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Zhao J, Lu Y, Ren X, Bian T, Feng J, Sun H, Liu L, She B, Liu Y, Ke H. Association of the SHOX2 and RASSF1A methylation levels with the pathological evolution of early-stage lung adenocarcinoma. BMC Cancer 2024; 24:687. [PMID: 38840077 PMCID: PMC11154976 DOI: 10.1186/s12885-024-12452-x] [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: 03/15/2024] [Accepted: 05/30/2024] [Indexed: 06/07/2024] Open
Abstract
Background The methylation of SHOX2 and RASSF1A shows promise as a potential biomarker for the early screening of lung cancer, offering a solution to remedy the limitations of morphological diagnosis. The aim of this study is to diagnose lung adenocarcinoma by measuring the methylation levels of SHOX2 and RASSF1A, and provide an accurate pathological diagnosis to predict the invasiveness of lung cancer prior to surgery.Material and methods The methylation levels of SHOX2 and RASSF1A were quantified using a LungMe® test kit through methylation-specific PCR (MS-PCR). The diagnostic efficacy of SHOX2 and RASSF1A and the cutoff values were validated using ROC curve analysis. The hazardous factors influencing the invasiveness of lung adenocarcinoma were calculated using multiple regression.Results: The cutoff values of SHOX2 and RASSF1A were 8.3 and 12.0, respectively. The sensitivities of LungMe® in IA, MIA and AIS patients were 71.3% (122/171), 41.7% (15/36), and 16.1% (5/31) under the specificity of 94.1% (32/34) for benign lesions. Additionally, the methylation level of SHOX2, RASSF1A and LungMe® correlated with the high invasiveness of clinicopathological features, such as age, gender, tumor size, TNM stage, pathological type, pleural invasion and STAS. The tumor size, age, CTR values and LungMe® methylation levels were identified as independent hazardous factors influencing the invasiveness of lung adenocarcinoma.Conclusion: SHOX2 and RASSF1A combined methylation can be used as an early detection indicator of lung adenocarcinoma. SHOX2 and RASSF1A combined (LungMe®) methylation is significantly correlated to age, gender, tumor size, TNM stage, pathological type, pleural invasion and STAS. The SHOX2 and RASSF1A methylation levels, tumor size and CTR values could predict the invasiveness of the tumor prior to surgery, thereby providing guidance for the surgical procedure.
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Affiliation(s)
- Jiaping Zhao
- Department of Thoracic Surgery, Affiliated Hospital of Nantong University, Nantong University, No.20 XISI road, ChongChuan District, NanTong, 226001, Jiangsu, China
- Medical School of Nantong University, Nantong University, ChongChuan District, NanTong, 226001, Jiangsu, China
| | - Yu Lu
- Department of Thoracic Surgery, Affiliated Hospital of Nantong University, Nantong University, No.20 XISI road, ChongChuan District, NanTong, 226001, Jiangsu, China
- Medical School of Nantong University, Nantong University, ChongChuan District, NanTong, 226001, Jiangsu, China
| | - Xiaosha Ren
- Department of Academic Development, Shanghai methyldia technology Co. Ltd, No. 412 Huiqing Road , Shanghai, 201203, China
| | - Tingting Bian
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong University, No.20 XISI road, ChongChuan District, NanTong, 226001, Jiangsu, China
| | - Jia Feng
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong University, No.20 XISI road, ChongChuan District, NanTong, 226001, Jiangsu, China
| | - Hui Sun
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong University, No.20 XISI road, ChongChuan District, NanTong, 226001, Jiangsu, China
| | - Lei Liu
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong University, No.20 XISI road, ChongChuan District, NanTong, 226001, Jiangsu, China
| | - Bin She
- Department of Academic Development, Shanghai methyldia technology Co. Ltd, No. 412 Huiqing Road , Shanghai, 201203, China
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong University, No.20 XISI road, ChongChuan District, NanTong, 226001, Jiangsu, China
- Tellgen Corporation Co. Ltd, No. 115, Lane 572, Bibo Road, Pilot Free Trade Zone, Shanghai, 201203, China
| | - Yifei Liu
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong University, No.20 XISI road, ChongChuan District, NanTong, 226001, Jiangsu, China.
| | - Honggang Ke
- Department of Thoracic Surgery, Affiliated Hospital of Nantong University, Nantong University, No.20 XISI road, ChongChuan District, NanTong, 226001, Jiangsu, China.
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Huo H, Zhang C, Wang K, Wang S, Chen W, Zhang Y, Yu W, Li S, Li S. A novel imprinted locus on bovine chromosome 18 homologous with human chromosome 16q24.1. Mol Genet Genomics 2024; 299:40. [PMID: 38546894 DOI: 10.1007/s00438-024-02123-8] [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: 08/28/2023] [Accepted: 02/02/2024] [Indexed: 04/02/2024]
Abstract
Genomic imprinting is an epigenetic regulation mechanism in mammals resulting in the parentally dependent monoallelic expression of genes. Imprinting disorders in humans are associated with several congenital syndromes and cancers and remain the focus of many medical studies. Cattle is a better model organism for investigating human embryo development than mice. Imprinted genes usually cluster on chromosomes and are regulated by different methylation regions (DMRs) located in imprinting control regions that control gene expression in cis. There is an imprinted locus on human chromosome 16q24.1 associated with congenital lethal developmental lung disease in newborns. However, genomic imprinting on bovine chromosome 18, which is homologous with human chromosome 16 has not been systematically studied. The aim of this study was to analyze the allelic expressions of eight genes (CDH13, ATP2C2, TLDC1, COTL1, CRISPLD2, ZDHHC7, KIAA0513, and GSE1) on bovine chromosome 18 and to search the DMRs associated gene allelic expression. Three transcript variants of the ZDHHC7 gene (X1, X2, and X5) showed maternal imprinting in bovine placentas. In addition, the monoallelic expression of X2 and X5 was tissue-specific. Five transcripts of the KIAA0513 gene showed tissue- and isoform-specific monoallelic expression. The CDH13, ATP2C2, and TLDC1 genes exhibited tissue-specific imprinting, however, COTL1, CRISLPLD2, and GSE1 escaped imprinting. Four DMRs, established after fertilization, were found in this region. Two DMRs were located between the ZDHHC7 and KIAA0513 genes, and two were in exon 1 of the CDH13 and ATP2C2 genes, respectively. The results from this study support future studies on the molecular mechanism to regulate the imprinting of candidate genes on bovine chromosome 18.
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Affiliation(s)
- Haonan Huo
- College of Life Science, Agricultural University of Hebei, Baoding, Hebei, China
| | - Cui Zhang
- College of Life Science, Agricultural University of Hebei, Baoding, Hebei, China
| | - Kun Wang
- Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
- Key Laboratory of Crop Cultivation Physiology and Green Production in Hebei Province, Shijiazhuang, China
| | - Siwei Wang
- Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
- Key Laboratory of Crop Cultivation Physiology and Green Production in Hebei Province, Shijiazhuang, China
| | - Weina Chen
- College of Medical Science, Hebei University, Baoding, Hebei, China
| | - Yinjiao Zhang
- College of Life Science, Agricultural University of Hebei, Baoding, Hebei, China
| | - Wenli Yu
- Shijiazhuang Tianquan Elite Dairy Ltd., Shijiazhuang, Hebei, China
| | - Shujing Li
- Shijiazhuang Tianquan Elite Dairy Ltd., Shijiazhuang, Hebei, China.
| | - Shijie Li
- College of Life Science, Agricultural University of Hebei, Baoding, Hebei, China.
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3
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Sun J, Chen J. [Research Progress of DNA Methylation in Cisplatin Resistance in Lung Cancer]. ZHONGGUO FEI AI ZA ZHI = CHINESE JOURNAL OF LUNG CANCER 2023; 26:52-58. [PMID: 36792081 PMCID: PMC9987084 DOI: 10.3779/j.issn.1009-3419.2023.101.03] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
As one of the most common malignant tumors, lung cancer poses a serious threat to human life and health. The platinum-based drug cisplatin (DDP) is used as the first-line treatment for lung cancer. The poor prognosis of lung cancer is mostly due to developed resistance to cisplatin, which poses a serious treatment challenge. The mechanism of cisplatin resistance is complex and unclear. Numerous studies have shown that DNA methylation plays a crucial role in the emergence of lung cancer cisplatin resistance. DNA hypermethylation results in the deactivation of numerous drug resistance genes and tumor suppressor genes through a change in chromatin conformation. Finding new therapeutic targets and indicators to predict the therapeutic effect can be aided by elucidating the complex mechanism. In order to discover novel strategies to overcome cisplatin resistance in lung cancer, this paper discusses DNA methylation-mediated cisplatin resistance and offers an overview of current demethylation procedures.
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Affiliation(s)
- Jinzhe Sun
- Department of Oncology, The Second Hospital of Dalian Medical University, Dalian 116000, China
| | - Jun Chen
- Department of Oncology, The Second Hospital of Dalian Medical University, Dalian 116000, China
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Nirgude S, Desai S, Choudhary B. Genome-wide differential DNA methylation analysis of MDA-MB-231 breast cancer cells treated with curcumin derivatives, ST08 and ST09. BMC Genomics 2022; 23:807. [PMID: 36474139 PMCID: PMC9727864 DOI: 10.1186/s12864-022-09041-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 10/17/2022] [Indexed: 12/12/2022] Open
Abstract
ST08 and ST09 are potent curcumin derivatives with antiproliferative, apoptotic, and migrastatic properties. Both ST08 and ST09 exhibit in vitro and in vivo anticancer properties. As reported earlier, these derivatives were highly cytotoxic towards MDA-MB-231 triple-negative breast cancer cells with IC50 values in the nanomolar (40-80nM) range.In this study,we performed whole-genome bisulfite sequencing(WGBS) of untreated (control), ST08 and ST09 (treated) triple-negative breast cancer cell line MDA-MB-231 to unravel epigenetic changes induced by the drug. We identified differentially methylated sites (DMSs) enriched in promoter regions across the genome. Analysis of the CpG island promoter methylation identified 12 genes common to both drugs, and 50% of them are known to be methylated in patient samples that were hypomethylated by drugs belonging to the homeobox family transcription factors.Methylation analysis of the gene body revealed 910 and 952 genes to be hypermethylatedin ST08 and ST09 treated MDA-MB-231 cells respectively. Correlation of the gene body hypermethylation with expression revealed CACNAH1 to be upregulated in ST08 treatment and CDH23 upregulation in ST09.Further, integrated analysis of the WGBS with RNA-seq identified uniquely altered pathways - ST08 altered ECM pathway, and ST09 cell cycle, indicating drug-specific signatures.
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Affiliation(s)
- Snehal Nirgude
- grid.418831.70000 0004 0500 991XInstitute of Bioinformatics and Applied Biotechnology, Electronic city phase 1, 560100 Bangalore, India ,grid.239552.a0000 0001 0680 8770Working at Division of Human Genetics, Children’s Hospital of Philadelphia, 19104 Philadelphia, PA USA
| | - Sagar Desai
- grid.418831.70000 0004 0500 991XInstitute of Bioinformatics and Applied Biotechnology, Electronic city phase 1, 560100 Bangalore, India
| | - Bibha Choudhary
- grid.418831.70000 0004 0500 991XInstitute of Bioinformatics and Applied Biotechnology, Electronic city phase 1, 560100 Bangalore, India
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Shao Y, Li W, Zhang L, Xue B, Chen Y, Zhang Z, Wang D, Wu B. CDH13 is a prognostic biomarker and a potential therapeutic target for patients with clear cell renal cell carcinoma. Am J Cancer Res 2022; 12:4520-4544. [PMID: 36381315 PMCID: PMC9641392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 09/15/2022] [Indexed: 06/16/2023] Open
Abstract
CDH13 is an atypical member of the cadherin family and is closely related to the clinicopathological factors and prognosis of many types of cancer. However, the role of CDH13 in clear cell renal cell carcinoma (ccRCC) remains unknown. Therefore, we comprehensively analyzed the expression level, diagnostic efficacy, clinical significance, prognostic value, immune infiltration, methylation status, genetic alteration, and biological functions of CDH13 in ccRCC patients. The results showed that CDH13 was significantly upregulated in ccRCC and strongly correlated with better survival, lower cancer stages, and lower tumor grades of ccRCC patients. Additionally, the immune infiltration analysis indicated that CDH13 might play a crucial role in regulating the tumor microenvironment of ccRCC. The results of methylation analysis showed that the epigenetic status of CDH13 was altered, and the prognosis of ccRCC patients was related not only to DNA methylation but also to m6A modification of CDH13. Finally, the results based on clinical samples further elucidated the expression pattern of CDH13 in ccRCC. In conclusion, CDH13 might be a novel prognostic biomarker and therapeutic target for patients with ccRCC. And our study provides new insights into the potential molecular changes and strategies for the treatment of ccRCC.
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Affiliation(s)
- Yuan Shao
- Department of Urology, The Second Hospital of Tianjin Medical UniversityTianjin 300070, China
- Shanxi Medical UniversityTaiyuan 030001, Shanxi, China
| | - Wenxia Li
- Clinical College of Neurology, Neurosurgery and Neurorehabilitation, Tianjin Medical UniversityTianjin 300350, China
- Shanxi Medical UniversityTaiyuan 030001, Shanxi, China
| | - Lin Zhang
- Shanxi Medical UniversityTaiyuan 030001, Shanxi, China
| | - Bo Xue
- Shanxi Medical UniversityTaiyuan 030001, Shanxi, China
| | - Yongquan Chen
- Shanxi Medical UniversityTaiyuan 030001, Shanxi, China
| | - Zikuan Zhang
- Shanxi Medical UniversityTaiyuan 030001, Shanxi, China
| | - Dongwen Wang
- Shanxi Medical UniversityTaiyuan 030001, Shanxi, China
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeShenzhen 518116, Guangdong, China
| | - Bo Wu
- Department of Urology, First Hospital of Shanxi Medical UniversityTaiyuan 030001, Shanxi, China
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Nirgude S, Desai S, Mahadeva R, Ravindran F, Choudhary B. ST08 Altered NF-κB Pathway in Breast Cancer Cells In Vitro as Revealed by miRNA-mRNA Analysis and Enhanced the Effect of Cisplatin on Tumour Reduction in EAC Mouse Model. Front Oncol 2022; 12:835027. [PMID: 35615145 PMCID: PMC9125255 DOI: 10.3389/fonc.2022.835027] [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: 12/14/2021] [Accepted: 03/22/2022] [Indexed: 12/17/2022] Open
Abstract
ST08 is a novel curcumin derivative that exhibited apoptotic and anti-migratory activity in MDA-MB-231, triple-negative breast cancer cells reported earlier. In this study, we further explored the anticancer properties of ST08. ST08 reduced tumor burden in vivo and induced apoptosis through the mitochondrial pathway both in vitro and in vivo. ST08 potentiated the effect of cisplatin in vitro and in vivo in mouse EAC breast cancer models with minimal toxicity. ST08 induced alterations in the gene expression were studied by parallel analysis of miRNA and mRNA. 74 differentially expressed miRNA regulated 114 mRNA in triple-negative (MDA-MB-231) cancer cells. Pathway related to the ECM was altered in mesenchymal MDA-MB-231 cells. We constructed a unique miRNA-mRNA interaction network, and one of the pathways regulated by miRNA was NF-κB. Targets of NF-κB like MMP1, PTX3, and MMP2 were downregulated in MDA-MB-231 in response to ST08 treatment. PMA induced cell proliferation was abrogated by ST08 treatment, and no additional cell cytotoxicity was observed when used in combination with IKK-16 indicating ST08 regulation of NF-κB pathway in MDA-MB-231 cells.
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Affiliation(s)
- Snehal Nirgude
- Institute of Bioinformatics and Applied Biotechnology, Bengaluru, India
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Sagar Desai
- Institute of Bioinformatics and Applied Biotechnology, Bengaluru, India
- Manipal Academy of Higher Education, Manipal, India
| | | | - Febina Ravindran
- Institute of Bioinformatics and Applied Biotechnology, Bengaluru, India
| | - Bibha Choudhary
- Institute of Bioinformatics and Applied Biotechnology, Bengaluru, India
- *Correspondence: Bibha Choudhary,
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Loaeza-Loaeza J, Illades-Aguiar B, Del Moral-Hernández O, Castro-Coronel Y, Leyva-Vázquez MA, Dircio-Maldonado R, Ortiz-Ortiz J, Hernández-Sotelo D. The CpG island methylator phenotype increases the risk of high-grade squamous intraepithelial lesions and cervical cancer. Clin Epigenetics 2022; 14:4. [PMID: 34991696 PMCID: PMC8740093 DOI: 10.1186/s13148-021-01224-0] [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: 05/13/2021] [Accepted: 12/23/2021] [Indexed: 02/06/2023] Open
Abstract
Background High-risk human papillomavirus (HR-HPV) infection is the main cause of cervical cancer, but additional alterations are necessary for its development. Abnormal DNA methylation has an important role in the origin and dissemination of cervical cancer and other human tumors. In this work, we analyzed the methylation of eight genes (AJAP1, CDH1, CDH13, MAGI2, MGMT, MYOD1, RASSF1A and SOX17) that participate in several biological processes for the maintenance of cell normality. We analyzed DNA methylation by methylation-specific PCR (MSP) and HPV infection using the INNO‑LiPA genotyping kit in 59 samples diagnostic of normal cervical tissue (non-SIL), 107 low-grade squamous intraepithelial lesions (LSILs), 29 high-grade squamous intraepithelial lesions (HSILs) and 51 cervical cancers (CCs). Results We found that all samples of LSIL, HSIL, and CC were HPV-positive, and the genotypes with higher frequencies were 16, 18, 51 and 56. In general, the genes analyzed displayed a significant tendency toward an increase in methylation levels according to increasing cervical lesion severity, except for the CDH13 gene. High CpG island methylator phenotype (CIMP) was associated with a 50.6-fold (95% CI 4.72–2267.3)-increased risk of HSIL and a 122-fold risk of CC (95% CI 10.04–5349.7). Conclusions We found that CIMP high was significantly associated with HSIL and CC risk. These results could indicate that CIMP together with HR-HPV infection and other factors participates in the development of HSIL and CC. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01224-0.
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Affiliation(s)
- Jaqueline Loaeza-Loaeza
- Laboratory of Cancer Epigenetics, School of Chemical and Biological Sciences, Autonomous University of Guerrero, Av. Lázaro Cárdenas S/N Col. Haciendita, 39070, Chilpancingo, Guerrero, Mexico
| | - Berenice Illades-Aguiar
- Laboratory of Molecular Biomedicine, School of Chemical and Biological Sciences, Autonomous University of Guerrero, Av. Lázaro Cárdenas S/N Col. Haciendita, 39070, Chilpancingo, Guerrero, Mexico
| | - Oscar Del Moral-Hernández
- Laboratory of Cancer Virology, School of Chemical and Biological Sciences, Autonomous University of Guerrero, Av. Lázaro Cárdenas S/N Col. Haciendita, 39070, Chilpancingo, Guerrero, Mexico
| | - Yaneth Castro-Coronel
- Laboratory of Cytopathology and Histochemistry, School of Chemical and Biological Sciences, Autonomous University of Guerrero, Av. Lázaro Cárdenas S/N Col. Haciendita, 39070, Chilpancingo, Guerrero, Mexico
| | - Marco A Leyva-Vázquez
- Laboratory of Molecular Biomedicine, School of Chemical and Biological Sciences, Autonomous University of Guerrero, Av. Lázaro Cárdenas S/N Col. Haciendita, 39070, Chilpancingo, Guerrero, Mexico
| | - Roberto Dircio-Maldonado
- Laboratory of Molecular Biomedicine, School of Chemical and Biological Sciences, Autonomous University of Guerrero, Av. Lázaro Cárdenas S/N Col. Haciendita, 39070, Chilpancingo, Guerrero, Mexico
| | - Julio Ortiz-Ortiz
- Laboratory of Molecular Biomedicine, School of Chemical and Biological Sciences, Autonomous University of Guerrero, Av. Lázaro Cárdenas S/N Col. Haciendita, 39070, Chilpancingo, Guerrero, Mexico
| | - Daniel Hernández-Sotelo
- Laboratory of Cancer Epigenetics, School of Chemical and Biological Sciences, Autonomous University of Guerrero, Av. Lázaro Cárdenas S/N Col. Haciendita, 39070, Chilpancingo, Guerrero, Mexico.
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8
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Li N, Zeng Y, Tai M, Lin B, Zhu D, Luo Y, Ren X, Zhu X, Li L, Wu H, Huang J. Analysis of the Prognostic Value and Gene Expression Mechanism of SHOX2 in Lung Adenocarcinoma. Front Mol Biosci 2021; 8:688274. [PMID: 34262939 PMCID: PMC8273341 DOI: 10.3389/fmolb.2021.688274] [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: 03/30/2021] [Accepted: 05/26/2021] [Indexed: 01/15/2023] Open
Abstract
Background: Detection of SHOX2 methylation has been used to assist in the early diagnosis of lung cancer in many hospitals as SHOX2 may be important in the tumorigenesis of lung cancer. However, there are few studies on the mRNA expression, methylation, and molecular mechanism of SHOX2 in lung cancer. We aimed to explore the role of SHOX2 in lung adenocarcinoma (LUAD). Methods: First, we examined the differential expression of SHOX2 mRNA and methylation in cancerous and normal tissues using databases. Second, we analyzed the relationship between SHOX2 expression and common clinical parameters in LUAD patients. Third, we further explored the methylated level and its specific location of SHOX2 and the mainly factors of SHOX2 gene expression. Finally, we screened the correlatively expressed genes to analyze the pathways from the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes using DAVID. Results: We found that the mRNA expression of SHOX2 was higher in multiple cancers, including LUAD and lung squamous cell carcinoma (LUSC), than in normal tissues. Among LUAD patients, SHOX2 expression was higher in patients of middle–young age, with smoking history, in advanced stages, and with nodal distant metastasis. In addition, our results showed that patients with high expression of SHOX2 are prone to recurrence, poor differentiation, and poor prognosis. Thus, we identified that SHOX2 might be an oncogene for LUAD progression. The main factor influencing the high expression of SHOX2 mRNA may be DNA methylation, followed by copy number variation (CNV), but not by gene mutations in LUAD. Unexpectedly, we found that SHOX2 undergoes hypomethylation in the gene body instead of hypermethylation in the promoter. Additionally, SHOX2 has cross talk in the PI3K–Akt signaling pathway and ECM–receptor interaction. Conclusion:SHOX2 is highly expressed in most cancers. SHOX2 gene expression might be mainly regulated by methylation of its gene body in LUAD, and its high expression or hypomethylation indicates poor differentiation and poor prognosis. SHOX2 could be involved in PI3K–Akt and other important cancer-related signaling pathways to promote tumorigenesis.
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Affiliation(s)
- Nanhong Li
- Institute of Nephrology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China.,The Center of Pathological Diagnosis and Research, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Yu Zeng
- Department of Respiration, The Second Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Min Tai
- Department of Pathology, Guangdong Medical University, Zhanjiang, China
| | - Biyun Lin
- The Center of Pathological Diagnosis and Research, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Di Zhu
- Department of Pathology, Guangdong Medical University, Zhanjiang, China
| | - Yi Luo
- Department of Pathology, Guangdong Medical University, Zhanjiang, China
| | - Xinle Ren
- Department of Pathology, Guangdong Medical University, Zhanjiang, China
| | - Xiaoying Zhu
- Department of Pathology, Guangdong Medical University, Zhanjiang, China
| | - Lanlan Li
- Department of Pathology, Guangdong Medical University, Zhanjiang, China
| | - Hongrong Wu
- The Center of Pathological Diagnosis and Research, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Jian Huang
- The Center of Pathological Diagnosis and Research, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China.,Department of Pathology, Guangdong Medical University, Zhanjiang, China
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Khan P, Siddiqui JA, Maurya SK, Lakshmanan I, Jain M, Ganti AK, Salgia R, Batra SK, Nasser MW. Epigenetic landscape of small cell lung cancer: small image of a giant recalcitrant disease. Semin Cancer Biol 2020; 83:57-76. [PMID: 33220460 PMCID: PMC8218609 DOI: 10.1016/j.semcancer.2020.11.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/10/2020] [Accepted: 11/11/2020] [Indexed: 12/12/2022]
Abstract
Small cell lung cancer (SCLC) is a particular subtype of lung cancer with high mortality. Recent advances in understanding SCLC genomics and breakthroughs of immunotherapy have substantially expanded existing knowledge and treatment modalities. However, challenges associated with SCLC remain enigmatic and elusive. Most of the conventional drug discovery approaches targeting altered signaling pathways in SCLC end up in the 'grave-yard of drug discovery', which mandates exploring novel approaches beyond inhibiting cell signaling pathways. Epigenetic modifications have long been documented as the key contributors to the tumorigenesis of almost all types of cancer, including SCLC. The last decade witnessed an exponential increase in our understanding of epigenetic modifications for SCLC. The present review highlights the central role of epigenetic regulations in acquiring neoplastic phenotype, metastasis, aggressiveness, resistance to chemotherapy, and immunotherapeutic approaches of SCLC. Different types of epigenetic modifications (DNA/histone methylation or acetylation) that can serve as predictive biomarkers for prognostication, treatment stratification, neuroendocrine lineage determination, and development of potential SCLC therapies are also discussed. We also review the utility of epigenetic targets/epidrugs in combination with first-line chemotherapy and immunotherapy that are currently under investigation in preclinical and clinical studies. Altogether, the information presents the inclusive landscape of SCLC epigenetics and epidrugs that will help to improve SCLC outcomes.
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Affiliation(s)
- Parvez Khan
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE-68198, USA
| | - Jawed Akhtar Siddiqui
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE-68198, USA
| | - Shailendra Kumar Maurya
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE-68198, USA
| | - Imayavaramban Lakshmanan
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE-68198, USA
| | - Maneesh Jain
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE-68198, USA; Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Apar Kishor Ganti
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA; Division of Oncology-Hematology, Department of Internal Medicine, VA-Nebraska Western Iowa Health Care System, Omaha, NE, 68105, USA; Division of Oncology-Hematology, Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Ravi Salgia
- Department of Medical Oncology and Therapeutics Research, City of Hope Comprehensive Cancer Center and Beckman Research Institute, Duarte 91010, CA, USA
| | - Surinder Kumar Batra
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE-68198, USA; Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA; Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Mohd Wasim Nasser
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE-68198, USA; Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA.
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He C, Qin H, Tang H, Yang D, Li Y, Huang Z, Zhang D, Lv C. Comprehensive bioinformatics analysis of the TP53 signaling pathway in Wilms' tumor. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:1228. [PMID: 33178760 PMCID: PMC7607069 DOI: 10.21037/atm-20-6047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Background Differential expression of tumor protein 53 (TP53, or p53) has been observed in multiple cancers. However, the expression levels and prognostic role of TP53 signaling pathway genes in Wilms' tumor (WT) have yet to be fully explored. Methods The expression levels of TP53 signaling pathway genes including TP53, mouse double minute 2 (MDM2), mouse double minute 4 (MDM4), cyclin-dependent kinase 2A (CDKN2A), cyclin-dependent kinase 2B (CDKN2B), and tumor suppressor p53-binding protein 1 (TP53BP1) in WT were analyzed using the Oncomine database. Aberration types, co-mutations, mutation locations, signaling pathways, and the prognostic role of TP53 in WT were investigated using cBioPortal. MicroRNA (miRNA) and transcription factor (TF) targets were identified with miRTarBase, miWalk, and ChIP-X Enrichment Analysis 3 (CheA3), respectively. A protein-protein network was constructed using GeneMANIA. The expression of TP53 signaling genes were confirmed in WT samples and normal kidney tissues using the Human Protein Atlas (HPA). Cancer Therapeutics Response Portal (CTRP) was used to analyze the small molecules potentially targeting TP53. Results TP53 was significantly expressed in the Cutcliffe Renal (P=0.010), but not in the Yusenko Renal (P=0.094). Meanwhile, MDM2 was significantly overexpressed in the Yusenko Renal (P=0.058), but not in the Cutcliffe Renal (P=0.058). The expression levels of MDM4 no significant difference between the tumor and normal tissue samples. The most common TP53 alteration was missense and the proportion of TP53 pathway-related mutations was 2.3%. Co-expressed genes included ZNF609 (zinc finger protein 609), WRAP53 (WD40-encoding RNA antisense to p53), CNOT2 (CC chemokine receptor 4-negative regulator of transcription 2), and CDH13 (cadherin 13). TP53 alterations indicated poor prognosis of WT (P=1.051e-4). The regulators of the TP53 pathway included miR-485-5p and TFs NR2F2 and KDM5B. The functions of TP53 signaling pathway were signal transduction in response to DNA damage and regulate the cell cycle. The small molecules targeting TP53 included PRIMA-1, RITA, SJ-172550, and SCH-529074. Conclusions TP53 was found to be differentially expressed in WT tissues. TP53 mutations indicated poor outcomes of WT. Therefore, pifithrin-mu, PRIMA-1, RITA, SJ-172550, and SCH-529074 could be used in combination with traditional chemotherapy to treat WT.
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Affiliation(s)
- Changjing He
- Department of Pediatric Surgery, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Huatao Qin
- Department of Nursing, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Haizhou Tang
- Department of Pediatric Surgery, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Di Yang
- Department of Pediatric Surgery, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Yufeng Li
- Department of Pediatric Surgery, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Zhenwen Huang
- Department of Pediatric Surgery, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Donghu Zhang
- Department of Pediatric Surgery, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Changheng Lv
- Department of Pediatric Surgery, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
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Jin C, Song P, Pang J. The CK2 inhibitor CX4945 reverses cisplatin resistance in the A549/DDP human lung adenocarcinoma cell line. Oncol Lett 2019; 18:3845-3856. [PMID: 31579410 DOI: 10.3892/ol.2019.10696] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 06/13/2019] [Indexed: 12/31/2022] Open
Abstract
Lung cancer negatively impacts global health, and the incidence of non-small cell lung cancer (NSCLC) is highest among all forms of lung cancer. Chemotherapy failure mainly occurs due to drug resistance; however, the associated molecular mechanism remains unclear. Casein kinase II (CK2), which plays important roles in the occurrence, development and metastasis of many tumours, regulates Wnt signaling by modulating β-catenin expression. In the present study the effects of the CK2 inhibitor, CX4945 on cisplatin [or cis-diamminedichloroplatinum (II); (DDP)]-resistant A549 cells (A549/DDP) were investigated to elucidate the underlying molecular mechanism. A549/DDP cells were divided into four groups (blank control, CX4945, cisplatin and CX4945+cisplatin). Cisplatin resistance was 5.16-fold greater in A549/DDP cells compared with that in A549 cells, with an optimal cisplatin concentration of 5 µg/ml. Moreover, levels of CK2, dishevelled-2 (DVL-2) phosphorylated (p) at Ser143 (p-DVL-2Ser143), and major Wnt-signaling proteins were significantly higher in A549/DDP cells compared with that in A549 cells (P<0.05), with these levels further increased following cisplatin treatment (P<0.05), whereas these levels significantly decreased in A549 cells after cisplatin treatment (P<0.05). Additionally, multidrug-resistance-associated protein 1 and lung resistance protein expression was significantly higher in A549/DDP cells compared with that in A549 cells (P<0.05), with these levels increasing further in A549/DDP (P<0.05) but not A549 cells upon cisplatin treatment (P>0.05). In addition, reduced expression of resistance proteins in A549/DDP cells was accompanied by a decline in the 50% growth inhibition after CX4945 pre-treatment. Furthermore, levels of p-DVL-2Ser143 and major Wnt-signaling proteins decreased significantly after treatment of A549/DDP cells with CX4945+cisplatin, whereas DVL-2 and p-DVL-2Thr224 levels remained unchanged. Additionally, significant elevations in apoptosis rates in the CX4945+cisplatin group relative to the control and cisplatin-only groups, was observed (P<0.001). These results suggested that inhibiting Wnt/β-catenin signaling with CX4945, which attenuates levels of drug-resistance-associated proteins and induces apoptosis, might reverse cisplatin resistance in NSCLC.
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Affiliation(s)
- Chengji Jin
- Respiratory Department, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, P.R. China
| | - Ping Song
- Respiratory Department, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, P.R. China
| | - Ji Pang
- Department of Physiology, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu 212013, P.R. China
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