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Sun Y, Wang HY, Liu B, Yue B, Liu Q, Liu Y, Rosa IF, Doretto LB, Han S, Lin L, Gong X, Shao C. CRISPR/dCas9-Mediated DNA Methylation Editing on emx2 in Chinese Tongue Sole ( Cynoglossus semilaevis) Testis Cells. Int J Mol Sci 2024; 25:7637. [PMID: 39062879 PMCID: PMC11277268 DOI: 10.3390/ijms25147637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 07/03/2024] [Accepted: 07/09/2024] [Indexed: 07/28/2024] Open
Abstract
DNA methylation is a key epigenetic mechanism orchestrating gene expression networks in many biological processes. Nonetheless, studying the role of specific gene methylation events in fish faces challenges. In this study, we validate the regulation of DNA methylation on empty spiracles homeobox 2 (emx2) expression with decitabine treatment in Chinese tongue sole testis cells. We used the emx2 gene as the target gene and developed a new DNA methylation editing system by fusing dnmt3a with catalytic dead Cas9 (dCas9) and demonstrated its ability for sequence-specific DNA methylation editing. Results revealed that utilizing dCas9-dnmt3a to target emx2 promoter region led to increased DNA methylation levels and decreased emx2 expression in Chinese tongue sole testis cells. More importantly, the DNA methylation editing significantly suppressed the expression of MYC proto-oncogene, bHLH transcription factor (myc), one target gene of emx2. Furthermore, we assessed the off-target effects of dCas9-dnmt3a and confirmed no significant impact on the predicted off-target gene expression. Taken together, we developed the first DNA methylation editing system in marine species and demonstrated its effective editing ability in Chinese tongue sole cells. This provides a new strategy for both epigenetic research and molecular breeding of marine species.
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Affiliation(s)
- Yanxu Sun
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China; (Y.S.); (B.Y.); (X.G.)
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (H.-Y.W.); (B.L.); (Q.L.); (Y.L.); (L.B.D.); (S.H.); (L.L.)
| | - Hong-Yan Wang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (H.-Y.W.); (B.L.); (Q.L.); (Y.L.); (L.B.D.); (S.H.); (L.L.)
| | - Binghua Liu
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (H.-Y.W.); (B.L.); (Q.L.); (Y.L.); (L.B.D.); (S.H.); (L.L.)
| | - Bowen Yue
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China; (Y.S.); (B.Y.); (X.G.)
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (H.-Y.W.); (B.L.); (Q.L.); (Y.L.); (L.B.D.); (S.H.); (L.L.)
| | - Qian Liu
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (H.-Y.W.); (B.L.); (Q.L.); (Y.L.); (L.B.D.); (S.H.); (L.L.)
| | - Yuyan Liu
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (H.-Y.W.); (B.L.); (Q.L.); (Y.L.); (L.B.D.); (S.H.); (L.L.)
| | - Ivana F. Rosa
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 01049-010, Brazil;
| | - Lucas B. Doretto
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (H.-Y.W.); (B.L.); (Q.L.); (Y.L.); (L.B.D.); (S.H.); (L.L.)
| | - Shenglei Han
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (H.-Y.W.); (B.L.); (Q.L.); (Y.L.); (L.B.D.); (S.H.); (L.L.)
| | - Lei Lin
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (H.-Y.W.); (B.L.); (Q.L.); (Y.L.); (L.B.D.); (S.H.); (L.L.)
| | - Xiaoling Gong
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China; (Y.S.); (B.Y.); (X.G.)
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, Shanghai 201306, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai 201306, China
| | - Changwei Shao
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (H.-Y.W.); (B.L.); (Q.L.); (Y.L.); (L.B.D.); (S.H.); (L.L.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao Marine Science and Technology Center, Qingdao 266237, China
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Zhou X, Dong S, Zhou Y, He Z, Zhang Z, Liao L, Zou B, Zheng X, Peng K, Duan X. EMX2 inhibits clear cell renal cell carcinoma progress via modulating Akt/FOXO3a pathway. Mol Carcinog 2024; 63:951-961. [PMID: 38362840 DOI: 10.1002/mc.23700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/19/2024] [Accepted: 02/01/2024] [Indexed: 02/17/2024]
Abstract
Empty spiracles homeobox 2 (EMX2) is initially identified as a key transcription factor that plays an essential role in the regulation of neuronal development and some brain disorders. Recently, several studies emphasized that EMX2 could as a tumor suppressor, but its role in human clear cell renal cell carcinoma (ccRCC) remains unclear. In the present study, we investigated the role and underlying mechanism of EMX2 in the regulation of ccRCC progress. Our results demonstrated that EMX2 expression was markedly decreased in ccRCC tissues and cell lines, and low EMX2 expression predicted the poor prognosis of ccRCC patients. In addition, forced expression of EMX2 significantly inhibited the cell growth, migration, and invasion in vitro, as well as ccRCC tumor growth in nude mice, via, at least in part, regulating Akt/FOXO3a pathway. In detail, EMX2 could attenuate the phosphorylation levels of Akt and FOXO3a, and increase FOXO3a expression without affecting total Akt expression in vivo and in vitro. Meanwhile, shRNA-mediated knockdown of FOXO3a expression could obviously attenuate the effects of EMX2 on cell growth, migration, invasion, and tumor growth. Furthermore, EMX2 could significantly attenuate the interaction between Akt and FOXO3a. Taken together, our results demonstrated that EMX2 could inhibit ccRCC progress through, at least in part, modulating Akt/FOXO3a signaling pathway, thus representing a novel role and underlying mechanism of EMX2 in the regulation of ccRCC progress.
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Affiliation(s)
- Xiaofeng Zhou
- Department of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Guangdong Key Laboratory of Urology, Guangzhou, China
- Guangdong Engineering Research Center of Urinary Minimally Invasive Surgery Robot and Intelligent Equipment, Guangzhou, China
- Guangzhou Institute of Urology, Guangzhou, China
| | - Sicheng Dong
- Department of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Guangdong Key Laboratory of Urology, Guangzhou, China
- Guangdong Engineering Research Center of Urinary Minimally Invasive Surgery Robot and Intelligent Equipment, Guangzhou, China
- Guangzhou Institute of Urology, Guangzhou, China
| | - Yuhao Zhou
- Department of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Guangdong Key Laboratory of Urology, Guangzhou, China
- Guangdong Engineering Research Center of Urinary Minimally Invasive Surgery Robot and Intelligent Equipment, Guangzhou, China
- Guangzhou Institute of Urology, Guangzhou, China
| | - Zhiqing He
- Department of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Guangdong Key Laboratory of Urology, Guangzhou, China
- Guangdong Engineering Research Center of Urinary Minimally Invasive Surgery Robot and Intelligent Equipment, Guangzhou, China
- Guangzhou Institute of Urology, Guangzhou, China
| | - Zhixiong Zhang
- Department of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Guangdong Key Laboratory of Urology, Guangzhou, China
- Guangdong Engineering Research Center of Urinary Minimally Invasive Surgery Robot and Intelligent Equipment, Guangzhou, China
- Guangzhou Institute of Urology, Guangzhou, China
| | - Liqiong Liao
- Department of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Guangdong Key Laboratory of Urology, Guangzhou, China
- Guangdong Engineering Research Center of Urinary Minimally Invasive Surgery Robot and Intelligent Equipment, Guangzhou, China
- Guangzhou Institute of Urology, Guangzhou, China
| | - Bangyu Zou
- Department of Urology, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Xiaopeng Zheng
- Department of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Guangdong Key Laboratory of Urology, Guangzhou, China
- Guangdong Engineering Research Center of Urinary Minimally Invasive Surgery Robot and Intelligent Equipment, Guangzhou, China
- Guangzhou Institute of Urology, Guangzhou, China
| | - Kaoqing Peng
- Department of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Guangdong Key Laboratory of Urology, Guangzhou, China
- Guangdong Engineering Research Center of Urinary Minimally Invasive Surgery Robot and Intelligent Equipment, Guangzhou, China
- Guangzhou Institute of Urology, Guangzhou, China
| | - Xiaolu Duan
- Department of Urology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Guangdong Key Laboratory of Urology, Guangzhou, China
- Guangdong Engineering Research Center of Urinary Minimally Invasive Surgery Robot and Intelligent Equipment, Guangzhou, China
- Guangzhou Institute of Urology, Guangzhou, China
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Wen DS, Huang LC, Bu XY, He MK, Lai ZC, Du ZF, Huang YX, Kan A, Shi M. DNA methylation-activated full-length EMX1 facilitates metastasis through EMX1-EGFR-ERK axis in hepatocellular carcinoma. Cell Death Dis 2023; 14:769. [PMID: 38007497 PMCID: PMC10676392 DOI: 10.1038/s41419-023-06293-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 11/01/2023] [Accepted: 11/13/2023] [Indexed: 11/27/2023]
Abstract
Altered DNA methylation is a crucial epigenetic event in hepatocellular carcinoma (HCC) development and progression. Through methylation-transcriptomic analysis, we identified a set of sixty potential DNA methylation-based epidriver genes. In this set of genes, we focused on the hypermethylation of EMX1, which is frequently observed in hepatobiliary tumors. Despite of its frequent occurrence, the function of EMX1 remains largely unknown. By utilizing bisulfite-next-generation sequencing, we have detected EMX1 DNA hypermethylation on the gene body, which is positively correlated with EMX1 mRNA expression. Further analysis revealed that EMX1 mRNA terminal exon splicing in HCC generated two protein isoforms: EMX1 full length (EMX1-FL) and alternative terminal exon splicing isoform (EMX1-X1). Cellular functional assays demonstrated that gain-of-function EMX1-FL, but not EMX1-X1, induced HCC cells migration and invasion while silencing EMX1-FL inhibited HCC cells motility. This result was further validated by in vivo tumor metastasis models. Mechanistically, EMX1-FL bound to EGFR promoter, promoting EGFR transcription and activating EGFR-ERK signaling to trigger tumor metastasis. Therefore, EGFR may be a potential therapeutic target for EMX1-high expression HCC. Our work illuminated the crucial role of gene body hypermethylation-activated EMX1-FL in promoting tumorigenesis and metastasis in HCC. These findings pave the way for targeting the EMX1-EGFR axis in HCC tumorigenicity and metastasis.
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Affiliation(s)
- Dong-Sheng Wen
- Department of Hepatobiliary Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, 510060, P. R. China
| | - Li-Chang Huang
- Department of Hepatobiliary Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, 510060, P. R. China
| | - Xiao-Yun Bu
- Department of Colorectal Surgery, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, P. R. China
| | - Min-Ke He
- Department of Hepatobiliary Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, 510060, P. R. China
| | - Zhi-Cheng Lai
- Department of Hepatobiliary Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, 510060, P. R. China
| | - Ze-Feng Du
- Department of Hepatobiliary Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, 510060, P. R. China
| | - Ye-Xing Huang
- Department of Hepatobiliary Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, 510060, P. R. China
| | - Anna Kan
- Department of Hepatobiliary Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, 510060, P. R. China.
| | - Ming Shi
- Department of Hepatobiliary Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, 510060, P. R. China.
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Shikhevich S, Chadaeva I, Khandaev B, Kozhemyakina R, Zolotareva K, Kazachek A, Oshchepkov D, Bogomolov A, Klimova NV, Ivanisenko VA, Demenkov P, Mustafin Z, Markel A, Savinkova L, Kolchanov NA, Kozlov V, Ponomarenko M. Differentially Expressed Genes and Molecular Susceptibility to Human Age-Related Diseases. Int J Mol Sci 2023; 24:ijms24043996. [PMID: 36835409 PMCID: PMC9966505 DOI: 10.3390/ijms24043996] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/02/2023] [Accepted: 02/13/2023] [Indexed: 02/18/2023] Open
Abstract
Mainstream transcriptome profiling of susceptibility versus resistance to age-related diseases (ARDs) is focused on differentially expressed genes (DEGs) specific to gender, age, and pathogeneses. This approach fits in well with predictive, preventive, personalized, participatory medicine and helps understand how, why, when, and what ARDs one can develop depending on their genetic background. Within this mainstream paradigm, we wanted to find out whether the known ARD-linked DEGs available in PubMed can reveal a molecular marker that will serve the purpose in anyone's any tissue at any time. We sequenced the periaqueductal gray (PAG) transcriptome of tame versus aggressive rats, identified rat-behavior-related DEGs, and compared them with their known homologous animal ARD-linked DEGs. This analysis yielded statistically significant correlations between behavior-related and ARD-susceptibility-related fold changes (log2 values) in the expression of these DEG homologs. We found principal components, PC1 and PC2, corresponding to the half-sum and the half-difference of these log2 values, respectively. With the DEGs linked to ARD susceptibility and ARD resistance in humans used as controls, we verified these principal components. This yielded only one statistically significant common molecular marker for ARDs: an excess of Fcγ receptor IIb suppressing immune cell hyperactivation.
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Affiliation(s)
- Svetlana Shikhevich
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
| | - Irina Chadaeva
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
| | - Bato Khandaev
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
- The Natural Sciences Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Rimma Kozhemyakina
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
| | - Karina Zolotareva
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
- The Natural Sciences Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Anna Kazachek
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
- The Natural Sciences Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Dmitry Oshchepkov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
- The Natural Sciences Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Anton Bogomolov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
- The Natural Sciences Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Natalya V. Klimova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
| | - Vladimir A. Ivanisenko
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
- The Natural Sciences Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Pavel Demenkov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
| | - Zakhar Mustafin
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
- The Natural Sciences Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Arcady Markel
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
- The Natural Sciences Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Ludmila Savinkova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
| | - Nikolay A. Kolchanov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
- The Natural Sciences Department, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Vladimir Kozlov
- Research Institute of Fundamental and Clinical Immunology (RIFCI) SB RAS, Novosibirsk 630099, Russia
| | - Mikhail Ponomarenko
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk 630090, Russia
- Correspondence: ; Tel.: +7-(383)-363-4963 (ext. 1311)
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Yi L, Qiang J, Yichen P, Chunna Y, Yi Z, Xun K, Jianwei Z, Rixing B, Wenmao Y, Xiaomin W, Parker L, Wenbin L. Identification of a 5-gene-based signature to predict prognosis and correlate immunomodulators for rectal cancer. Transl Oncol 2022; 26:101529. [PMID: 36130456 PMCID: PMC9493070 DOI: 10.1016/j.tranon.2022.101529] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 08/11/2022] [Accepted: 09/01/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Specific tumor markers have yet to be identified in rectal cancer. This study aims to identify a novel genetic signature in rectal cancer to provide clues for survival and immunotherapy. METHODS DEGs were obtained from two GEO datasets of rectal cancer. By using data from TCGA and GSE133057, two cohorts of rectal cancer were applied to establish and evaluate the signature. A nomogram was constructed for training and validation. We integrated the risk-score with clinicopathological features and assessed its interplay with immune cells and molecules. Finally, our study performed functional annotations, gene-targeted miRNAs, and single-cell analysis. RESULTS A total of 468 DEGs were identified, and a signature consisting of 5 genes (CLIC5, ENTPD8, PACSIN3, HGD, and GNG7) was selected to calculate the risk-score. The model exhibited high performance in time-dependent ROC and a nomogram. Further results showed that overall survival was significantly worse in the high-risk group. As an independent prognostic factor, the risk-score was associated with vascular invasion. There was a dramatic difference in nonregulatory CD4+ and CD8+ T cells between the high and low-risk groups, and the 5 genes were correlated with immune inhibitors. There was a considerable difference in autophagy, immune, cell cycle, infection, and apoptosis-associated terms and pathways in GO and KEGG. The functional states of differentiation, apoptosis, and quiescence were closely related to the 5-gene signature in single-cell analysis. CONCLUSION Our results suggest that the signature could serve as a novel prognostic biomarker in rectal cancer, which might benefit decision-making regarding immunotherapy.
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Affiliation(s)
- Lin Yi
- Department of General Surgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China; Department of Neuro-oncology, Cancer Center, China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Ji Qiang
- Department of Neuro-oncology, Cancer Center, China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China; Department of Epidemiology and Health Statistics, School of Public Health, Capital Medical University, Beijing, China
| | - Peng Yichen
- Department of Neuro-oncology, Cancer Center, China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yu Chunna
- Department of Neuro-oncology, Cancer Center, China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Zheng Yi
- Department of Neuro-oncology, Cancer Center, China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China; Department of Epidemiology and Health Statistics, School of Public Health, Capital Medical University, Beijing, China
| | - Kang Xun
- Department of Neuro-oncology, Cancer Center, China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Zheng Jianwei
- Department of General Surgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Bai Rixing
- Department of General Surgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yan Wenmao
- Department of General Surgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Wang Xiaomin
- Department of Neuro-oncology, Cancer Center, China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China; Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital & Institute, Beijing, China.
| | - Li Parker
- Clinical Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Li Wenbin
- Department of Neuro-oncology, Cancer Center, China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.
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Niu Y, Yang W, Qian H, Sun Y. Intracellular and extracellular factors of colorectal cancer liver metastasis: a pivotal perplex to be fully elucidated. Cancer Cell Int 2022; 22:341. [DOI: 10.1186/s12935-022-02766-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 10/19/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractMetastasis is the leading cause of death in colorectal cancer (CRC) patients, and the liver is the most common site of metastasis. Tumor cell metastasis can be thought of as an invasion-metastasis cascade and metastatic organotropism is thought to be a process that relies on the intrinsic properties of tumor cells and their interactions with molecules and cells in the microenvironment. Many studies have provided new insights into the molecular mechanism and contributing factors involved in CRC liver metastasis for a better understanding of the organ-specific metastasis process. The purpose of this review is to summarize the theories that explain CRC liver metastasis at multiple molecular dimensions (including genetic and non-genetic factors), as well as the main factors that cause CRC liver metastasis. Many findings suggest that metastasis may occur earlier than expected and with specific organ-anchoring property. The emergence of potential metastatic clones, the timing of dissemination, and the distinct routes of metastasis have been explained by genomic studies. The main force of CRC liver metastasis is also thought to be epigenetic alterations and dynamic phenotypic traits. Furthermore, we review key extrinsic factors that influence CRC cell metastasis and liver tropisms, such as pre-niches, tumor stromal cells, adhesion molecules, and immune/inflammatory responses in the tumor microenvironment. In addition, biomarkers associated with early diagnosis, prognosis, and recurrence of liver metastasis from CRC are summarized to enlighten potential clinical practice, including some markers that can be used as therapeutic targets to provide new perspectives for the treatment strategies of CRC liver metastasis.
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The tissue-specificity associated region and motif of an emx2 downstream enhancer CNE2.04 in zebrafish. Gene Expr Patterns 2022; 45:119269. [PMID: 35970322 DOI: 10.1016/j.gep.2022.119269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 07/04/2022] [Accepted: 07/29/2022] [Indexed: 11/22/2022]
Abstract
BACKGROUND Expression level of EMX2 plays an important role in the development of nervous system and cancers. CNE2.04, a conserved enhancer downstream of emx2, drives fluorescent protein expression in the similar pattern of emx2. METHODS CNE2.04 truncated or motif-mutated transgenic reporter plasmids were constructed and injected into the zebrafish fertilized egg with Tol2 mRNA at the unicellular stage of zebrafish eggs. The green fluorescence expression patterns were observed at 24, 48, and 72 hpf, and the fluorescence rates of different tissues were counted at 48 hpf. RESULTS Compared to CNE2.04, CNE2.04-R400 had comparable enhancer activity, while the tissue specificity of CNE2.04-L400 was obviously changed. Motif CCCCTC mutation obviously changed the enhancer activity, while motif CCGCTC mutations also changed it. CONCLUSION Due to their correlation with tissue specificity, CNE2.04-R400 is associated with the tissue-specificity of CNE2.04, and motif CCCCTC plays an important role in the enhancer activity of CNE2.04.
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Leung RF, George AM, Roussel EM, Faux MC, Wigle JT, Eisenstat DD. Genetic Regulation of Vertebrate Forebrain Development by Homeobox Genes. Front Neurosci 2022; 16:843794. [PMID: 35546872 PMCID: PMC9081933 DOI: 10.3389/fnins.2022.843794] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 03/14/2022] [Indexed: 01/19/2023] Open
Abstract
Forebrain development in vertebrates is regulated by transcription factors encoded by homeobox, bHLH and forkhead gene families throughout the progressive and overlapping stages of neural induction and patterning, regional specification and generation of neurons and glia from central nervous system (CNS) progenitor cells. Moreover, cell fate decisions, differentiation and migration of these committed CNS progenitors are controlled by the gene regulatory networks that are regulated by various homeodomain-containing transcription factors, including but not limited to those of the Pax (paired), Nkx, Otx (orthodenticle), Gsx/Gsh (genetic screened), and Dlx (distal-less) homeobox gene families. This comprehensive review outlines the integral role of key homeobox transcription factors and their target genes on forebrain development, focused primarily on the telencephalon. Furthermore, links of these transcription factors to human diseases, such as neurodevelopmental disorders and brain tumors are provided.
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Affiliation(s)
- Ryan F. Leung
- Murdoch Children’s Research Institute, The Royal Children’s Hospital Melbourne, Parkville, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
| | - Ankita M. George
- Murdoch Children’s Research Institute, The Royal Children’s Hospital Melbourne, Parkville, VIC, Australia
| | - Enola M. Roussel
- Murdoch Children’s Research Institute, The Royal Children’s Hospital Melbourne, Parkville, VIC, Australia
| | - Maree C. Faux
- Murdoch Children’s Research Institute, The Royal Children’s Hospital Melbourne, Parkville, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
- Department of Surgery, Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC, Australia
| | - Jeffrey T. Wigle
- Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
- Institute of Cardiovascular Sciences, St. Boniface Hospital Albrechtsen Research Centre, Winnipeg, MB, Canada
| | - David D. Eisenstat
- Murdoch Children’s Research Institute, The Royal Children’s Hospital Melbourne, Parkville, VIC, Australia
- Department of Paediatrics, University of Melbourne, Parkville, VIC, Australia
- Department of Medical Genetics, University of Alberta, Edmonton, AB, Canada
- Department of Pediatrics, University of Alberta, Edmonton, AB, Canada
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9
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Kołat D, Kałuzińska Ż, Bednarek AK, Płuciennik E. Prognostic significance of AP-2α/γ targets as cancer therapeutics. Sci Rep 2022; 12:5497. [PMID: 35361846 PMCID: PMC8971500 DOI: 10.1038/s41598-022-09494-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 03/24/2022] [Indexed: 02/07/2023] Open
Abstract
Identifying genes with prognostic importance could improve cancer treatment. An increasing number of reports suggest the existence of successful strategies based on seemingly "untargetable" transcription factors. In addition to embryogenesis, AP-2 transcription factors are known to play crucial roles in cancer development. Members of this family can be used as prognostic factors in oncological patients, and AP-2α/γ transcription factors were previously investigated in our pan-cancer comparative study using their target genes. The present study investigates tumors that were previously found similar with an emphasis on the possible role of AP-2 factors in specific cancer types. The RData workspace was loaded back to R environment and 3D trajectories were built via Monocle3. The genes that met the requirement of specificity were listed using top_markers(), separately for mutual and unique targets. Furthermore, the candidate genes had to meet the following requirements: correlation with AP-2 factor (through Correlation AnalyzeR) and validated prognostic importance (using GEPIA2 and subsequently KM-plotter or LOGpc). Eventually, the ROC analysis was applied to confirm their predictive value; co-dependence of expression was visualized via BoxPlotR. Some similar tumors were differentiated by AP-2α/γ targets with prognostic value. Requirements were met by only fifteen genes (EMX2, COL7A1, GRIA1, KRT1, KRT14, SLC12A5, SEZ6L, PTPRN, SCG5, DPP6, NTSR1, ARX, COL4A3, PPEF1 and TMEM59L); of these, the last four were excluded based on ROC curves. All the above genes were confronted with the literature, with an emphasis on the possible role played by AP-2 factors in specific cancers. Following ROC analysis, the genes were verified using immunohistochemistry data and progression-related signatures. Staining differences were observed, as well as co-dependence on the expression of e.g. CTNNB1, ERBB2, KRAS, SMAD4, EGFR or MKI67. In conclusion, prognostic value of targets suggested AP-2α/γ as candidates for novel cancer treatment. It was also revealed that AP-2 targets are related to tumor progression and that some mutual target genes could be inversely regulated.
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Affiliation(s)
- Damian Kołat
- Department of Molecular Carcinogenesis, Medical University of Lodz, 90-752, Lodz, Poland.
| | - Żaneta Kałuzińska
- Department of Molecular Carcinogenesis, Medical University of Lodz, 90-752, Lodz, Poland
| | - Andrzej K Bednarek
- Department of Molecular Carcinogenesis, Medical University of Lodz, 90-752, Lodz, Poland
| | - Elżbieta Płuciennik
- Department of Molecular Carcinogenesis, Medical University of Lodz, 90-752, Lodz, Poland
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Identification and Verification of Tumor Immune Microenvironment-Related Prognostic Genes in Kidney Renal Clear Cell Carcinoma. BIOMED RESEARCH INTERNATIONAL 2022; 2022:5563668. [PMID: 35127943 PMCID: PMC8813216 DOI: 10.1155/2022/5563668] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 12/12/2021] [Accepted: 12/17/2021] [Indexed: 12/12/2022]
Abstract
Background The tumor immune microenvironment is vital to kidney renal clear cell carcinoma (KIRC) progression, and immunotherapies have been shown to be effective in the management of KIRC. However, the prognostic genes associated with the tumor immune microenvironment in KIRC have not been fully identified. We obtained the KIRC RNA sequencing data and the clinical characteristics from The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC) database. We screened the gene modules associated with the tumor immune microenvironment based on the ESTIMATE algorithm and weighted gene coexpression network analysis (WGCNA). Univariate Cox analysis and the LASSO method were used to construct a prognostic model. Receiver Operating Characteristic (ROC) curve analysis was performed to evaluate the accuracy of our risk model. TIMER and Single-Sample Gene Set Enrichment Analysis (ssGSEA) were used to explore the correlation between prognostic genes and immune cell infiltration. Results Fifty-four genes in modules were significantly associated with the overall survival (OS) time of patients with KIRC. Furthermore, 12 hub genes were selected to construct the prognostic model. The prognostic model showed superior accuracy in both TCGA and ICGC cohorts using ROC curve analysis. Systematic analysis of immune cell infiltration revealed that nine genes were significantly correlated with levels of tumor-infiltrating immune cells. Conclusions Our findings indicated that the tumor immune microenvironment was an important determinant of KIRC outcomes and revealed potential biomarkers for predicting patient OS and for targeted immunotherapies.
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Jiang Y, Chen S. Functional New Transcription Factors (TFs) Associated with Cervical Cancer. JOURNAL OF HEALTHCARE ENGINEERING 2022; 2022:8381559. [PMID: 35126951 PMCID: PMC8808228 DOI: 10.1155/2022/8381559] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 12/10/2021] [Accepted: 12/20/2021] [Indexed: 11/17/2022]
Abstract
The goal of this research was to find noval transcription factors (TFs) that are involved in cervical carcinogenesis. The Gene Expression Omnibus (GEO) database was utilized to analyze ten cervical cancer datasets using the Robust Rank Aggregation (RRA) technique. Survival and differential expression were validated using GEPIA (Gene Expression Profiling Interactive Analysis). The transcriptional regulatory network and putative targets were built using Cytoscape. A real-time PCR (quantitative real-time polymerase chain reaction) experiment was used to confirm the mRNA expression. Using public cervical cancer single-cell RNA-sequencing (scRNA-seq), bulk TCGA-CESC RNA-seq, and microarray datasets, coexpression correlations between putative targets and TFs were confirmed. After combining the results of 10 datasets, 8 TFs, including EMX2 (Empty Spiracles Homeobox 2), were chosen among 385 robust DEGs. In the normal female reproductive tract, EMX2 is extensively expressed, but it is reduced in cervical cancer. Overexpression EMX2 suppresses the proliferation of HeLa cells. 12 potential targets of EMX2 were selected. Our research has revealed evidence that EMX2 acted as a tumor suppressor in cervical cancer and PDZRN3 might be possible target of EMX2 in cervical cancer. It might be a therapeutic target in the future.
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Affiliation(s)
- Yicheng Jiang
- Department of Oncology, People's Hospital of Chongqing Hechuan, Chongqing, China
| | - Shi Chen
- Department of Oncology, Chengdu Jinniu District People's Hospital, Chengdu, Sichuan, China
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12
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Liu GX, Tan YZ, He GC, Zhang QL, Liu P. EMX2OS plays a prognosis-associated enhancer RNA role in gastric cancer. Medicine (Baltimore) 2021; 100:e27535. [PMID: 34731149 PMCID: PMC8519253 DOI: 10.1097/md.0000000000027535] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 09/27/2021] [Indexed: 01/05/2023] Open
Abstract
Enhancer RNAs (eRNAs), a subclass of lncRNAs, are derived from enhancer regions. The function of eRNAs has been reported by many previous studies. However, the role of eRNAs in gastric cancer, especially the prognosis-associated eRNAs, has not been studied yet.In this study, we have used a novel approach to screened key eRNAs in gastric cancer. Kaplan-Meier correlation analysis and Co-expression analysis were used to find the most significant survival-associated eRNAs. Enrichment analysis is applied to explore the key functions and pathways of screened eRNAs. The correlation and survival analysis are used to evaluate targeted genes in the pan-cancer analysisA total of 63 prognostic-associated eRNAs in gastric cancer were identified, the top 6 eRNAs were LINC01714, ZNF192P1, AC079760.2, LINC01645, EMX2OS, and AC114489.2. The correlation analysis demonstrated the top 10 screened eRNAs and their targeted genes. The results demonstrated that EMX2OS was ranked as the top eRNA according to the results of the Kaplan-Meier analysis. The correlation analysis demonstrated that eRNA EMX2OS is correlated with age, grade, stage, and cancer status. The pan-cancer analysis demonstrated that EMX2OS was associated with poor survival outcomes in adrenocortical carcinoma, cervical squamous cell carcinoma and endocervical adenocarcinoma, kidney renal clear cell carcinoma, stomach adenocarcinoma, and uveal melanoma.In this study, survival-related eRNAs were screened and the correlation between survival-related eRNAs and their targeted genes was demonstrated. EMX2OS plays a prognosis-associated eRNA role in gastric cancer, which might be a novel therapeutic target in clinical practice.
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Affiliation(s)
- Ge-Xin Liu
- Department of Emergency, Zhuzhou Central Hospital, Zhuzhou, China
| | - Yu-Zhen Tan
- Department of Emergency, Zhuzhou Central Hospital, Zhuzhou, China
| | - Guo-Chao He
- Department of Emergency, Zhuzhou Central Hospital, Zhuzhou, China
| | - Qin-Lin Zhang
- Department of Neurology, Zhuzhou Central Hospital, Zhuzhou, China
| | - Pan Liu
- Department of Emergency, Zhuzhou Central Hospital, Zhuzhou, China
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Jimenez-García MP, Lucena-Cacace A, Otero-Albiol D, Carnero A. Empty spiracles homeobox genes EMX1 and EMX2 regulate WNT pathway activation in sarcomagenesis. J Exp Clin Cancer Res 2021; 40:247. [PMID: 34364391 PMCID: PMC8348834 DOI: 10.1186/s13046-021-02048-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 07/16/2021] [Indexed: 11/10/2022] Open
Abstract
Background Sarcomas are a very heterogeneous group of tumors with intrinsic developmental programs derived from the cell of origin. This implies a functional hierarchy inside tumors governed by sarcoma stem cells. Therefore, genetic and/or epigenetic changes profoundly affect the biology of sarcoma tumor stem cells. EMX genes are proposed to be transcription factors that are involved in the sarcomagenesis process, regardless of the neural or mesodermal embryological sarcoma origin. It has been shown that EMX1 or EMX2 overexpression reduces tumorigenic properties, while reducing the levels of these genes enhances these properties. Furthermore, it has been shown that EMX genes decrease the expression of stem cell regulatory genes and the stem cell phenotype. Taken together, these results indicate that the EMX1 and EMX2 genes negatively regulate these tumor-remodeling populations or sarcoma stem cells, acting as tumor suppressors in sarcoma. Methods Bioinformatic analysis, quantitative mRNA and protein expression analysis, cell models of sarcoma by ectopic expression of EMX genes. By cell biology methods we measured tumorigenesis and populations enriched on stem cell phenotypes, either in vitro or in vivo. Results In this work, we showed that the canonical Wnt pathway is one of the mechanisms that explains the relationships of EMX1/EMX2 and stem cell genes in sarcoma. The Wnt-EMX1/EMX2 relationship was validated in silico with sarcoma patient datasets, in vitro in primary derived sarcoma cell lines, and in vivo. EMX expression was found to negatively regulate the Wnt pathway. In addition, the constitutive activation of the Wnt pathway revers to a more aggressive phenotype with stem cell properties, and stemness gene transcription increased even in the presence of EMX1 and/or EMX2 overexpression, establishing the relationship among the Wnt pathway, stem cell genes and the EMX transcription factors. Conclusions Our data showed that Empty Spiracles Homeobox Genes EMX1 and EMX2 represses WNT signalling and activation of WNT pathway bypass EMX-dependent stemness repression and induces sarcomagenesis. These results also suggest the relevance of the Wnt/b-catenin/stemness axis as a therapeutic target in sarcoma. Supplementary Information The online version contains supplementary material available at 10.1186/s13046-021-02048-9.
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Affiliation(s)
- Manuel Pedro Jimenez-García
- Instituto de Biomedicina de Sevilla (IBIS), Hospital Universitario Virgen del Rocío, Universidad de Sevilla, Consejo Superior de Investigaciones Científicas, Sevilla, Spain.,CIBER de Cancer, IS Carlos III, Madrid, Spain
| | - Antonio Lucena-Cacace
- Present address: Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Daniel Otero-Albiol
- Instituto de Biomedicina de Sevilla (IBIS), Hospital Universitario Virgen del Rocío, Universidad de Sevilla, Consejo Superior de Investigaciones Científicas, Sevilla, Spain.,CIBER de Cancer, IS Carlos III, Madrid, Spain
| | - Amancio Carnero
- Instituto de Biomedicina de Sevilla (IBIS), Hospital Universitario Virgen del Rocío, Universidad de Sevilla, Consejo Superior de Investigaciones Científicas, Sevilla, Spain. .,CIBER de Cancer, IS Carlos III, Madrid, Spain. .,Instituto de Biomedicina de Sevilla/HUVR/CSIC, Hospital Universitario Virgen del Rocío, Avda. Manuel Siurot s/n, 41013, Sevilla, Spain.
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14
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Jimenez-García MP, Lucena-Cacace A, Otero-Albiol D, Carnero A. Regulation of sarcomagenesis by the empty spiracles homeobox genes EMX1 and EMX2. Cell Death Dis 2021; 12:515. [PMID: 34016958 PMCID: PMC8137939 DOI: 10.1038/s41419-021-03801-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 05/03/2021] [Accepted: 05/03/2021] [Indexed: 02/07/2023]
Abstract
The EMX (Empty Spiracles Homeobox) genes EMX1 and EMX2 are two homeodomain gene members of the EMX family of transcription factors involved in the regulation of various biological processes, such as cell proliferation, migration, and differentiation, during brain development and neural crest migration. They play a role in the specification of positional identity, the proliferation of neural stem cells, and the differentiation of certain neuronal cell phenotypes. In general, they act as transcription factors in early embryogenesis and neuroembryogenesis from metazoans to higher vertebrates. The EMX1 and EMX2's potential as tumor suppressor genes has been suggested in some cancers. Our work showed that EMX1/EMX2 act as tumor suppressors in sarcomas by repressing the activity of stem cell regulatory genes (OCT4, SOX2, KLF4, MYC, NANOG, NES, and PROM1). EMX protein downregulation, therefore, induced the malignance and stemness of cells both in vitro and in vivo. In murine knockout (KO) models lacking Emx genes, 3MC-induced sarcomas were more aggressive and infiltrative, had a greater capacity for tumor self-renewal, and had higher stem cell gene expression and nestin expression than those in wild-type models. These results showing that EMX genes acted as stemness regulators were reproduced in different subtypes of sarcoma. Therefore, it is possible that the EMX genes could have a generalized behavior regulating proliferation of neural crest-derived progenitors. Together, these results indicate that the EMX1 and EMX2 genes negatively regulate these tumor-altering populations or cancer stem cells, acting as tumor suppressors in sarcoma.
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Affiliation(s)
- Manuel Pedro Jimenez-García
- grid.411109.c0000 0000 9542 1158Instituto de Biomedicina de Sevilla (IBIS), Hospital Universitario Virgen del Rocío, Universidad de Sevilla, Consejo Superior de Investigaciones Científicas, Sevilla, Spain ,CIBER de Cancer, IS Carlos III, Madrid, Spain
| | - Antonio Lucena-Cacace
- grid.258799.80000 0004 0372 2033Department of Cell Growth and Differentiation, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Daniel Otero-Albiol
- grid.411109.c0000 0000 9542 1158Instituto de Biomedicina de Sevilla (IBIS), Hospital Universitario Virgen del Rocío, Universidad de Sevilla, Consejo Superior de Investigaciones Científicas, Sevilla, Spain ,CIBER de Cancer, IS Carlos III, Madrid, Spain
| | - Amancio Carnero
- grid.411109.c0000 0000 9542 1158Instituto de Biomedicina de Sevilla (IBIS), Hospital Universitario Virgen del Rocío, Universidad de Sevilla, Consejo Superior de Investigaciones Científicas, Sevilla, Spain ,CIBER de Cancer, IS Carlos III, Madrid, Spain
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15
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Ghafarpour V, Khansari M, Banaei-Moghaddam AM, Najafi A, Masoudi-Nejad A. DNA methylation association with stage progression of head and neck squamous cell carcinoma. Comput Biol Med 2021; 134:104473. [PMID: 34034219 DOI: 10.1016/j.compbiomed.2021.104473] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 04/27/2021] [Accepted: 05/02/2021] [Indexed: 01/13/2023]
Abstract
Head and Neck Squamous Cell Carcinoma (HNSCC) is the sixth most common cancer worldwide, which accounts for approximately 6% of all cases and is responsible for an estimated 2% of all cancer deaths. Despite progress in the treatment of squamous cell carcinomas, survival rates remain low. It is a fact that epigenetic modifications have numerous associations with biological processes and complex diseases such as cancer. Hence, a more systematic approach is needed to provide potential screening targets and have an effective therapy method. This study developed a workflow to analyze HM450 methylation arrays with mRNA expression profiles that identified novel signatures of epigenetic regulators for tumor progression. We identified differentially expressed genes and differentially methylated regions and the correlation between associated genes to identify epigenetic modifications underlying regulation roles. We have taken the differentiation direction of expressions into account during the integration of gene expression and DNA methylation modification to detect epigenetic regulators of core genes of tumor-stage progression. Enrichment analysis of selected key genes provides better insight into their functionality. Thus, we have investigated gene copy number alteration and mutations to filter differentially expressed genes, including some members of the fibroblast growth factor family and cyclin-dependent kinase inhibitor family with other potential known regulators. Our analysis has revealed the list of 61 commercial methylation probes positively correlated with 31 differentially expressed genes, which can be associated with HNSC metastasis stages. Most of these genes have already reported potential epigenetic regulators, and their role in cancer progression was studied. We suggest these selected probes of DNA methylation as potential targets of the epigenetic regulators in revealed genes that have displayed significant genetic and epigenetic modification behavior during cancer stage progression and tumor metastasis.
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Affiliation(s)
- Vahid Ghafarpour
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Mohammad Khansari
- Faculty of New Sciences and Technologies, University of Tehran, Tehran, Iran
| | - Ali M Banaei-Moghaddam
- Laboratory of Genomics and Epigenomics (LGE), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Ali Najafi
- Molecular Biology Research Center, Systems Biology and Poisonings Institute, Tehran, Iran
| | - Ali Masoudi-Nejad
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran. http://lbb.ut.ac.ir/
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Zheng W, Wu F, Fu K, Sun G, Sun G, Li X, Jiang W, Cao H, Wang H, Tang W. Emerging Mechanisms and Treatment Progress on Liver Metastasis of Colorectal Cancer. Onco Targets Ther 2021; 14:3013-3036. [PMID: 33986602 PMCID: PMC8110277 DOI: 10.2147/ott.s301371] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 03/24/2021] [Indexed: 12/24/2022] Open
Abstract
Colorectal cancer is currently the third largest malignant tumor in the world, with high new cases and high mortality. Metastasis is one of the most common causes of death of colorectal cancer, of which liver metastasis is the most fatal. Since the beginning of the Human Genome Project in 2001, people have gradually recognized the 3 billion base pairs that make up the human genome, of which only about 1.5% of the nucleic acid sequences are used for protein coding, including proto-oncogenes and tumor suppressor genes. A large number of differences in the expression of proto-oncogenes and tumor suppressor genes have also been found in the study of colorectal cancer, which proves that they are also actively involved in the progression of colorectal cancer and promote the occurrence of liver metastasis. Except for 1.5% of the coding sequence, the rest of the nucleic acid sequence does not encode any protein, which is called non-coding RNA. With the deepening of research, genome sequences without protein coding potential that were originally considered “junk sequences” may have important biological functions. Many years of studies have found that a large number of abnormal expression of ncRNA in colorectal cancer liver metastasis, indicating that ncRNA plays an important role in it. To explore the role and mechanism of these coding sequences and non-coding RNA in liver metastasis of colorectal cancer is very important for the early diagnosis and treatment of liver metastasis of colorectal cancer. This article reviews the coding genes and ncRNA that have been found in the study of liver metastasis of colorectal cancer in recent years, as well as the mechanisms that have been identified or are still under study, as well as the clinical treatment of liver metastasis of colorectal cancer.
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Affiliation(s)
- Wubin Zheng
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, People's Republic of China
| | - Fan Wu
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, People's Republic of China
| | - Kai Fu
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, People's Republic of China
| | - Guangshun Sun
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, People's Republic of China
| | - Guoqiang Sun
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, People's Republic of China
| | - Xiao Li
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, People's Republic of China
| | - Wei Jiang
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, People's Republic of China
| | - Hongyong Cao
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, People's Republic of China
| | - Hanjin Wang
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, People's Republic of China
| | - Weiwei Tang
- Hepatobiliary/Liver Transplantation Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Living Donor Transplantation, Chinese Academy of Medical Sciences, Nanjing, People's Republic of China
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17
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Zhou L, Zhang Y, Jin J, Gu X. Correlation between lncRNA SNHG16 gene polymorphism and its interaction with environmental factors and susceptibility to colorectal cancer. Medicine (Baltimore) 2020; 99:e23372. [PMID: 33235108 PMCID: PMC7710222 DOI: 10.1097/md.0000000000023372] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
OBJECTIVE To study the relationship between long-chain non-coding RNA small nucleolar RNA host gene 16 (lncRNA SNHG16) polymorphisms and its interaction with environmental factors and susceptibility to colorectal cancer (CRC). METHODS Sanger sequencing was used to analyze genotypes of lncRNA SNHG16 gene rs7353, rs8038, and rs15278 sites. Multifactor dimensionality reduction was used to analyze interactions between lncRNA SNHG16 gene rs7353, rs8038, rs15278 sites, and environmental factors. Haploview 4.1 software was used to analyze linkage disequilibrium of lncRNA SNHG16 gene rs7353, rs8038, and rs15278 sites. Quantitative real-time polymerase chain reaction was used to analyze plasma lncRNA SNHG16 levels of CRC patients and control subjects. RESULTS Variation of the lncRNA SNHG16 gene rs7353 site A>G variation was associated with decreased CRC susceptibility (Odds ratio [OR] = 0.50, 95% confidence interval [CI]: 0.40-0.62, P < .01). The rs8038 site G>A and rs15278 site A>G variation were associated with increased CRC susceptibility (OR = 1.87, 95% CI: 1.47-2.36, P < .01). The rs15278 site G>A variation was associated with increased CRC susceptibility (OR = 2.24, 95% CI: 1.61-3.11, P < .01). Interaction combinations featuring age, rs7353, rs8038, and rs15278 single nucleotide polymorphism are 13.53 times more susceptible to CRC than other interactions (95% CI: 9.43-19.41, P < .01). The rs15278, rs8038, and rs7353 site AGA haplotypes were significantly associated with a decreased CRC risk (OR = 0.65, 95% CI: 0.48-0.88, P = .01), AAG haplotypes were significantly associated with an increased CRC risk (OR = 2.00, 95% CI: 1.27-3.17, P < .01). High lncRNA SNHG16 expression was associated with tumor progression in CRC patients (χ = 8.85, P = .03). The rs7353 site A>G variation caused a significant decrease in plasma lncRNA SNHG16 level (P < .01), while the rs8038 site G>A variation and rs15278 site A>G variation resulted in increased plasma lncRNA SNHG16 levels. CONCLUSION Polymorphisms of lncRNA SNHG16 gene rs7353, rs8038, rs15278 loci and their interaction with age are significantly associated with CRC susceptibility.
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Affiliation(s)
- Li Zhou
- Department of Medical Oncology, First People's Hospital of Yuhang District, Hangzhou
| | - Yuefeng Zhang
- Department of Hematology, First People's Hospital of Yuhang District, Hangzhou
| | - Jianjiang Jin
- Department of Medical Oncology, First People's Hospital of Yuhang District, Hangzhou
| | - Xuewei Gu
- Department of Gastroenterology, Zhuji People's Hospital of Zhejiang Province (Zhuji Affiliated Hospital of Shaoxing University), Shaoxing, Zhejiang Province, China
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Patel KD, Vora HH, Trivedi TI, Patel JB, Pandya SJ, Jetly DH, Patel PS. Transcriptome profiling and pathway analysis in squamous cell carcinoma of buccal mucosa. Exp Mol Pathol 2020; 113:104378. [PMID: 31930966 DOI: 10.1016/j.yexmp.2020.104378] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Revised: 12/07/2019] [Accepted: 01/09/2020] [Indexed: 12/14/2022]
Abstract
BACKGROUND High recurrence and poor overall survival in buccal mucosa squamous cell carcinoma (BMSCC) are not well addressed due to lack of efficient prognostic biomarkers and targeted therapies. To uncover gene candidates for the same, transcriptome profiling has been examined in BMSCC, which is not explored yet. METHODS We compared 9 BMSCC and 2 normal oral FFPE tissues using Agilent SurePrint G3 Human gene expression v3 microarray chips. The obtained RNA signatures were interrogated in the cancer genome atlas (TCGA) dataset for alteration values and survival data. RESULTS We found total 237 protein coding RNAs and 85 long non-coding RNAs (lncRNAs) which displayed significant differential expression with criteria of at-least 2 fold change and Benjamini Hochberg FDR < .05. In protein coding RNAs, RUNX3 and EMX2 showed utmost degree of up-regulation and down-regulation, respectively. Likewise, among lncRNAs, ARGFXP2 and lnc-SYCP3-2 displayed highest degree of up-regulation and down-regulation, respectively. Besides, an analysis of the RNA list in TCGA dataset spotted deregulation of 21 genes in both, our cohort and TCGA cohort. Among which, MRTO4 and EIF3J genes, and LINC00310, a lncRNA showed greatest expression alterations. Strikingly, at RNA expression level, up-regulation of two genes, EIF3J and SDCBP, was significantly associated with disease free survival and poor overall survival, respectively. CONCLUSION Our data documented significant findings to enhance understanding of the disease biology. The proposed RNA candidates (RUNX3, EMX2, MRTO4, EIF3J, SDCBP and LINC00310) may serve as putative therapeutic targets and potential biomarkers for BMSCC diagnosis and prognosis.
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Affiliation(s)
- Kinjal D Patel
- The Gujarat Cancer & Research Institute, M.P. Shah Cancer Hospital, Civil Hospital Campus, Asarwa, Ahmedabad, Gujarat, India
| | - Hemangini H Vora
- The Gujarat Cancer & Research Institute, M.P. Shah Cancer Hospital, Civil Hospital Campus, Asarwa, Ahmedabad, Gujarat, India
| | - Trupti I Trivedi
- The Gujarat Cancer & Research Institute, M.P. Shah Cancer Hospital, Civil Hospital Campus, Asarwa, Ahmedabad, Gujarat, India
| | - Jayendra B Patel
- The Gujarat Cancer & Research Institute, M.P. Shah Cancer Hospital, Civil Hospital Campus, Asarwa, Ahmedabad, Gujarat, India
| | - Shashank J Pandya
- The Gujarat Cancer & Research Institute, M.P. Shah Cancer Hospital, Civil Hospital Campus, Asarwa, Ahmedabad, Gujarat, India
| | - Dhaval H Jetly
- The Gujarat Cancer & Research Institute, M.P. Shah Cancer Hospital, Civil Hospital Campus, Asarwa, Ahmedabad, Gujarat, India
| | - Prabhudas S Patel
- The Gujarat Cancer & Research Institute, M.P. Shah Cancer Hospital, Civil Hospital Campus, Asarwa, Ahmedabad, Gujarat, India.
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Monnier A, Boniface R, Bouvet R, Etcheverry A, Aubry M, Avril T, Quillien V, Chevet E, Mosser J. The expression of EMX2 lead to cell cycle arrest in glioblastoma cell line. BMC Cancer 2018; 18:1213. [PMID: 30514244 PMCID: PMC6280364 DOI: 10.1186/s12885-018-5094-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 11/14/2018] [Indexed: 01/22/2023] Open
Abstract
Background Glioblastoma (GB) is a highly invasive primary brain tumor that nearly always systematically recurs at the site of resection despite aggressive radio-chemotherapy. Previously, we reported a gene expression signature related to tumor infiltration. Within this signature, the EMX2 gene encodes a homeodomain transcription factor that we found was down regulated in glioblastoma. As EMX2 is reported to play a role in carcinogenesis, we investigated the impact of EMX2 overexpression in glioma-related cell lines. Methods For that purpose, we constructed tetracycline-inducible EMX2 expression lines. Transfected cell phenotypes (proliferation, cell death and cell cycle) were assessed in time-course experiments. Results Restoration of EMX2 expression in U87 glioblastoma cells significantly inhibited cell proliferation. This inhibition was reversible after EMX2 removal from cells. EMX2-induced proliferative inhibition was very likely due to cell cycle arrest in G1/S transition and was not accompanied by signs of cell death. Conclusion Our results suggest that EMX2 may constitute a putative therapeutic target for GB treatment. Further studies are required to decipher the gene networks and transduction signals involved in EMX2’s effect on cell proliferation. Electronic supplementary material The online version of this article (10.1186/s12885-018-5094-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Annabelle Monnier
- Univ Rennes, CNRS, IGDR [(Institut de génétique et développement de Rennes)]-UMR 6290, F-35000, Rennes, France.
| | - Rachel Boniface
- Univ Rennes, CNRS, IGDR [(Institut de génétique et développement de Rennes)]-UMR 6290, F-35000, Rennes, France
| | - Régis Bouvet
- CHU Rennes, Service de Génétique Moléculaire et Génomique Médicale, Rennes, France
| | - Amandine Etcheverry
- CHU Rennes, Service de Génétique Moléculaire et Génomique Médicale, Rennes, France
| | - Marc Aubry
- Univ Rennes, CNRS, IGDR [(Institut de génétique et développement de Rennes)]-UMR 6290, F-35000, Rennes, France.,Univ Rennes, Plateforme GEH, CNRS, Inserm, BIOSIT - UMS 3480, US_S 018, F-35000, Rennes, France
| | - Tony Avril
- Univ Rennes, Inserm, CLCC Eugène Marquis, COSS [(Chemistry Oncogenesis Stress Signaling)]-UMR_S 1242, F-35000, Rennes, France
| | - Véronique Quillien
- Univ Rennes, Inserm, CLCC Eugène Marquis, COSS [(Chemistry Oncogenesis Stress Signaling)]-UMR_S 1242, F-35000, Rennes, France
| | - Eric Chevet
- Univ Rennes, Inserm, CLCC Eugène Marquis, COSS [(Chemistry Oncogenesis Stress Signaling)]-UMR_S 1242, F-35000, Rennes, France
| | - Jean Mosser
- Univ Rennes, CNRS, IGDR [(Institut de génétique et développement de Rennes)]-UMR 6290, F-35000, Rennes, France.,CHU Rennes, Service de Génétique Moléculaire et Génomique Médicale, Rennes, France.,Univ Rennes, Plateforme GEH, CNRS, Inserm, BIOSIT - UMS 3480, US_S 018, F-35000, Rennes, France
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20
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Molecular and Immunohistochemical Markers with Prognostic and Predictive Significance in Liver Metastases from Colorectal Carcinoma. Int J Mol Sci 2018; 19:ijms19103014. [PMID: 30282914 PMCID: PMC6213422 DOI: 10.3390/ijms19103014] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 09/28/2018] [Accepted: 10/01/2018] [Indexed: 12/17/2022] Open
Abstract
Despite the significant recent achievements in the diagnosis and treatment of colorectal cancer (CRC), the prognosis of these patients has currently plateaued. During the past few years, the opportunity to consider multiple treatment modalities (including surgery and other locoregional treatments, systemic therapy, and targeted therapy) led to the research of novel prognostic and predictive biomarkers in CRC liver metastases (CRCLM) patients. In this review, we seek to describe the current state of knowledge of CRCLM biomarkers and to outline impending clinical perspectives, in particular focusing on the cutting-edge tools available for their characterization.
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