation, Polytechnic University of the Marche Region, Ancona, Italy
| | - Alessia Cimadamore
- Istituto di Anatomia Patologica, Dipartimento di Area Medica, Università di Udine
| | - Toyonori Tsuzuki
- Department of Surgical Pathology, Aichi Medical University, Aichi, Japan
| | - George J Netto
- Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, USA
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10
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Dong L, Lu D, Chen R, Lin Y, Zhu H, Zhang Z, Cai S, Cui P, Song G, Rao D, Yi X, Wu Y, Song N, Liu F, Zou Y, Zhang S, Zhang X, Wang X, Qiu S, Zhou J, Wang S, Zhang X, Shi Y, Figeys D, Ding L, Wang P, Zhang B, Rodriguez H, Gao Q, Gao D, Zhou H, Fan J. Proteogenomic characterization identifies clinically relevant subgroups of intrahepatic cholangiocarcinoma. Cancer Cell 2022; 40:70-87.e15. [PMID: 34971568 DOI: 10.1016/j.ccell.2021.12.006] [Citation(s) in RCA: 102] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 07/19/2021] [Accepted: 12/08/2021] [Indexed: 02/08/2023]
Abstract
We performed proteogenomic characterization of intrahepatic cholangiocarcinoma (iCCA) using paired tumor and adjacent liver tissues from 262 patients. Integrated proteogenomic analyses prioritized genetic aberrations and revealed hallmarks of iCCA pathogenesis. Aflatoxin signature was associated with tumor initiation, proliferation, and immune suppression. Mutation-associated signaling profiles revealed that TP53 and KRAS co-mutations may contribute to iCCA metastasis via the integrin-FAK-SRC pathway. FGFR2 fusions activated the Rho GTPase pathway and could be a potential source of neoantigens. Proteomic profiling identified four patient subgroups (S1-S4) with subgroup-specific biomarkers. These proteomic subgroups had distinct features in prognosis, genetic alterations, microenvironment dysregulation, tumor microbiota composition, and potential therapeutics. SLC16A3 and HKDC1 were further identified as potential prognostic biomarkers associated with metabolic reprogramming of iCCA cells. This study provides a valuable resource for researchers and clinicians to further identify molecular pathogenesis and therapeutic opportunities in iCCA.
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Affiliation(s)
- Liangqing Dong
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Fudan University, Shanghai 200032, China
| | - Dayun Lu
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; University of Chinese Academy of Sciences, Number 19A Yuquan Road, Beijing 100049, China
| | - Ran Chen
- University of Chinese Academy of Sciences, Number 19A Yuquan Road, Beijing 100049, China; State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Youpei Lin
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Fudan University, Shanghai 200032, China
| | - Hongwen Zhu
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Zhou Zhang
- Burning Rock Biotech, Shanghai 201114, China
| | - Shangli Cai
- Burning Rock Biotech, Shanghai 201114, China
| | - Peng Cui
- Burning Rock Biotech, Shanghai 201114, China
| | - Guohe Song
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Fudan University, Shanghai 200032, China
| | - Dongning Rao
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Fudan University, Shanghai 200032, China
| | - Xinpei Yi
- Lester and Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Yingcheng Wu
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Fudan University, Shanghai 200032, China
| | - Nixue Song
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; University of Chinese Academy of Sciences, Number 19A Yuquan Road, Beijing 100049, China
| | - Fen Liu
- University of Chinese Academy of Sciences, Number 19A Yuquan Road, Beijing 100049, China; State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Yunhao Zou
- University of Chinese Academy of Sciences, Number 19A Yuquan Road, Beijing 100049, China; State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Shu Zhang
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Fudan University, Shanghai 200032, China
| | - Xiaoming Zhang
- Key Laboratory of Molecular Virology and Immunology, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Xiaoying Wang
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Fudan University, Shanghai 200032, China
| | - Shuangjian Qiu
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Fudan University, Shanghai 200032, China
| | - Jian Zhou
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Fudan University, Shanghai 200032, China; Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Shisheng Wang
- Frontiers Science Center for Disease-related Molecular Network, Institutes for Systems Genetics, Key Lab of Transplant Engineering and Immunology, MOH, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xu Zhang
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada; Shanghai Institute of Materia Medica-University of Ottawa Joint Research Center in Systems and Personalized Pharmacology, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Yongyong Shi
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), The Collaborative Innovation Center for Brain Science, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China
| | - Daniel Figeys
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada; Shanghai Institute of Materia Medica-University of Ottawa Joint Research Center in Systems and Personalized Pharmacology, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Li Ding
- Department of Medicine, McDonnell Genome Institute, Siteman Cancer Center, Washington University, St. Louis, MI 63108, USA
| | - Pei Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, NewYork, NY 10029, USA
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Qiang Gao
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Fudan University, Shanghai 200032, China; Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China; State Key Laboratory of Genetic Engineering, Fudan University, Shanghai 200433, China.
| | - Daming Gao
- University of Chinese Academy of Sciences, Number 19A Yuquan Road, Beijing 100049, China; State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China; School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China.
| | - Hu Zhou
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China; University of Chinese Academy of Sciences, Number 19A Yuquan Road, Beijing 100049, China; Shanghai Institute of Materia Medica-University of Ottawa Joint Research Center in Systems and Personalized Pharmacology, 555 Zuchongzhi Road, Shanghai 201203, China.
| | - Jia Fan
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education, Fudan University, Shanghai 200032, China; Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China.
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11
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Iyer S, Ismail M, Tamrazi B, Salloum R, de Blank P, Margol A, Correa R, Chen J, Bera K, Statsevych V, Ho ML, Vaidya P, Verma R, Hawes D, Judkins A, Fu P, Madabhushi A, Tiwari P. Novel MRI deformation-heterogeneity radiomic features are associated with molecular subgroups and overall survival in pediatric medulloblastoma: Preliminary findings from a multi-institutional study. Front Oncol 2022; 12:915143. [PMID: 36620600 PMCID: PMC9811390 DOI: 10.3389/fonc.2022.915143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 11/30/2022] [Indexed: 12/24/2022] Open
Abstract
Introduction Medulloblastoma (MB) is a malignant, heterogenous brain tumor. Advances in molecular profiling have led to identifying four molecular subgroups of MB (WNT, SHH, Group 3, Group 4), each with distinct clinical behaviors. We hypothesize that (1) aggressive MB tumors, growing heterogeneously, induce pronounced local structural deformations in the surrounding parenchyma, and (b) these local deformations as captured on Gadolinium (Gd)-enhanced-T1w MRI are independently associated with molecular subgroups, as well as overall survival in MB patients. Methods In this work, a total of 88 MB studies from 2 institutions were analyzed. Following tumor delineation, Gd-T1w scan for every patient was registered to a normal age-specific T1w-MRI template via deformable registration. Following patient-atlas registration, local structural deformations in the brain parenchyma were obtained for every patient by computing statistics from deformation magnitudes obtained from every 5mm annular region, 0 < d < 60 mm, where d is the distance from the tumor infiltrating edge. Results Multi-class comparison via ANOVA yielded significant differences between deformation magnitudes obtained for Group 3, Group 4, and SHH molecular subgroups, observed up to 60-mm outside the tumor edge. Additionally, Kaplan-Meier survival analysis showed that the local deformation statistics, combined with the current clinical risk-stratification approaches (molecular subgroup information and Chang's classification), could identify significant differences between high-risk and low-risk survival groups, achieving better performance results than using any of these approaches individually. Discussion These preliminary findings suggest there exists significant association of our tumor-induced deformation descriptor with overall survival in MB, and that there could be an added value in using the proposed radiomic descriptor along with the current risk classification approaches, towards more reliable risk assessment in pediatric MB.
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Affiliation(s)
- Sukanya Iyer
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH, United States
| | - Marwa Ismail
- Department of Radiology and Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, United States
| | - Benita Tamrazi
- Department of Pathology, Children's Hospital Los Angeles, Los Angeles, CA, United States
| | - Ralph Salloum
- Division of Hematology, Oncology & Bone Marrow Transplant, Nationwide Children's Hospital, Columbus, OH, United States
| | - Peter de Blank
- Division of Oncology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Ashley Margol
- Department of Pathology, Children's Hospital Los Angeles, Los Angeles, CA, United States
| | - Ramon Correa
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH, United States
| | - Jonathan Chen
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH, United States
| | - Kaustav Bera
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH, United States
| | - Volodymyr Statsevych
- Department of Neuroradiology, Imaging Institute, Cleveland Clinic, Cleveland, OH, United States
| | - Mai-Lan Ho
- Department of Radiology, Nationwide Children's Hospital, Columbus, OH, United States
| | - Pranjal Vaidya
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH, United States
| | - Ruchika Verma
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH, United States
| | - Debra Hawes
- Department of Pathology, Children's Hospital Los Angeles, Los Angeles, CA, United States
| | - Alexander Judkins
- Department of Pathology, Children's Hospital Los Angeles, Los Angeles, CA, United States
| | - Pingfu Fu
- Radiology and Imaging Sciences, Biomedical Informatics (BMI) and Pathology, Georgia Institute of Technology and Emory University, Atlanta, GA, United States
| | - Anant Madabhushi
- Radiology and Imaging Sciences, Biomedical Informatics (BMI) and Pathology, Georgia Institute of Technology and Emory University, Atlanta, GA, United States
| | - Pallavi Tiwari
- Department of Radiology and Biomedical Engineering, University of Wisconsin-Madison, Madison, WI, United States
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12
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Liu Y, Liu S, Li G, Li Y, Chen L, Feng J, Yang Y, Jiang T, Qiu X. Association of high-dose radiotherapy with improved survival in patients with newly diagnosed low-grade gliomas. Cancer 2021; 128:1085-1092. [PMID: 34780673 PMCID: PMC9299029 DOI: 10.1002/cncr.34028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 10/28/2021] [Accepted: 10/29/2021] [Indexed: 11/10/2022]
Abstract
BACKGROUND The radiation dose for patients with low-grade gliomas (LGGs) is controversial. The objective of this study was to investigate the impact of the radiation dose on survival for patients with LGGs and especially for molecularly defined subgroups. METHODS Three hundred fifty-one patients with newly diagnosed LGGs from the multicenter Chinese Glioma Cooperative Group received postoperative radiotherapy (RT) in 2005-2018. The RT dose, as a continuous variable, was entered into a Cox regression model using penalized spline regression to allow for a nonlinear relationship between the RT dose and overall survival (OS) or progression-free survival (PFS). Inverse probability of treatment weighting (IPTW)-adjusted propensity scores were used to correct for potential confounders. Dose effects on survival within IDH mutation and 1p/19q codeletion defined subgroups were analyzed. RESULTS The risk of mortality and disease progression decreased sharply until 54 Gy. High-dose RT (≥54 Gy) was associated with significantly better 5-year OS (81.7% vs 64.0%; hazard ratio [HR], 0.33; P < .001) and PFS (77.4% vs 54.5%; HR, 0.46; P < .001) than low-dose RT (<54 Gy). IPTW correction confirmed the associations (HR for OS, 0.44; P = .001; HR for PFS, 0.48; P = .003). High-dose RT was associated with longer PFS (HR, 0.25; P = .002; HR, 0.21; P = .039) and OS (HR, 0.27; P = .006; HR, 0.07; P = .017) in IDH-mutant/1p/19q noncodeleted and IDH wild-type subgroups, respectively. No significant difference in survival was observed with high-dose RT in the IDH-mutant/1p/19q codeleted subgroup. CONCLUSIONS High-dose RT (≥54 Gy) was effective in LGGs. Patients with an IDH mutation/1p/19q noncodeletion or IDH wild-type may need to be considered for high-dose RT. LAY SUMMARY The radiotherapy dose-response was observed in patients with low-grade gliomas, and high-dose radiotherapy (≥54 Gy) was associated with improved survival. Patients with an IDH mutation/1p/19q noncodeletion or wild-type IDH may have improved survival with the administration of high-dose radiotherapy.
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Affiliation(s)
- Yanwei Liu
- Department of Radiation Oncology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Shuai Liu
- Department of Radiation Oncology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Guanzhang Li
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yanong Li
- Department of Radiation Oncology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Li Chen
- Department of Radiation Oncology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Jin Feng
- Department of Radiation Oncology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yong Yang
- Department of Radiation Oncology, Fujian Medical University Union Hospital, Fuzhou, China
| | - Tao Jiang
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Xiaoguang Qiu
- Department of Radiation Oncology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,National Clinical Research Center for Neurological Diseases, Beijing, China
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13
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Zhang P, Li S, Zhang T, Cui F, Shi JH, Zhao F, Sheng X. Characterization of Molecular Subtypes in Head and Neck Squamous Cell Carcinoma With Distinct Prognosis and Treatment Responsiveness. Front Cell Dev Biol 2021; 9:711348. [PMID: 34595167 PMCID: PMC8476885 DOI: 10.3389/fcell.2021.711348] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 08/10/2021] [Indexed: 12/20/2022] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is one of the most aggressive malignancies with complex phenotypic, etiological, biological, and clinical heterogeneities. Previous studies have proposed different clinically relevant subtypes of HNSCC, but little is known about its corresponding prognosis or suitable treatment strategy. Here, we identified 101 core genes from three prognostic pathways, including mTORC1 signaling, unfold protein response, and UV response UP, in 124 pairs of tumor and matched normal tissues of HNSCC. Moreover, we identified three robust subtypes associated with distinct molecular characteristics and clinical outcomes using consensus clustering based on the gene expression profiles of 944 HNSCC patients from four independent datasets. We then integrated the genomic information of The Cancer Genome Atlas (TCGA) HNSCC cohort to comprehensively evaluate the molecular features of different subtypes and screen for potentially effective therapeutic agents. Cluster 1 had more arrested oncogenic signaling, the highest immune cell infiltration, the highest immunotherapy and chemotherapeutic responsiveness, and the best prognosis. By contrast, Cluster 3 showed more activated oncogenic signaling, the lowest immune cell infiltration, the lowest immunotherapy and chemotherapy responsiveness, and the worst prognosis. Our findings corroborate the molecular diversity of HNSCC tumors and provide a novel classification strategy that may guide for prognosis and treatment allocation.
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Affiliation(s)
- Pei Zhang
- Department of Stomatology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Shue Li
- Department of Stomatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Hubei Province Key Laboratory of Oral and Maxillofacial Development and Regeneration, Wuhan, China
| | - Tingting Zhang
- Key Laboratory of Environment and Health, Ministry of Education & Ministry of Environmental Protection, State Key Laboratory of Environmental Health (Incubation), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Fengzhen Cui
- Key Laboratory of Environment and Health, Ministry of Education & Ministry of Environmental Protection, State Key Laboratory of Environmental Health (Incubation), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ji-Hua Shi
- Department of Hepatobiliary and Pancreatic Surgery, Henan Key Laboratory of Digestive Organ Transplantation, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Faming Zhao
- Key Laboratory of Environment and Health, Ministry of Education & Ministry of Environmental Protection, State Key Laboratory of Environmental Health (Incubation), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xia Sheng
- Key Laboratory of Environment and Health, Ministry of Education & Ministry of Environmental Protection, State Key Laboratory of Environmental Health (Incubation), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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14
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Guaitoli G, Tiseo M, Di Maio M, Friboulet L, Facchinetti F. Immune checkpoint inhibitors in oncogene-addicted non-small cell lung cancer: a systematic review and meta-analysis. Transl Lung Cancer Res 2021; 10:2890-2916. [PMID: 34295687 PMCID: PMC8264334 DOI: 10.21037/tlcr-20-941] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 10/23/2020] [Indexed: 12/12/2022]
Abstract
Background Treatment of oncogene-addicted non-small cell lung cancer (NSCLC) has been changed by the advent of tyrosine kinase inhibitors (TKIs). Albeit great benefits are achieved with target therapies, resistance invariably occurs and recourse to alternative treatments is unavoidable. Immune checkpoint inhibitors (ICIs) role and the best setting of immunotherapy administration in oncogene-driven NSCLC are matter of debate. Methods We performed a systematic literature review through PubMed, in order to gather all the available information regarding ICI activity and efficacy in oncogene-addicted NSCLC, from both prospective trials and retrospective series. A meta-analysis of objective response rate in different molecular subgroups was provided. Combinatorial strategies including ICIs and related toxicities were also recorded. Results Eighty-seven studies were included in the qualitative analysis. EGFR mutation may be a biomarker of poor response to single-agent ICIs (7% of EGFR-mutant NSCLC patients achieved disease response in prospective trials), while encouraging results have been shown with combination strategies. KRAS-mutated disease (response rate, RR, 22%) has different clinical and pathological characteristics, and the co-existence of additional mutations (e.g., STK11 or TP53) influence tumor microenvironment and response to immunotherapy. Other molecular alterations have been marginally considered prospectively, and data from clinical practice are variegated, given poor effectiveness of ICIs in ALK-rearranged disease (RR 9.5%, pooling the data of retrospective studies) or some encouraging results in BRAF-(RR 25%, retrospective data) or MET-driven one (with estimations conditioned by the presence of both exon 14 skipping mutations and gene amplification in reported series). Conclusions In oncogene-addicted NSCLC (with the exception of KRAS-mutated), ICIs are usually administered at the failure of other treatment options, but administering single-agent immunotherapy in later disease phases may limit its efficacy. With the progressive administration of TKIs and ICIs in early-stage disease, molecular characterization will become fundamental in this setting.
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Affiliation(s)
- Giorgia Guaitoli
- Division of Medical Oncology, University Hospital of Modena, Modena, Italy.,Université Paris-Saclay, Institut Gustave Roussy, Inserm, Biomarqueurs Prédictifs et Nouvelles Stratégies Thérapeutiques en Oncologie, Villejuif, France
| | - Marcello Tiseo
- Department of Medicine and Surgery, University of Parma, Parma, Italy.,Medical Oncology Unit, University Hospital of Parma, Parma, Italy
| | - Massimo Di Maio
- Department of Oncology, University of Turin at Ordine Mauriziano Hospital, Torino, Italy
| | - Luc Friboulet
- Université Paris-Saclay, Institut Gustave Roussy, Inserm, Biomarqueurs Prédictifs et Nouvelles Stratégies Thérapeutiques en Oncologie, Villejuif, France
| | - Francesco Facchinetti
- Université Paris-Saclay, Institut Gustave Roussy, Inserm, Biomarqueurs Prédictifs et Nouvelles Stratégies Thérapeutiques en Oncologie, Villejuif, France
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15
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Youngblood MW, Miyagishima DF, Jin L, Gupte T, Li C, Duran D, Montejo JD, Zhao A, Sheth A, Tyrtova E, Özduman K, Iacoangeli F, Peyre M, Boetto J, Pease M, Avşar T, Huttner A, Bilguvar K, Kilic T, Pamir MN, Amankulor N, Kalamarides M, Erson-Omay EZ, Günel M, Moliterno J. Associations of meningioma molecular subgroup and tumor recurrence. Neuro Oncol 2021; 23:783-794. [PMID: 33068421 DOI: 10.1093/neuonc/noaa226] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND We and others have identified mutually exclusive molecular subgroups of meningiomas; however, the implications of this classification for clinical prognostication remain unclear. Integrated genomic and epigenomic analyses implicate unique oncogenic processes associated with each subgroup, suggesting the potential for divergent clinical courses. The aim of this study was to understand the associated clinical outcomes of each subgroup, as this could optimize treatment for patients. METHODS We analyzed outcome data for 469 meningiomas of known molecular subgroup, including extent of resection, postoperative radiation, surveillance imaging, and time to recurrence, when applicable. Statistical relationships between outcome variables and subgroup were assessed. Features previously associated with recurrence were further investigated after stratification by subgroup. We used Kaplan-Meier analyses to compare progression-free survival, and identified factors significantly associated with recurrence using Cox proportional hazards modeling. RESULTS Meningioma molecular subgroups exhibited divergent clinical courses at 2 years of follow-up, with several aggressive subgroups (NF2, PI3K, HH, tumor necrosis factor receptor-associated factor 7 [TRAF7]) recurring at an average rate of 22 times higher than others (KLF4, POLR2A, SMARCB1). PI3K-activated tumors recurred earlier than other subgroups but had intermediate long-term outcome. Among low-grade tumors, HH and TRAF7 meningiomas exhibited elevated recurrence compared with other subgroups. Recurrence of NF2 tumors was associated with male sex, high grade, and elevated Ki-67. Multivariate analysis identified molecular subgroup as an independent predictor of recurrence, along with grade and previous recurrence. CONCLUSION We describe distinct clinical outcomes and recurrence rates associated with meningioma molecular subgroups. Our findings emphasize the importance of genomic characterization to guide postoperative management decisions for meningiomas.
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Affiliation(s)
- Mark W Youngblood
- Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut, USA.,Department of Neurological Surgery, Northwestern University, Chicago, Illinois, USA
| | - Danielle F Miyagishima
- Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut, USA.,Department of Neurosurgery, Yale School of Medicine, New Haven, Connecticut, USA.,Department of Genetics, Yale School of Medicine, New Haven, Connecticut, USA
| | - Lan Jin
- Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut, USA
| | - Trisha Gupte
- Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut, USA.,Department of Neurosurgery, Yale School of Medicine, New Haven, Connecticut, USA
| | - Chang Li
- Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut, USA.,Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China.,The Third Xiangya Hospital, Central South University, Changsha, China
| | - Daniel Duran
- Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut, USA.,Department of Neurosurgery, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Julio D Montejo
- Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut, USA.,Section of Neurosurgery, Dartmouth-Hitchcock Medical Center, One Medical Center Drive, Lebanon, New Hampshire, USA
| | - Amy Zhao
- Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut, USA
| | - Amar Sheth
- Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut, USA
| | - Evgeniya Tyrtova
- Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut, USA.,Department of Neurological Surgery, The University of Washington, Seattle, Washington, USA
| | - Koray Özduman
- Department of Neurosurgery, Acibadem Mehmet Ali Aydınlar University, School of Medicine, Istanbul, Turkey
| | - Francesco Iacoangeli
- Department of Neurosurgery, Yale School of Medicine, New Haven, Connecticut, USA.,Department of Neurosurgery, Pitie-Salpetriere Hospital and Sorbonne University, Paris, France
| | - Matthieu Peyre
- Department of Neurosurgery, Pitie-Salpetriere Hospital and Sorbonne University, Paris, France.,Department of Neurosurgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Julien Boetto
- Department of Neurosurgery, Pitie-Salpetriere Hospital and Sorbonne University, Paris, France
| | - Matthew Pease
- Department of Neurosurgery, Pitie-Salpetriere Hospital and Sorbonne University, Paris, France
| | - Timuçin Avşar
- Department of Medical Biology, Bahçeşehir University (BAU) Faculty of Medicine, Istanbul, Turkey
| | - Anita Huttner
- Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut, USA.,Department of Pathology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Kaya Bilguvar
- Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut, USA.,Yale Center for Genome Analysis, Yale University West Campus, Orange, Connecticut, USA
| | - Türker Kilic
- Department of Neurosurgery, BAU, School of Medicine, Istanbul, Turkey
| | - M Necmettin Pamir
- Department of Neurosurgery, Acibadem Mehmet Ali Aydınlar University, School of Medicine, Istanbul, Turkey
| | - Nduka Amankulor
- Department of Neurosurgery, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Michel Kalamarides
- Department of Neurosurgery, Pitie-Salpetriere Hospital and Sorbonne University, Paris, France
| | - E Zeynep Erson-Omay
- Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut, USA.,Department of Neurosurgery, Yale School of Medicine, New Haven, Connecticut, USA
| | - Murat Günel
- Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut, USA.,Department of Neurosurgery, Yale School of Medicine, New Haven, Connecticut, USA.,Yale Center for Genome Analysis, Yale University West Campus, Orange, Connecticut, USA
| | - Jennifer Moliterno
- Yale Program in Brain Tumor Research, Yale School of Medicine, New Haven, Connecticut, USA.,Department of Neurosurgery, Yale School of Medicine, New Haven, Connecticut, USA
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16
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Ho B, Johann PD, Grabovska Y, De Dieu Andrianteranagna MJ, Yao F, Frühwald M, Hasselblatt M, Bourdeaut F, Williamson D, Huang A, Kool M. Molecular subgrouping of atypical teratoid/rhabdoid tumors-a reinvestigation and current consensus. Neuro Oncol 2021; 22:613-624. [PMID: 31889194 PMCID: PMC7229260 DOI: 10.1093/neuonc/noz235] [Citation(s) in RCA: 109] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Background Atypical teratoid/rhabdoid tumors (ATRTs) are known to exhibit molecular and clinical heterogeneity even though SMARCB1 inactivation is the sole recurrent genetic event present in nearly all cases. Indeed, recent studies demonstrated 3 molecular subgroups of ATRTs that are genetically, epigenetically, and clinically distinct. As these studies included different numbers of tumors, various subgrouping techniques, and naming, an international working group sought to align previous findings and to reach a consensus on nomenclature and clinicopathological significance of ATRT subgroups. Methods We integrated various methods to perform a meta-analysis on published and unpublished DNA methylation and gene expression datasets of ATRTs and associated clinicopathological data. Results In concordance with previous studies, the analyses identified 3 main molecular subgroups of ATRTs, for which a consensus was reached to name them ATRT-TYR, ATRT-SHH, and ATRT-MYC. The ATRT-SHH subgroup exhibited further heterogeneity, segregating further into 2 subtypes associated with a predominant supratentorial (ATRT-SHH-1) or infratentorial (ATRT-SHH-2) location. For each ATRT subgroup we provide an overview of its main molecular and clinical characteristics, including SMARCB1 alterations and pathway activation. Conclusions The introduction of a common classification, characterization, and nomenclature of ATRT subgroups will facilitate future research and serve as a common ground for subgrouping patient samples and ATRT models, which will aid in refining subgroup-based therapies for ATRT patients.
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Affiliation(s)
- Ben Ho
- Division of Hematology and Oncology, Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Pascal D Johann
- Hopp Children's Cancer Center, Heidelberg, Germany.,Division of Pediatric Neuro-oncology, German Cancer Research Center and German Cancer Research Consortium, Heidelberg, Germany.,Department of Pediatric Hematology and Oncology, University Hospital Heidelberg, Heidelberg, Germany
| | - Yura Grabovska
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - Mamy Jean De Dieu Andrianteranagna
- Departments of Genetics and of Oncopediatry and Young Adults, Curie Institute, Paris, France.,INSERM U830, Laboratory of Translational Research in Pediatric Oncology, SIREDO Pediatric Oncology Center, Curie Institute, Paris, France
| | - Fupan Yao
- Department of Medical Biophysics, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Michael Frühwald
- University Children's Hospital Augsburg, Swabian Children's Cancer Center, Augsburg, Germany
| | - Martin Hasselblatt
- Institute of Neuropathology, University Hospital Münster, Münster, Germany
| | - Franck Bourdeaut
- Departments of Genetics and of Oncopediatry and Young Adults, Curie Institute, Paris, France.,INSERM U830, Laboratory of Translational Research in Pediatric Oncology, SIREDO Pediatric Oncology Center, Curie Institute, Paris, France
| | - Daniel Williamson
- Wolfson Childhood Cancer Research Centre, Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - Annie Huang
- Division of Hematology and Oncology, Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Marcel Kool
- Hopp Children's Cancer Center, Heidelberg, Germany.,Division of Pediatric Neuro-oncology, German Cancer Research Center and German Cancer Research Consortium, Heidelberg, Germany
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17
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Abstract
N6-methyladenosine (m6A) is a common form of mRNA modification regulated by m6A RNA methylation regulators and play an important role in the progression of gastric cancer (GC). However, the prognostic role of m6A-related lncRNA in gastric cancer has not been fully explored. This study aims at exploring the biological function and prognostic roles of the m6A-related lncRNA signature in gastric cancer. A total of 800 m6A-related lncRNAs were identified through Pearson correlation analysis between m6A regulators and all lncRNAs. Eleven m6A-related lncRNA signatures were identified through a survival analysis and the Kaplan-Meier (KM) curve analysis results suggest that patients in the low-risk group have a better overall survival (OS) and disease-free survival (DFS) outcome than the high-risk group. Also, the lncRNA signature can serve as an independent prognostic factor for OS and DFS. The gene set enrichment analysis (GSEA) result suggests that patients in the high-risk group were mainly enriched in the ECM receptor interaction, focal adhesion, and cytokine-cytokine receptor interaction pathway, while the low-risk group was characterized by the base excision repair pathway. We further constructed an individualized prognostic prediction model via the nomogram based on the independent prognostic factor for the OS and DFS, respectively. In addition, some candidate drugs aimed at GC risk group differentiation were identified using the Connective Map (CMAP) database. Lastly, four subgroups (C1, C2, C3, and C4) were identified based on the m6A-related lncRNA expression, through a consensus clustering algorithm. Among them, C1 and C2 have a greater likelihood to respond to immune checkpoint inhibitor immunotherapy, suggesting that the C1 and C2 subgroup might benefit from immunotherapy. In conclusion, the m6A-related lncRNA signature can independently predict the OS and DFS of GC and may aid in development of personalized immunotherapy strategies.
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Affiliation(s)
- Haixu Wang
- Postgraduate Training Base in General Hospital of The Northern Theater Command, China Medical University, Shenyang, China.,Department of Radiation Oncology, The General Hospital of Northern Theater Command, Shenyang, China
| | - Qingkai Meng
- Department of Colorectal Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Shenyang, China
| | - Bin Ma
- Department of Colorectal Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Shenyang, China
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18
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Randon G, Yaeger R, Hechtman JF, Manca P, Fucà G, Walch H, Lee J, Élez E, Seligmann J, Mussolin B, Pagani F, Germani MM, Ambrosini M, Rossini D, Ratti M, Salvà F, Richman SD, Wood H, Nanjangud G, Gloghini A, Milione M, Bardelli A, de Braud F, Morano F, Cremolini C, Pietrantonio F. EGFR Amplification in Metastatic Colorectal Cancer. J Natl Cancer Inst 2021; 113:1561-1569. [PMID: 33825902 DOI: 10.1093/jnci/djab069] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 03/05/2021] [Accepted: 04/05/2021] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND EGFR amplification occurs in about 1% of metastatic colorectal cancers (mCRCs) but is not routinely tested as a prognostic or predictive biomarker for patients treated with anti-EGFR monoclonal antibodies (mAbs). Herein, we aimed to characterize the clinical and molecular landscape of EGFR-amplified metastatic colorectal cancer (mCRC). METHODS In this multinational cohort study, we compared clinical data of 62 patients with EGFR-amplified vs. 1459 EGFR non-amplified mCRC, as well as comprehensive genomic data of 35 EGFR-amplified vs. 439 EGFR non-amplified RAS/BRAF wild-type and microsatellite stable (MSS) tumor samples. RESULTS EGFR amplification was statistically significantly associated with left primary tumor sidedness and RAS/BRAF wild-type status. All EGFR-amplified tumors were MSS and HER2 non-amplified. Overall, EGFR-amplified samples had higher median fraction of genome altered compared to EGFR non-amplified, RAS/BRAF wild-type MSS cohort. Patients with EGFR-amplified tumors reported longer overall survival (OS) (median OS = 71.3 months; 95% confidence interval [CI] = 50.7-NA) vs. EGFR non-amplified ones (24.0 months; 95% CI = 22.8-25.6; hazard ratio [HR] = 0.30, 95% CI = 0.20-0.44, P<.001; adjusted HR = 0.46, 95%CI = 0.30-0.69, P<.001). In the subgroup of patients with RAS/BRAF wild-type mCRC exposed to anti-EGFR-based therapy, EGFR amplification was again associated with better OS (median OS = 54.0 months [95% CI = 35.2-NA] vs. 29.1 months [95% CI = 27.0-31.9], respectively; HR = 0.46, 95%CI = 0.28-0.76, P=.002). CONCLUSION Patients with EGFR-amplified mCRC represent a biologically defined subgroup and merit dedicated clinical trials with novel and more potent EGFR targeting strategies beyond single-agent monoclonal antibodies.
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Affiliation(s)
- Giovanni Randon
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milano, Italy
| | - Rona Yaeger
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jaclyn F Hechtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Paolo Manca
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milano, Italy
| | - Giovanni Fucà
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milano, Italy
| | - Henry Walch
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jeeyun Lee
- Department of Medicine, Division of Hematology-Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Elena Élez
- Vall D'Hebron University Hospital (HUVH) and Vall D'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Jenny Seligmann
- St James's Institute of Oncology, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | | | - Filippo Pagani
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milano, Italy
| | - Marco Maria Germani
- Unit of Medical Oncology 2, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy.,Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Margherita Ambrosini
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milano, Italy
| | - Daniele Rossini
- Unit of Medical Oncology 2, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy.,Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Margherita Ratti
- Oncology Unit, Oncology Department, ASST of Cremona, 26100 Cremona, Italy
| | - Francesc Salvà
- Vall D'Hebron University Hospital (HUVH) and Vall D'Hebron Institute of Oncology (VHIO), Barcelona, Spain
| | - Susan D Richman
- St James's Institute of Oncology, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Henry Wood
- St James's Institute of Oncology, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Gouri Nanjangud
- Molecular Cytogenetics Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Annunziata Gloghini
- Department of the Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - Massimo Milione
- Department of the Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milan, Italy
| | - Alberto Bardelli
- Candiolo Cancer Institute, FPO - IRCCS, Candiolo, Torino, Italy.,University of Torino, Department of Oncology, Candiolo, Torino, Italy
| | - Filippo de Braud
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milano, Italy.,Oncology and Hemato-oncology Department, University of Milan, Milan, Italy
| | - Federica Morano
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milano, Italy
| | - Chiara Cremolini
- Unit of Medical Oncology 2, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy.,Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Filippo Pietrantonio
- Department of Medical Oncology, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milano, Italy.,Oncology and Hemato-oncology Department, University of Milan, Milan, Italy
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19
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Wolf J, Willscher E, Loeffler-Wirth H, Schmidt M, Flemming G, Zurek M, Uhlig HH, Händel N, Binder H. Deciphering the Transcriptomic Heterogeneity of Duodenal Coeliac Disease Biopsies. Int J Mol Sci 2021; 22:ijms22052551. [PMID: 33806322 PMCID: PMC7961974 DOI: 10.3390/ijms22052551] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 03/02/2021] [Accepted: 03/03/2021] [Indexed: 12/11/2022] Open
Abstract
Coeliac disease (CD) is a clinically heterogeneous autoimmune disease with variable presentation and progression triggered by gluten intake. Molecular or genetic factors contribute to disease heterogeneity, but the reasons for different outcomes are poorly understood. Transcriptome studies of tissue biopsies from CD patients are scarce. Here, we present a high-resolution analysis of the transcriptomes extracted from duodenal biopsies of 24 children and adolescents with active CD and 21 individuals without CD but with intestinal afflictions as controls. The transcriptomes of CD patients divide into three groups-a mixed group presenting the control cases, and CD-low and CD-high groups referring to lower and higher levels of CD severity. Persistence of symptoms was weakly associated with subgroup, but the highest marsh stages were present in subgroup CD-high, together with the highest cell cycle rates as an indicator of virtually complete villous atrophy. Considerable variation in inflammation-level between subgroups was further deciphered into immune cell types using cell type de-convolution. Self-organizing maps portrayal was applied to provide high-resolution landscapes of the CD-transcriptome. We find asymmetric patterns of miRNA and long non-coding RNA and discuss the effect of epigenetic regulation. Expression of genes involved in interferon gamma signaling represent suitable markers to distinguish CD from non-CD cases. Multiple pathways overlay in CD biopsies in different ways, giving rise to heterogeneous transcriptional patterns, which potentially provide information about etiology and the course of the disease.
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Affiliation(s)
- Johannes Wolf
- Department of Laboratory Medicine at Hospital “St. Georg” Leipzig, 04129 Leipzig, Germany;
- Immuno Deficiency Centre Leipzig (IDCL) at Hospital St. Georg Leipzig, Jeffrey Modell Diagnostic and Research Centre for Primary Immunodeficiency Diseases, 04129 Leipzig, Germany
| | - Edith Willscher
- IZBI, Interdisciplinary Centre for Bioinformatics, University Leipzig, Härtelstr. 16–18, 04107 Leipzig, Germany; (E.W.); (H.L.-W.); (M.S.)
| | - Henry Loeffler-Wirth
- IZBI, Interdisciplinary Centre for Bioinformatics, University Leipzig, Härtelstr. 16–18, 04107 Leipzig, Germany; (E.W.); (H.L.-W.); (M.S.)
| | - Maria Schmidt
- IZBI, Interdisciplinary Centre for Bioinformatics, University Leipzig, Härtelstr. 16–18, 04107 Leipzig, Germany; (E.W.); (H.L.-W.); (M.S.)
| | - Gunter Flemming
- Paediatric Gastroenterology Unit, University Hospital for Children and Adolescents, 04103 Leipzig, Germany;
| | - Marlen Zurek
- Children’s Hospital of the Clinical Centre “Sankt Georg”, 04129 Leipzig, Germany; (M.Z.); (N.H.)
| | - Holm H. Uhlig
- Translational Gastroenterology Unit, Oxford NIHR Biomedical Research Centre, Experimental Medicine, Department of Paediatrics, University of Oxford, John Radcliffe Hospital, Oxford OX4 2PG, UK;
| | - Norman Händel
- Children’s Hospital of the Clinical Centre “Sankt Georg”, 04129 Leipzig, Germany; (M.Z.); (N.H.)
| | - Hans Binder
- IZBI, Interdisciplinary Centre for Bioinformatics, University Leipzig, Härtelstr. 16–18, 04107 Leipzig, Germany; (E.W.); (H.L.-W.); (M.S.)
- Correspondence:
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20
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Zhang Z, Chen J, Zhu S, Zhu D, Xu J, He G. Construction and Validation of a Cell Cycle-Related Robust Prognostic Signature in Colon Cancer. Front Cell Dev Biol 2020; 8:611222. [PMID: 33304907 PMCID: PMC7701219 DOI: 10.3389/fcell.2020.611222] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 10/28/2020] [Indexed: 01/05/2023] Open
Abstract
Colon cancer is one of the most common cancers, great progress was taken place in the treatment of colon cancer, however, the prognostic assessment system remains lagging. Cell cycle plays a vital role in the whole procedure of cancers. In this study, we firstly identified cell cycle-related genes specific in colon cancer. Functional enrichment analysis proved our analysis reliable. Furthermore, we constructed a robust signature based on the cell cycle-related genes. The AUC of the signature to predict the overall survival was 0.808, 0.807, and 0.831 of AUC at 1, 3, and 5 years, respectively. Internal and external validation proved the signature efficient. The 9 genes involved in the signature also showed a great job in molecular subgrouping which indicated the significant value of the 9 genes for further experimental research. In conclusion, the present research provided a novel robust signature predicting the prognosis of colon cancer.
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Affiliation(s)
- Zhiyuan Zhang
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jingwen Chen
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Shichao Zhu
- Department of Cardiac Surgery, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Dexiang Zhu
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jianmin Xu
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Guodong He
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
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21
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Yan J, Liu L, Wang W, Zhao Y, Li KKW, Li K, Wang L, Yuan B, Geng H, Zhang S, Liu Z, Duan W, Zhan Y, Pei D, Zhao H, Sun T, Sun C, Wang W, Hong X, Wang X, Guo Y, Li W, Cheng J, Liu X, Ng HK, Li Z, Zhang Z. Radiomic Features From Multi-Parameter MRI Combined With Clinical Parameters Predict Molecular Subgroups in Patients With Medulloblastoma. Front Oncol 2020; 10:558162. [PMID: 33117690 PMCID: PMC7566191 DOI: 10.3389/fonc.2020.558162] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 09/01/2020] [Indexed: 12/11/2022] Open
Abstract
The 2016 WHO classification of central nervous system tumors has included four molecular subgroups under medulloblastoma (MB) as sonic hedgehog (SHH), wingless (WNT), Grade 3, and Group 4. We aimed to develop machine learning models for predicting MB molecular subgroups based on multi-parameter magnetic resonance imaging (MRI) radiomics, tumor locations, and clinical factors. A total of 122 MB patients were enrolled retrospectively. After selecting robust, non-redundant, and relevant features from 5,529 extracted radiomics features, a random forest model was constructed based on a training cohort (n = 92) and evaluated on a testing cohort (n = 30). By combining radiographic features and clinical parameters, two combined prediction models were also built. The subgroup can be classified using an 11-feature radiomics model with a high area under the curve (AUC) of 0.8264 for WNT and modest AUCs of 0.6683, 0.6004, and 0.6979 for SHH, Group 3, and Group 4 in the testing cohort, respectively. Incorporating location and hydrocephalus into the radiomics model resulted in improved AUCs of 0.8403 and 0.8317 for WNT and SHH, respectively. After adding gender and age, the AUCs for WNT and SHH were further improved to 0.9097 and 0.8654, while the accuracies were 70 and 86.67% for Group 3 and Group 4, respectively. Prediction performance was excellent for WNT and SHH, while that for Group 3 and Group 4 needs further improvements. Machine learning algorithms offer potentials to non-invasively predict the molecular subgroups of MB.
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Affiliation(s)
- Jing Yan
- Department of MRI, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Lei Liu
- Institute of Biomedical and Health Engineering, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Weiwei Wang
- Department of Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yuanshen Zhao
- Institute of Biomedical and Health Engineering, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Kay Ka-Wai Li
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Ke Li
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Li Wang
- Department of Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Binke Yuan
- Center for Language and Brain, Shenzhen Institute of Neuroscience, Shenzhen, China
| | - Haiyang Geng
- Shenzhen Key Laboratory of Affective and Social Neuroscience, Center for Brain Disorders and Cognitive Sciences, Shenzhen University, Shenzhen, China.,Department of Biomedical Sciences of Cells and Systems, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Shenghai Zhang
- Institute of Biomedical and Health Engineering, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Zhen Liu
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Wenchao Duan
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yunbo Zhan
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Dongling Pei
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Haibiao Zhao
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Tao Sun
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Chen Sun
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Wenqing Wang
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xuanke Hong
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiangxiang Wang
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yu Guo
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Wencai Li
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jingliang Cheng
- Department of MRI, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xianzhi Liu
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ho-Keung Ng
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong, China
| | - Zhicheng Li
- Institute of Biomedical and Health Engineering, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Zhenyu Zhang
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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22
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Zou H, Poore B, Broniscer A, Pollack IF, Hu B. Molecular Heterogeneity and Cellular Diversity: Implications for Precision Treatment in Medulloblastoma. Cancers (Basel) 2020; 12:cancers12030643. [PMID: 32164294 PMCID: PMC7139663 DOI: 10.3390/cancers12030643] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 03/03/2020] [Accepted: 03/05/2020] [Indexed: 12/31/2022] Open
Abstract
Medulloblastoma, the most common pediatric malignant brain tumor, continues to have a high rate of morbidity and mortality in childhood. Recent advances in cancer genomics, single-cell sequencing, and sophisticated tumor models have revolutionized the characterization and stratification of medulloblastoma. In this review, we discuss heterogeneity associated with four major subgroups of medulloblastoma (WNT, SHH, Group 3, and Group 4) on the molecular and cellular levels, including histological features, genetic and epigenetic alterations, proteomic landscape, cell-of-origin, tumor microenvironment, and therapeutic approaches. The intratumoral molecular heterogeneity and intertumoral cellular diversity clearly underlie the divergent biology and clinical behavior of these lesions and highlight the future role of precision treatment in this devastating brain tumor in children.
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Affiliation(s)
- Han Zou
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA; (H.Z.); (I.F.P.)
- Pediatric Neurosurgery, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
- Xiangya School of Medicine, Central South University, Changsha 410013, China
| | - Brad Poore
- Department of Pathology, Dartmouth Hitchcock Medical Center, Lebanon, NH 03766, USA;
| | - Alberto Broniscer
- Pediatric Neuro-Oncology Program, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA 15224, USA;
| | - Ian F. Pollack
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA; (H.Z.); (I.F.P.)
- Pediatric Neurosurgery, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Baoli Hu
- Department of Neurological Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA; (H.Z.); (I.F.P.)
- Pediatric Neurosurgery, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
- Molecular and Cellular Cancer Biology Program, UPMC Hillman Cancer Center, Pittsburgh, PA 15232, USA
- Correspondence: ; Tel.: +1-412-962-9457; Fax: +1-412-692-8906
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23
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Van Ommeren R, Garzia L, Holgado BL, Ramaswamy V, Taylor MD. The molecular biology of medulloblastoma metastasis. Brain Pathol 2020; 30:691-702. [PMID: 31883407 DOI: 10.1111/bpa.12811] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 12/11/2019] [Indexed: 12/16/2022] Open
Abstract
Medulloblastoma (MB) is the most common primary malignant brain tumor of childhood and a significant contributor to pediatric morbidity and death. While metastatic dissemination is the predominant cause of morbidity and mortality for patients with this disease, most research efforts and clinical trials to date have focused on the primary tumor; this is due mostly to the paucity of metastatic tumor samples and lack of robust mouse models of MB dissemination. Most current insights into the molecular drivers of metastasis have been derived from comparative molecular studies of metastatic and non-metastatic primary tumors. However, small studies on matched primary and metastatic tissues and recently developed mouse models of dissemination have begun to uncover the molecular biology of MB metastasis more directly. With respect to anatomical routes of dissemination, a hematogenous route for MB metastasis has recently been demonstrated, opening new avenues of investigation. The tumor micro-environment of the primary and metastatic niches has also been increasingly scrutinized in recent years, and further investigation of these tumor compartments is likely to result in a better understanding of the molecular mediators of MB colonization and growth in metastatic compartments.
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Affiliation(s)
- Randy Van Ommeren
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada.,The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Livia Garzia
- Department of Surgery, Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Borja L Holgado
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada.,The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Vijay Ramaswamy
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada.,The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada.,Division of Haematology/Oncology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Michael D Taylor
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada.,The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.,Division of Neurosurgery, The Hospital for Sick Children, Toronto, ON, Canada.,Senior Author
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24
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Chun HJE, Johann PD, Milne K, Zapatka M, Buellesbach A, Ishaque N, Iskar M, Erkek S, Wei L, Tessier-Cloutier B, Lever J, Titmuss E, Topham JT, Bowlby R, Chuah E, Mungall KL, Ma Y, Mungall AJ, Moore RA, Taylor MD, Gerhard DS, Jones SJM, Korshunov A, Gessler M, Kerl K, Hasselblatt M, Frühwald MC, Perlman EJ, Nelson BH, Pfister SM, Marra MA, Kool M. Identification and Analyses of Extra-Cranial and Cranial Rhabdoid Tumor Molecular Subgroups Reveal Tumors with Cytotoxic T Cell Infiltration. Cell Rep 2019; 29:2338-2354.e7. [PMID: 31708418 PMCID: PMC6905433 DOI: 10.1016/j.celrep.2019.10.013] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 08/20/2019] [Accepted: 10/02/2019] [Indexed: 11/23/2022] Open
Abstract
Extra-cranial malignant rhabdoid tumors (MRTs) and cranial atypical teratoid RTs (ATRTs) are heterogeneous pediatric cancers driven primarily by SMARCB1 loss. To understand the genome-wide molecular relationships between MRTs and ATRTs, we analyze multi-omics data from 140 MRTs and 161 ATRTs. We detect similarities between the MYC subgroup of ATRTs (ATRT-MYC) and extra-cranial MRTs, including global DNA hypomethylation and overexpression of HOX genes and genes involved in mesenchymal development, distinguishing them from other ATRT subgroups that express neural-like features. We identify five DNA methylation subgroups associated with anatomical sites and SMARCB1 mutation patterns. Groups 1, 3, and 4 exhibit cytotoxic T cell infiltration and expression of immune checkpoint regulators, consistent with a potential role for immunotherapy in rhabdoid tumor patients. Chun et al. report similarities between the MYC subgroup of cranial and extracranial rhabdoid tumors (RTs) at genetic, gene-expression, and epigenetic levels. They identify five DNA methylation subgroups of RTs across multiple organ sites, and some subgroups exhibit increased levels of immune cell infiltration and immune checkpoint expression.
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Affiliation(s)
- Hye-Jung E Chun
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V7Z 1L3, Canada
| | - Pascal D Johann
- Hopp Children's Cancer Center, Heidelberg 69120, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), and German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg 69120, Germany; Department of Pediatric Hematology and Oncology, University Hospital Heidelberg, Heidelberg 69120, Germany
| | - Katy Milne
- Deeley Research Centre, BC Cancer, Victoria, BC V8R 6V5, Canada
| | - Marc Zapatka
- Department of Molecular Genetics, DKFZ, Heidelberg 69120, Germany
| | - Annette Buellesbach
- Hopp Children's Cancer Center, Heidelberg 69120, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), and German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg 69120, Germany; Department of Pediatric Hematology and Oncology, University Hospital Heidelberg, Heidelberg 69120, Germany
| | - Naveed Ishaque
- Center for Digital Health, Berlin Institute of Health and Charité-Universitätsmedizin Berlin, Berlin 10117, Germany; Heidelberg Center for Personalized Oncology, DKFZ, Heidelberg 69120, Germany
| | - Murat Iskar
- Department of Molecular Genetics, DKFZ, Heidelberg 69120, Germany
| | - Serap Erkek
- Hopp Children's Cancer Center, Heidelberg 69120, Germany
| | - Lisa Wei
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V7Z 1L3, Canada
| | - Basile Tessier-Cloutier
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6H 3N1, Canada
| | - Jake Lever
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V7Z 1L3, Canada
| | - Emma Titmuss
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V7Z 1L3, Canada
| | - James T Topham
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V7Z 1L3, Canada
| | - Reanne Bowlby
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V7Z 1L3, Canada
| | - Eric Chuah
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V7Z 1L3, Canada
| | - Karen L Mungall
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V7Z 1L3, Canada
| | - Yussanne Ma
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V7Z 1L3, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V7Z 1L3, Canada
| | - Richard A Moore
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V7Z 1L3, Canada
| | - Michael D Taylor
- Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Daniela S Gerhard
- Office of Cancer Genomics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V7Z 1L3, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada
| | | | - Manfred Gessler
- Theodor-Boveri-Institute/Biocenter, Developmental Biochemistry; and Comprehensive Cancer Center Mainfranken, University of Wuerzburg, Wuerzburg 97074, Germany
| | - Kornelius Kerl
- Department of Pediatric Hematology and Oncology, University Children's Hospital Muenster, Muenster 48149, Germany
| | - Martin Hasselblatt
- Institute of Neuropathology, University Hospital Muenster, Muenster 48149, Germany
| | - Michael C Frühwald
- University Children's Hospital Augsburg, Swabian Children's Cancer Center, Augsburg 86156, Germany
| | - Elizabeth J Perlman
- Department of Pathology and Laboratory Medicine, Lurie Children's Hospital, Northwestern University's Feinberg School of Medicine and Robert H. Lurie Cancer Center, Chicago, IL 60611, USA
| | - Brad H Nelson
- Deeley Research Centre, BC Cancer, Victoria, BC V8R 6V5, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada; Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8P 3E6, Canada
| | - Stefan M Pfister
- Hopp Children's Cancer Center, Heidelberg 69120, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), and German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg 69120, Germany; Department of Pediatric Hematology and Oncology, University Hospital Heidelberg, Heidelberg 69120, Germany
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V7Z 1L3, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada.
| | - Marcel Kool
- Hopp Children's Cancer Center, Heidelberg 69120, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), and German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg 69120, Germany.
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25
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Leal LF, Evangelista AF, de Paula FE, Caravina Almeida G, Carloni AC, Saggioro F, Stavale JN, Malheiros SMF, Mançano B, de Oliveira MA, Luu B, Neder L, Taylor MD, Reis RM. Reproducibility of the NanoString 22-gene molecular subgroup assay for improved prognostic prediction of medulloblastoma. Neuropathology 2018; 38:475-483. [PMID: 30155928 DOI: 10.1111/neup.12508] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 06/22/2018] [Accepted: 07/25/2018] [Indexed: 11/30/2022]
Abstract
Medulloblastoma is the most frequent malignant brain tumor in children. Four medulloblastoma molecular subgroups, MBSHH , MBWNT , MBGRP3 and MBGRP4 , have been identified by integrated high-throughput platforms. Recently, a 22-gene panel NanoString-based assay was developed for medulloblastoma molecular subgrouping, but the robustness of this assay has not been widely evaluated. Mutations in the gene for human telomerase reverse transcriptase (hTERT) have been found in medulloblastomas and are associated with distinct molecular subtypes. This study aimed to implement the 22-gene panel in a Brazilian context, and to associate the molecular profile with patients' clinical-pathological features. Formalin-fixed, paraffin-embedded (FFPE) medulloblastoma samples (n = 104) from three Brazilian centers were evaluated. Expression profiling of the 22-gene panel was performed by NanoString and a Canadian series (n = 240) was applied for training phase. hTERT mutations were analyzed by PCR followed by direct Sanger sequencing and the molecular profile was associated with patients' clinicopathological features. Overall, 65% of the patients were male, average age at diagnosis was 18 years and 7% of the patients presented metastasis at diagnosis. The molecular classification was attained in 100% of the cases, with the following frequencies: MBSHH (n = 51), MBWNT (n = 19), MBGRP4 (n = 19) and MBGRP3 (n = 15). The MBSHH and MBGRP3 subgroups were associated with older and younger patients, respectively. The MBGRP4 subgroup exhibited the lowest 5-year cancer-specific overall survival (OS), yet in the multivariate analysis, only metastasis at diagnosis and surgical resection were associated with OS. hTERT mutations were detected in 29% of the cases and were associated with older patients, increased hTERT expression and MBSHH subgroup. The 22-gene panel provides a reproducible assay for molecular subgrouping of medulloblastoma FFPE samples in a routine setting and is well-suited for future clinical trials.
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Affiliation(s)
- Letícia F Leal
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil
| | | | - Flávia E de Paula
- Molecular Diagnostic Laboratory, Barretos Cancer Hospital, Barretos, Brazil
| | | | - Adriana C Carloni
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil
| | - Fabiano Saggioro
- Department of Pathology, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, Brazil
| | - João N Stavale
- Department of Pathology, Universidade Federal de São Paulo, São Paulo, Brazil
| | | | - Bruna Mançano
- Children and Young Adult's Cancer Hospital, Barretos Cancer Hospital, Barretos, Brazil
| | | | - Betty Luu
- Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Luciano Neder
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil.,Department of Pathology, Barretos Cancer Hospital, Barretos, Brazil
| | - Michael D Taylor
- Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Rui M Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil.,Molecular Diagnostic Laboratory, Barretos Cancer Hospital, Barretos, Brazil.,Life and Health Sciences Research Institute (ICVS), Health Sciences School, University of Minho, Braga, Portugal.,ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
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26
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Colafati GS, Voicu IP, Carducci C, Miele E, Carai A, Di Loreto S, Marrazzo A, Cacchione A, Cecinati V, Tornesello A, Mastronuzzi A. MRI features as a helpful tool to predict the molecular subgroups of medulloblastoma: state of the art. Ther Adv Neurol Disord 2018; 11:1756286418775375. [PMID: 29977341 PMCID: PMC6024494 DOI: 10.1177/1756286418775375] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 02/28/2018] [Indexed: 12/20/2022] Open
Abstract
Medulloblastoma is the most common malignant pediatric brain tumor. Medulloblastoma should not be viewed as a single disease, but as a heterogeneous mixture of various subgroups with distinct characteristics. Based on genomic profiles, four distinct molecular subgroups are identified: Wingless (WNT), Sonic Hedgehog (SHH), Group 3 and Group 4. Each of these subgroups are associated with specific genetic aberrations, typical age of onset as well as survival prognosis. Magnetic resonance imaging (MRI) is performed for all patients with brain tumors, and has a key role in the diagnosis, surgical guidance and follow up of patients with medulloblastoma. Several studies indicate MRI as a promising tool for early detection of medulloblastoma subgroups. The early identification of the subgroup can influence the extent of surgical resection, radiotherapy and chemotherapy targeted treatments. In this article, we review the state of the art in MRI-facilitated medulloblastoma subgrouping, with a summary of the main MRI features in medulloblastoma and a brief discussion on molecular characterization of medulloblastoma subgroups. The main focus of the article is MRI features that correlate with medulloblastoma subtypes, as well as features suggestive of molecular subgroups. Finally, we briefly discuss the latest trends in MRI studies and latest developments in molecular characterization.
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Affiliation(s)
| | - Ioan Paul Voicu
- Department of Imaging, Neuroradiology Unit and Department of Hematology/Oncology and Stem Cell Transplantation, Bambino Gesù Children's Hospital, Rome, Italy
| | - Chiara Carducci
- Department of Imaging, Neuroradiology Unit, Bambino Gesù Children's Hospital, Piazza Sant'Onofrio 4, 00165, Rome, Italy
| | - Evelina Miele
- Department of Hematology/Oncology and Stem Cell Transplantation, Bambino Gesù Children's Hospital, Rome, Italy
| | - Andrea Carai
- Department of Neuroscience and Neurorehabilitation, Neurosurgery Unit, Bambino Gesù Children's Hospital, Rome, Italy
| | - Simona Di Loreto
- Dipartimento di Pediatria, Università degli studi di Chieti, Chieti, Italy
| | - Antonio Marrazzo
- Department of Hematology/Oncology and Stem Cell Transplantation, Bambino Gesù Children's Hospital, Rome, Italy
| | - Antonella Cacchione
- Department of Hematology/Oncology and Stem Cell Transplantation, Bambino Gesù Children's Hospital, Rome, Italy
| | - Valerio Cecinati
- Pediatric Hematology and Oncology Unit, Department of Hematology, Transfusion Medicine and Biotechnology, Pescara, Italy
| | | | - Angela Mastronuzzi
- Department of Hematology/Oncology and Stem Cell Transplantation, Bambino Gesù Children's Hospital, Rome, Italy
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27
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Szucs Z, Jones RL. Perspectives on the evolving state of the art management of gastrointestinal stromal tumours. Transl Gastroenterol Hepatol 2018; 3:21. [PMID: 29780899 DOI: 10.21037/tgh.2018.04.02] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 03/30/2018] [Indexed: 12/12/2022] Open
Abstract
Gastrointestinal stromal tumours (GISTs) represent a very exciting tumour entity for the medical oncologist. There has been extensive clinical and preclinical research dissecting the natural behaviour, molecular landscape and therapeutic responsiveness of this rare mesenchymal tumour. Various molecular subtypes of GIST have a differing prognostic and predictive relevance in the state of the art management of the disease. Emerging mature clinical trial data gathered over the last one and half decade provided substantial molecular profiling information in understanding the success and eventual failure of treatment. In our review of the most relevant literature we aim to guide the clinician in tailoring neoadjuvant, adjuvant and palliative treatment of GIST alongside the different, now well established molecular subgroups of GISTs.
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Affiliation(s)
- Zoltan Szucs
- Consultant Medical Oncologist, Ipswich Hospital NHS Trust, UK
| | - Robin L Jones
- Consultant Medical Oncologist, Head of Sarcoma Unit, The Royal Marsden Hospital NHS Foundation Trust/Institute of Cancer Research, Fulham Road, London, SW3 6JJ, UK
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28
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Abstract
Brain tumors are the leading cause of cancer-related death in children, and medulloblastoma (MB) is the most common malignant pediatric brain tumor. Advances in surgery, radiation, and chemotherapy have improved the survival of MB patients. But despite these advances, 25-30% of patients still die from the disease, and survivors suffer severe long-term side effects from the aggressive therapies they receive. Although MB is often considered a single disease, molecular profiling has revealed a significant degree of heterogeneity, and there is a growing consensus that MB consists of multiple subgroups with distinct driver mutations, cells of origin, and prognosis. Here, we review recent progress in MB research, with a focus on the genes and pathways that drive tumorigenesis, the animal models that have been developed to study tumor biology, and the advances in conventional and targeted therapy.
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Affiliation(s)
- Jun Wang
- Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, USA;
| | - Alexandra Garancher
- Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, USA;
| | - Vijay Ramaswamy
- Division of Haematology/Oncology and Department of Paediatrics, Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada
| | - Robert J Wechsler-Reya
- Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, USA;
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29
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Lundberg IV, Wikberg ML, Ljuslinder I, Li X, Myte R, Zingmark C, Löfgren-Burström A, Edin S, Palmqvist R. MicroRNA Expression in KRAS- and BRAF-mutated Colorectal Cancers. Anticancer Res 2018; 38:677-683. [PMID: 29374690 DOI: 10.21873/anticanres.12272] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 12/03/2017] [Accepted: 12/04/2017] [Indexed: 11/10/2022]
Abstract
BACKGROUND/AIM KRAS and BRAF are two genes commonly mutated in colorectal cancer (CRC). Even though BRAF is a downstream target of KRAS in the MAPK signalling pathway, KRAS- and BRAF-mutated CRCs are found to display several different clinical and histopathological features. We investigated whether a differential expression of microRNAs (miRNAs) could explain the clinicopathological differences seen between KRAS- and BRAF-mutated CRCs. MATERIALS AND METHODS Using a PCR array, we analyzed the expression of 84 different miRNAs in CRC cell lines wild-type in KRAS and BRAF, or mutated in KRAS or BRAF. RESULTS Ten miRNAs were selected for further analyses in tumor tissue specimens (let-7a, let-7i, miR-10a, miR-10b, miR-31, miR-100, miR-181a, miR-181b, miR-372, and miR-373). BRAF-mutated tumors were found to express significantly higher levels of miR-31 as well as significantly lower levels of miR-373, compared to wild-type tumors. CONCLUSION Our results suggest that KRAS- and BRAF-mutated CRCs may have different miRNA signatures compared to CRC tumors wild-type in KRAS and BRAF. However, no difference in expression levels between KRAS- and BRAF-mutated tumors was evident for the miRNAs analyzed in this study.
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Affiliation(s)
- Ida V Lundberg
- Department of Medical Biosciences, Pathology, Umeå University, Umea, Sweden
| | - Maria L Wikberg
- Department of Medical Biosciences, Pathology, Umeå University, Umea, Sweden
| | - Ingrid Ljuslinder
- Department of Radiation Sciences, Oncology, Umeå University, Umea, Sweden
| | - Xingru Li
- Department of Medical Biosciences, Pathology, Umeå University, Umea, Sweden
| | - Robin Myte
- Department of Radiation Sciences, Oncology, Umeå University, Umea, Sweden
| | - Carl Zingmark
- Department of Medical Biosciences, Pathology, Umeå University, Umea, Sweden
| | | | - Sofia Edin
- Department of Medical Biosciences, Pathology, Umeå University, Umea, Sweden
| | - Richard Palmqvist
- Department of Medical Biosciences, Pathology, Umeå University, Umea, Sweden
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30
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Zapotocky M, Mata-Mbemba D, Sumerauer D, Liby P, Lassaletta A, Zamecnik J, Krskova L, Kyncl M, Stary J, Laughlin S, Arnoldo A, Hawkins C, Tabori U, Taylor MD, Bouffet E, Raybaud C, Ramaswamy V. Differential patterns of metastatic dissemination across medulloblastoma subgroups. J Neurosurg Pediatr 2018; 21:145-152. [PMID: 29219788 DOI: 10.3171/2017.8.peds17264] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Metastatic dissemination is a major treatment challenge and cause of death in patients with medulloblastoma. However, the influence of molecular biology on the pattern of metastatic dissemination at diagnosis is not known. In this study, the authors sought to define the location, pattern, and imaging characteristics of medulloblastoma metastases across subgroups at diagnosis. METHODS A consecutive cohort of patients with metastatic medulloblastoma at The Hospital for Sick Children and the University Hospital Motol, who underwent up-front MRI of the craniospinal axis, was assembled and allocated to subgroups using NanoString limited gene-expression profiling. Radiological characteristics (including location, morphology, size, diffusion restriction, and contrast enhancement) were discerned through a retrospective review. RESULTS Forty metastatic medulloblastomas were identified with up-front neuroimaging of the craniospinal axis: 5 sonic hedgehog (SHH), 16 Group 3, and 19 Group 4 metastases. Significant subgroup-specific differences were observed, particularly with respect to tumor location, size, and morphology. Group 3 metastases were most frequently laminar compared with a more nodular pattern in Group 4 (14 of 16 in Group 3 vs 8 of 19 in Group 4; p = 0.0004). Laminar metastases were not observed in patients with SHH medulloblastoma. Suprasellar metastases are highly specific to Group 4 (p = 0.016). Two of the 5 SHH cases had multifocal lesions in the cerebellum, raising the possibility that these were in fact synchronous primary tumors and not true metastases. A minority of patients with Group 4 metastases harbored metastatic deposits that did not enhance on MRI after contrast administration, often in patients whose primary tumor did not enhance. CONCLUSIONS The location, morphology, and imaging characteristics of metastatic medulloblastoma differ across molecular subgroups, with implications for diagnosis and management. This suggests that the biology of leptomeningeal dissemination differs among medulloblastoma subgroups.
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Affiliation(s)
- Michal Zapotocky
- 1Department of Paediatrics, Division of Haematology/Oncology.,2Pediatric Hematology and Oncology
| | | | | | | | | | | | | | - Martin Kyncl
- 6Radiology, 2nd Faculty of Medicine, Charles University and University Hospital Motol, Prague, Czech Republic
| | | | | | | | | | - Uri Tabori
- 1Department of Paediatrics, Division of Haematology/Oncology
| | | | - Eric Bouffet
- 1Department of Paediatrics, Division of Haematology/Oncology
| | - Charles Raybaud
- 3Department of Diagnostic Imaging, Division of Neuroradiology
| | - Vijay Ramaswamy
- 1Department of Paediatrics, Division of Haematology/Oncology.,9Programme in Neuroscience and Mental Health, University of Toronto and The Hospital for Sick Children, Toronto, Ontario, Canada; and Departments of
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31
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Jiang T, Zhang Y, Wang J, Du J, Raynald, Qiu X, Wang Y, Li C. A Retrospective Study of Progression-Free and Overall Survival in Pediatric Medulloblastoma Based on Molecular Subgroup Classification: A Single-Institution Experience. Front Neurol 2017; 8:198. [PMID: 28553259 PMCID: PMC5427081 DOI: 10.3389/fneur.2017.00198] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 04/24/2017] [Indexed: 01/09/2023] Open
Abstract
Background Medulloblastoma (MB) has been classified into four core subgroups according to the transcriptional profile in recent years. However, some disagreement among researchers remains regarding the prognoses and most effective treatments of the different subgroups with different age distributions. Objective The objective of this study was to analyze MB prognosis in children population based on the classification of four molecular subgroups. Methods From January 2011 to January 2013, 84 consecutive MB patients aged underwent tumor removal at Beijing Tiantan Hospital. A total of 55 patients who ranged in age from 4 to 18 years underwent detailed follow-up. Molecular subgrouping was performed using RT-PCR. Results The 2-year progression-free survival (PFS) and overall survival (OS) rates for the entire cohort were 76.2 ± 5.8 and 81.8 ± 5.2%, respectively. Univariate analysis revealed that the Group 4 patients had a better survival (2-year OS, 90.6 ± 5.2%) than the SHH subgroup (P = 0.002) and Group 3 patients (P = 0.008). Only two of the 23 non-metastasized Group 4 patients relapsed, and chemotherapy did significantly affect these patients (PFS, P = 0.685). One out of five WNT patients had tumor relapse and died at last. Large cell/anaplastic (LC/A) histology and chemotherapy were independent risk factors in multivariate analysis. Conclusion In our study, the non-metastasized Group 4 patients had an excellent prognosis. The SHH subgroup and Group 3 patients had worst prognoses. LC/A histology had a dismal prognosis in our cohorts, which warrants intensive treatment.
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Affiliation(s)
- Tao Jiang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Yuqi Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,Department of Neurosurgery, Yuquan Hospital, Medical Center, Tsinghua University, Beijing, China
| | - Junmei Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Jiang Du
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Raynald
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Xiaoguang Qiu
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Ying Wang
- Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Chunde Li
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China
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32
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Szucs Z, Thway K, Fisher C, Bulusu R, Constantinidou A, Benson C, van der Graaf WT, Jones RL. Molecular subtypes of gastrointestinal stromal tumors and their prognostic and therapeutic implications. Future Oncol 2016; 13:93-107. [PMID: 27600498 DOI: 10.2217/fon-2016-0192] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Gastrointestinal stromal tumors (GISTs) are composed of various molecular subtypes, with differing prognostic and predictive relevance. Previously, tumors lacking mutations in the KIT and PDGFRA genes have been designated as 'wild-type' GISTs; however, they represent a heterogeneous group currently undergoing further subclassification. Primary and secondary resistance to imatinib poses a significant clinical challenge, therefore ongoing research is trying to evaluate mechanisms to overcome resistance. Thorough understanding of the prognostic and predictive relevance of different genetic subtypes of GIST can guide clinical decision-making both in the adjuvant and the metastatic setting. Further work is required to identify tailored therapies for specific subgroups of GISTs wild-type for KIT and PDGFRA mutations and to identify predictive factors of resistance to currently approved systemic therapies.
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Affiliation(s)
- Zoltan Szucs
- The Royal Marsden Hospital NHS Foundation Trust, Fulham Road, London, SW3 6JJ, UK
| | - Khin Thway
- The Royal Marsden Hospital NHS Foundation Trust, Fulham Road, London, SW3 6JJ, UK
| | - Cyril Fisher
- The Royal Marsden Hospital NHS Foundation Trust, Fulham Road, London, SW3 6JJ, UK
| | - Ramesh Bulusu
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0QQ, UK
| | | | - Charlotte Benson
- The Royal Marsden Hospital NHS Foundation Trust, Fulham Road, London, SW3 6JJ, UK
| | - Winette Ta van der Graaf
- The Royal Marsden Hospital NHS Foundation Trust, Fulham Road, London, SW3 6JJ, UK.,The Institute of Cancer Research, Cotswold Road, Sutton, SM2 5NG, UK
| | - Robin L Jones
- The Royal Marsden Hospital NHS Foundation Trust, Fulham Road, London, SW3 6JJ, UK
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33
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Ling A, Lundberg IV, Eklöf V, Wikberg ML, Öberg Å, Edin S, Palmqvist R. The infiltration, and prognostic importance, of Th1 lymphocytes vary in molecular subgroups of colorectal cancer. J Pathol Clin Res 2015; 2:21-31. [PMID: 27499912 PMCID: PMC4858126 DOI: 10.1002/cjp2.31] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 10/05/2015] [Indexed: 12/11/2022]
Abstract
Giving strong prognostic information, T‐cell infiltration is on the verge of becoming an additional component in the routine clinical setting for classification of colorectal cancer (CRC). With a view to further improving the tools for prognostic evaluation, we have studied how Th1 lymphocyte infiltration correlates with prognosis not only by quantity, but also by subsite, within CRCs with different molecular characteristics (microsatellite instability, CpG island methylator phenotype status, and BRAF and KRAS mutational status). We evaluated the Th1 marker T‐bet by immunohistochemistry in 418 archival tumour tissue samples from patients who underwent surgical resection for CRC. We found that a high number of infiltrating Th1 lymphocytes is strongly associated with an improved prognosis in patients with CRC, irrespective of intratumoural subsite, and that both extent of infiltration and patient outcome differ according to molecular subgroup. In brief, microsatellite instability, CpG island methylator phenotype‐high and BRAF mutated tumours showed increased infiltration of Th1 lymphocytes, and the most pronounced prognostic effect of Th1 infiltration was found in these tumours. Interestingly, BRAF mutated tumours were found to be more highly infiltrated by Th1 lymphocytes than BRAF wild‐type tumours whereas the opposite was seen for KRAS mutated tumours. These differences could be explained at least partly by our finding that BRAF mutated, in contrast to KRAS mutated, CRC cell lines and tumour specimens expressed higher levels of the Th1‐attracting chemokine CXCL10, and reduced levels of CCL22 and TGFB1, stimulating Th2/Treg recruitment and polarisation. In conclusion, the strong prognostic importance of Th1 lymphocyte infiltration in CRC was found at all subsites evaluated, and it remained significant in multivariable analyses, indicating that T‐bet may be a valuable marker in the clinical setting. Our results also indicate that T‐bet is of value when analysed in molecular subgroups of CRC, allowing identification of patients with especially poor prognosis who are in need of extended treatment.
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Affiliation(s)
- Agnes Ling
- Department of Medical Biosciences Pathology, Umeå University Umeå Sweden
| | - Ida V Lundberg
- Department of Medical Biosciences Pathology, Umeå University Umeå Sweden
| | - Vincy Eklöf
- Department of Medical Biosciences Pathology, Umeå University Umeå Sweden
| | - Maria L Wikberg
- Department of Medical Biosciences Pathology, Umeå University Umeå Sweden
| | - Åke Öberg
- Department of Surgical and Perioperative Sciences Surgery, Umeå University Umeå Sweden
| | - Sofia Edin
- Department of Medical Biosciences Pathology, Umeå University Umeå Sweden
| | - Richard Palmqvist
- Department of Medical Biosciences Pathology, Umeå University Umeå Sweden
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Li KKW, Lau KM, Ng HK. Signaling pathway and molecular subgroups of medulloblastoma. Int J Clin Exp Pathol. 2013; 6(7): 1211-22. Int J Clin Exp Pathol 2015; 8:11945. [PMID: 26617952 PMCID: PMC4637768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 08/25/2015] [Indexed: 06/05/2023]
Abstract
Medulloblastoma (MB) is the most common malignant brain tumor in children. Although multimodality treatment regimens including surgery, radiotherapy and chemotherapy have greatly improved disease outcome, about one-third of MB patient remains incurable, and many long-term survivors are suffered from deleterious effects due to aggressive treatment. Understanding the signaling pathways and the genetic mechanisms contributed to MB development would be the key to develop novel therapeutic treatment strategies for improving survival and outcome of MB. In this review, we discuss the biological signaling pathways involved in MB pathogenesis. We also go through the current international consensus of four core MB subgroups namely, SHH, WNT, Group 3 and Group 4. This is adopted based on the knowledge of genomic complexity of MB as analyzed by recent high-throughput genomic technology. We talk about immunohistochemistry assays established to determine molecular subgroup affiliation. In the last part of review, we discuss how identification of molecular subgroups is going to change our routine disease diagnosis and clinical management.
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Affiliation(s)
- Kay Ka-Wai Li
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong KongHong Kong
- Shenzhen Research Institute, The Chinese University of Hong KongNo. 10, 2nd Yuexing Road, Nanshan District, Shenzhen 518057, China
| | - Kin-Mang Lau
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong KongHong Kong
| | - Ho-Keung Ng
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong KongHong Kong
- Shenzhen Research Institute, The Chinese University of Hong KongNo. 10, 2nd Yuexing Road, Nanshan District, Shenzhen 518057, China
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Margol AS, Robison NJ, Gnanachandran J, Hung LT, Kennedy RJ, Vali M, Dhall G, Finlay JL, Erdreich-Epstein A, Krieger MD, Drissi R, Fouladi M, Gilles FH, Judkins AR, Sposto R, Asgharzadeh S. Tumor-associated macrophages in SHH subgroup of medulloblastomas. Clin Cancer Res 2015; 21:1457-65. [PMID: 25344580 PMCID: PMC7654723 DOI: 10.1158/1078-0432.ccr-14-1144] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
PURPOSE Medulloblastoma in children can be categorized into at least four molecular subgroups, offering the potential for targeted therapeutic approaches to reduce treatment-related morbidities. Little is known about the role of tumor microenvironment in medulloblastoma or its contribution to these molecular subgroups. Tumor microenvironment has been shown to be an important source for therapeutic targets in both adult and pediatric neoplasms. In this study, we investigated the hypothesis that expression of genes related to tumor-associated macrophages (TAM) correlates with the medulloblastoma molecular subgroups and contributes to a diagnostic signature. METHODS Gene-expression profiling using human exon array (n = 168) was analyzed to identify medulloblastoma molecular subgroups and expression of inflammation-related genes. Expression of 45 tumor-related and inflammation-related genes was analyzed in 83 medulloblastoma samples to build a gene signature predictive of molecular subgroups. TAMs in medulloblastomas (n = 54) comprising the four molecular subgroups were assessed by immunohistochemistry (IHC). RESULTS A 31-gene medulloblastoma subgroup classification score inclusive of TAM-related genes (CD163 and CSF1R) was developed with a misclassification rate of 2%. Tumors in the Sonic Hedgehog (SHH) subgroup had increased expression of inflammation-related genes and significantly higher infiltration of TAMs than tumors in the Group 3 or Group 4 subgroups (P < 0.0001 and P < 0.0001, respectively). IHC data revealed a strong association between location of TAMs and proliferating tumor cells. CONCLUSIONS These data show that SHH tumors have a unique tumor microenvironment among medulloblastoma subgroups. The interactions of TAMs and SHH medulloblastoma cells may contribute to tumor growth revealing TAMs as a potential therapeutic target.
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Affiliation(s)
- Ashley S Margol
- Children's Hospital Los Angeles and The Saban Research Institute, Los Angeles, California. Department of Pediatrics, Keck School of Medicine of University of Southern California, Los Angeles, California
| | - Nathan J Robison
- Children's Hospital Los Angeles and The Saban Research Institute, Los Angeles, California. Department of Pediatrics, Keck School of Medicine of University of Southern California, Los Angeles, California
| | - Janahan Gnanachandran
- Children's Hospital Los Angeles and The Saban Research Institute, Los Angeles, California
| | - Long T Hung
- Children's Hospital Los Angeles and The Saban Research Institute, Los Angeles, California
| | - Rebekah J Kennedy
- Children's Hospital Los Angeles and The Saban Research Institute, Los Angeles, California
| | - Marzieh Vali
- Children's Hospital Los Angeles and The Saban Research Institute, Los Angeles, California
| | - Girish Dhall
- Children's Hospital Los Angeles and The Saban Research Institute, Los Angeles, California. Department of Pediatrics, Keck School of Medicine of University of Southern California, Los Angeles, California
| | - Jonathan L Finlay
- Children's Hospital Los Angeles and The Saban Research Institute, Los Angeles, California. Department of Pediatrics, Keck School of Medicine of University of Southern California, Los Angeles, California
| | - Anat Erdreich-Epstein
- Children's Hospital Los Angeles and The Saban Research Institute, Los Angeles, California. Department of Pediatrics, Keck School of Medicine of University of Southern California, Los Angeles, California. Department of Pathology, Keck School of Medicine of University of Southern California, Los Angeles, California
| | - Mark D Krieger
- Children's Hospital Los Angeles and The Saban Research Institute, Los Angeles, California. Department of Pediatrics, Keck School of Medicine of University of Southern California, Los Angeles, California
| | - Rachid Drissi
- Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Maryam Fouladi
- Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Floyd H Gilles
- Children's Hospital Los Angeles and The Saban Research Institute, Los Angeles, California. Department of Pediatrics, Keck School of Medicine of University of Southern California, Los Angeles, California
| | - Alexander R Judkins
- Children's Hospital Los Angeles and The Saban Research Institute, Los Angeles, California. Department of Pathology, Keck School of Medicine of University of Southern California, Los Angeles, California
| | - Richard Sposto
- Children's Hospital Los Angeles and The Saban Research Institute, Los Angeles, California. Department of Pediatrics, Keck School of Medicine of University of Southern California, Los Angeles, California
| | - Shahab Asgharzadeh
- Children's Hospital Los Angeles and The Saban Research Institute, Los Angeles, California. Department of Pediatrics, Keck School of Medicine of University of Southern California, Los Angeles, California. Department of Pathology, Keck School of Medicine of University of Southern California, Los Angeles, California.
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Schneider C, Ramaswamy V, Kulkarni AV, Rutka JT, Remke M, Tabori U, Hawkins C, Bouffet E, Taylor MD. Clinical implications of medulloblastoma subgroups: incidence of CSF diversion surgery. J Neurosurg Pediatr 2015; 15:236-42. [PMID: 25525930 DOI: 10.3171/2014.9.peds14280] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
OBJECT While medulloblastoma was initially thought to comprise a single homogeneous entity, it is now accepted that it in fact comprises 4 discrete subgroups, each with its own distinct demographics, clinical presentation, transcriptomics, genetics, and outcome. Hydrocephalus is a common complication of medulloblastoma and not infrequently requires CSF diversion. The authors report the incidence of CSF diversion surgery in each of the subgroups of medulloblastoma (Wnt, Shh, Group 3, and Group 4). METHODS The medical and imaging records for patients who underwent surgery for medulloblastoma at The Hospital for Sick Children were retrospectively reviewed. The primary outcome was the requirement for CSF diversion surgery either before or within 60 days of tumor resection. The modified Canadian Preoperative Prediction Rule for Hydrocephalus (mCPPRH) was compared among subgroups. RESULTS Of 143 medulloblastoma patients, treated from 1991 to 2013, sufficient data were available for 130 patients (15 with Wnt, 30 with Shh, 30 with Group 3, and 55 with Group 4 medulloblastomas). Of these, 28 patients (22%) ultimately underwent CSF diversion surgery: 0% with Wnt, 29% with Shh, 29% with Group 3, and 43% with Group 4 tumors. Patients in the Wnt subgroup had a lower incidence of CSF diversion than all other patients combined (p = 0.04). Wnt patients had a lower mCPPRH score (lower risk of CSF diversion, p = 0.045), were older, had smaller ventricles at diagnosis, and had no leptomeningeal metastases. CONCLUSIONS The overall rate of CSF diversion surgery for Shh, Group 3, and Group 4 medulloblastomas is around 30%, but no patients in the present series with a Wnt medulloblastoma required shunting. The low incidence of hydrocephalus in patients with Wnt medulloblastoma likely reflects both host factors (age) and disease factors (lack of metastases). The absence of hydrocephalus in patients with Wnt medulloblastomas likely contributes to their excellent rate of survival and may also contribute to a higher quality of life than for patients in other subgroups.
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Affiliation(s)
- Christian Schneider
- Developmental and Stem Cell Biology, Division of Neurosurgery, Neurooncology and Neuropathology, Arthur and Sonia Labatt Brain Tumor Research Center, The Hospital for Sick Children, Toronto, Ontario, Canada
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Abstract
Medulloblastoma is the commonest malignant brain tumor in children. Treatment with surgery, irradiation, and chemotherapy has improved outcomes in recent years, but patients are frequently left with devastating neurocognitive and other sequelae following such therapy. While the prognosis has traditionally been based on conventional histopathology and clinical staging (based on age, extent of resection, and presence or absence of metastasis), it has become apparent in recent years that the inherent biology of the tumor plays a significant part in predicting survival and sometimes supersedes clinical or pathologic risk factors. The advent of deep sequencing gene technology has provided invaluable clues to the molecular makeup of this tumor and allowed neuro-oncologists to understand that medulloblastoma is an amalgamation of several distinct disease entities with unique clinical associations and behavior. This review is a concise summary of the pathology, genetic syndromes, recent advances in molecular subgrouping, and the associated gene mutations and copy number variations in medulloblastoma. The association of molecular alterations with patient prognosis is also discussed, but it should be remembered that further validation is required in prospective clinical trials utilizing uniform treatment approaches.
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Affiliation(s)
- Kristin Schroeder
- Pediatric Clinical Services, Preston Robert Tisch Brain Tumor Center at Duke, Duke University Medical Center, Durham, NC, USA
| | - Sri Gururangan
- Pediatric Clinical Services, Preston Robert Tisch Brain Tumor Center at Duke, Duke University Medical Center, Durham, NC, USA
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Li KKW, Lau KM, Ng HK. Signaling pathway and molecular subgroups of medulloblastoma. Int J Clin Exp Pathol 2013; 6:1211-1222. [PMID: 23826403 PMCID: PMC3693187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Accepted: 05/21/2013] [Indexed: 06/02/2023]
Abstract
Medulloblastoma (MB) is the most common malignant brain tumor in children. Although multimodality treatment regimens including surgery, radiotherapy and chemotherapy have greatly improved disease outcome, about one-third of MB patient remains incurable, and many long-term survivors are suffered from deleterious effects due to aggressive treatment. Understanding the signaling pathways and the genetic mechanisms contributed to MB development would be the key to develop novel therapeutic treatment strategies for improving survival and outcome of MB. In this review, we discuss the biological signaling pathways involved in MB pathogenesis. We also go through the current international consensus of four core MB subgroups namely, SHH, WNT, Group 3, and Group 4. This is adopted based on the knowledge of genomic complexity of MB as analyzed by recent high-throughput genomic technology. We talk about immunohistochemistry assays established to determine molecular subgroup affiliation. In the last part of review, we discuss how identification of molecular subgroups is going to change our routine disease diagnosis and clinical management.
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Affiliation(s)
- Kay Ka-Wai Li
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong
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Lau J, Schmidt C, Markant SL, Taylor MD, Wechsler-Reya RJ, Weiss WA. Matching mice to malignancy: molecular subgroups and models of medulloblastoma. Childs Nerv Syst 2012; 28:521-32. [PMID: 22315164 PMCID: PMC3515664 DOI: 10.1007/s00381-012-1704-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2011] [Accepted: 01/17/2012] [Indexed: 12/28/2022]
Abstract
INTRODUCTION Medulloblastoma, the largest group of embryonal brain tumors, has historically been classified into five variants based on histopathology. More recently, epigenetic and transcriptional analyses of primary tumors have subclassified medulloblastoma into four to six subgroups, most of which are incongruous with histopathological classification. DISCUSSION Improved stratification is required for prognosis and development of targeted treatment strategies, to maximize cure and minimize adverse effects. Several mouse models of medulloblastoma have contributed both to an improved understanding of progression and to developmental therapeutics. In this review, we summarize the classification of human medulloblastoma subtypes based on histopathology and molecular features. We describe existing genetically engineered mouse models, compare these to human disease, and discuss the utility of mouse models for developmental therapeutics. Just as accurate knowledge of the correct molecular subtype of medulloblastoma is critical to the development of targeted therapy in patients, we propose that accurate modeling of each subtype of medulloblastoma in mice will be necessary for preclinical evaluation and optimization of those targeted therapies.
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Affiliation(s)
- Jasmine Lau
- Department of Neurology, University of California, San Francisco, CA, USA. Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA. Department of Neurological Surgery and Brain Tumor Research Center, University of California, San Francisco, CA, USA. Department of Pediatrics, University of California, San Francisco, CA, USA
| | - Christin Schmidt
- Department of Neurology, University of California, San Francisco, CA, USA. Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA. Department of Neurological Surgery and Brain Tumor Research Center, University of California, San Francisco, CA, USA. Department of Pediatrics, University of California, San Francisco, CA, USA
| | - Shirley L. Markant
- Tumor Development Program, Sanford-Burnham Medical Research Institute, La Jolla, CA, USA. Department of Pharmacology & Cancer Biology, Duke University Medical Center, Durham, NC, USA
| | - Michael D. Taylor
- Division of Neurosurgery, Hospital for Sick Children, University of Toronto, Toronto, ON, Canada. Arthur and Sonia Labatt Brain Tumour Research Centre, Program in Developmental and Stem Cell Biology, Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Robert J. Wechsler-Reya
- Tumor Development Program, Sanford-Burnham Medical Research Institute, La Jolla, CA, USA. Department of Pharmacology & Cancer Biology, Duke University Medical Center, Durham, NC, USA
| | - William A. Weiss
- Department of Neurology, University of California, San Francisco, CA, USA. Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA. Department of Neurological Surgery and Brain Tumor Research Center, University of California, San Francisco, CA, USA. Department of Pediatrics, University of California, San Francisco, CA, USA
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