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Qiu X, Guo R, Wang Y, Zheng S, Wang B, Gong Y. Mendelian randomization reveals potential causal relationships between cellular senescence-related genes and multiple cancer risks. Commun Biol 2024; 7:1069. [PMID: 39215079 PMCID: PMC11364673 DOI: 10.1038/s42003-024-06755-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Accepted: 08/20/2024] [Indexed: 09/04/2024] Open
Abstract
Cellular senescence is widely acknowledged as having strong associations with cancer. However, the intricate relationships between cellular senescence-related (CSR) genes and cancer risk remain poorly explored, with insights on causality remaining elusive. In this study, Mendelian Randomization (MR) analyses were used to draw causal inferences from 866 CSR genes as exposures and summary statistics for 18 common cancers as outcomes. We focused on genetic variants affecting gene expression, DNA methylation, and protein expression quantitative trait loci (cis-eQTL, cis-mQTL, and cis-pQTL, respectively), which were strongly linked to CSR genes alterations. Variants were selected as instrumental variables (IVs) and analyzed for causality with cancer using both summary-data-based MR (SMR) and two-sample MR (TSMR) approaches. Bayesian colocalization was used to unravel potential regulatory mechanisms underpinning risk variants in cancer, and further validate the robustness of MR results. We identified five CSR genes (CNOT6, DNMT3B, MAP2K1, TBPL1, and SREBF1), 18 DNA methylation genes, and LAYN protein expression which were all causally associated with different cancer types. Beyond causality, a comprehensive analysis of gene function, pathways, and druggability values was also conducted. These findings provide a robust foundation for unravelling CSR genes molecular mechanisms and promoting clinical drug development for cancer.
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Affiliation(s)
- Xunan Qiu
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, the First Hospital of China Medical University, Shenyang, 110001, China
- Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, the First Hospital of China Medical University, Shenyang, 110001, China
- Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, the First Hospital of China Medical University, Shenyang, 110001, China
| | - Rui Guo
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, the First Hospital of China Medical University, Shenyang, 110001, China
- Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, the First Hospital of China Medical University, Shenyang, 110001, China
- Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, the First Hospital of China Medical University, Shenyang, 110001, China
| | - Yingying Wang
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, the First Hospital of China Medical University, Shenyang, 110001, China
- Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, the First Hospital of China Medical University, Shenyang, 110001, China
- Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, the First Hospital of China Medical University, Shenyang, 110001, China
| | - Shuwen Zheng
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, the First Hospital of China Medical University, Shenyang, 110001, China
- Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, the First Hospital of China Medical University, Shenyang, 110001, China
- Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, the First Hospital of China Medical University, Shenyang, 110001, China
| | - Bengang Wang
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, the First Hospital of China Medical University, Shenyang, 110001, China.
- Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, the First Hospital of China Medical University, Shenyang, 110001, China.
- Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, the First Hospital of China Medical University, Shenyang, 110001, China.
| | - Yuehua Gong
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, the First Hospital of China Medical University, Shenyang, 110001, China.
- Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, the First Hospital of China Medical University, Shenyang, 110001, China.
- Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, the First Hospital of China Medical University, Shenyang, 110001, China.
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Batochir C, Kim IA, Jo EJ, Kim EB, Kim HJ, Hur JY, Kim DW, Park HK, Lee KY. Discrimination of Lung Cancer and Benign Lung Diseases Using BALF Exosome DNA Methylation Profile. Cancers (Basel) 2024; 16:2765. [PMID: 39123492 PMCID: PMC11311347 DOI: 10.3390/cancers16152765] [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: 06/05/2024] [Revised: 07/15/2024] [Accepted: 07/31/2024] [Indexed: 08/12/2024] Open
Abstract
Benign lung diseases are common and often do not require specific treatment, but they pose challenges in the distinguishing of them from lung cancer during low-dose computed tomography (LDCT). This study presents a comprehensive methylation analysis using real-time PCR for minimally invasive diagnoses of lung cancer via employing BALF exosome DNA. A panel of seven epigenetic biomarkers was identified, exhibiting specific methylation patterns in lung cancer BALF exosome DNA. This panel achieved an area under the curve (AUC) of 0.97, with sensitivity and specificity rates of 88.24% and 97.14%, respectively. Each biomarker showed significantly higher mean methylation levels (MMLs) in both non-small cell lung cancer (NSCLC) and small cell lung cancer (SCLC) compared to non-cancer groups, with fold changes from 1.7 to 13.36. The MMLs of the biomarkers were found to be moderately elevated with increasing patient age and smoking history, regardless of sex. A strong correlation was found between the MMLs and NSCLC stage progression, with detection sensitivities of 79% for early stages and 92% for advanced stages. In the validation cohort, the model demonstrated an AUC of 0.95, with 94% sensitivity and specificity. Sensitivity for early-stage NSCLC detection improved from 88.00% to 92.00% when smoking history was included as an additional risk factor.
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Affiliation(s)
- Chinbayar Batochir
- Seasun Biomaterials, Inc., Daejeon 34015, Republic of Korea; (C.B.); (E.J.J.); (E.-B.K.); (D.W.K.); (H.K.P.)
| | - In Ae Kim
- Precision Medicine Lung Cancer Center, Konkuk University Medical Center, Seoul 05030, Republic of Korea; (I.A.K.); (H.J.K.); (J.Y.H.)
| | - Eun Ji Jo
- Seasun Biomaterials, Inc., Daejeon 34015, Republic of Korea; (C.B.); (E.J.J.); (E.-B.K.); (D.W.K.); (H.K.P.)
| | - Eun-Bi Kim
- Seasun Biomaterials, Inc., Daejeon 34015, Republic of Korea; (C.B.); (E.J.J.); (E.-B.K.); (D.W.K.); (H.K.P.)
| | - Hee Joung Kim
- Precision Medicine Lung Cancer Center, Konkuk University Medical Center, Seoul 05030, Republic of Korea; (I.A.K.); (H.J.K.); (J.Y.H.)
| | - Jae Young Hur
- Precision Medicine Lung Cancer Center, Konkuk University Medical Center, Seoul 05030, Republic of Korea; (I.A.K.); (H.J.K.); (J.Y.H.)
| | - Do Won Kim
- Seasun Biomaterials, Inc., Daejeon 34015, Republic of Korea; (C.B.); (E.J.J.); (E.-B.K.); (D.W.K.); (H.K.P.)
| | - Hee Kyung Park
- Seasun Biomaterials, Inc., Daejeon 34015, Republic of Korea; (C.B.); (E.J.J.); (E.-B.K.); (D.W.K.); (H.K.P.)
| | - Kye Young Lee
- Precision Medicine Lung Cancer Center, Konkuk University Medical Center, Seoul 05030, Republic of Korea; (I.A.K.); (H.J.K.); (J.Y.H.)
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Caiado H, Cancela ML, Conceição N. Assessment of MGP gene expression in cancer and contribution to prognosis. Biochimie 2023; 214:49-60. [PMID: 37307958 DOI: 10.1016/j.biochi.2023.06.004] [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: 10/07/2022] [Revised: 05/30/2023] [Accepted: 06/09/2023] [Indexed: 06/14/2023]
Abstract
Matrix Gla protein (MGP) was first identified as a calcification physiological inhibitor and the causal agent of the Keutel syndrome. MGP has been suggested to play a role in development, cell differentiation, and tumorigenesis. This study aimed to compare MGP expression and methylation status in different tumors and adjacent tissues, using The Cancer Genome Atlas (TCGA) data repository. We investigated if changes in MGP mRNA expression were correlated to cancer progression and whether the correlation coefficients could be used for prognosis. Strong correlations were observed between altered MGP levels and disease progression in breast, kidney, liver, and thyroid cancers, suggesting that it could be used to complement current clinical biomarker assays, for early cancer diagnosis. We have also analyzed MGP methylation and identified CpG sites in its promoter and first intron with clear differences in methylation status between healthy and tumoral tissue providing evidence for epigenetic regulation of MGP transcription. Furthermore, we demonstrate that these alterations correlate with the overall survival of the patients suggesting that its assessment can serve as an independent prognostic indicator of patients' survival.
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Affiliation(s)
- Helena Caiado
- ProRegeM PhD Programme in Mechanisms of Disease and Regenerative Medicine, University of Algarve, Faro, 8005-139, Portugal; Centre of Marine Sciences (CCMAR), University of Algarve, Faro, 8005-139, Portugal; Faculty of Medicine and Biomedical Sciences, University of Algarve, Faro, 8005-139, Portugal
| | - M Leonor Cancela
- Centre of Marine Sciences (CCMAR), University of Algarve, Faro, 8005-139, Portugal; Faculty of Medicine and Biomedical Sciences, University of Algarve, Faro, 8005-139, Portugal; Algarve Biomedical Center, University of Algarve, Faro, 8005-139, Portugal.
| | - Natércia Conceição
- Centre of Marine Sciences (CCMAR), University of Algarve, Faro, 8005-139, Portugal; Faculty of Medicine and Biomedical Sciences, University of Algarve, Faro, 8005-139, Portugal; Algarve Biomedical Center, University of Algarve, Faro, 8005-139, Portugal.
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An G, Liu Y, Hou Y, Lei Y, Bai J, He L, Liu Y. RRP12 suppresses cell migration and invasion in colorectal cancer cell via regulation of epithelial-mesenchymal transition. J Gastrointest Oncol 2023; 14:2111-2123. [PMID: 37969827 PMCID: PMC10643574 DOI: 10.21037/jgo-23-254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 09/13/2023] [Indexed: 11/17/2023] Open
Abstract
Background The survival of patients with advanced colorectal cancer (CRC) is variable. The high rates of recurrence, metastasis, and drug resistance make clinical treatment difficult, which needs to further develop therapeutic and prognostic targets. Ribosomal RNA processing 12 homolog (RRP12), as a nucleolar protein involved in ribosome subunit maturation and export, plays important roles in cell cycle-related processes and the response to DNA damage, and regulates the occurrence and development of various cancers. The primary aim of this study was to identify the function of RRP12 in the process of epithelial-mesenchymal transition (EMT) in CRC. Methods In this study, the expression of RRP12 in tissue samples and the association with clinicopathological features in CRC was evaluated, and the correlation between RRP12 expression and aggressiveness of CRC was detected. After knockdown of RRP12 gene, the relationship between RRP12 and EMT-related indicators was verified in vivo and in vitro of CRC cells. Identification of RRP12-related genes and pathways through bioinformatic-based analyses was performed to find its potential mechanism. Results RRP12 is highly expressed in CRC cell lines and clinical samples and is associated with poor survival in CRC patients. RRP12 expression was positively associated with lymph node metastasis, tumor-node-metastasis (TNM) stage, and poor differentiation. Knockdown of RRP12 was found to suppress migration and invasion of CRC cells. RRP12 contributed to the EMT process of CRC cell lines in a ZEB1-mediated manner. RRP12 knockdown was found to reverse metastasis of CRC cells in vivo. Bioinformatic-based analyses indicated that RRP12 could serve as a potential biomarker for prognostic assessment of CRC patients. Conclusions RRP12 is involved in the tumorigenesis and metastasis of CRC by regulating the EMT process through ZEB1. Thus, RRP12 could be a potential therapeutic target for CRC therapy.
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Affiliation(s)
- Gaili An
- Department of Clinical Oncology, Shaanxi Provincial People’s Hospital, Xi’an, China
- Department of Oncology, the First Affiliated Hospital of Xi’an Jiaotong University Xi’an, China
| | - Ying Liu
- Department of Clinical Oncology, Shaanxi Provincial People’s Hospital, Xi’an, China
| | - Yinyin Hou
- Department of Clinical Oncology, Shaanxi Provincial People’s Hospital, Xi’an, China
| | - Yu Lei
- Department of Clinical Oncology, Shaanxi Provincial People’s Hospital, Xi’an, China
| | - Jun Bai
- Department of Clinical Oncology, Shaanxi Provincial People’s Hospital, Xi’an, China
| | - Li He
- Department of Clinical Oncology, Shaanxi Provincial People’s Hospital, Xi’an, China
| | - Yi Liu
- Department of Clinical Oncology, Shaanxi Provincial People’s Hospital, Xi’an, China
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Liu Y, Hu G, Li Y, Kong X, Yang K, Li Z, Lao W, Li J, Zhong J, Zhang S, Leng Y, Bi C, Zhai A. Research on the biological mechanism and potential application of CEMIP. Front Immunol 2023; 14:1222425. [PMID: 37662915 PMCID: PMC10471826 DOI: 10.3389/fimmu.2023.1222425] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 07/26/2023] [Indexed: 09/05/2023] Open
Abstract
Cell migration-inducing protein (CEMIP), also known as KIAA1199 and hyaluronan-binding protein involved in hyaluronan depolymerization, is a new member of the hyaluronidase family that degrades hyaluronic acid (HA) and remodels the extracellular matrix. In recent years, some studies have reported that CEMIP can promote the proliferation, invasion, and adhesion of various tumor cells and can play an important role in bacterial infection and arthritis. This review focuses on the pathological mechanism of CEMIP in a variety of diseases and expounds the function of CEMIP from the aspects of inhibiting cell apoptosis, promoting HA degradation, inducing inflammatory responses and related phosphorylation, adjusting cellular microenvironment, and regulating tissue fibrosis. The diagnosis and treatment strategies targeting CEMIP are also summarized. The various functions of CEMIP show its great potential application value.
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Affiliation(s)
- Yang Liu
- Department of Laboratory Medicine, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Gang Hu
- The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Yuetong Li
- Department of Endocrinology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Xinyi Kong
- Department of Laboratory Medicine, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Kaming Yang
- Department of Endocrinology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Zhenlin Li
- Department of Endocrinology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Wanwen Lao
- Department of Endocrinology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Jiaxin Li
- Department of Endocrinology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Jianhua Zhong
- Department of Endocrinology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Shitong Zhang
- Department of General Practice, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Yuxin Leng
- Department of Critical Care Medicine, Peking University Third Hospital, Beijing, China
| | - Changlong Bi
- Department of Endocrinology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Aixia Zhai
- Department of Laboratory Medicine, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
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Liu X, Feng D, Wang W, Liang J, Yu H, Ling B. Tumor Microenvironment CD8 T and Treg Cells-related Genes Signature Distinguishes Distinct Prognosis and Targeted Therapies Response in Endometrial Cancer. J Immunother 2023; 46:178-191. [PMID: 37098928 DOI: 10.1097/cji.0000000000000463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 02/14/2023] [Indexed: 04/27/2023]
Abstract
Although most endometrial cancer (EC) patients have a favorable prognosis, the overall survival (OS) of metastatic and recurrent EC could hardly be improved by the current chemoradiotherapy. We aimed to reveal the tumor microenvironment immune infiltration characteristics to elucidate the underlying mechanism of EC progression and guide clinical decisions. In the Cancer Genome Atlas (TCGA) cohort, Kaplan-Meier survival curves confirmed Tregs and CD8 T cells were prognosis-protective factors in OS of EC ( P <0.05). Weighted gene coexpression network analysis identified 2 gene modules closely correlated with Tregs and CD8 T-cell infiltration. We randomly split the TCGA EC cohort into the training and testing cohorts at a ratio of 7:3. An immune-related prognosis risk index (IRPRI), including NR3C1, E2F1, OTOG, TTK, PPP1R16B, and FOXP3, was established by univariate, Least Absolute Shrinkage and Selection Operator, and multivariate Cox regression with area under the curve >0.67. Distinct clinical, immune, and mutation characteristics existed between IRPRI groups by multiomics analysis. Cell proliferation and DNA damage repair-related pathways were activated, and immune-related pathways were inactivated in the IRPRI-high group. Furthermore, patients in the IRPRI-high group had lower tumor mutation burden, programmed death-ligand 1 expression, and Tumor Immune Dysfunction and Exclusion scores, indicating a poor response to immune checkpoint inhibitors therapy ( P <0.05), which was also validated in the TCGA testing cohort and independent cohorts, GSE78200, GSE115821, and GSE168204. Also, the higher mutation frequencies of BRCA1, BRCA2, and genes enrolled in homologous recombination repair in the IRPRI-low group predicted a good response to PARP inhibitors. Finally, a nomogram integrating the IRPRI group and prognosis significant clinicopathological factors for EC OS prediction was developed and validated with good discrimination and calibration.
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Affiliation(s)
- Xiaodie Liu
- Department of Obstetrics and Gynecology, China-Japan Friendship Hospital, Institute of Clinical Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Dingqing Feng
- Department of Obstetrics and Gynecology, China-Japan Friendship Hospital, Beijing, China
| | - Wenhui Wang
- Department of Obstetrics and Gynecology, China-Japan Friendship Hospital, Beijing, China
| | - Jing Liang
- Department of Obstetrics and Gynecology, China-Japan Friendship Hospital, Beijing, China
| | - Huan Yu
- Department of Obstetrics and Gynecology, China-Japan Friendship Hospital, Beijing, China
| | - Bin Ling
- Department of Obstetrics and Gynecology, China-Japan Friendship Hospital, Institute of Clinical Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Department of Obstetrics and Gynecology, China-Japan Friendship Hospital, Beijing, China
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Li H, Li C, Zhang B, Jiang H. Lactoferrin suppresses the progression of colon cancer under hyperglycemia by targeting WTAP/m 6A/NT5DC3/HKDC1 axis. J Transl Med 2023; 21:156. [PMID: 36855062 PMCID: PMC9972781 DOI: 10.1186/s12967-023-03983-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 02/13/2023] [Indexed: 03/02/2023] Open
Abstract
BACKGROUND Although the relationship between type 2 diabetes (T2D) and the increased risk of colorectal carcinogenesis is widely defined in clinical studies, the therapeutic methods and molecular mechanism of T2D-induced colon cancer and how does hyperglycemia affect the progression is still unknown. Here, we studied the function of lactoferrin (LF) in suppressing the progression of colon cancer in T2D mice, and uncovered the related molecular mechanisms in DNA 5mC and RNA m6A levels. METHODS We examined the effects of LF (50% iron saturation) on the migration and invasion of colon tumor cells under high concentration of glucose. Then, transcriptomics and DNA methylation profilings of colon tumor cells was co-analyzed to screen out the special gene (NT5DC3), and the expression level of NT5DC3 in 75 clinical blood samples was detected by q-PCR and western blot, to investigate whether NT5DC3 was a biomarker to distinguish T2D patients and T2D-induced colon cancer patients from healthy volunteers. Futhermore, in T2D mouse with xenografted colon tumor models, the inhibitory effects of LF and NT5DC3 protein on colon tumors were investigated. In addition, epigenetic alterations were measured to examine the 5mC/m6A modification sites of NT5DC3 regulated by LF. Utilizing siRNA fragments of eight m6A-related genes, the special gene (WTAP) regulating m6A of NT5DC was proved, and the effect of LF on WTAP/NT5DC3/HKDC1 axis was finally evaluated. RESULTS A special gene NT5DC3 was screened out through co-analysis of transcriptomics and DNA methylation profiling, and HKDC1 might be a downstream sensor of NT5DC3. Mechanistically, LF-dependent cellular DNA 5mC and RNA m6A profiling remodeling transcriptionally regulate NT5DC3 expression. WTAP plays a key role in regulating NT5DC3 m6A modification and subsequently controls NT5DC3 downstream target HKDC1 expression. Moreover, co-treatment of lactoferrin and NT5DC3 protein restrains the growth of colon tumors by altering the aberrant epigenetic markers. Strikingly, clinical blood samples analysis demonstrates NT5DC3 protein expression is required to direct the distinction of T2D or T2D-induced colon cancer with healthy humans. CONCLUSIONS Together, this study reveals that lactoferrin acts as a major factor to repress the progression of colon cancer under hyperglycemia, thus, significantly expanding the landscape of natural dietary mediated tumor suppression.
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Affiliation(s)
- Huiying Li
- College of Biological Sciences and Technology, Beijing Key Laboratory of Food Processing and Safety in Forestry, Beijing Forestry University, Beijing, 100083, People's Republic of China.
| | - Chaonan Li
- College of Biological Sciences and Technology, Beijing Key Laboratory of Food Processing and Safety in Forestry, Beijing Forestry University, Beijing, 100083, People's Republic of China
| | - Boyang Zhang
- Department of Nutrition and Health, China Agricultural University, Beijing, 100083, People's Republic of China
| | - Hongpeng Jiang
- Department of General Surgery, Beijing Key Laboratory of Cancer Invasion and Metastasis Research and National Clinical Research Center for Digestive Diseases, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, People's Republic of China.
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Bi YH, Wang J, Guo ZJ, Jia KN. Characterization of Ferroptosis-Related Molecular Subtypes with Immune Infiltrations in Neuropathic Pain. J Pain Res 2022; 15:3327-3348. [PMID: 36311291 PMCID: PMC9601606 DOI: 10.2147/jpr.s385228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 10/18/2022] [Indexed: 11/23/2022] Open
Abstract
Background Neuropathic pain (NP) caused by a lesion or disease of the somatosensory nervous system is a common chronic pain condition that has a major impact on quality of life. However, NP pathogenesis remains unclear. The purpose of this study was to identify differentially expressed genes (DEGs) and specific and meaningful gene targets for the diagnosis and treatment of NP. Methods Data from rat spinal nerve ligations and the sham group were downloaded from the Gene Expression Omnibus (GEO) database. Based on the single-sample gene set enrichment analysis (ssGSEA) method, 29 immune gene sets were identified in each sample, and these samples were correlated with the immune infiltration phenotype. LASSO regression modeling was used to screen key genes to identify diagnostic gene markers. According to GSEA and GSVA, NP is concentrated in a large number of immune-related pathways and genes. Additionally, we used the DGIdb database and correlation test to construct gene-drug and transcription factor interaction networks for differentially expressed genes relevant to NP-related ferroptosis. We used WGCNA to identify gene co-expression modules of NP, and explored the relationship between gene networks and phenotypes. Finally, we crossed core genes with diagnostic markers and analyzed gene correlation with molecular subtypes and immune cells. Results We identified 224 DEGs, including 191 upregulated genes and 33 downregulated genes. APC co-stimulation, CCR, cytolytic activity, humid-promoting, neutrophils, NK cells, and RGS4, CXCL2, DRD4 and other 7 genes related to ferroptosis were involved in NP development. Key genes of RGS4 and HIF-1 signaling pathway were screened. Conclusion This study contributes to our understanding of the neuroimmune mechanism of neuropathic pain, provides a reference for NP biomarkers and drug targets. Ferroptosis may be the next research direction to explore NP mechanism.
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Affiliation(s)
- Yan-Hua Bi
- Neurosurgery Department, Huabei Petroleum Administration Bureau General Hospital, Renqiu, People’s Republic of China
| | - Jia Wang
- Neurosurgery Department, Huabei Petroleum Administration Bureau General Hospital, Renqiu, People’s Republic of China
| | - Zhi-Jun Guo
- Medical Imaging Department, Huabei Petroleum Administration Bureau General Hospital, Renqiu, People’s Republic of China
| | - Kai-Ning Jia
- Clinical Trials Center, Huabei Petroleum Administration Bureau General Hospital, Renqiu, People’s Republic of China,Correspondence: Kai-Ning Jia, Clinical Trials Center, Huabei Petroleum Administration Bureau General Hospital, Renqiu, 062550, People’s Republic of China, Email
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Bayrak T, Çetin Z, Saygılı Eİ, Ogul H. Identifying the tumor location-associated candidate genes in development of new drugs for colorectal cancer using machine-learning-based approach. Med Biol Eng Comput 2022; 60:2877-2897. [DOI: 10.1007/s11517-022-02641-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 07/28/2022] [Indexed: 02/07/2023]
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10
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Welsh J, Bak MJ, Narvaez CJ. New insights into vitamin K biology with relevance to cancer. Trends Mol Med 2022; 28:864-881. [PMID: 36028390 PMCID: PMC9509427 DOI: 10.1016/j.molmed.2022.07.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 06/23/2022] [Accepted: 07/22/2022] [Indexed: 10/24/2022]
Abstract
Phylloquinone (vitamin K1) and menaquinones (vitamin K2 family) are essential for post-translational γ-carboxylation of a small number of proteins, including clotting factors. These modified proteins have now been implicated in diverse physiological and pathological processes including cancer. Vitamin K intake has been inversely associated with cancer incidence and mortality in observational studies. Newly discovered functions of vitamin K in cancer cells include activation of the steroid and xenobiotic receptor (SXR) and regulation of oxidative stress, apoptosis, and autophagy. We provide an update of vitamin K biology, non-canonical mechanisms of vitamin K actions, the potential functions of vitamin K-dependent proteins in cancer, and observational trials on vitamin K intake and cancer.
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Affiliation(s)
- JoEllen Welsh
- Cancer Research Center and Department of Environmental Health Sciences, University at Albany, Rensselaer, NY 12144, USA.
| | - Min Ji Bak
- Cancer Research Center and Department of Environmental Health Sciences, University at Albany, Rensselaer, NY 12144, USA
| | - Carmen J Narvaez
- Cancer Research Center and Department of Environmental Health Sciences, University at Albany, Rensselaer, NY 12144, USA
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Lamare FA, Khongsti S, Marthong L, Ghosh S, Chenkual S, Dkhar H, Maitra A, Ghosh S. Genome-wide DNA methylation profiling of stomach cancer in the ethnic population of Mizoram, North East India. Genomics 2022; 114:110478. [PMID: 36064073 DOI: 10.1016/j.ygeno.2022.110478] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 08/10/2022] [Accepted: 08/31/2022] [Indexed: 12/01/2022]
Abstract
Stomach cancer is the fifth most common cancer in terms of prevalence and incidence and the fourth leading cause of mortality in men and women worldwide. It is well-established that aberrant DNA methylation in cells can lead to carcinogenesis. The primary objective of our study was to investigate the aberrant DNA methylation status of genes associated with stomach cancer with a particular reference to the ethnic population of Mizoram, North East India. The site-level analysis identified 2883 CpG sites differentially methylated, representing ~922 genes. Out of which 476 Differentially Methylated Positions (DMPs) were promoter-associated, 452 DMPs were hypermethylated, and 24 were hypomethylated. The region-level analysis identified 462 Differentially Methylated Regions (DMRs) corresponding to ~320 genes, of which ~281 genes were hypermethylated and ~ 40 genes were hypomethylated. TCGA analysis showed that some of the genes had been previously implicated in other cancers including stomach cancer. Five hypermethylated genes were selected as candidate genes for further investigations and they have shown to be novel and could serve as candidate hypermethylation biomarkers for stomach cancer in this particular ethnic group.
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Affiliation(s)
- F A Lamare
- Department of Zoology, North-Eastern Hill University (NEHU), Shillong, India
| | - S Khongsti
- Department of Zoology, North-Eastern Hill University (NEHU), Shillong, India
| | - L Marthong
- Department of Zoology, North-Eastern Hill University (NEHU), Shillong, India
| | - S Ghosh
- National Institute of Biomedical Genomics (NIBMG), Kalyani, West Bengal, India
| | | | - H Dkhar
- Nazareth Hospital, Shillong, India
| | - A Maitra
- National Institute of Biomedical Genomics (NIBMG), Kalyani, West Bengal, India
| | - S Ghosh
- Department of Zoology, North-Eastern Hill University (NEHU), Shillong, India.
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12
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Fatemi N, Tierling S, Es HA, Varkiani M, Nazemalhosseini Mojarad E, Asadzadeh Aghdaei H, Walter J, Totonchi M. DNA Methylation Biomarkers in Colorectal Cancer: Clinical Applications for Precision Medicine. Int J Cancer 2022; 151:2068-2081. [PMID: 35730647 DOI: 10.1002/ijc.34186] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 04/29/2022] [Accepted: 06/08/2022] [Indexed: 11/06/2022]
Abstract
Colorectal cancer (CRC) is the second leading cause of cancer death worldwide that is attributed to gradual long-term accumulation of both genetic and epigenetic changes. To reduce the mortality rate of CRC and to improve treatment efficacy, it will be important to develop accurate noninvasive diagnostic tests for screening, acute, and personalized diagnosis. Epigenetic changes such as DNA methylation play an important role in the development and progression of CRC. Over the last decade, a panel of DNA methylation markers has been reported showing a high accuracy and reproducibility in various semi-invasive or noninvasive biosamples. Research to obtain comprehensive panels of markers allowing a highly sensitive and differentiating diagnosis of CRC is ongoing. Moreover, the epigenetic alterations for cancer therapy, as a precision medicine strategy will increase their therapeutic potential over time. Here, we discuss the current state of DNA methylation-based biomarkers and their impact on CRC diagnosis. We emphasize the need to further identify and stratify methylation-biomarkers and to develop robust and effective detection methods that are applicable for a routine clinical setting of CRC diagnostics particularly at the early stage of the disease.
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Affiliation(s)
- Nayeralsadat Fatemi
- Basic & Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology & Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sascha Tierling
- Department of Genetics/Epigenetics, Faculty NT, Life Sciences, Saarland University, Saarbrücken, Germany
| | | | - Maryam Varkiani
- Department of Molecular Genetics, Faculty of Basic Sciences and Advanced Technologies in Biology, University of Science and Culture, Tehran, Iran
| | - Ehsan Nazemalhosseini Mojarad
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamid Asadzadeh Aghdaei
- Basic & Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology & Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Jörn Walter
- Department of Genetics/Epigenetics, Faculty NT, Life Sciences, Saarland University, Saarbrücken, Germany
| | - Mehdi Totonchi
- Basic & Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology & Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
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13
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Yang M, He H, Peng T, Lu Y, Yu J. Identification of 9 Gene Signatures by WGCNA to Predict Prognosis for Colon Adenocarcinoma. COMPUTATIONAL INTELLIGENCE AND NEUROSCIENCE 2022; 2022:8598046. [PMID: 35392038 PMCID: PMC8983226 DOI: 10.1155/2022/8598046] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 03/01/2022] [Accepted: 03/10/2022] [Indexed: 11/17/2022]
Abstract
Background A risk assessment model for prognostic prediction of colon adenocarcinoma (COAD) was established based on weighted gene co-expression network analysis (WGCNA). Methods From the Cancer Genome Atlas (TCGA) database, RNA-seq data and clinical data of COAD patients were retrieved. After screening of differentially expressed genes (DEGs), WGCNA was performed to identify gene modules and screen those associated with COAD progression. Then, via protein-protein interaction (PPI) network construction of module genes, hub genes were obtained, which were then subjected to the least absolute shrinkage and selection operator (LASSO) and Cox regression to build a hub gene-based prognostic scoring model. The receiver operating characteristic curve (ROC curve) was plotted for the optimal cutoff (OCO) of the risk score, based on which, patients were assigned to high or low-risk groups. Areas under the ROC curve (AUCs) were calculated, and model performance was visualized using Kaplan-Meier (KM) survival curves and verified in the external dataset GSE29621. Finally, the model's independent prognostic value was evaluated by univariate and multivariate Cox regression analyses, and a nomogram was built. Results Totally 2840 DEGs were screened from COAD dataset of TCGA, including 1401 upregulated ones and 1439 downregulated ones, which were divided into 10 modules by WGCNA. The eigenvalue of the black module was found to have a high correlation with COAD progression. PPI interaction networks were constructed for genes in the black module, and 34 hub genes were obtained by using the MCODE plug-in. A LASSO-Cox regression approach was utilized to analyze the hub genes, and a prognostic risk score model based on the signatures of 9 genes (CHEK1, DEPDC1B, FANCI, MCM10, NCAPG, PARPBP, PLK4, RAD51AP1, and RFC4) was constructed. KM analysis identified shorter overall lower survival in the high-risk group. The model was verified to have favorable predictive ability through training set and validation set. The nomogram, composed of tumor node metastasis (TNM) staging and risk score, was of good predictability. Conclusions The COAD prognostic risk model constructed upon the signatures of 9 genes (CHEK1, DEPDC1B, FANCI, MCM10, NCAPG, PARPBP, PLK4, RAD51AP1, and RFC4) can effectively predict the survival status of COAD patients.
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Affiliation(s)
- Mian Yang
- Department of Colon Anorectal Surgery, Lihuili Hospital, Ningbo Medical Center, Ningbo, Zhejiang, China
| | - Haibin He
- Department of Gastrointestinal Surgery, Lihuili Hospital, Ningbo Medical Center, Ningbo, Zhejiang, China
| | - Tao Peng
- Department of Colon Anorectal Surgery, Lihuili Hospital, Ningbo Medical Center, Ningbo, Zhejiang, China
| | - Yi Lu
- Department of Chemoradiotherapy, Lihuili Hospital, Ningbo Medical Center, Ningbo, Zhejiang, China
| | - Jiazi Yu
- Department of Colon Anorectal Surgery, Lihuili Hospital, Ningbo Medical Center, Ningbo, Zhejiang, China
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14
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Whole exome and transcriptome sequencing reveal clonal evolution and exhibit immune-related features in metastatic colorectal tumors. Cell Death Discov 2021; 7:222. [PMID: 34453042 PMCID: PMC8397721 DOI: 10.1038/s41420-021-00607-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 07/14/2021] [Accepted: 07/29/2021] [Indexed: 01/05/2023] Open
Abstract
Liver is the most common site where metastatic lesions of colorectal cancer (CRC) arise. Although researches have shown mutations in driver genes, copy number variations (CNV) and alterations in relevant signaling pathways promoted the tumor evolution and immune escape during colorectal liver metastasis (CLM), the underlying mechanism remains largely elusive. Tumor and matched metastatic tissues were collected from 16 patients diagnosed with colorectal cancer and subjected to whole-exome sequencing (WES) and RNA sequencing (RNA-seq) for studying colorectal cancer clonal evolution and immune escape during CLM. Shared somatic mutations between primary and metastatic tissues with a commonly observed subclonal-clonal (S-C) changing pattern indicated a common clonal origin between two lesions. The recurrent mutations with S-C changing pattern included those in KRAS, SYNE1, CACNA1H, PCLO, FBXL2, and DNAH11. The main CNV events underwent clonal-clonal evolution (20q amplification (amp), 17p deletion (del), 18q del and 8p del), subclonal-clonal evolution (8q amp, 13q amp, 8p del) and metastasis-specific evolution (8q amp) during the process of CLM. In addition, we revealed a potential mechanism of tumor cell immune escape by analyzing human leukocytes antigens (HLA) related clonal neoantigens and immune cell components in CLM. Our study proposed a novel liver metastasis-related evolutionary process in colorectal cancer and emphasized the theory of neo-immune escape in colorectal liver metastasis.
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15
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Jin H, Pang L, Li H, Xu M, Yan H, Li R. [Value of combined detection of ITGA4 and SFRP2 gene methylation in stool DNA in diagnosis and prognostic evaluation of colorectal tumors]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2021; 41:891-897. [PMID: 34238742 DOI: 10.12122/j.issn.1673-4254.2021.06.12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
OBJECTIVE To investigate the value of quantitative detection of ITGA4 and SFRP2 gene methylation in stool DNA for the early diagnosis and prognostic evaluation of colorectal tumors. OBJECTIVE Real-time PCR was used for quantitative assessment of ITGA4 and SFRP2 gene methylation levels in stool samples of 85 patients with colorectal cancer, 65 patients with colorectal adenoma and 40 healthy subjects. OBJECTIVE The 3 groups were comparable for age and gender composition. Methylated ITGA4 and SFRP2 promoters were detected in 48.2% and 62.4% of patients with colorectal cancer, respectively, with a combined positivity of 81.2%. ITGA4 and SFRP2 promoter methylation was detected in 23.1% and 43.1% of patients with colorectal adenoma, respectively, with a combined positivity of 69.2%. The positivity rates of ITGA4 and SFRP2 methylation were significantly higher in patients with colorectal cancer than in those with colorectal adenoma (P < 0.001; P= 0.001) and healthy subjects (P < 0.001; P < 0.001). In colorectal cancer group, ITGA4 and SFRP2 promoter methylation levels were correlated with postoperative tumor recurrence in colorectal cancer group, and the relapse-free survival rate was significantly lower in positive patients for ITGA4 and SFRP2 promoter methylation than in the negative patients (P=0.0002; P=0.007). Multivariate analysis with the COX proportional hazard regression model showed that methylation of ITGA4 and SFRP2 gene promoters (P=0.01) and the degree of tumor differentiation (P=0.03) were associated with the recurrence of colorectal cancer, and were independent risk factors for the recurrence of colorectal cancer. OBJECTIVE Combined detection of ITGA4 and SFRP2 gene methylation levels in stool DNA can improve the early diagnosis rate of colorectal tumor. ITGA4 and SFRP2 promoter methylation and the degree of tumor differentiation are independent risk factors for colorectal cancer recurrence.
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Affiliation(s)
- H Jin
- Department of Clinical Laboratory, Affiliated Hongqi Hospital, Mudanjiang Medical University, Mudanjiang 157011, China
| | - L Pang
- First School of Clinical Medicine, Mudanjiang Medical University, Mudanjiang 157011, China
| | - H Li
- Department of Quality Control, Affiliated Hongqi Hospital, Mudanjiang Medical University, Mudanjiang 157011, China
| | - M Xu
- Department of Clinical Laboratory, Affiliated Hongqi Hospital, Mudanjiang Medical University, Mudanjiang 157011, China
| | - H Yan
- Department of Clinical Laboratory, Affiliated Hongqi Hospital, Mudanjiang Medical University, Mudanjiang 157011, China
| | - R Li
- Department of Clinical Laboratory, Affiliated Hongqi Hospital, Mudanjiang Medical University, Mudanjiang 157011, China
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16
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Zhu L, Sun H, Tian G, Wang J, Zhou Q, Liu P, Tang X, Shi X, Yang L, Liu G. Development and validation of a risk prediction model and nomogram for colon adenocarcinoma based on methylation-driven genes. Aging (Albany NY) 2021; 13:16600-16619. [PMID: 34182539 PMCID: PMC8266312 DOI: 10.18632/aging.203179] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 05/13/2021] [Indexed: 12/13/2022]
Abstract
Evidence suggests that abnormal DNA methylation patterns play a crucial role in the etiology and pathogenesis of colon adenocarcinoma (COAD). In this study, we identified a total of 97 methylation-driven genes (MDGs) through a comprehensive analysis of the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. Univariate Cox regression analysis identified four MDGs (CBLN2, RBM47, SLCO4C1, and TMEM220) associated with overall survival (OS) in COAD patients. A risk prediction model was then developed based on these four MDGs to predict the prognosis of COAD patients. We also created a nomogram that incorporated risk scores, age, and TNM stage to promote a personalized prediction of OS in COAD patients. Compared with the traditional TNM staging system, our new nomogram was better at predicting the OS of COAD patients. In cell experiments, we confirmed that the mRNA expression levels of CLBN2 and TMEM220 were regulated by the methylation of their promoter regions. Moreover, immunohistochemistry showed that CBLN2 and TMEM220 were potential prognostic biomarkers for COAD patients. In summary, we have established a risk prediction model and nomogram that might be effectively utilized to promote the prediction of OS in COAD patients.
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Affiliation(s)
- Liangyu Zhu
- Department of Epidemiology and Statistics, School of Public Health, Hebei Key Laboratory of Environment and Human Health, Hebei Medical University, Shijiazhuang 050017, P.R. China
| | - Hongyu Sun
- Department of Epidemiology and Statistics, School of Public Health, Hebei Key Laboratory of Environment and Human Health, Hebei Medical University, Shijiazhuang 050017, P.R. China
| | - Guo Tian
- Department of Medical Record, The Fourth Hospital of Hebei Medical University, Shijiazhuang 050011, P.R. China
| | - Juan Wang
- Department of Pathology, The Second Hospital of Hebei Medical University, Shijiazhuang 050000, P.R. China
| | - Qian Zhou
- Department of Clinical Pharmacology, The Fourth Hospital of Hebei Medical University, Shijiazhuang 050011, P.R. China
| | - Pu Liu
- Department of Epidemiology and Statistics, School of Public Health, Hebei Key Laboratory of Environment and Human Health, Hebei Medical University, Shijiazhuang 050017, P.R. China
| | - Xuejiao Tang
- Department of Epidemiology and Statistics, School of Public Health, Hebei Key Laboratory of Environment and Human Health, Hebei Medical University, Shijiazhuang 050017, P.R. China
| | - Xinrui Shi
- Department of Epidemiology and Statistics, School of Public Health, Hebei Key Laboratory of Environment and Human Health, Hebei Medical University, Shijiazhuang 050017, P.R. China
| | - Lei Yang
- Department of Epidemiology and Statistics, School of Public Health, Hebei Key Laboratory of Environment and Human Health, Hebei Medical University, Shijiazhuang 050017, P.R. China
| | - Guangjie Liu
- Department of Thoracic Surgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang 050011, P.R. China
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17
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Li R, Qu B, Wan K, Lu C, Li T, Zhou F, Lin J. Identification of two methylated fragments of an SDC2 CpG island using a sliding window technique for early detection of colorectal cancer. FEBS Open Bio 2021; 11:1941-1952. [PMID: 33955718 PMCID: PMC8255834 DOI: 10.1002/2211-5463.13180] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 04/06/2021] [Accepted: 05/04/2021] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most common cancer types globally with a 5‐year survival rate of < 50% in China. Aberrant DNA methylation is one of the hallmarks of tumor initiation, progression, and metastasis. Here, we investigated the clinical performance of two differentially methylated regions (DMRs) in SDC2 CpG islands for the detection of CRC. A sliding window technique was used to identify the DMRs, and methylation‐specific PCR assay was used to assess the DMRs in 198 CRC samples and 54 normal controls. Two DMRs (DMR2 and DMR5) were identified using The Cancer Genome Atlas (TCGA) data, and the hypermethylation of DMR2 and DMR5 was detected in 90.91% (180/198) and 89.90% (178/198) of CRC samples, respectively. When combining DMR2 and DMR5, the sensitivity for CRC detection was 94.4% higher than that of DMR2 or DMR5 alone. Based on the above results, we propose using DMR2 and DMR5 as a sensitive biomarker to detect CRC.
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Affiliation(s)
- Ruibin Li
- Hubei Key Laboratory of Tumor Biological Behavior, Hubei Cancer Clinical Study Center, Zhongnan Hospital of Wuhan University, China.,Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Bing Qu
- Department of Reproductive Medicine Center, Renmin Hospital of Wuhan University & Hubei Clinic Research Center for Assisted Reproductive Technology and Embryonic Development, China.,Department of Science and Education, China Resources & WISCO General Hospital, Wuhan University of Science and Technology, Wuhan, China
| | | | | | - Tingting Li
- Wuhan Ammunition Life-tech Company, Ltd., China
| | - Fuxiang Zhou
- Hubei Key Laboratory of Tumor Biological Behavior, Hubei Cancer Clinical Study Center, Zhongnan Hospital of Wuhan University, China.,Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jun Lin
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, China
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18
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Qu Y, Gao N, Wu T. Expression and clinical significance of SYNE1 and MAGI2 gene promoter methylation in gastric cancer. Medicine (Baltimore) 2021; 100:e23788. [PMID: 33530176 PMCID: PMC7850698 DOI: 10.1097/md.0000000000023788] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 11/13/2020] [Indexed: 02/07/2023] Open
Abstract
Gastric cancer is the fifth most common cancer and the third leading cause of cancer-related mortality globally. Abnormal DNA methylation is closely related to gastric cancer. The purpose of the study was to investigate the methylation of the SYNE1 and MAGI2 gene promoter and its relationship with the clinical-pathological factors, chemotherapy efficacy, and survival, thus providing a new biomarker for the prognosis and chemotherapy efficacy in gastric cancer.The methylation status of SYNE1 and MAGI2 in gastric cancer and adjacent tissues was detected by MSP method in 70 cases of advanced gastric cancer paraffin specimens.The methylation rate of the SYNE1 and MAGI2 gene promoter region was higher in gastric cancer tissues compared with adjacent tissues. The methylation status of SYNE1 was associated with the age at diagnosis and the size of the primary tumors, but no clinical or pathological factors have been found to be related with the methylation status of MAGI2 promoter. A high level of SYNE1 promoter methylation was associated with poorer chemotherapy efficacy in recurrent patients with gastric cancer. Thirty-three percent of the 70 patients exhibited highly methylated MAGI2; in this group, the median progression-free survival time was 4.1 months, shorter than those with negative methylated MAGI2 whose PFS was 5.1 months.MAGI2 is more methylated in gastric cancer than in adjacent tissues suggesting that hypermethylation changes in MAGI2 may be one of the mechanisms of tumorigenesis in gastric cancer. The methylation status of the SYNE1 and MAGI2 promoter regions may affect the chemotherapy efficacy of advanced gastric cancer. The prognosis of MAGI2-negative patients was better than that of positive ones, suggesting that MAGI2 may be an independent prognostic factor for PFS in patients with advanced gastric cancer.
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Affiliation(s)
- Yanjun Qu
- Department of Oncology, the Second Hospital of Dalian Medical University
| | - Na Gao
- Department of Obstetrics and Gynecology, the First Hospital of Dalian Medical University, Dalian, Liaoning, P.R. China
| | - Tao Wu
- Department of Oncology, the Second Hospital of Dalian Medical University
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19
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Li M, Du M, Cong H, Gu Y, Fang Y, Li J, Gan Y, Tu H, Gu J, Xia Q. Characterization of hepatitis B virus DNA integration patterns in intrahepatic cholangiocarcinoma. Hepatol Res 2021; 51:102-115. [PMID: 33037855 DOI: 10.1111/hepr.13580] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 09/19/2020] [Accepted: 09/24/2020] [Indexed: 12/13/2022]
Abstract
AIM Hepatitis B virus (HBV) integration is one of the mechanisms contributing to hepatocellular carcinoma (HCC) development. However, the status of HBV integration in intrahepatic cholangiocarcinoma (ICC) is poorly understood. This study aims to characterize the viral integration in HBV-related ICC. METHODS The presence of HBV S and C gene in ICCs and the paratumor tissue was determined by polymerase chain reaction direct sequencing. Hepatitis B virus integration was detected by a high-throughput capture sequencing method. The expression analysis of the genes targeted by HBV in ICC was undertaken in The Cancer Genome Atlas dataset. RESULTS Hepatitis B virus S and/or C gene fragments were detected in 71.43% (10/14) ICCs and 57.14% (8/14) paratumor tissues. Using the high-throughput capture sequencing approach, 139 and 183 HBV integration breakpoints were identified from seven ICC and seven paired paratumor tissues, respectively. Seven genes (TERT, CEACAM20, SPATA18, TRERF1, ZNF23, LINC01449, and LINC00486) were recurrently targeted by HBV-DNA in different ICC tissues or different cell populations of the same tissue. TERT, which is the most preferential HBV target gene in HCC, was found to be repeatedly interrupted by HBV-DNA in three different ICC tissues. Based on The Cancer Genome Atlas dataset, TERT, as well as three other HBV recurrently targeted genes (SPATA18, TRERF1, and ZNF23), showed differential expression levels between ICC and para-ICC tissues. CONCLUSIONS Taken together, HBV integration is a common event in HBV-related ICC. The HBV recurrent integration genes identified from this study, such as TERT, provide new clues for further research on the causative link between HBV infection and ICC.
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Affiliation(s)
- Mengge Li
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Min Du
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hui Cong
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuanyuan Gu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of Emergency, Nanjing First Hospital, Nanjing, China
| | - Yuan Fang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Organ Transplantation Center, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Jin Li
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yu Gan
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hong Tu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jinyang Gu
- Department of Transplantation, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qiang Xia
- Department of Liver Surgery, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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20
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Involvement of Actin and Actin-Binding Proteins in Carcinogenesis. Cells 2020; 9:cells9102245. [PMID: 33036298 PMCID: PMC7600575 DOI: 10.3390/cells9102245] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 09/18/2020] [Accepted: 10/05/2020] [Indexed: 12/13/2022] Open
Abstract
The actin cytoskeleton plays a crucial role in many cellular processes while its reorganization is important in maintaining cell homeostasis. However, in the case of cancer cells, actin and ABPs (actin-binding proteins) are involved in all stages of carcinogenesis. Literature has reported that ABPs such as SATB1 (special AT-rich binding protein 1), WASP (Wiskott-Aldrich syndrome protein), nesprin, and villin take part in the initial step of carcinogenesis by regulating oncogene expression. Additionally, changes in actin localization promote cell proliferation by inhibiting apoptosis (SATB1). In turn, migration and invasion of cancer cells are based on the formation of actin-rich protrusions (Arp2/3 complex, filamin A, fascin, α-actinin, and cofilin). Importantly, more and more scientists suggest that microfilaments together with the associated proteins mediate tumor vascularization. Hence, the presented article aims to summarize literature reports in the context of the potential role of actin and ABPs in all steps of carcinogenesis.
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21
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Bacolod MD, Mirza AH, Huang J, Giardina SF, Feinberg PB, Soper SA, Barany F. Application of Multiplex Bisulfite PCR-Ligase Detection Reaction-Real-Time Quantitative PCR Assay in Interrogating Bioinformatically Identified, Blood-Based Methylation Markers for Colorectal Cancer. J Mol Diagn 2020; 22:885-900. [PMID: 32407802 DOI: 10.1016/j.jmoldx.2020.03.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 02/14/2020] [Accepted: 03/31/2020] [Indexed: 02/07/2023] Open
Abstract
The analysis of CpG methylation in circulating tumor DNA fragments has emerged as a promising approach for the noninvasive early detection of solid tumors, including colorectal cancer (CRC). The most commonly employed assay involves bisulfite conversion of circulating tumor DNA, followed by targeted PCR, then real-time quantitative PCR (alias methylation-specific PCR). This report demonstrates the ability of a multiplex bisulfite PCR-ligase detection reaction-real-time quantitative PCR assay to detect seven methylated CpG markers (CRC or colon specific), in both simulated (approximately 30 copies of fragmented CRC cell line DNA mixed with approximately 3000 copies of fragmented peripheral blood DNA) and CRC patient-derived cell-free DNAs. This scalable assay is designed for multiplexing and incorporates steps for improved sensitivity and specificity, including the enrichment of methylated CpG fragments, ligase detection reaction, the incorporation of ribose bases in primers, and use of uracil DNA glycosylase. Six of the seven CpG markers (located in promoter regions of PPP1R16B, KCNA3, CLIP4, GDF6, SEPT9, and GSG1L) were identified through integrated analyses of genome-wide methylation data sets for 31 different types of cancer. These markers were mapped to CpG sites at the promoter region of VIM; VIM and SEPT9 are established epigenetic markers of CRC. Additional bioinformatics analyses show that the methylation at these CpG sites negatively correlates with the transcription of their corresponding genes.
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Affiliation(s)
- Manny D Bacolod
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York
| | - Aashiq H Mirza
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York
| | - Jianmin Huang
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York
| | - Sarah F Giardina
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York
| | - Philip B Feinberg
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York
| | - Steven A Soper
- Department of Mechanical Engineering, The University of Kansas, Lawrence, Kansas
| | - Francis Barany
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York.
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22
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Sun J, Xie T, Jamal M, Tu Z, Li X, Wu Y, Li J, Zhang Q, Huang X. CLEC3B as a potential diagnostic and prognostic biomarker in lung cancer and association with the immune microenvironment. Cancer Cell Int 2020; 20:106. [PMID: 32265595 PMCID: PMC7110733 DOI: 10.1186/s12935-020-01183-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 03/23/2020] [Indexed: 02/06/2023] Open
Abstract
Background Lung cancer is the leading cause of cancer-related mortality globally. Discovering effective biomarkers for early diagnosis and prognosis is important to reduce the mortality rate and ensure efficient therapy for lung cancer patients. C-type lectin domain family 3 member B (CLEC3B) has been reported in various cancers, but its correlation with lung cancer remains elusive. Methods The GEO, TCGA and Oncomine databases were analyzed to examine the expression of CLEC3B in lung cancer. The CLEC3B mRNA levels in 15 patient tissue samples were detected by real-time PCR and the CLEC3B protein levels in 34 patient tissue samples were detected by immunohistochemistry. A Chi-square test was performed to analyze the correlation of CLEC3B expression and clinicopathological factors. The diagnostic value of CLEC3B was revealed by receiver operating characteristic (ROC) curves. Univariate and multivariate Cox proportional hazards regression models and Kaplan–Meier plots were used to evaluate the prognostic value of CLEC3B in lung cancer. The TIMER database was used to evaluate the correlation of CLEC3B and immune infiltration. Gene set enrichment analysis revealed tumor‐associated biological processes related to CLEC3B. Results CLEC3B is significantly downregulated in lung cancer patients compared with nontumor controls according to database analysis and patient tissue sample detection (p < 0.001). Specifically, CLEC3B is significantly downregulated in stage IA lung cancer patients (p < 0.001) and has a high diagnostic accuracy (area under the receiver operating characteristic curve > 0.9). Moreover, low expression of CLEC3B is related to poor progression-free survival (HR = 0.60, 95% CI 0.49–0.74, p = 8.3e−07) and overall survival (HR = 0.66, 95% CI 0.58–0.75, p = 2.1e−10), indicating it as a risk factor for lung cancer. Multivariate analysis value showed that low expression of CLEC3B may be an independent risk factor for disease‐free survival in lung cancer patients (HR = 0.655, 95% CI 0.430–0.996, Cox p = 0.048). In addition, we also investigated the potential role of CLEC3B in tumor-immune interactions and found that CLEC3B might be associated with the immune infiltration and immune activation of lung cancer, especially in squamous cell carcinoma. Conclusions Our findings indicate that CLEC3B expression is downregulated in lung cancer and reveal the diagnostic and prognostic potential of CLEC3B in lung cancer and its potential as an immune-related therapeutic target in lung cancer.
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Affiliation(s)
- Jiaxing Sun
- 1Department of Blood Transfusion, Zhongnan Hospital of Wuhan University, Wuhan, China.,2Department of Immunology, School of Basic Medical Science, Wuhan University, Wuhan, China
| | - Tian Xie
- 1Department of Blood Transfusion, Zhongnan Hospital of Wuhan University, Wuhan, China.,2Department of Immunology, School of Basic Medical Science, Wuhan University, Wuhan, China
| | - Muhammad Jamal
- 2Department of Immunology, School of Basic Medical Science, Wuhan University, Wuhan, China
| | - Zhenbo Tu
- 2Department of Immunology, School of Basic Medical Science, Wuhan University, Wuhan, China
| | - Xinran Li
- 3School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Yingjie Wu
- 4Department of Pathology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jingyuan Li
- 2Department of Immunology, School of Basic Medical Science, Wuhan University, Wuhan, China
| | - Qiuping Zhang
- 2Department of Immunology, School of Basic Medical Science, Wuhan University, Wuhan, China
| | - Xiaoxing Huang
- 1Department of Blood Transfusion, Zhongnan Hospital of Wuhan University, Wuhan, China
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23
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Caiado H, Conceição N, Tiago D, Marreiros A, Vicente S, Enriquez JL, Vaz AM, Antunes A, Guerreiro H, Caldeira P, Cancela ML. Evaluation of MGP gene expression in colorectal cancer. Gene 2020; 723:144120. [PMID: 31589964 DOI: 10.1016/j.gene.2019.144120] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 09/10/2019] [Accepted: 09/11/2019] [Indexed: 01/14/2023]
Abstract
PURPOSE Matrix Gla protein (MGP) is a vitamin K-dependent, γ-carboxylated protein that was initially found to be a physiological inhibitor of ectopic calcifications affecting mainly cartilage and the vascular system. Mutations in the MGP gene were found to be responsible for a human pathology, the Keutel syndrome, characterized by abnormal calcifications in cartilage, lungs, brain and vascular system. MGP was recently implicated in tumorigenic processes such as angiogenesis and shown to be abnormally regulated in several tumors, including cervical, ovarian, urogenital and breast. This fact has triggered our interest in analyzing the expression of MGP and of its regulator, the transcription factor runt related transcription factor 2 (RUNX2), in colorectal cancer (CRC). METHODS MGP and RUNX2 expression were analyzed in cancer and non-tumor biopsies samples from 33 CRC patients and 9 healthy controls by RT-qPCR. Consequently, statistical analyses were performed to evaluate the clinical-pathological significance of MGP and RUNX2 in CRC. MGP protein was also detected by immunohistochemical analysis. RESULTS Showed an overall overexpression of MGP in the tumor mucosa of patients at mRNA level when compared to adjacent normal mucosa and healthy control tissues. In addition, analysis of the expression of RUNX2 mRNA demonstrated an overexpression in CRC tissue samples and a positive correlation with MGP expression (Pearson correlation coefficient 0.636; p ≤ 0.01) in tumor mucosa. However correlations between MGP gene expression and clinical-pathological characteristics, such as gender, age and pathology classification did not provide relevant information that may shed light towards the differences of MGP expression observed between normal and malignant tissue. CONCLUSIONS We were able to associate the high levels of MGP mRNA expression with a worse prognosis and survival rate lower than five years. These results contributed to improve our understanding of the molecular mechanism underlying MGP deregulation in cancer.
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Affiliation(s)
- Helena Caiado
- ProRegeM PhD Programme in Mechanisms of Disease and Regenerative Medicine, University of Algarve, Faro 8005-139, Portugal; Centre of Marine Sciences (CCMAR), University of Algarve, Faro 8005-139, Portugal; Department of Biomedical Sciences and Medicine, University of Algarve, Faro 8005-139, Portugal
| | - Natércia Conceição
- Centre of Marine Sciences (CCMAR), University of Algarve, Faro 8005-139, Portugal; Department of Biomedical Sciences and Medicine, University of Algarve, Faro 8005-139, Portugal; Algarve Biomedical Center, University of Algarve, Faro 8005-139, Portugal.
| | - Daniel Tiago
- Centre of Marine Sciences (CCMAR), University of Algarve, Faro 8005-139, Portugal
| | - Ana Marreiros
- Department of Biomedical Sciences and Medicine, University of Algarve, Faro 8005-139, Portugal; Algarve Biomedical Center, University of Algarve, Faro 8005-139, Portugal
| | - Susana Vicente
- Pathology Department, University Hospital of Algarve, Faro 8000-386, Portugal
| | - Jose Luis Enriquez
- Pathology Department, University Hospital of Algarve, Faro 8000-386, Portugal
| | - Ana Margarida Vaz
- Gastroenterology Department, University Hospital of Algarve, Faro 8000-386, Portugal
| | - Artur Antunes
- Gastroenterology Department, University Hospital of Algarve, Faro 8000-386, Portugal
| | - Horácio Guerreiro
- Gastroenterology Department, University Hospital of Algarve, Faro 8000-386, Portugal
| | - Paulo Caldeira
- Department of Biomedical Sciences and Medicine, University of Algarve, Faro 8005-139, Portugal; Gastroenterology Department, University Hospital of Algarve, Faro 8000-386, Portugal
| | - M Leonor Cancela
- Centre of Marine Sciences (CCMAR), University of Algarve, Faro 8005-139, Portugal; Department of Biomedical Sciences and Medicine, University of Algarve, Faro 8005-139, Portugal; Algarve Biomedical Center, University of Algarve, Faro 8005-139, Portugal; Centre for Biomedical Research, University of Algarve, Faro 8005-139, Portugal.
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Liu X, Fu J, Bi H, Ge A, Xia T, Liu Y, Sun H, Li D, Zhao Y. DNA methylation of SFRP1, SFRP2, and WIF1 and prognosis of postoperative colorectal cancer patients. BMC Cancer 2019; 19:1212. [PMID: 31830937 PMCID: PMC6909551 DOI: 10.1186/s12885-019-6436-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 12/05/2019] [Indexed: 12/24/2022] Open
Abstract
Background As biomarkers, DNA methylation is used to detect colorectal cancer (CRC) and make assessment of CRC prognosis. The published findings showed the association between the methylation of SFRP1, SFRP2, and WIF1, located in the Wnt signaling pathway, and the prognosis of CRC were not consistent. Our study aimed to explore the potential possibility of SFRP1, SFRP2, and WIF1 concomitant promoter methylation as prognostic biomarkers of postoperative CRC patients. Methods As a total of 307 sporadic postoperative CRC patients were followed up, we detected SFRP1, SFRP2, and WIF1 methylation obtained from tumor tissues and adjacent non-tumor tissues respectively on the basis of methylation-sensitive high resolution melting analysis. Univariate and multivariate Cox regressions were carried out so as to assess the potential possibility of SFRP1, SFRP2, and WIF1 promoter methylation as predictors of prognosis. Confounders in our study were controlled by Propensity Score (PS) analysis. Results The SFRP1, SFRP2, and WIF1 methylation levels in tumor tissues were significantly higher than that in adjacent non-tumor tissues (P < 0.001). SFRP2 hypermethylation was significantly associated with a favorable clinical outcome at the hazard ratio (HR) of 0.343 [95% confidence intervals (CI): 0.164–0.718, P = 0.005] and 0.410 (95% CI: 0.200–0.842, P = 0.015) in multivariate Cox regression and PS analysis, respectively. Co-hypermethylation of SFRP1 and SFRP2 was significantly associated with a favorable clinical outcome at the HR of 0.333 (95% CI: 0.159–0.694, P = 0.003) and 0.398 (95% CI: 0.192–0.821, P = 0.013) in multivariate Cox regression and PS analysis, respectively. Co-hypermethylation of SFRP1, SFRP2 and WIF1 was significantly associated with a favorable clinical outcome at the HR of 0.326 (95% CI: 0.117–0.908, P = 0.032) and 0.401 (95% CI: 0.146–1.106, P = 0.077) in multivariate Cox regression and PS analysis, respectively. Conclusions SFRP1, SFRP2, and WIF1 were frequently hypermethylated in CRC tumor tissues. It was apparent that the promoter hypermethylation of SFRP2 and co-hypermethylation of SFRP1 and SFRP2 might be considered as independent prognostic predictors for survival advantage of postoperative CRC patients.
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Affiliation(s)
- Xinyan Liu
- Department of Epidemiology, School of Public Health, Harbin Medical University, 157 Baojian Street, Nangang District, Harbin, 150086, Heilongjiang Province, People's Republic of China
| | - Jinming Fu
- Department of Epidemiology, School of Public Health, Harbin Medical University, 157 Baojian Street, Nangang District, Harbin, 150086, Heilongjiang Province, People's Republic of China
| | - Haoran Bi
- Department of Epidemiology, School of Public Health, Harbin Medical University, 157 Baojian Street, Nangang District, Harbin, 150086, Heilongjiang Province, People's Republic of China
| | - Anqi Ge
- Department of Epidemiology, School of Public Health, Harbin Medical University, 157 Baojian Street, Nangang District, Harbin, 150086, Heilongjiang Province, People's Republic of China
| | - Tingting Xia
- Department of Epidemiology, School of Public Health, Harbin Medical University, 157 Baojian Street, Nangang District, Harbin, 150086, Heilongjiang Province, People's Republic of China
| | - Yupeng Liu
- Department of Epidemiology, School of Public Health, Harbin Medical University, 157 Baojian Street, Nangang District, Harbin, 150086, Heilongjiang Province, People's Republic of China
| | - Hongru Sun
- Department of Epidemiology, School of Public Health, Harbin Medical University, 157 Baojian Street, Nangang District, Harbin, 150086, Heilongjiang Province, People's Republic of China
| | - Dapeng Li
- Department of Epidemiology, School of Public Health, Harbin Medical University, 157 Baojian Street, Nangang District, Harbin, 150086, Heilongjiang Province, People's Republic of China
| | - Yashuang Zhao
- Department of Epidemiology, School of Public Health, Harbin Medical University, 157 Baojian Street, Nangang District, Harbin, 150086, Heilongjiang Province, People's Republic of China.
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25
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Zhu T, Gao Y, Wang J, Li X, Shang S, Wang Y, Guo S, Zhou H, Liu H, Sun D, Chen H, Wang L, Ning S. CancerClock: A DNA Methylation Age Predictor to Identify and Characterize Aging Clock in Pan-Cancer. Front Bioeng Biotechnol 2019; 7:388. [PMID: 31867319 PMCID: PMC6905170 DOI: 10.3389/fbioe.2019.00388] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 11/18/2019] [Indexed: 01/12/2023] Open
Abstract
Many biological indicators related to chronological age have been proposed. Recent studies found that epigenetic clock or DNA methylation age is highly correlated with chronological age. In particular, a significant difference between DNA methylation age (m-age) and chronological age was observed in cancers. However, the prediction and characterization of m-age in pan-cancer remains an explored area. In this study, 1,631 age-related methylation sites in normal tissues were discovered and analyzed. A comprehensive computational model named CancerClock was constructed to predict the m-age for normal samples based on methylation levels of the extracted methylation sites. LASSO linear regression model was used to screen and train the CancerClock model in normal tissues. The accuracy of CancerClock has proved to be 81%, and the correlation value between chronological age and m-age was 0.939 (P < 0.01). Next, CancerClock was used to evaluate the difference between m-age and chronological age for 33 cancer types from TCGA. There were significant differences between predicted m-age and chronological age in large number of cancer samples. These cancer samples were defined as “age-related cancer samples” and they have some differential methylation sites. The differences between predicted m-age and chronological age may contribute to cancer development. Some of these differential methylation sites were associated with cancer survival. CancerClock provided assistance in estimating the m-age in normal and cancer samples. The changes between m-age and chronological age may improve the diagnosis and prognosis of cancers.
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Affiliation(s)
- Tongtong Zhu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yue Gao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Junwei Wang
- Department of Respiratory Medicine, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xin Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Shipeng Shang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yanxia Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Shuang Guo
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Hanxiao Zhou
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Hongjia Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Dailin Sun
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Hong Chen
- Department of Respiratory Medicine, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Li Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Shangwei Ning
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
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Usefulness of bevacizumab-induced hypertension in patients with metastatic colorectal cancer: an updated meta-analysis. Aging (Albany NY) 2019; 10:1424-1441. [PMID: 29969436 PMCID: PMC6046235 DOI: 10.18632/aging.101478] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 06/10/2018] [Indexed: 12/17/2022]
Abstract
We tested the hypothesis that bevacizumab-induced hypertension may be a useful predictor for objective response rate, progression-free and overall survival in patients with metastatic colorectal cancer via a comprehensive meta-analysis. Search process, article selection and data extraction were independently performed by two investigators. Statistical analyses were conducted using the STATA/SE software. Fourteen independent studies and 2292 study subjects were synthesized. Overall relative risk of objective response rate for bevacizumab-induced hypertension was 2.03 (95% confidence interval [CI]: 1.18-3.48, p=0.01), with significant heterogeneity and publication bias, whereas unbiased estimate was nonsignificant after considering potentially missing studies. Overall hazard ratio for progression-free survival was 0.58 (95% CI: 0.43-0.77, p<0.001), with significant heterogeneity and publication bias, and unbiased estimate was significant (hazard ratio: 0.52, 95% CI: 0.41-0.66, p<0.001). Overall hazard ratio for overall survival was 0.51 (95% CI: 0.39-0.65, p<0.001), and this estimate was not likely confounded by heterogeneity or publication bias. Subgroup and meta-regression analyses suggested that hypertension grade of controls, sample size, age and gender were possible causes of heterogeneity. Taken together, our findings indicate that bevacizumab-induced hypertension can predict progress-free survival and overall survival in patients with metastatic colorectal cancer, whereas its prediction for objective response rate was nonsignificant.
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27
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Song Y, Pan Y, Liu J. The relevance between the immune response-related gene module and clinical traits in head and neck squamous cell carcinoma. Cancer Manag Res 2019; 11:7455-7472. [PMID: 31496804 PMCID: PMC6689548 DOI: 10.2147/cmar.s201177] [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: 01/13/2019] [Accepted: 07/17/2019] [Indexed: 02/05/2023] Open
Abstract
Purpose Head and neck squamous cell carcinoma (HNSCC) is the sixth most prevalent cancer in the world, accounting for more than 90% of head and neck malignant tumors. However, its molecular mechanism is largely unknown. To help elucidate the potential mechanism of HNSCC tumorigenesis, we investigated the gene interaction patterns associated with tumorigenesis. Methods Weighted gene co-expression network analysis (WGCNA) can help us to predict the intrinsic relationship or correlation between gene expression. Additionally, we further explored the combination of clinical information and module construction. Results Sixteen modules were constructed, among which the key module most closely associated with clinical information was identified. By analyzing the genes in this module, we found that the latter may be related to the immune response, inflammatory response and formation of the tumor microenvironment. Sixteen hub genes were identified-ARHGAP9, SASH3, CORO1A, ITGAL, PPP1R16B, TBC1D10C, IL10RA, ITK, AKNA, PRKCB, TRAF3IP3, GIMAP4, CCR7, P2RY8, GIMAP7, and SP140. We further validated these genes at the transcriptional and translation levels. Conclusion The innovative use of a weighted network to analyze HNSCC samples provides new insights into the molecular mechanism and prognosis of HNSCC. Additionally, the hub genes we identified can be used as biomarkers and therapeutic targets of HNSCC, laying the foundation for the accurate diagnosis and treatment of HNSCC in clinical and research in the future.
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Affiliation(s)
- Yidan Song
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, People's Republic of China
| | - Yihua Pan
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, People's Republic of China
| | - Jun Liu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, People's Republic of China
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28
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Li C, Gao W, Gao Y, Yu C, Lv J, Lv R, Duan J, Sun Y, Guo X, Cao W, Li L. Age prediction of children and adolescents aged 6-17 years: an epigenome-wide analysis of DNA methylation. Aging (Albany NY) 2019; 10:1015-1026. [PMID: 29754148 PMCID: PMC5990383 DOI: 10.18632/aging.101445] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 05/08/2018] [Indexed: 02/06/2023]
Abstract
The DNA methylation age, a good reflection of human aging process, has been used to predict chronological age of adults and newborns. However, the prediction model for children and adolescents was absent. In this study, we aimed to generate a prediction model of chronological age for children and adolescents aged 6-17 years by using age-specific DNA methylation patterns from 180 Chinese twin individuals. We identified 6,350 age-related CpGs from the epigenome-wide association analysis (N=179). 116 known age-related sites in children were confirmed. 83 novel CpGs were selected as predictors from all age-related loci by elastic net regression and they could accurately predict the chronological age of the pediatric population, with a correlation of 0.99 and the error of 0.23 years in the training dataset (N=90). The predictive accuracy in the testing dataset (N=89) was high (correlation=0.93, error=0.62 years). Among the 83 predictors, 49 sites were novel probes not existing on the Illumina 450K BeadChip. The top two predictors of age were on the PRKCB and REG4 genes, which are associated with diabetes and cancer, respectively. Our results suggest that the chronological age can be accurately predicted among children and adolescents aged 6-17 years by 83 newly identified CpG sites.
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Affiliation(s)
- Chunxiao Li
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing 100191, China
| | - Wenjing Gao
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing 100191, China
| | - Ying Gao
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing 100191, China
| | - Canqing Yu
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing 100191, China
| | - Jun Lv
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing 100191, China
| | - Ruoran Lv
- Beijing Center for Disease Control and Prevention, Beijing 100013, China
| | - Jiali Duan
- Beijing Center for Disease Control and Prevention, Beijing 100013, China
| | - Ying Sun
- Beijing Center for Disease Control and Prevention, Beijing 100013, China
| | - Xianghui Guo
- Chaoyang District Center for Disease Control and Prevention, Beijing 100021, China
| | - Weihua Cao
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing 100191, China
| | - Liming Li
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing 100191, China
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Berral-Gonzalez A, Riffo-Campos AL, Ayala G. OMICfpp: a fuzzy approach for paired RNA-Seq counts. BMC Genomics 2019; 20:259. [PMID: 30940089 PMCID: PMC6444640 DOI: 10.1186/s12864-019-5496-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 01/29/2019] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND RNA sequencing is a widely used technology for differential expression analysis. However, the RNA-Seq do not provide accurate absolute measurements and the results can be different for each pipeline used. The major problem in statistical analysis of RNA-Seq and in the omics data in general, is the small sample size with respect to the large number of variables. In addition, experimental design must be taken into account and few tools consider it. RESULTS We propose OMICfpp, a method for the statistical analysis of RNA-Seq paired design data. First, we obtain a p-value for each case-control pair using a binomial test. These p-values are aggregated using an ordered weighted average (OWA) with a given orness previously chosen. The aggregated p-value from the original data is compared with the aggregated p-value obtained using the same method applied to random pairs. These new pairs are generated using between-pairs and complete randomization distributions. This randomization p-value is used as a raw p-value to test the differential expression of each gene. The OMICfpp method is evaluated using public data sets of 68 sample pairs from patients with colorectal cancer. We validate our results through bibliographic search of the reported genes and using simulated data set. Furthermore, we compared our results with those obtained by the methods edgeR and DESeq2 for paired samples. Finally, we propose new target genes to validate these as gene expression signatures in colorectal cancer. OMICfpp is available at http://www.uv.es/ayala/software/OMICfpp_0.2.tar.gz . CONCLUSIONS Our study shows that OMICfpp is an accurate method for differential expression analysis in RNA-Seq data with paired design. In addition, we propose the use of randomized p-values pattern graphic as a powerful and robust method to select the target genes for experimental validation.
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Affiliation(s)
- Alberto Berral-Gonzalez
- Grupo de Investigación Bioinformática y Genómica Funcional. Laboratorio 19. Centro de Investigación del Cáncer (CiC-IBMCC, Universidad de Salamanca-CSIC, Campus Universitario Miguel de Unamuno s/n, Salamanca, 37007 Spain
| | - Angela L. Riffo-Campos
- Universidad de La Frontera. Centro De Excelencia de Modelación y Computación Científica, C/ Montevideo 740, Temuco, Chile
| | - Guillermo Ayala
- Universidad de Valencia. Departamento de Estadística e Investigación Operativa, Avda. Vicent Andrés Estellés, 1, Burjasot, 46100 Spain
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Deng W, Lu YF. Methylation of tumor suppressor genes and risk factors of colorectal cancer. Shijie Huaren Xiaohua Zazhi 2018; 26:2088-2095. [DOI: 10.11569/wcjd.v26.i36.2088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Although the diagnostic methods and treatment options are continuously optimized, the incidence and mortality of colorectal cancer (CRC) are still rising. Therefore, "preventive treatment of disease" is the key to solving this problem. In recent years, hypermethylation of promoter CpG islands (CGIs) in tumor suppressor genes has been a hot research topic because it is reversible and early events in the development of CRC, and affects drug resistance, disease treatment, and patient prognosis. CRC risk factors such as poor dietary choice, lack of physical activity, excessive drinking, and unhealthy weight can regulate promoter CGI hypermethylation, which will help develop new methylation-related cancer prevention strategies. This article mainly introduces the significance and regulatory mechanism of methylation of tumor suppressor genes and its relationship with risk factors in CRC.
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Affiliation(s)
- Wei Deng
- Department of Gastroenterology, the Affiliated Hospital of Qinghai University, Xining 810000, Qinghai Province, China
| | - Yong-Fu Lu
- Department of Gastroenterology, the Affiliated Hospital of Qinghai University, Xining 810000, Qinghai Province, China
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31
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Duan B, Bai J, Qiu J, Wang J, Tong C, Wang X, Miao J, Li Z, Li W, Yang J, Huang C. Histone-lysine N-methyltransferase SETD7 is a potential serum biomarker for colorectal cancer patients. EBioMedicine 2018; 37:134-143. [PMID: 30361067 PMCID: PMC6284455 DOI: 10.1016/j.ebiom.2018.10.036] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 10/04/2018] [Accepted: 10/11/2018] [Indexed: 01/14/2023] Open
Abstract
Background There is an urgent need for the identification of new, clinically useful biomarkers of CRC to enhance diagnostic and prognostic capabilities. Methods We performed proteomic profiling on serum samples from paired pre- and post-operative CRC patients, colorectal polyps patients and healthy controls using an approach combining magnetic bead-based weak cation exchange and matrix-assisted laser desorption ionization-time of flight mass spectrometry. We next performed liquid chromatography-electrospray ionization-tandem mass spectrometry to identify the proteins and selected potential biomarker based on bioinformatics analysis of the TCGA and GEO dataset. We examined SETD7 expression in serum and tissue samples by ELISA and immunohistochemistry respectively and explored the biological function of SETD7 in vitro. Findings 85 differentially expressed peptides were identified. Five peptides showing the most significant changes in abundance across paired pre- and post-operation CRC patients, colorectal polyps patients and healthy controls were identified as peptide regions of FGA, MUC5AC and SETD7. Bioinformatics analysis suggested that the up-regulation of SETD7 in CRC is relatively specific. Validation studies showed that SETD7 expression increased from healthy controls to those with colorectal polyps and finally CRC patients, and decreased after surgery. The sensitivity and specificity of SETD7 were 92.17% and 81.08%, with a high diagnostic value (AUC = 0.9477). In addition, SETD7 expression was significantly correlated with tumor stage and microsatellite instability. Knockdown of SETD7 inhibited cancer cell proliferation, induced G1/S cell cycle arrest and increased apoptosis. Interpretation Our data indicate that SETD7 could serve as a potential diagnostic and prognostic biomarker for CRC.
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Affiliation(s)
- Baojun Duan
- Key Laboratory of Environment and Disease-Related Gene, Ministry of Education, Department of Cell Biology and Genetics, School of Basic Medical sciences, Xi'an Jiaotong University, Health Science Center, Shaanxi, Xi'an 710061, China; Department of Medical Oncology of Shaanxi Provincial People's Hospital, Shaanxi, Xi'an 710068, China
| | - Jun Bai
- Department of Medical Oncology of Shaanxi Provincial People's Hospital, Shaanxi, Xi'an 710068, China
| | - Jian Qiu
- Department of General Surgery of Shaanxi Provincial People's Hospital, Shaanxi, Xi'an 710068, China
| | - Jianhua Wang
- Department of General Surgery of Shaanxi Provincial People's Hospital, Shaanxi, Xi'an 710068, China
| | - Cong Tong
- Department of General Surgery of Shaanxi Provincial People's Hospital, Shaanxi, Xi'an 710068, China
| | - Xiaofei Wang
- Key Laboratory of Environment and Disease-Related Gene, Ministry of Education, Department of Cell Biology and Genetics, School of Basic Medical sciences, Xi'an Jiaotong University, Health Science Center, Shaanxi, Xi'an 710061, China
| | - Jiyu Miao
- Key Laboratory of Environment and Disease-Related Gene, Ministry of Education, Department of Cell Biology and Genetics, School of Basic Medical sciences, Xi'an Jiaotong University, Health Science Center, Shaanxi, Xi'an 710061, China
| | - Zongfang Li
- National & Local Joint Engineering Research Center of Biodiagnostics and Biotherapy, the Second Affiliated Hospital of Xi'an Jiaotong University, Shaanxi, Xi'an 710004, China
| | - Wensheng Li
- Department of Pathology of Shaanxi Provincial People's Hospital, Shaanxi, Xi'an 710068, China
| | - Juan Yang
- Key Laboratory of Environment and Disease-Related Gene, Ministry of Education, Department of Cell Biology and Genetics, School of Basic Medical sciences, Xi'an Jiaotong University, Health Science Center, Shaanxi, Xi'an 710061, China.
| | - Chen Huang
- Key Laboratory of Environment and Disease-Related Gene, Ministry of Education, Department of Cell Biology and Genetics, School of Basic Medical sciences, Xi'an Jiaotong University, Health Science Center, Shaanxi, Xi'an 710061, China.
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Soda K. Polyamine Metabolism and Gene Methylation in Conjunction with One-Carbon Metabolism. Int J Mol Sci 2018; 19:E3106. [PMID: 30309036 PMCID: PMC6213949 DOI: 10.3390/ijms19103106] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 10/01/2018] [Accepted: 10/05/2018] [Indexed: 02/07/2023] Open
Abstract
Recent investigations have revealed that changes in DNA methylation status play an important role in aging-associated pathologies and lifespan. The methylation of DNA is regulated by DNA methyltransferases (DNMT1, DNMT3a, and DNMT3b) in the presence of S-adenosylmethionine (SAM), which serves as a methyl group donor. Increased availability of SAM enhances DNMT activity, while its metabolites, S-adenosyl-l-homocysteine (SAH) and decarboxylated S-adenosylmethionine (dcSAM), act to inhibit DNMT activity. SAH, which is converted from SAM by adding a methyl group to cytosine residues in DNA, is an intermediate precursor of homocysteine. dcSAM, converted from SAM by the enzymatic activity of adenosylmethionine decarboxylase, provides an aminopropyl group to synthesize the polyamines spermine and spermidine. Increased homocysteine levels are a significant risk factor for the development of a wide range of conditions, including cardiovascular diseases. However, successful homocysteine-lowering treatment by vitamins (B6, B12, and folate) failed to improve these conditions. Long-term increased polyamine intake elevated blood spermine levels and inhibited aging-associated pathologies in mice and humans. Spermine reversed changes (increased dcSAM, decreased DNMT activity, aberrant DNA methylation, and proinflammatory status) induced by the inhibition of ornithine decarboxylase. The relation between polyamine metabolism, one-carbon metabolism, DNA methylation, and the biological mechanism of spermine-induced lifespan extension is discussed.
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Affiliation(s)
- Kuniyasu Soda
- Cardiovascular Research Institute, Saitama Medical Center, Jichi Medical University, 1-847 Amanuma, Omiya, Saitama-city, Saitama Prefecture 330-8503, Japan.
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Luebeck GE, Hazelton WD, Curtius K, Maden SK, Yu M, Carter KT, Burke W, Lampe PD, Li CI, Ulrich CM, Newcomb PA, Westerhoff M, Kaz AM, Luo Y, Inadomi JM, Grady WM. Implications of Epigenetic Drift in Colorectal Neoplasia. Cancer Res 2018; 79:495-504. [PMID: 30291105 DOI: 10.1158/0008-5472.can-18-1682] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 08/15/2018] [Accepted: 09/25/2018] [Indexed: 12/11/2022]
Abstract
Many normal tissues undergo age-related drift in DNA methylation, providing a quantitative measure of tissue age. Here, we identify and validate 781 CpG islands (CGI) that undergo significant methylomic drift in 232 normal colorectal tissues and show that these CGI continue to drift in neoplasia while retaining significant correlations across samples. However, compared with normal colon, this drift advanced (∼3-4-fold) faster in neoplasia, consistent with increased cell proliferation during neoplastic progression. The observed drift patterns were broadly consistent with modeled adenoma-to-carcinoma sojourn time distributions from colorectal cancer incidence data. These results support the hypothesis that, beginning with the founder premalignant cell, cancer precursors frequently sojourn for decades before turning into cancer, implying that the founder cell typically arises early in life. At least 77% to 89% of the observed drift variance in distal and rectal tumors was explained by stochastic variability associated with neoplastic progression, whereas only 55% of the variance was explained for proximal tumors. However, gene-CGI pairs in the proximal colon that underwent drift were significantly and primarily negatively correlated with cancer gene expression, suggesting that methylomic drift participates in the clonal evolution of colorectal cancer. Methylomic drift advanced in colorectal neoplasia, consistent with extended sojourn time distributions, which accounts for a significant fraction of epigenetic heterogeneity in colorectal cancer. Importantly, these estimated long-duration premalignant sojourn times suggest that early dietary and lifestyle interventions may be more effective than later changes in reducing colorectal cancer incidence. SIGNIFICANCE: These findings present age-related methylomic drift in colorectal neoplasia as evidence that premalignant cells can persist for decades before becoming cancerous.See related commentary by Sapienza, p. 437.
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Affiliation(s)
- Georg E Luebeck
- Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington.
| | - William D Hazelton
- Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington.
| | - Kit Curtius
- Centre for Tumour Biology, Barts Cancer Institute, London, United Kingdom
| | - Sean K Maden
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Ming Yu
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Kelly T Carter
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Wynn Burke
- Division of Gastroenterology, Department of Medicine, University of Washington, Seattle, Washington
| | - Paul D Lampe
- Molecular Diagnostics, Public Health and Human Biology Divisions, Fred Hutchinson Cancer Research Center, Seattle, Washington.,School of Public Health and Community Medicine, University of Washington, Seattle, Washington
| | - Christopher I Li
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.,Epidemiology, School of Public Health, University of Washington, Seattle, Washington
| | - Cornelia M Ulrich
- Huntsman Cancer Institute and Department of Population Health Sciences, University of Utah, Salt Lake City, Utah
| | - Polly A Newcomb
- Epidemiology, School of Public Health, University of Washington, Seattle, Washington.,Cancer Prevention Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Maria Westerhoff
- Department of Pathology, University of Michigan, Ann Arbor, Michigan
| | - Andrew M Kaz
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.,Division of Gastroenterology, Department of Medicine, University of Washington, Seattle, Washington.,Gastroenterology Section, VA Puget Sound Health Care System, Seattle, Washington
| | - Yanxin Luo
- Department of Colorectal Surgery, the Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou China.,Gastrointestinal Institute, Sun Yat-Sen University, Guangzhou, China
| | - John M Inadomi
- Division of Gastroenterology, Department of Medicine, University of Washington, Seattle, Washington.,GI Cancer Prevention Program, Seattle Cancer Care Alliance, Seattle, Washington
| | - William M Grady
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.,Division of Gastroenterology, Department of Medicine, University of Washington, Seattle, Washington.,GI Cancer Prevention Program, Seattle Cancer Care Alliance, Seattle, Washington
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Aberrantly Expressed Genes and miRNAs in Slow Transit Constipation Based on RNA-Seq Analysis. BIOMED RESEARCH INTERNATIONAL 2018; 2018:2617432. [PMID: 30186855 PMCID: PMC6112260 DOI: 10.1155/2018/2617432] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 06/26/2018] [Accepted: 07/18/2018] [Indexed: 02/06/2023]
Abstract
Background This study aims to identify the key genes and miRNAs in slow transit constipation (STC). Methods MRNA and miRNA expression profiling were obtained. Differentially expressed genes (DEGs) and miRNAs were identified followed by the regulatory network construction. Functional annotation analysis and protein-protein interaction (PPI) network were conducted. The electronic validation was performed. Results Hsa-miR-2116-3p, hsa-miR-3622a-5p, hsa-miR-424-5p, and hsa-miR-1273-3p covered most DEGs. HLA-DRB1, HLA-DRB5, C3, and ICAM were significantly involved in staphylococcus aureus infection. The PPI network generated several hub proteins including ZBTB16, FBN1, CCNF, and CDK1. Electronic validation of HLA-DRB1, PTGDR, MKI67, BIRC5, CCNF, and CDK1 was consistent with the RNA-sequencing analysis. Conclusion Our study might be helpful in understanding the pathology of STC at the molecular level.
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Nwanaji-Enwerem JC, Weisskopf MG, Baccarelli AA. Multi-tissue DNA methylation age: Molecular relationships and perspectives for advancing biomarker utility. Ageing Res Rev 2018; 45:15-23. [PMID: 29698722 PMCID: PMC6047923 DOI: 10.1016/j.arr.2018.04.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 03/29/2018] [Accepted: 04/18/2018] [Indexed: 12/31/2022]
Abstract
The multi-tissue DNA methylation estimator of chronological age (DNAm-age) has been associated with a wide range of exposures and health outcomes. Still, it is unclear how DNAm-age can have such broad relationships and how it can be best utilized as a biomarker. Understanding DNAm-age's molecular relationships is a promising approach to address this critical knowledge gap. In this review, we discuss the existing literature regarding DNAm-age's molecular relationships in six major categories: animal model systems, cancer processes, cellular aging processes, immune system processes, metabolic processes, and nucleic acid processes. We also present perspectives regarding the future of DNAm-age research, including the need to translate a greater number of ongoing research efforts to experimental and animal model systems.
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Affiliation(s)
- Jamaji C Nwanaji-Enwerem
- Department of Environmental Health, Harvard T.H. Chan School of Public Health and MD-PhD Program, Harvard Medical School, Boston, MA, USA.
| | - Marc G Weisskopf
- Department of Environmental Health and Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Andrea A Baccarelli
- Department of Environmental Health Sciences, Columbia Mailman School of Public Health, New York, NY, USA
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36
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Krasnov GS, Melnikova NV, Lakunina VA, Snezhkina AV, Kudryavtseva AV, Dmitriev AA. MethyMer: Design of combinations of specific primers for bisulfite sequencing of complete CpG islands. J Bioinform Comput Biol 2018; 16:1840004. [PMID: 29382254 DOI: 10.1142/s0219720018400048] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
We present MethyMer, a Python-based tool aimed at selecting primers for amplification of complete CpG islands. These regions are difficult in terms of selecting appropriate primers because of their low-complexity, high GC content. Moreover, bisulfite treatment, in fact, leads to the reduction of the 4-letter alphabet (ATGC) to 3-letter one (ATG, except for methylated cytosines), and this also reduces region complexity and increases mispriming potential. MethyMer has a flexible scoring system, which optimizes the balance between various characteristics such as nucleotide composition, thermodynamic features (melting temperature, dimers [Formula: see text]G, etc.), the presence of CpG sites and polyN tracts, and primer specificity, which is assessed with aligning primers to the bisulfite-treated genome using bowtie (up to three mismatches are allowed). Users are able to customize desired or limit ranges of various parameters as well as penalties for non-desired values. Moreover, MethyMer allows picking up the optimal combination of PCR primer pairs to perform the amplification of a large genomic locus, e.g. CpG island or other hard-to-study region, with minimal overlap of the individual amplicons. MethyMer incorporates ENCODE genome annotation records (promoter/enhancer/insulator), The Cancer Genome Atlas (TCGA) CpG methylation data derived with Illumina Infinium 450K microarrays, and records on correlations between TCGA RNA-Seq and CpG methylation data for 20 cancer types. These databases are included in the MethyMer release. Our tool is available at https://sourceforge.net/projects/methymer/ .
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Affiliation(s)
- George S Krasnov
- 1 Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Nataliya V Melnikova
- 1 Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Valentina A Lakunina
- 1 Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Anastasiya V Snezhkina
- 1 Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Anna V Kudryavtseva
- 1 Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Alexey A Dmitriev
- 1 Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia
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Silencing of CEMIP suppresses Wnt/β-catenin/Snail signaling transduction and inhibits EMT program of colorectal cancer cells. Acta Histochem 2018; 120:56-63. [PMID: 29173982 DOI: 10.1016/j.acthis.2017.11.002] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 11/10/2017] [Accepted: 11/13/2017] [Indexed: 12/20/2022]
Abstract
Cell migration inducing hyaluronan binding protein (CEMIP) is a hyaluronic acid binding protein, the abnormal elevation of which is suggested as a contributor in the carcinogenesis of colorectal cancer (CRC). Cancer cells lose their adhesive properties and acquire an enhanced mobility by undergoing epithelial-mesenchymal transition (EMT). This study is performed to investigate whether and how CEMIP orchestrates the EMT process of CRC cells. To avoid the unexpected off-target effects possibly caused by one single shRNA, two shRNAs targeting different mRNA regions of CEMIP gene were used to knock down the mRNA and protein expression of CEMIP. Our data showed that the proliferation, migration and invasion of two CRC cell lines, HCT116 and SW480 cells, were inhibited by CEMIP shRNA. We here defined EMT as the complete or partial loss of E-cadherin and zona occludens protein 1 (ZO-1) (epithelial markers) and the gain of Vimentin and N-cadherin (mesenchymal markers), and found that the EMT process was attenuated in CEMIP-silenced SW480 cells. Snail, a direct target of β-catenin/T cell factor complex, is known to activate the EMT program during cancer metastasis. CEMIP shRNA was further found to suppress the Wnt/β-catenin/Snail signaling transduction in CRC cells as manifested by the decreased nuclear β-catenin and Snail. Collectively, our work demonstrates that CEMIP contributes to metastatic phenotype of CRC cells in vitro.
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