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Hu X, Wang Y, Zhang X, Li C, Zhang X, Yang D, Liu Y, Li L. DNA methylation of HOX genes and its clinical implications in cancer. Exp Mol Pathol 2023; 134:104871. [PMID: 37696326 DOI: 10.1016/j.yexmp.2023.104871] [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: 03/29/2023] [Revised: 09/06/2023] [Accepted: 09/08/2023] [Indexed: 09/13/2023]
Abstract
Homeobox (HOX) genes encode highly conserved transcription factors that play vital roles in embryonic development. DNA methylation is a pivotal regulatory epigenetic signaling mark responsible for regulating gene expression. Abnormal DNA methylation is largely associated with the aberrant expression of HOX genes, which is implicated in a broad range of human diseases, including cancer. Numerous studies have clarified the mechanisms of DNA methylation in both physiological and pathological processes. In this review, we focus on how DNA methylation regulates HOX genes and briefly discuss drug development approaches targeting these mechanisms.
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Affiliation(s)
- Xin Hu
- Department of Immunology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250117, Shandong, China
| | - Yong Wang
- Shandong Xinchuang Biotechnology Co., LTD, Jinan 250102, Shandong, China; Laboratory of Precision Medicine, Zhangqiu District People's Hospital of Jinan, Jinan 250200, Shandong, China
| | - Xiaoyu Zhang
- Department of Immunology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250117, Shandong, China
| | - Chensheng Li
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250021, Shandong, China
| | - Xikun Zhang
- Department of Minimally Invasive Interventional, The Third Affiliated Hospital of Shandong First Medical University, Jinan 250031, Shandong, China
| | - Dongxia Yang
- Shandong Xinchuang Biotechnology Co., LTD, Jinan 250102, Shandong, China
| | - Yuanyuan Liu
- Shandong Xinchuang Biotechnology Co., LTD, Jinan 250102, Shandong, China
| | - Lianlian Li
- Department of Oncology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250021, Shandong, China; Department of Immunology, School of Clinical and Basic Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250117, Shandong, China.
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Li Y, Li B, Jiang R, Liao L, Zheng C, Yuan J, Zeng L, Hu K, Zhang Y, Mei W, Hong Z, Xiao B, Kong L, Han K, Tang J, Jiang W, Pan Z, Zhang S, Ding P. A novel screening method of DNA methylation biomarkers helps to improve the detection of colorectal cancer and precancerous lesions. Cancer Med 2023; 12:20626-20638. [PMID: 37881109 PMCID: PMC10660402 DOI: 10.1002/cam4.6511] [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: 04/28/2023] [Revised: 07/22/2023] [Accepted: 08/30/2023] [Indexed: 10/27/2023] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is one of the most common malignancies, and early detection plays a crucial role in enhancing curative outcomes. While colonoscopy is considered the gold standard for CRC diagnosis, noninvasive screening methods of DNA methylation biomarkers can improve the early detection of CRC and precancerous lesions. METHODS Bioinformatics and machine learning methods were used to evaluate CRC-related genes within the TCGA database. By identifying the overlapped genes, potential biomarkers were selected for further validation. Methylation-specific PCR (MSP) was utilized to identify the associated genes as biomarkers. Subsequently, a real-time PCR assay for detecting the presence of neoplasia or cancer of the colon or rectum was established. This screening approach involved the recruitment of 978 participants from five cohorts. RESULTS The genes with the highest specificity and sensitivity were Septin9, AXL4, and SDC2. A total of 940 participants were involved in the establishment of the final PCR system and the subsequent performance evaluation test. A multiplex TaqMan real-time PCR system has been illustrated to greatly enhance the ability to detect precancerous lesions and achieved an accuracy of 87.8% (95% CI 82.9-91.5), a sensitivity of 82.7% (95% CI 71.8-90.1), and a specificity of 90.1% (95% CI 84.3-93.9). Moreover, the detection rate of precancerous lesions of this assay reached 55.0% (95% CI 38.7-70.4). CONCLUSION The combined detection of the methylation status of SEPT9, SDC2, and ALX4 in plasma holds the potential to further enhance the sensitivity of CRC detection.
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Affiliation(s)
- Yuan Li
- Department of Colorectal SurgerySun Yat‐sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer MedicineGuangzhouChina
| | - Bin Li
- Beijing BGI‐GBI Biotech Co., LtdBeijingChina
| | - Rou Jiang
- Department of Cancer Prevention CenterSun Yat‐sen University Cancer CenterGuangzhouChina
| | - Leen Liao
- Department of Colorectal SurgerySun Yat‐sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer MedicineGuangzhouChina
| | | | - Jie Yuan
- Department of General SurgeryThe Fifth Affiliated Hospital of Southern Medical UniversityGuangzhouChina
| | | | - Kunling Hu
- Beijing BGI‐GBI Biotech Co., LtdBeijingChina
| | | | - Weijian Mei
- Department of Colorectal SurgerySun Yat‐sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer MedicineGuangzhouChina
| | - Zhigang Hong
- Department of Colorectal SurgerySun Yat‐sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer MedicineGuangzhouChina
| | - Binyi Xiao
- Department of Colorectal SurgerySun Yat‐sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer MedicineGuangzhouChina
| | - Lingheng Kong
- Department of Colorectal SurgerySun Yat‐sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer MedicineGuangzhouChina
| | - Kai Han
- Department of Colorectal SurgerySun Yat‐sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer MedicineGuangzhouChina
| | - Jinghua Tang
- Department of Colorectal SurgerySun Yat‐sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer MedicineGuangzhouChina
| | - Wu Jiang
- Department of Colorectal SurgerySun Yat‐sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer MedicineGuangzhouChina
| | - Zhizhong Pan
- Department of Colorectal SurgerySun Yat‐sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer MedicineGuangzhouChina
| | | | - Peirong Ding
- Department of Colorectal SurgerySun Yat‐sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer MedicineGuangzhouChina
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Dong M, Li P, Luo J, Chen B, Jiang H. Oligopeptide/Histidine Transporter PHT1 and PHT2 - Function, Regulation, and Pathophysiological Implications Specifically in Immunoregulation. Pharm Res 2023; 40:2585-2596. [PMID: 37610621 DOI: 10.1007/s11095-023-03589-8] [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: 05/28/2023] [Accepted: 08/15/2023] [Indexed: 08/24/2023]
Abstract
The oligopeptide/histidine transporters PHT1 and PHT2, two mammalian solute carrier family 15A proteins, mediate the transmembrane transport of histidine and some di/tripeptides via proton gradient. PHT1 and PHT2 are distributed in a variety of tissues but are preferentially expressed in immune cells and localize to the lysosome-related organelles. Studies have reported the relationships between PHT1/PHT2 and immune diseases. PHT1 and PHT2 participate in the regulation of lysosomal homeostasis and lysosome-associated signaling pathways through their transport and nontransport functions, playing important roles in inflammatory diseases. In this review, we summarize recent research on PHT1 and PHT2, aiming to provide reference for their further biological research and as targets for drug design.
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Affiliation(s)
- Minlei Dong
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Ping Li
- Department of Clinical Pharmacy, Key Laboratory of Clinical Cancer Pharmacology and Toxicology Research of Zhejiang Province, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jun Luo
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Binxin Chen
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Huidi Jiang
- Institute of Drug Metabolism and Pharmaceutical Analysis, Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China.
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Li S, Wang Y, Xuan Z, Zhang Y, Miao Z. High expression of homeobox B2 predicts poor survival of colon adenocarcinoma by enhancing tumor proliferation and invasion. Ir J Med Sci 2023; 192:89-97. [PMID: 35320486 DOI: 10.1007/s11845-022-02964-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 12/27/2021] [Indexed: 02/04/2023]
Abstract
OBJECTIVE Homeobox B2 (HOXB2) is known to be correlated with the development and prognosis of various cancers. However, its role in colon cancer remains unclear. AIMS In this study, we explored the prognostic value of HOXB2 in colon adenocarcinoma (COAD). METHODS A total of 264 colon adenocarcinoma cases were retrospectively enrolled to evaluate HOXB2 expression and clinical significance. Chi-square test was applied to identify relationship between clinical features and HOXB2 expression. The effect of HOXB2 expression and clinical features on the survival of COAD patients was evaluated using Kaplan-Meier and Cox regression analyses. Cellular assays and mice models were conducted to validate the tumor-related role of HOXB2 in COAD. RESULTS Higher expression of HOXB2 in COAD tissues was significantly associated with tumor size, invasion depth, and lymph node metastasis (all P < 0.05). Univariate and multivariate analyses showed that high expression of HOXB2 was significantly correlated with a poor overall survival. In vitro cellular assays combined with knockdown strategies demonstrated that HOXB2 can promote tumor proliferation and invasion of COAD, which was further confirmed by in vivo xenograft experiments. CONCLUSIONS HOXB2 may be a valuable biomarker and potential therapeutic target for the treatment of COAD.
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Affiliation(s)
- Shengjie Li
- Department of Gastroenterology Surgery, Dalian Municipal Central Hospital, Liaoning, 116033, China
| | - Yujie Wang
- Department of Gastroenterology Surgery, Dalian Municipal Central Hospital, Liaoning, 116033, China
| | - Zhiqiang Xuan
- Department of Gastroenterology Surgery, Dalian Municipal Central Hospital, Liaoning, 116033, China
| | - Yue Zhang
- Department of Gastroenterology Surgery, Dalian Municipal Central Hospital, Liaoning, 116033, China
| | - Zhongxing Miao
- Department of Gastroenterology Surgery, Dalian Municipal Central Hospital, Liaoning, 116033, China.
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Wu M, Wei B, Duan SL, Liu M, Ou-Yang DJ, Huang P, Chang S. Methylation-Driven Gene PLAU as a Potential Prognostic Marker for Differential Thyroid Carcinoma. Front Cell Dev Biol 2022; 10:819484. [PMID: 35141223 PMCID: PMC8818873 DOI: 10.3389/fcell.2022.819484] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 01/07/2022] [Indexed: 11/16/2022] Open
Abstract
Purpose: Aberrant DNA methylation plays a crucial role in the tumorigenesis of differentiated thyroid cancer (DTC); nevertheless, the factors leading to the local and regional recurrence of DTC are not well understood. This study aimed to establish the connection between DNA methylation-driven genes and the recurrence of DTC. Methods: RNA sequencing profiles and DNA methylation profiles of DTC were downloaded from The Cancer Genome Atlas (TCGA) database. Combined application of the methylmix R package and univariate Cox regression analyses were used to screen and distinguish prognosis-related methylation-driven genes. Multivariate Cox regression analyses were utilized to identify the target genes that were closely associated with the recurrence of DTC. Then, correlations between the expression levels of the target genes and the clinicopathological features were verified, as well as their potential biological functions. Results: A total of 168 Methylation-driven genes were differentially expressed in thyroid cancer, among which 10 genes (GSTO2, GSTM5, GSTM1, GPX7, FGF2, LIF, PLAU, BCL10, SHARPIN and TNFRSF1A) were identified as Hub genes. We selected PLAU for further analysis because PLAU was most strongly correlated with DTC recurrence and the DNA methylation levels of PLAU were closely associated with multiple clinicopathological features of DTC. PLAU was significantly upregulated in DTC, and patients with a high expression level of PLAU had a higher risk of recurrence (p < 0.05). Functional predictions suggested that PLAU-related genes were mainly involved in the regulation of immune-related signaling pathways. Moreover, the mRNA level of PLAU was found to be positively correlated with the cell markers of neutrophils and dendritic cells. In addition, we found that two DNA methylation sites (cg06829584, cg19399285) were associated with abnormal expression of PLAU in DTC. Conclusion: The methylation-driven gene PLAU is an independent risk factor for the recurrence of DTC and it functions as an oncogene through the regulation of immune-related signaling pathways, which offers new insight into the molecular mechanisms of thyroid cancer and provides new possibilities for individualized treatment of thyroid cancer patients.
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Affiliation(s)
- Min Wu
- Department of General Surgery, Xiangya Hospital Central South University, Changsha, China
| | - Bo Wei
- Department of General Surgery, Xiangya Hospital Central South University, Changsha, China
| | - Sai-Li Duan
- Department of General Surgery, Xiangya Hospital Central South University, Changsha, China
| | - Mian Liu
- Department of General Surgery, Xiangya Hospital Central South University, Changsha, China
| | - Deng-Jie Ou-Yang
- Department of General Surgery, Xiangya Hospital Central South University, Changsha, China
| | - Peng Huang
- Department of General Surgery, Xiangya Hospital Central South University, Changsha, China
- *Correspondence: Peng Huang,
| | - Shi Chang
- Department of General Surgery, Xiangya Hospital Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, China
- Clinical Research Center for Thyroid Disease in Hunan Province, Changsha, China
- Hunan Provincial Engineering Research Center for Thyroid and Related Diseases Treatment Technology, Changsha, China
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Qin Y, Zhou J, Fan Z, Gu J, Li X, Lin D, Deng D, Wei W. Evaluation of the Impact of Intratumoral Heterogeneity of Esophageal Cancer on Pathological Diagnosis and P16 Methylation and the Representativity of Endoscopic Biopsy. Front Oncol 2021; 11:683876. [PMID: 34485122 PMCID: PMC8416173 DOI: 10.3389/fonc.2021.683876] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 07/27/2021] [Indexed: 01/22/2023] Open
Abstract
Background P16 methylation is expected to be potential diagnostic and therapeutic targets for esophageal cancer (EC). The intratumoral heterogeneity (ITH) of EC has been mentioned but has not been quantitatively measured yet. We aimed to clarify the impact of ITH on pathological diagnosis and P16 methylation, and the concordance between endoscopic biopsy and the corresponding surgically resected tissue. Methods We designed a systematic sampling method (SSM) compared with a general sampling method (GSM) to obtain EC tumor tissue, tumor biopsy, and normal squamous epithelium biopsy. MethyLight assay was utilized to test P16 methylation. All specimens obtained by the SSM were pathologically diagnosed. Results A total of 81 cases were collected by the GSM, and 91.4% and 8.6% of them were esophageal squamous cell carcinomas (ESCCs) and esophageal adenocarcinomas (EADs), respectively. Nine SSM cases were 100.0% ESCCs. The positive rates of P16 methylation of the GSM tumor and normal tissues were 63.0% (51/81) and 32.1% (26/81), respectively. For SSM samples, tumor tissues were 100.0% (40/40) EC and 85.0% (34/40) P16 methylated; tumor biopsy was 64.4% (29/45) diagnosed of EC and 68.9% P16 methylated; the corresponding normal biopsies were 15.7% (8/51) dysplasia and 54.9% (28/51) P16 methylated. The concordance of pathological diagnosis and P16 methylation between tumor biopsy and the corresponding tumor tissue was 75.0% and 62.5%, respectively. Conclusion The SSM we designed was efficient in measuring the ITH of EC. We found inadequate concordance between tumor biopsy and tissue in pathological diagnosis and P16 methylation.
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Affiliation(s)
- Yu Qin
- National Cancer Registry Office, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jing Zhou
- Key Laboratory of Carcinogenesis and Translational Research, Peking University Cancer Hospital, Beijing, China
| | - Zhiyuan Fan
- National Cancer Registry Office, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jianhua Gu
- National Cancer Registry Office, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xinqing Li
- National Cancer Registry Office, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Dongmei Lin
- Department of Pathology, Peking University Cancer Hospital, Beijing, China
| | - Dajun Deng
- Key Laboratory of Carcinogenesis and Translational Research, Peking University Cancer Hospital, Beijing, China
| | - Wenqiang Wei
- National Cancer Registry Office, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Takemoto A, Tanimoto K, Mori S, Inoue J, Fujiwara N, Noda T, Inazawa J. Integrative genome-wide analyses reveal the transcriptional aberrations in Japanese esophageal squamous cell carcinoma. Cancer Sci 2021; 112:4377-4392. [PMID: 34263978 PMCID: PMC8486213 DOI: 10.1111/cas.15063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 07/06/2021] [Accepted: 07/09/2021] [Indexed: 01/14/2023] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) is a malignant disease. At present, the genomic profiles of ESCC are known to a considerable extent, and DNA methylation and gene expression profiles have been mainly used for the classification of ESCC subtypes, but integrative genomic, transcriptomic, and epigenomic analyses remain insufficient. Therefore, we performed integrative analyses using whole-exome sequencing, DNA methylation, and RNA sequencing (RNA-seq) analyses of Japanese patients with ESCC. In cancer-related genes, such as NOTCH family genes, RTK/PI3K pathway genes, and NFE2L2 pathway genes, variants and copy number amplification were detected frequently. Japanese ESCC cases were clustered into two mutational signatures: an APOBEC-associated signature and an age-related signature. In imprinted genes, DNA methylation was aberrant in gene promoter regions and correlated well with gene expression profiles. Nonsynonymous single-nucleotide variants and allelic expression imbalance were detected frequently in FAT family genes. Our integrative genome-wide analyses, including DNA methylation and allele-specific gene expression profiles, revealed altered gene regulation of imprinted genes and FAT family genes in ESCC.
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Affiliation(s)
- Akira Takemoto
- Bioresource Research Center, Tokyo Medical and Dental University (TMDU) Yushima, Tokyo, Japan
| | - Kousuke Tanimoto
- Genome Laboratory, Medical Research Institute, TMDU, Tokyo, Japan.,Genomics Research Support Unit, Research Core, TMDU, Tokyo, Japan
| | - Seiichi Mori
- Division of Cancer Genomics, Cancer Institute, Japanese Foundation for Cancer Research (JFCR), Tokyo, Japan
| | - Jun Inoue
- Department of Molecular Cytogenetics, Medical Research Institute, TMDU, Tokyo, Japan
| | - Naoto Fujiwara
- Department of Gastrointestinal Surgery, TMDU, Tokyo, Japan
| | - Tetsuo Noda
- Cancer Institute, Japanese Foundation for Cancer Research (JFCR), Tokyo, Japan
| | - Johji Inazawa
- Bioresource Research Center, Tokyo Medical and Dental University (TMDU) Yushima, Tokyo, Japan.,Department of Molecular Cytogenetics, Medical Research Institute, TMDU, Tokyo, Japan
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Peng Y, Zhao J, Yin F, Sharen G, Wu Q, Chen Q, Sun X, Yang J, Wang H, Zhang D. A methylation-driven gene panel predicts survival in patients with colon cancer. FEBS Open Bio 2021; 11:2490-2506. [PMID: 34184409 PMCID: PMC8409306 DOI: 10.1002/2211-5463.13242] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 05/14/2021] [Accepted: 06/28/2021] [Indexed: 02/06/2023] Open
Abstract
The accumulation of various genetic and epigenetic changes in colonic epithelial cells has been identified as one of the fundamental processes that drive the initiation and progression of colorectal cancer (CRC). This study aimed to explore functional genes regulated by DNA methylation and their potential utilization as biomarkers for the prediction of CRC prognoses. Methylation‐driven genes (MDGs) were explored by applying the integrative analysis tool (methylmix) to The Cancer Genome Atlas CRC project. The prognostic MDG panel was identified by combining the Cox regression model with the least absolute shrinkage and selection operator regularization. Gene set enrichment analysis was used to determine the pathways associated with the six‐MDG panel. Cluster of differentiation 40 (CD40) expression and methylation in CRC samples were validated by using additional datasets from the Gene Expression Omnibus. Methylation‐specific PCR and bisulfite sequencing were used to confirm DNA methylation in CRC cell lines. A prognostic MDG panel consisting of six gene members was identified: TMEM88, HOXB2, FGD1, TOGARAM1, ARHGDIB and CD40. The high‐risk phenotype classified by the six‐MDG panel was associated with cancer‐related biological processes, including invasion and metastasis, angiogenesis and the tumor immune microenvironment. The prognostic value of the six‐MDG panel was found to be independent of tumor node metastasis stage and, in combination with tumor node metastasis stage and age, could help improve survival prediction. In addition, the expression of CD40 was confirmed to be regulated by promoter region methylation in CRC samples and cell lines. The proposed six‐MDG panel represents a promising signature for estimating the prognosis of patients with CRC.
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Affiliation(s)
- Yaojun Peng
- Emergency Department, The First Medical Center, Chinese PLA General Hospital, Beijing, China.,College of Graduate, Chinese PLA General Hospital, Beijing, China
| | - Jing Zhao
- Department of Scientific Research Administration, Chinese PLA General Hospital, Beijing, China
| | - Fan Yin
- Department of Oncology, The Second Medical Center & National Clinical Research Center of Geriatric Disease, Chinese PLA General Hospital, Beijing, China
| | - Gaowa Sharen
- Department of Pathology, The First Affiliated Hospital of Inner Mongolia Medical University, Hohhot City, China
| | - Qiyan Wu
- Department of Oncology, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Qi Chen
- Department of Traditional Chinese Medicine, The First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Xiaoxuan Sun
- National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, China.,Department of Oncology Surgery, Tianjin Cancer Hospital Airport Free Trade Zone Hospital, China
| | - Juan Yang
- Department of Cardiothoracic Surgery, Tianjin Fourth Center Hospital, China
| | - Huan Wang
- Department of Scientific Research Administration, Chinese PLA General Hospital, Beijing, China
| | - Dong Zhang
- Department of Oncology, The Second Medical Center & National Clinical Research Center of Geriatric Disease, Chinese PLA General Hospital, Beijing, China
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Estrogen suppresses HOXB2 expression via ERα in breast cancer cells. Gene 2021; 794:145746. [PMID: 34062258 DOI: 10.1016/j.gene.2021.145746] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 04/27/2021] [Accepted: 05/27/2021] [Indexed: 11/20/2022]
Abstract
The expression of HOXB2, a homeobox transcription factor, is altered in a variety of solid tumors. Using an in vivo screen to identify regulators of breast tumor growth in murine mammary fat pads, Boimel and co-workers recently identified HOXB2 as a tumor suppressor. However, the mechanistic underpinnings of its role in breast cancer is not understood. Given the emerging interaction of estrogen-regulated gene expression and altered HOX gene expression network in the pathophysiology of breast cancer, this study addressed the relationship between estrogen signaling and HOXB2 expression. Using a mouse model and human breast cancer cell lines, we show that estrogen suppresses HOXB2 expression. Suppression of HOXB2 by PPT, a known ERα agonist, in MCF-7 and T47D cells indicated the involvement of ERα, which was confirmed by siRNA-mediated ERα knockdown experiments. In-silico analysis of the upstream promoter region revealed the presence of three putative EREs. Chromatin immunoprecipitation experiments showed that upon estrogen binding, ERα engaged with EREs in the 5' upstream region of HOXB2 in MCF-7 and T47D cells. Future investigations should address the implications of estrogen-mediated suppression on the proposed tumor suppressor function of HOXB2.
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Inoue J, Kishikawa M, Tsuda H, Nakajima Y, Asakage T, Inazawa J. Identification of PDHX as a metabolic target for esophageal squamous cell carcinoma. Cancer Sci 2021; 112:2792-2802. [PMID: 33964039 PMCID: PMC8253269 DOI: 10.1111/cas.14938] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 04/27/2021] [Accepted: 04/28/2021] [Indexed: 12/13/2022] Open
Abstract
The metabolism in tumors is reprogrammed to meet its energetic and substrate demands. However, this metabolic reprogramming creates metabolic vulnerabilities, providing new opportunities for cancer therapy. Metabolic vulnerability as a therapeutic target in esophageal squamous cell carcinoma (ESCC) has not been adequately clarified. Here, we identified pyruvate dehydrogenase (PDH) component X (PDHX) as a metabolically essential gene for the cell growth of ESCC. PDHX expression was required for the maintenance of PDH activity and the production of ATP, and its knockdown inhibited the proliferation of cancer stem cells (CSCs) and in vivo tumor growth. PDHX was concurrently upregulated with the CD44 gene, a marker of CSCs, by co-amplification at 11p13 in ESCC tumors and these genes coordinately functioned in cancer stemness. Furthermore, CPI-613, a PDH inhibitor, inhibited the proliferation of CSCs in vitro and the growth of ESCC xenograft tumors in vivo. Thus, our study provides new insights related to the development of novel therapeutic strategies for ESCC by targeting the PDH complex-associated metabolic vulnerability.
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Affiliation(s)
- Jun Inoue
- Department of Molecular Cytogenetics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Masahiro Kishikawa
- Department of Molecular Cytogenetics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan.,Department of Head and Neck Surgery, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hitoshi Tsuda
- Department of Basic Pathology, National Defense Medical College, Saitama, Japan
| | - Yasuaki Nakajima
- Department of Surgical Gastroenterology, Graduate School, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takahiro Asakage
- Department of Head and Neck Surgery, Tokyo Medical and Dental University, Tokyo, Japan
| | - Johji Inazawa
- Department of Molecular Cytogenetics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan.,Bioresource Research Center, Tokyo Medical and Dental University, Tokyo, Japan
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Paço A, Aparecida de Bessa Garcia S, Leitão Castro J, Costa-Pinto AR, Freitas R. Roles of the HOX Proteins in Cancer Invasion and Metastasis. Cancers (Basel) 2020; 13:E10. [PMID: 33375038 PMCID: PMC7792759 DOI: 10.3390/cancers13010010] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/16/2020] [Accepted: 12/17/2020] [Indexed: 02/06/2023] Open
Abstract
Invasion and metastasis correspond to the foremost cause of cancer-related death, and the molecular networks behind these two processes are extremely complex and dependent on the intra- and extracellular conditions along with the prime of the premetastatic niche. Currently, several studies suggest an association between the levels of HOX genes expression and cancer cell invasion and metastasis, which favour the formation of novel tumour masses. The deregulation of HOX genes by HMGA2/TET1 signalling and the regulatory effect of noncoding RNAs generated by the HOX loci can also promote invasion and metastasis, interfering with the expression of HOX genes or other genes relevant to these processes. In this review, we present five molecular mechanisms of HOX deregulation by which the HOX clusters products may affect invasion and metastatic processes in solid tumours.
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Affiliation(s)
- Ana Paço
- BLC3—Biomassa Lenho-Celulósica de 3ª Geração, Campus of Technology and Innovation, 3405-169 Oliveira do Hospital, Portugal
| | - Simone Aparecida de Bessa Garcia
- I3S—Institute for Innovation & Health Research, University of Porto, 4200-135 Porto, Portugal; (S.A.d.B.G.); (J.L.C.); (A.R.C.-P.); (R.F.)
| | - Joana Leitão Castro
- I3S—Institute for Innovation & Health Research, University of Porto, 4200-135 Porto, Portugal; (S.A.d.B.G.); (J.L.C.); (A.R.C.-P.); (R.F.)
| | - Ana Rita Costa-Pinto
- I3S—Institute for Innovation & Health Research, University of Porto, 4200-135 Porto, Portugal; (S.A.d.B.G.); (J.L.C.); (A.R.C.-P.); (R.F.)
| | - Renata Freitas
- I3S—Institute for Innovation & Health Research, University of Porto, 4200-135 Porto, Portugal; (S.A.d.B.G.); (J.L.C.); (A.R.C.-P.); (R.F.)
- ICBAS—Institute of Biomedical Sciences Abel Salazar, University of Porto, 4050-313 Porto, Portugal
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12
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Organoids and Liquid Biopsy in Oral Cancer Research. J Clin Med 2020; 9:jcm9113701. [PMID: 33218071 PMCID: PMC7698863 DOI: 10.3390/jcm9113701] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 11/15/2020] [Indexed: 12/22/2022] Open
Abstract
To promote the newest discoveries in oral cancer research, a special issue "Frontiers in Oral Cancer-Basic and Clinical Sciences" in the Journal of Clinical Medicine (JCM) was opened from September 2019 to April 2020 [...].
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13
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Paço A, de Bessa Garcia SA, Freitas R. Methylation in HOX Clusters and Its Applications in Cancer Therapy. Cells 2020; 9:cells9071613. [PMID: 32635388 PMCID: PMC7408435 DOI: 10.3390/cells9071613] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 06/26/2020] [Accepted: 06/29/2020] [Indexed: 02/08/2023] Open
Abstract
HOX genes are commonly known for their role in embryonic development, defining the positional identity of most structures along the anterior–posterior axis. In postembryonic life, HOX gene aberrant expression can affect several processes involved in tumorigenesis such as proliferation, apoptosis, migration and invasion. Epigenetic modifications are implicated in gene expression deregulation, and it is accepted that methylation events affecting HOX gene expression play crucial roles in tumorigenesis. In fact, specific methylation profiles in the HOX gene sequence or in HOX-associated histones are recognized as potential biomarkers in several cancers, helping in the prediction of disease outcomes and adding information for decisions regarding the patient’s treatment. The methylation of some HOX genes can be associated with chemotherapy resistance, and its identification may suggest the use of other treatment options. The use of epigenetic drugs affecting generalized or specific DNA methylation profiles, an approach that now deserves much attention, seems likely to be a promising weapon in cancer therapy in the near future. In this review, we summarize these topics, focusing particularly on how the regulation of epigenetic processes may be used in cancer therapy.
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Affiliation(s)
- Ana Paço
- Centre Bio: Bioindustries, Biorefineries and Bioproducts, BLC3 Association—Technology and Innovation Campus, 3405-169 Oliveira do Hospital, Portugal;
| | | | - Renata Freitas
- I3S—Institute for Innovation & Health Research, University of Porto, 4200-135 Porto, Portugal;
- ICBAS—Institute of Biomedical Sciences Abel Salazar, University of Porto, 4050-313 Porto, Portugal
- Correspondence:
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Li N, Lin H, Zhou H, Zheng D, Xu G, Shi H, Zhu X, Gao J, Shao G, Sun L. Efficient detection of differentially methylated regions in the genome of patients with thoracic aortic dissection and association with MMP2 hypermethylation. Exp Ther Med 2020; 20:1073-1081. [PMID: 32765660 PMCID: PMC7388572 DOI: 10.3892/etm.2020.8753] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 04/01/2020] [Indexed: 12/13/2022] Open
Abstract
DNA methylation is known to regulate the expression of numerous genes but its role in the pathogenesis of thoracic aortic dissection (TAD) has remained largely elusive. In the present study, the DNA methylome of patients with TAD was analyzed using a methylation microarray and bisulfite pyrosequencing was used to determine whether the hypermethylation of matrix metalloproteinase 2 (MMP2) specifically is associated with TAD. Chip-based whole-DNA methylome analysis was performed on 4 male patients with TAD and 4 male healthy controls using an Illumina HumanMethylation EPIC 850K BeadChip. The resulting data were analyzed by clustering and principal component analysis, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed on the differentially methylated genes to interrogate their biological functions. Compared to the healthy controls, 3,362 loci were differentially methylated in the patients with TAD with a statistical significance of P<0.05, while 1,223 loci had a significance of P<0.01. Among these loci, 2,019 were hypermethylated and 1,343 were hypomethylated. From GO analysis within the biological process category, the MMP2, MMP14 and WNT2B genes were identified. enrichment was observed for loci involved in cellular component organization, enzyme-linked receptor protein signaling pathways (potentially having a key role in the development of cardiopulmonary function disorders) and vascular reconstruction. Bisulfite pyrosequencing of plasma samples indicated significantly increased methylation (P<0.01) of the CpG site at position 2 in the promoter of MMP2 in the TAD group relative to the healthy controls, and the mean methylation level of four CpG sites on the MMP2 gene in the TAD group was slightly higher than that in the control group, but not significantly. Hypermethylation of the MMP2 promoter may be a promising novel diagnostic and prognostic biomarker for TAD. Future studies on the epigenetics of biomarkers linked to vascular reconstruction and immune function may provide further insight into the pathogenesis and progression of TAD.
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Affiliation(s)
- Ni Li
- Department of Cardiothoracic Surgery, Lihuili Hospital Affiliated to Ningbo University, Ningbo, Zhejiang 315041, P.R. China.,Institute of Pharmaceutics, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, P.R. China
| | - Hangjuan Lin
- Department of Pharmacy, Ningbo Traditional Chinese Medicine Hospital, Ningbo, Zhejiang 315041, P.R. China
| | - Hua Zhou
- Department of Cardiothoracic Surgery, Lihuili Hospital Affiliated to Ningbo University, Ningbo, Zhejiang 315041, P.R. China
| | - Dawei Zheng
- Department of Cardiothoracic Surgery, Lihuili Hospital Affiliated to Ningbo University, Ningbo, Zhejiang 315041, P.R. China
| | - Guodong Xu
- Department of Cardiothoracic Surgery, Lihuili Hospital Affiliated to Ningbo University, Ningbo, Zhejiang 315041, P.R. China
| | - Huoshun Shi
- Department of Cardiothoracic Surgery, Lihuili Hospital Affiliated to Ningbo University, Ningbo, Zhejiang 315041, P.R. China
| | - Xiuying Zhu
- Department of Cardiothoracic Surgery, Lihuili Hospital Affiliated to Ningbo University, Ningbo, Zhejiang 315041, P.R. China
| | - Jianqing Gao
- Institute of Pharmaceutics, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, P.R. China
| | - Guofeng Shao
- Department of Cardiothoracic Surgery, Lihuili Hospital Affiliated to Ningbo University, Ningbo, Zhejiang 315041, P.R. China
| | - Lebo Sun
- Department of Cardiothoracic Surgery, Lihuili Hospital Affiliated to Ningbo University, Ningbo, Zhejiang 315041, P.R. China
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15
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Yu YH, Xin F, Dong L, Ge L, Zhai CY, Shen XL. Weighted gene coexpression network analysis identifies critical genes in different subtypes of acute myeloid leukaemia. BIOTECHNOL BIOTEC EQ 2020. [DOI: 10.1080/13102818.2020.1811767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- Yan-Hui Yu
- Department of Hematology, Heping Hospital Affiliated to Changzhi Medical College, Changzhi, Shanxi, PR China
| | - Fei Xin
- Department of Hematology, Heping Hospital Affiliated to Changzhi Medical College, Changzhi, Shanxi, PR China
| | - Lu Dong
- Department of Hematology, Heping Hospital Affiliated to Changzhi Medical College, Changzhi, Shanxi, PR China
| | - Li Ge
- Department of Hematology, Heping Hospital Affiliated to Changzhi Medical College, Changzhi, Shanxi, PR China
| | - Chun-Yan Zhai
- Department of Hematology, Heping Hospital Affiliated to Changzhi Medical College, Changzhi, Shanxi, PR China
| | - Xu-Liang Shen
- Department of Hematology, Heping Hospital Affiliated to Changzhi Medical College, Changzhi, Shanxi, PR China
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16
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Shen N, Wang T, Li D, Zhu Y, Xie H, Lu Y. Hypermethylation of the SEPT9 Gene Suggests Significantly Poor Prognosis in Cancer Patients: A Systematic Review and Meta-Analysis. Front Genet 2019; 10:887. [PMID: 31608117 PMCID: PMC6761278 DOI: 10.3389/fgene.2019.00887] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 08/22/2019] [Indexed: 12/27/2022] Open
Abstract
Background: Aberrant hypermethylation of the Septin 9 (SEPT9) is an early event in several human cancers, and increasing studies have reported good performance of methylated SEPT9 (mSEPT9) in cancer diagnosis. Recent studies further focused on its value in cancer prognosis, but results are not clearly elucidated. Methods: A comprehensive search to identify relevant studies about the association between mSEPT9 and cancer prognosis was conducted through the EMBASE, PubMed, and Web of Science databases (up to January 2019). The main outcomes were overall survival (OS) and disease-free survival (DFS). The hazard ratio (HR) and 95% confidence interval (CI) for OS and DFS were extracted from each included study and pooled using a random-effects model. Results: Ten eligible studies comprising 1,266 cancer patients were included. Results demonstrated that mSEPT9 was associated with poor OS (HR = 2.07, 95% CI = 1.40–3.06). Specially, mSEPT9 detected in preoperative plasma predicted worse OS in cancer patients (HR = 3.25, 95% CI = 1.93–5.48). In addition, we also identified a significant association of mSEPT9 with decreased DFS of cancer (HR = 3.24, 95% CI = 1.81–5.79). Conclusion: Our meta-analysis supports that mSEPT9 is associated with reduced OS and DFS in cancer patients. Moreover, detection of mSEPT9 using plasma appears to be a convenient and promising way to predict long-term survival of cancer patients.
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Affiliation(s)
- Na Shen
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ting Wang
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Delei Li
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yaowu Zhu
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Huaping Xie
- Department of Gastroenterology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yanjun Lu
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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17
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Zeng B, Zhang X, Zhao J, Wei Z, Zhu H, Fu M, Zou D, Feng Y, Luo H, Lei Y. The role of DNMT1/hsa-miR-124-3p/BCAT1 pathway in regulating growth and invasion of esophageal squamous cell carcinoma. BMC Cancer 2019; 19:609. [PMID: 31226958 PMCID: PMC6588861 DOI: 10.1186/s12885-019-5815-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 06/10/2019] [Indexed: 01/16/2023] Open
Abstract
Background Esophageal squamous cell carcinoma (ESCC) is the major subtype of esophageal cancer with high aggressiveness and poor prognosis. There is an urgent need for understanding the molecular mechanism underlying the development and progression of ESCC. Methods ESCC tissues and corresponding non-neoplastic tissues were collected. The expression and function of miR-124-3p and BCAT1 in two cell lines KYSE-150 and Eca109 were determined. Results We show downregulation of miR-124-3p expression in ESCC tissues, which is highly correlated with proliferation and migration of ESCC cell lines KYSE-150 and Eca109. miR-124-3p show high correlation with TNM stage and differentiation grade. Furthermore, miR-124-3p directly targets mRNA 3’UTR region of BCAT1, which results in upregulation of BCAT1 expression as observed in ESCC tissues and cell lines. Also, our data indicates that BCAT1 high expression is strongly linked to the disease-free survival, tumor size, pathologic stage, T classification and differentiation grade. On the other hand, we clarified the upstream mechanism regulating miR-124-3p expression in ESCC, which involves in the hypermethylation-silencing regulation mediated by DNA methyltransferase 1(DNMT1), which is of high expression in ESCC tissues and cell lines in the present study. In addition, DNMT1 knockdown or inhibition of DNMT1 function contributes to downregulation of miR-124-3p and BCAT1 expression. Conclusions Our study thus clarifies a new mechanism that DNMT1/miR-124/BCAT1 axis regulates the development and progression of ESCC.
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Affiliation(s)
- Bo Zeng
- Department of Thoracic Surgery, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xin Zhang
- Department of Thoracic Surgery, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jingling Zhao
- Department of Burns, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zhewei Wei
- Department of Gastrointestinal Surgery, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Haoshuai Zhu
- Department of Thoracic Surgery, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Minyi Fu
- Surgical and anesthesia center, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Dawei Zou
- Department of Thoracic Surgery, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yanfen Feng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China. .,Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, China. .,, Guangzhou, China.
| | - Honghe Luo
- Department of Thoracic Surgery, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China. .,, Guangzhou, China.
| | - Yiyan Lei
- Department of Thoracic Surgery, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China. .,, Guangzhou, China.
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18
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Sadeghpour S, Ghorbian S. Evaluation of the potential clinical prognostic value of lncRNA-BANCR gene in esophageal squamous cell carcinoma. Mol Biol Rep 2018; 46:991-995. [PMID: 30552615 DOI: 10.1007/s11033-018-4556-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 12/04/2018] [Indexed: 01/28/2023]
Abstract
Esophageal squamous cell carcinoma (ESCC) is the seventh most common cause of cancer death in worldwide. LncRNA-BANCR is a long non-coding RNA (lncRNA), which has made new windows in cancer investigations. The aim of this survey was to determine the lncRNA-BANCR gene expression changes in patients with ESCC. In case-control investigation was performed on 150 formalin fixed-paraffin embedded tissues (75 cancerous and 75 non-cancerous tissues) of ESCC patients. The lncRNA-BANCR gene expression alteration was assessed by Real-Time PCR technique. Our findings revealed that lncRNA-BANCR gene expression was increased significantly in tumor tissues compared with the non-cancerous tissues (p = 0.0025). In addition, lncRNA-BANCR gene expression changes was positively associated with the lymph node metastasis (p = 0.013), tumor differentiation (p = 0.019) and tumor stage (p = 0.017). Our results suggest a possible role of lncRNA-BANCR in proliferation of esophageal tissues and may be considered as a potential prognostic value for ESCC metastasis.
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Affiliation(s)
- Shiva Sadeghpour
- Department of Molecular Genetics, Ahar Branch, Islamic Azad University, Ahar, Iran
| | - Saeid Ghorbian
- Department of Molecular Genetics, Ahar Branch, Islamic Azad University, Ahar, Iran.
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19
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Talukdar FR, di Pietro M, Secrier M, Moehler M, Goepfert K, Lima SSC, Pinto LFR, Hendricks D, Parker MI, Herceg Z. Molecular landscape of esophageal cancer: implications for early detection and personalized therapy. Ann N Y Acad Sci 2018; 1434:342-359. [PMID: 29917250 DOI: 10.1111/nyas.13876] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 05/08/2018] [Accepted: 05/14/2018] [Indexed: 12/12/2022]
Abstract
Esophageal cancer (EC) is one of the most lethal cancers and a public health concern worldwide, owing to late diagnosis and lack of efficient treatment. Esophageal squamous cell carcinoma (ESCC) and esophageal adenocarcinoma (EAC) are main histopathological subtypes of EC that show striking differences in geographical distribution, possibly due to differences in exposure to risk factors and lifestyles. ESCC and EAC are distinct diseases in terms of cell of origin, epidemiology, and molecular architecture of tumor cells. Past efforts aimed at translating potential molecular candidates into clinical practice proved to be challenging, underscoring the need for identifying novel candidates for early diagnosis and therapy of EC. Several major international efforts have brought about important advances in identifying molecular landscapes of ESCC and EAC toward understanding molecular mechanisms and critical molecular events driving the progression and pathological features of the disease. In our review, we summarize recent advances in the areas of genomics and epigenomics of ESCC and EAC, their mutational signatures and immunotherapy. We also discuss implications of recent advances in characterizing the genome and epigenome of EC for the discovery of diagnostic/prognostic biomarkers and development of new targets for personalized treatment and prevention.
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Affiliation(s)
- Fazlur Rahman Talukdar
- Section of Mechanisms of Carcinogenesis, International Agency for Research on Cancer (WHO), Lyon, France
| | | | - Maria Secrier
- Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Markus Moehler
- First Department of Internal Medicine, Johannes Gutenberg-University of Mainz, Mainz, Germany
| | - Katrin Goepfert
- First Department of Internal Medicine, Johannes Gutenberg-University of Mainz, Mainz, Germany
| | | | | | - Denver Hendricks
- Division of Medical Biochemistry & Structural Biology, University of Cape Town, Cape Town, South Africa
| | - Mohamed Iqbal Parker
- Division of Medical Biochemistry & Structural Biology, University of Cape Town, Cape Town, South Africa
| | - Zdenko Herceg
- Section of Mechanisms of Carcinogenesis, International Agency for Research on Cancer (WHO), Lyon, France
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Roy R, Kandimalla R, Sonohara F, Koike M, Kodera Y, Takahashi N, Yamada Y, Goel A. A comprehensive methylation signature identifies lymph node metastasis in esophageal squamous cell carcinoma. Int J Cancer 2018; 144:1160-1169. [PMID: 30006931 DOI: 10.1002/ijc.31755] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 06/25/2018] [Indexed: 01/01/2023]
Abstract
Treatment modalities in esophageal squamous cell carcinoma (ESCC) depend largely on lymph node metastasis (LNM) status. With suboptimal detection sensitivity of existing imaging techniques, we propose a methylation signature which identifies patients with LNM with greater accuracy. This would allow precise stratification of high-risk patients requiring more aggressive treatment from low-risk ESCC patients who can forego radical surgery. An unbiased genome-wide methylation signature for LNM detection was established from an initial in silico discovery phase. The signature was tested in independent clinical cohorts comprising of 249 ESCC patients. The prognostic potential of the methylation signature was compared to clinical variables including LNM status. A 10-probe LNM associated signature (LNAS) was developed using stringent bioinformatics analyses. The area under the curve values for LNAS risk scores were 0.81 and 0.88 in the training and validation cohorts respectively, in association with lymphatic vessel invasion and tumor stage. High LNAS risk-score was also associated with worse overall survival [HR (95% CI) 3 (1.8-4.8), p < 0.0001 training and 3.9 (1.5-10.2), p = 0.001 validation cohort]. In conclusion, our novel methylation signature is a powerful biomarker that identifies LNM status robustly and is also associated with worse prognosis in ESCC patients.
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Affiliation(s)
- Roshni Roy
- Center for Gastrointestinal Research; Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute and Charles A Sammons Cancer Center, Baylor University Medical Center, Dallas, Texas
| | - Raju Kandimalla
- Center for Gastrointestinal Research; Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute and Charles A Sammons Cancer Center, Baylor University Medical Center, Dallas, Texas
| | - Fuminori Sonohara
- Department of Gastroenterological Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Masahiko Koike
- Department of Gastroenterological Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yasuhiro Kodera
- Department of Gastroenterological Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Naoki Takahashi
- Department of Gastrointestinal Medical Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Yasuhide Yamada
- Department of Gastrointestinal Medical Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Ajay Goel
- Center for Gastrointestinal Research; Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute and Charles A Sammons Cancer Center, Baylor University Medical Center, Dallas, Texas
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21
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Pu W, Wang C, Chen S, Zhao D, Zhou Y, Ma Y, Wang Y, Li C, Huang Z, Jin L, Guo S, Wang J, Wang M. Targeted bisulfite sequencing identified a panel of DNA methylation-based biomarkers for esophageal squamous cell carcinoma (ESCC). Clin Epigenetics 2017; 9:129. [PMID: 29270239 PMCID: PMC5732523 DOI: 10.1186/s13148-017-0430-7] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 11/29/2017] [Indexed: 12/20/2022] Open
Abstract
Background DNA methylation has been implicated as a promising biomarker for precise cancer diagnosis. However, limited DNA methylation-based biomarkers have been described in esophageal squamous cell carcinoma (ESCC). Methods A high-throughput DNA methylation dataset (100 samples) of ESCC from The Cancer Genome Atlas (TCGA) project was analyzed and validated along with another independent dataset (12 samples) from the Gene Expression Omnibus (GEO) database. The methylation status of peripheral blood mononuclear cells and peripheral blood leukocytes from healthy controls was also utilized for biomarker selection. The candidate CpG sites as well as their adjacent regions were further validated in 94 pairs of ESCC tumor and adjacent normal tissues from the Chinese Han population using the targeted bisulfite sequencing method. Logistic regression and several machine learning methods were applied for evaluation of the diagnostic ability of our panel. Results In the discovery stage, five hyper-methylated CpG sites were selected as candidate biomarkers for further analysis as shown below: cg15830431, P = 2.20 × 10−4; cg19396867, P = 3.60 × 10−4; cg20655070, P = 3.60 × 10−4; cg26671652, P = 5.77 × 10−4; and cg27062795, P = 3.60 × 10−4. In the validation stage, the methylation status of both the five CpG sites and their adjacent genomic regions were tested. The diagnostic model based on the combination of these five genomic regions yielded a robust performance (sensitivity = 0.75, specificity = 0.88, AUC = 0.85). Eight statistical models along with five-fold cross-validation were further applied, in which the SVM model reached the best accuracy in both training and test dataset (accuracy = 0.82 and 0.80, respectively). In addition, subgroup analyses revealed a significant difference in diagnostic performance between the alcohol use and non-alcohol use subgroups. Conclusions Methylation profiles of the five genomic regions covering cg15830431 (STK3), cg19396867, cg20655070, cg26671652 (ZNF418), and cg27062795 (ZNF542) can be used for effective methylation-based testing for ESCC diagnosis. Electronic supplementary material The online version of this article (10.1186/s13148-017-0430-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Weilin Pu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Chenji Wang
- Department of Biochemistry and Molecular Biology, Medical College, Soochow University, Suzhou, Jiangsu China
| | - Sidi Chen
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Dunmei Zhao
- Department of Biochemistry and Molecular Biology, Medical College, Soochow University, Suzhou, Jiangsu China
| | - Yinghui Zhou
- Department of Biochemistry and Molecular Biology, Medical College, Soochow University, Suzhou, Jiangsu China
| | - Yanyun Ma
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Ying Wang
- Genesky Biotechnologies Inc., Shanghai, China
| | - Caihua Li
- Genesky Biotechnologies Inc., Shanghai, China
| | - Zebin Huang
- Genesky Biotechnologies Inc., Shanghai, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Shicheng Guo
- Center for Human Genetics, Marshfield Clinic Research Foundation, 9500 Gilman Drive, MC0412, Marshfield, Wisconsin 54449 United States
| | - Jiucun Wang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Minghua Wang
- Department of Biochemistry and Molecular Biology, Medical College, Soochow University, Suzhou, Jiangsu China
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