Expression and DNA methylation levels of prolyl hydroxylases PHD1, PHD2, PHD3 and asparaginyl hydroxylase FIH in colorectal cancer

Cancer tissues have characteristic DNA methylation profiles compared with their corresponding normal tissues that can be utilized for cancer diagnosis with liquid biopsy. Using a genome-scale DNA methylation approach, we sought to identify a panel of DNA methylation markers specific for cell-free DNA (cfDNA) from patients with colorectal cancer (CRC). By comparing DNA methylomes between CRC and normal mucosal tissues or blood leukocytes, we identified eight cancer-specific methylated loci (ADGRB1, ANKRD13, FAM123A, GLI3, PCDHG, PPP1R16B, SLIT3, and TMEM90B) and developed a five-marker panel (FAM123A, GLI3, PPP1R16B, SLIT3, and TMEM90B) that detected CRC in liquid biopsies with a high sensitivity and specificity with a droplet digital MethyLight assay. In a set of cfDNA samples from CRC patients (n = 117) and healthy volunteers (n = 60), a panel of five markers on the platform of the droplet digital MethyLight assay detected stages I–III and stage IV CRCs with sensitivities of 45.9% and 95.7%, respectively, and a specificity of 95.0%. The number of detected markers was correlated with the cancer stage, perineural invasion, lymphatic emboli, and venous invasion. Our five-marker panel with the droplet digital MethyLight assay showed a high sensitivity and specificity for the detection of CRC with cfDNA samples from patients with metastatic CRC.

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Progressive alteration of DNA methylation of Alu, MGMT, MINT2, and TFPI2 genes in colonic mucosa during colorectal cancer development

Cancer Biomarkers ◽

10.3233/cbm-203259 ◽

2021 ◽

pp. 1-6

Author(s):

Ben Kang ◽

Hyun Seok Lee ◽

Seong Woo Jeon ◽

Soo Yeun Park ◽

Gyu Seog Choi ◽

...

Keyword(s):

Colorectal Cancer ◽

Dna Methylation ◽

Healthy Subjects ◽

Large Scale ◽

Methylation Status ◽

Clinical Information ◽

Field Cancerization ◽

Aberrant Methylation ◽

Clinical Value ◽

Mortality And Morbidity

BACKGROUND: Colorectal cancer (CRC) is one of the leading causes of mortality and morbidity in the world. It is characterized by different pathways of carcinogenesis and is a heterogeneous disease with diverse molecular landscapes that reflect histopathological and clinical information. Changes in the DNA methylation status of colon epithelial cells have been identified as critical components in CRC development and appear to be emerging biomarkers for the early detection and prognosis of CRC. OBJECTIVE: To explore the underlying disease mechanisms and identify more effective biomarkers of CRC. METHODS: We compared the levels and frequencies of DNA methylation in 11 genes (Alu, APC, DAPK, MGMT, MLH1, MINT1, MINT2, MINT3, p16, RGS6, and TFPI2) in colorectal cancer and its precursor adenomatous polyp with normal tissue of healthy subjects using pyrosequencing and then evaluated the clinical value of these genes. RESULTS: Aberrant methylation of Alu, MGMT, MINT2, and TFPI2 genes was progressively accumulated during the normal-adenoma-carcinoma progression. Additionally, CGI methylation occurred either as an adenoma-associated event for APC, MLH1, MINT1, MINT31, p16, and RGS6 or a tumor-associated event for DAPK. Moreover, relatively high levels and frequencies of DAPK, MGMT, and TFPI2 methylation were detected in the peritumoral nonmalignant mucosa of cancer patients in a field-cancerization manner, as compared to normal mucosa from healthy subjects. CONCLUSION: This study identified several biomarkers associated with the initiation and progression of CRC. As novel findings, they may have important clinical implications for CRC diagnostic and prognostic applications. Further large-scale studies are needed to confirm these findings.

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Genome-wide analysis identifies critical DNA methylations within NTRKs genes in colorectal cancer

Journal of Translational Medicine ◽

10.1186/s12967-021-02740-6 ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Zijian Chen ◽

Zenghong Huang ◽

Yanxin Luo ◽

Qi Zou ◽

Liangliang Bai ◽

...

Keyword(s):

Colorectal Cancer ◽

Dna Methylation ◽

Promoter Methylation ◽

Expression Profiles ◽

Methylation Status ◽

Gene Promoter ◽

Normal Mucosa ◽

Suppressor Gene ◽

Survival Outcome ◽

Prognostic Models

Abstract Background Neurotrophic tropomyosin receptor kinases (NTRKs) are a gene family function as oncogene or tumor suppressor gene in distinct cancers. We aimed to investigate the methylation and expression profiles and prognostic value of NTRKs gene in colorectal cancer (CRC). Methods An analysis of DNA methylation and expression profiles in CRC patients was performed to explore the critical methylations within NTRKs genes. The methylation marker was validated in a retrospectively collected cohort of 229 CRC patients and tested in other tumor types from TCGA. DNA methylation status was determined by quantitative methylation-specific PCR (QMSP). Results The profiles in six CRC cohorts showed that NTRKs gene promoter was more frequently methylated in CRC compared to normal mucosa, which was associated with suppressed gene expression. We identified a specific methylated region within NTRK3 promoter targeted by cg27034819 and cg11525479 that best predicted survival outcome in CRC. NTRK3 promoter methylation showed independently predictive value for survival outcome in the validation cohort (P = 0.004, HR 2.688, 95% CI [1.355, 5.333]). Based on this, a nomogram predicting survival outcome was developed with a C-index of 0.705. Furthermore, the addition of NTRK3 promoter methylation improved the performance of currently-used prognostic model (AIC: 516.49 vs 513.91; LR: 39.06 vs 43.64, P = 0.032). Finally, NTRK3 promoter methylation also predicted survival in other tumors, including pancreatic cancer, glioblastoma and stomach adenocarcinoma. Conclusions This study highlights the essential value of NTRK3 methylation in prognostic evaluation and the potential to improve current prognostic models in CRC and other tumors.

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The importance of stool DNA methylation in colorectal cancer diagnosis: A meta-analysis

PLoS ONE ◽

10.1371/journal.pone.0200735 ◽

2018 ◽

Vol 13 (7) ◽

pp. e0200735 ◽

Cited By ~ 9

Author(s):

Afsaneh Mojtabanezhad Shariatpanahi ◽

Maryam Yassi ◽

Mehdi Nouraie ◽

Amirhossein Sahebkar ◽

Fatemeh Varshoee Tabrizi ◽

...

Keyword(s):

Colorectal Cancer ◽

Dna Methylation ◽

Cancer Diagnosis ◽

Meta Analysis ◽

Stool Dna

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Clinical Relevance of Plasma DNA Methylation in Colorectal Cancer Patients Identified by Using a Genome-Wide High-Resolution Array

Annals of Surgical Oncology ◽

10.1245/s10434-014-4277-2 ◽

2014 ◽

Vol 22 (S3) ◽

pp. 1419-1427 ◽

Cited By ~ 26

Author(s):

Pei-Ching Lin ◽

Jen-Kou Lin ◽

Chien-Hsing Lin ◽

Hung-Hsin Lin ◽

Shung-Haur Yang ◽

...

Keyword(s):

Colorectal Cancer ◽

Dna Methylation ◽

High Resolution ◽

Cancer Patients ◽

Clinical Relevance ◽

Plasma Dna ◽

Genome Wide ◽

A Genome ◽

Colorectal Cancer Patients

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Su1892 Sept9 DNA Methylation in Healthy, Adenoma and Colorectal Cancer Patients: A Comparison Between Tissue and Plasma Specimens

Gastroenterology ◽

10.1016/s0016-5085(12)62031-9 ◽

2012 ◽

Vol 142 (5) ◽

pp. S-528-S-529

Author(s):

Kinga Tóth ◽

Orsolya Galamb ◽

Ferenc Sipos ◽

Katalin Leiszter ◽

Gabor Valcz ◽

...

Keyword(s):

Colorectal Cancer ◽

Dna Methylation ◽

Cancer Patients ◽

Colorectal Cancer Patients

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DNA Methylation and Colorectal Cancer

Current Colorectal Cancer Reports ◽

10.1007/s11888-014-0245-2 ◽

2014 ◽

Vol 10 (4) ◽

pp. 425-430 ◽

Cited By ~ 26

Author(s):

Hassan Ashktorab ◽

Hassan Brim

Keyword(s):

Colorectal Cancer ◽

Dna Methylation

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Analysis of DNA Methylation in Bowel Lavage Fluid for Detection of Colorectal Cancer

Cancer Prevention Research ◽

10.1158/1940-6207.capr-14-0162 ◽

2014 ◽

Vol 7 (10) ◽

pp. 1002-1010 ◽

Cited By ~ 23

Author(s):

Taku Harada ◽

Eiichiro Yamamoto ◽

Hiro-o Yamano ◽

Masanori Nojima ◽

Reo Maruyama ◽

...

Keyword(s):

Colorectal Cancer ◽

Dna Methylation ◽

Lavage Fluid

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Biochemical characterization of human HIF hydroxylases using HIF protein substrates that contain all three hydroxylation sites

Biochemical Journal ◽

10.1042/bj20101201 ◽

2011 ◽

Vol 436 (2) ◽

pp. 363-369 ◽

Cited By ~ 25

Author(s):

Melissa B. Pappalardi ◽

Dean E. McNulty ◽

John D. Martin ◽

Kelly E. Fisher ◽

Yong Jiang ◽

...

Keyword(s):

Biochemical Characterization ◽

Hypoxia Inducible Factor ◽

Prolyl Hydroxylase ◽

Transactivation Domain ◽

Prolyl Hydroxylases ◽

Proline Residue ◽

Protein Substrates ◽

Steady State Kinetic ◽

Asparaginyl Hydroxylase

The HIF (hypoxia-inducible factor) plays a central regulatory role in oxygen homoeostasis. HIF proteins are regulated by three Fe(II)- and α-KG (α-ketoglutarate)-dependent prolyl hydroxylase enzymes [PHD (prolyl hydroxylase domain) isoenzymes 1–3 or PHD1, PHD2 and PHD3] and one asparaginyl hydroxylase [FIH (factor inhibiting HIF)]. The prolyl hydroxylases control the abundance of HIF through oxygen-dependent hydroxylation of specific proline residues in HIF proteins, triggering subsequent ubiquitination and proteasomal degradation. FIH inhibits the HIF transcription activation through asparagine hydroxylation. Understanding the precise roles and regulation of these four Fe(II)- and α-KG-dependent hydroxylases is of great importance. In the present paper, we report the biochemical characterization of the first HIF protein substrates that contain the CODDD (C-terminal oxygen-dependent degradation domain), the NODDD (N-terminal oxygen-dependent degradation domain) and the CAD (C-terminal transactivation domain). Using LC-MS/MS (liquid chromatography–tandem MS) detection, we show that all three PHD isoenzymes have a strong preference for hydroxylation of the CODDD proline residue over the NODDD proline residue and the preference is observed for both HIF1α and HIF2α protein substrates. In addition, steady-state kinetic analyses show differential substrate selectivity for HIF and α-KG in reference to the three PHD isoforms and FIH.

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Gene expression and DNA methylation analyses suggest that two immune related genes are prognostic factors of colorectal cancer

BMC Medical Genomics ◽

10.1186/s12920-021-00966-3 ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Xiao-Liang Xing ◽

Zhi-Yong Yao ◽

Chaoqun Xing ◽

Zhi Huang ◽

Jing Peng ◽

...

Keyword(s):

Gene Expression ◽

Colorectal Cancer ◽

Risk Assessment ◽

Dna Methylation ◽

Differentially Expressed Genes ◽

Risk Score ◽

Immune Cells ◽

Assessment Model ◽

Differentially Expressed ◽

Risk Assessment Model

Abstract Background Colorectal cancer (CRC) is the second most prevalent cancer, as it accounts for approximately 10% of all annually diagnosed cancers. Studies have indicated that DNA methylation is involved in cancer genesis. The purpose of this study was to investigate the relationships among DNA methylation, gene expression and the tumor-immune microenvironment of CRC, and finally, to identify potential key genes related to immune cell infiltration in CRC. Methods In the present study, we used the ChAMP and DESeq2 packages, correlation analyses, and Cox regression analyses to identify immune-related differentially expressed genes (IR-DEGs) that were correlated with aberrant methylation and to construct a risk assessment model. Results Finally, we found that HSPA1A expression and CCRL2 expression were positively and negatively associated with the risk score of CRC, respectively. Patients in the high-risk group were more positively correlated with some types of tumor-infiltrating immune cells, whereas they were negatively correlated with other tumor-infiltrating immune cells. After the patients were regrouped according to the median risk score, we could more effectively distinguish them based on survival outcome, clinicopathological characteristics, specific tumor-immune infiltration status and highly expressed immune-related biomarkers. Conclusion This study suggested that the risk assessment model constructed by pairing immune-related differentially expressed genes correlated with aberrant DNA methylation could predict the outcome of CRC patients and might help to identify those patients who could benefit from antitumor immunotherapy.

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