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Tsumura K, Fujimoto M, Tian Y, Kawahara T, Fujimoto H, Maeshima AM, Nakagawa T, Kume H, Yoshida T, Kanai Y, Arai E. Aberrant cell adhesiveness due to DNA hypermethylation of KLF11 in papillary urothelial carcinomas. Exp Mol Pathol 2024; 137:104908. [PMID: 38824688 DOI: 10.1016/j.yexmp.2024.104908] [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: 12/12/2023] [Revised: 05/15/2024] [Accepted: 05/24/2024] [Indexed: 06/04/2024]
Abstract
PURPOSE The aim of this study was to clarify DNA methylation profiles determining the clinicopathological diversity of urothelial carcinomas. METHODS Genome-wide DNA methylation analysis was performed using the Infinium HumanMethylation450 BeadChip in 46 paired samples of non-cancerous urothelium (N) and corresponding cancerous tissue (T), and 26 samples of normal control urothelium obtained from patients without urothelial carcinomas (C). For genes of interest, correlation between DNA methylation and mRNA expression was examined using the Cancer Genome Atlas database. In addition, the role of a selected target for cancer-relevant endpoints was further examined in urothelial carcinoma cell lines. RESULTS The genes showing significant differences in DNA methylation levels between papillary carcinomas and more aggressive non-papillary (nodular) carcinomas were accumulated in signaling pathways participating in cell adhesion and cytoskeletal remodeling. Five hundred ninety-six methylation sites showed differences in DNA methylation levels between papillary and nodular carcinomas. Of those sites, that were located in CpG-islands around transcription start site, 5'-untranslated region or 1st exon, 16 genes exhibited inverse correlations between DNA methylation and mRNA expression levels. Among the latter, only the KLF11 gene showed papillary T sample-specific DNA hypermethylation in comparison to C and N samples. The DNA methylation levels of KLF11 were not significantly different between T samples and N samples or T samples and C samples for patients with papillo-nodular or nodular carcinomas. Knockdown experiments using the urothelial carcinoma cell lines HT1376 and 5637, which are considered models for papillary carcinoma, revealed that KLF11 participates in altering the adhesiveness of cells to laminin-coated dishes, although cell growth was not affected. CONCLUSION These data indicate that DNA hypermethylation of KLF11 may participate in the generation of papillary urothelial carcinomas through induction of aberrant cancer cell adhesion to the basement membrane.
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Affiliation(s)
- Koji Tsumura
- Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8654, Japan
| | - Mao Fujimoto
- Department of Pathology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Ying Tian
- Department of Pathology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Toru Kawahara
- Department of Pathology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Hiroyuki Fujimoto
- Department of Urology, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Akiko Miyagi Maeshima
- Department of Diagnostic Pathology, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Tohru Nakagawa
- Department of Urology, Teikyo University School of Medicine, Tokyo 173-8605, Japan
| | - Haruki Kume
- Department of Urology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8654, Japan
| | - Teruhiko Yoshida
- Fundamental Innovative Oncology Core Center, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Yae Kanai
- Department of Pathology, Keio University School of Medicine, Tokyo 160-8582, Japan.
| | - Eri Arai
- Department of Pathology, Keio University School of Medicine, Tokyo 160-8582, Japan.
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Kanai Y. Molecular pathological approach to cancer epigenomics and its clinical application. Pathol Int 2024; 74:167-186. [PMID: 38482965 DOI: 10.1111/pin.13418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/15/2024] [Accepted: 02/26/2024] [Indexed: 04/11/2024]
Abstract
Careful microscopic observation of histopathological specimens, accumulation of large numbers of high-quality tissue specimens, and analysis of molecular pathology in relation to morphological features are considered to yield realistic data on the nature of multistage carcinogenesis. Since the morphological hallmark of cancer is disruption of the normal histological structure maintained through cell-cell adhesiveness and cellular polarity, attempts have been made to investigate abnormalities of the cadherin-catenin cell adhesion system in human cancer cells. It has been shown that the CDH1 tumor suppressor gene encoding E-cadherin is silenced by DNA methylation, suggesting that a "double hit" involving DNA methylation and loss of heterozygosity leads to carcinogenesis. Therefore, in the 1990s, we focused on epigenomic mechanisms, which until then had not received much attention. In chronic hepatitis and liver cirrhosis associated with hepatitis virus infection, DNA methylation abnormalities were found to occur frequently, being one of the earliest indications that such abnormalities are present even in precancerous tissue. Aberrant expression and splicing of DNA methyltransferases, such as DNMT1 and DNMT3B, was found to underlie the mechanism of DNA methylation alterations in various organs. The CpG island methylator phenotype in renal cell carcinoma was identified for the first time, and its therapeutic targets were identified by multilayer omics analysis. Furthermore, the DNA methylation profile of nonalcoholic steatohepatitis (NASH)-related hepatocellular carcinoma was clarified in groundbreaking studies. Since then, we have developed diagnostic markers for carcinogenesis risk in NASH patients and noninvasive diagnostic markers for upper urinary tract cancer, as well as developing a new high-performance liquid chromatography-based diagnostic system for DNA methylation diagnosis. Research on the cancer epigenome has revealed that DNA methylation alterations occur from the precancerous stage as a result of exposure to carcinogenic factors such as inflammation, smoking, and viral infections, and continuously contribute to multistage carcinogenesis through aberrant expression of cancer-related genes and genomic instability. DNA methylation alterations at the precancerous stages are inherited by or strengthened in cancers themselves and determine the clinicopathological aggressiveness of cancers as well as patient outcome. DNA methylation alterations have applications as biomarkers, and are expected to contribute to diagnosis, as well as preventive and preemptive medicine.
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Affiliation(s)
- Yae Kanai
- Department of Pathology, Keio University School of Medicine, Tokyo, Japan
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Tahara S, Tahara T, Yamazaki J, Shijimaya T, Horiguchi N, Funasaka K, Fukui T, Nakagawa Y, Shibata T, Naganuma M, Tsukamoto T, Ohmiya N. Helicobacter pylori infection associated DNA methylation in primary gastric cancer significantly correlates with specific molecular and clinicopathological features. Mol Carcinog 2024; 63:266-274. [PMID: 37846801 DOI: 10.1002/mc.23650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 08/23/2023] [Accepted: 10/01/2023] [Indexed: 10/18/2023]
Abstract
Helicobacter pylori induces DNA methylation in gastric mucosa, which links to gastric cancer (GC) risk. In contrast, CpG island methylator phenotype (CIMP) is defined as high levels of cancer-specific methylation and provides distinct molecular and clinicopathological features of GC. The association between those two types of methylation in GC remains unclear. We examined DNA methylation of well-validated H. pylori infection associated genes in GC and its adjacent mucosa and investigated its association with CIMP, various molecular subtypes and clinical features. We studied 50 candidate loci in 24 gastric samples to identify H. pylori infection associated genes. Identified loci were further examined in 624 gastric tissue from 217 primary GC, 217 adjacent mucosa, and 190 mucosae from cancer-free subjects. We identified five genes (IGF2, SLC16A2, SOX11, P2RX7, and MYOD1) as hypermethylated in H. pylori infected gastric mucosa. In non-neoplastic mucosa, methylation of H. pylori infection associated genes was higher in patients with GC than those without. In primary GC tissues, higher methylation of H. pylori infection associated genes correlated with CIMP-positive and its related features, such as MLH1 methylated cases. On the other hand, GC with lower methylation of these genes presented aggressive clinicopathological features including undifferentiated histopathology, advanced stage at diagnosis. H. pylori infection associated DNA methylation is correlated with CIMP, specific molecular and clinicopathological features in GC, supporting its utility as promising biomarker in this tumor type.
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Affiliation(s)
- Sayumi Tahara
- Department of Diagnostic Pathology I, Fujita Health University School of Medicine, Toyoake, Japan
| | - Tomomitsu Tahara
- Department of Gastroenterology, Fujita Health University School of Medicine, Toyoake, Japan
- Third Department of Internal Medicine, Kansai Medical University, Hirakata, Japan
| | - Jumpei Yamazaki
- Translational Research Unit, Veterinary Teaching Hospital, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
| | - Takuya Shijimaya
- Third Department of Internal Medicine, Kansai Medical University, Hirakata, Japan
| | - Noriyuki Horiguchi
- Department of Gastroenterology, Fujita Health University School of Medicine, Toyoake, Japan
| | - Kohei Funasaka
- Department of Gastroenterology, Fujita Health University School of Medicine, Toyoake, Japan
| | - Toshiro Fukui
- Third Department of Internal Medicine, Kansai Medical University, Hirakata, Japan
| | - Yoshihito Nakagawa
- Department of Gastroenterology, Fujita Health University School of Medicine, Toyoake, Japan
| | - Tomoyuki Shibata
- Department of Gastroenterology, Fujita Health University School of Medicine, Toyoake, Japan
| | - Makoto Naganuma
- Third Department of Internal Medicine, Kansai Medical University, Hirakata, Japan
| | - Tetsuya Tsukamoto
- Department of Diagnostic Pathology I, Fujita Health University School of Medicine, Toyoake, Japan
| | - Naoki Ohmiya
- Department of Advanced Endoscopy, Fujita Health University, Toyoake, Aichi, Japan
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Liu Y, Cheng X, Xi P, Zhang Z, Sun T, Gong B. Bioinformatic analysis highlights SNHG6 as a putative prognostic biomarker for kidney renal papillary cell carcinoma. BMC Urol 2023; 23:54. [PMID: 37004005 PMCID: PMC10067223 DOI: 10.1186/s12894-023-01218-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 03/20/2023] [Indexed: 04/03/2023] Open
Abstract
PURPOSE Kidney renal papillary cell carcinoma (KIRP) is a highly heterogeneous malignancy and current systemic therapeutic strategies are difficult to achieve a satisfactory outcome for advanced disease. Meanwhile, there is a lack of effective biomarkers to predict the prognosis of KIRP. METHODS Using TCGA, GTEx, UALCAN, TIMER, TIMER 2.0 and STRING databases, we analyzed the relationship of SNHG6 with KIRP subtypes, tumor-infiltrating immune cells and potential target mRNAs. Based on TCGA data, ROC curves, Kaplan-Meier survival analysis and COX regression analysis were performed to evaluate the diagnostic and prognostic value of SNHG6 in KIRP. Nomogram was used to predict 3- and 5-year disease-specific survival in KIRP patients. In addition, with the help of Genetic ontology and Gene set enrichment analysis, the biological processes and signalling pathways that SNHG6 may be involved in KIRP were initially explored. RESULTS In patients with KIRP, SNHG6 was significantly upregulated and associated with a more aggressive subtype (lymph node involvement, pathological stage IV, CIMP phenotype) and poor prognosis. The ROC curve showed good diagnostic efficacy (AUC value: 0.828) and the C-index of the Nomogram for predicting DSS at 3 and 5 years was 0.920 (0.898-0.941). In the immune microenvironment of KIRP, SNHG6 expression levels were negatively correlated with macrophage abundance and positively correlated with cancer-associated fibroblasts. Furthermore, SNHG6 may promote KIRP progression by regulating the expression of molecules such as AURKB, NDC80, UBE2C, NUF2, PTTG1, CENPH, SPC25, CDCA3, CENPM, BIRC5, TROAP, EZH2. Last, GSEA suggests that SNHG6 may be involved in the regulation of the PPAR signalling pathway and the SLIT/ROBO signalling pathway. CONCLUSIONS Our analysis suggests that a high SNHG6 expression status in KIRP is associated with a poorer prognosis for patients, and also elucidates some potential mechanisms contributing to this poorer outcome. This may provide new insights into the treatment and management of KIRP in the foreseeable future.
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Affiliation(s)
- Yifu Liu
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, China
- Jiangxi Institute of Urology, Nanchang, 330006, Jiangxi, China
| | - Xiaofeng Cheng
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, China
- Jiangxi Institute of Urology, Nanchang, 330006, Jiangxi, China
| | - Ping Xi
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, China
- Jiangxi Institute of Urology, Nanchang, 330006, Jiangxi, China
| | - Zhicheng Zhang
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, China
- Jiangxi Institute of Urology, Nanchang, 330006, Jiangxi, China
| | - Ting Sun
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, China
- Jiangxi Institute of Urology, Nanchang, 330006, Jiangxi, China
| | - Binbin Gong
- Department of Urology, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, Jiangxi, China.
- Jiangxi Institute of Urology, Nanchang, 330006, Jiangxi, China.
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Hu J, Yang Q, Yue Z, Liao B, Cheng H, Li W, Zhang H, Wang S, Tian Q. Emerging advances in engineered macrophages for tumor immunotherapy. Cytotherapy 2023; 25:235-244. [PMID: 36008206 DOI: 10.1016/j.jcyt.2022.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 07/02/2022] [Accepted: 07/08/2022] [Indexed: 02/07/2023]
Abstract
Macrophages are versatile antigen-presenting cells. Recent studies suggest that engineered modifications of macrophages may confer better tumor therapy. Genetic engineering of macrophages with specific chimeric antigen receptors offers new possibilities for treatment of solid tumors and has received significant attention. In vitro gene editing of macrophages and infusion into the body can inhibit the immunosuppressive effect of the tumor microenvironment in solid tumors. This strategy is flexible and can be applied to all stages of cancer treatment. In contrast, nongenetic engineering tools are used to block relevant signaling pathways in immunosuppressive responses. In addition, macrophages can be loaded with drugs and engineered into cellular drug delivery systems. Here, we analyze the effect of the chimeric antigen receptor platform on macrophages and other existing engineering modifications of macrophages, highlighting their status, challenges and future perspectives. Indeed, our analyses show that new approaches in the treatment of solid tumors will likely exploit macrophages, an innate immune cell.
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Affiliation(s)
- Jing Hu
- College of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang, China; Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Qian Yang
- College of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang, China; Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Zhongyu Yue
- College of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang, China; Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Boting Liao
- College of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang, China; Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Huijuan Cheng
- College of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang, China; Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Wenqi Li
- College of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang, China; Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Honghua Zhang
- College of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang, China; Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Shuling Wang
- College of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang, China; Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Qingchang Tian
- College of Pharmacy, Hangzhou Normal University, Hangzhou, Zhejiang, China; Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou, Zhejiang, China.
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Ochoa S, Hernández-Lemus E. Functional impact of multi-omic interactions in breast cancer subtypes. Front Genet 2023; 13:1078609. [PMID: 36685900 PMCID: PMC9850112 DOI: 10.3389/fgene.2022.1078609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 12/15/2022] [Indexed: 01/07/2023] Open
Abstract
Multi-omic approaches are expected to deliver a broader molecular view of cancer. However, the promised mechanistic explanations have not quite settled yet. Here, we propose a theoretical and computational analysis framework to semi-automatically produce network models of the regulatory constraints influencing a biological function. This way, we identified functions significantly enriched on the analyzed omics and described associated features, for each of the four breast cancer molecular subtypes. For instance, we identified functions sustaining over-representation of invasion-related processes in the basal subtype and DNA modification processes in the normal tissue. We found limited overlap on the omics-associated functions between subtypes; however, a startling feature intersection within subtype functions also emerged. The examples presented highlight new, potentially regulatory features, with sound biological reasons to expect a connection with the functions. Multi-omic regulatory networks thus constitute reliable models of the way omics are connected, demonstrating a capability for systematic generation of mechanistic hypothesis.
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Affiliation(s)
- Soledad Ochoa
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico,Programa de Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Enrique Hernández-Lemus
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico,Center for Complexity Sciences, Universidad Nacional Autónoma de México, Mexico City, Mexico,*Correspondence: Enrique Hernández-Lemus,
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Hassan Ibrahim I, Balah A, Gomaa Abd Elfattah Hassan A, Gamal Abd El-Aziz H. Role of motor proteins in human cancers. Saudi J Biol Sci 2022; 29:103436. [PMID: 36131778 PMCID: PMC9483653 DOI: 10.1016/j.sjbs.2022.103436] [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: 03/29/2022] [Revised: 08/04/2022] [Accepted: 09/01/2022] [Indexed: 11/30/2022] Open
Abstract
Motor proteins include several protein families (Kinesin, Dynein and Myosin) responsible for intracellular transport, intercellular communication, among other functions. In cancer cells, motor proteins along with microtubules (MT) and other tubulin and actin structures, are crucial for cell proliferation and invasion. The cBioPortal platform for Cancer Genomics database was queried for solid cancers in a combined cohort of 9204 patients with complete cancer genomics data. To assess the importance of motor proteins in cancer, copy number alterations (CNAs) and survival rates were analyzed in the combined dataset. Kinesin, Dynein, and Myosin families showed CNAs in 47%, 49%, and 57 % of patients, respectively, in at least one of their members. Survival analysis showed that CNAs in Kinesin and Dynein, families' genes in the same patients were significantly correlated to decreased overall survival. These results added more evidence to previous literature highlighting the importance of motor proteins as a target in cancer therapy. Kinesin inhibitors could act by several mechanisms such as inhibiting spindle assembly or centrosome separation during mitosis, leading to cell cycle arrest and eventually apoptosis. Dynein inhibitors modulate Dynein's activity and MT binding, inhibiting cell proliferation and invasion. Myosin inhibitors act by stabilizing MT, inducing cell cycle arrest and inhibiting invasiveness. Increasing the specificity of motor proteins targeting drugs could improve cancer therapy and patient survival.
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Affiliation(s)
- Iman Hassan Ibrahim
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy (Girls), Al-Azhar University, Postal code 11765, Egypt
| | - Amany Balah
- Department of Pharmacology and Toxicology, Faculty of Pharmacy (Girls), Al- Azhar University, Postal code 11765, Egypt
| | - Abrar Gomaa Abd Elfattah Hassan
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy (Girls), Al-Azhar University, Postal code 11765, Egypt
| | - Heba Gamal Abd El-Aziz
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy (Girls), Al-Azhar University, Postal code 11765, Egypt
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DNA methylation status of the SPHK1 and LTB genes underlies the clinicopathological diversity of non-alcoholic steatohepatitis-related hepatocellular carcinomas. J Cancer Res Clin Oncol 2022:10.1007/s00432-022-04445-9. [DOI: 10.1007/s00432-022-04445-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 10/19/2022] [Indexed: 11/09/2022]
Abstract
Abstract
Purpose
This study was performed to identify the DNA methylation profiles underlying the clinicopathological diversity of non-alcoholic steatohepatitis (NASH)-related hepatocellular carcinomas (HCCs).
Methods
Genome-wide DNA methylation analysis of 88 liver tissue samples was performed using the Infinium assay.
Results
Principal component analysis revealed that distinct DNA methylation profiles differing from such profiles in normal control liver tissue had already been established in non-cancerous liver tissue showing NASH, which is considered to be a precancerous condition. Hierarchical clustering separated 26 NASH-related HCCs into Cluster I (n = 8) and Cluster II (n = 18). Such epigenetic clustering was significantly correlated with histopathological diversity, i.e. poorer tumor differentiation, tumor steatosis and development of a scirrhous HCC component. Significant differences in DNA methylation levels between the two clusters were accumulated in molecular pathways participating in cell adhesion and cytoskeletal remodeling, as well as cell proliferation and apoptosis. Among tumor-related genes characterizing Clusters I and II, differences in the levels of DNA methylation and mRNA expression for the SPHK1, INHBA, LTB and PDE3B genes were correlated with poorer tumor differentiation. 5-Aza-2′-deoxycytidine treatment of HCC cells revealed epigenetic regulation of the SPHK1 and LTB genes. Knockdown experiments showed that SPHK1 promotes cell proliferation, represses apoptosis and enhances migration, whereas LTB enhances migration of HCC cells. DNA hypomethylation resulting in increased expression of SPHK1 and LTB in poorly differentiated HCCs may underlie the aggressive phenotype of such HCCs.
Conclusion
These data indicate that DNA methylation profiles may determine the clinicopathological heterogeneity of NASH-related HCCs via alterations of tumor-related gene expression.
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Zhang L, Liu M, Zhang Z, Chen D, Chen G, Liu M. Machine learning based identification of hub genes in renal clear cell carcinoma using multi-omics data. Methods 2022; 207:110-117. [PMID: 36179770 DOI: 10.1016/j.ymeth.2022.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/12/2022] [Accepted: 09/24/2022] [Indexed: 11/18/2022] Open
Abstract
Renal cell carcinoma is one of the most universal urinary system cancers in the world. The most common renal cell carcinoma subtype is renal clear cell carcinoma. It is usually associated with high rates of metastasis and mortality. Therefore, finding effective therapeutic targets and prognostic molecular markers is of great significance to improve the early diagnosis rate and prognostic accuracy of renal clear cell carcinoma. In this work, we successfully identified six hub genes that are closely related to the occurrence, development and prognosis of renal clear cell carcinoma and proposed three new potential prognostic markers, namely ATP4B, AC144831.1 and Tfcp2l1 through differentially expressed genes (DEGs) analysis, GO functional enrichment and KEGG pathway analysis, WGCNA analysis, and survival analysis. In addition, we established machine learning models to predict the occurrence of tumors through the gene expression data of patients. It is expected that the results of this study can provide reference value for the treatment of renal clear cell carcinoma.
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Affiliation(s)
- Lichao Zhang
- School of Intelligent Manufacturing and Equipment, Shenzhen Institute of Information Technology, Shenzhen, China
| | - Mingjun Liu
- School of Intelligent Manufacturing and Equipment, Shenzhen Institute of Information Technology, Shenzhen, China
| | - Zhenjiu Zhang
- School of Intelligent Manufacturing and Equipment, Shenzhen Institute of Information Technology, Shenzhen, China
| | | | | | - Mingyang Liu
- Beidahuang Industry Group General Hospital, Harbin, China.
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Marchocki Z, Tone A, Virtanen C, de Borja R, Clarke B, Brown T, May T. Impact of neoadjuvant chemotherapy on somatic mutation status in high-grade serous ovarian carcinoma. J Ovarian Res 2022; 15:50. [PMID: 35501919 PMCID: PMC9059396 DOI: 10.1186/s13048-022-00983-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 04/13/2022] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Patients treated with neoadjuvant chemotherapy (NACT) for advanced high-grade serous ovarian carcinoma (HGSC) have a higher rate and shorter time to platinum-resistant recurrence compared to patients treated with primary cytoreductive surgery (PCS) and adjuvant chemotherapy. The purpose of this study is to determine the impact of NACT on somatic mutation status in platinum-sensitive and resistant HGSC. Patients with advanced HGSC who had a documented response to platinum-based NACT, a banked blood sample, and a banked tumor sample before and after NACT were identified. Whole exome and/or targeted deep sequencing was performed in matched normal and pre/post-NACT tumor samples from 3 platinum-resistant and 2 platinum-sensitive patients to identify somatic non-synonymous mutations at each time point. RESULTS When comparing exonic non-synonymous mutations in pre-NACT and post-NACT samples from the same patient, an average of 41% (1-68%) of genes were mutated at both time points. There were no trends detected in the mutational burden following exposure to NACT in platinum-resistant vs. platinum-sensitive cases. The majority of mutated genes were unique to each case. We identified several genes that were commonly mutated in pre-NACT samples specific to platinum-resistant (CSPG4, SLC35G5, TUBA3D) or sensitive (CYP2D6, NUTM1, DNAH5) cases. Four mutated genes emerged exclusively in the platinum-resistant cases (ADGRV1, MUC17, MUC20, PAK2) following NACT. CONCLUSIONS Patients with advanced HGSC present with significant intra-tumor heterogeneity. NACT significantly impacts the somatic mutation status irrespective of the time to recurrence. The mutated genes detected in chemo-naive pre-NACT tumor samples from either resistant or sensitive cases could potentially have a role in the prediction of chemotherapy response in patients scheduled to receive NACT; larger studies are required to further validate these genes.
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Affiliation(s)
- Zibi Marchocki
- Department of Surgical Oncology, Division of Gynecologic Oncology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Obstetrics and Gynecology, University of Toronto, Toronto, ON, Canada
| | - Alicia Tone
- Department of Surgical Oncology, Division of Gynecologic Oncology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Carl Virtanen
- Bioinformatics and HPC Services Core, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Richard de Borja
- Department of Obstetrics and Gynecology, University of Toronto, Toronto, ON, Canada
| | - Blaise Clarke
- Department of Pathology, University Health Network, Toronto, Ontario, Canada
| | - Theodore Brown
- Department of Obstetrics and Gynecology, University of Toronto, Toronto, ON, Canada
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Taymaa May
- Department of Surgical Oncology, Division of Gynecologic Oncology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
- Department of Obstetrics and Gynecology, University of Toronto, Toronto, ON, Canada.
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Harville EW, Mishra PP, Kähönen M, Raitoharju E, Marttila S, Raitakari O, Lehtimäki T. Reproductive history and blood cell DNA methylation later in life: the Young Finns Study. Clin Epigenetics 2021; 13:227. [PMID: 34930449 PMCID: PMC8690999 DOI: 10.1186/s13148-021-01215-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 12/09/2021] [Indexed: 01/16/2023] Open
Abstract
Background Women with a history of complications of pregnancy, including hypertensive disorders, gestational diabetes or an infant fetal growth restriction or preterm birth, are at higher risk for cardiovascular disease later in life. We aimed to examine differences in maternal DNA methylation following pregnancy complications. Methods Data on women participating in the Young Finns study (n = 836) were linked to the national birth registry. DNA methylation in whole blood was assessed using the Infinium Methylation EPIC BeadChip. Epigenome-wide analysis was conducted on differential CpG methylation at 850 K sites. Reproductive history was also modeled as a predictor of four epigenetic age indices. Results Fourteen significant differentially methylated sites were found associated with both history of pre-eclampsia and overall hypertensive disorders of pregnancy. No associations were found between reproductive history and any epigenetic age acceleration measure. Conclusions Differences in epigenetic methylation profiles could represent pre-existing risk factors, or changes that occurred as a result of experiencing these complications. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01215-1.
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Affiliation(s)
- Emily W Harville
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, 70112, USA. .,Department of Clinical Chemistry, Faculty of Medicine and Health Technology, Tampere University, 33520, Tampere, Finland.
| | - Pashupati P Mishra
- Department of Clinical Chemistry, Faculty of Medicine and Health Technology, Tampere University, 33520, Tampere, Finland.,Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, 33521, Tampere, Finland.,Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital, and Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, 33521, Tampere, Finland
| | - Emma Raitoharju
- Department of Clinical Chemistry, Faculty of Medicine and Health Technology, Tampere University, 33520, Tampere, Finland.,Department of Molecular Epidemiology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Saara Marttila
- Department of Clinical Chemistry, Faculty of Medicine and Health Technology, Tampere University, 33520, Tampere, Finland.,Department of Molecular Epidemiology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,Gerontology Research Center, Tampere University, Tampere, Finland
| | - Olli Raitakari
- Research Center of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Faculty of Medicine and Health Technology, Tampere University, 33520, Tampere, Finland.,Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, 33521, Tampere, Finland.,Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
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12
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The role of ZNF384, DNAH17, and NDST2 gene expression in non-Hodgkin's lymphoma patients. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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13
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Duerinckx S, Désir J, Perazzolo C, Badoer C, Jacquemin V, Soblet J, Maystadt I, Tunca Y, Blaumeiser B, Ceulemans B, Courtens W, Debray F, Destree A, Devriendt K, Jansen A, Keymolen K, Lederer D, Loeys B, Meuwissen M, Moortgat S, Mortier G, Nassogne M, Sekhara T, Van Coster R, Van Den Ende J, Van der Aa N, Van Esch H, Vanakker O, Verhelst H, Vilain C, Weckhuysen S, Passemard S, Verloes A, Aeby A, Deconinck N, Van Bogaert P, Pirson I, Abramowicz M. Phenotypes and genotypes in non-consanguineous and consanguineous primary microcephaly: High incidence of epilepsy. Mol Genet Genomic Med 2021; 9:e1768. [PMID: 34402213 PMCID: PMC8457702 DOI: 10.1002/mgg3.1768] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 05/06/2021] [Accepted: 07/03/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Primary microcephaly (PM) is defined as a significant reduction in occipitofrontal circumference (OFC) of prenatal onset. Clinical and genetic heterogeneity of PM represents a diagnostic challenge. METHODS We performed detailed phenotypic and genomic analyses in a large cohort (n = 169) of patients referred for PM and could establish a molecular diagnosis in 38 patients. RESULTS Pathogenic variants in ASPM and WDR62 were the most frequent causes in non-consanguineous patients in our cohort. In consanguineous patients, microarray and targeted gene panel analyses reached a diagnostic yield of 67%, which contrasts with a much lower rate in non-consanguineous patients (9%). Our series includes 11 novel pathogenic variants and we identify novel candidate genes including IGF2BP3 and DNAH2. We confirm the progression of microcephaly over time in affected children. Epilepsy was an important associated feature in our PM cohort, affecting 34% of patients with a molecular confirmation of the PM diagnosis, with various degrees of severity and seizure types. CONCLUSION Our findings will help to prioritize genomic investigations, accelerate molecular diagnoses, and improve the management of PM patients.
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Affiliation(s)
- Sarah Duerinckx
- Institut de Recherche Interdisciplinaire en Biologie Humaine et moléculaireUniversité Libre de BruxellesBrusselsBelgium
| | - Julie Désir
- Centre de Génétique HumaineInstitut de Pathologie et de GénétiqueGosseliesBelgium
| | - Camille Perazzolo
- Institut de Recherche Interdisciplinaire en Biologie Humaine et moléculaireUniversité Libre de BruxellesBrusselsBelgium
| | - Cindy Badoer
- Department of GeneticsHôpital ErasmeULB Center of Human GeneticsUniversité Libre de BruxellesBrusselsBelgium
| | - Valérie Jacquemin
- Institut de Recherche Interdisciplinaire en Biologie Humaine et moléculaireUniversité Libre de BruxellesBrusselsBelgium
| | - Julie Soblet
- Department of GeneticsHôpital ErasmeULB Center of Human GeneticsUniversité Libre de BruxellesBrusselsBelgium
- Hôpital Universitaire des Enfants Reine Fabiola (HUDERF)Université Libre de BruxellesBrusselsBelgium
| | - Isabelle Maystadt
- Centre de Génétique HumaineInstitut de Pathologie et de GénétiqueGosseliesBelgium
| | - Yusuf Tunca
- Department of Medical GeneticsGülhane Faculty of Medicine & Gülhane Training and Research HospitalUniversity of Health Sciences TurkeyAnkaraTurkey
| | | | | | | | | | - Anne Destree
- Centre de Génétique HumaineInstitut de Pathologie et de GénétiqueGosseliesBelgium
| | | | - Anna Jansen
- Universitair Ziekenhuis Brussel (UZ Brussel)Centrum Medische GeneticaUniversiteit Brussel (VUB)BrusselsBelgium
| | - Kathelijn Keymolen
- Universitair Ziekenhuis Brussel (UZ Brussel)Centrum Medische GeneticaUniversiteit Brussel (VUB)BrusselsBelgium
| | - Damien Lederer
- Centre de Génétique HumaineInstitut de Pathologie et de GénétiqueGosseliesBelgium
| | - Bart Loeys
- University and University Hospital of AntwerpAntwerpBelgium
| | | | - Stéphanie Moortgat
- Centre de Génétique HumaineInstitut de Pathologie et de GénétiqueGosseliesBelgium
| | - Geert Mortier
- University and University Hospital of AntwerpAntwerpBelgium
| | | | | | | | | | | | - Hilde Van Esch
- Center for Human GeneticsUniversity Hospitals LeuvenLeuvenBelgium
| | | | | | - Catheline Vilain
- Department of GeneticsHôpital ErasmeULB Center of Human GeneticsUniversité Libre de BruxellesBrusselsBelgium
- Hôpital Universitaire des Enfants Reine Fabiola (HUDERF)Université Libre de BruxellesBrusselsBelgium
| | | | | | - Alain Verloes
- Department of GeneticsAPHPRobert Debré University HospitalParisFrance
| | - Alec Aeby
- Hôpital Universitaire des Enfants Reine Fabiola (HUDERF)Université Libre de BruxellesBrusselsBelgium
| | - Nicolas Deconinck
- Hôpital Universitaire des Enfants Reine Fabiola (HUDERF)Université Libre de BruxellesBrusselsBelgium
| | | | - Isabelle Pirson
- Institut de Recherche Interdisciplinaire en Biologie Humaine et moléculaireUniversité Libre de BruxellesBrusselsBelgium
| | - Marc Abramowicz
- Institut de Recherche Interdisciplinaire en Biologie Humaine et moléculaireUniversité Libre de BruxellesBrusselsBelgium
- Department of Genetic Medicine and DevelopmentUniversity of GenevaGenèveSwitzerland
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14
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Wu Y, Sa Y, Guo Y, Li Q, Zhang N. Identification of WHO II/III gliomas by 16 prognostic-related gene signatures using machine learning methods. Curr Med Chem 2021; 29:1622-1639. [PMID: 34455959 DOI: 10.2174/0929867328666210827103049] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND It is found that the prognosis of gliomas of the same grade has large differences among World Health Organization(WHO) grade II and III in clinical observation. Therefore, a better understanding of the genetics and molecular mechanisms underlying WHO grade II and III gliomas is required, with the aim of developing a classification scheme at the molecular level rather than the conventional pathological morphology level. METHOD We performed survival analysis combined with machine learning methods of Least Absolute Shrinkage and Selection Operator using expression datasets downloaded from the Chinese Glioma Genome Atlas as well as The Cancer Genome Atlas. Risk scores were calculated by the product of expression level of overall survival-related genes and their multivariate Cox proportional hazards regression coefficients. WHO grade II and III gliomas were categorized into the low-risk subgroup, medium-risk subgroup, and high-risk subgroup. We used the 16 prognostic-related genes as input features to build a classification model based on prognosis using a fully connected neural network. Gene function annotations were also performed. RESULTS The 16 genes (AKNAD1, C7orf13, CDK20, CHRFAM7A, CHRNA1, EFNB1, GAS1, HIST2H2BE, KCNK3, KLHL4, LRRK2, NXPH3, PIGZ, SAMD5, ERINC2, and SIX6) related to the glioma prognosis were screened. The 16 selected genes were associated with the development of gliomas and carcinogenesis. The accuracy of an external validation data set of the fully connected neural network model from the two cohorts reached 95.5%. Our method has good potential capability in classifying WHO grade II and III gliomas into low-risk, medium-risk, and high-risk subgroups. The subgroups showed significant (P<0.01) differences in overall survival. CONCLUSION This resulted in the identification of 16 genes that were related to the prognosis of gliomas. Here we developed a computational method to discriminate WHO grade II and III gliomas into three subgroups with distinct prognoses. The gene expression-based method provides a reliable alternative to determine the prognosis of gliomas.
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Affiliation(s)
- YaMeng Wu
- Department of Biomedical Engineering, Tianjin Key Lab of BME Measurement, Tianjin University, Tianjin. China
| | - Yu Sa
- Department of Biomedical Engineering, Tianjin Key Lab of BME Measurement, Tianjin University, Tianjin. China
| | - Yu Guo
- Department of Biomedical Engineering, Tianjin Key Lab of BME Measurement, Tianjin University, Tianjin. China
| | - QiFeng Li
- Department of Biomedical Engineering, Tianjin Key Lab of BME Measurement, Tianjin University, Tianjin. China
| | - Ning Zhang
- Department of Biomedical Engineering, Tianjin Key Lab of BME Measurement, Tianjin University, Tianjin. China
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15
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Hamada K, Tian Y, Fujimoto M, Takahashi Y, Kohno T, Tsuta K, Watanabe SI, Yoshida T, Asamura H, Kanai Y, Arai E. DNA hypermethylation of the ZNF132 gene participates in the clinicopathological aggressiveness of 'pan-negative'-type lung adenocarcinomas. Carcinogenesis 2021; 42:169-179. [PMID: 33152763 PMCID: PMC7905838 DOI: 10.1093/carcin/bgaa115] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 10/12/2020] [Accepted: 10/29/2020] [Indexed: 11/26/2022] Open
Abstract
Although some previous studies have examined epigenomic alterations in lung adenocarcinomas, correlations between epigenomic events and genomic driver mutations have not been fully elucidated. Single-CpG resolution genome-wide DNA methylation analysis with the Infinium HumanMethylation27 BeadChip was performed using 162 paired samples of adjacent normal lung tissue (N) and the corresponding tumorous tissue (T) from patients with lung adenocarcinomas. Correlations between DNA methylation data on the one hand and clinicopathological parameters and genomic driver mutations, i.e. mutations of EGFR, KRAS, BRAF and HER2 and fusions involving ALK, RET and ROS1, were examined. DNA methylation levels in 12 629 probes from N samples were significantly correlated with recurrence-free survival. Principal component analysis revealed that distinct DNA methylation profiles at the precancerous N stage tended not to induce specific genomic driver aberrations. Most of the genes showing significant DNA methylation alterations during transition from N to T were shared by two or more driver aberration groups. After small interfering RNA knockdown of ZNF132, which showed DNA hypermethylation only in the pan-negative group and was correlated with vascular invasion, the proliferation, apoptosis and migration of cancer cell lines were examined. ZNF132 knockdown led to increased cell migration ability, rather than increased cell growth or reduced apoptosis. We concluded that DNA hypermethylation of the ZNF132 gene participates in the clinicopathological aggressiveness of ‘pan-negative’ lung adenocarcinomas. In addition, DNA methylation alterations at the precancerous stage may determine tumor aggressiveness, and such alterations that accumulate after driver mutation may additionally modify clinicopathological features through alterations of gene expression.
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Affiliation(s)
- Kenichi Hamada
- Department of Pathology, Keio University School of Medicine, Tokyo, Japan
- Division of Thoracic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Ying Tian
- Department of Pathology, Keio University School of Medicine, Tokyo, Japan
| | - Mao Fujimoto
- Department of Pathology, Keio University School of Medicine, Tokyo, Japan
| | - Yoriko Takahashi
- Bioscience Department, Solution Knowledge Center, Mitsui Knowledge Industry Co., Ltd., Tokyo, Japan
| | - Takashi Kohno
- Division of Genome Biology, National Cancer Center Research Institute, Tokyo, Japan
| | - Koji Tsuta
- Department of Pathology & Laboratory Medicine, Kansai Medical University, Osaka, Japan
| | - Shun-ichi Watanabe
- Department of Thoracic Surgery, National Cancer Center Hospital, Tokyo, Japan
| | - Teruhiko Yoshida
- Fundamental Innovative Oncology Core Center, National Cancer Center Research Institute, Tokyo, Japan
| | - Hisao Asamura
- Division of Thoracic Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Yae Kanai
- Department of Pathology, Keio University School of Medicine, Tokyo, Japan
| | - Eri Arai
- Department of Pathology, Keio University School of Medicine, Tokyo, Japan
- To whom correspondence should be addressed. Tel: +81 3 3353 1211; Fax: +81 3 3353 3290;
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16
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Yang M, Arai E, Takahashi Y, Totsuka H, Chiku S, Taniguchi H, Katai H, Sakamoto H, Yoshida T, Kanai Y. Cooperative participation of epigenomic and genomic alterations in the clinicopathological diversity of gastric adenocarcinomas: significance of cell adhesion and epithelial-mesenchymal transition-related signaling pathways. Carcinogenesis 2021; 41:1473-1484. [PMID: 32710740 PMCID: PMC7665242 DOI: 10.1093/carcin/bgaa079] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 06/27/2020] [Accepted: 07/21/2020] [Indexed: 02/06/2023] Open
Abstract
The present study was conducted to clarify the cooperative significance of epigenomic and genomic abnormalities during gastric carcinogenesis. Using 21 samples of normal control gastric mucosa (C), 109 samples of non-cancerous gastric mucosa (N) and 105 samples of cancerous tissue (T) from 109 patients with primary gastric adenocarcinomas, genome-wide DNA methylation analysis was performed using Infinium assay. Among these samples, 66 paired N and corresponding T samples were subjected to whole-exome and single nucleotide polymorphism array analyses. As had been shown in our previous study, 109 patients were clustered clinicopathologically into least aggressive Cluster A (n = 20), most aggressive Cluster B1 (n = 20) and Cluster B2 (n = 69). Most DNA methylation alterations in each cluster had already occurred even in N samples compared with C samples, and DNA methylation alterations at the precancerous N stage were inherited by the established cancers themselves. Recurrent single nucleotide variants and insertions/deletions resulting in functional disruption of the proteins encoded by the ABCA10, BNC2, CDH1, CTNNB1, SMAD4 and VAV2 genes were specific to Cluster B1, whereas those of the APC, EGFR, ERBB2, ERBB3, MLH1 and MUC6 genes were specific to Cluster A. MetaCore pathway analysis revealed that the epigenomically affected TWIST1 gene and genomically affected CDH1, CTNNB1, MMP9, TLN2, ROCK1 and SMAD4 genes were accumulated in signaling pathways related to cell adhesion, cytoskeleton remodeling and epithelial–mesenchymal transition in Cluster B1. These data indicate that epigenomic alterations at the precancerous stage are important in gastric carcinogenesis and that epigenomic and genomic alterations cooperatively underlie the aggressiveness of gastric adenocarcinomas.
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Affiliation(s)
- Menghan Yang
- Department of Pathology, Keio University School of Medicine, Tokyo, Japan
| | - Eri Arai
- Department of Pathology, Keio University School of Medicine, Tokyo, Japan
| | - Yoriko Takahashi
- Biomedical Department, Cloud Service Division, IT Infrastructure Services Unit, Mitsui Knowledge Industry Co., Ltd., Tokyo, Japan
| | - Hirohiko Totsuka
- Bioinformatics Group, Research and Development Center, Solution Division 4, Hitachi Government and Public Corporation System Engineering Ltd., Tokyo, Japan
| | - Suenori Chiku
- Information and Communication Research Division, Mizuho Information and Research Institute, Inc., Tokyo, Japan
| | - Hirokazu Taniguchi
- Department of Clinical Laboratories, JR Tokyo General Hospital, Tokyo, Japan
| | - Hitoshi Katai
- Department of Gastric Surgery, National Cancer Center Hospital, Tokyo, Japan
| | - Hiromi Sakamoto
- Fundamental Innovative Oncology Core Center, National Cancer Center Research Institute, Tokyo, Japan
| | - Teruhiko Yoshida
- Department of Genetic Medicine and Services, National Cancer Center Hospital, Tokyo, Japan
| | - Yae Kanai
- Department of Pathology, Keio University School of Medicine, Tokyo, Japan
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17
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Sorgini A, Kim HAJ, Zeng PYF, Shaikh MH, Mundi N, Ghasemi F, Di Gravio E, Khan H, MacNeil D, Khan MI, Mendez A, Yoo J, Fung K, Lang P, Palma DA, Mymryk JS, Barrett JW, Patel KB, Boutros PC, Nichols AC. Analysis of the TCGA Dataset Reveals that Subsites of Laryngeal Squamous Cell Carcinoma are Molecularly Distinct. Cancers (Basel) 2020; 13:cancers13010105. [PMID: 33396315 PMCID: PMC7794818 DOI: 10.3390/cancers13010105] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 12/16/2020] [Accepted: 12/26/2020] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Squamous cell carcinomas from different parts of the larynx have distinct presentations and prognoses, but the molecular basis for this discrepancy has yet to be characterized. We aimed to determine whether different types of mutations at the DNA, mRNA, and protein levels exist to explain the differential prognoses observed. We found that cancers of the supraglottis had higher overall and smoking-associated genome mutations. Further, supraglottic cancers had a significantly poorer prognosis when other clinical variables and mutational status were controlled for. Different protein pathways were enriched in each subsite: muscle-related in the glottis and neural in the supraglottis. Specific cancer-related proteins were also differentially abundant between the supraglottis and glottis. Our findings may partially explain therapeutic response differences, but further study is required for validation. Abstract Laryngeal squamous cell carcinoma (LSCC) from different subsites have distinct presentations and prognosis. In this study, we carried out a multiomic comparison of LSCC subsites. The Cancer Genome Atlas (TCGA) LSCC cohort was analyzed in the R statistical environment for differences between supraglottic and glottic cancers in single nucleotide variations (SNVs), copy number alterations (CNAs), mRNA abundance, protein abundance, pathway overrepresentation, tumor microenvironment (TME), hypoxia status, and patient outcome. Supraglottic cancers had significantly higher overall and smoking-associated SNV mutational load. Pathway analysis revealed upregulation of muscle related pathways in glottic cancer and neural pathways in supraglottic cancer. Proteins involved in cancer relevant signaling pathways including PI3K/Akt/mTOR, the cell cycle, and PDL1 were differentially abundant between subsites. Glottic and supraglottic tumors have different molecular profiles, which may partially account for differences in presentation and response to therapy.
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Affiliation(s)
- Alana Sorgini
- Department of Otolaryngology, Head and Neck Surgery, University of Western Ontario, London, ON N6A 5W9, Canada; (A.S.); (H.A.J.K.); (P.Y.F.Z.); (M.H.S.); (N.M.); (E.D.G.); (H.K.); (D.M.); (M.I.K.); (A.M.); (J.Y.); (K.F.); (D.A.P.); (J.S.M.); (J.W.B.)
| | - Hugh Andrew Jinwook Kim
- Department of Otolaryngology, Head and Neck Surgery, University of Western Ontario, London, ON N6A 5W9, Canada; (A.S.); (H.A.J.K.); (P.Y.F.Z.); (M.H.S.); (N.M.); (E.D.G.); (H.K.); (D.M.); (M.I.K.); (A.M.); (J.Y.); (K.F.); (D.A.P.); (J.S.M.); (J.W.B.)
| | - Peter Y. F. Zeng
- Department of Otolaryngology, Head and Neck Surgery, University of Western Ontario, London, ON N6A 5W9, Canada; (A.S.); (H.A.J.K.); (P.Y.F.Z.); (M.H.S.); (N.M.); (E.D.G.); (H.K.); (D.M.); (M.I.K.); (A.M.); (J.Y.); (K.F.); (D.A.P.); (J.S.M.); (J.W.B.)
| | - Mushfiq Hassan Shaikh
- Department of Otolaryngology, Head and Neck Surgery, University of Western Ontario, London, ON N6A 5W9, Canada; (A.S.); (H.A.J.K.); (P.Y.F.Z.); (M.H.S.); (N.M.); (E.D.G.); (H.K.); (D.M.); (M.I.K.); (A.M.); (J.Y.); (K.F.); (D.A.P.); (J.S.M.); (J.W.B.)
| | - Neil Mundi
- Department of Otolaryngology, Head and Neck Surgery, University of Western Ontario, London, ON N6A 5W9, Canada; (A.S.); (H.A.J.K.); (P.Y.F.Z.); (M.H.S.); (N.M.); (E.D.G.); (H.K.); (D.M.); (M.I.K.); (A.M.); (J.Y.); (K.F.); (D.A.P.); (J.S.M.); (J.W.B.)
| | - Farhad Ghasemi
- Department of General Surgery, University of Western Ontario, London, ON N6A 5C5, Canada;
| | - Eric Di Gravio
- Department of Otolaryngology, Head and Neck Surgery, University of Western Ontario, London, ON N6A 5W9, Canada; (A.S.); (H.A.J.K.); (P.Y.F.Z.); (M.H.S.); (N.M.); (E.D.G.); (H.K.); (D.M.); (M.I.K.); (A.M.); (J.Y.); (K.F.); (D.A.P.); (J.S.M.); (J.W.B.)
| | - Halema Khan
- Department of Otolaryngology, Head and Neck Surgery, University of Western Ontario, London, ON N6A 5W9, Canada; (A.S.); (H.A.J.K.); (P.Y.F.Z.); (M.H.S.); (N.M.); (E.D.G.); (H.K.); (D.M.); (M.I.K.); (A.M.); (J.Y.); (K.F.); (D.A.P.); (J.S.M.); (J.W.B.)
| | - Danielle MacNeil
- Department of Otolaryngology, Head and Neck Surgery, University of Western Ontario, London, ON N6A 5W9, Canada; (A.S.); (H.A.J.K.); (P.Y.F.Z.); (M.H.S.); (N.M.); (E.D.G.); (H.K.); (D.M.); (M.I.K.); (A.M.); (J.Y.); (K.F.); (D.A.P.); (J.S.M.); (J.W.B.)
- Department of Oncology, University of Western Ontario, London, ON N6A 5W9, Canada;
| | - Mohammed Imran Khan
- Department of Otolaryngology, Head and Neck Surgery, University of Western Ontario, London, ON N6A 5W9, Canada; (A.S.); (H.A.J.K.); (P.Y.F.Z.); (M.H.S.); (N.M.); (E.D.G.); (H.K.); (D.M.); (M.I.K.); (A.M.); (J.Y.); (K.F.); (D.A.P.); (J.S.M.); (J.W.B.)
| | - Adrian Mendez
- Department of Otolaryngology, Head and Neck Surgery, University of Western Ontario, London, ON N6A 5W9, Canada; (A.S.); (H.A.J.K.); (P.Y.F.Z.); (M.H.S.); (N.M.); (E.D.G.); (H.K.); (D.M.); (M.I.K.); (A.M.); (J.Y.); (K.F.); (D.A.P.); (J.S.M.); (J.W.B.)
- Department of Oncology, University of Western Ontario, London, ON N6A 5W9, Canada;
| | - John Yoo
- Department of Otolaryngology, Head and Neck Surgery, University of Western Ontario, London, ON N6A 5W9, Canada; (A.S.); (H.A.J.K.); (P.Y.F.Z.); (M.H.S.); (N.M.); (E.D.G.); (H.K.); (D.M.); (M.I.K.); (A.M.); (J.Y.); (K.F.); (D.A.P.); (J.S.M.); (J.W.B.)
- Department of Oncology, University of Western Ontario, London, ON N6A 5W9, Canada;
| | - Kevin Fung
- Department of Otolaryngology, Head and Neck Surgery, University of Western Ontario, London, ON N6A 5W9, Canada; (A.S.); (H.A.J.K.); (P.Y.F.Z.); (M.H.S.); (N.M.); (E.D.G.); (H.K.); (D.M.); (M.I.K.); (A.M.); (J.Y.); (K.F.); (D.A.P.); (J.S.M.); (J.W.B.)
- Department of Oncology, University of Western Ontario, London, ON N6A 5W9, Canada;
| | - Pencilla Lang
- Department of Oncology, University of Western Ontario, London, ON N6A 5W9, Canada;
| | - David A. Palma
- Department of Otolaryngology, Head and Neck Surgery, University of Western Ontario, London, ON N6A 5W9, Canada; (A.S.); (H.A.J.K.); (P.Y.F.Z.); (M.H.S.); (N.M.); (E.D.G.); (H.K.); (D.M.); (M.I.K.); (A.M.); (J.Y.); (K.F.); (D.A.P.); (J.S.M.); (J.W.B.)
- Department of Oncology, University of Western Ontario, London, ON N6A 5W9, Canada;
| | - Joe S. Mymryk
- Department of Otolaryngology, Head and Neck Surgery, University of Western Ontario, London, ON N6A 5W9, Canada; (A.S.); (H.A.J.K.); (P.Y.F.Z.); (M.H.S.); (N.M.); (E.D.G.); (H.K.); (D.M.); (M.I.K.); (A.M.); (J.Y.); (K.F.); (D.A.P.); (J.S.M.); (J.W.B.)
- Department of Oncology, University of Western Ontario, London, ON N6A 5W9, Canada;
- Department of Microbiology & Immunology, University of Western Ontario, London, ON N6A 5C1, Canada
| | - John W. Barrett
- Department of Otolaryngology, Head and Neck Surgery, University of Western Ontario, London, ON N6A 5W9, Canada; (A.S.); (H.A.J.K.); (P.Y.F.Z.); (M.H.S.); (N.M.); (E.D.G.); (H.K.); (D.M.); (M.I.K.); (A.M.); (J.Y.); (K.F.); (D.A.P.); (J.S.M.); (J.W.B.)
- Department of Oncology, University of Western Ontario, London, ON N6A 5W9, Canada;
| | - Krupal B. Patel
- Department of Otolaryngology, Moffitt Cancer Center, Tampa, FL 33612, USA;
| | - Paul C. Boutros
- Department of Human Genetics, University of California, Los Angeles, CA 90095, USA;
- Department of Urology, University of California, Los Angeles, CA 90095, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA 90095, USA
- Institute for Precision Health, University of California, Los Angeles, CA 90095, USA
- Jonsson Comprehensive Cancer Centre, University of California, Los Angeles, CA 90095, USA
| | - Anthony C. Nichols
- Department of Otolaryngology, Head and Neck Surgery, University of Western Ontario, London, ON N6A 5W9, Canada; (A.S.); (H.A.J.K.); (P.Y.F.Z.); (M.H.S.); (N.M.); (E.D.G.); (H.K.); (D.M.); (M.I.K.); (A.M.); (J.Y.); (K.F.); (D.A.P.); (J.S.M.); (J.W.B.)
- Department of Oncology, University of Western Ontario, London, ON N6A 5W9, Canada;
- Correspondence: ; Tel.: +519-685-8804
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Yang H, Wang Y, Zhang Z, Li H. Identification of KIF18B as a Hub Candidate Gene in the Metastasis of Clear Cell Renal Cell Carcinoma by Weighted Gene Co-expression Network Analysis. Front Genet 2020; 11:905. [PMID: 32973873 PMCID: PMC7468490 DOI: 10.3389/fgene.2020.00905] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 07/21/2020] [Indexed: 12/13/2022] Open
Abstract
Background Clear cell renal cell carcinoma (ccRCC) is a common type of fatal malignancy in the urinary system. As the therapeutic strategies of ccRCC are severely limited at present, the prognosis of patients with metastatic carcinoma is usually not promising. Revealing the pathogenesis and identifying hub candidate genes for prognosis prediction and precise treatment are urgently needed in metastatic ccRCC. Methods In the present study, we conducted a series of bioinformatics studies with the gene expression profiles of ccRCC samples from Gene Expression Omnibus (GEO) and the cancer genome atlas (TCGA) database for identifying and validating the hub gene of metastatic ccRCC. We constructed a co-expression network, divided genes into co-expression modules, and identified ccRCC-related modules by weighted gene co-expression network analysis (WGCNA) with data from GEO. Then, we investigated the functions of genes in the ccRCC-related modules by enrichment analyses and built a sub-network accordingly. A hub candidate gene of the metastatic ccRCC was identified by maximal clique centrality (MCC) method. We validate the hub gene by differentially expressed gene analysis, overall survival analysis, and correlation analysis with clinical traits with the external dataset (TCGA). Finally, we explored the function of the hub gene by correlation analysis with targets of precise therapies and single-gene gene set enrichment analysis. Results We conducted WGCNA with the expression profiles of GSE73731 from GEO and divided all genes into 8 meaningful co-expression modules. One module is proved to be positively correlated with pathological stage and tumor grade of ccRCC. Genes in the ccRCC-related module were mainly enriched in functions of mitotic cell division and several proverbial tumor related signal pathways. We then identified KIF18B as a hub gene of the metastasis of ccRCC. Validating analyses in external dataset observed the up-regulation of KIF18B in ccRCC and its correlation with worse outcomes. Further analyses found that the expression of KIF18B is related to that of targets of precise therapies. Conclusion Our study proposed KIF18B as a hub candidate gene of ccRCC for the first time. Our conclusion may provide a brand-new clue for prognosis evaluating and precise treatment for ccRCC in the future.
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Affiliation(s)
- Huiying Yang
- Department of Nephrology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yukun Wang
- Department of Urology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Ziyi Zhang
- Department of Endocrinology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Hua Li
- Department of Nephrology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
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19
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Fujimoto M, Arai E, Tsumura K, Yotani T, Yamada Y, Takahashi Y, Maeshima AM, Fujimoto H, Yoshida T, Kanai Y. Establishment of diagnostic criteria for upper urinary tract urothelial carcinoma based on genome-wide DNA methylation analysis. Epigenetics 2020; 15:1289-1301. [PMID: 32498593 PMCID: PMC7678936 DOI: 10.1080/15592294.2020.1767374] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The aim of this study was to develop a less invasive and accurate diagnostic system for upper urinary tract urothelial carcinoma (UTUC) based on genome-wide DNA methylation profiling. Genome-wide DNA methylation screening was performed using the Infinium HumanMethylation450 BeadChip, and DNA methylation quantification was verified using pyrosequencing. We analysed 26 samples of normal control urothelial tissue (C), an initial cohort of 62 samples (31 samples of non-cancerous urothelium [N] from UTUC patients and 31 samples of the corresponding UTUCs), a validation cohort of 82 samples (41 N and 41 UTUC samples), and 14 samples of urinary bladder urothelial carcinoma (BUC). In the initial cohort, we identified 2,448 CpG sites showing significant differences in DNA methylation levels between both C and UTUC and N and UTUC, but not showing differences between C and N. Among these CpG sites, 10 were located within CpG islands or their shores and shelves included in genomic domains where DNA methylation levels are stably controlled, allowing discrimination of UTUC even from BUC. Receiver operating characteristic curve analysis for discrimination of UTUC from N in these 10 CpG and neighbouring sites (37 diagnostic panels in total) yielded area under the curve values of 0.959-1.000, with a sensitivity and specificity of 86.6-100% and 93.5-100%, respectively. The diagnostic impact was successfully confirmed in the validation cohort. Our criteria were useful for diagnosis of UTUC, regardless of its clinicopathological features. Application of our criteria to voided urine samples will ultimately allow non-invasive DNA methylation diagnosis of UTUC.
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Affiliation(s)
- Mao Fujimoto
- Department of Pathology, Keio University School of Medicine , Tokyo, Japan
| | - Eri Arai
- Department of Pathology, Keio University School of Medicine , Tokyo, Japan
| | - Koji Tsumura
- Department of Urology, Graduate School of Medicine, the University of Tokyo , Tokyo, Japan
| | - Takuya Yotani
- Tsukuba Research Institute, Research and Development Division, Sekisui Medical Co., Ltd ., Ryugasaki, Japan
| | - Yuriko Yamada
- Tsukuba Research Institute, Research and Development Division, Sekisui Medical Co., Ltd ., Ryugasaki, Japan
| | - Yoriko Takahashi
- Bioscience Department, Solution Knowledge Center, Mitsui Knowledge Industry Co., Ltd ., Tokyo, Japan
| | - Akiko Miyagi Maeshima
- Department of Pathology and Clinical Laboratories, National Cancer Center Hospital , Tokyo, Japan
| | - Hiroyuki Fujimoto
- Department of Urology, National Cancer Center Hospital , Tokyo, Japan
| | - Teruhiko Yoshida
- Fundamental Innovative Oncology Core Center, National Cancer Center Research Institute , Tokyo, Japan
| | - Yae Kanai
- Department of Pathology, Keio University School of Medicine , Tokyo, Japan
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20
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Li C, Zou H, Xiong Z, Xiong Y, Miyagishima DF, Wanggou S, Li X. Construction and Validation of a 13-Gene Signature for Prognosis Prediction in Medulloblastoma. Front Genet 2020; 11:429. [PMID: 32508873 PMCID: PMC7249855 DOI: 10.3389/fgene.2020.00429] [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] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 04/07/2020] [Indexed: 01/28/2023] Open
Abstract
Background: Recent studies have identified several molecular subgroups of medulloblastoma associated with distinct clinical outcomes; however, no robust gene signature has been established for prognosis prediction. Our objective was to construct a robust gene signature-based model to predict the prognosis of patients with medulloblastoma. Methods: Expression data of medulloblastomas were acquired from the Gene Expression Omnibus (GSE85217, n = 763; GSE37418, n = 76). To identify genes associated with overall survival (OS), we performed univariate survival analysis and least absolute shrinkage and selection operator (LASSO) Cox regression. A risk score model was constructed based on selected genes and was validated using multiple datasets. Differentially expressed genes (DEGs) between the risk groups were identified. Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Ontology (GO), and protein–protein interaction (PPI) analyses were performed. Network modules and hub genes were identified using Cytoscape. Furthermore, tumor microenvironment (TME) was evaluated using ESTIMATE algorithm. Tumor-infiltrating immune cells (TIICs) were inferred using CIBERSORTx. Results: A 13-gene model was constructed and validated. Patients classified as high-risk group had significantly worse OS than those as low-risk group (Training set: p < 0.0001; Validation set 1: p < 0.0001; Validation set 2: p = 0.00052). The area under the curve (AUC) of the receiver operating characteristic (ROC) analysis indicated a good performance in predicting 1-, 3-, and 5-year OS in all datasets. Multivariate analysis integrating clinical factors demonstrated that the risk score was an independent predictor for the OS (validation set 1: p = 0.001, validation set 2: p = 0.004). We then identified 265 DEGs between risk groups and PPI analysis predicted modules that were highly related to central nervous system and embryonic development. The risk score was significantly correlated with programmed death-ligand 1 (PD-L1) expression (p < 0.001), as well as immune score (p = 0.035), stromal score (p = 0.010), and tumor purity (p = 0.010) in Group 4 medulloblastomas. Correlations between the 13-gene signature and the TIICs in Sonic hedgehog and Group 4 medulloblastomas were revealed. Conclusion: Our study constructed and validated a robust 13-gene signature model estimating the prognosis of medulloblastoma patients. We also revealed genes and pathways that may be related to the development and prognosis of medulloblastoma, which might provide candidate targets for future investigation.
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Affiliation(s)
- Chang Li
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China.,Xiangya School of Medicine, Central South University, Changsha, China.,Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, China
| | - Han Zou
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China.,Xiangya School of Medicine, Central South University, Changsha, China.,Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, China
| | - Zujian Xiong
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China.,Xiangya School of Medicine, Central South University, Changsha, China.,Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, China
| | - Yi Xiong
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China.,Xiangya School of Medicine, Central South University, Changsha, China.,Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, China
| | - Danielle F Miyagishima
- Department of Neurosurgery, Yale School of Medicine, New Haven, CT, United States.,Department of Genetics, Yale School of Medicine, New Haven, CT, United States
| | - Siyi Wanggou
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China.,Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, China
| | - Xuejun Li
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China.,Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, China
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21
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Wang Z, Cheng H, Qi L, Sui D. Comprehensive analysis of long non‑coding RNA using an associated competitive endogenous RNA network in Wilms tumor. Mol Med Rep 2020; 22:105-116. [PMID: 32377711 PMCID: PMC7252721 DOI: 10.3892/mmr.2020.11124] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 02/26/2020] [Indexed: 12/27/2022] Open
Abstract
Wilms tumor (WT) is the most common malignant renal neoplasm in children; however, the underlying molecular mechanisms are not well understood. According to the competing endogenous RNA (ceRNA) theory, long non-coding RNAs (lncRNAs) can regulate the expression of target genes by adsorbing microRNAs (miRNAs/miRs). However, the role of lncRNAs in WT has not been fully elucidated. The aim of the present study was to construct a ceRNA network to identify the potential lncRNAs involved in WT. The expression profiles of lncRNAs, miRNAs and mRNAs in 120 WT and six normal tissues were obtained from the Therapeutically Applicable Research to Generate Effective Treatments database. A total of 442 lncRNAs, 214 miRNAs and 4,912 mRNAs were identified as differentially expressed in WT and were enriched in 472 Gene Ontology terms (355 biological processes, 89 cellular components and 29 molecular functions) and 18 Kyoto Encyclopedia of Genes and Genomes pathways. A lncRNA-miRNA-mRNA ceRNA network of WT consisting of with 32 lncRNAs, 14 miRNAs and 158 mRNAs was constructed, based on the bioinformatics analysis of the miR target prediction database and the miRNAcode, miRTarBase and TargetScan databases. Subsequently, three lncRNAs, three miRNAs and 17 mRNAs, which had a significant effect on the overall survival rate of patients with WT, were identified based on the survival analysis. The three lncRNAs were also differentially expressed in the late and early stages of WT and were validated using the GSE66405 dataset obtained from the Gene Expression Omnibus database. In conclusion, the present study generated a specific lncRNA-related ceRNA network of WT, which may provide a novel perspective on the molecular mechanisms underlying the progression and prognosis of the disease.
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Affiliation(s)
- Zhichao Wang
- Department of Pharmacology, School of Pharmaceutical Sciences, Jilin University, Changchun, Jilin 130021, P.R. China
| | - Huiyan Cheng
- Department of Gynecology, First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Lingli Qi
- Department of Pediatric Gastroenterology, First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Dayun Sui
- Department of Pharmacology, School of Pharmaceutical Sciences, Jilin University, Changchun, Jilin 130021, P.R. China
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22
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Peters I, Merseburger AS, Tezval H, Lafos M, Tabrizi PF, Mazdak M, Wolters M, Kuczyk MA, Serth J, von Klot CA. The Prognostic Value of DNA Methylation Markers in Renal Cell Cancer: A Systematic Review. KIDNEY CANCER 2020. [DOI: 10.3233/kca-190069] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Inga Peters
- Department of Urology and Urologic Oncology, Hannover Medical School, Hannover, Germany
| | | | - Hossein Tezval
- Department of Urology and Urologic Oncology, Hannover Medical School, Hannover, Germany
| | - Marcel Lafos
- Department of Pathology, Hannover Medical School, Hannover, Germany
| | - Pouriya Faraj Tabrizi
- Department of Urology and Urologic Oncology, Hannover Medical School, Hannover, Germany
| | - Mehrdad Mazdak
- Department of Urology and Urologic Oncology, Hannover Medical School, Hannover, Germany
| | - Mathias Wolters
- Department of Urology and Urologic Oncology, Hannover Medical School, Hannover, Germany
| | - Markus A. Kuczyk
- Department of Urology and Urologic Oncology, Hannover Medical School, Hannover, Germany
| | - Jürgen Serth
- Department of Urology and Urologic Oncology, Hannover Medical School, Hannover, Germany
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23
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Zhu C, Yang Q, Xu J, Zhao W, Zhang Z, Xu D, Zhang Y, Zhao E, Zhao G. Somatic mutation of DNAH genes implicated higher chemotherapy response rate in gastric adenocarcinoma patients. J Transl Med 2019; 17:109. [PMID: 30944005 PMCID: PMC6448266 DOI: 10.1186/s12967-019-1867-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Accepted: 03/29/2019] [Indexed: 12/13/2022] Open
Abstract
Background The dynein axonemal heavy chain (DNAH) family of genes encode the dynein axonemal heavy chain, which is involved in cell motility. Genomic variations of DNAH family members have been frequently reported in diverse kinds of malignant tumors. In this study, we analyzed the genomic database to evaluate the mutation status of DNAH genes in gastric adenocarcinoma and further identified the significance of mutant DNAH genes as effective molecular biomarkers for predicting chemotherapy response in gastric cancer patients. Methods We analyzed the clinical and genomic data of gastric cancer patients published in The Cancer Genome Atlas (TCGA) project. Data on chemotherapy response, overall survival (OS) and chemotherapy-free survival were retrieved. Then, we verified the results via targeted sequencing of gastric cancer patients with similar clinical characteristics but different chemotherapeutic outcomes. Results In total, 132 gastric adenocarcinoma patients undergoing chemotherapy treatment from TCGA were included in our study. Somatic mutations in all 13 members of the DNAH family of genes were associated with different chemotherapy responses. Compared with patients with wild-type DNAH genes (n = 59), a significantly higher proportion of those with mutations in DNAH genes (n = 73) (55.9% vs 80.8%) responded to chemotherapy (P = 0.002). Moreover, DNAH mutations were correlated with significantly better OS (P = 0.027), chemotherapy-free survival (P = 0.027), fluoropyrimidine-free survival (P = 0.048) and platinum-free survival (P = 0.014). DNAH mutation status was an independent risk factor for OS (P = 0.015), chemotherapy-free survival (P = 0.015) and platinum-free survival (P = 0.011). We identified somatic mutations in 27 (42.2%) of the 64 stage III gastric adenocarcinoma patients receiving fluoropyrimidine-based chemotherapy by targeted exon sequencing with strict screening conditions. In our own cohort, a significantly higher proportion of patients (n = 32) with DNAH mutations than patients with wild-type DNAH genes (n = 32) had a good prognosis (OS > 48 months) (70.4% vs 35.1%) (P = 0.005). Conclusions Dynein axonemal heavy chain gene mutations contribute positively to chemotherapy sensitivity in gastric cancer patients. Electronic supplementary material The online version of this article (10.1186/s12967-019-1867-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chunchao Zhu
- Department of Gastrointestinal Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, People's Republic of China.,State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Qin Yang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Jia Xu
- Department of Gastrointestinal Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, People's Republic of China.,State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Wenyi Zhao
- Department of Gastrointestinal Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, People's Republic of China.,State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Zizhen Zhang
- Department of Gastrointestinal Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, People's Republic of China.,State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Danhua Xu
- Department of Gastrointestinal Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, People's Republic of China.,State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Yeqian Zhang
- Department of Gastrointestinal Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, People's Republic of China.,State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Enhao Zhao
- Department of Gastrointestinal Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, People's Republic of China.
| | - Gang Zhao
- Department of Gastrointestinal Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, People's Republic of China.
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24
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Kanai Y, Nishihara H, Miyagi Y, Tsuruyama T, Taguchi K, Katoh H, Takeuchi T, Gotoh M, Kuramoto J, Arai E, Ojima H, Shibuya A, Yoshida T, Akahane T, Kasajima R, Morita KI, Inazawa J, Sasaki T, Fukayama M, Oda Y. The Japanese Society of Pathology Guidelines on the handling of pathological tissue samples for genomic research: Standard operating procedures based on empirical analyses. Pathol Int 2018; 68:63-90. [PMID: 29431262 DOI: 10.1111/pin.12631] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 12/12/2017] [Indexed: 12/19/2022]
Abstract
Genome research using appropriately collected pathological tissue samples is expected to yield breakthroughs in the development of biomarkers and identification of therapeutic targets for diseases such as cancers. In this connection, the Japanese Society of Pathology (JSP) has developed "The JSP Guidelines on the Handling of Pathological Tissue Samples for Genomic Research" based on an abundance of data from empirical analyses of tissue samples collected and stored under various conditions. Tissue samples should be collected from appropriate sites within surgically resected specimens, without disturbing the features on which pathological diagnosis is based, while avoiding bleeding or necrotic foci. They should be collected as soon as possible after resection: at the latest within about 3 h of storage at 4°C. Preferably, snap-frozen samples should be stored in liquid nitrogen (about -180°C) until use. When intending to use genomic DNA extracted from formalin-fixed paraffin-embedded tissue, 10% neutral buffered formalin should be used. Insufficient fixation and overfixation must both be avoided. We hope that pathologists, clinicians, clinical laboratory technicians and biobank operators will come to master the handling of pathological tissue samples based on the standard operating procedures in these Guidelines to yield results that will assist in the realization of genomic medicine.
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Affiliation(s)
- Yae Kanai
- Department of Pathology, Keio University School of Medicine, Tokyo, Japan
| | - Hiroshi Nishihara
- Department of Translational Pathology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Yohei Miyagi
- Molecular Pathology and Genetics Division, Kanagawa Cancer Center Research Institute, Yokohama, Japan
| | | | - Kenichi Taguchi
- Department of Pathology, National Kyushu Cancer Center, Fukuoka, Japan
| | - Hiroto Katoh
- Department of Genomic Pathology, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Tomoyo Takeuchi
- Department of Pathology, Institute of Basic Medical Science, University of Tsukuba, Tsukuba, Japan
| | - Masahiro Gotoh
- Fundamental Innovative Oncology Core, National Cancer Center Research Institute, Tokyo, Japan
| | - Junko Kuramoto
- Department of Pathology, Keio University School of Medicine, Tokyo, Japan
| | - Eri Arai
- Department of Pathology, Keio University School of Medicine, Tokyo, Japan
| | - Hidenori Ojima
- Department of Pathology, Keio University School of Medicine, Tokyo, Japan
| | | | - Teruhiko Yoshida
- Fundamental Innovative Oncology Core, National Cancer Center Research Institute, Tokyo, Japan
| | | | - Rika Kasajima
- Molecular Pathology and Genetics Division, Kanagawa Cancer Center Research Institute, Yokohama, Japan
| | - Kei-Ichi Morita
- Tokyo Medical and Dental University, Bioresource Research Center, Tokyo, Japan
| | - Johji Inazawa
- Tokyo Medical and Dental University, Bioresource Research Center, Tokyo, Japan
| | - Takeshi Sasaki
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masashi Fukayama
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yoshinao Oda
- Department of Anatomic Pathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
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25
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Abstract
Renal cell carcinoma (RCC) is the most common kidney cancer and includes several molecular and histological subtypes with different clinical characteristics. While survival rates are high if RCC is diagnosed when still confined to the kidney and treated definitively, there are no specific diagnostic screening tests available and symptoms are rare in early stages of the disease. Management of advanced RCC has changed significantly with the advent of targeted therapies, yet survival is usually increased by months due to acquired resistance to these therapies. DNA methylation, the covalent addition of a methyl group to a cytosine, is essential for normal development and transcriptional regulation, but becomes altered commonly in cancer. These alterations result in broad transcriptional changes, including in tumor suppressor genes. Because DNA methylation is one of the earliest molecular changes in cancer and is both widespread and stable, its role in cancer biology, including RCC, has been extensively studied. In this review, we examine the role of DNA methylation in RCC disease etiology and progression, the preclinical use of DNA methylation alterations as diagnostic, prognostic and predictive biomarkers, and the potential for DNA methylation-directed therapies.
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Affiliation(s)
- Brittany N Lasseigne
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35806-2908, USA.
| | - James D Brooks
- Department of Urology, Stanford University Medical Center, 300 Pasteur Drive, Stanford, CA, 94305-5118, USA
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26
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Arai E, Miura F, Totoki Y, Yamashita S, Tian Y, Gotoh M, Ojima H, Nakagawa H, Takahashi Y, Nakamura H, Hama N, Kato M, Kimura H, Suzuki Y, Ito T, Shibata T, Kanai Y. Epigenome mapping of human normal purified hepatocytes: personal epigenome variation and genome-epigenome correlation. Epigenomics 2018; 10:955-979. [PMID: 29972026 DOI: 10.2217/epi-2017-0111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
AIM The aim of this study was to reveal the epigenome landscape of human normal hepatocytes. MATERIALS & METHODS Cells purified from partial hepatectomy specimens of Japanese patients were subjected to whole-genome bisulfite sequencing using postbisulfite adaptor tagging, chromatin immunoprecipitation sequencing, RNA sequencing and whole-genome sequencing. RESULTS CHG and CHH methylations were inversely associated with gene expression. Histone modification profiles of personal differentially methylated regions (pDMRs) differed considerably among samples. pDMRs were observed around the transcription start sites of genes whose expression is reportedly regulated by CpG methylation. pDMRs were frequently observed in the vicinity of single-nucleotide variations and insertions/deletions. CONCLUSION Genetic variations may induce epigenetic variations, generating individual differences in the phenotypes of normal hepatocytes through variations in expression.
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Affiliation(s)
- Eri Arai
- Department of Pathology, Keio University School of Medicine, Tokyo 160-8582, Japan.,Division of Molecular Pathology, National Cancer Center Research Institute, Tokyo 104-0045, Japan.,AMED-CREST, Japan Agency for Medical Research & Development, Tokyo 100-0004, Japan
| | - Fumihito Miura
- AMED-CREST, Japan Agency for Medical Research & Development, Tokyo 100-0004, Japan.,Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan
| | - Yasushi Totoki
- AMED-CREST, Japan Agency for Medical Research & Development, Tokyo 100-0004, Japan.,Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Satoshi Yamashita
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Ying Tian
- Department of Pathology, Keio University School of Medicine, Tokyo 160-8582, Japan.,AMED-CREST, Japan Agency for Medical Research & Development, Tokyo 100-0004, Japan
| | - Masahiro Gotoh
- Division of Molecular Pathology, National Cancer Center Research Institute, Tokyo 104-0045, Japan.,AMED-CREST, Japan Agency for Medical Research & Development, Tokyo 100-0004, Japan
| | - Hidenori Ojima
- Department of Pathology, Keio University School of Medicine, Tokyo 160-8582, Japan.,AMED-CREST, Japan Agency for Medical Research & Development, Tokyo 100-0004, Japan
| | - Hiroyuki Nakagawa
- Biomedical Department, Cloud Service Division, IT Infrastructure Services Unit, Mitsui Knowledge Industry Co., Ltd, Tokyo 105-6215, Japan
| | - Yoriko Takahashi
- Biomedical Department, Cloud Service Division, IT Infrastructure Services Unit, Mitsui Knowledge Industry Co., Ltd, Tokyo 105-6215, Japan
| | - Hiromi Nakamura
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Natsuko Hama
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Mamoru Kato
- Department of Bioinformatics, National Cancer Center Research Institute, Tokyo 104-0045, Japan
| | - Hiroshi Kimura
- AMED-CREST, Japan Agency for Medical Research & Development, Tokyo 100-0004, Japan.,Graduate School of Bioscience & Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Yutaka Suzuki
- AMED-CREST, Japan Agency for Medical Research & Development, Tokyo 100-0004, Japan.,Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8561, Japan
| | - Takashi Ito
- AMED-CREST, Japan Agency for Medical Research & Development, Tokyo 100-0004, Japan.,Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan
| | - Tatsuhiro Shibata
- AMED-CREST, Japan Agency for Medical Research & Development, Tokyo 100-0004, Japan.,Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo 104-0045, Japan.,Laboratory of Molecular Medicine, Human Genome Center, The Institute of Medical Sciences, The University of Tokyo, Tokyo 108-8639, Japan
| | - Yae Kanai
- Department of Pathology, Keio University School of Medicine, Tokyo 160-8582, Japan.,Division of Molecular Pathology, National Cancer Center Research Institute, Tokyo 104-0045, Japan.,AMED-CREST, Japan Agency for Medical Research & Development, Tokyo 100-0004, Japan
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27
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Yotani T, Yamada Y, Arai E, Tian Y, Gotoh M, Komiyama M, Fujimoto H, Sakamoto M, Kanai Y. Novel method for DNA methylation analysis using high-performance liquid chromatography and its clinical application. Cancer Sci 2018; 109:1690-1700. [PMID: 29520901 PMCID: PMC5980336 DOI: 10.1111/cas.13566] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 02/17/2018] [Accepted: 02/25/2018] [Indexed: 12/21/2022] Open
Abstract
The aim of this study was to develop a new methodology that is suitable for DNA methylation diagnostics and to demonstrate its clinical applicability. We developed a new anion-exchange column for high-performance liquid chromatography (HPLC) with electrostatic and hydrophobic properties. Both cytosine and thymine, corresponding to methylated and unmethylated cytosine after bisulfite modification, respectively, are captured by electrostatic interaction and then discriminated from each other by their hydrophobic interactions. The DNA methylation levels of synthetic DNA were quantified accurately and reproducibly within 10 minutes without time-consuming pretreatment of PCR products, and the measured values were unaffected by the distribution of methylated CpG within the synthetic DNA fragments. When the DNA methylation status of the FAM150A gene, a marker of the CpG island methylator phenotype specific to clear cell renal cell carcinoma (ccRCC), was examined in 98 patients with ccRCC, bulk specimens of tumorous tissue including cancer cells showing DNA methylation of the FAM150A gene were easily identifiable by simply viewing the differentiated chromatograms, even when the cancer cell content was low. Sixteen ccRCC showing DNA methylation more frequently exhibited clinicopathological parameters reflecting tumor aggressiveness (ie, a larger diameter, higher histological grade, vascular involvement, renal vein tumor thrombi, infiltrating growth, tumor necrosis, renal pelvis invasion and higher pathological TNM stage), and had significantly lower recurrence-free and overall survival rates. These data indicate that HPLC analysis using this newly developed anion-exchange column could be a powerful tool for DNA methylation diagnostics, including prognostication of patients with cancers, in a clinical setting.
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Affiliation(s)
- Takuya Yotani
- Department of PathologyKeio University School of MedicineTokyoJapan
- Tsukuba Research InstituteResearch and Development DivisionSekisui Medical Co., Ltd.RyugasakiJapan
- Division of Molecular PathologyNational Cancer Center Research InstituteTokyoJapan
| | - Yuriko Yamada
- Tsukuba Research InstituteResearch and Development DivisionSekisui Medical Co., Ltd.RyugasakiJapan
- Division of Molecular PathologyNational Cancer Center Research InstituteTokyoJapan
| | - Eri Arai
- Department of PathologyKeio University School of MedicineTokyoJapan
- Division of Molecular PathologyNational Cancer Center Research InstituteTokyoJapan
| | - Ying Tian
- Department of PathologyKeio University School of MedicineTokyoJapan
| | - Masahiro Gotoh
- Division of Molecular PathologyNational Cancer Center Research InstituteTokyoJapan
| | | | | | - Michiie Sakamoto
- Department of PathologyKeio University School of MedicineTokyoJapan
| | - Yae Kanai
- Department of PathologyKeio University School of MedicineTokyoJapan
- Division of Molecular PathologyNational Cancer Center Research InstituteTokyoJapan
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28
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Yanagita T, Murata Y, Tanaka D, Motegi SI, Arai E, Daniwijaya EW, Hazama D, Washio K, Saito Y, Kotani T, Ohnishi H, Oldenborg PA, Garcia NV, Miyasaka M, Ishikawa O, Kanai Y, Komori T, Matozaki T. Anti-SIRP α antibodies as a potential new tool for cancer immunotherapy. JCI Insight 2017; 2:e89140. [PMID: 28097229 DOI: 10.1172/jci.insight.89140] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Tumor cells are thought to evade immune surveillance through interaction with immune cells. Much recent attention has focused on the modification of immune responses as a basis for new cancer treatments. SIRPα is an Ig superfamily protein that inhibits phagocytosis in macrophages upon interaction with its ligand CD47 expressed on the surface of target cells. Here, we show that SIRPα is highly expressed in human renal cell carcinoma and melanoma. Furthermore, an anti-SIRPα Ab that blocks the interaction with CD47 markedly suppressed tumor formation by renal cell carcinoma or melanoma cells in immunocompetent syngeneic mice. This inhibitory effect of the Ab appeared to be mediated by dual mechanisms: direct induction of Ab-dependent cellular phagocytosis of tumor cells by macrophages and blockade of CD47-SIRPα signaling that negatively regulates such phagocytosis. The antitumor effect of the Ab was greatly attenuated by selective depletion not only of macrophages but also of NK cells or CD8+ T cells. In addition, the anti-SIRPα Ab also enhances the inhibitory effects of Abs against CD20 and programmed cell death 1 (PD-1) on tumor formation in mice injected with SIRPα-nonexpressing tumor cells. Anti-SIRPα Abs thus warrant further study as a potential new therapy for a broad range of cancers.
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Affiliation(s)
- Tadahiko Yanagita
- Division of Molecular and Cellular Signaling, Department of Biochemistry and Molecular Biology.,Department of Oral and Maxillofacial Surgery, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Yoji Murata
- Division of Molecular and Cellular Signaling, Department of Biochemistry and Molecular Biology
| | - Daisuke Tanaka
- Division of Molecular and Cellular Signaling, Department of Biochemistry and Molecular Biology
| | - Sei-Ichiro Motegi
- Department of Dermatology, Gunma University Graduate School of Medicine, Gunma, Japan
| | - Eri Arai
- Division of Molecular Pathology, National Cancer Center Research Institute, Tokyo, Japan.,Department of Pathology, Keio University School of Medicine, Tokyo, Japan
| | | | - Daisuke Hazama
- Division of Molecular and Cellular Signaling, Department of Biochemistry and Molecular Biology
| | - Ken Washio
- Division of Molecular and Cellular Signaling, Department of Biochemistry and Molecular Biology
| | - Yasuyuki Saito
- Division of Molecular and Cellular Signaling, Department of Biochemistry and Molecular Biology
| | - Takenori Kotani
- Division of Molecular and Cellular Signaling, Department of Biochemistry and Molecular Biology
| | - Hiroshi Ohnishi
- Department of Laboratory Sciences, Gunma University Graduate School of Health Sciences, Gunma, Japan
| | - Per-Arne Oldenborg
- Department of Integrative Medical Biology, Section for Histology and Cell Biology, Umeå University, Umeå, Sweden
| | - Noel Verjan Garcia
- Laboratory of Immunodynamics, Department of Microbiology and Immunology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Masayuki Miyasaka
- Laboratory of Immunodynamics, Department of Microbiology and Immunology, Osaka University Graduate School of Medicine, Osaka, Japan.,MediCity Research Laboratory, University of Turku, Turku, Finland
| | - Osamu Ishikawa
- Department of Dermatology, Gunma University Graduate School of Medicine, Gunma, Japan
| | - Yae Kanai
- Division of Molecular Pathology, National Cancer Center Research Institute, Tokyo, Japan.,Department of Pathology, Keio University School of Medicine, Tokyo, Japan
| | - Takahide Komori
- Department of Oral and Maxillofacial Surgery, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Takashi Matozaki
- Division of Molecular and Cellular Signaling, Department of Biochemistry and Molecular Biology
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29
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Chinello C, L'imperio V, Stella M, Smith AJ, Bovo G, Grasso A, Grasso M, Raimondo F, Pitto M, Pagni F, Magni F. The proteomic landscape of renal tumors. Expert Rev Proteomics 2016; 13:1103-1120. [PMID: 27748142 DOI: 10.1080/14789450.2016.1248415] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Renal cell carcinoma (RCC) is the most fatal of the common urologic cancers, with approximately 35% of patients dying within 5 years following diagnosis. Therefore, there is a need for non-invasive markers that are capable of detecting and determining the severity of small renal masses at an early stage in order to tailor treatment and follow-up. Proteomic studies have proved to be very useful in the study of tumors. Areas covered: In this review, we will detail the current knowledge obtained by the different proteomic approaches, focusing on MS-based strategies, used to investigate RCC biology in order to identify diagnostic, prognostic and predictive biomarkers on tissue, cultured cells and biological fluids. Expert commentary: Currently, no reliable biomarkers or targets for RCC have been translated into the clinical setting. Moreover, despite the efforts of proteomics and other -omics disciplines, only a small number of them have been observed as shared targets between the different analytical platforms and biological specimens. The difficulty to define a specific molecular pattern for RCC and its subtypes highlights a peculiar profile and a heterogeneity that must be taken into account in future studies.
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Affiliation(s)
- Clizia Chinello
- a Department of Medicine and Surgery , University Milan Bicocca , Monza , Italy
| | - Vincenzo L'imperio
- a Department of Medicine and Surgery , University Milan Bicocca , Monza , Italy
| | - Martina Stella
- a Department of Medicine and Surgery , University Milan Bicocca , Monza , Italy
| | - Andrew James Smith
- a Department of Medicine and Surgery , University Milan Bicocca , Monza , Italy
| | - Giorgio Bovo
- b Pathology unit , San Gerardo Hospital , Monza , Italy
| | - Angelica Grasso
- c Department of Specialistic Surgical Sciences, Urology unit , Ospedale Maggiore Policlinico Foundation , Milano , Italy
| | - Marco Grasso
- d Department of Urology , San Gerardo Hospital , Monza , Italy
| | - Francesca Raimondo
- a Department of Medicine and Surgery , University Milan Bicocca , Monza , Italy
| | - Marina Pitto
- a Department of Medicine and Surgery , University Milan Bicocca , Monza , Italy
| | - Fabio Pagni
- a Department of Medicine and Surgery , University Milan Bicocca , Monza , Italy
| | - Fulvio Magni
- a Department of Medicine and Surgery , University Milan Bicocca , Monza , Italy
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30
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Liu S, Mitra R, Zhao MM, Fan W, Eischen CM, Yin F, Zhao Z. The Potential Roles of Long Noncoding RNAs (lncRNA) in Glioblastoma Development. Mol Cancer Ther 2016; 15:2977-2986. [PMID: 27784795 DOI: 10.1158/1535-7163.mct-16-0320] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 09/17/2016] [Accepted: 09/20/2016] [Indexed: 01/06/2023]
Abstract
Long noncoding RNA (lncRNA) may contribute to the initiation and progression of tumor. In this study, we first systematically compared lncRNA and mRNA expression between glioblastoma and paired normal brain tissues using microarray data. We found 27 lncRNA and 82 mRNA significantly upregulated in glioblastoma, as well as 198 lncRNA and 285 mRNA significantly downregulated in glioblastoma. We identified 138 coexpressed lncRNA-mRNA pairs from these differentially expressed lncRNA and genes. Subsequent pathway analysis of the lncRNA-paired genes indicated that EphrinB-EPHB, p75-mediated signaling, TNFα/NF-κB, and ErbB2/ErbB3 signaling pathways might be altered in glioblastoma. Specifically, lncRNA RAMP2-AS1 had significant decrease of expression in glioblastoma tissues and showed coexpressional relationship with NOTCH3, an important tumor promoter in many neoplastic diseases. Our follow up experiment indicated that (i) an overexpression of RAMP2-AS1 reduced glioblastoma cell proliferation in vitro and also reduced glioblastoma xenograft tumors in vivo; (ii) NOTCH3 and RAMP2-AS1 coexpression rescued the inhibitory action of RAMP2-AS1 in glioblastoma cells; and (iii) RNA pull-down assay revealed a direct interaction of RAMP2-AS1 with DHC10, which may consequently inhibit, as we hypothesize, the expression of NOTCH3 and its downstream signaling molecule HES1 in glioblastoma. Taken together, our data revealed that lncRNA expression profile in glioblastoma tissue was significantly altered; and RAMP2-AS1 might play a tumor suppressive role in glioblastoma through an indirect inhibition of NOTCH3 Our results provided some insights into understanding the key roles of lncRNA-mRNA coregulation in human glioblastoma and the mechanisms responsible for glioblastoma progression and pathogenesis. Mol Cancer Ther; 15(12); 2977-86. ©2016 AACR.
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Affiliation(s)
- Shuang Liu
- Department of Neurosurgery, Navy General Hospital, PLA. Beijing, 100048, China
| | - Ramkrishna Mitra
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA.,Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37203, USA
| | - Ming-Ming Zhao
- Department of Neurosurgery, Navy General Hospital, PLA. Beijing, 100048, China
| | - Wenhong Fan
- Department of Recombinant Drugs, National Institutes for Food and Drug Control, Beijing, 100050, China
| | - Christine M Eischen
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA
| | - Feng Yin
- Department of Neurosurgery, Navy General Hospital, PLA. Beijing, 100048, China
| | - Zhongming Zhao
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37203, USA.,Department of Cancer Biology, Vanderbilt University Medical Center, Nashville, TN 37212, USA.,Center for Precision Health, School of Biomedical University, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
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31
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Sheng Y, Wang H, Liu D, Zhang C, Deng Y, Yang F, Zhang T, Zhang C. Methylation of tumor suppressor gene CDH13 and SHP1 promoters and their epigenetic regulation by the UHRF1/PRMT5 complex in endometrial carcinoma. Gynecol Oncol 2015; 140:145-51. [PMID: 26597461 DOI: 10.1016/j.ygyno.2015.11.017] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 10/24/2015] [Accepted: 11/17/2015] [Indexed: 12/19/2022]
Abstract
OBJECTIVE Epigenetic changes in cancer and precancerous lesions could be utilized as biomarkers for cancer early detection. This study aims to investigate the novel biomarkers in endometrial carcinoma, and explore their epigenetic regulation. METHODS Methylation of six tumor suppressor genes (CDH13, SHP1, HIN1, DKK3, CTNNA1 and PCDH8) was evaluated in 155 endometrium samples. Changes of methylation and mRNA expression after treatment with 5-Aza-2'-deoxycytidine (5-Aza-CdR) or/and trichostatin A (TSA) were investigated by MSP and qRT-PCR respectively. Co-immunoprecipitation was used to detect the interactions between UHRF1 and PRMT5 proteins. RESULTS CDH13 and SHP1 promoters were highly methylated (81.36% and 86.44%, respectively) in endometrial carcinoma, while CDH13 promoter methylation was also present in complex hyperplasia and atypical hyperplasia (51.72% and 50.00%, respectively). Methylation of CDH13 and SHP1 promoters was associated with age and tumor differentiation or muscular infiltration depth. CDH13 and SHP1 promoters were completely methylated in endometrial carcinoma cell lines and were partially reversed by 5-Aza-CdR or TSA to induce mRNA levels (P<0.01). After combined treatment with these two agents, methylation of CDH13 and SHP1 promoters was completely reversed and expression of their mRNA was significantly increased (P<0.01). Moreover, PRMT5 could bind to UHRF1 and down-regulated by 5-Aza-CdR and/or TSA treatment (P<0.05). CONCLUSIONS Our data demonstrate for the first time that SHP1 methylation has high specificity for diagnosis of endometrial carcinoma, while CDH13 promoter methylation plays a role in the earlier stage. Furthermore, UHRF1 could form a complex with PRMT5 to contribute to the endometrial carcinogenesis.
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Affiliation(s)
- Yan Sheng
- Institute of Pathology and Pathophysiology, Shandong University School of Medicine, Jinan 250012, China; Department of Gynecology and Obstetrics, Tianjin Medical University General Hospital, Tianjin, China
| | - Hongtao Wang
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research for Cancer, The Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, China
| | - Dongchen Liu
- Institute of Pathology and Pathophysiology, Shandong University School of Medicine, Jinan 250012, China
| | - Cheng Zhang
- Institute of Pathology and Pathophysiology, Shandong University School of Medicine, Jinan 250012, China
| | - Yupeng Deng
- Institute of Pathology and Pathophysiology, Shandong University School of Medicine, Jinan 250012, China
| | - Fan Yang
- Institute of Pathology and Pathophysiology, Shandong University School of Medicine, Jinan 250012, China
| | - Tingguo Zhang
- Institute of Pathology and Pathophysiology, Shandong University School of Medicine, Jinan 250012, China.
| | - Cuijuan Zhang
- Institute of Pathology and Pathophysiology, Shandong University School of Medicine, Jinan 250012, China.
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