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Yasumizu Y, Hagiwara M, Umezu Y, Fuji H, Iwaisako K, Asagiri M, Uemoto S, Nakamura Y, Thul S, Ueyama A, Yokoi K, Tanemura A, Nose Y, Saito T, Wada H, Kakuda M, Kohara M, Nojima S, Morii E, Doki Y, Sakaguchi S, Ohkura N. Neural-net-based cell deconvolution from DNA methylation reveals tumor microenvironment associated with cancer prognosis. NAR Cancer 2024; 6:zcae022. [PMID: 38751935 PMCID: PMC11094754 DOI: 10.1093/narcan/zcae022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 04/18/2024] [Accepted: 05/01/2024] [Indexed: 05/18/2024] Open
Abstract
DNA methylation is a pivotal epigenetic modification that defines cellular identity. While cell deconvolution utilizing this information is considered useful for clinical practice, current methods for deconvolution are limited in their accuracy and resolution. In this study, we collected DNA methylation data from 945 human samples derived from various tissues and tumor-infiltrating immune cells and trained a neural network model with them. The model, termed MEnet, predicted abundance of cell population together with the detailed immune cell status from bulk DNA methylation data, and showed consistency to those of flow cytometry and histochemistry. MEnet was superior to the existing methods in the accuracy, speed, and detectable cell diversity, and could be applicable for peripheral blood, tumors, cell-free DNA, and formalin-fixed paraffin-embedded sections. Furthermore, by applying MEnet to 72 intrahepatic cholangiocarcinoma samples, we identified immune cell profiles associated with cancer prognosis. We believe that cell deconvolution by MEnet has the potential for use in clinical settings.
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Affiliation(s)
- Yoshiaki Yasumizu
- Department of Experimental Immunology, Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Osaka, Japan
| | - Masaki Hagiwara
- Department of Experimental Immunology, Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan
- Department of Basic Research in Tumor Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
- Pharmaceutical Research Division, Shionogi & Co., Ltd., Toyonaka, Osaka, Japan
| | - Yuto Umezu
- Faculty of Medicine, Osaka University, Suita, Osaka, Japan
| | - Hiroaki Fuji
- Department of Hepato-Biliary-Pancreatic Surgery, Hyogo Medical University, Nishinomiya, Hyogo, Japan
- Division of Hepato-Biliary-Pancreatic Surgery and Transplantation, Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Kyoto, Japan
| | - Keiko Iwaisako
- Division of Hepato-Biliary-Pancreatic Surgery and Transplantation, Department of Surgery, Graduate School of Medicine, Kyoto University, Kyoto, Kyoto, Japan
- Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, Kyoto, Japan
| | - Masataka Asagiri
- Department of Pharmacology, Yamaguchi University Graduate School of Medicine, Ube, Yamaguchi, Japan
| | - Shinji Uemoto
- Shiga University Medical Science, Otsu, Shiga, Japan
| | - Yamami Nakamura
- Department of Experimental Immunology, Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan
| | - Sophia Thul
- Department of Experimental Immunology, Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan
| | - Azumi Ueyama
- Pharmaceutical Research Division, Shionogi & Co., Ltd., Toyonaka, Osaka, Japan
- Department of Clinical Research in Tumor Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Kazunori Yokoi
- Department of Dermatology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Atsushi Tanemura
- Department of Dermatology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Yohei Nose
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Takuro Saito
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Hisashi Wada
- Department of Clinical Research in Tumor Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Mamoru Kakuda
- Department of Obstetrics and Gynecology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Masaharu Kohara
- Department of Pathology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Satoshi Nojima
- Department of Pathology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Eiichi Morii
- Department of Pathology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Yuichiro Doki
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Shimon Sakaguchi
- Department of Experimental Immunology, Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan
- Department of Experimental Immunology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Kyoto, Japan
| | - Naganari Ohkura
- Department of Experimental Immunology, Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan
- Department of Basic Research in Tumor Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
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Keller JA, Sigurdsson S, Schmitz Abecassis B, Kant IMJ, Van Buchem MA, Launer LJ, van Osch MJP, Gudnason V, de Bresser J. Identification of Distinct Brain MRI Phenotypes and Their Association With Long-Term Dementia Risk in Community-Dwelling Older Adults. Neurology 2024; 102:e209176. [PMID: 38471053 PMCID: PMC11033985 DOI: 10.1212/wnl.0000000000209176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 12/13/2023] [Indexed: 03/14/2024] Open
Abstract
BACKGROUND AND OBJECTIVES Individual brain MRI markers only show at best a modest association with long-term occurrence of dementia. Therefore, it is challenging to accurately identify individuals at increased risk for dementia. We aimed to identify different brain MRI phenotypes by hierarchical clustering analysis based on combined neurovascular and neurodegenerative brain MRI markers and to determine the long-term dementia risk within the brain MRI phenotype subgroups. METHODS Hierarchical clustering analysis based on 32 combined neurovascular and neurodegenerative brain MRI markers in community-dwelling individuals of the Age-Gene/Environment Susceptibility Reykjavik Study was applied to identify brain MRI phenotypes. A Cox proportional hazards regression model was used to determine the long-term risk for dementia per subgroup. RESULTS We included 3,056 participants and identified 15 subgroups with distinct brain MRI phenotypes. The phenotypes ranged from limited burden, mostly irregular white matter hyperintensity (WMH) shape and cerebral atrophy, mostly irregularly WMHs and microbleeds, mostly cortical infarcts and atrophy, mostly irregularly shaped WMH and cerebral atrophy to multiburden subgroups. Each subgroup showed different long-term risks for dementia (min-max range hazard ratios [HRs] 1.01-6.18; mean time to follow-up 9.9 ± 2.6 years); especially the brain MRI phenotype with mainly WMHs and atrophy showed a large increased risk (HR 6.18, 95% CI 3.37-11.32). DISCUSSION Distinct brain MRI phenotypes can be identified in community-dwelling older adults. Our results indicate that distinct brain MRI phenotypes are related to varying long-term risks of developing dementia. Brain MRI phenotypes may in the future assist in an improved understanding of the structural correlates of dementia predisposition.
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Affiliation(s)
- Jasmin Annica Keller
- From the Department of Radiology (J.A.K., B.S.A., M.A.V.B., M.J.P.v.O., J.d.B.), Leiden University Medical Center, the Netherlands; Icelandic Heart Association (S.S., V.G.), Kópavogur, Iceland; Clinical Artificial Intelligence Implementation and Research Lab (CAIRELab) and Department of Information Technology & Digital Innovation, Department of Digital Health (I.M.J.K.), University Medical Center Utrecht, the Netherlands; Laboratory of Epidemiology and Population Science (L.J.L.), National Institute on Aging, Bethesda, MD; and Faculty of Medicine (V.G.), University of Iceland, Reykjavik
| | - Sigurdur Sigurdsson
- From the Department of Radiology (J.A.K., B.S.A., M.A.V.B., M.J.P.v.O., J.d.B.), Leiden University Medical Center, the Netherlands; Icelandic Heart Association (S.S., V.G.), Kópavogur, Iceland; Clinical Artificial Intelligence Implementation and Research Lab (CAIRELab) and Department of Information Technology & Digital Innovation, Department of Digital Health (I.M.J.K.), University Medical Center Utrecht, the Netherlands; Laboratory of Epidemiology and Population Science (L.J.L.), National Institute on Aging, Bethesda, MD; and Faculty of Medicine (V.G.), University of Iceland, Reykjavik
| | - Bárbara Schmitz Abecassis
- From the Department of Radiology (J.A.K., B.S.A., M.A.V.B., M.J.P.v.O., J.d.B.), Leiden University Medical Center, the Netherlands; Icelandic Heart Association (S.S., V.G.), Kópavogur, Iceland; Clinical Artificial Intelligence Implementation and Research Lab (CAIRELab) and Department of Information Technology & Digital Innovation, Department of Digital Health (I.M.J.K.), University Medical Center Utrecht, the Netherlands; Laboratory of Epidemiology and Population Science (L.J.L.), National Institute on Aging, Bethesda, MD; and Faculty of Medicine (V.G.), University of Iceland, Reykjavik
| | - Ilse M J Kant
- From the Department of Radiology (J.A.K., B.S.A., M.A.V.B., M.J.P.v.O., J.d.B.), Leiden University Medical Center, the Netherlands; Icelandic Heart Association (S.S., V.G.), Kópavogur, Iceland; Clinical Artificial Intelligence Implementation and Research Lab (CAIRELab) and Department of Information Technology & Digital Innovation, Department of Digital Health (I.M.J.K.), University Medical Center Utrecht, the Netherlands; Laboratory of Epidemiology and Population Science (L.J.L.), National Institute on Aging, Bethesda, MD; and Faculty of Medicine (V.G.), University of Iceland, Reykjavik
| | - Mark A Van Buchem
- From the Department of Radiology (J.A.K., B.S.A., M.A.V.B., M.J.P.v.O., J.d.B.), Leiden University Medical Center, the Netherlands; Icelandic Heart Association (S.S., V.G.), Kópavogur, Iceland; Clinical Artificial Intelligence Implementation and Research Lab (CAIRELab) and Department of Information Technology & Digital Innovation, Department of Digital Health (I.M.J.K.), University Medical Center Utrecht, the Netherlands; Laboratory of Epidemiology and Population Science (L.J.L.), National Institute on Aging, Bethesda, MD; and Faculty of Medicine (V.G.), University of Iceland, Reykjavik
| | - Lenore J Launer
- From the Department of Radiology (J.A.K., B.S.A., M.A.V.B., M.J.P.v.O., J.d.B.), Leiden University Medical Center, the Netherlands; Icelandic Heart Association (S.S., V.G.), Kópavogur, Iceland; Clinical Artificial Intelligence Implementation and Research Lab (CAIRELab) and Department of Information Technology & Digital Innovation, Department of Digital Health (I.M.J.K.), University Medical Center Utrecht, the Netherlands; Laboratory of Epidemiology and Population Science (L.J.L.), National Institute on Aging, Bethesda, MD; and Faculty of Medicine (V.G.), University of Iceland, Reykjavik
| | - Matthias J P van Osch
- From the Department of Radiology (J.A.K., B.S.A., M.A.V.B., M.J.P.v.O., J.d.B.), Leiden University Medical Center, the Netherlands; Icelandic Heart Association (S.S., V.G.), Kópavogur, Iceland; Clinical Artificial Intelligence Implementation and Research Lab (CAIRELab) and Department of Information Technology & Digital Innovation, Department of Digital Health (I.M.J.K.), University Medical Center Utrecht, the Netherlands; Laboratory of Epidemiology and Population Science (L.J.L.), National Institute on Aging, Bethesda, MD; and Faculty of Medicine (V.G.), University of Iceland, Reykjavik
| | - Vilmundur Gudnason
- From the Department of Radiology (J.A.K., B.S.A., M.A.V.B., M.J.P.v.O., J.d.B.), Leiden University Medical Center, the Netherlands; Icelandic Heart Association (S.S., V.G.), Kópavogur, Iceland; Clinical Artificial Intelligence Implementation and Research Lab (CAIRELab) and Department of Information Technology & Digital Innovation, Department of Digital Health (I.M.J.K.), University Medical Center Utrecht, the Netherlands; Laboratory of Epidemiology and Population Science (L.J.L.), National Institute on Aging, Bethesda, MD; and Faculty of Medicine (V.G.), University of Iceland, Reykjavik
| | - Jeroen de Bresser
- From the Department of Radiology (J.A.K., B.S.A., M.A.V.B., M.J.P.v.O., J.d.B.), Leiden University Medical Center, the Netherlands; Icelandic Heart Association (S.S., V.G.), Kópavogur, Iceland; Clinical Artificial Intelligence Implementation and Research Lab (CAIRELab) and Department of Information Technology & Digital Innovation, Department of Digital Health (I.M.J.K.), University Medical Center Utrecht, the Netherlands; Laboratory of Epidemiology and Population Science (L.J.L.), National Institute on Aging, Bethesda, MD; and Faculty of Medicine (V.G.), University of Iceland, Reykjavik
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Shakyawar SK, Sajja BR, Patel JC, Guda C. iCluF: an unsupervised iterative cluster-fusion method for patient stratification using multiomics data. BIOINFORMATICS ADVANCES 2024; 4:vbae015. [PMID: 38698887 PMCID: PMC11063539 DOI: 10.1093/bioadv/vbae015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/10/2023] [Accepted: 01/26/2024] [Indexed: 05/05/2024]
Abstract
Motivation Patient stratification is crucial for the effective treatment or management of heterogeneous diseases, including cancers. Multiomic technologies facilitate molecular characterization of human diseases; however, the complexity of data warrants the need for the development of robust data integration tools for patient stratification using machine-learning approaches. Results iCluF iteratively integrates three types of multiomic data (mRNA, miRNA, and DNA methylation) using pairwise patient similarity matrices built from each omic data. The intermediate omic-specific neighborhood matrices implement iterative matrix fusion and message passing among the similarity matrices to derive a final integrated matrix representing all the omics profiles of a patient, which is used to further cluster patients into subtypes. iCluF outperforms other methods with significant differences in the survival profiles of 8581 patients belonging to 30 different cancers in TCGA. iCluF also predicted the four intrinsic subtypes of Breast Invasive Carcinomas with adjusted rand index and Fowlkes-Mallows scores of 0.72 and 0.83, respectively. The Gini importance score showed that methylation features were the primary decisive players, followed by mRNA and miRNA to identify disease subtypes. iCluF can be applied to stratify patients with any disease containing multiomic datasets. Availability and implementation Source code and datasets are available at https://github.com/GudaLab/iCluF_core.
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Affiliation(s)
- Sushil K Shakyawar
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, United States
| | - Balasrinivasa R Sajja
- Department of Radiology, University of Nebraska Medical Center, Omaha, NE 68198, United States
| | - Jai Chand Patel
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, United States
| | - Chittibabu Guda
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, United States
- Department of Genetics, Cell Biology and Anatomy, Center for Biomedical Informatics Research and Innovation, University of Nebraska Medical Center, Omaha, NE 68198-5805, United States
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Wang HC, Chan LP, Wu CC, Hsiao HH, Liu YC, Cho SF, Du JS, Liu TC, Yang CH, Pan MR, Moi SH. Progression Risk Score Estimation Based on Immunostaining Data in Oral Cancer Using Unsupervised Hierarchical Clustering Analysis: A Retrospective Study in Taiwan. J Pers Med 2021; 11:jpm11090908. [PMID: 34575686 PMCID: PMC8466609 DOI: 10.3390/jpm11090908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/09/2021] [Accepted: 09/10/2021] [Indexed: 11/16/2022] Open
Abstract
This study aimed to investigate whether the progression risk score (PRS) developed from cytoplasmic immunohistochemistry (IHC) biomarkers is available and applicable for assessing risk and prognosis in oral cancer patients. Participants in this retrospective case-control study were diagnosed between 2012 and 2014 and subsequently underwent surgical intervention. The specimens from surgery were stained by IHC for 16 cytoplasmic target markers. We evaluated the results of IHC staining, clinical and pathological features, progression-free survival (PFS), and overall survival (OS) of 102 oral cancer patients using a novel estimation approach with unsupervised hierarchical clustering analysis. Patients were stratified into high-risk (52) and low-risk (50) groups, according to their PRS; a metric consisting of cytoplasmic PLK1, PhosphoMet, SGK2, and SHC1 expression. Moreover, PRS could be extended for use in the Cox proportional hazard regression model to estimate survival outcomes with associated clinical parameters. Our study findings revealed that the high-risk patients had a significantly increased risk in cancer progression compared with low-risk patients (hazard ratio (HR) = 2.20, 95% confidence interval (CI) = 1.10-2.42, p = 0.026). After considering the influences of demographics, risk behaviors, and tumor characteristics, risk estimation with PRS provided distinct PFS groups for patients with oral cancer (p = 0.017, p = 0.019, and p = 0.020). Our findings support that PRS could serve as an ideal biomarker for clinical use in risk stratification and progression assessment in oral cancer.
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Affiliation(s)
- Hui-Ching Wang
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (H.-C.W.); (J.-S.D.); (M.-R.P.)
- Department of Internal Medicine, Division of Hematology and Oncology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (H.-H.H.); (Y.-C.L.); (S.-F.C.)
- Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
| | - Leong-Perng Chan
- Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
- Department of Otolaryngology-Head and Neck Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department of Otorhinolaryngology-Head and Neck Surgery, Kaohsiung Municipal Ta-Tung Hospital and Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
| | - Chun-Chieh Wu
- Department of Pathology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
| | - Hui-Hua Hsiao
- Department of Internal Medicine, Division of Hematology and Oncology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (H.-H.H.); (Y.-C.L.); (S.-F.C.)
- Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
| | - Yi-Chang Liu
- Department of Internal Medicine, Division of Hematology and Oncology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (H.-H.H.); (Y.-C.L.); (S.-F.C.)
- Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
| | - Shih-Feng Cho
- Department of Internal Medicine, Division of Hematology and Oncology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (H.-H.H.); (Y.-C.L.); (S.-F.C.)
- Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
| | - Jeng-Shiun Du
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (H.-C.W.); (J.-S.D.); (M.-R.P.)
- Department of Internal Medicine, Division of Hematology and Oncology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (H.-H.H.); (Y.-C.L.); (S.-F.C.)
- Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
| | - Ta-Chih Liu
- Department of Hematology-Oncology, Chang Bing Show Chwan Memorial Hospital, Changhua 505, Taiwan;
| | - Cheng-Hong Yang
- Department of Electronic Engineering, National Kaohsiung University of Science and Technology, Kaohsiung 807, Taiwan;
- Ph.D. Program in Biomedical Engineering, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Mei-Ren Pan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan; (H.-C.W.); (J.-S.D.); (M.-R.P.)
- Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Sin-Hua Moi
- Center of Cancer Program Development, E-Da Cancer Hospital, I-Shou University, Kaohsiung 807, Taiwan
- Correspondence: ; Tel.: +886-7-6150022 (ext. 6135); Fax: +886-7-6150940
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Phenomapping of Patients with Primary Breast Cancer Using Machine Learning-Based Unsupervised Cluster Analysis. J Pers Med 2021; 11:jpm11040272. [PMID: 33916398 PMCID: PMC8067194 DOI: 10.3390/jpm11040272] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 03/23/2021] [Accepted: 04/01/2021] [Indexed: 12/15/2022] Open
Abstract
Primary breast cancer (PBC) is a heterogeneous disease at the clinical, histopathological, and molecular levels. The improved classification of PBC might be important to identify subgroups of the disease, relevant to patient management. Machine learning algorithms may allow a better understanding of the relationships within heterogeneous clinical syndromes. This work aims to show the potential of unsupervised learning techniques for improving classification in PBC. A dataset of 712 women with PBC is used as a motivating example. A set of variables containing biological prognostic parameters is considered to define groups of individuals. Four different clustering methods are used: K-means, self-organising maps, hierarchical agglomerative (HAC), and Gaussian mixture models clustering. HAC outperforms the other clustering methods. With an optimal partitioning parameter, the methods identify two clusters with different clinical profiles. Patients in the first cluster are younger and have lower values of the oestrogen receptor (ER) and progesterone receptor (PgR) than patients in the second cluster. Moreover, cathepsin D values are lower in the first cluster. The three most important variables identified by the HAC are: age, ER, and PgR. Unsupervised learning seems a suitable alternative for the analysis of PBC data, opening up new perspectives in the particularly active domain of dissecting clinical heterogeneity.
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Luo C, Huang J, Guo Z, Guo J, Zeng X, Li Y, Liu M. Methylated biomarkers for breast cancer identified through public database analysis and plasma target capture sequencing. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:683. [PMID: 33987381 PMCID: PMC8106113 DOI: 10.21037/atm-21-1128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Background Aberrant methylation is common during the early stage of cancer development. This study was designed to investigate DNA methylation as biomarker for breast cancer. Methods Public database analysis and methylation-specific whole-gene sequencing were conducted to identify methylated biomarkers that would enable early non-invasive diagnosis of breast cancer. Firstly, the data was obtained from the TCGA Database and the Blueprint Epigenome Database. Secondly, methylation-specific whole-gene sequencing was conducted in 10 female patients with early-stage breast cancer and 10 healthy female volunteers from Nanfang Hospital of Southern Medical University between March 2018 and July 2018. Thirdly, the R language was used for data analysis, and KEGG and DAVID online tool was used for annotations. Results We found that methylation levels at 13 cytosine-phosphate-guanine (CpG) sites (cg04066177, cg04281344, cg05995576, cg06221609, cg08642731, cg11388802, cg12665414, cg14557216, cg19404723, cg19457909, cg24570211, cg25818763, and cg26215982) in the malignant tissue DNA were highly comparable to those of circulating cell-free DNA (cfDNA) of breast cancer patients, but were significantly different from those of normal tissue DNA, cfDNA of healthy women, and leukocyte DNA. In addition, three CpG sites (cg04281344, cg24570211, and cg26215982) were confirmed in clinical research, which showed that the sensitivity and specificity of these CpGs as biomarkers for breast cancer were 69.4–83.7% and 85.7–88.6%, respectively. Conclusions New biomarkers were identified and confirmed for breast cancer by comparing the methylation of tumour tissues, leukocytes, and non-plasma DNA.
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Affiliation(s)
- Can Luo
- Breast Center, Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jiaheng Huang
- Department of Surgery, First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Zhaoze Guo
- Breast Center, Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jingyun Guo
- Breast Center, Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xiaoqi Zeng
- Breast Center, Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yimin Li
- General Surgery, Yangjiang Hospital, Qiongzhong, China
| | - Minfeng Liu
- Breast Center, Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, China
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Uhrig S, Ellermann J, Walther T, Burkhardt P, Fröhlich M, Hutter B, Toprak UH, Neumann O, Stenzinger A, Scholl C, Fröhling S, Brors B. Accurate and efficient detection of gene fusions from RNA sequencing data. Genome Res 2021; 31:448-460. [PMID: 33441414 PMCID: PMC7919457 DOI: 10.1101/gr.257246.119] [Citation(s) in RCA: 200] [Impact Index Per Article: 66.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 12/30/2020] [Indexed: 12/17/2022]
Abstract
The identification of gene fusions from RNA sequencing data is a routine task in cancer research and precision oncology. However, despite the availability of many computational tools, fusion detection remains challenging. Existing methods suffer from poor prediction accuracy and are computationally demanding. We developed Arriba, a novel fusion detection algorithm with high sensitivity and short runtime. When applied to a large collection of published pancreatic cancer samples (n = 803), Arriba identified a variety of driver fusions, many of which affected druggable proteins, including ALK, BRAF, FGFR2, NRG1, NTRK1, NTRK3, RET, and ROS1. The fusions were significantly associated with KRAS wild-type tumors and involved proteins stimulating the MAPK signaling pathway, suggesting that they substitute for activating mutations in KRAS In addition, we confirmed the transforming potential of two novel fusions, RRBP1-RAF1 and RASGRP1-ATP1A1, in cellular assays. These results show Arriba's utility in both basic cancer research and clinical translation.
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Affiliation(s)
- Sebastian Uhrig
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT) Heidelberg, 69120 Heidelberg, Germany
- Computational Oncology Group, Molecular Diagnostics Program at the NCT and DKFZ, 69120 Heidelberg, Germany
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Julia Ellermann
- Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
- Division of Translational Medical Oncology, NCT Heidelberg and DKFZ, 69120 Heidelberg, Germany
| | - Tatjana Walther
- Division of Translational Medical Oncology, NCT Heidelberg and DKFZ, 69120 Heidelberg, Germany
| | - Pauline Burkhardt
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT) Heidelberg, 69120 Heidelberg, Germany
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Martina Fröhlich
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT) Heidelberg, 69120 Heidelberg, Germany
- Computational Oncology Group, Molecular Diagnostics Program at the NCT and DKFZ, 69120 Heidelberg, Germany
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Barbara Hutter
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT) Heidelberg, 69120 Heidelberg, Germany
- Computational Oncology Group, Molecular Diagnostics Program at the NCT and DKFZ, 69120 Heidelberg, Germany
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Umut H Toprak
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
- Division of Neuroblastoma Genomics, DKFZ, 69120 Heidelberg, Germany
| | - Olaf Neumann
- Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Albrecht Stenzinger
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
- Institute of Pathology, University Hospital Heidelberg, 69120 Heidelberg, Germany
- German Center for Lung Research (DZL), Heidelberg site, 69120 Heidelberg, Germany
| | - Claudia Scholl
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
- Division of Applied Functional Genomics, DKFZ and NCT Heidelberg, 69120 Heidelberg, Germany
| | - Stefan Fröhling
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
- Division of Translational Medical Oncology, NCT Heidelberg and DKFZ, 69120 Heidelberg, Germany
- NCT Molecular Diagnostics Program, NCT Heidelberg and DKFZ, 69120 Heidelberg, Germany
| | - Benedikt Brors
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT) Heidelberg, 69120 Heidelberg, Germany
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
- NCT Molecular Diagnostics Program, NCT Heidelberg and DKFZ, 69120 Heidelberg, Germany
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8
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Lu H, Shi C, Liu X, Liang C, Yang C, Wan X, Li L, Liu Y. Identification of ZG16B as a prognostic biomarker in breast cancer. Open Med (Wars) 2020; 16:1-13. [PMID: 33336077 PMCID: PMC7718615 DOI: 10.1515/med-2021-0004] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/01/2020] [Accepted: 10/14/2020] [Indexed: 02/06/2023] Open
Abstract
Zymogen granule protein 16B (ZG16B) has been identified in various cancers, while so far the association between ZG16B and breast cancer hasn’t been explored. Our aim is to confirm whether it can serve as a prognostic biomarker in breast cancer. In this study, Oncomine, Cancer Cell Line Encyclopedia (CCLE), Ualcan, and STRING database analyses were conducted to detect the expression level of ZG16B in breast cancer with different types. Kaplan–Meier plotter was used to analyze the prognosis of patients with high or low expression of ZG16B. We found that ZG16B was significantly upregulated in breast cancer. Moreover, ZG16B was closely associated with foregone biomarkers and crucial factors in breast cancer. In the survival analysis, high expression of ZG16B represents a favorable prognosis in patients. Our work demonstrates the latent capacity of ZG16B to be a biomarker for prognosis of breast cancer.
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Affiliation(s)
- Haotian Lu
- School of Basic Medicine, College of Medicine, Qingdao University, Qingdao, 266071, China
| | - Chunying Shi
- Department of Human Anatomy, Histology and Embryology, School of Basic Medicine, College of Medicine, Qingdao University, Qingdao, 266071, China
| | - Xinyu Liu
- School of Basic Medicine, College of Medicine, Qingdao University, Qingdao, 266071, China
| | - Chen Liang
- School of Basic Medicine, College of Medicine, Qingdao University, Qingdao, 266071, China
| | - Chaochao Yang
- School of Basic Medicine, College of Medicine, Qingdao University, Qingdao, 266071, China
| | - Xueqi Wan
- School of Basic Medicine, College of Medicine, Qingdao University, Qingdao, 266071, China
| | - Ling Li
- Department of Human Anatomy, Histology and Embryology, School of Basic Medicine, College of Medicine, Qingdao University, Qingdao, 266071, China
| | - Ying Liu
- School of Basic Medicine, College of Medicine, Qingdao University, Qingdao, 266071, China.,Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, 266071, China
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9
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Zhang Y, Wang P, Li X, Ning S, Li X, Cao Y, Chen SX. GABC: A comprehensive resource and Genome Atlas for Breast Cancer. Int J Cancer 2020; 148:988-994. [PMID: 33064305 DOI: 10.1002/ijc.33347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 09/07/2020] [Accepted: 09/14/2020] [Indexed: 11/09/2022]
Abstract
We developed the Genome Atlas of Breast Cancer (GABC), a global map of noncoding events in the human genome associated with breast cancer that provides a valuable reference resource for users to investigate the underlying genome abnormalities in breast cancer patients. Although significant progress has been made in breast cancer treatment, its morbidity and recurrence rates in women are still high worldwide. Curation and integration of breast cancer-related dysregulations from multiple aspects is essential for disease prevention and diagnosis. In this study, we developed the GABC, which contains 10 172 aberrant noncoding events occurring at multiomics levels, including the genome (single nucleotide polymorphism and somatic mutation), transcriptome (long noncoding RNA and microRNA) and epigenome (DNA methylation, enhancer and superenhancer). Each event entry provides descriptions of detailed biological mechanisms specific to the region or element. Users can also check the genome locations and relationships of functional regulators. The GABC provides a flexible and user-friendly interface for users to search, browse and download data. In addition, the GABC provides an interface to submit newly discovered noncoding events that can be included in the database. Therefore, the GABC aims to constantly enhance our understanding of noncoding genomic events in breast cancer.
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Affiliation(s)
- Yunpeng Zhang
- Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, Florida, USA.,Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida, USA.,College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Peng Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Xin Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Shangwei Ning
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Xia Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yan Cao
- Department of Urology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Steven Xi Chen
- Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, Florida, USA.,Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida, USA
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10
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Jaarsma-Coes MG, Ghaznawi R, Hendrikse J, Slump C, Witkamp TD, van der Graaf Y, Geerlings MI, de Bresser J. MRI phenotypes of the brain are related to future stroke and mortality in patients with manifest arterial disease: The SMART-MR study. J Cereb Blood Flow Metab 2020; 40:354-364. [PMID: 30547694 PMCID: PMC6985990 DOI: 10.1177/0271678x18818918] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Neurodegenerative and neurovascular diseases lead to heterogeneous brain abnormalities. A combined analysis of these abnormalities by phenotypes of the brain might give a more accurate representation of the underlying aetiology. We aimed to identify different MRI phenotypes of the brain and assessed the risk of future stroke and mortality within these subgroups. In 1003 patients (59 ± 10 years) from the Second Manifestations of ARTerial disease-Magnetic Resonance (SMART-MR) study, different quantitative 1.5T brain MRI markers were used in a hierarchical clustering analysis to identify 11 distinct subgroups with a different distribution in brain MRI markers and cardiovascular risk factors, and a different risk of stroke (Cox regression: from no increased risk compared to the reference group with relatively few brain abnormalities to HR = 10.34; 95% CI 3.80↔28.12 for the multi-burden subgroup) and mortality (from no increased risk compared to the reference group to HR = 4.00; 95% CI 2.50↔6.40 for the multi-burden subgroup). In conclusion, within a group of patients with manifest arterial disease, we showed that different MRI phenotypes of the brain can be identified and that these were associated with different risks of future stroke and mortality. These MRI phenotypes can possibly classify individual patients and assess their risk of future stroke and mortality.
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Affiliation(s)
- Myriam G Jaarsma-Coes
- Department of Radiology, University Medical Center Utrecht, and Utrecht University, Utrecht, The Netherlands.,MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, Enschede, The Netherlands.,Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Rashid Ghaznawi
- Department of Radiology, University Medical Center Utrecht, and Utrecht University, Utrecht, The Netherlands.,Julius Center for Health Sciences and Primary Care, Department of Epidemiology, University Medical Center Utrecht, and Utrecht University, Utrecht, the Netherlands
| | - Jeroen Hendrikse
- Department of Radiology, University Medical Center Utrecht, and Utrecht University, Utrecht, The Netherlands
| | - Cornelis Slump
- MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, Enschede, The Netherlands
| | - Theo D Witkamp
- Department of Radiology, University Medical Center Utrecht, and Utrecht University, Utrecht, The Netherlands
| | - Yolanda van der Graaf
- Julius Center for Health Sciences and Primary Care, Department of Epidemiology, University Medical Center Utrecht, and Utrecht University, Utrecht, the Netherlands
| | - Mirjam I Geerlings
- Julius Center for Health Sciences and Primary Care, Department of Epidemiology, University Medical Center Utrecht, and Utrecht University, Utrecht, the Netherlands
| | - Jeroen de Bresser
- Department of Radiology, University Medical Center Utrecht, and Utrecht University, Utrecht, The Netherlands.,Department of Radiology, Leiden University Medical Center, Leiden, The Netherlands
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11
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Lv P, Yang S, Liu W, Qin H, Tang X, Wu F, Liu Z, Gao H, Liu X. Circulating plasma lncRNAs as novel markers of EGFR mutation status and monitors of epidermal growth factor receptor-tyrosine kinase inhibitor therapy. Thorac Cancer 2019; 11:29-40. [PMID: 31691525 PMCID: PMC6938758 DOI: 10.1111/1759-7714.13216] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 09/20/2019] [Accepted: 09/22/2019] [Indexed: 12/23/2022] Open
Abstract
Background Epidermal growth factor receptor (EGFR) gene mutations predict tumor response to EGFR tyrosine kinase inhibitors (EGFR‐TKIs) in non‐small cell lung cancer (NSCLC). However, even patients with EGFR‐sensitive mutations in NSCLC have limited efficacy with EGFR‐TKI. Studies have shown that long noncoding RNA (lncRNA) is related to diagnosis and prognosis with NSCLC. This study aimed to explore the correlation between lncRNA in NSCLC patients with EGFR mutation status and EGFR‐TKI efficacy. Methods The amplification‐refractory mutation system method was used to test the EGFR mutation status in tumor tissues and pleural effusions of NSCLC patients. Three EGFR‐mutant patients and three EGFR wild‐type patients were selected. Differential lncRNA was performed on the pleural effusions of the two selected groups of patients using Clariom D Human chip technology. Five lncRNAs significantly associated with EGFR mutation status were screened by FC value and GO analysis, and then evaluated by real‐time quantitative polymerase chain reaction in NSCLC patients' pleural effusions. Three were further analyzed in NSCLC patients' plasma. Results There were 61 significant differences in lncRNA between EGFR mutation‐positive and wild‐type patients. Among them, SCARNA7, MALAT1, NONHSAT017369, NONHSAT051892, and FTH1P2 were significantly associated with EGFR mutation status. SCARNA7, MALAT1, and NONHSAT017369 showed consistent results with plasma in pleural effusions compared to EGFR wild‐type, all upregulated in the EGFR mutation group. Conclusion This study shows that lncRNAs can be used not only as potential biomarkers for predicting the mutation status of EGFR and the efficacy of EGFR‐TKI, but also for monitoring the efficacy of EGFR‐TKI.
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Affiliation(s)
- Panpan Lv
- Academy of Military Medical Science, Beijing, China.,PLA Rocket Force Characteristic Medical Center, Beijing, China
| | - Shaoxing Yang
- Department of Pulmonary Oncology, The Fifth Medical Centre, Chinese PLA General Hospital, Beijing, China
| | - Wenjing Liu
- Department of Pulmonary Oncology, The Fifth Medical Centre, Chinese PLA General Hospital, Beijing, China
| | - Haifeng Qin
- Department of Pulmonary Oncology, The Fifth Medical Centre, Chinese PLA General Hospital, Beijing, China
| | - Xiuhua Tang
- Department of Pulmonary Oncology, The Fifth Medical Centre, Chinese PLA General Hospital, Beijing, China
| | - Fangfang Wu
- Department of Pulmonary Oncology, The Fifth Medical Centre, Chinese PLA General Hospital, Beijing, China
| | - Zeyuan Liu
- Department of Pulmonary Oncology, The Fifth Medical Centre, Chinese PLA General Hospital, Beijing, China
| | - Hongjun Gao
- Department of Pulmonary Oncology, The Fifth Medical Centre, Chinese PLA General Hospital, Beijing, China
| | - Xiaoqing Liu
- Department of Pulmonary Oncology, The Fifth Medical Centre, Chinese PLA General Hospital, Beijing, China
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12
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Chen J, Haanpää MK, Gruber JJ, Jäger N, Ford JM, Snyder MP. High-Resolution Bisulfite-Sequencing of Peripheral Blood DNA Methylation in Early-Onset and Familial Risk Breast Cancer Patients. Clin Cancer Res 2019; 25:5301-5314. [PMID: 31175093 DOI: 10.1158/1078-0432.ccr-18-2423] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 04/11/2019] [Accepted: 06/05/2019] [Indexed: 12/14/2022]
Abstract
PURPOSE Understanding and explaining hereditary predisposition to cancer has focused on the genetic etiology of the disease. However, mutations in known genes associated with breast cancer, such as BRCA1 and BRCA2, account for less than 25% of familial cases of breast cancer. Recently, specific epigenetic modifications at BRCA1 have been shown to promote hereditary breast cancer, but the broader potential for epigenetic contribution to hereditary breast cancer is not yet well understood. EXPERIMENTAL DESIGN We examined DNA methylation through deep bisulfite sequencing of CpG islands and known promoter or regulatory regions in peripheral blood DNA from 99 patients with familial or early-onset breast or ovarian cancer, 6 unaffected BRCA mutation carriers, and 49 unaffected controls. RESULTS In 9% of patients, we observed altered methylation in the promoter regions of genes known to be involved in cancer, including hypermethylation at the tumor suppressor PTEN and hypomethylation at the proto-oncogene TEX14. These alterations occur in the form of allelic methylation that span up to hundreds of base pairs in length. CONCLUSIONS Our observations suggest a broader role for DNA methylation in early-onset, familial risk breast cancer. Further studies are warranted to clarify these mechanisms and the benefits of DNA methylation screening for early risk prediction of familial cancers.
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Affiliation(s)
- Justin Chen
- Department of Genetics, Stanford University, Stanford, California
| | - Maria K Haanpää
- Department of Medicine, Oncology Division, Stanford University, Stanford, California
| | - Joshua J Gruber
- Department of Genetics, Stanford University, Stanford, California.,Department of Medicine, Oncology Division, Stanford University, Stanford, California
| | - Natalie Jäger
- Department of Genetics, Stanford University, Stanford, California
| | - James M Ford
- Department of Genetics, Stanford University, Stanford, California. .,Department of Medicine, Oncology Division, Stanford University, Stanford, California
| | - Michael P Snyder
- Department of Genetics, Stanford University, Stanford, California.
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13
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Lima EU, Rubio IGS, Da Silva JC, Galrão AL, Pêssoa D, Oliveira TC, Carrijo F, Silva Campos I, Fonseca Espinheira L, Sampaio LJ, Lima CR, Cerutti JM, Ramos HE. HOPX homeobox methylation in differentiated thyroid cancer and its clinical relevance. Endocr Connect 2018; 7:1333-1342. [PMID: 30400039 PMCID: PMC6280589 DOI: 10.1530/ec-18-0380] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 10/24/2018] [Indexed: 12/29/2022]
Abstract
BACKGROUND The inactivation of the tumor-suppressor homeodomain-only protein X (HOPX) usually involves promoter methylation in several cancer types. This study aimed to investigate the HOPX-β mRNA expression and promoter methylation and their clinical relevance in differentiated thyroid cancer (DTC). PATIENTS AND METHODS Clinicopathological data and paraffin-embedded thyroid tumor tissues from 21 patients with DTC and 6 with benign tumors (T) and their non-tumor parenchyma (NT) were investigated. Tumor cell lines (FTC238, FTC236 and WRO) were treated with demethylating agent. HOPX-β mRNA expression was assessed by qRT-PCR and methylation status by Q-MSP. Thyroid cancer data from Cancer Genome Atlas (TCGA) was also collected. RESULTS HOPX-β mRNA re-expression in two cell lines treated with demethylating agent was observed concomitantly with reduced promoter methylation. Reduced mRNA expression in T group compared to their NT was observed, and reduced protein expression in T compared to NT was observed in three cases. Low mRNA expression with high methylation status was detected in 6/14 DTC samples. High methylation status was associated with older age at diagnosis, recurrent or progressive disease and with the presence of new neoplasm event post initial therapy while hyper-methylation correlated with worse overall survival, worse disease-free status and older age. CONCLUSION A moderate coupling of downregulation of HOPX-β mRNA expression in DTC followed by high HOPX-β promoter methylation was observed however; high HOPX promoter methylation status was associated with the worse prognosis of DTC patients.
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Affiliation(s)
- Erika Urbano Lima
- Biological Science Department, Thyroid Molecular Sciences Laboratory, Universidade Federal de São Paulo, São Paulo, Brazil
- Structural and Functional Biology Program, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Ileana G S Rubio
- Biological Science Department, Thyroid Molecular Sciences Laboratory, Universidade Federal de São Paulo, São Paulo, Brazil
- Structural and Functional Biology Program, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Joaquim Custodio Da Silva
- Department of Bio-regulation, Thyroid Study Laboratory, Health & Science Institute, Federal University of Bahia, Salvador, Brazil
- Post-graduate Program in Interactive Processes of Organs and Systems, Health & Science Institute, Federal University of Bahia, Salvador, Brazil
| | - Ana Luiza Galrão
- Biological Science Department, Thyroid Molecular Sciences Laboratory, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Danielle Pêssoa
- Department of Bio-regulation, Thyroid Study Laboratory, Health & Science Institute, Federal University of Bahia, Salvador, Brazil
- Post-graduate Program in Interactive Processes of Organs and Systems, Health & Science Institute, Federal University of Bahia, Salvador, Brazil
| | - Taise Cerqueira Oliveira
- Department of Bio-regulation, Thyroid Study Laboratory, Health & Science Institute, Federal University of Bahia, Salvador, Brazil
| | - Fabiane Carrijo
- Department of Bio-regulation, Thyroid Study Laboratory, Health & Science Institute, Federal University of Bahia, Salvador, Brazil
- Post-graduate Program in Interactive Processes of Organs and Systems, Health & Science Institute, Federal University of Bahia, Salvador, Brazil
| | | | - Luciano Fonseca Espinheira
- Department of Pathology, Sao Rafael Hospital, Salvador, Brazil
- Department of Anatomic Pathology & Legal Medicine, Bahia Federal Medical School, Federal University of Bahia, Salvador, Brazil
| | | | | | - Janete Maria Cerutti
- Structural and Functional Biology Program, Universidade Federal de São Paulo, São Paulo, Brazil
- Division of Genetics, Department of Morphology and Genetics, Genetic Basis of Thyroid Tumors Laboratory, Paulista School of Medicine, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Helton Estrela Ramos
- Department of Bio-regulation, Thyroid Study Laboratory, Health & Science Institute, Federal University of Bahia, Salvador, Brazil
- Post-graduate Program in Interactive Processes of Organs and Systems, Health & Science Institute, Federal University of Bahia, Salvador, Brazil
- Correspondence should be addressed to H E Ramos:
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14
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Salhab A, Nordström K, Gasparoni G, Kattler K, Ebert P, Ramirez F, Arrigoni L, Müller F, Polansky JK, Cadenas C, G Hengstler J, Lengauer T, Manke T, Walter J. A comprehensive analysis of 195 DNA methylomes reveals shared and cell-specific features of partially methylated domains. Genome Biol 2018; 19:150. [PMID: 30266094 PMCID: PMC6161375 DOI: 10.1186/s13059-018-1510-5] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 08/20/2018] [Indexed: 12/12/2022] Open
Abstract
Background Partially methylated domains are extended regions in the genome exhibiting a reduced average DNA methylation level. They cover gene-poor and transcriptionally inactive regions and tend to be heterochromatic. We present a comprehensive comparative analysis of partially methylated domains in human and mouse cells, to identify structural and functional features associated with them. Results Partially methylated domains are present in up to 75% of the genome in human and mouse cells irrespective of their tissue or cell origin. Each cell type has a distinct set of partially methylated domains, and genes expressed in such domains show a strong cell type effect. The methylation level varies between cell types with a more pronounced effect in differentiating and replicating cells. The lowest level of methylation is observed in highly proliferating and immortal cancer cell lines. A decrease of DNA methylation within partially methylated domains tends to be linked to an increase in heterochromatic histone marks and a decrease of gene expression. Characteristic combinations of heterochromatic signatures in partially methylated domains are linked to domains of early and middle S-phase and late S-G2 phases of DNA replication. Conclusions Partially methylated domains are prominent signatures of long-range epigenomic organization. Integrative analysis identifies them as important general, lineage- and cell type-specific topological features. Changes in partially methylated domains are hallmarks of cell differentiation, with decreased methylation levels and increased heterochromatic marks being linked to enhanced cell proliferation. In combination with broad histone marks, partially methylated domains demarcate distinct domains of late DNA replication. Electronic supplementary material The online version of this article (10.1186/s13059-018-1510-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Abdulrahman Salhab
- Department of Genetics, Saarland University, Campus Saarbrücken, Saarbrücken, 66123, Germany
| | - Karl Nordström
- Department of Genetics, Saarland University, Campus Saarbrücken, Saarbrücken, 66123, Germany
| | - Gilles Gasparoni
- Department of Genetics, Saarland University, Campus Saarbrücken, Saarbrücken, 66123, Germany
| | - Kathrin Kattler
- Department of Genetics, Saarland University, Campus Saarbrücken, Saarbrücken, 66123, Germany
| | - Peter Ebert
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, 66123, Germany
| | - Fidel Ramirez
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, 79108, Germany
| | - Laura Arrigoni
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, 79108, Germany
| | - Fabian Müller
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, 66123, Germany
| | - Julia K Polansky
- Berlin-Brandenburg Center for Regenerative Therapies at the Charité, Berlin, Germany.,University Medicine Berlin and German Rheumatism Research Centre, Berlin, Germany
| | - Cristina Cadenas
- Leibniz Research Center for working Environment and Human Factors IfADo, Dortmund, 44139, Germany
| | - Jan G Hengstler
- Leibniz Research Center for working Environment and Human Factors IfADo, Dortmund, 44139, Germany
| | - Thomas Lengauer
- Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrücken, 66123, Germany
| | - Thomas Manke
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, 79108, Germany
| | | | - Jörn Walter
- Department of Genetics, Saarland University, Campus Saarbrücken, Saarbrücken, 66123, Germany.
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15
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Kalinkova L, Zmetakova I, Smolkova B, Minarik G, Sedlackova T, Horvathova Kajabova V, Cierna Z, Mego M, Fridrichova I. Decreased methylation in the SNAI2 and ADAM23 genes associated with de-differentiation and haematogenous dissemination in breast cancers. BMC Cancer 2018; 18:875. [PMID: 30189837 PMCID: PMC6127923 DOI: 10.1186/s12885-018-4783-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 08/29/2018] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND In breast cancer (BC), deregulation of DNA methylation leads to aberrant expressions and functions of key regulatory genes. In our study, we investigated the relationship between the methylation profiles of genes associated with cancer invasivity and clinico-pathological parameters. In detail, we studied differences in the methylation levels between BC patients with haematogenous and lymphogenous cancer dissemination. METHODS We analysed samples of primary tumours (PTs), lymph node metastases (LNMs) and peripheral blood cells (PBCs) from 59 patients with sporadic disseminated BC. Evaluation of the DNA methylation levels of six genes related to invasivity, ADAM23, uPA, CXCL12, TWIST1, SNAI1 and SNAI2, was performed by pyrosequencing. RESULTS Among the cancer-specific methylated genes, we found lower methylation levels of the SNAI2 gene in histologic grade 3 tumours (OR = 0.61; 95% CI, 0.39-0.97; P = 0.038) than in fully or moderately differentiated cancers. We also evaluated the methylation profiles in patients with different cancer cell dissemination statuses (positivity for circulating tumour cells (CTCs) and/or LNMs). We detected the significant association between reduced DNA methylation of ADAM23 in PTs and presence of CTCs in the peripheral blood of patients (OR = 0.45; 95% CI, 0.23-0.90; P = 0.023). CONCLUSION The relationships between the decreased methylation levels of the SNAI2 and ADAM23 genes and cancer de-differentiation and haematogenous dissemination, respectively, indicate novel functions of those genes in the invasive processes. After experimental validation of the association between the lower values of SNAI2 and ADAM23 methylation and clinical features of aggressive BCs, these methylation profiles could improve the management of metastatic disease.
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Affiliation(s)
- Lenka Kalinkova
- Department of Genetics, Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, v.v.i., Dubravska cesta 9, 845 05, Bratislava, Slovak Republic
| | - Iveta Zmetakova
- Department of Genetics, Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, v.v.i., Dubravska cesta 9, 845 05, Bratislava, Slovak Republic
| | - Bozena Smolkova
- Department of Genetics, Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, v.v.i., Dubravska cesta 9, 845 05, Bratislava, Slovak Republic
| | - Gabriel Minarik
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, Sasinkova 4, 811 08, Bratislava, Slovak Republic
| | - Tatiana Sedlackova
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, Sasinkova 4, 811 08, Bratislava, Slovak Republic
| | - Viera Horvathova Kajabova
- Department of Genetics, Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, v.v.i., Dubravska cesta 9, 845 05, Bratislava, Slovak Republic
| | - Zuzana Cierna
- Institute of Pathological Anatomy, Faculty of Medicine, Comenius University, University Hospital, Sasinkova 4, 811 08, Bratislava, Slovak Republic
| | - Michal Mego
- 2nd Department of Oncology, Faculty of Medicine, Comenius University, National Cancer Institute, Klenova 1, 83310, Bratislava, Slovak Republic
| | - Ivana Fridrichova
- Department of Genetics, Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, v.v.i., Dubravska cesta 9, 845 05, Bratislava, Slovak Republic.
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16
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Croes L, Beyens M, Fransen E, Ibrahim J, Vanden Berghe W, Suls A, Peeters M, Pauwels P, Van Camp G, Op de Beeck K. Large-scale analysis of DFNA5 methylation reveals its potential as biomarker for breast cancer. Clin Epigenetics 2018; 10:51. [PMID: 29682089 PMCID: PMC5896072 DOI: 10.1186/s13148-018-0479-y] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 03/26/2018] [Indexed: 12/17/2022] Open
Abstract
Background Breast cancer is the most frequent cancer among women worldwide. Biomarkers for early detection and prognosis of these patients are needed. We hypothesized that deafness, autosomal dominant 5 (DFNA5) may be a valuable biomarker, based upon strong indications for its role as tumor suppressor gene and its function in regulated cell death. In this study, we aimed to analyze DFNA5 methylation and expression in the largest breast cancer cohort to date using publicly available data from TCGA, in order to further unravel the role of DFNA5 as detection and/or prognostic marker in breast cancer. We analyzed Infinium HumanMethylation450k data, covering 22 different CpGs in the DFNA5 gene (668 breast adenocarcinomas and 85 normal breast samples) and DFNA5 expression (Agilent 244K Custom Gene Expression: 476 breast adenocarcinomas and 56 normal breast samples; RNA-sequencing: 666 breast adenocarcinomas and 71 normal breast samples). Results DFNA5 methylation and expression were significantly different between breast cancer and normal breast samples. Overall, breast cancer samples showed higher DFNA5 methylation in the putative gene promoter compared to normal breast samples, whereas in the gene body and upstream of the putative gene promoter, the opposite is true. Furthermore, DFNA5 methylation, in 10 out of 22 CpGs, and expression were significantly higher in lobular compared to ductal breast cancers. An important result of this study was the identification of a combination of one CpG in the gene promoter (CpG07504598) and one CpG in the gene body (CpG12922093) of DFNA5, which was able to discriminate between breast cancer and normal breast samples (AUC = 0.93). This model was externally validated in three independent datasets. Moreover, we showed that estrogen receptor state is associated with DFNA5 methylation and expression. Finally, we were able to find a significant effect of DFNA5 gene body methylation on a 5-year overall survival time. Conclusions We conclude that DFNA5 methylation shows strong potential as detection and prognostic biomarker for breast cancer.
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Affiliation(s)
- Lieselot Croes
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Prins Boudewijnlaan 43/6, BE-2650 Edegem, Antwerp Belgium.,Center for Oncological Research, University of Antwerp and Antwerp University Hospital, Universiteitsplein 1, BE-2610 Wilrijk, Antwerp Belgium
| | - Matthias Beyens
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Prins Boudewijnlaan 43/6, BE-2650 Edegem, Antwerp Belgium.,Center for Oncological Research, University of Antwerp and Antwerp University Hospital, Universiteitsplein 1, BE-2610 Wilrijk, Antwerp Belgium
| | - Erik Fransen
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Prins Boudewijnlaan 43/6, BE-2650 Edegem, Antwerp Belgium.,3StatUa Center for Statistics, University of Antwerp, Prinsstraat 13, BE-2000 Antwerp, Belgium
| | - Joe Ibrahim
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Prins Boudewijnlaan 43/6, BE-2650 Edegem, Antwerp Belgium.,Center for Oncological Research, University of Antwerp and Antwerp University Hospital, Universiteitsplein 1, BE-2610 Wilrijk, Antwerp Belgium
| | - Wim Vanden Berghe
- 4Laboratory of Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), University of Antwerp, Universiteitsplein 1, BE-2610 Wilrijk, Antwerp Belgium
| | - Arvid Suls
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Prins Boudewijnlaan 43/6, BE-2650 Edegem, Antwerp Belgium
| | - Marc Peeters
- Center for Oncological Research, University of Antwerp and Antwerp University Hospital, Universiteitsplein 1, BE-2610 Wilrijk, Antwerp Belgium
| | - Patrick Pauwels
- Center for Oncological Research, University of Antwerp and Antwerp University Hospital, Universiteitsplein 1, BE-2610 Wilrijk, Antwerp Belgium
| | - Guy Van Camp
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Prins Boudewijnlaan 43/6, BE-2650 Edegem, Antwerp Belgium
| | - Ken Op de Beeck
- Center of Medical Genetics, University of Antwerp and Antwerp University Hospital, Prins Boudewijnlaan 43/6, BE-2650 Edegem, Antwerp Belgium.,Center for Oncological Research, University of Antwerp and Antwerp University Hospital, Universiteitsplein 1, BE-2610 Wilrijk, Antwerp Belgium
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17
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Huang YS, Chang CC, Lee SS, Jou YS, Shih HM. Xist reduction in breast cancer upregulates AKT phosphorylation via HDAC3-mediated repression of PHLPP1 expression. Oncotarget 2017; 7:43256-43266. [PMID: 27248326 PMCID: PMC5190021 DOI: 10.18632/oncotarget.9673] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 05/12/2016] [Indexed: 11/30/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) dysregulated in cancer potentially play oncogenic or tumor-suppressive roles. While the X inactivate-specific transcript (Xist) lncRNA is important for X-chromosome inactivation in female cells, very little is known about the role of Xist in human breast cancer in modulating cellular pathway(s). Here, we show that Xist expression is significantly reduced in breast tumor samples and cancer cell lines. Xist knockdown or overexpression resulted in increased or decreased levels, respectively, of AKT phosphorylation and cell viability. Further studies revealed an inverse correlation between Xist and phospho-AKT levels in breast cancer samples. Additionally, Xist knockdown-elicited increase of cell viability was attenuated by AKT inhibitor. These results suggest that Xist negatively regulates cell viability via inhibition of AKT activation. Interestingly, decreased Xist expression in breast cancer samples was associated with reduced levels of Jpx RNA, an lncRNA that positively regulates Xist promoter activity. Accordingly, Jpx knockdown enhanced AKT activation and cell viability. We also demonstrate that knockdown of Xist or SPEN, an intermediator protein to link Xist, SMRT co-repressor and HDAC3 complexes for X-chromosome inactivation, decreased expression of PHLPP1, a phosphatase to remove AKT phosphorylation, via increased HDAC3 recruitment to the PHLPP1 promoter, correlating with increased AKT phosphorylation. Our findings elucidate the tumor suppressor role of Xist in breast cancer and provide the molecular basis of Xist in downregulating AKT activation.
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Affiliation(s)
- Yen-Sung Huang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Che-Chang Chang
- Graduate Institute of Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Szu-Shuo Lee
- Program in Molecular Medicine, National Yang-Ming University and Academia Sinica, Taipei, Taiwan
| | - Yuh-Shan Jou
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.,Program in Molecular Medicine, National Yang-Ming University and Academia Sinica, Taipei, Taiwan
| | - Hsiu-Ming Shih
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.,Graduate Institute of Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan.,Program in Molecular Medicine, National Yang-Ming University and Academia Sinica, Taipei, Taiwan
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18
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Soozangar N, Sadeghi MR, Jeddi F, Somi MH, Shirmohamadi M, Samadi N. Comparison of genome‐wide analysis techniques to DNA methylation analysis in human cancer. J Cell Physiol 2017; 233:3968-3981. [DOI: 10.1002/jcp.26176] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 08/24/2017] [Indexed: 12/11/2022]
Affiliation(s)
- Narges Soozangar
- Liver and Gastrointestinal Diseases Research CenterTabriz University of Medical SciencesTabrizIran
- Department of Molecular Medicine, Faculty of Advanced Medical Sciences,Tabriz University of Medical SciencesTabrizIran
- Molecular Medicine Research CenterTabriz University of Medical SciencesTabrizIran
| | - Mohammad R. Sadeghi
- Liver and Gastrointestinal Diseases Research CenterTabriz University of Medical SciencesTabrizIran
- Department of Molecular Medicine, Faculty of Advanced Medical Sciences,Tabriz University of Medical SciencesTabrizIran
| | - Farhad Jeddi
- Liver and Gastrointestinal Diseases Research CenterTabriz University of Medical SciencesTabrizIran
- Department of Molecular Medicine, Faculty of Advanced Medical Sciences,Tabriz University of Medical SciencesTabrizIran
| | - Mohammad H. Somi
- Liver and Gastrointestinal Diseases Research CenterTabriz University of Medical SciencesTabrizIran
- Department of Molecular Medicine, Faculty of Advanced Medical Sciences,Tabriz University of Medical SciencesTabrizIran
| | - Masoud Shirmohamadi
- Liver and Gastrointestinal Diseases Research CenterTabriz University of Medical SciencesTabrizIran
| | - Nasser Samadi
- Department of Molecular Medicine, Faculty of Advanced Medical Sciences,Tabriz University of Medical SciencesTabrizIran
- Department of Biochemistry, Faculty of MedicineTabriz University of Medical SciencesTabrizIran
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19
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Wippermann A, Noll T. DNA methylation in CHO cells. J Biotechnol 2017; 258:206-210. [DOI: 10.1016/j.jbiotec.2017.08.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 08/06/2017] [Accepted: 08/07/2017] [Indexed: 01/22/2023]
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20
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Lee YJ, Moon SU, Park MG, Jung WY, Park YK, Song SK, Ryu JG, Lee YS, Heo HJ, Gu HN, Cho SJ, Ali BA, Al-Khedhairy AA, Lee I, Kim S. Multiplex bioimaging of piRNA molecular pathway-regulated theragnostic effects in a single breast cancer cell using a piRNA molecular beacon. Biomaterials 2016; 101:143-55. [PMID: 27289065 DOI: 10.1016/j.biomaterials.2016.05.052] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 05/18/2016] [Accepted: 05/24/2016] [Indexed: 12/17/2022]
Abstract
Recently, PIWI-interacting small non-coding RNAs (piRNAs) have emerged as novel cancer biomarkers candidate because of their high expression level in various cancer types and role in the control of tumor suppressor genes. In this study, a novel breast cancer theragnostics probe based on a single system targeting the piRNA-36026 (piR-36026) molecular pathway was developed using a piR-36026 molecular beacon (MB). The piR-36026 MB successfully visualized endogenous piR-36026 biogenesis, which is highly expressed in MCF7 cells (a human breast cancer cell line), and simultaneously inhibited piR-36026-mediated cancer progression in vitro and in vivo. We discovered two tumor suppressor proteins, SERPINA1 and LRAT, that were directly regulated as endogenous piR-36026 target genes in MCF7 cells. Furthermore, multiplex bioimaging of a single MCF7 cell following treatment with piR-36026 MB clearly visualized the direct molecular interaction of piRNA-36026 with SERPINA1 or LRAT and subsequent molecular therapeutic responses including caspase-3 and PI in the nucleus.
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Affiliation(s)
- Youn Jung Lee
- Institute for Bio-Medical Convergence, College of Medicine, Catholic Kwandong University, Gangneung-si, Gangwon-do, 270-701, Republic of Korea
| | - Sung Ung Moon
- Institute for Bio-Medical Convergence, College of Medicine, Catholic Kwandong University, Gangneung-si, Gangwon-do, 270-701, Republic of Korea
| | - Min Geun Park
- Department of Surgery, Catholic Kwandong University International St. Mary's Hospital, Incheon Metropolitan City, 404-834, Republic of Korea
| | - Woon Yong Jung
- Department of Pathology, Catholic Kwandong University International St. Mary's Hospital, Incheon Metropolitan City, 404-834, Republic of Korea
| | - Yong Keun Park
- Department of Surgery, Catholic Kwandong University International St. Mary's Hospital, Incheon Metropolitan City, 404-834, Republic of Korea
| | - Sung Kyu Song
- Department of Surgery, Catholic Kwandong University International St. Mary's Hospital, Incheon Metropolitan City, 404-834, Republic of Korea
| | - Je Gyu Ryu
- Department of Surgery, Catholic Kwandong University International St. Mary's Hospital, Incheon Metropolitan City, 404-834, Republic of Korea
| | - Yong Seung Lee
- Institute for Bio-Medical Convergence, College of Medicine, Catholic Kwandong University, Gangneung-si, Gangwon-do, 270-701, Republic of Korea
| | - Hye Jung Heo
- Institute for Bio-Medical Convergence, College of Medicine, Catholic Kwandong University, Gangneung-si, Gangwon-do, 270-701, Republic of Korea
| | - Ha Na Gu
- Institute for Bio-Medical Convergence, College of Medicine, Catholic Kwandong University, Gangneung-si, Gangwon-do, 270-701, Republic of Korea
| | - Su Jeong Cho
- Institute for Bio-Medical Convergence, College of Medicine, Catholic Kwandong University, Gangneung-si, Gangwon-do, 270-701, Republic of Korea
| | - Bahy A Ali
- Al-Jeraisy DNA Research Chair, Department of Zoology, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia; Department of Nucleic Acids Research, Genetic Engineering and Biotechnology Research Institute, City for Scientific Research and Technological Applications, Alexandria, Egypt
| | - Abdulaziz A Al-Khedhairy
- Al-Jeraisy DNA Research Chair, Department of Zoology, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Ilkyun Lee
- Department of Surgery, Catholic Kwandong University International St. Mary's Hospital, Incheon Metropolitan City, 404-834, Republic of Korea.
| | - Soonhag Kim
- Institute for Bio-Medical Convergence, College of Medicine, Catholic Kwandong University, Gangneung-si, Gangwon-do, 270-701, Republic of Korea; Catholic Kwandong University International St. Mary's Hospital, Incheon Metropolitan City, 404-834, Republic of Korea.
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21
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Soto J, Rodriguez-Antolin C, Vallespín E, de Castro Carpeño J, Ibanez de Caceres I. The impact of next-generation sequencing on the DNA methylation-based translational cancer research. Transl Res 2016; 169:1-18.e1. [PMID: 26687736 DOI: 10.1016/j.trsl.2015.11.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 10/29/2015] [Accepted: 11/14/2015] [Indexed: 01/08/2023]
Abstract
Epigenetics is currently in an exponential phase of growth, constituting one of the most promising fields in science, particularly in cancer research. Impaired epigenetic processes can lead to abnormal gene activity or inactivity, causing cellular disorders that are closely associated with tumor initiation and progression. Thus, there is a pivotal role of massive sequencing techniques for epigenetics, which aim to find novel biomarkers, factors of prognosis and prediction, and targets for achieving personalized treatments. We present a brief description of the evolution of next-generation sequencing technologies and its coupling with DNA methylation analysis techniques, highlighting its future in translational medicine and presenting significant findings in several malignancies. We also expose critical topics related to the implementation of these approaches, which is expected to be affordable for most research centers in the near future.
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Affiliation(s)
- Javier Soto
- Cancer Epigenetics Laboratory, INGEMM, La Paz University Hospital, Madrid, Spain; Biomarkers and Experimental Therapeutics in Cancer, IdiPAZ, Madrid, Spain
| | - Carlos Rodriguez-Antolin
- Cancer Epigenetics Laboratory, INGEMM, La Paz University Hospital, Madrid, Spain; Biomarkers and Experimental Therapeutics in Cancer, IdiPAZ, Madrid, Spain
| | - Elena Vallespín
- Structural and Functional Genomics, INGEMM-IdiPAZ-CIBERER, La Paz University Hospital, Madrid, Spain
| | | | - Inmaculada Ibanez de Caceres
- Cancer Epigenetics Laboratory, INGEMM, La Paz University Hospital, Madrid, Spain; Biomarkers and Experimental Therapeutics in Cancer, IdiPAZ, Madrid, Spain.
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22
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Di Oto E, Monti V, Cucchi MC, Masetti R, Varga Z, Foschini MP. X chromosome gain in male breast cancer. Hum Pathol 2015; 46:1908-12. [PMID: 26475094 DOI: 10.1016/j.humpath.2015.08.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 08/07/2015] [Accepted: 08/16/2015] [Indexed: 10/23/2022]
Abstract
Male breast cancer (MBC) is an uncommon disease whose molecular profile is not well known. X chromosome gain has been described as a marker of aggressive behavior in female breast cancer. The aim of this study is to investigate the role of the X chromosome in male breast cancer. Twenty cases of male breast invasive ductal carcinoma were retrieved and compared with 10 cases of gynecomastia. Cases were tested by fluorescence in situ hybridization to assess a cytogenetic profile for the X chromosome. The X chromosome status was compared with histopathologic features and stage at presentation. All MBC cases harbored an X chromosome gain (100%) in a variable percentage of neoplastic cells, ranging from 31% to 85% (mean, 59%). On the contrary, all cases of gynecomastia showed wild X chromosome asset. The patients' age at surgery and tumor grading showed a statistically significant correlation (P = .0188-.04), with the percentages of neoplastic cells showing an X chromosome gain. These data suggest that this X chromosome gain plays a role in the neoplastic transformation of male breast epithelial cells.
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Affiliation(s)
- Enrico Di Oto
- Anatomic Pathology, Department of Biomedical and Neuromotor Sciences, University of Bologna, 40139, Bologna, Italy
| | - Valentina Monti
- Anatomic Pathology, Department of Biomedical and Neuromotor Sciences, University of Bologna, 40139, Bologna, Italy
| | - Maria C Cucchi
- Breast Surgery Unit, Bellaria Hospital, 40139, Bologna, Italy
| | - Riccardo Masetti
- Breast Surgery Unit, Policlinico Universitario A. Gemelli, 30151, Rome, Italy
| | - Zsuzsanna Varga
- Institute of Surgical Pathology University Hospital Zurich, 8091, Zurich, Switzerland
| | - Maria P Foschini
- Anatomic Pathology, Department of Biomedical and Neuromotor Sciences, University of Bologna, 40139, Bologna, Italy.
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