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Hushmandi K, Einollahi B, Saadat SH, Lee EHC, Farani MR, Okina E, Huh YS, Nabavi N, Salimimoghadam S, Kumar AP. Amino acid transporters within the solute carrier superfamily: Underappreciated proteins and novel opportunities for cancer therapy. Mol Metab 2024; 84:101952. [PMID: 38705513 PMCID: PMC11112377 DOI: 10.1016/j.molmet.2024.101952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 04/24/2024] [Accepted: 04/27/2024] [Indexed: 05/07/2024] Open
Abstract
BACKGROUND Solute carrier (SLC) transporters, a diverse family of membrane proteins, are instrumental in orchestrating the intake and efflux of nutrients including amino acids, vitamins, ions, nutrients, etc, across cell membranes. This dynamic process is critical for sustaining the metabolic demands of cancer cells, promoting their survival, proliferation, and adaptation to the tumor microenvironment (TME). Amino acids are fundamental building blocks of cells and play essential roles in protein synthesis, nutrient sensing, and oncogenic signaling pathways. As key transporters of amino acids, SLCs have emerged as crucial players in maintaining cellular amino acid homeostasis, and their dysregulation is implicated in various cancer types. Thus, understanding the intricate connections between amino acids, SLCs, and cancer is pivotal for unraveling novel therapeutic targets and strategies. SCOPE OF REVIEW In this review, we delve into the significant impact of amino acid carriers of the SLCs family on the growth and progression of cancer and explore the current state of knowledge in this field, shedding light on the molecular mechanisms that underlie these relationships and highlighting potential avenues for future research and clinical interventions. MAJOR CONCLUSIONS Amino acids transportation by SLCs plays a critical role in tumor progression. However, some studies revealed the tumor suppressor function of SLCs. Although several studies evaluated the function of SLC7A11 and SLC1A5, the role of some SLC proteins in cancer is not studied well. To exert their functions, SLCs mediate metabolic rewiring, regulate the maintenance of redox balance, affect main oncogenic pathways, regulate amino acids bioavailability within the TME, and alter the sensitivity of cancer cells to therapeutics. However, different therapeutic methods that prevent the function of SLCs were able to inhibit tumor progression. This comprehensive review provides insights into a rapidly evolving area of cancer biology by focusing on amino acids and their transporters within the SLC superfamily.
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Affiliation(s)
- Kiavash Hushmandi
- Nephrology and Urology Research Center, Clinical Sciences Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran.
| | - Behzad Einollahi
- Nephrology and Urology Research Center, Clinical Sciences Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Seyed Hassan Saadat
- Nephrology and Urology Research Center, Clinical Sciences Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - E Hui Clarissa Lee
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore; NUS Center for Cancer Research (N2CR), Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Marzieh Ramezani Farani
- NanoBio High-Tech Materials Research Center, Department of Biological Sciences and Bioengineering, Inha University, Incheon 22212, Republic of Korea
| | - Elena Okina
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore; NUS Center for Cancer Research (N2CR), Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Yun Suk Huh
- NanoBio High-Tech Materials Research Center, Department of Biological Sciences and Bioengineering, Inha University, Incheon 22212, Republic of Korea
| | - Noushin Nabavi
- Department of Urologic Sciences and Vancouver Prostate Centre, University of British Columbia, V6H3Z6, Vancouver, BC, Canada
| | - Shokooh Salimimoghadam
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Shahid Chamran University of Ahvaz, Ahvaz, Iran.
| | - Alan Prem Kumar
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore; NUS Center for Cancer Research (N2CR), Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
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2
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Xu SM, Cheng Y, Fisher H, Janitz M. Recent advances in the investigation of fusion RNAs and their role in molecular pathology of cancer. Int J Biochem Cell Biol 2024; 168:106529. [PMID: 38246262 DOI: 10.1016/j.biocel.2024.106529] [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: 09/23/2023] [Revised: 01/16/2024] [Accepted: 01/17/2024] [Indexed: 01/23/2024]
Abstract
Gene fusions have had a significant role in the development of various types of cancer, oftentimes involved in oncogenic activities through dysregulation of gene expression or signalling pathways. Some cancer-associated chromosomal translocations can undergo backsplicing, resulting in fusion-circular RNAs, a more stable isoform immune to RNase degradation. This stability makes fusion circular RNAs a promising diagnostic biomarker for cancer. While the detection of linear fusion RNAs and their function in certain cancers have been described in literature, fusion circular RNAs lag behind due to their low abundance in cancer cells. This review highlights current literature on the role of linear and circular fusion transcripts in cancer, tools currently available for detecting of these chimeric RNAs and their function and how they play a role in tumorigenesis.
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Affiliation(s)
- Si-Mei Xu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Yuning Cheng
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Harry Fisher
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Michael Janitz
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia.
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Abomoelak B, Prather R, Pragya SU, Pragya SC, Mehta ND, Uddin P, Veeramachaneni P, Mehta N, Young A, Kapoor S, Mehta D. Cognitive Skills and DNA Methylation Are Correlating in Healthy and Novice College Students Practicing Preksha Dhyāna Meditation. Brain Sci 2023; 13:1214. [PMID: 37626570 PMCID: PMC10452635 DOI: 10.3390/brainsci13081214] [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: 06/21/2023] [Revised: 08/15/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023] Open
Abstract
The impact of different meditation protocols on human health is explored at the cognitive and cellular levels. Preksha Dhyana meditation has been observed to seemingly affect the cognitive performance, transcriptome, and methylome of healthy and novice participant practitioners. In this study, we performed correlation analyses to investigate the presence of any relationships in the changes in cognitive performance and DNA methylation in a group of college students practicing Preksha Dhyāna (N = 34). Nine factors of cognitive performance were assessed at baseline and 8 weeks postintervention timepoints in the participants. Statistically significant improvements were observed in six of the nine assessments, which were predominantly relating to memory and affect. Using Illumina 850 K microarray technology, 470 differentially methylated sites (DMS) were identified between the two timepoints (baseline and 8 weeks), using a threshold of p-value < 0.05 and methylation levels beyond -3% to 3% at every site. Correlation analysis between the changes in performance on each of the nine assessments and every DMS unveiled statistically significant positive and negative relationships at several of these sites. The identified DMS were in proximity of essential genes involved in signaling and other important metabolic processes. Interestingly, we identified a set of sites that can be considered as biomarkers for Preksha meditation improvements at the genome level.
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Affiliation(s)
- Bassam Abomoelak
- Gastrointestinal Translational Laboratory, Arnold Palmer Hospital for Children, Orlando, FL 32806, USA;
| | - Ray Prather
- Pediatric Cardiothoracic Surgery Department, Arnold Palmer Hospital for Children, Orlando, FL 32806, USA;
| | - Samani U. Pragya
- Department of Religions and Philosophies, University of London, London WC1H 0XG, UK;
| | - Samani C. Pragya
- Department of Biostatistics, Robert Stempel College of Public Health and Social Work, Florida International University, Miami, FL 33199, USA;
| | - Neelam D. Mehta
- Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA 19107, USA;
| | - Parvin Uddin
- College of Arts, Sciences and Education, Florida International University, Miami, FL 33199, USA;
| | | | - Naina Mehta
- Neurodevelopmental Pediatrician, Behavioral and Developmental Center, Orlando Health, Orlando, FL 32805, USA;
| | - Amanda Young
- Institute for Simulation and Training, University of Central Florida, Orlando, FL 32765, USA;
| | - Saumya Kapoor
- Medical School, University of Central Florida, Orlando, FL 32827, USA;
| | - Devendra Mehta
- Gastrointestinal Translational Laboratory, Arnold Palmer Hospital for Children, Orlando, FL 32806, USA;
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Lin Z, Lei Y, Wen M, He Q, Tian D, Xie H. MTAP-ANRIL gene fusion promotes melanoma epithelial-mesenchymal transition-like process by activating the JNK and p38 signaling pathways. Sci Rep 2023; 13:9073. [PMID: 37277447 DOI: 10.1038/s41598-023-36404-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 06/02/2023] [Indexed: 06/07/2023] Open
Abstract
Gene fusions caused by cytogenetic aberrations play important roles in the initiation and progression of cancers. The recurrent MTAP-ANRIL fusion gene was reported to have a frequency of greater than 7% in melanoma in our previous study. However, its functions remain unclear. Truncated MTAP proteins resulting from point mutations in the last three exons of MTAP can physically interact with the wild-type MTAP protein, a tumor suppressor in several human cancers. Similarly, MTAP-ANRIL, which is translated into a truncated MTAP protein, would influence wild-type MTAP to act as an oncogene. Here, we found that MTAP-ANRIL gene fusion downregulated the expression of wild-type MTAP and promoted epithelial-mesenchymal transition-like process through the activation of JNK and p38 MAPKs in vitro and in vivo. Our results suggest that MTAP-ANRIL is a potential molecular prognostic biomarker and therapeutic target for melanoma.
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Affiliation(s)
- Zhuoying Lin
- Department of Gastroenterology, Shangrao People's Hospital, Shangrao, 334000, Jiangxi Province, China
| | - Yu Lei
- Department of Gastroenterology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei Province, China
- Institute of Liver and Gastrointestinal Diseases, Huazhong University of Science and Technology, Tongji Hospital of Tongji Medical CollegeWuhan, 430030, Hubei Province, China
| | - Mingyao Wen
- Department of Otolaryngology-Head and Neck Surgery, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei Province, China
| | - Qin He
- Department of Gastroenterology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei Province, China
- Institute of Liver and Gastrointestinal Diseases, Huazhong University of Science and Technology, Tongji Hospital of Tongji Medical CollegeWuhan, 430030, Hubei Province, China
| | - Dean Tian
- Department of Gastroenterology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei Province, China
- Institute of Liver and Gastrointestinal Diseases, Huazhong University of Science and Technology, Tongji Hospital of Tongji Medical CollegeWuhan, 430030, Hubei Province, China
| | - Huaping Xie
- Department of Gastroenterology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei Province, China.
- Institute of Liver and Gastrointestinal Diseases, Huazhong University of Science and Technology, Tongji Hospital of Tongji Medical CollegeWuhan, 430030, Hubei Province, China.
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Chen S, Zang Y, Xu B, Lu B, Ma R, Miao P, Chen B. An Unsupervised Deep Learning-Based Model Using Multiomics Data to Predict Prognosis of Patients with Stomach Adenocarcinoma. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:5844846. [PMID: 36339684 PMCID: PMC9633210 DOI: 10.1155/2022/5844846] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 09/25/2022] [Accepted: 10/08/2022] [Indexed: 09/08/2023]
Abstract
METHODS Patients (363 in total) with stomach adenocarcinoma from The Cancer Genome Atlas (TCGA) cohort were included. An autoencoder was constructed to integrate the RNA sequencing, miRNA sequencing, and methylation data. The features of the bottleneck layer were used to perform the k-means clustering algorithm to obtain different subgroups for evaluating the prognosis-related risk of stomach adenocarcinoma. The model's robustness was verified using a 10-fold cross-validation (CV). Survival was analyzed by the Kaplan-Meier method. Univariate and multivariate Cox regression was used to estimate hazard risk. The model was validated in three independent cohorts with different endpoints. RESULTS The patients were divided into low-risk and high-risk groups according to the k-means clustering algorithm. The high-risk group had a significantly higher risk of poor survival (log-rank P value = 2.80e - 06; adjusted hazard ratio = 2.386, 95% confidence interval: 1.607~3.543), a concordance index (C-index) of 0.714, and a Brier score of 0.184. The model performed well both in the 10-fold CV procedure and three independent cohorts from the Gene Expression Omnibus (GEO) repository. CONCLUSIONS A robust and generalizable model based on the autoencoder was proposed to integrate multiomics data and predict the prognosis of patients with stomach adenocarcinoma. The model demonstrates better performance than two alternative approaches on prognosis prediction. The results might provide the grounds for further exploring the potential biomarkers to predict the prognosis of patients with stomach adenocarcinoma.
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Affiliation(s)
- Sizhen Chen
- Department of Epidemiology and Biostatistics, School of Public Health, Southeast University, Nanjing 210009, China
| | - Yiteng Zang
- Department of Epidemiology and Biostatistics, School of Public Health, Southeast University, Nanjing 210009, China
| | - Biyun Xu
- Department of Biostatistics, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing 210008, China
| | - Beier Lu
- Department of Epidemiology and Biostatistics, School of Public Health, Southeast University, Nanjing 210009, China
| | - Rongji Ma
- Department of Epidemiology and Biostatistics, School of Public Health, Southeast University, Nanjing 210009, China
| | - Pengcheng Miao
- Department of Epidemiology and Biostatistics, School of Public Health, Southeast University, Nanjing 210009, China
| | - Bingwei Chen
- Department of Epidemiology and Biostatistics, School of Public Health, Southeast University, Nanjing 210009, China
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6
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Kato T, Kusakizako T, Jin C, Zhou X, Ohgaki R, Quan L, Xu M, Okuda S, Kobayashi K, Yamashita K, Nishizawa T, Kanai Y, Nureki O. Structural insights into inhibitory mechanism of human excitatory amino acid transporter EAAT2. Nat Commun 2022; 13:4714. [PMID: 35953475 PMCID: PMC9372063 DOI: 10.1038/s41467-022-32442-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 08/01/2022] [Indexed: 11/18/2022] Open
Abstract
Glutamate is a pivotal excitatory neurotransmitter in mammalian brains, but excessive glutamate causes numerous neural disorders. Almost all extracellular glutamate is retrieved by the glial transporter, Excitatory Amino Acid Transporter 2 (EAAT2), belonging to the SLC1A family. However, in some cancers, EAAT2 expression is enhanced and causes resistance to therapies by metabolic disturbance. Despite its crucial roles, the detailed structural information about EAAT2 has not been available. Here, we report cryo-EM structures of human EAAT2 in substrate-free and selective inhibitor WAY213613-bound states at 3.2 Å and 2.8 Å, respectively. EAAT2 forms a trimer, with each protomer consisting of transport and scaffold domains. Along with a glutamate-binding site, the transport domain possesses a cavity that could be disrupted during the transport cycle. WAY213613 occupies both the glutamate-binding site and cavity of EAAT2 to interfere with its alternating access, where the sensitivity is defined by the inner environment of the cavity. We provide the characterization of the molecular features of EAAT2 and its selective inhibition mechanism that may facilitate structure-based drug design for EAAT2. EAAT2 is an amino acid transporter implicated in glutamate homeostasis in brain and therapy resistance of cancer cells. Here, the authors report cryo-EM structures and reveal inhibitory mechanisms via selective inhibitor WAY213613.
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Affiliation(s)
- Takafumi Kato
- Department of Biological Science, Graduate School of Science, The University of Tokyo, Tokyo, Japan.,Department of Biochemistry, The University of Oxford, Oxford, UK
| | - Tsukasa Kusakizako
- Department of Biological Science, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
| | - Chunhuan Jin
- Department of Bio-system Pharmacology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Xinyu Zhou
- Department of Bio-system Pharmacology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Ryuichi Ohgaki
- Department of Bio-system Pharmacology, Graduate School of Medicine, Osaka University, Osaka, Japan.,Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiative (OTRI), Osaka University, Osaka, Japan
| | - LiLi Quan
- Department of Bio-system Pharmacology, Graduate School of Medicine, Osaka University, Osaka, Japan.,Department of Molecular Pharmacology, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Minhui Xu
- Department of Bio-system Pharmacology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Suguru Okuda
- Department of Bio-system Pharmacology, Graduate School of Medicine, Osaka University, Osaka, Japan.,Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Kan Kobayashi
- Department of Biological Science, Graduate School of Science, The University of Tokyo, Tokyo, Japan.,Peptidream Inc, Kawasaki, Japan
| | - Keitaro Yamashita
- Department of Biological Science, Graduate School of Science, The University of Tokyo, Tokyo, Japan.,Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Tomohiro Nishizawa
- Department of Biological Science, Graduate School of Science, The University of Tokyo, Tokyo, Japan.,Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Yoshikatsu Kanai
- Department of Bio-system Pharmacology, Graduate School of Medicine, Osaka University, Osaka, Japan. .,Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiative (OTRI), Osaka University, Osaka, Japan.
| | - Osamu Nureki
- Department of Biological Science, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
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Freidman N, Briot C, Ryan R. Characterizing unexpected interactions of a glutamine transporter inhibitor with members of the SLC1A transporter family. J Biol Chem 2022; 298:102178. [PMID: 35752361 PMCID: PMC9293768 DOI: 10.1016/j.jbc.2022.102178] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 06/14/2022] [Accepted: 06/19/2022] [Indexed: 11/29/2022] Open
Abstract
The solute carrier 1A family comprises a group of membrane proteins that act as dual-function amino acid transporters and chloride (Cl−) channels and includes the alanine serine cysteine transporters (ASCTs) as well as the excitatory amino acid transporters. ASCT2 is regarded as a promising target for cancer therapy, as it can transport glutamine and other neutral amino acids into cells and is upregulated in a range of solid tumors. The compound L-γ-glutamyl-p-nitroanilide (GPNA) is widely used in studies probing the role of ASCT2 in cancer biology; however, the mechanism by which GPNA inhibits ASCT2 is not entirely clear. Here, we used electrophysiology and radiolabelled flux assays to demonstrate that GPNA activates the Cl− conductance of ASCT2 to the same extent as a transported substrate, whilst not undergoing the full transport cycle. This is a previously unreported phenomenon for inhibitors of the solute carrier 1A family but corroborates a body of literature suggesting that the structural requirements for transport are distinct from those for Cl− channel formation. We also show that in addition to its currently known targets, GPNA inhibits several of the excitatory amino acid transporters. Together, these findings raise questions about the true mechanisms of its anticancer effects.
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Affiliation(s)
- Natasha Freidman
- School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, NSW, Australia
| | - Chelsea Briot
- School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, NSW, Australia
| | - Renae Ryan
- School of Medical Sciences, Faculty of Medicine and Health, University of Sydney, NSW, Australia.
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8
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Roles of fusion genes in digestive system cancers: dawn for cancer precision therapy. Crit Rev Oncol Hematol 2022; 171:103622. [PMID: 35124200 DOI: 10.1016/j.critrevonc.2022.103622] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 02/01/2022] [Accepted: 02/02/2022] [Indexed: 11/21/2022] Open
Abstract
For advanced and advanced tumors of the digestive system, personalized, precise treatment could be a lifesaving medicine. With the development of next-generation sequencing technology, detection of fusion genes in solid tumors has become more extensive. Some fusion gene targeting therapies have been written into the guidelines for digestive tract tumors, such as for neurotrophic receptor tyrosine kinase, fibroblast growth factor receptor 2. There are also many fusion genes being investigated as potential future therapeutic targets. This review focuses on the current detection methods for fusion genes, fusion genes written into the digestive system tumor guidelines, and potential fusion gene therapy targets in different organs to discuss the possibility of clinical treatments for these targets in digestive system tumors.
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9
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Zhong X, Yao L, Xu L, Ma Q, Huang G, Yang M, Gao C, Cheng J, Zhou X, Li Q, Guo X. Comprehensive Analysis of Potential Correlation Between Solute Carrier 1A (SLC1A) Family and Lung Adenocarcinoma. Int J Gen Med 2022; 15:2101-2117. [PMID: 35241927 PMCID: PMC8886152 DOI: 10.2147/ijgm.s350986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 02/15/2022] [Indexed: 12/12/2022] Open
Abstract
Background Lung adenocarcinoma (LUAD) is the most common dangerous malignant tumor and the leading cause of global cancer incidence and mortality. The Solute Carrier 1A (SLC1A) family play a significant part in cellular biological process, inflammation, and immunity. Specific functions of the SLC1A family in lung cancer are still not systematically described. Objective This study aimed to explore the best biological understanding of SLC1A family in lung cancer. Methods To study the expression and role of the SLC1A family in lung cancer, researchers used a variety of bioinformatics databases and tools. Results Aberrant expression of SLC1A family genes were demonstrated and analyzed the association with gender, tumor grade, cancer stages, and nodal metastasis status. The ectopic expression of SLC1A family genes has prognostic value for LUAD patients. Immune infiltration revealed a significant correlation between SLC1A family genes expression in LUAD. SLC1A family genes were involved in manifold biological processes and have different levels of DNA methylation and genetic alteration. Conclusions These findings suggested that members of the SLC1A family could be a potential target for the development of LUAD therapeutics as well as a reliable indicator of LUAD prognostic value.
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Affiliation(s)
- Xiaowu Zhong
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, People’s Republic of China
- Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, 637000, People’s Republic of China
- Translational Medicine Research Center, North Sichuan Medical College, Nanchong, 637000, People’s Republic of China
| | - Lihua Yao
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, People’s Republic of China
- Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, 637000, People’s Republic of China
| | - Lei Xu
- Translational Medicine Research Center, North Sichuan Medical College, Nanchong, 637000, People’s Republic of China
| | - Qiang Ma
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, People’s Republic of China
- Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, 637000, People’s Republic of China
| | - Guangcheng Huang
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, People’s Republic of China
- Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, 637000, People’s Republic of China
| | - Miyuan Yang
- Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, 637000, People’s Republic of China
| | - Chuanli Gao
- Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, 637000, People’s Republic of China
| | - Jibing Cheng
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, People’s Republic of China
- Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, 637000, People’s Republic of China
| | - Xi Zhou
- Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, 637000, People’s Republic of China
| | - Qinrong Li
- Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, 637000, People’s Republic of China
| | - Xiaolan Guo
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, People’s Republic of China
- Department of Laboratory Medicine, North Sichuan Medical College, Nanchong, 637000, People’s Republic of China
- Translational Medicine Research Center, North Sichuan Medical College, Nanchong, 637000, People’s Republic of China
- Correspondence: Xiaolan Guo, Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, People’s Republic of China, Tel +86-817-2282059, Fax +86-817-2282059, Email
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10
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García-Gaytán AC, Hernández-Abrego A, Díaz-Muñoz M, Méndez I. Glutamatergic system components as potential biomarkers and therapeutic targets in cancer in non-neural organs. Front Endocrinol (Lausanne) 2022; 13:1029210. [PMID: 36457557 PMCID: PMC9705578 DOI: 10.3389/fendo.2022.1029210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 10/24/2022] [Indexed: 11/17/2022] Open
Abstract
Glutamate is one of the most abundant amino acids in the blood. Besides its role as a neurotransmitter in the brain, it is a key substrate in several metabolic pathways and a primary messenger that acts through its receptors outside the central nervous system (CNS). The two main types of glutamate receptors, ionotropic and metabotropic, are well characterized in CNS and have been recently analyzed for their roles in non-neural organs. Glutamate receptor expression may be particularly important for tumor growth in organs with high concentrations of glutamate and might also influence the propensity of such tumors to set metastases in glutamate-rich organs, such as the liver. The study of glutamate transporters has also acquired relevance in the physiology and pathologies outside the CNS, especially in the field of cancer research. In this review, we address the recent findings about the expression of glutamatergic system components, such as receptors and transporters, their role in the physiology and pathology of cancer in non-neural organs, and their possible use as biomarkers and therapeutic targets.
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11
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Hao W, Wu L, Cao L, Yu J, Ning L, Wang J, Lin X, Chen Y. Radioresistant Nasopharyngeal Carcinoma Cells Exhibited Decreased Cisplatin Sensitivity by Inducing SLC1A6 Expression. Front Pharmacol 2021; 12:629264. [PMID: 33927617 PMCID: PMC8077170 DOI: 10.3389/fphar.2021.629264] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 03/02/2021] [Indexed: 12/29/2022] Open
Abstract
Cisplatin-based regimens are commonly used for the treatment of nasopharyngeal carcinoma (NPC) in patients who receive concurrent chemoradiotherapy. The sensitivity of NPC cells to cisplatin is closely associated with the efficacy of radiation therapy. In this study, we established two radioresistant NPC cell lines, HONE1-IR and CNE2-IR, and found that both cell lines showed reduced sensitivity to cisplatin. RNA-sequence analysis showed that SLC1A6 was upregulated in both HONE1-IR and CNE2-IR cell lines. Downregulation of SLC1A6 enhanced cisplatin sensitivity in these two radioresistant NPC cell lines. It was also found that the expression of SLC1A6 was induced during radiation treatment and correlated with poor prognosis of NPC patients. Notably, we observed that upregulation of SLC1A6 led to elevating level of glutamate and the expression of drug-resistant genes, resulted in reduced cisplatin sensitivity. Our findings provide a rationale for developing a novel therapeutic target for NPC patients with cisplatin resistance.
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Affiliation(s)
- Wenwen Hao
- Department of Nasopharyngeal Carcinoma, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, China.,Department of Head and Neck Surgery, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Lisha Wu
- Department of Oncology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Linhui Cao
- Department of Traditional Chinese Medicine, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jinxiu Yu
- Department of Radiotherapy, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Li Ning
- Department of Head and Neck Surgery, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jingshu Wang
- Department of Oncology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xiaoping Lin
- Department of Nuclear Medicine, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yanfeng Chen
- Department of Head and Neck Surgery, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
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12
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Díaz Del Arco C, Estrada Muñoz L, Ortega Medina L, Fernández Aceñero MJ. [Update on gastric cancer. New molecular classifications]. REVISTA ESPANOLA DE PATOLOGIA : PUBLICACION OFICIAL DE LA SOCIEDAD ESPANOLA DE ANATOMIA PATOLOGICA Y DE LA SOCIEDAD ESPANOLA DE CITOLOGIA 2021; 54:102-113. [PMID: 33726886 DOI: 10.1016/j.patol.2020.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 05/17/2020] [Accepted: 06/01/2020] [Indexed: 06/12/2023]
Abstract
Gastric cancer (GC) is an aggressive tumor, which is usually diagnosed at an advanced stage and shows high mortality rates. Several GC classifications have been published, based on features such as tumor location, endoscopic features or microscopic architecture. However, TNM stage remains the mainstay of GC management and treatment. In the last years, technical advances have allowed us to investigate the biological heterogeneity of GC and develop new molecular classifications. This knowledge may enhance current classifications, and has the potential to refine GC management and aid in the identification of new molecular targets. In this literature review we have summarized the main findings in epidemiology, screening, classification systems and treatment of GC, focusing on the molecular alterations and new molecular classifications published in the last years.
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Affiliation(s)
- Cristina Díaz Del Arco
- Universidad Complutense de Madrid, España; Anatomía Patológica, Hospital Clínico San Carlos, Madrid, España.
| | | | - Luis Ortega Medina
- Universidad Complutense de Madrid, España; Anatomía Patológica, Hospital Clínico San Carlos, Madrid, España
| | - Ma Jesús Fernández Aceñero
- Universidad Complutense de Madrid, España; Anatomía Patológica, Hospital General Universitario Gregorio Marañón, Madrid, España
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13
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Bacci M, Lorito N, Ippolito L, Ramazzotti M, Luti S, Romagnoli S, Parri M, Bianchini F, Cappellesso F, Virga F, Gao Q, Simões BM, Marangoni E, Martin LA, Comito G, Ferracin M, Giannoni E, Mazzone M, Chiarugi P, Morandi A. Reprogramming of Amino Acid Transporters to Support Aspartate and Glutamate Dependency Sustains Endocrine Resistance in Breast Cancer. Cell Rep 2020; 28:104-118.e8. [PMID: 31269432 PMCID: PMC6616584 DOI: 10.1016/j.celrep.2019.06.010] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 05/13/2019] [Accepted: 06/03/2019] [Indexed: 01/08/2023] Open
Abstract
Endocrine therapy (ET) is the standard of care for estrogen receptor-positive (ER+) breast cancers. Despite its efficacy, ∼40% of women relapse with ET-resistant (ETR) disease. A global transcription analysis in ETR cells reveals a downregulation of the neutral and basic amino acid transporter SLC6A14 governed by enhanced miR-23b-3p expression, resulting in impaired amino acid metabolism. This altered amino acid metabolism in ETR cells is supported by the activation of autophagy and the enhanced import of acidic amino acids (aspartate and glutamate) mediated by the SLC1A2 transporter. The clinical significance of these findings is validated by multiple orthogonal approaches in a large cohort of ET-treated patients, in patient-derived xenografts, and in in vivo experiments. Targeting these amino acid metabolic dependencies resensitizes ETR cells to therapy and impairs the aggressive features of ETR cells, offering predictive biomarkers and potential targetable pathways to be exploited to combat or delay ETR in ER+ breast cancers.
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Affiliation(s)
- Marina Bacci
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Florence 50134, Italy
| | - Nicla Lorito
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Florence 50134, Italy
| | - Luigi Ippolito
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Florence 50134, Italy
| | - Matteo Ramazzotti
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Florence 50134, Italy
| | - Simone Luti
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Florence 50134, Italy
| | - Simone Romagnoli
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Florence 50134, Italy
| | - Matteo Parri
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Florence 50134, Italy
| | - Francesca Bianchini
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Florence 50134, Italy
| | - Federica Cappellesso
- VIB Center for Cancer Biology, Department of Oncology, University of Leuven, Leuven 3000, Belgium
| | - Federico Virga
- VIB Center for Cancer Biology, Department of Oncology, University of Leuven, Leuven 3000, Belgium; Molecular Biotechnology Center (MBC), Department of Molecular Biotechnology and Health Sciences, University of Turin, Turin 10126, Italy
| | - Qiong Gao
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London SW3 6JB, UK
| | - Bruno M Simões
- Breast Cancer Now Research Unit, Division of Cancer Sciences, Manchester Cancer Research Centre, University of Manchester, Manchester M20 4GJ, UK
| | - Elisabetta Marangoni
- Institut Curie, PSL Research University, Translational Research Department, Paris 75248, France
| | - Lesley-Ann Martin
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London SW3 6JB, UK
| | - Giuseppina Comito
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Florence 50134, Italy
| | - Manuela Ferracin
- Department of Experimental, Diagnostic, and Specialty Medicine (DIMES), University of Bologna, Bologna 40126, Italy
| | - Elisa Giannoni
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Florence 50134, Italy
| | - Massimiliano Mazzone
- VIB Center for Cancer Biology, Department of Oncology, University of Leuven, Leuven 3000, Belgium
| | - Paola Chiarugi
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Florence 50134, Italy
| | - Andrea Morandi
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, Florence 50134, Italy.
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14
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Ooi WF, Nargund AM, Lim KJ, Zhang S, Xing M, Mandoli A, Lim JQ, Ho SWT, Guo Y, Yao X, Lin SJ, Nandi T, Xu C, Ong X, Lee M, Tan ALK, Lam YN, Teo JX, Kaneda A, White KP, Lim WK, Rozen SG, Teh BT, Li S, Skanderup AJ, Tan P. Integrated paired-end enhancer profiling and whole-genome sequencing reveals recurrent CCNE1 and IGF2 enhancer hijacking in primary gastric adenocarcinoma. Gut 2020; 69:1039-1052. [PMID: 31542774 DOI: 10.1136/gutjnl-2018-317612] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 08/22/2019] [Accepted: 09/01/2019] [Indexed: 12/21/2022]
Abstract
OBJECTIVE Genomic structural variations (SVs) causing rewiring of cis-regulatory elements remain largely unexplored in gastric cancer (GC). To identify SVs affecting enhancer elements in GC (enhancer-based SVs), we integrated epigenomic enhancer profiles revealed by paired-end H3K27ac ChIP-sequencing from primary GCs with tumour whole-genome sequencing (WGS) data (PeNChIP-seq/WGS). DESIGN We applied PeNChIP-seq to 11 primary GCs and matched normal tissues combined with WGS profiles of >200 GCs. Epigenome profiles were analysed alongside matched RNA-seq data to identify tumour-associated enhancer-based SVs with altered cancer transcription. Functional validation of candidate enhancer-based SVs was performed using CRISPR/Cas9 genome editing, chromosome conformation capture assays (4C-seq, Capture-C) and Hi-C analysis of primary GCs. RESULTS PeNChIP-seq/WGS revealed ~150 enhancer-based SVs in GC. The majority (63%) of SVs linked to target gene deregulation were associated with increased tumour expression. Enhancer-based SVs targeting CCNE1, a key driver of therapy resistance, occurred in 8% of patients frequently juxtaposing diverse distal enhancers to CCNE1 proximal regions. CCNE1-rearranged GCs were associated with high CCNE1 expression, disrupted CCNE1 topologically associating domain (TAD) boundaries, and novel TAD interactions in CCNE1-rearranged primary tumours. We also observed IGF2 enhancer-based SVs, previously noted in colorectal cancer, highlighting a common non-coding genetic driver alteration in gastric and colorectal malignancies. CONCLUSION Integrated paired-end NanoChIP-seq and WGS of gastric tumours reveals tumour-associated regulatory SV in regions associated with both simple and complex genomic rearrangements. Genomic rearrangements may thus exploit enhancer-hijacking as a common mechanism to drive oncogene expression in GC.
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Affiliation(s)
- Wen Fong Ooi
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore
| | - Amrita M Nargund
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Kevin Junliang Lim
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore.,Centre for Computational Biology, Duke-NUS Medical School, Singapore
| | - Shenli Zhang
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Manjie Xing
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore
| | - Amit Mandoli
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Jing Quan Lim
- Lymphoma Genomic Translational Laboratory, National Cancer Centre Singapore, Singapore
| | - Shamaine Wei Ting Ho
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Yu Guo
- Computational and Systems Biology, Genome Institute of Singapore, Singapore
| | - Xiaosai Yao
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore
| | - Suling Joyce Lin
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore
| | - Tannistha Nandi
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore
| | - Chang Xu
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Xuewen Ong
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Minghui Lee
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Angie Lay-Keng Tan
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Yue Ning Lam
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore
| | - Jing Xian Teo
- SingHealth/Duke-NUS Institute of Precision Medicine, National Heart Centre, Singapore
| | - Atsushi Kaneda
- Department of Molecular Oncology, Chiba University, Chiba, Japan
| | - Kevin P White
- Institute for Genomics and Systems Biology, University of Chicago and Argonne National Laboratory, Chicago, Illinois, USA.,Tempus Labs, Chicago, Illinois, USA
| | - Weng Khong Lim
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore.,SingHealth/Duke-NUS Institute of Precision Medicine, National Heart Centre, Singapore
| | - Steven G Rozen
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore.,Centre for Computational Biology, Duke-NUS Medical School, Singapore.,SingHealth/Duke-NUS Institute of Precision Medicine, National Heart Centre, Singapore
| | - Bin Tean Teh
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore.,SingHealth/Duke-NUS Institute of Precision Medicine, National Heart Centre, Singapore.,Laboratory of Cancer Epigenome, National Cancer Centre Singapore, Singapore
| | - Shang Li
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Anders J Skanderup
- Computational and Systems Biology, Genome Institute of Singapore, Singapore
| | - Patrick Tan
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore .,Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore.,Cancer Science Institute of Singapore, National University of Singapore, Singapore.,SingHealth/Duke-NUS Institute of Precision Medicine, National Heart Centre, Singapore
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15
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Amino Acid Transporters and Exchangers from the SLC1A Family: Structure, Mechanism and Roles in Physiology and Cancer. Neurochem Res 2020; 45:1268-1286. [DOI: 10.1007/s11064-019-02934-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 12/10/2019] [Accepted: 12/13/2019] [Indexed: 12/13/2022]
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16
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Sun Y, Zhao C, Ye Y, Wang Z, He Y, Li Y, Mao H. High expression of fibronectin 1 indicates poor prognosis in gastric cancer. Oncol Lett 2019; 19:93-102. [PMID: 31897119 PMCID: PMC6923922 DOI: 10.3892/ol.2019.11088] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 08/01/2019] [Indexed: 02/06/2023] Open
Abstract
Fibronectin 1 (FN1) is involved in the occurrence and development of various tumors and is upregulated in multiple cancer types. FN1 has been demonstrated to promote cell proliferation and migration in gastric cancer cell lines. However, the relationship between the expression of FN1 and clinicopathological factors and prognosis is not clear in gastric cancer (GC). The aim of the present study was to investigate the association between FN1 expression and clinicopathology and prognosis of gastric cancer. In this study, 17 publicly available GC cohorts (n=2,376) with gene expression data from the Gene Expression Omnibus (GEO), The Cancer Genome Atlas (TCGA) and Oncomine databases were tested. In addition, FN1 protein expression was validated by immunohistochemistry in a separate cohort (n=190). The meta-analysis results demonstrated an increase in FN1 expression at the protein and mRNA level in GC tissues, and the FN1 gene was highly expressed at the mRNA level in the advanced T stage (T2 + T3 + T4) group compared with that in the early T stage (T1) group. In addition, the expression of epithelial FN1 at the protein level was positively correlated with tumor size. FN1 expression at the protein and mRNA level was a predictor of poor prognosis following radical resection of GC. In conclusion, the expression of FN1 in GC tissues is upregulated compared with adjacent normal tissues, and it is a potential biomarker of poor prognosis in patients with GC.
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Affiliation(s)
- Yang Sun
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China.,Department of Breast and Thyroid Surgery, Nanyang Central Hospital, Nanyang, Henan 473000, P.R. China
| | - Chunlin Zhao
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Yanwei Ye
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Zhen Wang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Yuanhang He
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Yulin Li
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
| | - Haoxun Mao
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, P.R. China
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17
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Abstract
Glutamine and glutamate are major bioenergy substrates for normal and cancer cell growth. Cancer cells need more biofuel than normal tissues for energy supply, anti-oxidation activity and biomass production. Genes related to metabolic chains in many cancers are somehow mutated, which makes cancer cells more glutamate dependent. Meanwhile, glutamate is an excitatory neurotransmitter for conducting signals through binding with different types of receptors in central neuron system. Interestingly, increasing evidences have shown involvement of glutamate signaling, guided through their receptors, in human malignancy. Dysregulation of glutamate transporters, such as excitatory amino acid transporter and cystine/glutamate antiporter system, also generates excessive extracellular glutamate, which in turn, activates glutamate receptors on cancer cells and results in malignant growth. These features make glutamate an attractive target for anti-cancer drug development with some glutamate targeted but blood brain barrier impermeable anti-psychosis drugs under consideration. We discussed the relevant progressions and drawbacks in this field herein.
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Affiliation(s)
- Haowei Yi
- Department of Genetics, Cell Biology and Anatomy
| | | | - Jing Wang
- Department of Genetics, Cell Biology and Anatomy
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18
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Song L, Wang XY, He XF. A 5-Gene Prognostic Combination for Predicting Survival of Patients with Gastric Cancer. Med Sci Monit 2019; 25:6313-6320. [PMID: 31422414 PMCID: PMC6713029 DOI: 10.12659/msm.914815] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Background The aim of the study was to identify a multigene prognostic factor in patients with gastric cancer (GC). Material/Methods Random survival forest (RSF) was performed to screen survival-related genes and develop a multigene combination based on the cumulative hazard function of each GC patient in TCGA-STAD and GSE15459. Kaplan-Meier curve and univariate and multivariable Cox proportional hazards regression model were applied to evaluate the prognostic performance of the 5-gene combination. C-index was used to compare the prognostic performance of the 5-gene combination and another 9-gene signature in GC. Gene set enrichment analysis (GSEA) was conducted. Results We obtained 19 survival-related genes through univariate Cox proportional hazards analysis in the training set, 5 of which were identified and were used to develop a 5-gene combination through RSF. Patients in the 5-gene combination low-risk group had better overall survival (OS) than those in the 5-gene combination high-risk group, and the 5-gene combination was demonstrated to be an independent prognostic factor in patients with GC. The 5-gene combination outperformed the 9-gene signature in predicting the OS of GC patients, and it might affect the prognosis of GC patients through E2F signaling, MYC signaling, and G2M checkpoint. Conclusions We introduce a 5-gene combination that can predict the survival of GC patients and might be an independent prognostic factor in GC.
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Affiliation(s)
- Liang Song
- Endoscopy Room, Heping Hospital Affiliated to Changzhi Medical College, Changzhi, Shanxi, China (mainland)
| | - Xiao-Yan Wang
- Department of Epidemiology and Health Statistics, Basic Medical College of Zhejiang University of Traditional Chinese Medicine, Hangzhou, Zhejiang, China (mainland)
| | - Xiao-Feng He
- Department of Science and Education, Heping Hospital Affiliated to Changzhi Medical College, Changzhi, Shanxi, China (mainland)
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19
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Xu XF, Gao F, Wang JJ, Long C, Chen X, Tao L, Yang L, Ding L, Ji Y. BMX-ARHGAP fusion protein maintains the tumorigenicity of gastric cancer stem cells by activating the JAK/STAT3 signaling pathway. Cancer Cell Int 2019; 19:133. [PMID: 31130822 PMCID: PMC6525346 DOI: 10.1186/s12935-019-0847-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 05/02/2019] [Indexed: 12/19/2022] Open
Abstract
Background Cancer stem cells (CSCs), drug-resistant cancer cell subsets, are known to be responsible for tumor metastasis and relapse. The JAK/STAT pathway, activated by SH2 domain, is known to regulate the tumor growth in gastric cancer (GC). Now, this study was designed to examine whether BMX-ARHGAP affects the GC stem cell properties and the underlying regulatory network via JAK/STAT axis. Methods BMX-ARHGAP expression was characterized in GC tissues and cells by RT-qPCR and western blot assay. When BMX-ARHGAP was overexpressed or silenced via plasmids or siRNA transfection, the stem cell properties were assessed by determining stem cell markers CD133, CD44, SOX2 and Nanog, followed by cell sphere and colony formation assays. Subsequently, cell proliferation and invasion were examined by conducting EdU and Transwell assays. The JAK/STAT3 signaling pathway activation was inhibited using AG490. ARHGAP12, BMX exon 10-11, BXM-SH2, JAK2 and STAT3 expression patterns were all determined to examine the regulatory network. The stem cell property in nude mice was also tested. Results BMX-ARHGAP was determined to be enriched in the GC. Overexpression of BMX-ARHGAP resulted in increased expression of CD133, CD44, SOX2 and Nanog protein, and accelerated proliferation and invasion of CD133+CD44+ cells as well as facilitated self-renewal potential of GC cells. However, the inhibition of the JAK/STAT3 signaling pathway reversed the stimulating effect of BMX-ARHGAP on proliferative and invasion abilities of CD133+CD44+ cells. The overexpression of BMX-ARHGAP was suggested to increase the BMX-SH2 protein expression via ARHGAP 5'UTR, and activate the JAK/STAT3 signaling pathway. Also, BMX-ARHGAP promoted tumor growth in nude mice. Conclusions The aforementioned results demonstrated that the BMX-ARHGAP-dependent SH2 domain-JAK/STAT3 axis mediates the maintenance of GC stem cells, benefiting the development of new potential therapeutic targets for GC.
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Affiliation(s)
- Xiao-Feng Xu
- Clinical Laboratory, Jingjiang People's Hospital, Jingjiang, 214500 People's Republic of China
| | - Feng Gao
- Department of Surgery, Jingjiang People's Hospital, No. 28, Zhongzhou Road, Jingjiang, 214500 Jiangsu People's Republic of China
| | - Jian-Jiang Wang
- Department of Surgery, Jingjiang People's Hospital, No. 28, Zhongzhou Road, Jingjiang, 214500 Jiangsu People's Republic of China
| | - Cong Long
- Clinical Laboratory, Jingjiang People's Hospital, Jingjiang, 214500 People's Republic of China
| | - Xing Chen
- Department of Surgery, Jingjiang People's Hospital, No. 28, Zhongzhou Road, Jingjiang, 214500 Jiangsu People's Republic of China
| | - Lan Tao
- Central Laboratory, Jingjiang People's Hospital, Jingjiang, 214500 People's Republic of China
| | - Liu Yang
- Clinical Laboratory, Jingjiang People's Hospital, Jingjiang, 214500 People's Republic of China
| | - Li Ding
- Clinical Laboratory, Jingjiang People's Hospital, Jingjiang, 214500 People's Republic of China
| | - Yong Ji
- Department of Surgery, Jingjiang People's Hospital, No. 28, Zhongzhou Road, Jingjiang, 214500 Jiangsu People's Republic of China
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20
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The significance of gene mutations across eight major cancer types. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2019; 781:88-99. [PMID: 31416581 DOI: 10.1016/j.mrrev.2019.04.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 04/11/2019] [Accepted: 04/30/2019] [Indexed: 12/12/2022]
Abstract
Mutations occur spontaneously, which can be induced by either chemicals (e.g. benzene) or biological factors (e.g. virus). Not all mutations cause noticeable changes in cellular functions. However, mutation in key cellular genes leads to developmental disorders. It is one of the main ways in which proto-oncogenes can be changed into their oncogenic state. The progressive accumulation of multiple mutations throughout life leads to cancer. In the past few decades, extensive research on cancer biology has discovered many genes and pathways having role in cancer development. In this review, we tried to summarize the current knowledge of mutational effect on different cancer types and its consequences in brief for future reference and guidance of researchers in cancer biology.
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21
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Hu Z, Yang D, Tang Y, Zhang X, Wei Z, Fu H, Xu J, Zhu Z, Cai Q. Five-long non-coding RNA risk score system for the effective prediction of gastric cancer patient survival. Oncol Lett 2019; 17:4474-4486. [PMID: 30988816 PMCID: PMC6447923 DOI: 10.3892/ol.2019.10124] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 12/12/2018] [Indexed: 12/13/2022] Open
Abstract
The prognosis for patients with gastric cancer (GC) is usually poor, as the majority of patients have reached the advanced stages of disease at the point of diagnosis. Therefore, revealing the mechanisms of GC is necessary for the identification of key biomarkers and the development of effective targeted therapies. The present study aimed to identify long non-coding RNAs (lncRNAs) prominently expressed in patients with GC. The GC dataset (including 384 GC samples) was downloaded from The Cancer Genome Atlas database as the training set. A number of other GC datasets were obtained from the Gene Expression Omnibus database as validation sets. Following data processing, lncRNAs were annotated, followed by co-expression module analysis to identify stable modules, using the weighted gene co-expression network analysis (WGCNA) package. Prognosis-associated lncRNAs were screened using the ‘survival’ package. Following the selection of the optimal lncRNA combinations using the ‘penalized’ package, risk score systems were constructed and assessed. Consensus differentially-expressed RNAs (DE-RNAs) were screened using the MetaDE package, and an lncRNA-mRNA network was constructed. Additionally, pathway enrichment analysis was conducted for the network nodes using gene set enrichment analysis (GSEA). A total of seven modules (blue, brown, green, grey, red, turquoise and yellow) were obtained following WGCNA analysis, among which the green and turquoise modules were stable and associated with the histological grade of GC. A total of 12 prognosis-associated lncRNAs were identified in the two modules. Combined with the optimal lncRNA combinations, risk score systems were constructed. The risk score system based on the green module [including ITPK1 antisense RNA 1 (ITPK1-AS1), KCNQ1 downstream neighbor (KCNQ1DN), long intergenic non-protein coding RNA 167 (LINC00167), LINC00173 and LINC00307] was the more efficient at predicting risk compared with those based on the turquoise, or the green + turquoise modules. A total of 1,105 consensus DE-RNAs were identified; GSEA revealed that LINC00167, LINC00173 and LINC00307 had the same association directions with 4 pathways and the 32 genes involved in those pathways. In conclusion, a risk score system based on the green module may be applied to predict the survival of patients with GC. Furthermore, ITPK1-AS1, KCNQ1DN, LINC00167, LINC00173 and LINC00307 may serve as biomarkers for GC pathogenesis.
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Affiliation(s)
- Zunqi Hu
- Department of Gastrointestinal Surgery, Changzheng Hospital, Second Military Medical University, Shanghai 200003, P.R. China
| | - Dejun Yang
- Department of Gastrointestinal Surgery, Changzheng Hospital, Second Military Medical University, Shanghai 200003, P.R. China
| | - Yuan Tang
- Department of Gastrointestinal Surgery, Changzheng Hospital, Second Military Medical University, Shanghai 200003, P.R. China
| | - Xin Zhang
- Department of Gastrointestinal Surgery, Changzheng Hospital, Second Military Medical University, Shanghai 200003, P.R. China
| | - Ziran Wei
- Department of Gastrointestinal Surgery, Changzheng Hospital, Second Military Medical University, Shanghai 200003, P.R. China
| | - Hongbing Fu
- Department of Gastrointestinal Surgery, Changzheng Hospital, Second Military Medical University, Shanghai 200003, P.R. China
| | - Jiapeng Xu
- Department of Gastrointestinal Surgery, Changzheng Hospital, Second Military Medical University, Shanghai 200003, P.R. China
| | - Zhenxin Zhu
- Department of Gastrointestinal Surgery, Changzheng Hospital, Second Military Medical University, Shanghai 200003, P.R. China
| | - Qingping Cai
- Department of Gastrointestinal Surgery, Changzheng Hospital, Second Military Medical University, Shanghai 200003, P.R. China
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22
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RhoGAP domain-containing fusions and PPAPDC1A fusions are recurrent and prognostic in diffuse gastric cancer. Nat Commun 2018; 9:4439. [PMID: 30361512 PMCID: PMC6202325 DOI: 10.1038/s41467-018-06747-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 09/21/2018] [Indexed: 01/22/2023] Open
Abstract
We conducted an RNA sequencing study to identify novel gene fusions in 80 discovery dataset tumors collected from young patients with diffuse gastric cancer (DGC). Twenty-five in-frame fusions are associated with DGC, three of which (CLDN18-ARHGAP26, CTNND1-ARHGAP26, and ANXA2-MYO9A) are recurrent in 384 DGCs based on RT-PCR. All three fusions contain a RhoGAP domain in their 3’ partner genes. Patients with one of these three fusions have a significantly worse prognosis than those without. Ectopic expression of CLDN18-ARHGAP26 promotes the migration and invasion capacities of DGC cells. Parallel targeted RNA sequencing analysis additionally identifies TACC2-PPAPDC1A as a recurrent and poor prognostic in-frame fusion. Overall, PPAPDC1A fusions and in-frame fusions containing a RhoGAP domain clearly define the aggressive subset (7.5%) of DGCs, and their prognostic impact is greater than, and independent of, chromosomal instability and CDH1 mutations. Our study may provide novel genomic insights guiding future strategies for managing DGCs. Diffuse Gastric Cancer (DGC) is increasingly being considered separate to intestinal type gastric cancer; several fusions events have been reported as drivers of the disease but few of those have been subsequently validated. Here the authors perform RNA-seq on early-onset DGC patients who had not been treated with chemotherapy or radiation and identify a previously unknown fusion.
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23
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Su X, Xue Y, Wei J, Huo X, Gong Y, Zhang H, Han R, Chen Y, Chen H, Chen J. Establishment and Characterization of gc-006-03, a Novel Human Signet Ring Cell Gastric Cancer Cell Line Derived from Metastatic Ascites. J Cancer 2018; 9:3236-3246. [PMID: 30271482 PMCID: PMC6160672 DOI: 10.7150/jca.26051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 07/17/2018] [Indexed: 12/15/2022] Open
Abstract
Signet ring cell gastric cancer (SRCGC) is a special type of gastric cancer with rapid progression and poor prognosis. However, few available SRCGC cell lines from Chinese patients can be used for research, the molecular mechanism of its growth and metastasis is still incompletely understood. In this study, we established and characterized a novel SRCGC cell line, gc-006-03.The cells showed a tendency to pile up without contact inhibition. G-band karyotypes of gc-006-03 were revealed hypotriploid with a modal chromosome number of 51. Immunohistochemistry analysis showed that the cells were positive for CEA, CK7, CDX2 and Ki-67(45%), and negative for CK20, TTF1and Li-cadherin. Flow cytometry analysis showed that gc-006-3 had 25% of CD44+ cells. The cells possessed strong clonality and high plating efficiency, and the doubling time was 36h. The cells grew vigorously for more than 100 passages in serial culture. Meanwhile, the cells showed a high rate of tumor formation. Tumors were observed in all of the nude mice (5/5) given injections of the cells. The metastatic capability of the cell line was found in zebrafish injected the cells. The results of whole genome sequencing revealed the unique genomic characteristics of gc-006-03. In summary, this new stable cell line may be useful in basic and clinical research on gastric signet ring cell carcinoma.
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Affiliation(s)
- Xinyu Su
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China.,Department of Radiation Oncology, the Affiliated Huai'an Hospital of Xuzhou Medical College, Huai'an, China
| | - Yiqi Xue
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Jingsun Wei
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Xinying Huo
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Yang Gong
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Honghong Zhang
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Rongbo Han
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Yuetong Chen
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Hong Chen
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Jinfei Chen
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
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24
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Transcriptome-wide analysis of alternative mRNA splicing signature in the diagnosis and prognosis of stomach adenocarcinoma. Oncol Rep 2018; 40:2014-2022. [PMID: 30106437 PMCID: PMC6111597 DOI: 10.3892/or.2018.6623] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Accepted: 07/17/2018] [Indexed: 12/12/2022] Open
Abstract
Alternative mRNA splicing (AS) contributes greatly to expanding the diversity and function of the proteome. Increasing evidence has suggested that dysregulation of mRNA splicing may be associated with various types of cancer. In the present study, RNA sequencing data were used to investigate alterations to the global mRNA splicing landscape of cellular genes from 452 stomach adenocarcinoma (STAD) tissues available in The Cancer Genome Atlas. Seven types of AS events, including the profiles of exon skipping events, were analyzed using SpliceSeq software. A total of 60,754 AS events in 10,611 genes were detected, more than half of which were exon skipping events. The AS events were compared between 415 STAD tissues and 37 normal tissues, and 3,895 differentially spliced cancer-specific events were identified. In addition, the association of the AS events with the overall survival of 373 STAD patients was analyzed. Multivariate Cox regression analysis revealed that prognosis prediction models based on the AS events with clinical parameters had an excellent performance in predicting the survival of STAD patients. This study provides a comprehensive portrait of global changes in mRNA splicing signatures that occur in gastric cancer. These results allowed the identification of a core set of AS in gastric cancer and indicated that AS events may serve as prognostic indicators.
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25
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Xie H, Rachakonda PS, Heidenreich B, Nagore E, Sucker A, Hemminki K, Schadendorf D, Kumar R. Mapping of deletion breakpoints at the CDKN2A locus in melanoma: detection of MTAP-ANRIL fusion transcripts. Oncotarget 2017; 7:16490-504. [PMID: 26909863 PMCID: PMC4941330 DOI: 10.18632/oncotarget.7503] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Accepted: 02/11/2016] [Indexed: 12/17/2022] Open
Abstract
Genomic locus at chromosome 9p21 that contains the CDKN2A and CDKN2B tumor suppressor genes is inactivated through mutations, deletions and promoter methylation in multiple human cancers. Additionally, the locus encodes an anti-sense RNA (ANRIL). Both hemizygous and homozygous deletions at the locus targeting multiple genes are fairly common in different cancers. We in this study investigated breakpoints in five melanoma cell lines, derived from metastasized tumors, with previously identified homozygous deletions using array comparative genomic hybridization (aCGH). For breakpoint mapping, we used primer approximation multiplex PCR (PAMP) and inverse PCR techniques. Our results showed that three cell lines carried complex rearrangements. In two other cell lines, with focal deletions of 141 kb and 181 kb, we identified fusion gene products, involving MTAP and ANRIL. We also confirmed the complex rearrangements and focal deletions in DNA from tumor tissues corresponding to three cell lines. The rapid amplification of 3′cDNA ends (3′RACE) carried out on transcripts resulted in identification of three isoforms of MTAP-ANRIL fusion gene. Screening of cDNA from 64 melanoma cell lines resulted in detection of fusion transcripts in 13 (20%) cell lines that involved exons 4-7 of the MTAP and exon 2 or 5 of the ANRIL genes. We also detected fusion transcripts involving MTAP and ANRIL in two of the seven primary melanoma tumors with focal deletion at the locus. The results from the study, besides identifying complex rearrangements involving CDKN2A locus, show frequent occurrence of fusion transcripts involving MTAP and ANRIL genes.
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Affiliation(s)
- Huaping Xie
- Department of Gastroenterology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Division of Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | | | - Barbara Heidenreich
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany
| | - Eduardo Nagore
- Department of Dermatology, Instituto Valenciano de Oncologia, Valencia, Spain
| | - Antje Sucker
- Department of Dermatology, University Hospital Essen, Essen, Germany
| | - Kari Hemminki
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany.,Center for Primary Health Care Research, Lund University, Malmö, Sweden
| | - Dirk Schadendorf
- Department of Dermatology, University Hospital Essen, Essen, Germany.,German Cancer Consortium (DKTK), Essen, Germany
| | - Rajiv Kumar
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, Heidelberg, Germany
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26
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Novel chimeric transcript RRM2-c2orf48 promotes metastasis in nasopharyngeal carcinoma. Cell Death Dis 2017; 8:e3047. [PMID: 28906488 PMCID: PMC5636969 DOI: 10.1038/cddis.2017.402] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Revised: 06/29/2017] [Accepted: 07/14/2017] [Indexed: 12/13/2022]
Abstract
Recently, chimeric transcripts have been found to be associated with the pathogenesis and poor prognosis of malignant tumors. Through our preliminary experiment, a novel chimeric transcript called chimeric transcript RRM2-c2orf48 was detected in C666-1, a classical cell line of human nasopharyngeal carcinoma (NPC). Therefore, the objective of this study was to demonstrate the existence and expression of novel chimeric transcript RRM2-c2orf48 and to explore the main functions and mechanisms of RRM2-c2orf48 in NPC. In this study, the expression of RRM2-c2orf48 was evaluated in NPC cells and specimens. Effects of RRM2-c2orf48 on migration and invasive capacities were detected invivo and vitro. Moreover, ways in which RRM2-c2orf48 increases the invasive capacities of NPC were explored. As a result, the presence of novel chimeric transcript RRM2-c2orf48 was confirmed in C666-1 by RT-PCR and sequencing, and it was a read-through between RRM2 and c2orf48 through the transcription of interchromosome. Higher expressions of novel RRM2-c2orf48 were detected in NPC cell lines and NPC tissue specimens relative to the controls and its expression was be statistically relevant to TNM staging. High level of RRM2-c2orf48 could increase the migration and invasive capacities of NPC cells, potentially as a result of NPC cell epithelial–mesenchymal transition. RRM2-c2orf48 could also enhance resistance of chemotherapy. In vivo, RRM2-c2orf48 could enhance lung and lymph node metastasis in nude mice. These results demonstrate that high levels of RRM2-c2orf48 expression may be a useful predictor of NPC patients of metastatic potency, presenting potential implications for NPC diagnosis and therapy.
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27
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Abstract
Gastric cancer is the fifth most incident and the third most common cause of cancer-related death in the world. Infection with Helicobacter pylori is the major risk factor for this disease. Gastric cancer is the final outcome of a cascade of events that takes decades to occur and results from the accumulation of multiple genetic and epigenetic alterations. These changes are crucial for tumor cells to expedite and sustain the array of pathways involved in the cancer development, such as cell cycle, DNA repair, metabolism, cell-to-cell and cell-to-matrix interactions, apoptosis, angiogenesis, and immune surveillance. Comprehensive molecular analyses of gastric cancer have disclosed the complex heterogeneity of this disease. In particular, these analyses have confirmed that Epstein-Barr virus (EBV)-positive gastric cancer is a distinct entity. The identification of gastric cancer subtypes characterized by recognizable molecular profiles may pave the way for a more personalized clinical management and to the identification of novel therapeutic targets and biomarkers for screening, prognosis, prediction of response to treatment, and monitoring of gastric cancer progression.
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28
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Liu X, Meltzer SJ. Gastric Cancer in the Era of Precision Medicine. Cell Mol Gastroenterol Hepatol 2017; 3:348-358. [PMID: 28462377 PMCID: PMC5404028 DOI: 10.1016/j.jcmgh.2017.02.003] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 02/13/2017] [Indexed: 12/14/2022]
Abstract
Gastric cancer (GC) remains the third most common cause of cancer death worldwide, with limited therapeutic strategies available. With the advent of next-generation sequencing and new preclinical model technologies, our understanding of its pathogenesis and molecular alterations continues to be revolutionized. Recently, the genomic landscape of GC has been delineated. Molecular characterization and novel therapeutic targets of each molecular subtype have been identified. At the same time, patient-derived tumor xenografts and organoids now comprise effective tools for genetic evolution studies, biomarker identification, drug screening, and preclinical evaluation of personalized medicine strategies for GC patients. These advances are making it feasible to integrate clinical, genome-based and phenotype-based diagnostic and therapeutic methods and apply them to individual GC patients in the era of precision medicine.
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Key Words
- CIMP, CpG island methylator phenotype
- CIN, chromosomally unstable/chromosomal instability
- Cancer Genomics
- EBV, Epstein-Barr virus
- GAPPS, gastric adenocarcinoma and proximal polyposis of the stomach
- GC, gastric cancer
- GTPase, guanosine triphosphatase
- Gastric Cancer
- HDGC, hereditary diffuse gastric cancer
- LOH, loss of heterozygosity
- MSI, microsatellite unstable/instability
- MSI-H, high microsatellite instability
- MSS/EMT, microsatellite stable with epithelial-to-mesenchymal transition features
- Molecular Classification
- NGS, next-generation sequencing
- PDX, patient-derived tumor xenografts
- Preclinical Models
- TCGA, The Cancer Genome Atlas
- TGF, transforming growth factor
- hPSC, human pluripotent stem cell
- lncRNA, long noncoding RNA
- miRNA, microRNA
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Affiliation(s)
- Xi Liu
- Department of Pathology, First Affiliated Hospital of Xi’ an Jiaotong University, Xi’ an, Shaanxi, China,Division of Gastroenterology, Department of Medicine, and Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, Maryland
| | - Stephen J. Meltzer
- Division of Gastroenterology, Department of Medicine, and Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, Maryland,Correspondence Address correspondence to: Stephen J. Meltzer, MD, Johns Hopkins University School of Medicine, 1503 East Jefferson Street, Room 112, Baltimore, Maryland 21287. fax: (410) 502-1329.Johns Hopkins University School of Medicine1503 East Jefferson Street, Room 112BaltimoreMaryland21287
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29
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Figueiredo C, Camargo MC, Leite M, Fuentes-Pananá EM, Rabkin CS, Machado JC. Pathogenesis of Gastric Cancer: Genetics and Molecular Classification. Curr Top Microbiol Immunol 2017. [PMID: 28124158 DOI: 10.1007/978-3-319-50520-6_12.erratum.in:currtopmicrobiolimmunol.2017;400:e1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2023]
Abstract
Gastric cancer is the fifth most incident and the third most common cause of cancer-related death in the world. Infection with Helicobacter pylori is the major risk factor for this disease. Gastric cancer is the final outcome of a cascade of events that takes decades to occur and results from the accumulation of multiple genetic and epigenetic alterations. These changes are crucial for tumor cells to expedite and sustain the array of pathways involved in the cancer development, such as cell cycle, DNA repair, metabolism, cell-to-cell and cell-to-matrix interactions, apoptosis, angiogenesis, and immune surveillance. Comprehensive molecular analyses of gastric cancer have disclosed the complex heterogeneity of this disease. In particular, these analyses have confirmed that Epstein-Barr virus (EBV)-positive gastric cancer is a distinct entity. The identification of gastric cancer subtypes characterized by recognizable molecular profiles may pave the way for a more personalized clinical management and to the identification of novel therapeutic targets and biomarkers for screening, prognosis, prediction of response to treatment, and monitoring of gastric cancer progression.
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Affiliation(s)
- Ceu Figueiredo
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Institute of Molecular Pathology and Immunology of the University of Porto (Ipatimup), Rua Júlio Amaral de Carvalho 45, 4200-135, Porto, Portugal.,Faculty of Medicine of the University of Porto, Porto, Portugal
| | - M C Camargo
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, ML, USA
| | - Marina Leite
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Institute of Molecular Pathology and Immunology of the University of Porto (Ipatimup), Rua Júlio Amaral de Carvalho 45, 4200-135, Porto, Portugal
| | - Ezequiel M Fuentes-Pananá
- Research Unit of Cancer and Virology, Children's Hospital of Mexico "Federico Gomez", Mexico City, Mexico
| | - Charles S Rabkin
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, ML, USA
| | - José C Machado
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal. .,Institute of Molecular Pathology and Immunology of the University of Porto (Ipatimup), Rua Júlio Amaral de Carvalho 45, 4200-135, Porto, Portugal. .,Faculty of Medicine of the University of Porto, Porto, Portugal.
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30
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Okuda T, Taki T, Nishida K, Chinen Y, Nagoshi H, Sakakura C, Taniwaki M. Molecular heterogeneity in the novel fusion gene APIP-FGFR2: Diversity of genomic breakpoints in gastric cancer with high-level amplifications at 11p13 and 10q26. Oncol Lett 2016; 13:215-221. [PMID: 28123544 PMCID: PMC5244987 DOI: 10.3892/ol.2016.5386] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 09/28/2016] [Indexed: 01/14/2023] Open
Abstract
Several novel fusion transcripts were identified by next-generation sequencing in gastric cancer; however, the breakpoint junctions have yet to be characterized. The present study characterized a plethora of APIP-FGFR2 genomic breakpoints in the SNU-16 gastric cancer cell line, which harbored homogeneously staining regions (hsrs) and double minute chromosomes. Oligonucleotide microarrays revealed high-level amplifications at chromosomes 8q24.1 (0.8 Mb region), 10q26 (1.1 Mb) and 11p13 (1.1 Mb). These amplicons contained MYC and PVT1 at chromosome 8q24.1, BRWD2, FGFR2 and ATE1 at chromosome 10q26, and 24 genes, including APIP, CD44, RAG1 and RAG2, at chromosome 11p13. Based on these findings, reverse transcription-polymerase chain reaction (PCR) was performed using various candidate gene primers to detect possible fusion transcripts, and several products using primer sets for the APIP and FGFR2 genes were detected. Eventually, three in-frame and two out-of-frame fusion transcripts were detected. Notably, PCR analysis of the entire genomic DNA detected three distinct genomic junctions. The breakpoints were within intron 5 of APIP, which contained three distinct breakpoints, and introns 5, 7 and 9 of FGFR2. Fluorescence in situ hybridization showed several fusion signals within hsrs using two short probes (~10-kb segments of a bacterial artificial chromosome clone) containing exons 2–5 of APIP or exons 11–13 of FGFR2. Although, for any given fusion, a multiplicity of transcripts is thought to be created by alternative splicing of one rearranged allele, the results of the present study suggested that genomic fusions of APIP and FGFR2 are generated in hsrs with a diversity of breakpoints that are then faithfully transcribed.
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Affiliation(s)
- Takashi Okuda
- Department of Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine Graduate School of Medical Science, Kyoto 602-8566, Japan; Department of Hematology and Oncology, Kyoto Prefectural University of Medicine Graduate School of Medical Science, Kyoto 602-8566, Japan
| | - Tomohiko Taki
- Department of Molecular Diagnostics and Therapeutics, Kyoto Prefectural University of Medicine Graduate School of Medical Science, Kyoto 602-8566, Japan
| | - Kazuhiro Nishida
- Department of Hematology and Oncology, Kyoto Prefectural University of Medicine Graduate School of Medical Science, Kyoto 602-8566, Japan
| | - Yoshiaki Chinen
- Department of Hematology and Oncology, Kyoto Prefectural University of Medicine Graduate School of Medical Science, Kyoto 602-8566, Japan
| | - Hisao Nagoshi
- Department of Hematology and Oncology, Kyoto Prefectural University of Medicine Graduate School of Medical Science, Kyoto 602-8566, Japan
| | - Chouhei Sakakura
- Department of Digestive Surgery, Kyoto Prefectural University of Medicine Graduate School of Medical Science, Kyoto 602-8566, Japan
| | - Masafumi Taniwaki
- Department of Hematology and Oncology, Kyoto Prefectural University of Medicine Graduate School of Medical Science, Kyoto 602-8566, Japan
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31
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Chan THM, Qamra A, Tan KT, Guo J, Yang H, Qi L, Lin JS, Ng VHE, Song Y, Hong H, Tay ST, Liu Y, Lee J, Rha SY, Zhu F, So JBY, Teh BT, Yeoh KG, Rozen S, Tenen DG, Tan P, Chen L. ADAR-Mediated RNA Editing Predicts Progression and Prognosis of Gastric Cancer. Gastroenterology 2016; 151:637-650.e10. [PMID: 27373511 PMCID: PMC8286172 DOI: 10.1053/j.gastro.2016.06.043] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2015] [Revised: 06/23/2016] [Accepted: 06/24/2016] [Indexed: 12/13/2022]
Abstract
BACKGROUD & AIMS Gastric cancer (GC) is the third leading cause of global cancer mortality. Adenosine-to-inosine RNA editing is a recently described novel epigenetic mechanism involving sequence alterations at the RNA but not DNA level, primarily mediated by ADAR (adenosine deaminase that act on RNA) enzymes. Emerging evidence suggests a role for RNA editing and ADARs in cancer, however, the relationship between RNA editing and GC development and progression remains unknown. METHODS In this study, we leveraged on the next-generation sequencing transcriptomics to demarcate the GC RNA editing landscape and the role of ADARs in this deadly malignancy. RESULTS Relative to normal gastric tissues, almost all GCs displayed a clear RNA misediting phenotype with ADAR1/2 dysregulation arising from the genomic gain and loss of the ADAR1 and ADAR2 gene in primary GCs, respectively. Clinically, patients with GCs exhibiting ADAR1/2 imbalance demonstrated extremely poor prognoses in multiple independent cohorts. Functionally, we demonstrate in vitro and in vivo that ADAR-mediated RNA misediting is closely associated with GC pathogenesis, with ADAR1 and ADAR2 playing reciprocal oncogenic and tumor suppressive roles through their catalytic deaminase domains, respectively. Using an exemplary target gene PODXL (podocalyxin-like), we demonstrate that the ADAR2-regulated recoding editing at codon 241 (His to Arg) confers a loss-of-function phenotype that neutralizes the tumorigenic ability of the unedited PODXL. CONCLUSIONS Our study highlights a major role for RNA editing in GC disease and progression, an observation potentially missed by previous next-generation sequencing analyses of GC focused on DNA alterations alone. Our findings also suggest new GC therapeutic opportunities through ADAR1 enzymatic inhibition or the potential restoration of ADAR2 activity.
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Affiliation(s)
- Tim Hon Man Chan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Aditi Qamra
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, Singapore,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Kar Tong Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Jing Guo
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Henry Yang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Lihua Qi
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Jaymie Siqi Lin
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Vanessa Hui En Ng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Yangyang Song
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Huiqi Hong
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Su Ting Tay
- Cancer and Stem Cell Biology Program, Duke–National University of Singapore Graduate Medical School, Singapore
| | - Yujing Liu
- Cancer and Stem Cell Biology Program, Duke–National University of Singapore Graduate Medical School, Singapore,Singapore–Massachusetts Institute of Technology Alliance, Singapore
| | - Jeeyun Lee
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Sun Yong Rha
- Yonsei Cancer Center, Seodaemun-gu, Seoul, South Korea
| | - Feng Zhu
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Jimmy Bok Yan So
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Bin Tean Teh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore,Cancer and Stem Cell Biology Program, Duke–National University of Singapore Graduate Medical School, Singapore,Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, Singapore
| | - Khay Guan Yeoh
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore,Department of Gastroenterology and Hepatology, National University Health System, Singapore
| | - Steve Rozen
- Cancer and Stem Cell Biology Program, Duke–National University of Singapore Graduate Medical School, Singapore,Centre for Computational Biology, Duke–National University of Singapore Graduate Medical School, Singapore
| | - Daniel G. Tenen
- Cancer Science Institute of Singapore, National University of Singapore, Singapore,Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts
| | - Patrick Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore; Cancer and Stem Cell Biology Program, Duke-National University of Singapore Graduate Medical School, Singapore; Cellular and Molecular Research, National Cancer Centre, Singapore; Genome Institute of Singapore, Singapore.
| | - Leilei Chen
- Cancer Science Institute of Singapore, National University of Singapore, Singapore; Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
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32
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Liu L, Zhao X, Zou H, Bai R, Yang K, Tian Z. Hypoxia Promotes Gastric Cancer Malignancy Partly through the HIF-1α Dependent Transcriptional Activation of the Long Non-coding RNA GAPLINC. Front Physiol 2016; 7:420. [PMID: 27729869 PMCID: PMC5037220 DOI: 10.3389/fphys.2016.00420] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 09/06/2016] [Indexed: 01/16/2023] Open
Abstract
Hypoxia-inducible factor (HIF) activates the transcription of genes involved in cancer progression. Recently, HIF was reported to regulate the transcription of non-coding RNAs. Here, we show that the transcription of a long non-coding RNA (lncRNA), Gastric Adenocarcinoma Associated, Positive CD44 Regulator, Long Intergenic Non-Coding RNA (GAPLINC), is directly activated by HIF-1α in gastric cancer (GC). GAPLINC was overexpressed in GC tissues and promoted tumor migration and invasive behavior. GAPLINC overexpression was associated with poor prognosis in GC patients. Luciferase reporter assays and chromatin immunoprecipitation assays confirmed that HIF-1α binds to the promoter region of GAPLINC and activates its transcription. GAPLINC knockdown inhibited hypoxia-induced tumor proliferation in vivo. Taken together, our results identified a novel role for HIF transcriptional pathways in GC tumorigenesis mediated by the regulation of the lncRNA GAPLINC, and suggest GAPLINC as a novel therapeutic target for reversing chemoradioresistance and prolonging survival.
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Affiliation(s)
- Lei Liu
- General Surgery Department, Shengjing Hospital, China Medical University Shenyang, China
| | - Xihe Zhao
- Oncology Department, Shengjing Hospital, China Medical University Shenyang, China
| | - Huawei Zou
- Oncology Department, Shengjing Hospital, China Medical University Shenyang, China
| | - Rubing Bai
- General Surgery Department, The Forth Hospital, China Medical University Shenyang, China
| | - Keyu Yang
- General Surgery Department, The Forth Hospital, China Medical University Shenyang, China
| | - Zhong Tian
- General Surgery Department, Shengjing Hospital, China Medical University Shenyang, China
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Skierucha M, Milne ANA, Offerhaus GJA, Polkowski WP, Maciejewski R, Sitarz R. Molecular alterations in gastric cancer with special reference to the early-onset subtype. World J Gastroenterol 2016; 22:2460-74. [PMID: 26937134 PMCID: PMC4768192 DOI: 10.3748/wjg.v22.i8.2460] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Revised: 11/06/2015] [Accepted: 12/30/2015] [Indexed: 02/06/2023] Open
Abstract
Currently, gastric cancer (GC) is one of the most frequently diagnosed neoplasms, with a global burden of 723000 deaths in 2012. It is the third leading cause of cancer-related death worldwide. There are numerous possible factors that stimulate the pro-carcinogenic activity of important genes. These factors include genetic susceptibility expressed in a single-nucleotide polymorphism, various acquired mutations (chromosomal instability, microsatellite instability, somatic gene mutations, epigenetic alterations) and environmental circumstances (e.g., Helicobcter pylori infection, EBV infection, diet, and smoking). Most of the aforementioned pathways overlap, and authors agree that a clear-cut pathway for GC may not exist. Thus, the categorization of carcinogenic events is complicated. Lately, it has been claimed that research on early-onset gastric carcinoma (EOGC) and hereditary GC may contribute towards unravelling some part of the mystery of the GC molecular pattern because young patients are less exposed to environmental carcinogens and because carcinogenesis in this setting may be more dependent on genetic factors. The comparison of various aspects that differ and coexist in EOGCs and conventional GCs might enable scientists to: distinguish which features in the pathway of gastric carcinogenesis are modifiable, discover specific GC markers and identify a specific target. This review provides a summary of the data published thus far concerning the molecular characteristics of GC and highlights the outstanding features of EOGC.
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Chia NY, Tan P. Molecular classification of gastric cancer. Ann Oncol 2016; 27:763-9. [PMID: 26861606 DOI: 10.1093/annonc/mdw040] [Citation(s) in RCA: 195] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 01/19/2016] [Indexed: 12/14/2022] Open
Abstract
Gastric cancer (GC), a heterogeneous disease characterized by epidemiologic and histopathologic differences across countries, is a leading cause of cancer-related death. Treatment of GC patients is currently suboptimal due to patients being commonly treated in a uniform fashion irrespective of disease subtype. With the advent of next-generation sequencing and other genomic technologies, GCs are now being investigated in great detail at the molecular level. High-throughput technologies now allow a comprehensive study of genomic and epigenomic alterations associated with GC. Gene mutations, chromosomal aberrations, differential gene expression and epigenetic alterations are some of the genetic/epigenetic influences on GC pathogenesis. In addition, integrative analyses of molecular profiling data have led to the identification of key dysregulated pathways and importantly, the establishment of GC molecular classifiers. Recently, The Cancer Genome Atlas (TCGA) network proposed a four subtype classification scheme for GC based on the underlying tumor molecular biology of each subtype. This landmark study, together with other studies, has expanded our understanding on the characteristics of GC at the molecular level. Such knowledge may improve the medical management of GC in the future.
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Affiliation(s)
- N-Y Chia
- Cancer and Stem Cell Biology Program, Duke-National University of Singapore Graduate Medical School
| | - P Tan
- Cancer and Stem Cell Biology Program, Duke-National University of Singapore Graduate Medical School Genome Institute of Singapore, Agency for Science, Technology, and Research Cancer Science Institute of Singapore, National University of Singapore Cellular and Molecular Research, National Cancer Centre Singapore, Singapore
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Kumar-Sinha C, Kalyana-Sundaram S, Chinnaiyan AM. Landscape of gene fusions in epithelial cancers: seq and ye shall find. Genome Med 2015; 7:129. [PMID: 26684754 PMCID: PMC4683719 DOI: 10.1186/s13073-015-0252-1] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Enabled by high-throughput sequencing approaches, epithelial cancers across a range of tissue types are seen to harbor gene fusions as integral to their landscape of somatic aberrations. Although many gene fusions are found at high frequency in several rare solid cancers, apart from fusions involving the ETS family of transcription factors which have been seen in approximately 50% of prostate cancers, several other common solid cancers have been shown to harbor recurrent gene fusions at low frequencies. On the other hand, many gene fusions involving oncogenes, such as those encoding ALK, RAF or FGFR kinase families, have been detected across multiple different epithelial carcinomas. Tumor-specific gene fusions can serve as diagnostic biomarkers or help define molecular subtypes of tumors; for example, gene fusions involving oncogenes such as ERG, ETV1, TFE3, NUT, POU5F1, NFIB, PLAG1, and PAX8 are diagnostically useful. Tumors with fusions involving therapeutically targetable genes such as ALK, RET, BRAF, RAF1, FGFR1-4, and NOTCH1-3 have immediate implications for precision medicine across tissue types. Thus, ongoing cancer genomic and transcriptomic analyses for clinical sequencing need to delineate the landscape of gene fusions. Prioritization of potential oncogenic "drivers" from "passenger" fusions, and functional characterization of potentially actionable gene fusions across diverse tissue types, will help translate these findings into clinical applications. Here, we review recent advances in gene fusion discovery and the prospects for medicine.
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Affiliation(s)
- Chandan Kumar-Sinha
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
| | - Shanker Kalyana-Sundaram
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
| | - Arul M Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
- Howard Hughes Medical Institute, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
- Department of Urology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
- Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
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Tan P, Yeoh KG. Genetics and Molecular Pathogenesis of Gastric Adenocarcinoma. Gastroenterology 2015; 149:1153-1162.e3. [PMID: 26073375 DOI: 10.1053/j.gastro.2015.05.059] [Citation(s) in RCA: 318] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 05/18/2015] [Accepted: 05/20/2015] [Indexed: 02/07/2023]
Abstract
Gastric cancer (GC) is globally the fifth most common cancer and third leading cause of cancer death. A complex disease arising from the interaction of environmental and host-associated factors, key contributors to GC's high mortality include its silent nature, late clinical presentation, and underlying biological and genetic heterogeneity. Achieving a detailed molecular understanding of the various genomic aberrations associated with GC will be critical to improving patient outcomes. The recent years has seen considerable progress in deciphering the genomic landscape of GC, identifying new molecular components such as ARID1A and RHOA, cellular pathways, and tissue populations associated with gastric malignancy and progression. The Cancer Genome Atlas (TCGA) project is a landmark in the molecular characterization of GC. Key challenges for the future will involve the translation of these molecular findings to clinical utility, by enabling novel strategies for early GC detection, and precision therapies for individual GC patients.
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Affiliation(s)
- Patrick Tan
- Cancer and Stem Cell Biology Program, Duke-National University of Singapore Graduate Medical School, Singapore; Genome Institute of Singapore, Agency for Science, Technology, and Research, Singapore; Cancer Science Institute of Singapore, National University of Singapore, Singapore; Cellular and Molecular Research, National Cancer Centre Singapore, Singapore; Singapore Gastric Cancer Consortium, Singapore.
| | - Khay-Guan Yeoh
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Department of Gastroenterology and Hepatology, National University Health System, Singapore; Singapore Gastric Cancer Consortium, Singapore.
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Genomic assays for Epstein-Barr virus-positive gastric adenocarcinoma. Exp Mol Med 2015; 47:e134. [PMID: 25613731 PMCID: PMC4314585 DOI: 10.1038/emm.2014.93] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2014] [Accepted: 10/06/2014] [Indexed: 12/13/2022] Open
Abstract
A small set of gastric adenocarcinomas (9%) harbor Epstein–Barr virus (EBV) DNA within malignant cells, and the virus is not an innocent bystander but rather is intimately linked to pathogenesis and tumor maintenance. Evidence comes from unique genomic features of host DNA, mRNA, microRNA and CpG methylation profiles as revealed by recent comprehensive genomic analysis by The Cancer Genome Atlas Network. Their data show that gastric cancer is not one disease but rather comprises four major classes: EBV-positive, microsatellite instability (MSI), genomically stable and chromosome instability. The EBV-positive class has even more marked CpG methylation than does the MSI class, and viral cancers have a unique pattern of methylation linked to the downregulation of CDKN2A (p16) but not MLH1. EBV-positive cancers often have mutated PIK3CA and ARID1A and an amplified 9p24.1 locus linked to overexpression of JAK2, CD274 (PD-L1) and PDCD1LG2 (PD-L2). Multiple noncoding viral RNAs are highly expressed. Patients who fail standard therapy may qualify for enrollment in clinical trials targeting cancer-related human gene pathways or promoting destruction of infected cells through lytic induction of EBV genes. Genomic tests such as the GastroGenus Gastric Cancer Classifier are available to identify actionable variants in formalin-fixed cancer tissue of affected patients.
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Xu X, Xu L, Gao F, Wang J, Ye J, Zhou M, Zhu Y, Tao L. Identification of a novel gene fusion (BMX-ARHGAP) in gastric cardia adenocarcinoma. Diagn Pathol 2014; 9:218. [PMID: 25499959 PMCID: PMC4282731 DOI: 10.1186/s13000-014-0218-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 10/27/2014] [Indexed: 12/31/2022] Open
Abstract
Background Gastric cardia adenocarcinoma (GCA) is one of the major causes of cancer related mortality worldwide. We aim to provide new understanding in the pathogenesis of GCA through investigations on gene expression alterations. Methods We preformed RNA-Seq for one pair of GCA and matched non-tumor tissues. Differentially expressed genes (DEGs) and fusion genes were acquired. PCR and gel analysis in additional 14 pairs of samples were performed to validate the chimeric transcripts. Results 1590 up-regulated and 709 down-regulated genes were detected. Functional analysis revealed that these DEGs were significantly overrepresented in gene ontology items of cell cycle, tumor invasion and proliferation. Moreover, we firstly discovered 3 fusion genes in GCA, including BMX-ARHGAP, LRP5- LITAF and CBX3-C15orf57. The chimeric transcript BMX-ARHGAP was validated and recurrently occurred in 4/15 independent tumor tissues. Conclusions Our results may provide new understanding of GCA and biomarkers for further therapeutic studies. Virtual Slides The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/13000_2014_218
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Affiliation(s)
- Xiaofeng Xu
- Clinical Laboratory, People's hospital, Jingjiang, 214500, Jiangsu, China.
| | - Lifang Xu
- Department of Gastroenterology, People's hospital, Jingjiang, 214500, Jiangsu, China.
| | - Feng Gao
- Department of General Surgery, People's hospital, Jingjiang, 214500, Jiangsu, China.
| | - Jianjiang Wang
- Department of General Surgery, People's hospital, Jingjiang, 214500, Jiangsu, China.
| | - Jinsong Ye
- Clinical Laboratory, People's hospital, Jingjiang, 214500, Jiangsu, China.
| | - Mingxian Zhou
- Clinical Laboratory, People's hospital, Jingjiang, 214500, Jiangsu, China.
| | - Yunling Zhu
- Clinical Laboratory, People's hospital, Jingjiang, 214500, Jiangsu, China.
| | - Lan Tao
- Clinical Laboratory, People's hospital, Jingjiang, 214500, Jiangsu, China.
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Abstract
Gastric cancer remains highly prevalent and accounts for a notable proportion of global cancer mortality. This cancer is also associated with poor survival rates. Understanding the genetic basis of gastric cancer will offer insights into its pathogenesis, help identify new biomarkers and novel treatment targets, aid prognostication and could be central to developing individualized treatment strategies in the future. An inherited component contributes to <3% of gastric cancers; the majority of genetic changes associated with gastric cancer are acquired. Over the past few decades, advances in technology and high-throughput analysis have improved understanding of the molecular aspects of the pathogenesis of gastric cancer. These aspects are multifaceted and heterogeneous and represent a wide spectrum of several key genetic influences, such as chromosomal instability, microsatellite instability, changes in microRNA profile, somatic gene mutations or functional single nucleotide polymorphisms. These genetic aspects of the pathogenesis of gastric cancer will be addressed in this Review.
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Affiliation(s)
- Mairi H McLean
- National Cancer Institute, Laboratory of Molecular Immunoregulation, Cancer &Inflammation Program, 1050 Boyles Street, Frederick, MD 21702-1201, USA
| | - Emad M El-Omar
- Division of Applied Medicine, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB51 5ER, UK
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40
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Shi J, Qu YP, Hou P. Pathogenetic mechanisms in gastric cancer. World J Gastroenterol 2014; 20:13804-13819. [PMID: 25320518 PMCID: PMC4194564 DOI: 10.3748/wjg.v20.i38.13804] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 01/15/2014] [Accepted: 05/29/2014] [Indexed: 02/06/2023] Open
Abstract
Gastric cancer (GC) is a major public health issue as the fourth most common cancer and the second leading cause of cancer-related death. Recent advances have improved our understanding of its molecular pathogenesis, as best exemplified by elucidating the fundamental role of several major signaling pathways and related molecular derangements. Central to these mechanisms are the genetic and epigenetic alterations in these signaling pathways, such as gene mutations, copy number variants, aberrant gene methylation and histone modification, nucleosome positioning, and microRNAs. Some of these genetic/epigenetic alterations represent effective diagnostic and prognostic biomarkers and therapeutic targets for GC. This information has now opened unprecedented opportunities for better understanding of the molecular mechanisms of gastric carcinogenesis and the development of novel therapeutic strategies for this cancer. The pathogenetic mechanisms of GC are the focus of this review.
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Yun SM, Yoon K, Lee S, Kim E, Kong SH, Choe J, Kang JM, Han TS, Kim P, Choi Y, Jho S, Yoo H, Bhak J, Yang HK, Kim SJ. PPP1R1B-STARD3 chimeric fusion transcript in human gastric cancer promotes tumorigenesis through activation of PI3K/AKT signaling. Oncogene 2013; 33:5341-7. [DOI: 10.1038/onc.2013.472] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Revised: 09/24/2013] [Accepted: 10/04/2013] [Indexed: 12/28/2022]
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Kim HP, Cho GA, Han SW, Shin JY, Jeong EG, Song SH, Lee WC, Lee KH, Bang D, Seo JS, Kim JI, Kim TY. Novel fusion transcripts in human gastric cancer revealed by transcriptome analysis. Oncogene 2013; 33:5434-41. [PMID: 24240688 DOI: 10.1038/onc.2013.490] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Revised: 10/01/2013] [Accepted: 10/04/2013] [Indexed: 12/20/2022]
Abstract
Gene fusion is involved in the development of various types of malignancies. Recent advances in sequencing technology have facilitated identification of gene fusions and have stimulated the research of this field in cancer. In the present study, we performed next-generation transcriptome sequencing in order to discover novel gene fusions in gastric cancer. A total of 282 fusion transcript candidates were detected from 12 gastric cancer cell lines by bioinformatic filtering. Among the candidates, we have validated 19 fusion transcripts, which are 7 inter-chromosomal and 12 intra-chromosomal fusions. A novel DUS4L-BCAP29 fusion transcript was found in 2 out of 12 cell lines and 10 out of 13 gastric cancer tissues. Knockdown of DUS4L-BCAP29 transcript using siRNA inhibited cell proliferation. Soft agar assay further confirmed that this novel fusion transcript has tumorigenic potential. We also identified that microRNA-coding gene PVT1, which is amplified in double minute chromosomes in SNU-16 cells, is recurrently involved in gene fusion. PVT1 produced six different fusion transcripts involving four different genes as fusion partners. Our findings provide better insight into transcriptional and genetic alterations of gastric cancer: namely, the tumorigenic effects of transcriptional read-through and a candidate region for genetic instability.
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Affiliation(s)
- H-P Kim
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - G-A Cho
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - S-W Han
- 1] Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea [2] Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - J-Y Shin
- 1] Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Korea [2] Psoma Therapeutic Inc, Seoul, Korea
| | - E-G Jeong
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - S-H Song
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - W-C Lee
- 1] Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Korea [2] Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Korea
| | - K-H Lee
- 1] Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea [2] Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - D Bang
- Department of Chemistry, College of Science, Yonsei University, Seoul, Korea
| | - J-S Seo
- 1] Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Korea [2] Psoma Therapeutic Inc, Seoul, Korea [3] Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Korea [4] Department of Biochemistry, Seoul National University College of Medicine, Seoul, Korea [5] Macrogen Inc., Seoul, Korea
| | - J-Il Kim
- 1] Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Korea [2] Psoma Therapeutic Inc, Seoul, Korea [3] Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Korea [4] Department of Biochemistry, Seoul National University College of Medicine, Seoul, Korea
| | - T-Y Kim
- 1] Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea [2] Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea [3] Department of Molecular Medicine & Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University College of Medicine, Seoul, Korea
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Giacomini CP, Sun S, Varma S, Shain AH, Giacomini MM, Balagtas J, Sweeney RT, Lai E, Del Vecchio CA, Forster AD, Clarke N, Montgomery KD, Zhu S, Wong AJ, van de Rijn M, West RB, Pollack JR. Breakpoint analysis of transcriptional and genomic profiles uncovers novel gene fusions spanning multiple human cancer types. PLoS Genet 2013; 9:e1003464. [PMID: 23637631 PMCID: PMC3636093 DOI: 10.1371/journal.pgen.1003464] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Accepted: 03/05/2013] [Indexed: 02/07/2023] Open
Abstract
Gene fusions, like BCR/ABL1 in chronic myelogenous leukemia, have long been recognized in hematologic and mesenchymal malignancies. The recent finding of gene fusions in prostate and lung cancers has motivated the search for pathogenic gene fusions in other malignancies. Here, we developed a “breakpoint analysis” pipeline to discover candidate gene fusions by tell-tale transcript level or genomic DNA copy number transitions occurring within genes. Mining data from 974 diverse cancer samples, we identified 198 candidate fusions involving annotated cancer genes. From these, we validated and further characterized novel gene fusions involving ROS1 tyrosine kinase in angiosarcoma (CEP85L/ROS1), SLC1A2 glutamate transporter in colon cancer (APIP/SLC1A2), RAF1 kinase in pancreatic cancer (ATG7/RAF1) and anaplastic astrocytoma (BCL6/RAF1), EWSR1 in melanoma (EWSR1/CREM), CDK6 kinase in T-cell acute lymphoblastic leukemia (FAM133B/CDK6), and CLTC in breast cancer (CLTC/VMP1). Notably, while these fusions involved known cancer genes, all occurred with novel fusion partners and in previously unreported cancer types. Moreover, several constituted druggable targets (including kinases), with therapeutic implications for their respective malignancies. Lastly, breakpoint analysis identified new cell line models for known rearrangements, including EGFRvIII and FIP1L1/PDGFRA. Taken together, we provide a robust approach for gene fusion discovery, and our results highlight a more widespread role of fusion genes in cancer pathogenesis. Gene fusions represent an important class of cancer genes, created by rearrangements of the genome that bring together two different genes. Because they are unique to cancer cells, gene fusions are ideal diagnostic markers and therapeutic targets. While gene fusions were once thought restricted mainly to blood cancers, recent discoveries suggest they are more widespread. Here, we have developed an approach for mining DNA microarray data to detect the tell-tale signatures of gene fusions, as “breakpoints” occurring within the encoding DNA or expressed transcripts. We apply this approach to a large collection of nearly 1,000 human cancer specimens. From this analysis, we discover and verify twelve new gene fusions occurring in diverse cancer types. We verify that some of these rearrangements recur in other samples of the same cancer type (supporting a causal role) and that the cancers show dependency on the fusion for cancer cell growth. Notably, some of these fusions (e.g. CEP85L/ROS1 in angiosarcoma) represent the first for that cancer type and thus provide important new biological insight. Some are also good drug targets (including rearrangements of ROS1, RAF1, and CDK6 kinases), with clear implications for therapy.
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Affiliation(s)
- Craig P. Giacomini
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Steven Sun
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Sushama Varma
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - A. Hunter Shain
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Marilyn M. Giacomini
- Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Jay Balagtas
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, United States of America
| | - Robert T. Sweeney
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Everett Lai
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Catherine A. Del Vecchio
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, California, United States of America
| | - Andrew D. Forster
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Nicole Clarke
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Kelli D. Montgomery
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Shirley Zhu
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Albert J. Wong
- Department of Neurosurgery, Stanford University School of Medicine, Stanford, California, United States of America
| | - Matt van de Rijn
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Robert B. West
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Jonathan R. Pollack
- Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
- * E-mail:
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44
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McCracken AN, Edinger AL. Nutrient transporters: the Achilles' heel of anabolism. Trends Endocrinol Metab 2013; 24:200-8. [PMID: 23402769 PMCID: PMC3617053 DOI: 10.1016/j.tem.2013.01.002] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Revised: 01/03/2013] [Accepted: 01/04/2013] [Indexed: 01/08/2023]
Abstract
Highly proliferative cells, including cancer cells, require a constant supply of molecular building blocks to support their growth. To acquire substrates such as glucose and amino acids from the extracellular space, dividing cells rely on transporter proteins in the plasma membrane. Numerous studies link transcriptional and post-translational control of nutrient transporter expression with proliferation, highlighting the importance of nutrient transporters in both physiologic and pathologic growth. Here we review recent work that spotlights the crucial role of nutrient transporters in cell growth and proliferation, discuss post-translational mechanisms for coordinating expression of different transporters, and consider the therapeutic potential of targeting these proteins in cancer and other diseases characterized by inappropriate cell division.
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Affiliation(s)
| | - Aimee L. Edinger
- Corresponding Author: Aimee L. Edinger 2128 Natural Sciences 1 University of California, Irvine Irvine, CA 92697-2300 Tel: 949-824-1921 FAX: 949-824-4709
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45
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Zhang Z, Fan J, Ren Y, Zhou W, Yin G. The release of glutamate from cortical neurons regulated by BDNF via the TrkB/Src/PLC-γ1 pathway. J Cell Biochem 2012; 114:144-51. [DOI: 10.1002/jcb.24311] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Accepted: 07/26/2012] [Indexed: 12/29/2022]
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46
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Abstract
Recurrent gene fusions have been thought to play a central role in leukemias, lymphomas, and sarcomas, but they have been neglected in carcinomas, largely because of technical limitations of cytogenetics. In the past few years, an increasing number of recurrent gene fusions have been recognized in epithelial cancers. The majority of prostate cancers, for example, have an androgen-regulated fusion of one of the ETS transcription factor gene family. Notably, the fusion genes can often serve as specific diagnostic markers, criteria of molecular classification and therefore potential therapeutic targets. Recent studies have focused on investigations of morphologic features (phenotype) of recurrent gene fusions (genotype) in malignancies. In this review, we will summarize the histologic features of known recurrent genomic rearrangements in carcinomas, especially focusing on TMPRSS2-ERG fusion in prostate cancer, EML4-ALK in lung cancer, ETV6-NTRK3 in secretory breast cancer, RET/PTC and PAX8/PPARγ1 rearrangements in thyroid cancer. In addition, we will describe how these features could potentially be used to alert the pathologists of the diagnosis of fusion-positive tumor. A combination of histologic validation with other screening strategies (eg, immunohistochemistry) for recognition of recurrent gene fusions is also highlighted.
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47
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Tan IB, Ng I, Tai WM, Tan P. Understanding the genetic basis of gastric cancer: recent advances. Expert Rev Gastroenterol Hepatol 2012; 6:335-41. [PMID: 22646255 DOI: 10.1586/egh.12.7] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Two major gastric cancer histological subtypes are recognized with distinct morphology, epidemiology, pathogenesis and clinical behavior. Genetically, the intestinal and diffuse subtypes are also characterized by distinct germline susceptibility patterns and somatic aberrations. Helicobacter pylori is strongly associated with both Lauren's subtypes, although the underlying carcinogenic mechanisms are unique. Risk is modulated by strain-specific virulence factors, host responses and specific host-microbe interactions. Somatic aberrations in gastric cancer are driven by three major mechanisms, namely chromosomal instability, microsatellite instability and epigenetic alterations. These processes drive carcinogenesis in both Lauren's subtypes; however, the relative contribution of these processes and the specific genes aberrated differ. Moving beyond Lauren's subtypes, next-generation techniques have identified major genomic subtypes that have prognostic impact and exhibit distinct response patterns to standard cytotoxics.
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Affiliation(s)
- Iain Beehuat Tan
- Department of Medical Oncology, National Cancer Centre Singapore, Singapore.
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A transforming KIF5B and RET gene fusion in lung adenocarcinoma revealed from whole-genome and transcriptome sequencing. Genome Res 2011; 22:436-45. [PMID: 22194472 DOI: 10.1101/gr.133645.111] [Citation(s) in RCA: 375] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The identification of the molecular events that drive cancer transformation is essential to the development of targeted agents that improve the clinical outcome of lung cancer. Many studies have reported genomic driver mutations in non-small-cell lung cancers (NSCLCs) over the past decade; however, the molecular pathogenesis of >40% of NSCLCs is still unknown. To identify new molecular targets in NSCLCs, we performed the combined analysis of massively parallel whole-genome and transcriptome sequencing for cancer and paired normal tissue of a 33-yr-old lung adenocarcinoma patient, who is a never-smoker and has no familial cancer history. The cancer showed no known driver mutation in EGFR or KRAS and no EML4-ALK fusion. Here we report a novel fusion gene between KIF5B and the RET proto-oncogene caused by a pericentric inversion of 10p11.22-q11.21. This fusion gene overexpresses chimeric RET receptor tyrosine kinase, which could spontaneously induce cellular transformation. We identified the KIF5B-RET fusion in two more cases out of 20 primary lung adenocarcinomas in the replication study. Our data demonstrate that a subset of NSCLCs could be caused by a fusion of KIF5B and RET, and suggest the chimeric oncogene as a promising molecular target for the personalized diagnosis and treatment of lung cancer.
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Greenhill C. Cancer: Gene fusion identified in gastric cancer. Nat Rev Gastroenterol Hepatol 2011; 8:301. [PMID: 21643030 DOI: 10.1038/nrgastro.2011.78] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
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