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Nakasone ES, Zemla TJ, Yu M, Lin SY, Ou FS, Carter K, Innocenti F, Saltz L, Grady WM, Cohen SA. Evaluating the utility of ZNF331 promoter methylation as a prognostic and predictive marker in stage III colon cancer: results from CALGB 89803 (Alliance). Epigenetics 2024; 19:2349980. [PMID: 38716804 PMCID: PMC11085945 DOI: 10.1080/15592294.2024.2349980] [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: 09/20/2023] [Accepted: 04/23/2024] [Indexed: 05/12/2024] Open
Abstract
While epigenomic alterations are common in colorectal cancers (CRC), few epigenomic biomarkers that risk-stratify patients have been identified. We thus sought to determine the potential of ZNF331 promoter hypermethylation (mZNF331) as a prognostic and predictive marker in colon cancer. We examined the association of mZNF331 with clinicopathologic features, relapse, survival, and treatment efficacy in patients with stage III colon cancer treated within a randomized adjuvant chemotherapy trial (CALGB/Alliance89803). Residual tumour tissue was available for genomic DNA extraction and methylation analysis for 385 patients. ZNF331 promoter methylation status was determined by bisulphite conversion and fluorescence-based real-time polymerase chain reaction. Kaplan-Meier estimator and Cox proportional hazard models were used to assess the prognostic and predictive role of mZNF331 in this well-annotated dataset, adjusting for clinicopathologic features and standard molecular markers. mZNF331 was observed in 267/385 (69.4%) evaluable cases. Histopathologic features were largely similar between patients with mZNF331 compared to unmethylated ZNF331 (unmZNFF31). There was no significant difference in disease-free or overall survival between patients with mZNF331 versus unmZNF331 colon cancers, even when adjusting for clinicopathologic features and molecular marker status. Similarly, there was no difference in disease-free or overall survival across treatment arms when stratified by ZNF331 methylation status. While ZNF331 promoter hypermethylation is frequently observed in CRC, our current study of a small subset of patients with stage III colon cancer suggests limited applicability as a prognostic marker. Larger studies may provide more insight and clarity into the applicability of mZNF331 as a prognostic and predictive marker.
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Affiliation(s)
- Elizabeth S Nakasone
- Division of Oncology, University of Washington, Seattle, WA, USA
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Tyler J Zemla
- Alliance Statistics and Data Management Center, Mayo Clinic, Rochester, MN, USA
| | - Ming Yu
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - She Yu Lin
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- School of Life Sciences, Nantong University, Nantong, P.R. China
| | - Fang-Shu Ou
- Alliance Statistics and Data Management Center, Mayo Clinic, Rochester, MN, USA
| | - Kelly Carter
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Federico Innocenti
- Division of Pharmacotherapy and Experimental Therapeutics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Leonard Saltz
- Department of Gastrointestinal Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - William M Grady
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Division of Gastroenterology, University of Washington, Seattle, WA, USA
| | - Stacey A Cohen
- Division of Oncology, University of Washington, Seattle, WA, USA
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
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2
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Mirbahari SN, Fatemi N, Savabkar S, Chaleshi V, Zali N, Taleghani MY, Mirzaei E, Rejali L, Moghadam PK, Mojarad EN. Unmasking early colorectal cancer clues: in silico and in vitro investigation of downregulated IGF2, SOCS1, MLH1, and CACNA1G in SSA polyps. Mol Biol Rep 2024; 51:764. [PMID: 38874740 PMCID: PMC11178608 DOI: 10.1007/s11033-024-09683-3] [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: 01/16/2024] [Accepted: 05/29/2024] [Indexed: 06/15/2024]
Abstract
BACKGROUND AND AIM Colorectal cancer (CRC) originates from pre-existing polyps in the colon. The development of different subtypes of CRC is influenced by various genetic and epigenetic characteristics. CpG island methylator phenotype (CIMP) is found in about 15-20% of sporadic CRCs and is associated with hypermethylation of certain gene promoters. This study aims to find prognostic genes and compare their expression and methylation status as potential biomarkers in patients with serrated sessile adenomas/polyps (SSAP) and CRC, in order to evaluate which, one is a better predictor of disease. METHOD This study employed a multi-phase approach to investigate genes associated with CRC and SSAP. Initially, two gene expression datasets were analyzed using R and Limma package to identify differentially expressed genes (DEGs). Venn diagram analysis further refined the selection, revealing four genes from the Weissenberg panel with significant changes. These genes, underwent thorough in silico evaluations. Once confirmed, they proceeded to wet lab experimentation, focusing on expression and methylation status. This comprehensive methodology ensured a robust examination of the genes involved in CRC and SSAP. RESULT This study identified cancer-specific genes, with 8,351 and 1,769 genes specifically down-regulated in SSAP and CRC tissues, respectively. The down-regulated genes were associated with cell adhesion, negative regulation of cell proliferation, and drug response. Four highly downregulated genes in the Weissenberg panel, including CACNA1G, IGF2, MLH1, and SOCS1. In vitro analysis showed that they are hypermethylated in both SSAP and CRC samples while their expressions decreased only in CRC samples. CONCLUSION This suggests that the decrease in gene expression could help determine whether a polyp will become cancerous. Using both methylation status and gene expression status of genes in the Weissenberg panel in prognostic tests may lead to better prognoses for patients.
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Affiliation(s)
- Seyedeh Nasim Mirbahari
- Faculty of Sciences and Advanced Technologies in Biology, University of Science and Culture, ACECR, Tehran, Iran
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Nayeralsadat Fatemi
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sanaz Savabkar
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Vahid Chaleshi
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Neda Zali
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Yaghoob Taleghani
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Ebrahim Mirzaei
- Department of Medical Genetics, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Leili Rejali
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Pardis Ketabi Moghadam
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, P. O. Box: 1985717413, Tehran, Iran
| | - Ehsan Nazemalhosseini Mojarad
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, P. O. Box: 1985717413, Tehran, Iran.
- Department of Surgery, Leiden University Medical Center, P.O. Box 2333 ZA, Leiden, Netherlands.
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3
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Ouchi K, Takahashi S, Sasaki K, Yoshida Y, Taniguchi S, Kasahara Y, Komine K, Imai H, Saijo K, Shirota H, Takahashi M, Ishioka C. Genome-wide DNA methylation status is a predictor of the efficacy of anti-EGFR antibodies in the second-line treatment of metastatic colorectal cancer: Translational research of the EPIC trial. Int J Colorectal Dis 2024; 39:89. [PMID: 38862615 PMCID: PMC11166830 DOI: 10.1007/s00384-024-04659-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/26/2024] [Indexed: 06/13/2024]
Abstract
PURPOSE The genome-wide DNA methylation status (GWMS) predicts of therapeutic response to anti-epidermal growth factor receptor (EGFR) antibodies in treating metastatic colorectal cancer. We verified the significance of GWMS as a predictive factor for the efficacy of anti-EGFR antibodies in the second-line treatment of metastatic colorectal cancer. METHODS Clinical data were obtained from a prospective trial database, and a genome-wide DNA methylation analysis was performed. GWMS was classified into high-methylated colorectal cancer (HMCC) and low-methylated colorectal cancer (LMCC). The patients were divided into subgroups according to the treatment arm (cetuximab plus irinotecan or irinotecan alone) and GWMS, and the clinical outcomes were compared between the subgroups. RESULTS Of the 112 patients, 58 (51.8%) were in the cetuximab plus irinotecan arm, and 54 (48.2%) were in the irinotecan arm; 47 (42.0%) were in the HMCC, and 65 (58.0%) were in the LMCC group regarding GWMS. Compared with the LMCC group, the progression-free survival (PFS) was significantly shortened in the HMCC group in the cetuximab plus irinotecan arm (median 1.4 vs. 4.1 months, p = 0.001, hazard ratio = 2.56), whereas no significant differences were observed in the irinotecan arm. A multivariate analysis showed that GWMS was an independent predictor of PFS and overall survival (OS) in the cetuximab plus irinotecan arm (p = 0.002, p = 0.005, respectively), whereas GWMS did not contribute to either PFS or OS in the irinotecan arm. CONCLUSIONS GWMS was a predictive factor for the efficacy of anti-EGFR antibodies in the second-line treatment of metastatic colorectal cancer.
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Affiliation(s)
- Kota Ouchi
- Department of Medical Oncology, Tohoku University Hospital, Miyagi, Japan. 4-1 Seiryo-Machi, Aobaku, Sendai, Miyagi, 980-8575, Japan
- Department of Clinical Oncology, Graduate School of Medicine, Tohoku University, Miyagi, Japan. 4-1 Seiryo-Machi, Aobaku, Sendai, Miyagi, 980-8575, Japan
| | - Shin Takahashi
- Department of Medical Oncology, Tohoku University Hospital, Miyagi, Japan. 4-1 Seiryo-Machi, Aobaku, Sendai, Miyagi, 980-8575, Japan
- Department of Clinical Oncology, Graduate School of Medicine, Tohoku University, Miyagi, Japan. 4-1 Seiryo-Machi, Aobaku, Sendai, Miyagi, 980-8575, Japan
| | - Keiju Sasaki
- Department of Medical Oncology, Tohoku University Hospital, Miyagi, Japan. 4-1 Seiryo-Machi, Aobaku, Sendai, Miyagi, 980-8575, Japan
- Department of Clinical Oncology, Graduate School of Medicine, Tohoku University, Miyagi, Japan. 4-1 Seiryo-Machi, Aobaku, Sendai, Miyagi, 980-8575, Japan
| | - Yuya Yoshida
- Department of Medical Oncology, Tohoku University Hospital, Miyagi, Japan. 4-1 Seiryo-Machi, Aobaku, Sendai, Miyagi, 980-8575, Japan
- Department of Clinical Oncology, Graduate School of Medicine, Tohoku University, Miyagi, Japan. 4-1 Seiryo-Machi, Aobaku, Sendai, Miyagi, 980-8575, Japan
| | - Sakura Taniguchi
- Department of Medical Oncology, Tohoku University Hospital, Miyagi, Japan. 4-1 Seiryo-Machi, Aobaku, Sendai, Miyagi, 980-8575, Japan
- Department of Clinical Oncology, Graduate School of Medicine, Tohoku University, Miyagi, Japan. 4-1 Seiryo-Machi, Aobaku, Sendai, Miyagi, 980-8575, Japan
| | - Yuki Kasahara
- Department of Medical Oncology, Tohoku University Hospital, Miyagi, Japan. 4-1 Seiryo-Machi, Aobaku, Sendai, Miyagi, 980-8575, Japan
- Department of Clinical Oncology, Graduate School of Medicine, Tohoku University, Miyagi, Japan. 4-1 Seiryo-Machi, Aobaku, Sendai, Miyagi, 980-8575, Japan
| | - Keigo Komine
- Department of Medical Oncology, Tohoku University Hospital, Miyagi, Japan. 4-1 Seiryo-Machi, Aobaku, Sendai, Miyagi, 980-8575, Japan
- Department of Clinical Oncology, Graduate School of Medicine, Tohoku University, Miyagi, Japan. 4-1 Seiryo-Machi, Aobaku, Sendai, Miyagi, 980-8575, Japan
| | - Hiroo Imai
- Department of Medical Oncology, Tohoku University Hospital, Miyagi, Japan. 4-1 Seiryo-Machi, Aobaku, Sendai, Miyagi, 980-8575, Japan
- Department of Clinical Oncology, Graduate School of Medicine, Tohoku University, Miyagi, Japan. 4-1 Seiryo-Machi, Aobaku, Sendai, Miyagi, 980-8575, Japan
| | - Ken Saijo
- Department of Medical Oncology, Tohoku University Hospital, Miyagi, Japan. 4-1 Seiryo-Machi, Aobaku, Sendai, Miyagi, 980-8575, Japan
- Department of Clinical Oncology, Graduate School of Medicine, Tohoku University, Miyagi, Japan. 4-1 Seiryo-Machi, Aobaku, Sendai, Miyagi, 980-8575, Japan
| | - Hidekazu Shirota
- Department of Medical Oncology, Tohoku University Hospital, Miyagi, Japan. 4-1 Seiryo-Machi, Aobaku, Sendai, Miyagi, 980-8575, Japan
- Department of Clinical Oncology, Graduate School of Medicine, Tohoku University, Miyagi, Japan. 4-1 Seiryo-Machi, Aobaku, Sendai, Miyagi, 980-8575, Japan
| | - Masanobu Takahashi
- Department of Medical Oncology, Tohoku University Hospital, Miyagi, Japan. 4-1 Seiryo-Machi, Aobaku, Sendai, Miyagi, 980-8575, Japan
- Department of Clinical Oncology, Graduate School of Medicine, Tohoku University, Miyagi, Japan. 4-1 Seiryo-Machi, Aobaku, Sendai, Miyagi, 980-8575, Japan
- Department of Clinical Oncology, Institute of Development, Aging and Cancer, Tohoku University, Miyagi, Japan 4-1 Seiryo-Machi, Aobaku, Sendai, Miyagi, 980-8575, Japan
| | - Chikashi Ishioka
- Department of Medical Oncology, Tohoku University Hospital, Miyagi, Japan. 4-1 Seiryo-Machi, Aobaku, Sendai, Miyagi, 980-8575, Japan.
- Department of Clinical Oncology, Graduate School of Medicine, Tohoku University, Miyagi, Japan. 4-1 Seiryo-Machi, Aobaku, Sendai, Miyagi, 980-8575, Japan.
- Department of Clinical Oncology, Institute of Development, Aging and Cancer, Tohoku University, Miyagi, Japan 4-1 Seiryo-Machi, Aobaku, Sendai, Miyagi, 980-8575, Japan.
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Liu Z, Hu Y, Xie H, Chen K, Wen L, Fu W, Zhou X, Tang F. Single-Cell Chromatin Accessibility Analysis Reveals the Epigenetic Basis and Signature Transcription Factors for the Molecular Subtypes of Colorectal Cancers. Cancer Discov 2024; 14:1082-1105. [PMID: 38445965 DOI: 10.1158/2159-8290.cd-23-1445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 02/06/2024] [Accepted: 03/04/2024] [Indexed: 03/07/2024]
Abstract
Colorectal cancer is a highly heterogeneous disease, with well-characterized subtypes based on genome, DNA methylome, and transcriptome signatures. To chart the epigenetic landscape of colorectal cancers, we generated a high-quality single-cell chromatin accessibility atlas of epithelial cells for 29 patients. Abnormal chromatin states acquired in adenomas were largely retained in colorectal cancers, which were tightly accompanied by opposite changes of DNA methylation. Unsupervised analysis on malignant cells revealed two epigenetic subtypes, exactly matching the iCMS classification, and key iCMS-specific transcription factors (TFs) were identified, including HNF4A and PPARA for iCMS2 tumors and FOXA3 and MAFK for iCMS3 tumors. Notably, subtype-specific TFs bind to distinct target gene sets and contribute to both interpatient similarities and diversities for both chromatin accessibilities and RNA expressions. Moreover, we identified CpG-island methylator phenotypes and pinpointed chromatin state signatures and TF regulators for the CIMP-high subtype. Our work systematically revealed the epigenetic basis of the well-known iCMS and CIMP classifications of colorectal cancers. SIGNIFICANCE Our work revealed the epigenetic basis of the well-known iCMS and CIMP classifications of colorectal cancers. Moreover, interpatient minor similarities and major diversities of chromatin accessibility signatures of TF target genes can faithfully explain the corresponding interpatient minor similarities and major diversities of RNA expression signatures of colorectal cancers, respectively. This article is featured in Selected Articles from This Issue, p. 897.
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Affiliation(s)
- Zhenyu Liu
- School of Life Sciences, Biomedical Pioneering Innovation Center, Department of General Surgery, Third Hospital, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
| | - Yuqiong Hu
- School of Life Sciences, Biomedical Pioneering Innovation Center, Department of General Surgery, Third Hospital, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
- Key Laboratory of Organ Regeneration and Reconstruction, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Haoling Xie
- School of Life Sciences, Biomedical Pioneering Innovation Center, Department of General Surgery, Third Hospital, Peking University, Beijing, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Kexuan Chen
- School of Life Sciences, Biomedical Pioneering Innovation Center, Department of General Surgery, Third Hospital, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
| | - Lu Wen
- School of Life Sciences, Biomedical Pioneering Innovation Center, Department of General Surgery, Third Hospital, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
| | - Wei Fu
- School of Life Sciences, Biomedical Pioneering Innovation Center, Department of General Surgery, Third Hospital, Peking University, Beijing, China
- Peking University Third Hospital Cancer Center, Beijing, China
| | - Xin Zhou
- School of Life Sciences, Biomedical Pioneering Innovation Center, Department of General Surgery, Third Hospital, Peking University, Beijing, China
- Peking University Third Hospital Cancer Center, Beijing, China
| | - Fuchou Tang
- School of Life Sciences, Biomedical Pioneering Innovation Center, Department of General Surgery, Third Hospital, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
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5
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Lee AV, Nestler KA, Chiappinelli KB. Therapeutic targeting of DNA methylation alterations in cancer. Pharmacol Ther 2024; 258:108640. [PMID: 38570075 DOI: 10.1016/j.pharmthera.2024.108640] [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: 12/13/2023] [Revised: 03/13/2024] [Accepted: 03/22/2024] [Indexed: 04/05/2024]
Abstract
DNA methylation is a critical component of gene regulation and plays an important role in the development of cancer. Hypermethylation of tumor suppressor genes and silencing of DNA repair pathways facilitate uncontrolled cell growth and synergize with oncogenic mutations to perpetuate cancer phenotypes. Additionally, aberrant DNA methylation hinders immune responses crucial for antitumor immunity. Thus, inhibiting dysregulated DNA methylation is a promising cancer therapy. Pharmacologic inhibition of DNA methylation reactivates silenced tumor suppressors and bolster immune responses through induction of viral mimicry. Now, with the advent of immunotherapies and discovery of the immune-modulatory effects of DNA methylation inhibitors, there is great interest in understanding how targeting DNA methylation in combination with other therapies can enhance antitumor immunity. Here, we describe the role of aberrant DNA methylation in cancer and mechanisms by which it promotes tumorigenesis and modulates immune responses. Finally, we review the initial discoveries and ongoing efforts to target DNA methylation as a cancer therapeutic.
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Affiliation(s)
- Abigail V Lee
- Department of Microbiology, Immunology, & Tropical Medicine, The George Washington University, Washington, DC, USA
| | - Kevin A Nestler
- Department of Microbiology, Immunology, & Tropical Medicine, The George Washington University, Washington, DC, USA
| | - Katherine B Chiappinelli
- Department of Microbiology, Immunology, & Tropical Medicine, The George Washington University, Washington, DC, USA.
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6
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Shu J, Jelinek J, Chen H, Zhang Y, Qin T, Li M, Liu L, Issa JPJ. Genome-wide screening and functional validation of methylation barriers near promoters. Nucleic Acids Res 2024; 52:4857-4871. [PMID: 38647050 PMCID: PMC11109949 DOI: 10.1093/nar/gkae302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 03/13/2024] [Accepted: 04/09/2024] [Indexed: 04/25/2024] Open
Abstract
CpG islands near promoters are normally unmethylated despite being surrounded by densely methylated regions. Aberrant hypermethylation of these CpG islands has been associated with the development of various human diseases. Although local genetic elements have been speculated to play a role in protecting promoters from methylation, only a limited number of methylation barriers have been identified. In this study, we conducted an integrated computational and experimental investigation of colorectal cancer methylomes. Our study revealed 610 genes with disrupted methylation barriers. Genomic sequences of these barriers shared a common 41-bp sequence motif (MB-41) that displayed homology to the chicken HS4 methylation barrier. Using the CDKN2A (P16) tumor suppressor gene promoter, we validated the protective function of MB-41 and showed that loss of such protection led to aberrant hypermethylation. Our findings highlight a novel sequence signature of cis-acting methylation barriers in the human genome that safeguard promoters from silencing.
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Affiliation(s)
- Jingmin Shu
- College of Health Solutions, Arizona State University, Phoenix, AZ, USA
- Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Jaroslav Jelinek
- Fels Institute for Cancer Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
- Cooper Medical School at Rowan University, Camden, NJ 08103, USA
- Coriell Institute for Medical Research, Camden, NJ 08103, USA
| | - Hai Chen
- College of Health Solutions, Arizona State University, Phoenix, AZ, USA
- Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Yan Zhang
- Fels Institute for Cancer Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
| | - Taichun Qin
- Fels Institute for Cancer Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
| | - Ming Li
- Phoenix VA Health Care System, Phoenix, AZ 85012, USA
- University of Arizona College of Medicine, Phoenix, AZ 85004, USA
| | - Li Liu
- College of Health Solutions, Arizona State University, Phoenix, AZ, USA
- Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Jean-Pierre J Issa
- Fels Institute for Cancer Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
- Cooper Medical School at Rowan University, Camden, NJ 08103, USA
- Coriell Institute for Medical Research, Camden, NJ 08103, USA
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7
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Weng YY, Huang MY. The CpG Island Methylator Phenotype Status in Synchronous and Solitary Primary Colorectal Cancers: Prognosis and Effective Therapeutic Drug Prediction. Int J Mol Sci 2024; 25:5243. [PMID: 38791280 PMCID: PMC11121449 DOI: 10.3390/ijms25105243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 05/08/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024] Open
Abstract
Synchronous colorectal cancer (sCRC) is characterized by the occurrence of more than one tumor within six months of detecting the first tumor. Evidence suggests that sCRC might be more common in the serrated neoplasia pathway, marked by the CpG island methylator phenotype (CIMP), than in the chromosomal instability pathway (CIN). An increasing number of studies propose that CIMP could serve as a potential epigenetic predictor or prognostic biomarker of sCRC. Therapeutic drugs already used for treating CIMP-positive colorectal cancers (CRCs) are reviewed and drug selections for sCRC patients are discussed.
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Affiliation(s)
- Yun-Yun Weng
- Department of Radiation Oncology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
| | - Ming-Yii Huang
- Department of Radiation Oncology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
- Department of Radiation Oncology, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
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8
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Chen X, Ding Y, Yi Y, Chen Z, Fu J, Chang Y. Review of Animal Models of Colorectal Cancer in Different Carcinogenesis Pathways. Dig Dis Sci 2024; 69:1583-1592. [PMID: 38526618 DOI: 10.1007/s10620-024-08384-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Accepted: 03/05/2024] [Indexed: 03/27/2024]
Abstract
Colorectal cancer (CRC) is a common malignant tumor of the gastrointestinal tract with increasing morbidity and mortality. Exploring the factors affecting colorectal carcinogenesis and controlling its occurrence at its root is as important as studying post-cancer treatment and management. Establishing ideal animal models of CRC is crucial, which can occur through various pathways, such as adenoma-carcinoma sequence, inflammation-induced carcinogenesis, serrated polyp pathway and de-novo pathway. This article aims to categorize the existing well-established CRC animal models based on different carcinogenesis pathways, and to describe their mechanisms, methods, advantages and limitations using domestic and international literature sources. This will provide suggestions for the selection of animal models in early-stage CRC research.
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Affiliation(s)
- Xue Chen
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Diseases, Wuhan, 430071, China
| | - Yirong Ding
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Diseases, Wuhan, 430071, China
| | - Yun Yi
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Diseases, Wuhan, 430071, China
| | - Zhishan Chen
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Diseases, Wuhan, 430071, China
| | - Jiaping Fu
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
- Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Diseases, Wuhan, 430071, China
| | - Ying Chang
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China.
- Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Diseases, Wuhan, 430071, China.
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9
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Ogurchenok NE, Khalin KD, Bryukhovetskiy IS. Chemoprophylaxis of precancerous lesions in patients who are at a high risk of developing colorectal cancer (Review). MEDICINE INTERNATIONAL 2024; 4:25. [PMID: 38628384 PMCID: PMC11019464 DOI: 10.3892/mi.2024.149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Accepted: 03/07/2024] [Indexed: 04/19/2024]
Abstract
The diagnostics of colorectal cancer (CRC) and precancerous lesions in the colon is one of the most urgent matters to be considered for the modern protocols of complex examination, recommended for use from the age of 45 years, and including both instrumental and laboratory methods of research: Colonoscopy, CT colonography, flexible sigmoidoscopy, fecal occult blood test, fecal immunohistochemistry test and stool DNA test Nevertheless, the removal of those precancerous lesions does not solve the issue, and, apart from the regular endoscopic monitoring of patients who are at a high risk of developing CRC, the pharmacological treatment of certain key pathogenic mechanisms leading to the development of CRC is required. The present review to discusses the function of β-catenin in the transformation of precancerous colorectal lesions into CRC, when collaborating with PI3K/AKT/mTOR signaling pathway and other mechanisms. The existing methods for the early diagnostics and prevention of discovered anomalies are described and categorized. The analysis of the approaches to chemoprophylaxis of CRC, depending on the results of endoscopic, morphological and molecular-genetic tests, is presented.
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Affiliation(s)
- Nonna E. Ogurchenok
- Far Eastern Federal University, School of Medicine and Life Sciences, FEFU Medical Center, Russky Island, 690091 Vladivostok, Russian Federation
- Primorskiy Regional Clinical Hospital N1, Medical Center, Russky Island, 690091 Vladivostok, Russian Federation
| | - Konstantin D. Khalin
- Far Eastern Federal University, School of Medicine and Life Sciences, FEFU Medical Center, Russky Island, 690091 Vladivostok, Russian Federation
- Far Eastern Federal University, Medical Center, Russky Island, 690091 Vladivostok, Russian Federation
| | - Igor S. Bryukhovetskiy
- Far Eastern Federal University, Medical Center, Russky Island, 690091 Vladivostok, Russian Federation
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10
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Abolghasemi Fard A, Mahmoodzadeh A. Unraveling the Progression of Colon Cancer Pathogenesis Through Epigenetic Alterations and Genetic Pathways. Cureus 2024; 16:e59503. [PMID: 38826873 PMCID: PMC11143495 DOI: 10.7759/cureus.59503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/02/2024] [Indexed: 06/04/2024] Open
Abstract
In the modern age, colon cancer has attained a widespread status, affecting a considerable number of people. It develops due to the progressive accumulation of genetic and epigenetic alterations. While genetic mutations have been extensively studied in the context of colon cancer, emerging evidence highlights the pivotal role of epigenetic alterations in its pathogenesis. These alterations ultimately result in the transformation of normal colonic epithelium into colon adenocarcinoma. Key mechanisms of epigenetic modifications include DNA methylation, histone modification, and nucleosome positioning. Research findings have linked these modifications to the development, progression, or metastasis of tumors. Through the assessment of the colon cancer epigenome, it has been discovered that practically all colorectal cancers (CRCs) display gene methylation abnormalities and changes in miRNA expression. Advancements in this area indicate that epigenetic modifications will likely be commonly used in the near future to direct the prevention and treatment of CRC. The maintenance of genome stability is essential for preserving cellular integrity. The development of CRC is primarily influenced by the loss of genomic stability, which allows for the emergence of new mutations contributing to tumor characteristics. Although genetic mutations have been extensively researched in the realm of colon cancer, recent evidence underscores the pivotal role of epigenetic changes in its pathogenesis. The following types of genomic instability will be discussed: chromosomal instability, microsatellite instability, CpG island methylation phenotype, and aberrant DNA methylation.
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Affiliation(s)
- Asal Abolghasemi Fard
- Department of Cellular and Molecular Biology, Faculty of Modern Science and Technologies, Tehran Medical Sciences, Islamic Azad University, Tehran, IRN
| | - Afshin Mahmoodzadeh
- Department of Biology, Roudehen Branch, Islamic Azad University, Tehran, IRN
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11
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Choi Y, Kim N. Sex Difference of Colon Adenoma Pathway and Colorectal Carcinogenesis. World J Mens Health 2024; 42:256-282. [PMID: 37652658 PMCID: PMC10949019 DOI: 10.5534/wjmh.230085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 05/09/2023] [Indexed: 09/02/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most common causes of cancer morbidity in both sexes but shows sex differences. First, sex-specific differences in tumor recurrence and survival rates have been reported. For example, the development of CRC is found about 1.5 times higher and 4-8 years earlier in males compared to females, suggesting the protective role of estrogen in the disease. Furthermore, female patients have a higher risk of developing right-sided (proximal) colon cancer than male patients, which is known to have more aggressive clinical character compared to left-sided (distal) colon cancer. That is, left and right CRCs show differences in carcinogenic mechanism, that the chromosomal instability pathway is more common in left colon cancer while the microsatellite instability and serrated pathways are more common in right colon cancer. It is thought that there are sex-based differences on the background of carcinogenesis of CRC. Sex differences of CRC have two aspects, sexual dimorphism (biological differences in hormones and genes) and gender differences (non-biological differences in societal attitudes and behavior). Recently, sex difference of colon adenoma pathway and sexual dimorphism in the biology of gene and protein expression, and in endocrine cellular signaling in the CRC carcinogenesis have been accumulated. In addition, behavioral patterns can lead to differences in exposure to risk factors such as drinking or smoking, diet and physical activity. Therefore, understanding sex/gender-related biological and sociocultural differences in CRC risk will help in providing strategies for screening, treatment and prevention protocols to reduce the mortality and improve the quality of life. In this review, sex/gender differences in colon adenoma pathway and various aspects such as clinicopathological, biological, molecular, and socio-cultural aspects of CRC were described.
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Affiliation(s)
- Yonghoon Choi
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Nayoung Kim
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
- Department of Internal Medicine and Liver Research Institute, Seoul National University College of Medicine, Seoul, Korea.
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12
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Gretarsson KH, Abini-Agbomson S, Gloor SL, Weinberg DN, McCuiston JL, Kumary VUS, Hickman AR, Sahu V, Lee R, Xu X, Lipieta N, Flashner S, Adeleke OA, Popova IK, Taylor HF, Noll K, Windham CL, Maryanski DN, Venters BJ, Nakagawa H, Keogh MC, Armache KJ, Lu C. Cancer-associated DNA Hypermethylation of Polycomb Targets Requires DNMT3A Dual Recognition of Histone H2AK119 Ubiquitination and the Nucleosome Acidic Patch. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.18.585588. [PMID: 38562823 PMCID: PMC10983913 DOI: 10.1101/2024.03.18.585588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
During tumor development, promoter CpG islands (CGIs) that are normally silenced by Polycomb repressive complexes (PRCs) become DNA hypermethylated. The molecular mechanism by which de novo DNA methyltransferase(s) catalyze CpG methylation at PRC-regulated regions remains unclear. Here we report a cryo-EM structure of the DNMT3A long isoform (DNMT3A1) N-terminal region in complex with a nucleosome carrying PRC1-mediated histone H2A lysine 119 monoubiquitination (H2AK119Ub). We identify regions within the DNMT3A1 N-terminus that bind H2AK119Ub and the nucleosome acidic patch. This bidentate interaction is required for effective DNMT3A1 engagement with H2AK119Ub-modified chromatin in cells. Furthermore, aberrant redistribution of DNMT3A1 to Polycomb target genes inhibits their transcriptional activation during cell differentiation and recapitulates the cancer-associated DNA hypermethylation signature. This effect is rescued by disruption of the DNMT3A1-acidic patch interaction. Together, our analyses reveal a binding interface critical for countering promoter CGI DNA hypermethylation, a major molecular hallmark of cancer.
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13
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van Toledo DEFWM, Bleijenberg AGC, Venema A, de Wit MJ, van Eeden S, Meijer GA, Carvalho B, Dekker E, Henneman P, IJspeert JEG, van Noesel CJM. Aberrant PRDM2 methylation as an early event in serrated lesions destined to evolve into microsatellite-instable colorectal cancers. J Pathol Clin Res 2024; 10:e348. [PMID: 38380944 PMCID: PMC10880511 DOI: 10.1002/cjp2.348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 08/17/2023] [Accepted: 10/15/2023] [Indexed: 02/22/2024]
Abstract
Up to 30% of colorectal cancers (CRCs) develop from sessile serrated lesions (SSLs). Within the serrated neoplasia pathway, at least two principally distinct oncogenetic routes exist generating microsatellite-stable and microsatellite-instable CRCs, respectively. Aberrant DNA methylation (DNAm) is found early in the serrated pathway and might play a role in both oncogenetic routes. We studied a cohort of 23 SSLs with a small focus (<10 mm) of dysplasia or cancer, 10 of which were MLH1 deficient and 13 MLH1 proficient. By comparing, for each SSL, the methylation status of (1) the region of dysplasia or cancer (SSL-D), (2) the nondysplastic SSL (SSL), and (3) adjacent normal mucosa, differentially methylated probes (DMPs) and regions (DMRs) were assessed both genome-wide as well as in a tumor-suppressor gene-focused approach. By comparing DNAm of MLH1-deficient SSL-Ds with their corresponding SSLs, we identified five DMRs, including those annotating for PRDM2 and, not unexpectedly, MLH1. PRDM2 gene promotor methylation was associated with MLH1 expression status, as it was largely hypermethylated in MLH1-deficient SSL-Ds and hypomethylated in MLH1-proficient SSL-Ds. Significantly increased DNAm levels of PRDM2 and MLH1, in particular at 'critical' MLH1 probe sites, were to some extent already visible in SSLs as compared to normal mucosa (p = 0.02, p = 0.01, p < 0.0001, respectively). No DMRs, nor DMPs, were identified for SSLs destined to evolve into MLH1-proficient SSL-Ds. Our data indicate that, within both arms of the serrated CRC pathway, the majority of the epigenetic alterations are introduced early during SSL formation. Promoter hypermethylation of PRDM2 and MLH1 on the other hand specifically initiates in SSLs destined to transform into MLH1-deficient CRCs suggesting that the fate of SSLs may not necessarily result from a stochastic process but possibly is already imprinted and predisposed.
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Affiliation(s)
- David EFWM van Toledo
- Department of Gastroenterology and HepatologyAmsterdam University Medical Centers, location Academic Medical CenterAmsterdamThe Netherlands
- Amsterdam Gastroenterology Endocrinology and MetabolismAmsterdamThe Netherlands
- Cancer Center AmsterdamAmsterdam University Medical Centers, Location Academic Medical CenterAmsterdamThe Netherlands
| | - Arne GC Bleijenberg
- Department of Gastroenterology and HepatologyAmsterdam University Medical Centers, location Academic Medical CenterAmsterdamThe Netherlands
- Amsterdam Gastroenterology Endocrinology and MetabolismAmsterdamThe Netherlands
- Cancer Center AmsterdamAmsterdam University Medical Centers, Location Academic Medical CenterAmsterdamThe Netherlands
| | - Andrea Venema
- Department of Human Genetics, Epigenetics of disease, Amsterdam Gastroenterology Endocrinology and MetabolismAmsterdam University Medical Centers, Location Academic Medical CenterAmsterdamThe Netherlands
| | - Mireille J de Wit
- Department of PathologyAmsterdamAmsterdam University Medical Centers, Location Academic Medical CenterThe Netherlands
| | - Susanne van Eeden
- Department of PathologyAmsterdamAmsterdam University Medical Centers, Location Academic Medical CenterThe Netherlands
| | - Gerrit A Meijer
- Department of PathologyNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Beatrice Carvalho
- Department of PathologyNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Evelien Dekker
- Department of Gastroenterology and HepatologyAmsterdam University Medical Centers, location Academic Medical CenterAmsterdamThe Netherlands
- Amsterdam Gastroenterology Endocrinology and MetabolismAmsterdamThe Netherlands
- Cancer Center AmsterdamAmsterdam University Medical Centers, Location Academic Medical CenterAmsterdamThe Netherlands
| | - Peter Henneman
- Department of Human Genetics, Epigenetics of disease, Amsterdam Gastroenterology Endocrinology and MetabolismAmsterdam University Medical Centers, Location Academic Medical CenterAmsterdamThe Netherlands
| | - Joep EG IJspeert
- Department of Gastroenterology and HepatologyAmsterdam University Medical Centers, location Academic Medical CenterAmsterdamThe Netherlands
- Amsterdam Gastroenterology Endocrinology and MetabolismAmsterdamThe Netherlands
- Cancer Center AmsterdamAmsterdam University Medical Centers, Location Academic Medical CenterAmsterdamThe Netherlands
| | - Carel JM van Noesel
- Department of PathologyAmsterdamAmsterdam University Medical Centers, Location Academic Medical CenterThe Netherlands
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14
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Chen ZG, Ji XM, Xu YX, Fong WP, Liu XY, Liang JY, Tan Q, Wen L, Cai YY, Wang DS, Li YH. Methylated ctDNA predicts early recurrence risk in patients undergoing resection of initially unresectable colorectal cancer liver metastases. Ther Adv Med Oncol 2024; 16:17588359241230752. [PMID: 38425989 PMCID: PMC10903215 DOI: 10.1177/17588359241230752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 01/18/2024] [Indexed: 03/02/2024] Open
Abstract
Background Patients with initially unresectable colorectal cancer liver metastases (IU-CRLM) might benefit from using an effective systemic treatment followed by resection of liver metastases but the curative success rate is quite low. Indeed, nearly one-third of patients exhibit early recurrence within the first 6 months after surgery, and these individuals often have poor overall survival. Objectives This study aims to clarify the application value of serial circulating tumor DNA (ctDNA) analysis in predicting the clinical outcome of IU-CRLM patients following liver metastasectomy. Design A retrospective study was conducted on a cohort of patients with IU-CRLM between February 2018 and April 2021. Methods Plasma samples at different time points during CRLM treatment [baseline (BL), preoperation (PRE), postoperation (POST), end-of-treatment (EOT), and progressive disease (PD)] were retrospectively collected from patients with initially unresectable CRLM enrolled at the Sun Yat-sen University Cancer Center. Dynamic changes of SEPTIN 9 (SEPT9) and Neuropeptide Y (NPY) methylated circulating tumor DNA (MetctDNA) levels in serial plasma samples were detected using droplet-digital PCR (ddPCR). Results SEPT9 and NPY genes were hypermethylated in colon cancer cell lines and tissues while no difference was observed between primary and metastatic tumors. Patients with MetctDNA positive at POST or EOT had significantly lower recurrence-free survival (RFS) compared to patients with MetctDNA negative at these time points [POST: Hazard ratio (HR) 9.44, 95% confidence interval (CI) 5.15-17.30, p < 0.001; EOT: HR 11.48, 95% CI 3.27-40.31, p < 0.001]. Multivariate analysis demonstrated that POST (OR 33.96, 95% CI 4.03-286.10, p = 0.001) and EOT (OR 18.36, 95% CI 1.14-295.71, p = 0.04) MetctDNA was an independent risk factor for early recurrence. Time-dependent receiver operating characteristic curve (T-ROC) analysis revealed that area under the curve (AUC) value was greatest at the relapse time point of 6 months post-intervention, with POST-AUC and EOT-AUC values of 0.74 (95% CI 0.66-0.81) and 0.73 (95% CI 0.53-0.94), respectively. Serial MetctDNA analysis showed that RFS was significantly lower in patients with no MetctDNA clearance compared with those with MetctDNA clearance (HR 26.05, 95% CI 4.92-137.81, p < 0.001). Conclusion Our study confirmed that serial ctDNA analysis of NPY and SEPT9 gene methylation could effectively predict early recurrence in IU-CRLM patients, especially at POST and EOT.
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Affiliation(s)
- Zhi-Gang Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, P.R. China
- Department of Medical Oncology, Sun Yat-Sen University Cancer Center, Guangzhou, P.R. China
| | - Xiao-Meng Ji
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, P.R. China
- Department of Radiation Oncology, The Affiliated Hospital of Qingdao University, Qingdao, P.R. China
| | - Yu-Xia Xu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, P.R. China
- Department of Molecular Diagnostics Sun Yat-Sen University Cancer Center, Guangzhou, P.R. China
| | - William Pat Fong
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, P.R. China
- Department of Medical Oncology, Sun Yat-Sen University Cancer Center, Guangzhou, P.R. China
| | - Xiao-Yun Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, P.R. China
- Department of Molecular Diagnostics Sun Yat-Sen University Cancer Center, Guangzhou, P.R. China
| | - Jie-Ying Liang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, P.R. China
- Department of Medical Oncology, Sun Yat-Sen University Cancer Center, Guangzhou, P.R. China
| | - Qiong Tan
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, P.R. China
- Department of Medical Oncology, Sun Yat-Sen University Cancer Center, Guangzhou, P.R. China
| | - Lei Wen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, P.R. China
- Department of Medical Oncology, Sun Yat-Sen University Cancer Center, Guangzhou, P.R. China
| | - Yan-Yu Cai
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, P.R. China
- Department of Medical Oncology, Sun Yat-Sen University Cancer Center, Guangzhou, P.R. China
| | - De-Shen Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, P.R. China
- Department of Medical Oncology, Sun Yat-Sen University Cancer Center, 651 Dongfeng East Road, Guangzhou 510060, P.R. China
| | - Yu-Hong Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, P.R. China
- Department of Medical Oncology, Sun Yat-Sen University Cancer Center, 651 Dongfeng East Road, Guangzhou 510060, P.R. China
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15
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Cicirò Y, Ragusa D, Sala A. Expression of the checkpoint kinase BUB1 is a predictor of response to cancer therapies. Sci Rep 2024; 14:4461. [PMID: 38396175 PMCID: PMC10891059 DOI: 10.1038/s41598-024-55080-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 02/19/2024] [Indexed: 02/25/2024] Open
Abstract
The identification of clinically-relevant biomarkers is of upmost importance for the management of cancer, from diagnosis to treatment choices. We performed a pan-cancer analysis of the mitotic checkpoint budding uninhibited by benzimidazole 1 gene BUB1, in the attempt to ascertain its diagnostic and prognostic values, specifically in the context of drug response. BUB1 was found to be overexpressed in the majority of cancers, and particularly elevated in clinically aggressive molecular subtypes. Its expression was correlated with clinico-phenotypic features, notably tumour staging, size, invasion, hypoxia, and stemness. In terms of prognostic value, the expression of BUB1 bore differential clinical outcomes depending on the treatment administered in TCGA cancer cohorts, suggesting sensitivity or resistance, depending on the expression levels. We also integrated in vitro drug sensitivity data from public projects based on correlation between drug efficacy and BUB1 expression to produce a list of candidate compounds with differential responses according to BUB1 levels. Gene Ontology enrichment analyses revealed that BUB1 overexpression in cancer is associated with biological processes related to mitosis and chromosome segregation machinery, reflecting the mechanisms of action of drugs with a differential effect based on BUB1 expression.
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Affiliation(s)
- Ylenia Cicirò
- Centre for Inflammation Research and Translational Medicine (CIRTM), Brunel University London, Uxbridge, UB8 3PH, UK
| | - Denise Ragusa
- Centre for Genome Engineering and Maintenance (CenGEM), Brunel University London, Uxbridge, UB8 3PH, UK.
| | - Arturo Sala
- Centre for Inflammation Research and Translational Medicine (CIRTM), Brunel University London, Uxbridge, UB8 3PH, UK.
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16
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Yang L, Tu L, Bisht S, Mao Y, Petkovich D, Thursby SJ, Liang J, Patel N, Yen RWC, Largent T, Zahnow C, Brock M, Gabrielson K, Salimian KJ, Baylin SB, Easwaran H. Tissue-location-specific transcription programs drive tumor dependencies in colon cancer. Nat Commun 2024; 15:1384. [PMID: 38360902 PMCID: PMC10869357 DOI: 10.1038/s41467-024-45605-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 01/30/2024] [Indexed: 02/17/2024] Open
Abstract
Cancers of the same tissue-type but in anatomically distinct locations exhibit different molecular dependencies for tumorigenesis. Proximal and distal colon cancers exemplify such characteristics, with BRAFV600E predominantly occurring in proximal colon cancers along with increased DNA methylation phenotype. Using mouse colon organoids, here we show that proximal and distal colon stem cells have distinct transcriptional programs that regulate stemness and differentiation. We identify that the homeobox transcription factor, CDX2, which is silenced by DNA methylation in proximal colon cancers, is a key mediator of the differential transcriptional programs. Cdx2-mediated proximal colon-specific transcriptional program concurrently is tumor suppressive, and Cdx2 loss sufficiently creates permissive state for BRAFV600E-driven transformation. Human proximal colon cancers with CDX2 downregulation showed similar transcriptional program as in mouse proximal organoids with Cdx2 loss. Developmental transcription factors, such as CDX2, are thus critical in maintaining tissue-location specific transcriptional programs that create tissue-type origin specific dependencies for tumor development.
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Affiliation(s)
- Lijing Yang
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD, 21287, USA
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, 430071, PR China
| | - Lei Tu
- Division of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Shilpa Bisht
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD, 21287, USA
| | - Yiqing Mao
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD, 21287, USA
| | - Daniel Petkovich
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD, 21287, USA
| | - Sara-Jayne Thursby
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD, 21287, USA
| | - Jinxiao Liang
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD, 21287, USA
| | - Nibedita Patel
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD, 21287, USA
| | - Ray-Whay Chiu Yen
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD, 21287, USA
| | - Tina Largent
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD, 21287, USA
| | - Cynthia Zahnow
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD, 21287, USA
| | - Malcolm Brock
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD, 21287, USA
| | - Kathy Gabrielson
- Department of Comparative Medicine, Johns Hopkins Medical Institutions, 863 Broadway Research Building, 733 N. Broadway, Baltimore, MD, 21205-2196, USA
| | - Kevan J Salimian
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Stephen B Baylin
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD, 21287, USA
| | - Hariharan Easwaran
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Room 530, Baltimore, MD, 21287, USA.
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17
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Shim H, Jang K, Bang YH, Chu HBK, Kang J, Lee JY, Cho S, Lee HS, Jeon J, Hwang T, Joe S, Lim J, Choi JH, Joo EH, Park K, Moon JH, Han KY, Hong Y, Lee WY, Kim HC, Yun SH, Cho YB, Park YA, Huh JW, Shin JK, Pyo DH, Hong H, Lee HO, Park WY, Yang JO, Kim YJ. Comprehensive profiling of DNA methylation in Korean patients with colorectal cancer. BMB Rep 2024; 57:110-115. [PMID: 37605617 PMCID: PMC10910091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 06/27/2023] [Accepted: 08/21/2023] [Indexed: 08/23/2023] Open
Abstract
Alterations in DNA methylation play an important pathophysiological role in the development and progression of colorectal cancer. We comprehensively profiled DNA methylation alterations in 165 Korean patients with colorectal cancer (CRC), and conducted an in-depth investigation of cancer-specific methylation patterns. Our analysis of the tumor samples revealed a significant presence of hypomethylated probes, primarily within the gene body regions; few hypermethylated sites were observed, which were mostly enriched in promoter-like and CpG island regions. The CpG Island Methylator PhenotypeHigh (CIMP-H) exhibited notable enrichment of microsatellite instability-high (MSI-H). Additionally, our findings indicated a significant correlation between methylation of the MLH1 gene and MSI-H status. Furthermore, we found that the CIMP-H had a higher tendency to affect the right-side of the colon tissues and was slightly more prevalent among older patients. Through our methylome profile analysis, we successfully verified the thylation patterns and clinical characteristics of Korean patients with CRC. This valuable dataset lays a strong foundation for exploring novel molecular insights and potential therapeutic targets for the treatment of CRC. [BMB Reports 2024; 57(2): 110-115].
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Affiliation(s)
- Hyeran Shim
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Kiwon Jang
- Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
| | - Yeong Hak Bang
- Department of Digital Health, Samsung Advanced Institute for Health Science & Technology (SAIHST), Sungkyunkwan University, Seoul 06355, Korea
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea
| | - Hoang Bao Khanh Chu
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Jisun Kang
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Jin-Young Lee
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Sheehyun Cho
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Hong Seok Lee
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Jongbum Jeon
- Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
| | - Taeyeon Hwang
- Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
| | - Soobok Joe
- Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
| | - Jinyeong Lim
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul 06355, Korea
| | - Ji-Hye Choi
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul 06355, Korea
| | - Eun Hye Joo
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul 06355, Korea
| | - Kyunghee Park
- Samsung Genome Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea, Seoul 04779, Korea
| | - Ji Hwan Moon
- Samsung Genome Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea, Seoul 04779, Korea
| | - Kyung Yeon Han
- Samsung Genome Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea, Seoul 04779, Korea
| | - Yourae Hong
- Department of Oncology, Katholieke Universiteit Leuven, B-3000 Leuven, Belgium, Seoul 04779, Korea
| | - Woo Yong Lee
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea
| | - Hee Cheol Kim
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea
| | - Seong Hyeon Yun
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea
| | - Yong Beom Cho
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea
| | - Yoon Ah Park
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea
| | - Jung Wook Huh
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea
| | - Jung Kyong Shin
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea
| | - Dae Hee Pyo
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea
| | - Hyekyung Hong
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea
| | - Hae-Ock Lee
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
- Department of Biomedicine and Health Sciences, Graduate School, The Catholic University of Korea, Seoul 06591, Korea
| | - Woong-Yang Park
- Department of Digital Health, Samsung Advanced Institute for Health Science & Technology (SAIHST), Sungkyunkwan University, Seoul 06355, Korea
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul 06355, Korea
- Samsung Genome Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea, Seoul 04779, Korea
| | - Jin Ok Yang
- Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
| | - Young-Joon Kim
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
- LepiDyne Co., Ltd., Seoul 04779, Korea
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Tahara S, Tahara T, Yamazaki J, Shijimaya T, Horiguchi N, Funasaka K, Fukui T, Nakagawa Y, Shibata T, Naganuma M, Tsukamoto T, Ohmiya N. Helicobacter pylori infection associated DNA methylation in primary gastric cancer significantly correlates with specific molecular and clinicopathological features. Mol Carcinog 2024; 63:266-274. [PMID: 37846801 DOI: 10.1002/mc.23650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 08/23/2023] [Accepted: 10/01/2023] [Indexed: 10/18/2023]
Abstract
Helicobacter pylori induces DNA methylation in gastric mucosa, which links to gastric cancer (GC) risk. In contrast, CpG island methylator phenotype (CIMP) is defined as high levels of cancer-specific methylation and provides distinct molecular and clinicopathological features of GC. The association between those two types of methylation in GC remains unclear. We examined DNA methylation of well-validated H. pylori infection associated genes in GC and its adjacent mucosa and investigated its association with CIMP, various molecular subtypes and clinical features. We studied 50 candidate loci in 24 gastric samples to identify H. pylori infection associated genes. Identified loci were further examined in 624 gastric tissue from 217 primary GC, 217 adjacent mucosa, and 190 mucosae from cancer-free subjects. We identified five genes (IGF2, SLC16A2, SOX11, P2RX7, and MYOD1) as hypermethylated in H. pylori infected gastric mucosa. In non-neoplastic mucosa, methylation of H. pylori infection associated genes was higher in patients with GC than those without. In primary GC tissues, higher methylation of H. pylori infection associated genes correlated with CIMP-positive and its related features, such as MLH1 methylated cases. On the other hand, GC with lower methylation of these genes presented aggressive clinicopathological features including undifferentiated histopathology, advanced stage at diagnosis. H. pylori infection associated DNA methylation is correlated with CIMP, specific molecular and clinicopathological features in GC, supporting its utility as promising biomarker in this tumor type.
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Affiliation(s)
- Sayumi Tahara
- Department of Diagnostic Pathology I, Fujita Health University School of Medicine, Toyoake, Japan
| | - Tomomitsu Tahara
- Department of Gastroenterology, Fujita Health University School of Medicine, Toyoake, Japan
- Third Department of Internal Medicine, Kansai Medical University, Hirakata, Japan
| | - Jumpei Yamazaki
- Translational Research Unit, Veterinary Teaching Hospital, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
| | - Takuya Shijimaya
- Third Department of Internal Medicine, Kansai Medical University, Hirakata, Japan
| | - Noriyuki Horiguchi
- Department of Gastroenterology, Fujita Health University School of Medicine, Toyoake, Japan
| | - Kohei Funasaka
- Department of Gastroenterology, Fujita Health University School of Medicine, Toyoake, Japan
| | - Toshiro Fukui
- Third Department of Internal Medicine, Kansai Medical University, Hirakata, Japan
| | - Yoshihito Nakagawa
- Department of Gastroenterology, Fujita Health University School of Medicine, Toyoake, Japan
| | - Tomoyuki Shibata
- Department of Gastroenterology, Fujita Health University School of Medicine, Toyoake, Japan
| | - Makoto Naganuma
- Third Department of Internal Medicine, Kansai Medical University, Hirakata, Japan
| | - Tetsuya Tsukamoto
- Department of Diagnostic Pathology I, Fujita Health University School of Medicine, Toyoake, Japan
| | - Naoki Ohmiya
- Department of Advanced Endoscopy, Fujita Health University, Toyoake, Aichi, Japan
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19
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Satomi K, Ichimura K, Shibahara J. Decoding the DNA methylome of central nervous system tumors: An emerging modality for integrated diagnosis. Pathol Int 2024; 74:51-67. [PMID: 38224248 DOI: 10.1111/pin.13402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/16/2023] [Accepted: 12/18/2023] [Indexed: 01/16/2024]
Abstract
The definitive diagnosis and classification of individual cancers are crucial for patient care and cancer research. To achieve a robust diagnosis of central nervous system (CNS) tumors, a genotype-phenotype integrated diagnostic approach was introduced in recent versions of the World Health Organization classification, followed by the incorporation of a genome-wide DNA methylome-based classification. Microarray-based platforms are widely used to obtain DNA methylome data, and the German Cancer Research Center (Deutsches Krebsforschungszentrum [DKFZ]) has a webtool for a DNA methylation-based classifier (DKFZ classifier). Integration of DNA methylome will further enhance the precision of CNS tumor classification, especially in diagnostically challenging cases. However, in the clinical application of DNA methylome-based classification, challenges related to data interpretation persist, in addition to technical caveats, regulations, and limited accessibility. Dimensionality reduction (DMR) can complement integrated diagnosis by visualizing a profile and comparing it with other known samples. Therefore, DNA methylome-based classification is a highly useful research tool for auxiliary analysis in challenging diagnostic and rare disease cases, and for establishing novel tumor concepts. Decoding the DNA methylome, especially by DMR in addition to DKFZ classifier, emphasizes the capability of grasping the fundamental biological principles that provide new perspectives on CNS tumors.
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Affiliation(s)
- Kaishi Satomi
- Department of Pathology, Kyorin University Faculty of Medicine, Tokyo, Japan
| | - Koichi Ichimura
- Department of Brain Disease Translational Research, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Junji Shibahara
- Department of Pathology, Kyorin University Faculty of Medicine, Tokyo, Japan
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20
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Weber R, Weller M, Reifenberger G, Vasella F. Epigenetic modification and characterization of the MGMT promoter region using CRISPRoff in glioblastoma cells. Front Oncol 2024; 14:1342114. [PMID: 38357209 PMCID: PMC10864556 DOI: 10.3389/fonc.2024.1342114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 01/04/2024] [Indexed: 02/16/2024] Open
Abstract
The methylation status of the O6-methylguanine DNA methyltransferase (MGMT) promoter region is a critical predictor of response to alkylating agents in glioblastoma. However, current approaches to study the MGMT status focus on analyzing models with non-identical backgrounds. Here, we present an epigenetic editing approach using CRISPRoff to introduce site-specific CpG methylation in the MGMT promoter region of glioma cell lines. Sanger sequencing revealed successful introduction of methylation, effectively generating differently methylated glioma cell lines with an isogenic background. The introduced methylation resulted in reduced MGMT mRNA and protein levels. Furthermore, the cell lines with MGMT promoter region methylation exhibited increased sensitivity to temozolomide, consistent with the impact of methylation on treatment outcomes in patients with glioblastoma. This precise epigenome-editing approach provides valuable insights into the functional relevance of MGMT promoter regional methylation and its potential for prognostic and predictive assessments, as well as epigenetic-targeted therapies.
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Affiliation(s)
- Remi Weber
- Laboratory of Molecular Neuro-Oncology, Department of Neurology, Clinical Neuroscience Center, University of Zurich, Zurich, Switzerland
| | - Michael Weller
- Laboratory of Molecular Neuro-Oncology, Department of Neurology, Clinical Neuroscience Center, University of Zurich, Zurich, Switzerland
- Laboratory of Molecular Neuro-Oncology, Department of Neurology, Clinical Neuroscience Center, University Hospital Zurich, Zurich, Switzerland
| | - Guido Reifenberger
- Institute of Neuropathology, Medical Faculty, Heinrich Heine University and University Hospital Düsseldorf, Düsseldorf, Germany
| | - Flavio Vasella
- Laboratory of Molecular Neuro-Oncology, Department of Neurology, Clinical Neuroscience Center, University Hospital Zurich, Zurich, Switzerland
- Department of Neurosurgery, Clinical Neuroscience Center, University Hospital and University of Zurich, Zurich, Switzerland
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21
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Krumpolec P, Kodada D, Hadžega D, Petrovič O, Babišová K, Dosedla E, Turcsányiová Z, Minárik G. Changes in DNA methylation associated with a specific mode of delivery: a pilot study. Front Med (Lausanne) 2024; 11:1291429. [PMID: 38314203 PMCID: PMC10835804 DOI: 10.3389/fmed.2024.1291429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 01/05/2024] [Indexed: 02/06/2024] Open
Abstract
Background The mode of delivery represents an epigenetic factor with potential to affect further development of the individual by multiple mechanisms. DNA methylation may be one of them, representing a major epigenetic mechanism involving direct chemical modification of the individual's DNA. This pilot study aims to examine whether a specific mode of delivery induces changes of DNA methylation by comparing the umbilical cord blood and peripheral blood of the newborns. Methods Blood samples from infants born by vaginal delivery and caesarean section were analysed to prepare the Methylseq library according to NEBNext enzymatic Methyl-seq Methylation Library Preparation Kit with further generation of target-enriched DNA libraries using the Twist Human Methylome Panel. DNA methylation status was determined using Illumina next-generation sequencing (NGS). Results We identified 168 differentially methylated regions in umbilical cord blood samples and 157 regions in peripheral blood samples. These were associated with 59 common biological, metabolic and signalling pathways for umbilical cord and peripheral blood samples. Conclusion Caesarean section is likely to represent an important epigenetic factor with the potential to induce changes in the genome that could play an important role in development of a broad spectrum of disorders. Our results could contribute to the elucidation of how epigenetic factors, such as a specific mode of delivery, could have adverse impact on health of an individual later in their life.
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Affiliation(s)
| | - Dominik Kodada
- Medirex Group Academy n.o., Nitra, Slovakia
- Department of Clinical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University in Bratislava, Bratislava, Slovakia
| | | | | | | | - Erik Dosedla
- Department of Gynaecology and Obstetrics, Faculty of Medicine, Pavol Jozef Šafárik University in Košice, Košice, Slovakia
| | - Zuzana Turcsányiová
- Department of Gynaecology and Obstetrics, Faculty of Medicine, Pavol Jozef Šafárik University in Košice, Košice, Slovakia
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22
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Park PH, Keith K, Calendo G, Jelinek J, Madzo J, Gharaibeh RZ, Ghosh J, Sapienza C, Jobin C, Issa JPJ. Association between gut microbiota and CpG island methylator phenotype in colorectal cancer. Gut Microbes 2024; 16:2363012. [PMID: 38860458 PMCID: PMC11174071 DOI: 10.1080/19490976.2024.2363012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 05/29/2024] [Indexed: 06/12/2024] Open
Abstract
The intestinal microbiota is an important environmental factor implicated in CRC development. Intriguingly, modulation of DNA methylation by gut microbiota has been reported in preclinical models, although the relationship between tumor-infiltrating bacteria and CIMP status is currently unexplored. In this study, we investigated tumor-associated bacteria in 203 CRC tumor cases and validated the findings using The Cancer Genome Atlas datasets. We assessed the abundance of Bacteroides fragilis, Escherichia coli, Fusobacterium nucleatum, and Klebsiella pneumoniae through qPCR analysis and observed enrichment of all four bacterial species in CRC samples. Notably, except for E. coli, all exhibited significant enrichment in cases of CIMP. This enrichment was primarily driven by a subset of cases distinguished by high levels of these bacteria, which we labeled as "Superhigh". The bacterial Superhigh status showed a significant association with CIMP (odds ratio 3.1, p-value = 0.013) and with MLH1 methylation (odds ratio 4.2, p-value = 0.0025). In TCGA CRC cases (393 tumor and 45 adj. normal), bacterial taxa information was extracted from non-human whole exome sequencing reads, and the bacterial Superhigh status was similarly associated with CIMP (odds ratio 2.9, p < 0.001) and MLH1 methylation (odds ratio 3.5, p < 0.001). Finally, 16S ribosomal RNA gene sequencing revealed high enrichment of Bergeyella spp. C. concisus, and F. canifelinum in CIMP-Positive tumor cases. Our findings highlight that specific bacterial taxa may influence DNA methylation, particularly in CpG islands, and contribute to the development and progression of CIMP in colorectal cancer.
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Affiliation(s)
- Pyoung Hwa Park
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
- Research, Coriell Institute for Medical Research, Camden, NJ, USA
| | - Kelsey Keith
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
- Research, Coriell Institute for Medical Research, Camden, NJ, USA
| | - Gennaro Calendo
- Research, Coriell Institute for Medical Research, Camden, NJ, USA
| | - Jaroslav Jelinek
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
- Research, Coriell Institute for Medical Research, Camden, NJ, USA
- Biomedical Sciences, Cooper Medical School at Rowan University, Camden, NJ, USA
| | - Jozef Madzo
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
- Research, Coriell Institute for Medical Research, Camden, NJ, USA
- Biomedical Sciences, Cooper Medical School at Rowan University, Camden, NJ, USA
| | - Raad Z. Gharaibeh
- Department of Medicine, University of Florida, Gainesville, FL, USA
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL, USA
| | - Jayashri Ghosh
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
| | - Carmen Sapienza
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
| | - Christian Jobin
- Department of Medicine, University of Florida, Gainesville, FL, USA
| | - Jean-Pierre J. Issa
- Fels Cancer Institute for Personalized Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, PA, USA
- Research, Coriell Institute for Medical Research, Camden, NJ, USA
- Biomedical Sciences, Cooper Medical School at Rowan University, Camden, NJ, USA
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23
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Deshmukh R, Prajapati M, Harwansh RK. Management of Colorectal Cancer Using Nanocarriers-based Drug Delivery for Herbal Bioactives: Current and Emerging Approaches. Curr Pharm Biotechnol 2024; 25:599-622. [PMID: 38807329 DOI: 10.2174/0113892010242028231002075512] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 08/14/2023] [Accepted: 08/21/2023] [Indexed: 05/30/2024]
Abstract
Colorectal cancer (CRC) is a complex and multifactorial disorder in middle-aged people. Several modern medicines are available for treating and preventing it. However, their therapeutic uses are limited due to drawbacks, such as gastric perforation, diarrhea, intestinal bleeding, abdominal cramps, hair loss, nausea, vomiting, weight loss, and adverse reactions. Hence, there is a continuous quest for safe and effective medicines to manage human health problems, like CRC. In this context, herbal medicines are considered an alternative disease control system. It has become popular in countries, like American, European, and Asian, due to its safety and effectiveness, which has been practiced for 1000 years. During the last few decades, herbal medicines have been widely explored through multidisciplinary fields for getting active compounds against human diseases. Several herbal bioactives, like curcumin, glycyrrhizin, paclitaxel, chlorogenic acid, gallic acid, catechin, berberine, ursolic acid, betulinic acid, chrysin, resveratrol, quercetin, etc., have been found to be effective against CRC. However, their pharmacological applications are limited due to low bioavailability and therapeutic efficacy apart from their several health benefits. An effective delivery system is required to increase their bioavailability and efficacy. Therefore, targeted novel drug delivery approaches are promising for improving these substances' solubility, bioavailability, and therapeutic effects. Novel carrier systems, such as liposomes, nanoparticles, micelles, microspheres, dendrimers, microbeads, and hydrogels, are promising for delivering poorly soluble drugs to the target site, i.e., the colon. Thus, the present review is focused on the pathophysiology, molecular pathways, and diagnostic and treatment approaches for CRC. Moreover, an emphasis has been laid especially on herbal bioactive-based novel delivery systems and their clinical updates.
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Affiliation(s)
- Rohitas Deshmukh
- Institute of Pharmaceutical Research, GLA University, Mathura, 281406, India
| | - Mahendra Prajapati
- Institute of Pharmaceutical Research, GLA University, Mathura, 281406, India
| | - Ranjit K Harwansh
- Institute of Pharmaceutical Research, GLA University, Mathura, 281406, India
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24
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Kwao-Zigah G, Bediako-Bowan A, Boateng PA, Aryee GK, Abbang SM, Atampugbire G, Quaye O, Tagoe EA. Microbiome Dysbiosis, Dietary Intake and Lifestyle-Associated Factors Involve in Epigenetic Modulations in Colorectal Cancer: A Narrative Review. Cancer Control 2024; 31:10732748241263650. [PMID: 38889965 DOI: 10.1177/10732748241263650] [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] [Indexed: 06/20/2024] Open
Abstract
Background: Colorectal cancer is the second cause of cancer mortality and the third most commonly diagnosed cancer worldwide. Current data available implicate epigenetic modulations in colorectal cancer development. The health of the large bowel is impacted by gut microbiome dysbiosis, which may lead to colon and rectum cancers. The release of microbial metabolites and toxins by these microbiotas has been shown to activate epigenetic processes leading to colorectal cancer development. Increased consumption of a 'Westernized diet' and certain lifestyle factors such as excessive consumption of alcohol have been associated with colorectal cancer.Purpose: In this review, we seek to examine current knowledge on the involvement of gut microbiota, dietary factors, and alcohol consumption in colorectal cancer development through epigenetic modulations.Methods: A review of several published articles focusing on the mechanism of how changes in the gut microbiome, diet, and excessive alcohol consumption contribute to colorectal cancer development and the potential of using these factors as biomarkers for colorectal cancer diagnosis.Conclusions: This review presents scientific findings that provide a hopeful future for manipulating gut microbiome, diet, and alcohol consumption in colorectal cancer patients' management and care.
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Affiliation(s)
- Genevieve Kwao-Zigah
- Department of Biochemistry, Cell and Molecular Biology/West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana
| | - Antionette Bediako-Bowan
- Department of Surgery, University of Ghana Medical School, Accra, Ghana
- Department of Surgery, Korle Bu Teaching Hospital, Accra, Ghana
| | - Pius Agyenim Boateng
- Department of Biochemistry, Cell and Molecular Biology/West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana
| | - Gloria Kezia Aryee
- Department of Medical Laboratory Sciences, University of Ghana, Accra, Ghana
| | - Stacy Magdalene Abbang
- Department of Biochemistry, Cell and Molecular Biology/West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana
| | - Gabriel Atampugbire
- Department of Biochemistry, Cell and Molecular Biology/West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana
| | - Osbourne Quaye
- Department of Biochemistry, Cell and Molecular Biology/West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana
| | - Emmanuel A Tagoe
- Department of Medical Laboratory Sciences, University of Ghana, Accra, Ghana
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25
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Emiloju OE, Sinicrope FA. Neoadjuvant Immune Checkpoint Inhibitor Therapy for Localized Deficient Mismatch Repair Colorectal Cancer: A Review. JAMA Oncol 2023; 9:1708-1715. [PMID: 37676680 DOI: 10.1001/jamaoncol.2023.3323] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/08/2023]
Abstract
Importance Colorectal cancers (CRCs) with deficient DNA mismatch repair (dMMR) account for 15% of all CRCs. Deficient MMR is a predictive biomarker associated with responsiveness to immune checkpoint inhibitors (ICIs) in solid tumors, including CRC. The remarkable effectiveness of ICIs in metastatic CRC has led to their evaluation in the neoadjuvant and adjuvant treatment of localized disease. Observations Multiple prospective phase 2 studies in limited numbers of patients with localized dMMR CRC demonstrate high complete clinical and pathological response rates (60%-100%) to neoadjuvant ICIs, with low rates of grade 3 or higher ICI-related toxic effects. Given the median follow-up of 12 to 25 months in these studies, longer-term monitoring is needed to determine the durability of response and to ensure that oncologic outcomes are not compromised in patients undergoing nonoperative management. Neoadjuvant ICI therapy is especially attractive for patients with rectal cancer given the significant morbidity that accompanies pelvic irradiation and total mesorectal excision. Ongoing and planned prospective phase 2 trials will provide further data on important issues, including optimal neoadjuvant treatment duration, ICI monotherapy vs combination, and the need for adjuvant ICI therapy. Conclusions and Relevance While this review found that early results of neoadjuvant immunotherapy for localized dMMR CRC show high rates of major and complete pathological response, longer-term follow-up data are needed to ensure that oncologic outcomes are not compromised and are ideally improved. Neoadjuvant ICI therapy in localized dMMR CRC represents a potential paradigm shift with implications for organ preservation.
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Affiliation(s)
| | - Frank A Sinicrope
- Division of Medical Oncology, Mayo Clinic, Rochester, Minnesota
- Department of Medicine, Mayo Clinic Alix School of Medicine, Rochester, Minnesota
- Mayo Clinic Comprehensive Cancer Center, Rochester, Minnesota
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26
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Lee SW, Frankston CM, Kim J. Epigenome editing in cancer: Advances and challenges for potential therapeutic options. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2023; 383:191-230. [PMID: 38359969 DOI: 10.1016/bs.ircmb.2023.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
Cancers are diseases caused by genetic and non-genetic environmental factors. Epigenetic alterations, some attributed to non-genetic factors, can lead to cancer development. Epigenetic changes can occur in tumor suppressors or oncogenes, or they may contribute to global cell state changes, making cells abnormal. Recent advances in gene editing technology show potential for cancer treatment. Herein, we will discuss our current knowledge of epigenetic alterations occurring in cancer and epigenetic editing technologies that can be applied to developing therapeutic options.
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Affiliation(s)
- Seung-Won Lee
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, United States; Department of Molecular and Medical Genetics, School of Medicine, Oregon Health & Science University, Portland, OR, United States
| | - Connor Mitchell Frankston
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, United States; Biomedical Engineering Graduate Program, Department of Biomedical Engineering, School of Medicine, Oregon Health & Science University, Portland, OR, United States
| | - Jungsun Kim
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, United States; Department of Molecular and Medical Genetics, School of Medicine, Oregon Health & Science University, Portland, OR, United States; Cancer Biology Research Program, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, United States.
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27
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Moreta-Moraleda C, Queralt C, Vendrell-Ayats C, Forcales S, Martínez-Balibrea E. Chromatin factors: Ready to roll as biomarkers in metastatic colorectal cancer? Pharmacol Res 2023; 196:106924. [PMID: 37709185 DOI: 10.1016/j.phrs.2023.106924] [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] [Received: 04/14/2023] [Revised: 08/29/2023] [Accepted: 09/12/2023] [Indexed: 09/16/2023]
Abstract
Colorectal cancer (CRC) ranks as the third most prevalent cancer globally and stands as the fourth leading cause of cancer-related fatalities in 2020. Survival rates for metastatic disease have slightly improved in recent decades, with clinical trials showing median overall survival of approximately 24-30 months. This progress can be attributed to the integration of chemotherapeutic treatments alongside targeted therapies and immunotherapy. Despite these modest improvements, the primary obstacle to successful treatment for advanced CRC lies in the development of chemoresistance, whether inherent or acquired, which remains the major cause of treatment failure. Epigenetics has emerged as a hallmark of cancer, contributing to master transcription regulation and genome stability maintenance. As a result, epigenetic factors are starting to appear as potential clinical biomarkers for diagnosis, prognosis, and prediction of treatment response in CRC.In recent years, numerous studies have investigated the influence of DNA methylation, histone modifications, and chromatin remodelers on responses to chemotherapeutic treatments. While there is accumulating evidence indicating their significant involvement in various types of cancers, the exact relationship between chromatin landscapes and treatment modulation in CRC remains elusive. This review aims to provide a comprehensive summary of the most pertinent and extensively researched epigenetic-associated mechanisms described between 2015 and 2022 and their potential usefulness as predictive biomarkers in the metastatic disease.
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Affiliation(s)
- Cristina Moreta-Moraleda
- Immunology Unit, Department of Pathology and Experimental Therapeutics, Faculty of Medicine and Health Sciences, University of Barcelona, c/Feixa Llarga s/n, 08917 L'Hospitalet de Llobregat, Barcelona, Spain; Group of Inflammation, Immunity and Cancer, Molecular Mechanisms and Experimental Therapy in Oncology Program (Oncobell), The Bellvitge Biomedical Research Institute ( IDIBELL), Hospital Duran i Reynals 3a Planta, Av. Gran Via de l'Hospitalet 199, 08908 L'Hospitalet de Llobregat, Spain
| | - Cristina Queralt
- ProCURE Program, Catalan Instiute of Oncology, Carretera de Can Ruti, camí de les escoles s/n, 08916 Badalona, Spain
| | - Carla Vendrell-Ayats
- ProCURE Program, Catalan Instiute of Oncology, Carretera de Can Ruti, camí de les escoles s/n, 08916 Badalona, Spain; CARE Program, Germans Trias I Pujol Research Institute (IGTP), Carretera de Can Ruti, camí de les escoles s/n, 08916 Badalona, Spain
| | - Sonia Forcales
- Serra Húnter Programme, Immunology Unit, Department of Pathology and Experimental Therapeutics, Faculty of Medicine and Health Sciences, University of Barcelona, c/Feixa Llarga s/n, 08917 L'Hospitalet de Llobregat, Barcelona, Spain; Group of Inflammation, Immunity and Cancer, Molecular Mechanisms and Experimental Therapy in Oncology Program (Oncobell), The Bellvitge Biomedical Research Institute ( IDIBELL), Hospital Duran i Reynals 3a Planta, Av. Gran Via de l'Hospitalet 199, 08908 L'Hospitalet de Llobregat, Spain.
| | - Eva Martínez-Balibrea
- ProCURE Program, Catalan Instiute of Oncology, Carretera de Can Ruti, camí de les escoles s/n, 08916 Badalona, Spain; CARE Program, Germans Trias I Pujol Research Institute (IGTP), Carretera de Can Ruti, camí de les escoles s/n, 08916 Badalona, Spain.
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28
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Joe S, Kim J, Lee JY, Jeon J, Byeon I, Han SW, Ryoo SB, Park KJ, Song SH, Cho S, Shim H, Chu HBK, Kang J, Lee HS, Kim D, Kim YJ, Kim TY, Kim SY. Epigenetic insights into colorectal cancer: comprehensive genome-wide DNA methylation profiling of 294 patients in Korea. BMB Rep 2023; 56:563-568. [PMID: 37574809 PMCID: PMC10618077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 06/20/2023] [Accepted: 08/14/2023] [Indexed: 08/15/2023] Open
Abstract
DNA methylation regulates gene expression and contributes to tumorigenesis in the early stages of cancer. In colorectal cancer (CRC), CpG island methylator phenotype (CIMP) is recognized as a distinct subset that is associated with specific molecular and clinical features. In this study, we investigated the genomewide DNA methylation patterns among patients with CRC. The methylation data of 1 unmatched normal, 142 adjacent normal, and 294 tumor samples were analyzed. We identified 40,003 differentially methylated positions with 6,933 (79.8%) hypermethylated and 16,145 (51.6%) hypomethylated probes in the genic region. Hypermethylated probes were predominantly found in promoter-like regions, CpG islands, and N shore sites; hypomethylated probes were enriched in open-sea regions. CRC tumors were categorized into three CIMP subgroups, with 90 (30.6%) in the CIMP-high (CIMP-H), 115 (39.1%) in the CIMP-low (CIMP-L), and 89 (30.3%) in the non-CIMP group. The CIMP-H group was associated with microsatellite instabilityhigh tumors, hypermethylation of MLH1, older age, and rightsided tumors. Our results showed that genome-wide methylation analyses classified patients with CRC into three subgroups according to CIMP levels, with clinical and molecular features consistent with previous data. [BMB Reports 2023; 56(10): 563-568].
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Affiliation(s)
- Soobok Joe
- Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
| | - Jinyong Kim
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Jin-Young Lee
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Jongbum Jeon
- Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
| | - Iksu Byeon
- Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
| | - Sae-Won Han
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul 03080, Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Seung-Bum Ryoo
- Department of Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Kyu Joo Park
- Department of Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Sang-Hyun Song
- Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Sheehyun Cho
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Hyeran Shim
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Hoang Bao Khanh Chu
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Jisun Kang
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Hong Seok Lee
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | | | - Young-Joon Kim
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
- LepiDyne Co., Ltd., Seoul 04779, Korea
| | - Tae-You Kim
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul 03080, Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, Korea
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 08826, Korea
- IMBdx, Inc., Seoul 08506, Korea
| | - Seon-Young Kim
- Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
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29
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Choudhury H, Pandey M, Saravanan V, Mun ATY, Bhattamisra SK, Parikh A, Garg S, Gorain B. Recent progress of targeted nanocarriers in diagnostic, therapeutic, and theranostic applications in colorectal cancer. BIOMATERIALS ADVANCES 2023; 153:213556. [PMID: 37478770 DOI: 10.1016/j.bioadv.2023.213556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 06/28/2023] [Accepted: 07/06/2023] [Indexed: 07/23/2023]
Abstract
Cancer at the lower end of the digestive tract, colorectal cancer (CRC), starts with asymptomatic polyps, which can be diagnosed as cancer at a later stage. It is the fourth leading cause of malignancy-associated mortality worldwide. Despite progress in conventional treatment strategies, the possibility to overcome the mortality and morbidity issues with the enhancement of the lifespan of CRC patients is limited. With the advent of nanocarrier-based drug delivery systems, a promising revolution has been made in diagnosis, treatment, and theranostic purposes for cancer management. Herein, we reviewed the progress of miniaturized nanocarriers, such as liposomes, niosomes, solid lipid nanoparticles, micelles, and polymeric nanoparticles, employed in passive and active targeting and their role in theranostic applications in CRC. With this novel scope, the diagnosis and treatment of CRC have proceeded to the forefront of innovation, where specific characteristics of the nanocarriers, such as processability, flexibility in developing precise architecture, improved circulation, site-specific delivery, and rapid response, facilitate the management of cancer patients. Furthermore, surface-engineered technologies for the nanocarriers could involve receptor-mediated deliveries towards the overexpressed receptors on the CRC microenvironment. Moreover, the potential of clinical translation of these targeted miniaturized formulations as well as the possible limitations and barriers that could impact this translation into clinical practice were highlighted. The advancement of these newest developments in clinical research and progress into the commercialization stage gives hope for a better tomorrow.
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Affiliation(s)
- Hira Choudhury
- Department of Pharmaceutical Technology, School of Pharmacy, International Medical University, Bukit Jalil 57000, Kuala Lumpur, Malaysia
| | - Manisha Pandey
- Department of Pharmaceutical Technology, School of Pharmacy, International Medical University, Bukit Jalil 57000, Kuala Lumpur, Malaysia.
| | - Vilashini Saravanan
- Department of Pharmaceutical Technology, School of Pharmacy, International Medical University, Bukit Jalil 57000, Kuala Lumpur, Malaysia
| | - Amanda Tan Yee Mun
- Department of Pharmaceutical Technology, School of Pharmacy, International Medical University, Bukit Jalil 57000, Kuala Lumpur, Malaysia
| | - Subrat Kumar Bhattamisra
- Department of Life Sciences, School of Pharmacy, International Medical University, Bukit Jalil 57000, Kuala Lumpur, Malaysia
| | - Ankit Parikh
- Centre for Pharmaceutical Innovation (CPI), Clinical and Health Sciences, University of South Australia, Adelaide, SA 5000, Australia
| | - Sanjay Garg
- Centre for Pharmaceutical Innovation (CPI), Clinical and Health Sciences, University of South Australia, Adelaide, SA 5000, Australia
| | - Bapi Gorain
- Department of Pharmaceutical Sciences and Technology, Birla Institute of Technology, Mesra, Ranchi 835215, Jharkhand, India.
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30
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Téllez T, Martin-García D, Redondo M, García-Aranda M. Clusterin Expression in Colorectal Carcinomas. Int J Mol Sci 2023; 24:14641. [PMID: 37834086 PMCID: PMC10572822 DOI: 10.3390/ijms241914641] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/25/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023] Open
Abstract
Colorectal cancer is the third most diagnosed cancer, behind only breast and lung cancer. In terms of overall mortality, it ranks second due to, among other factors, problems with screening programs, which means that one of the factors that directly impacts survival and treatment success is early detection of the disease. Clusterin (CLU) is a molecular chaperone that has been linked to tumorigenesis, cancer progression and resistance to anticancer treatments, which has made it a promising drug target. However, it is still necessary to continue this line of research and to adjust the situations in which its use is more favorable. The aim of this paper is to review the current genetic knowledge on the role of CLU in tumorigenesis and cancer progression in general, and discuss its possible use as a therapeutic target in colorectal cancer.
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Affiliation(s)
- Teresa Téllez
- Surgical Specialties, Biochemistry and Immunology Department, Faculty of Medicine, University of Málaga, 29010 Malaga, Spain; (T.T.); (D.M.-G.)
- Red de Investigación en Servicios de Salud en Enfermedades Crónicas (REDISSEC), Red de Investigación en Cronicidad, Atención Primaria y Promoción de la Salud (RICAPPS), Instituto de Investigación Biomédica de Málaga (IBIMA), 29590 Malaga, Spain;
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina—IBIMA Plataforma BIONAND, 29590 Malaga, Spain
| | - Desirée Martin-García
- Surgical Specialties, Biochemistry and Immunology Department, Faculty of Medicine, University of Málaga, 29010 Malaga, Spain; (T.T.); (D.M.-G.)
- Red de Investigación en Servicios de Salud en Enfermedades Crónicas (REDISSEC), Red de Investigación en Cronicidad, Atención Primaria y Promoción de la Salud (RICAPPS), Instituto de Investigación Biomédica de Málaga (IBIMA), 29590 Malaga, Spain;
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina—IBIMA Plataforma BIONAND, 29590 Malaga, Spain
- Research and Innovation Unit, Hospital Costa del Sol, 29602 Marbella, Spain
| | - Maximino Redondo
- Surgical Specialties, Biochemistry and Immunology Department, Faculty of Medicine, University of Málaga, 29010 Malaga, Spain; (T.T.); (D.M.-G.)
- Red de Investigación en Servicios de Salud en Enfermedades Crónicas (REDISSEC), Red de Investigación en Cronicidad, Atención Primaria y Promoción de la Salud (RICAPPS), Instituto de Investigación Biomédica de Málaga (IBIMA), 29590 Malaga, Spain;
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina—IBIMA Plataforma BIONAND, 29590 Malaga, Spain
- Research and Innovation Unit, Hospital Costa del Sol, 29602 Marbella, Spain
| | - Marilina García-Aranda
- Red de Investigación en Servicios de Salud en Enfermedades Crónicas (REDISSEC), Red de Investigación en Cronicidad, Atención Primaria y Promoción de la Salud (RICAPPS), Instituto de Investigación Biomédica de Málaga (IBIMA), 29590 Malaga, Spain;
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina—IBIMA Plataforma BIONAND, 29590 Malaga, Spain
- Research and Innovation Unit, Hospital Costa del Sol, 29602 Marbella, Spain
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31
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Grassadonia A, Carletti E, De Luca A, Vici P, Di Lisa FS, Filomeno L, Cicero G, De Lellis L, Veschi S, Florio R, Brocco D, Di Marino P, Alberti S, Gamucci T, Borrelli P, Cama A, Tinari N. Prognostic value of gender and primary tumor location in metastatic colon cancer. J Cancer 2023; 14:2751-2758. [PMID: 37781086 PMCID: PMC10539565 DOI: 10.7150/jca.85748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 07/07/2023] [Indexed: 10/03/2023] Open
Abstract
Sex might influence prognosis in patients affected by colorectal cancer. We retrospectively studied a cohort of patients affected by metastatic colon cancer (mCC) stratified by sex and primary tumor location. RAS mutational status was also included in the analysis. Overall, 616 patients met the eligibility criteria, 261 women and 355 men. Neither gender, nor RAS mutational status influenced overall survival (OS) in the entire population. As expected, patients with right-sided colon cancer (RCC) had a significant shorter OS compared to those with left-sided colon cancer (LCC) (21.3 vs 33.1 months, p= 0.002). When the analysis was performed stratifying for gender, RCC retained worse prognosis among men (OS 20.5 vs 33.9 months, p= 0.008), but not among women (p= 0.132). Similarly, the presence of RAS mutations had no prognostic effect in women, but was significantly associate with shorter survival in men (OS 29.5 vs 33.7 months, p= 0.046). In addition, when comparing clinical outcome of women or men according to sidedness and RAS mutational status, RCC was associated with dismal prognosis only in men with RAS mutated tumor (OS 17.2 vs 32.3 months, p= 0.008). Our study highlights the importance of gender in the outcome of patients with mCC.
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Affiliation(s)
- Antonino Grassadonia
- Department of Innovative Technologies in Medicine and Dentistry, and Center for Advanced Studies and Technology (CAST), G. D'Annunzio University Chieti-Pescara, 66100 Chieti, Italy
| | - Erminia Carletti
- Department of Medical, Oral and Biotechnological Sciences, and Center for Advanced Studies and Technology (CAST), G. D'Annunzio University Chieti-Pescara, 66100 Chieti, Italy
| | - Antonella De Luca
- Department of Medical, Oral and Biotechnological Sciences, and Center for Advanced Studies and Technology (CAST), G. D'Annunzio University Chieti-Pescara, 66100 Chieti, Italy
| | - Patrizia Vici
- Unit of Phase IV Trials, IRCCS Regina Elena National Cancer Institute, 00144 Rome, Italy
| | | | - Lorena Filomeno
- Unit of Phase IV Trials, IRCCS Regina Elena National Cancer Institute, 00144 Rome, Italy
| | - Giuseppe Cicero
- Department of Surgical, Oncological and Oral Sciences, Section of Medical Oncology, University of Palermo, 90133 Palermo, Italy
| | - Laura De Lellis
- Department of Pharmacy, G. D'Annunzio University, Chieti-Pescara, 66100 Chieti, Italy
| | - Serena Veschi
- Department of Pharmacy, G. D'Annunzio University, Chieti-Pescara, 66100 Chieti, Italy
| | - Rosalba Florio
- Department of Pharmacy, G. D'Annunzio University, Chieti-Pescara, 66100 Chieti, Italy
| | - Davide Brocco
- Department of Pharmacy, G. D'Annunzio University, Chieti-Pescara, 66100 Chieti, Italy
| | - Pietro Di Marino
- Clinical Oncology, S.S. Annunziata Hospital, 66100 Chieti, Italy
| | - Saverio Alberti
- Unit of Medical Genetics, Department of Biomedical Sciences-BIOMORF, University of Messina, 98125 Messina, Italy
| | - Teresa Gamucci
- Medical Oncology, Sandro Pertini Hospital, 00159 Rome, Italy
| | - Paola Borrelli
- Laboratory of Biostatistics, Department of Medical, Oral and Biotechnological Sciences, G. D'Annunzio University Chieti-Pescara, 66100 Chieti, Italy
| | - Alessandro Cama
- Department of Pharmacy, G. D'Annunzio University, Chieti-Pescara, 66100 Chieti, Italy
| | - Nicola Tinari
- Department of Medical, Oral and Biotechnological Sciences, and Center for Advanced Studies and Technology (CAST), G. D'Annunzio University Chieti-Pescara, 66100 Chieti, Italy
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32
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Asari Y, Yamazaki J, Thandar O, Suzuki T, Aoshima K, Takeuchi K, Kinoshita R, Kim S, Hosoya K, Ishizaki T, Kagawa Y, Jelinek J, Yokoyama S, Sasaki N, Ohta H, Nakamura K, Takiguchi M. Diverse genome-wide DNA methylation alterations in canine hepatocellular tumours. Vet Med Sci 2023; 9:2006-2014. [PMID: 37483163 PMCID: PMC10508506 DOI: 10.1002/vms3.1204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 06/02/2023] [Accepted: 07/06/2023] [Indexed: 07/25/2023] Open
Abstract
BACKGROUND Canine hepatocellular tumours (HCTs) are common primary liver tumours. However, the exact mechanisms of tumourigenesis remain unclear. Although some genetic mutations have been reported, DNA methylation alterations in canine HCT have not been well studied. OBJECTIVES In this study, we aimed to analyse the DNA methylation status of canine HCT. METHODS Tissues from 33 hepatocellular carcinomas, 3 hepatocellular adenomas, 1 nodular hyperplasia, 21 non-tumour livers from the patients and normal livers from 5 healthy dogs were used. We analysed the DNA methylation levels of 72,367 cytosine-guanine dinucleotides (CpG sites) in all 63 samples. RESULTS AND CONCLUSIONS Although a large fraction of CpG sites that were highly methylated in the normal liver became hypomethylated in tumours from most patients, we also found some patients with less remarkable change or no change in DNA methylation. Hierarchical clustering analysis revealed that 32 of 37 tumour samples differed from normal livers, although the remaining 5 tumour livers fell into the same cluster as normal livers. In addition, the number of hypermethylated genes in tumour livers varied among tumour cases, suggesting various DNA methylation patterns in different tumour groups. However, patient and clinical parameters, such as age, were not associated with DNA methylation status. In conclusion, we found that HCTs undergo aberrant and diverse patterns of genome-wide DNA methylation compared with normal liver tissue, suggesting a complex epigenetic mechanism in canine HCT.
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Affiliation(s)
- Yu Asari
- Laboratory of Veterinary Internal Medicine, Graduate School of Veterinary MedicineHokkaido UniversitySapporoJapan
| | - Jumpei Yamazaki
- Veterinary Teaching HospitalGraduate School of Veterinary MedicineHokkaido UniversitySapporoJapan
- Translational Research Unit, Veterinary Teaching Hospital, Graduate School of Veterinary MedicineHokkaido UniversitySapporoJapan
- One Health Research Center, Cancer Research UnitHokkaido UniversitySapporoJapan
| | - Oo Thandar
- Laboratory of Veterinary Internal Medicine, Graduate School of Veterinary MedicineHokkaido UniversitySapporoJapan
| | - Tamami Suzuki
- Laboratory of Comparative Pathology, Graduate School of Veterinary MedicineHokkaido UniversitySapporoJapan
| | - Keisuke Aoshima
- One Health Research Center, Cancer Research UnitHokkaido UniversitySapporoJapan
- Laboratory of Comparative Pathology, Graduate School of Veterinary MedicineHokkaido UniversitySapporoJapan
| | - Kyosuke Takeuchi
- Veterinary Teaching HospitalGraduate School of Veterinary MedicineHokkaido UniversitySapporoJapan
| | - Ryohei Kinoshita
- Veterinary Teaching HospitalGraduate School of Veterinary MedicineHokkaido UniversitySapporoJapan
- One Health Research Center, Cancer Research UnitHokkaido UniversitySapporoJapan
| | - Sangho Kim
- One Health Research Center, Cancer Research UnitHokkaido UniversitySapporoJapan
- Laboratory of Veterinary Surgery, Graduate School of Veterinary MedicineHokkaido UniversitySapporoJapan
| | - Kenji Hosoya
- One Health Research Center, Cancer Research UnitHokkaido UniversitySapporoJapan
- Laboratory of Veterinary Surgery, Graduate School of Veterinary MedicineHokkaido UniversitySapporoJapan
| | - Teita Ishizaki
- Veterinary Teaching HospitalGraduate School of Veterinary MedicineHokkaido UniversitySapporoJapan
- Laboratory of Comparative Pathology, Graduate School of Veterinary MedicineHokkaido UniversitySapporoJapan
- North LabSapporoJapan
| | | | | | - Shoko Yokoyama
- Veterinary Teaching HospitalGraduate School of Veterinary MedicineHokkaido UniversitySapporoJapan
- Translational Research Unit, Veterinary Teaching Hospital, Graduate School of Veterinary MedicineHokkaido UniversitySapporoJapan
- One Health Research Center, Cancer Research UnitHokkaido UniversitySapporoJapan
| | - Noboru Sasaki
- Laboratory of Veterinary Internal Medicine, Graduate School of Veterinary MedicineHokkaido UniversitySapporoJapan
| | - Hiroshi Ohta
- Laboratory of Veterinary Internal Medicine, Graduate School of Veterinary MedicineHokkaido UniversitySapporoJapan
| | - Kensuke Nakamura
- Laboratory of Veterinary Internal Medicine, Graduate School of Veterinary MedicineHokkaido UniversitySapporoJapan
| | - Mitsuyoshi Takiguchi
- Laboratory of Veterinary Internal Medicine, Graduate School of Veterinary MedicineHokkaido UniversitySapporoJapan
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33
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Kim J, Nath K, Schmidlin K, Schaufelberger H, Quattropani C, Vannini S, Mossi S, Thumshirn M, Manz M, Litichevskiy L, Fan J, Dmitrieva-Posocco O, Li M, Levy M, Schär P, Zwahlen M, Thaiss CA, Truninger K. Hierarchical contribution of individual lifestyle factors and their interactions on adenomatous and serrated polyp risk. J Gastroenterol 2023; 58:856-867. [PMID: 37300599 PMCID: PMC10423128 DOI: 10.1007/s00535-023-02004-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 05/28/2023] [Indexed: 06/12/2023]
Abstract
BACKGROUND Individual colorectal polyp risk factors are well characterized; however, insights into their pathway-specific interactions are scarce. We aimed to identify the impact of individual risk factors and their joint effects on adenomatous (AP) and serrated polyp (SP) risk. METHODS We collected information on 363 lifestyle and metabolic parameters from 1597 colonoscopy participants, resulting in over 521,000 data points. We used multivariate statistics and machine-learning approaches to assess associations of single variables and their interactions with AP and SP risk. RESULTS Individual factors and their interactions showed common and polyp subtype-specific effects. Abdominal obesity, high body mass index (BMI), metabolic syndrome, and red meat consumption globally increased polyp risk. Age, gender, and western diet associated with AP risk, while smoking was associated with SP risk. CRC family history was associated with advanced adenomas and diabetes with sessile serrated lesions. Regarding lifestyle factor interactions, no lifestyle or dietary adjustments mitigated the adverse smoking effect on SP risk, whereas its negative effect was exacerbated by alcohol in the conventional pathway. The adverse effect of red meat on SP risk was not ameliorated by any factor, but was further exacerbated by western diet along the conventional pathway. No modification of any factor reduced the negative impact of metabolic syndrome on AP risk, whereas increased fatless fish or meat substitutes' intake mitigated its effect on SP risk. CONCLUSIONS Individual risk factors and their interactions for polyp formation along the adenomatous and serrated pathways are strongly heterogeneous. Our findings may facilitate tailored lifestyle recommendations and contribute to a better understanding of how risk factor combinations impact colorectal carcinogenesis.
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Affiliation(s)
- Jihee Kim
- Microbiology Department and Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, 3610 Hamilton Walk, Philadelphia, PA, 19104, USA
| | - Kirti Nath
- Microbiology Department and Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, 3610 Hamilton Walk, Philadelphia, PA, 19104, USA
| | - Kurt Schmidlin
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | | | | | | | | | | | - Michael Manz
- Clarunis, University Hospital of Basel, Basel, Switzerland
| | - Lev Litichevskiy
- Microbiology Department and Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, 3610 Hamilton Walk, Philadelphia, PA, 19104, USA
| | - Jiaxin Fan
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Oxana Dmitrieva-Posocco
- Microbiology Department and Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, 3610 Hamilton Walk, Philadelphia, PA, 19104, USA
| | - Mingyao Li
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Maayan Levy
- Microbiology Department and Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, 3610 Hamilton Walk, Philadelphia, PA, 19104, USA
| | - Primo Schär
- Department of Biomedicine, Genome Plasticity Group, University of Basel, Basel, Switzerland
| | - Marcel Zwahlen
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Christoph A Thaiss
- Microbiology Department and Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, 3610 Hamilton Walk, Philadelphia, PA, 19104, USA.
| | - Kaspar Truninger
- Department of Biomedicine, Genome Plasticity Group, University of Basel, Basel, Switzerland.
- Gastroenterologie Oberaargau, Langenthal, Switzerland.
- Clinic of Gastroenterology and Hepatology, Stadtspital Triemli, Zurich, Switzerland.
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34
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Jevšinek Skok D, Hauptman N. In Silico Gene Prioritization Highlights the Significance of Bone Morphogenetic Protein 4 ( BMP4) Promoter Methylation across All Methylation Clusters in Colorectal Cancer. Int J Mol Sci 2023; 24:12692. [PMID: 37628872 PMCID: PMC10454928 DOI: 10.3390/ijms241612692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 08/03/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023] Open
Abstract
The cytosine-phosphate-guanine (CpG) island methylator phenotype (CIMP) represents one of the pathways involved in the development of colorectal cancer, characterized by genome-wide hypermethylation. To identify samples exhibiting hypermethylation, we used unsupervised hierarchical clustering on genome-wide methylation data. This clustering analysis revealed the presence of four distinct subtypes within the tumor samples, namely, CIMP-H, CIMP-L, cluster 3, and cluster 4. These subtypes demonstrated varying levels of methylation, categorized as high, intermediate, and very low. To gain further insights, we mapped significant probes from all clusters to Ensembl Regulatory build 89, with a specific focus on those located within promoter regions or bound regions. By intersecting the methylated promoter and bound regions across all methylation subtypes, we identified a total of 253 genes exhibiting aberrant methylation patterns in the promoter regions across all four subtypes of colorectal cancer. Among these genes, our comprehensive genome-wide analysis highlights bone morphogenic protein 4 (BMP4) as the most prominent candidate. This significant finding was derived through the utilization of various bioinformatics tools, emphasizing the potential role of BMP4 in colorectal cancer development and progression.
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Affiliation(s)
- Daša Jevšinek Skok
- Agricultural Institute of Slovenia, Hacquetova ulica 17, SI-1000 Ljubljana, Slovenia;
| | - Nina Hauptman
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, Korytkova 2, SI-1000 Ljubljana, Slovenia
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35
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Kerdivel G, Amrouche F, Calmejane MA, Carallis F, Hamroune J, Hantel C, Bertherat J, Assié G, Boeva V. DNA hypermethylation driven by DNMT1 and DNMT3A favors tumor immune escape contributing to the aggressiveness of adrenocortical carcinoma. Clin Epigenetics 2023; 15:121. [PMID: 37528470 PMCID: PMC10394822 DOI: 10.1186/s13148-023-01534-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 07/16/2023] [Indexed: 08/03/2023] Open
Abstract
BACKGROUND Adrenocortical carcinoma is rare and aggressive endocrine cancer of the adrenal gland. Within adrenocortical carcinoma, a recently described subtype characterized by a CpG island methylator phenotype (CIMP) has been associated with an especially poor prognosis. However, the drivers of CIMP remain unknown. Furthermore, the functional relation between CIMP and poor clinical outcomes of patients with adrenocortical carcinoma stays elusive. RESULTS Here, we show that CIMP in adrenocortical carcinoma is linked to the increased expression of DNA methyltransferases DNMT1 and DNMT3A driven by a gain of gene copy number and cell hyperproliferation. Importantly, we demonstrate that CIMP contributes to tumor aggressiveness by favoring tumor immune escape. This effect could be at least partially reversed by treatment with the demethylating agent 5-azacytidine. CONCLUSIONS In sum, our findings suggest that co-treatment with demethylating agents might enhance the efficacy of immunotherapy and could represent a novel therapeutic approach for patients with high CIMP adrenocortical carcinoma.
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Affiliation(s)
- Gwenneg Kerdivel
- INSERM, U1016, Cochin Institute, CNRS UMR8104, University of Paris, 24 rue du Faubourg Saint-Jacques, Paris, France
| | - Floriane Amrouche
- INSERM, U1016, Cochin Institute, CNRS UMR8104, University of Paris, 24 rue du Faubourg Saint-Jacques, Paris, France
| | - Marie-Ange Calmejane
- INSERM, U1016, Cochin Institute, CNRS UMR8104, University of Paris, 24 rue du Faubourg Saint-Jacques, Paris, France
| | | | - Juliette Hamroune
- INSERM, U1016, Cochin Institute, CNRS UMR8104, University of Paris, 24 rue du Faubourg Saint-Jacques, Paris, France
| | - Constanze Hantel
- Department of Endocrinology, Diabetology and Clinical Nutrition, University Hospital Zurich (USZ) and University of Zurich (UZH), Zurich, Switzerland
- Medizinische Klinik und Poliklinik III, University Hospital Carl Gustav Carus Dresden, Dresden, Germany
| | - Jérôme Bertherat
- INSERM, U1016, Cochin Institute, CNRS UMR8104, University of Paris, 24 rue du Faubourg Saint-Jacques, Paris, France
| | - Guillaume Assié
- INSERM, U1016, Cochin Institute, CNRS UMR8104, University of Paris, 24 rue du Faubourg Saint-Jacques, Paris, France
| | - Valentina Boeva
- INSERM, U1016, Cochin Institute, CNRS UMR8104, University of Paris, 24 rue du Faubourg Saint-Jacques, Paris, France.
- Department of Computer Science, Institute for Machine Learning, ETH Zurich, Universitätstrasse 6, 8092, Zurich, Switzerland.
- Swiss Institute of Bioinformatics (SIB), Zurich, Switzerland.
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Taghehchian N, Samsami Y, Maharati A, Zangouei AS, Boroumand-Noughabi S, Moghbeli M. Molecular biology of microRNA-342 during tumor progression and invasion. Pathol Res Pract 2023; 248:154672. [PMID: 37413875 DOI: 10.1016/j.prp.2023.154672] [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] [Received: 06/02/2023] [Accepted: 07/02/2023] [Indexed: 07/08/2023]
Abstract
Cancer is considered as one of the main causes of human deaths and health challenges in the world. Various factors are involved in the high death rate of cancer patients, including late diagnosis and drug resistance that result in treatment failure and tumor recurrence. Invasive diagnostic methods are one of the main reasons of late tumor detection in cancer patients. Therefore, it is necessary to investigate the molecular tumor biology to introduce efficient non-invasive markers. MicroRNAs (miRNAs) are involved in regulation of the cellular mechanisms such as cell proliferation, apoptosis, and migration. MiRNAs deregulations have been also frequently shown in different tumor types. Here, we discussed the molecular mechanisms of miR-342 during tumor growth. MiR-342 mainly functions as a tumor suppressor by the regulation of transcription factors and signaling pathways such as WNT, PI3K/AKT, NF-kB, and MAPK. Therefore, miR-342 mimics can be used as a reliable therapeutic strategy to inhibit the tumor cells growth. The present review can also pave the way to introduce the miR-342 as a non-invasive diagnostic/prognostic marker in cancer patients.
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Affiliation(s)
- Negin Taghehchian
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Yalda Samsami
- Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Amirhosein Maharati
- Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Amir Sadra Zangouei
- Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Samaneh Boroumand-Noughabi
- Department of Hematology and Blood Bank, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Meysam Moghbeli
- Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
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Bhandari YR, Krishna V, Powers R, Parmar S, Thursby SJ, Gupta E, Kulak O, Gokare P, Reumers J, Van Wesenbeeck L, Bachman KE, Baylin SB, Easwaran H. Transcription factor expression repertoire basis for epigenetic and transcriptional subtypes of colorectal cancers. Proc Natl Acad Sci U S A 2023; 120:e2301536120. [PMID: 37487069 PMCID: PMC10401032 DOI: 10.1073/pnas.2301536120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 06/15/2023] [Indexed: 07/26/2023] Open
Abstract
Colorectal cancers (CRCs) form a heterogenous group classified into epigenetic and transcriptional subtypes. The basis for the epigenetic subtypes, exemplified by varying degrees of promoter DNA hypermethylation, and its relation to the transcriptional subtypes is not well understood. We link cancer-specific transcription factor (TF) expression alterations to methylation alterations near TF-binding sites at promoter and enhancer regions in CRCs and their premalignant precursor lesions to provide mechanistic insights into the origins and evolution of the CRC molecular subtypes. A gradient of TF expression changes forms a basis for the subtypes of abnormal DNA methylation, termed CpG-island promoter DNA methylation phenotypes (CIMPs), in CRCs and other cancers. CIMP is tightly correlated with cancer-specific hypermethylation at enhancers, which we term CpG-enhancer methylation phenotype (CEMP). Coordinated promoter and enhancer methylation appears to be driven by downregulation of TFs with common binding sites at the hypermethylated enhancers and promoters. The altered expression of TFs related to hypermethylator subtypes occurs early during CRC development, detectable in premalignant adenomas. TF-based profiling further identifies patients with worse overall survival. Importantly, altered expression of these TFs discriminates the transcriptome-based consensus molecular subtypes (CMS), thus providing a common basis for CIMP and CMS subtypes.
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Affiliation(s)
- Yuba R. Bhandari
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD21287
| | - Vinod Krishna
- Infectious Diseases and Vaccines Therapeutic Area, Janssen Research and Development, Spring House, PA19477
| | - Rachael Powers
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD21287
| | - Sehej Parmar
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD21287
| | - Sara-Jayne Thursby
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD21287
| | - Ekta Gupta
- Division of Gastroenterology and Hepatology, The Johns Hopkins University School of Medicine, Baltimore, MD21287
| | - Ozlem Kulak
- Division of Gastrointestinal and Liver Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD21287
| | - Prashanth Gokare
- Oncology Therapeutic Area, Janssen Research and Development, Spring House, PA19477
| | - Joke Reumers
- Discovery Technologies and Molecular Pharmacology, Therapeutics Discovery, Janssen Research and Development, Turnhoutseweg 30, 2340Beerse, Belgiumg
| | - Liesbeth Van Wesenbeeck
- Infectious Diseases and Vaccines Therapeutic Area, Janssen Research and Development, Turnhoutseweg 30, 2340Beerse, Belgium
| | - Kurtis E. Bachman
- Oncology Therapeutic Area, Janssen Research and Development, Spring House, PA19477
| | - Stephen B. Baylin
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD21287
| | - Hariharan Easwaran
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD21287
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Utsumi T, Yamada Y, Diaz-Meco MT, Moscat J, Nakanishi Y. Sessile serrated lesions with dysplasia: is it possible to nip them in the bud? J Gastroenterol 2023; 58:705-717. [PMID: 37219625 PMCID: PMC10366009 DOI: 10.1007/s00535-023-02003-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 05/14/2023] [Indexed: 05/24/2023]
Abstract
The serrated neoplasia pathway constitutes an "alternative route" to colorectal cancer (CRC), and sessile serrated lesions with dysplasia (SSLDs) are an intermediate step between sessile serrated lesions (SSLs) and invasive CRC in this pathway. While SSLs show indolent growth before becoming dysplastic (> 10-15 years), SSLDs are considered to rapidly progress to either immunogenic microsatellite instable-high (MSI-H) CRC (presumably 75% of cases) or mesenchymal microsatellite stable (MSS) CRC. Their flat shapes and the relatively short window of this intermediate state make it difficult to detect and diagnose SSLDs; thus, these lesions are potent precursors of post-colonoscopy/interval cancers. Confusing terminology and the lack of longitudinal observation data of serrated polyps have hampered the accumulation of knowledge about SSLDs; however, a growing body of evidence has started to clarify their characteristics and biology. Together with recent efforts to incorporate terminology, histological studies of SSLDs have identified distinct dysplastic patterns and revealed alterations in the tumor microenvironment (TME). Molecular studies at the single-cell level have identified distinct gene alterations in both the epithelium and the TME. Mouse serrated tumor models have demonstrated the importance of TME in disease progression. Advances in colonoscopy provide clues to distinguish pre-malignant from non-malignant-SSLs. Recent progress in all aspects of the field has enhanced our understanding of the biology of SSLDs. The aim of this review article was to assess the current knowledge of SSLDs and highlight their clinical implications.
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Affiliation(s)
- Takahiro Utsumi
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, 54 Kawaharacho, Shogoin, Sakyo-Ku, Kyoto, 606-8507, Japan
| | - Yosuke Yamada
- Department of Diagnostic Pathology, Kyoto University Hospital, Kyoto, Japan
| | - Maria Teresa Diaz-Meco
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York City, NY, USA
| | - Jorge Moscat
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York City, NY, USA
| | - Yuki Nakanishi
- Department of Gastroenterology and Hepatology, Kyoto University Graduate School of Medicine, 54 Kawaharacho, Shogoin, Sakyo-Ku, Kyoto, 606-8507, Japan.
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van Toledo DEFWM, IJspeert JE, Boersma H, Musler AR, Bleijenberg AGC, Dekker E, van Noesel CJM. Polyps and Colorectal Cancer in Serrated Polyposis Syndrome: Contribution of the Classical Adenoma-Carcinoma and Serrated Neoplasia Pathways. Clin Transl Gastroenterol 2023; 14:e00611. [PMID: 37352472 PMCID: PMC10461936 DOI: 10.14309/ctg.0000000000000611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 06/07/2023] [Indexed: 06/25/2023] Open
Abstract
INTRODUCTION Patients with serrated polyposis syndrome (SPS) have an increased risk to develop colorectal cancer (CRC). Due to an abundance of serrated polyps, these CRCs are assumed to arise mainly through the serrated neoplasia pathway rather than through the classical adenoma-carcinoma pathway. We aimed to evaluate the pathogenetic routes of CRCs in patients with SPS. METHODS We collected endoscopy and pathology data on CRCs and polyps of patients with SPS under treatment in our center. Our primary end point was the proportion of BRAFV600E mutated CRCs, indicating serrated pathway CRCs (sCRCs). CRCs lacking BRAFV600E most likely inferred a classical adenoma-carcinoma origin (aCRCs). We assessed patient, polyp, and CRC characteristics and stratified for BRAFV600E mutation status. RESULTS Thirty-five patients with SPS harbored a total of 43 CRCs. Twenty-one CRCs (48.8%) carried a BRAFV600E mutation, 10 of which lacked MLH1 staining and 17 (81%) were located in the proximal colon. Twenty-two CRCs (51.1%) did not carry a BRAFV600E mutation and were MLH1 proficient. Of these 22 putatively aCRCs, 17 (77.3%) were located distally and one-third (36.4%) harbored a pathogenic KRAS or NRAS mutation. In patients with BRAFwt -CRCs, a higher ratio of the median number of conventional adenomas versus serrated polyps was found (4 vs 13) than patients with BRAFV600E -CRCs (1 vs 14). DISCUSSION Our study indicates that in patients with SPS, the ratio of sCRCs:aCRCs on average is 50:50. This elevated sCRC:aCRC ratio in patients with SPS, when compared with non-SPS patients, correlates well with the differences in the ratios of the numbers of sessile serrated lesions and conventional adenomas in patients with SPS and non-SPS patients, respectively.
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Affiliation(s)
- David E. F. W. M. van Toledo
- Department of Gastroenterology and Hepatology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands;
- Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, the Netherlands;
- Cancer Center Amsterdam, Amsterdam, the Netherlands;
| | - Joep E.G. IJspeert
- Department of Gastroenterology and Hepatology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands;
- Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, the Netherlands;
- Cancer Center Amsterdam, Amsterdam, the Netherlands;
| | - Hannah Boersma
- Department of Gastroenterology and Hepatology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands;
| | - Alex R. Musler
- Amsterdam University Medical Centers, University of Amsterdam, Department of Pathology, Amsterdam, the Netherlands.
| | - Arne G. C. Bleijenberg
- Department of Gastroenterology and Hepatology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands;
- Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, the Netherlands;
- Cancer Center Amsterdam, Amsterdam, the Netherlands;
| | - Evelien Dekker
- Department of Gastroenterology and Hepatology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands;
- Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, the Netherlands;
- Cancer Center Amsterdam, Amsterdam, the Netherlands;
| | - Carel J. M. van Noesel
- Amsterdam University Medical Centers, University of Amsterdam, Department of Pathology, Amsterdam, the Netherlands.
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Sun JM, Chow WY, Xu G, Hicks MJ, Nakka M, Shen J, Ng PKS, Taylor AM, Yu A, Farrar JE, Barkauskas DA, Gorlick R, Guidry Auvil JM, Gerhard D, Meltzer P, Guerra R, Man TK, Lau CC. The Role of FAS Receptor Methylation in Osteosarcoma Metastasis. Int J Mol Sci 2023; 24:12155. [PMID: 37569529 PMCID: PMC10418590 DOI: 10.3390/ijms241512155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/26/2023] [Accepted: 07/27/2023] [Indexed: 08/13/2023] Open
Abstract
Osteosarcoma is the most frequent primary malignant bone tumor with an annual incidence of about 400 cases in the United States. Osteosarcoma primarily metastasizes to the lungs, where FAS ligand (FASL) is constitutively expressed. The interaction of FASL and its cell surface receptor, FAS, triggers apoptosis in normal cells; however, this function is altered in cancer cells. DNA methylation has previously been explored as a mechanism for altering FAS expression, but no variability was identified in the CpG island (CGI) overlapping the promoter. Analysis of an expanded region, including CGI shores and shelves, revealed high variability in the methylation of certain CpG sites that correlated significantly with FAS mRNA expression in a negative manner. Bisulfite sequencing revealed additional CpG sites, which were highly methylated in the metastatic LM7 cell line but unmethylated in its parental non-metastatic SaOS-2 cell line. Treatment with the demethylating agent, 5-azacytidine, resulted in a loss of methylation in CpG sites located within the FAS promoter and restored FAS protein expression in LM7 cells, resulting in reduced migration. Orthotopic implantation of 5-azacytidine treated LM7 cells into severe combined immunodeficient mice led to decreased lung metastases. These results suggest that DNA methylation of CGI shore sites may regulate FAS expression and constitute a potential target for osteosarcoma therapy, utilizing demethylating agents currently approved for the treatment of other cancers.
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Affiliation(s)
- Jiayi M. Sun
- Program of Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA; (J.M.S.); (A.M.T.); (T.-K.M.)
- Department of Pediatrics-Oncology, Baylor College of Medicine, Houston, TX 77030, USA; (W.-Y.C.); (G.X.); (M.N.); (J.S.); (A.Y.)
| | - Wing-Yuk Chow
- Department of Pediatrics-Oncology, Baylor College of Medicine, Houston, TX 77030, USA; (W.-Y.C.); (G.X.); (M.N.); (J.S.); (A.Y.)
- Texas Children’s Cancer and Hematology Center, Houston, TX 77030, USA
| | - Gufeng Xu
- Department of Pediatrics-Oncology, Baylor College of Medicine, Houston, TX 77030, USA; (W.-Y.C.); (G.X.); (M.N.); (J.S.); (A.Y.)
- Texas Children’s Cancer and Hematology Center, Houston, TX 77030, USA
| | - M. John Hicks
- Department of Pathology, Texas Children’s Hospital, Baylor College of Medicine, Houston, TX 77030, USA;
| | - Manjula Nakka
- Department of Pediatrics-Oncology, Baylor College of Medicine, Houston, TX 77030, USA; (W.-Y.C.); (G.X.); (M.N.); (J.S.); (A.Y.)
- Texas Children’s Cancer and Hematology Center, Houston, TX 77030, USA
| | - Jianhe Shen
- Department of Pediatrics-Oncology, Baylor College of Medicine, Houston, TX 77030, USA; (W.-Y.C.); (G.X.); (M.N.); (J.S.); (A.Y.)
- Texas Children’s Cancer and Hematology Center, Houston, TX 77030, USA
| | | | - Aaron M. Taylor
- Program of Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA; (J.M.S.); (A.M.T.); (T.-K.M.)
- Department of Pediatrics-Oncology, Baylor College of Medicine, Houston, TX 77030, USA; (W.-Y.C.); (G.X.); (M.N.); (J.S.); (A.Y.)
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA;
| | - Alexander Yu
- Department of Pediatrics-Oncology, Baylor College of Medicine, Houston, TX 77030, USA; (W.-Y.C.); (G.X.); (M.N.); (J.S.); (A.Y.)
- Texas Children’s Cancer and Hematology Center, Houston, TX 77030, USA
| | - Jason E. Farrar
- Arkansas Children’s Research Institute and Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA;
| | - Donald A. Barkauskas
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA;
| | - Richard Gorlick
- Division of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - Jaime M. Guidry Auvil
- Office of Cancer Genomics, National Cancer Institute, Bethesda, MD 20892, USA; (J.M.G.A.)
| | - Daniela Gerhard
- Office of Cancer Genomics, National Cancer Institute, Bethesda, MD 20892, USA; (J.M.G.A.)
| | - Paul Meltzer
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA;
| | - Rudy Guerra
- Department of Statistics, Rice University, Houston, TX 77005, USA;
| | - Tsz-Kwong Man
- Program of Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA; (J.M.S.); (A.M.T.); (T.-K.M.)
- Department of Pediatrics-Oncology, Baylor College of Medicine, Houston, TX 77030, USA; (W.-Y.C.); (G.X.); (M.N.); (J.S.); (A.Y.)
- Texas Children’s Cancer and Hematology Center, Houston, TX 77030, USA
| | - Ching C. Lau
- Program of Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX 77030, USA; (J.M.S.); (A.M.T.); (T.-K.M.)
- Department of Pediatrics-Oncology, Baylor College of Medicine, Houston, TX 77030, USA; (W.-Y.C.); (G.X.); (M.N.); (J.S.); (A.Y.)
- Texas Children’s Cancer and Hematology Center, Houston, TX 77030, USA
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA;
- Center for Cancer and Blood Disorders, Connecticut Children’s Medical Center, Hartford, CT 06106, USA
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Lukacova E, Burjanivova T, Podlesniy P, Grendar M, Turyova E, Kasubova I, Laca L, Mikolajcik P, Kudelova E, Vanochova A, Miklusica J, Mersakova S, Lasabova Z. Hypermethylated GRIA4, a potential biomarker for an early non-invasive detection of metastasis of clinically known colorectal cancer. Front Oncol 2023; 13:1205791. [PMID: 37476382 PMCID: PMC10354553 DOI: 10.3389/fonc.2023.1205791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/12/2023] [Indexed: 07/22/2023] Open
Abstract
Introduction Colorectal cancer (CRC) can develop through several dysregulated molecular pathways, including the serrated pathway, characterized by CpG island methylator (CIMP) phenotype. Although the tumor tissue is a commonly tested material, sample types such as stool or plasma, bring a new, non-invasive approach. Several cancer-related methylated genes have been identified in CRC patients, including gene GRIA4, showing promising diagnostic potential. The aim of our study was to develop a sensitive droplet digital PCR (ddPCR) assay to examine GRIA4 hypermethylation status in CRC patients and evaluate its diagnostic potential in tissue and liquid biopsy samples. Methods In total, 23 patients participated in this study, 7 patients with primary CRC and 16 patients with liver metastasis of clinically known CRC. We obtained tumor and non-tumor tissues (N=17), blood samples pre- and post-surgery (N=22), and blood of five volunteers without a personal cancer history. We have developed and optimized a ddPCR assay for GRIA4 hypermethylation detection, from tissue and plasma samples. Results We detected significantly increased GRIA4 methylation in tumor tissues compared to their adjacent non-tumor tissue, p<0.0001. Receiver operating characteristic (ROC) analysis defined cutoff values to separate primary tumors and metastases from non-tumor colon/rectum, specifically 36.85% for primary tumors and 34.81% for metastases. All primary tumors were above this threshold. When comparing the methylation levels of metastatic vs. non-tumor tissue, a smaller increase was observed in liver metastasis versus colon tissue (3.6× gain; p=0.001), then in liver metastasis versus adjacent liver tissue (17.4× gain; p<0.0001). On average, GRIA4 hypermethylation in primary tumor plasma was 2.8-fold higher (p=0.39), and in metastatic plasma, 16.4-fold higher (p=0.0011) compared to healthy individuals. Hypermethylation in metastatic plasma was on average 5.9 times higher (p=0.051) than in primary tumor plasma. After tumor removal surgery, average hypermethylation decrease in plasma was 1.6× for primary (p=0.037) and 4.5× for metastatic patients (p=0.023). Discussion Based on our data, it can be inferred that GRIA4 serves as a tissue specific biomarker for the colon/rectum tissue, thus is suitable for cancer classification. This biomarker showed the potential to be an attractive target for early non-invasive detection of metastases of clinically known CRC, although additional analysis has to be performed.
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Affiliation(s)
- Eva Lukacova
- Department of Molecular Biology and Genomics, Comenius University in Bratislava, Jessenius Faculty of Medicine in Martin (JFM CU), Martin, Slovakia
| | - Tatiana Burjanivova
- Department of Molecular Biology and Genomics, Comenius University in Bratislava, Jessenius Faculty of Medicine in Martin (JFM CU), Martin, Slovakia
| | - Petar Podlesniy
- Centro Investigacion Biomedica en Red Enfermedades Neurodegenerativas (CiberNed), Madrid, Spain
| | - Marian Grendar
- Laboratory of Bioinformatics and Biostatistics, Biomedical Center Martin JFM CU, Commenius University in Bratislava, Jessenius Faculty of Medicine in Martin (JFM CU), Martin, Slovakia
| | - Eva Turyova
- Department of Molecular Biology and Genomics, Comenius University in Bratislava, Jessenius Faculty of Medicine in Martin (JFM CU), Martin, Slovakia
| | - Ivana Kasubova
- Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Ludovit Laca
- Clinic of Surgery and Transplant Center, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Peter Mikolajcik
- Clinic of Surgery and Transplant Center, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Eva Kudelova
- Clinic of Surgery and Transplant Center, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Andrea Vanochova
- Department of Molecular Biology and Genomics, Comenius University in Bratislava, Jessenius Faculty of Medicine in Martin (JFM CU), Martin, Slovakia
| | - Juraj Miklusica
- Clinic of Surgery and Transplant Center, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Sandra Mersakova
- Biomedical Center Martin, Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Martin, Slovakia
| | - Zora Lasabova
- Department of Molecular Biology and Genomics, Comenius University in Bratislava, Jessenius Faculty of Medicine in Martin (JFM CU), Martin, Slovakia
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Mohan DR, Borges KS, Finco I, LaPensee CR, Rege J, Solon AL, Little DW, Else T, Almeida MQ, Dang D, Haggerty-Skeans J, Apfelbaum AA, Vinco M, Wakamatsu A, Mariani BMP, Amorim LC, Latronico AC, Mendonca BB, Zerbini MCN, Lawlor ER, Ohi R, Auchus RJ, Rainey WE, Marie SKN, Giordano TJ, Venneti S, Fragoso MCBV, Breault DT, Lerario AM, Hammer GD. β-Catenin-Driven Differentiation Is a Tissue-Specific Epigenetic Vulnerability in Adrenal Cancer. Cancer Res 2023; 83:2123-2141. [PMID: 37129912 PMCID: PMC10330305 DOI: 10.1158/0008-5472.can-22-2712] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 03/19/2023] [Accepted: 04/28/2023] [Indexed: 05/03/2023]
Abstract
Adrenocortical carcinoma (ACC) is a rare cancer in which tissue-specific differentiation is paradoxically associated with dismal outcomes. The differentiated ACC subtype CIMP-high is prevalent, incurable, and routinely fatal. CIMP-high ACC possess abnormal DNA methylation and frequent β-catenin-activating mutations. Here, we demonstrated that ACC differentiation is maintained by a balance between nuclear, tissue-specific β-catenin-containing complexes, and the epigenome. On chromatin, β-catenin bound master adrenal transcription factor SF1 and hijacked the adrenocortical super-enhancer landscape to maintain differentiation in CIMP-high ACC; off chromatin, β-catenin bound histone methyltransferase EZH2. SF1/β-catenin and EZH2/β-catenin complexes present in normal adrenals persisted through all phases of ACC evolution. Pharmacologic EZH2 inhibition in CIMP-high ACC expelled SF1/β-catenin from chromatin and favored EZH2/β-catenin assembly, erasing differentiation and restraining cancer growth in vitro and in vivo. These studies illustrate how tissue-specific programs shape oncogene selection, surreptitiously encoding targetable therapeutic vulnerabilities. SIGNIFICANCE Oncogenic β-catenin can use tissue-specific partners to regulate cellular differentiation programs that can be reversed by epigenetic therapies, identifying epigenetic control of differentiation as a viable target for β-catenin-driven cancers.
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Affiliation(s)
- Dipika R. Mohan
- Medical Scientist Training Program, University of Michigan, Ann Arbor, MI, USA
- Doctoral Program in Cancer Biology, University of Michigan, Ann Arbor, MI, USA
| | - Kleiton S. Borges
- Division of Endocrinology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Isabella Finco
- Department of Internal Medicine, Division of Metabolism, Endocrinology, and Diabetes, University of Michigan, Ann Arbor, MI, USA
| | - Christopher R. LaPensee
- Department of Internal Medicine, Division of Metabolism, Endocrinology, and Diabetes, University of Michigan, Ann Arbor, MI, USA
| | - Juilee Rege
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - April L. Solon
- Department of Cell & Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Donald W. Little
- Department of Internal Medicine, Division of Metabolism, Endocrinology, and Diabetes, University of Michigan, Ann Arbor, MI, USA
| | - Tobias Else
- Department of Internal Medicine, Division of Metabolism, Endocrinology, and Diabetes, University of Michigan, Ann Arbor, MI, USA
| | - Madson Q. Almeida
- Unidade de Suprarrenal, Laboratório de Hormônios e Genética Molecular/LIM42, Hospital das Clínicas, Departamento de Clínica Médica, Disciplina de Endocrinologia, Faculdade de Medicina da Universidade de São Paulo, SP, Brazil
- Instituto do Câncer do Estado de São Paulo (ICESP), Faculdade de Medicina da Universidade de São Paulo, SP, Brazil
| | - Derek Dang
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Laboratory of Brain Tumor Metabolism and Epigenetics, University of Michigan, Ann Arbor, MI, USA
| | - James Haggerty-Skeans
- Medical Scientist Training Program, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Laboratory of Brain Tumor Metabolism and Epigenetics, University of Michigan, Ann Arbor, MI, USA
| | - April A. Apfelbaum
- Doctoral Program in Cancer Biology, University of Michigan, Ann Arbor, MI, USA
- Seattle Children’s Research Institute, University of Washington, Seattle, WA, USA
| | - Michelle Vinco
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Alda Wakamatsu
- Departamento de Patologia, Faculdade de Medicina da Universidade de São Paulo, SP, Brazil
| | - Beatriz M. P. Mariani
- Unidade de Suprarrenal, Laboratório de Hormônios e Genética Molecular/LIM42, Hospital das Clínicas, Departamento de Clínica Médica, Disciplina de Endocrinologia, Faculdade de Medicina da Universidade de São Paulo, SP, Brazil
| | - Larissa Costa Amorim
- Unidade de Suprarrenal, Laboratório de Hormônios e Genética Molecular/LIM42, Hospital das Clínicas, Departamento de Clínica Médica, Disciplina de Endocrinologia, Faculdade de Medicina da Universidade de São Paulo, SP, Brazil
- Instituto do Câncer do Estado de São Paulo (ICESP), Faculdade de Medicina da Universidade de São Paulo, SP, Brazil
| | - Ana Claudia Latronico
- Unidade de Suprarrenal, Laboratório de Hormônios e Genética Molecular/LIM42, Hospital das Clínicas, Departamento de Clínica Médica, Disciplina de Endocrinologia, Faculdade de Medicina da Universidade de São Paulo, SP, Brazil
| | - Berenice B. Mendonca
- Unidade de Suprarrenal, Laboratório de Hormônios e Genética Molecular/LIM42, Hospital das Clínicas, Departamento de Clínica Médica, Disciplina de Endocrinologia, Faculdade de Medicina da Universidade de São Paulo, SP, Brazil
| | | | - Elizabeth R. Lawlor
- Seattle Children’s Research Institute, University of Washington, Seattle, WA, USA
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Ryoma Ohi
- Department of Cell & Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Richard J. Auchus
- Department of Internal Medicine, Division of Metabolism, Endocrinology, and Diabetes, University of Michigan, Ann Arbor, MI, USA
- Lieutenant Colonel Charles S. Kettles Veterans Affairs Medical Center, Ann Arbor, MI, USA
- Department of Pharmacology, University of Michigan, Ann Arbor, MI, USA
| | - William E. Rainey
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Suely K. N. Marie
- Laboratório de Biologia Molecular e Celular/LIM15, Departamento de Neurologia, Faculdade de Medicina da Universidade de São Paulo, SP, Brazil
| | - Thomas J. Giordano
- Department of Internal Medicine, Division of Metabolism, Endocrinology, and Diabetes, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center Endocrine Oncology Program, University of Michigan, Ann Arbor, MI, USA
| | - Sriram Venneti
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Laboratory of Brain Tumor Metabolism and Epigenetics, University of Michigan, Ann Arbor, MI, USA
- Department of Pediatrics and Communicable Diseases, University of Michigan, Ann Arbor, MI, USA
| | - Maria Candida Barisson Villares Fragoso
- Unidade de Suprarrenal, Laboratório de Hormônios e Genética Molecular/LIM42, Hospital das Clínicas, Departamento de Clínica Médica, Disciplina de Endocrinologia, Faculdade de Medicina da Universidade de São Paulo, SP, Brazil
- Instituto do Câncer do Estado de São Paulo (ICESP), Faculdade de Medicina da Universidade de São Paulo, SP, Brazil
| | - David T. Breault
- Division of Endocrinology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA
- Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, USA
| | - Antonio Marcondes Lerario
- Department of Internal Medicine, Division of Metabolism, Endocrinology, and Diabetes, University of Michigan, Ann Arbor, MI, USA
- Co-senior authors
| | - Gary D. Hammer
- Department of Internal Medicine, Division of Metabolism, Endocrinology, and Diabetes, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
- Department of Cell & Developmental Biology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center Endocrine Oncology Program, University of Michigan, Ann Arbor, MI, USA
- Co-senior authors
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Gunn K, Myllykoski M, Cao JZ, Ahmed M, Huang B, Rouaisnel B, Diplas BH, Levitt MM, Looper R, Doench JG, Ligon KL, Kornblum HI, McBrayer SK, Yan H, Duy C, Godley LA, Koivunen P, Losman JA. (R)-2-Hydroxyglutarate Inhibits KDM5 Histone Lysine Demethylases to Drive Transformation in IDH-Mutant Cancers. Cancer Discov 2023; 13:1478-1497. [PMID: 36847506 PMCID: PMC10238656 DOI: 10.1158/2159-8290.cd-22-0825] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 12/21/2022] [Accepted: 02/22/2023] [Indexed: 03/01/2023]
Abstract
Oncogenic mutations in isocitrate dehydrogenase 1 (IDH1) and IDH2 occur in a wide range of cancers, including acute myeloid leukemia (AML) and glioma. Mutant IDH enzymes convert 2-oxoglutarate (2OG) to (R)-2-hydroxyglutarate [(R)-2HG], an oncometabolite that is hypothesized to promote cellular transformation by dysregulating 2OG-dependent enzymes. The only (R)-2HG target that has been convincingly shown to contribute to transformation by mutant IDH is the myeloid tumor suppressor TET2. However, there is ample evidence to suggest that (R)-2HG has other functionally relevant targets in IDH-mutant cancers. Here, we show that (R)-2HG inhibits KDM5 histone lysine demethylases and that this inhibition contributes to cellular transformation in IDH-mutant AML and IDH-mutant glioma. These studies provide the first evidence of a functional link between dysregulation of histone lysine methylation and transformation in IDH-mutant cancers. SIGNIFICANCE Mutant IDH is known to induce histone hypermethylation. However, it is not known if this hypermethylation is functionally significant or is a bystander effect of (R)-2HG accumulation in IDH-mutant cells. Here, we provide evidence that KDM5 inhibition by (R)-2HG contributes to mutant IDH-mediated transformation in AML and glioma. This article is highlighted in the In This Issue feature, p. 1275.
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Affiliation(s)
- Kathryn Gunn
- Division of Molecular and Cellular Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Matti Myllykoski
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, FI-90220, Oulu, Finland; Oulu Center for Cell-Matrix Research, University of Oulu, FI-90220, Oulu, Finland
| | - John Z. Cao
- Committee on Cancer Biology, Biological Sciences Division, University of Chicago, Chicago, IL 60637, USA
| | - Manna Ahmed
- Cancer Signaling and Epigenetics Program, Cancer Epigenetic Institute, Fox Chase Cancer Center, Philadelphia, PA 19111
| | - Bofu Huang
- Division of Molecular and Cellular Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Betty Rouaisnel
- Division of Molecular and Cellular Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Bill H. Diplas
- Department of Pathology, Duke University Medical Center, Durham, NC 27710, USA
| | - Michael M. Levitt
- Children’s Medical Center Research Institute and Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ryan Looper
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, USA
| | - John G. Doench
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Keith L. Ligon
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Pathology, Boston Children’s Hospital and Brigham and Women’s Hospital, Boston, MA 02115, USA
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Harley I. Kornblum
- Intellectual and Developmental Disabilities Research Center, David Geffen School of Medicine at UCLA, Los Angeles, California 90095, USA
| | - Samuel K. McBrayer
- Children’s Medical Center Research Institute and Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Hai Yan
- Department of Pathology, Duke University Medical Center, Durham, NC 27710, USA
| | - Cihangir Duy
- Cancer Signaling and Epigenetics Program, Cancer Epigenetic Institute, Fox Chase Cancer Center, Philadelphia, PA 19111
| | - Lucy A. Godley
- Committee on Cancer Biology, Biological Sciences Division, University of Chicago, Chicago, IL 60637, USA
- Section of Hematology/Oncology, Departments of Medicine and Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Peppi Koivunen
- Biocenter Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, FI-90220, Oulu, Finland; Oulu Center for Cell-Matrix Research, University of Oulu, FI-90220, Oulu, Finland
| | - Julie-Aurore Losman
- Division of Molecular and Cellular Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Division of Hematology, Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
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MacLennan SA, Marra MA. Oncogenic Viruses and the Epigenome: How Viruses Hijack Epigenetic Mechanisms to Drive Cancer. Int J Mol Sci 2023; 24:ijms24119543. [PMID: 37298494 DOI: 10.3390/ijms24119543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 05/26/2023] [Accepted: 05/29/2023] [Indexed: 06/12/2023] Open
Abstract
Globally, viral infections substantially contribute to cancer development. Oncogenic viruses are taxonomically heterogeneous and drive cancers using diverse strategies, including epigenomic dysregulation. Here, we discuss how oncogenic viruses disrupt epigenetic homeostasis to drive cancer and focus on how virally mediated dysregulation of host and viral epigenomes impacts the hallmarks of cancer. To illustrate the relationship between epigenetics and viral life cycles, we describe how epigenetic changes facilitate the human papillomavirus (HPV) life cycle and how changes to this process can spur malignancy. We also highlight the clinical impact of virally mediated epigenetic changes on cancer diagnosis, prognosis, and treatment.
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Affiliation(s)
- Signe A MacLennan
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Marco A Marra
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
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Kanai R, Uehara T, Yoshizawa T, Kamakura M, Nakajima T, Kinugawa Y, Iwaya M, Asaka S, Kitazawa M, Nagaya T, Ota H. ARL4C is associated with epithelial-to-mesenchymal transition in colorectal cancer. BMC Cancer 2023; 23:478. [PMID: 37237373 DOI: 10.1186/s12885-023-10958-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Accepted: 05/13/2023] [Indexed: 05/28/2023] Open
Abstract
BACKGROUND ADP-ribosylation factor-like protein 4 C (ARL4C) is a member of the ARF small GTP-binding protein subfamily. The ARL4C gene is highly expressed in colorectal cancer (CRC). ARL4C protein promotes cell motility, invasion, and proliferation. METHODS We investigated the characteristics of ARL4C by comparing its expression at the invasion front and relationships with clinicopathological data using RNAscope, a highly sensitive RNA in situ method. RESULTS In all cases, ARL4C expression was observed in cancer stromal cells and cancer cells. ARL4C expression in cancer cells was localized at the invasion front. In cancer stromal cells, ARL4C expression was significantly stronger in cases with high-grade tumor budding than in cases with low-grade tumor budding (P = 0.0002). Additionally, ARL4C expression was significantly increased in patients with high histological grade compared with those with low histological grade (P = 0.0227). Furthermore, ARL4C expression was significantly stronger in lesions with the epithelial-to-mesenchymal transition (EMT) phenotype compared with the non-EMT phenotype (P = 0.0289). In CRC cells, ARL4C expression was significantly stronger in cells that had the EMT phenotype compared with those with a non-EMT phenotype (P = 0.0366). ARL4C expression was significantly higher in cancer stromal cells than in CRC cells (P < 0.0001). CONCLUSION Our analysis reinforces the possibility that ARL4C expression worsens the prognosis of patients with CRC. Further elucidation of the function of ARL4C is desired.
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Affiliation(s)
- Ryo Kanai
- Department of Laboratory Medicine, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano, 390-8621, Japan
| | - Takeshi Uehara
- Department of Laboratory Medicine, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano, 390-8621, Japan.
| | - Takahiro Yoshizawa
- Division of Gastroenterological, Hepato-Biliary-Pancreatic, Transplantation and Pediatric Surgery, Shinshu University School of Medicine, Matsumoto, Japan
| | - Masato Kamakura
- Department of Gastroenterology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Tomoyuki Nakajima
- Department of Laboratory Medicine, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano, 390-8621, Japan
| | - Yasuhiro Kinugawa
- Department of Laboratory Medicine, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano, 390-8621, Japan
| | - Mai Iwaya
- Department of Laboratory Medicine, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano, 390-8621, Japan
| | - Shiho Asaka
- Department of Laboratory Medicine, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano, 390-8621, Japan
| | - Masato Kitazawa
- Division of Gastroenterological, Hepato-Biliary-Pancreatic, Transplantation and Pediatric Surgery, Shinshu University School of Medicine, Matsumoto, Japan
| | - Tadanobu Nagaya
- Department of Gastroenterology, Shinshu University School of Medicine, Matsumoto, Japan
| | - Hiroyoshi Ota
- Department of Laboratory Medicine, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano, 390-8621, Japan
- Department of Biomedical Laboratory Medicine, Shinshu University School of Medicine, Matsumoto, Japan
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Yang G, Yu XR, Weisenberger DJ, Lu T, Liang G. A Multi-Omics Overview of Colorectal Cancer to Address Mechanisms of Disease, Metastasis, Patient Disparities and Outcomes. Cancers (Basel) 2023; 15:cancers15112934. [PMID: 37296894 DOI: 10.3390/cancers15112934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 05/16/2023] [Accepted: 05/23/2023] [Indexed: 06/12/2023] Open
Abstract
Human colorectal cancer (CRC) is one of the most common malignancies in men and women across the globe, albeit CRC incidence and mortality shows a substantial racial and ethnic disparity, with the highest burden in African American patients. Even with effective screening tools such as colonoscopy and diagnostic detection assays, CRC remains a substantial health burden. In addition, primary tumors located in the proximal (right) or distal (left) sides of the colorectum have been shown to be unique tumor types that require unique treatment schema. Distal metastases in the liver and other organ systems are the major causes of mortality in CRC patients. Characterizing genomic, epigenomic, transcriptomic and proteomic (multi-omics) alterations has led to a better understanding of primary tumor biology, resulting in targeted therapeutic advancements. In this regard, molecular-based CRC subgroups have been developed that show correlations with patient outcomes. Molecular characterization of CRC metastases has highlighted similarities and differences between metastases and primary tumors; however, our understanding as to how to improve patient outcomes based on metastasis biology is lagging and remains a major obstacle to improving CRC patient outcomes. In this review, we will summarize the multi-omics features of primary CRC tumors and their metastases across racial and ethnic groups, the differences in proximal and distal tumor biology, molecular-based CRC subgroups, treatment strategies and challenges for improving patient outcomes.
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Affiliation(s)
- Guang Yang
- School of Sciences, China Pharmaceutical University, Nanjing 211121, China
- China Grand Enterprises, Beijing 100101, China
| | - Xi Richard Yu
- China Grand Enterprises, Beijing 100101, China
- Huadong Medicine Co., Ltd., Hangzhou 310011, China
| | - Daniel J Weisenberger
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- USC Institute of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Tao Lu
- School of Sciences, China Pharmaceutical University, Nanjing 211121, China
- State Key Laboratory of Natural Sciences, China Pharmaceutical University, Nanjing 211121, China
| | - Gangning Liang
- USC Institute of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
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Rejali L, Seifollahi Asl R, Sanjabi F, Fatemi N, Asadzadeh Aghdaei H, Saeedi Niasar M, Ketabi Moghadam P, Nazemalhosseini Mojarad E, Mini E, Nobili S. Principles of Molecular Utility for CMS Classification in Colorectal Cancer Management. Cancers (Basel) 2023; 15:2746. [PMID: 37345083 DOI: 10.3390/cancers15102746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 05/05/2023] [Accepted: 05/09/2023] [Indexed: 06/23/2023] Open
Abstract
Colorectal cancer (CRC) is the second cause of cancer-related deaths in both sexes globally and presents different clinical outcomes that are described by a range of genomic and epigenomic alterations. Despite the advancements in CRC screening plans and treatment strategies, the prognosis of CRC is dismal. In the last two decades, molecular biomarkers predictive of prognosis have been identified in CRC, although biomarkers predictive of treatment response are only available for specific biological drugs used in stage IV CRC. Translational clinical trials mainly based on "omic" strategies allowed a better understanding of the biological heterogeneity of CRCs. These studies were able to classify CRCs into subtypes mainly related to prognosis, recurrence risk, and, to some extent, also to treatment response. Accordingly, the comprehensive molecular characterizations of CRCs, including The Cancer Genome Atlas (TCGA) and consensus molecular subtype (CMS) classifications, were presented to improve the comprehension of the genomic and epigenomic landscapes of CRCs for a better patient management. The CMS classification obtained by the CRC subtyping consortium categorizes CRC into four consensus molecular subtypes (CMS1-4) characterized by different prognoses. In this review, we discussed the CMS classification in different settings with a focus on its relationships with precursor lesions, tumor immunophenotype, and gut microbiota, as well as on its role in predicting prognosis and/or response to pharmacological treatments, as a crucial step towards precision medicine.
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Affiliation(s)
- Leili Rejali
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran P.O. Box 19875-17411, Iran
| | - Romina Seifollahi Asl
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran P.O. Box 19875-17411, Iran
| | - Fatemeh Sanjabi
- Department of Medical Biotechnology, School of Allied Medicine, Iran University of Medical Sciences, Tehran P.O. Box 14496-14535, Iran
| | - Nayeralsadat Fatemi
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran P.O. Box 19875-17411, Iran
| | - Hamid Asadzadeh Aghdaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran P.O. Box 19875-17411, Iran
| | - Mahsa Saeedi Niasar
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran P.O. Box 19875-17411, Iran
| | - Pardis Ketabi Moghadam
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran P.O. Box 19875-17411, Iran
| | - Ehsan Nazemalhosseini Mojarad
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Yaman Street, Chamran Expressway, Tehran P.O. Box 19857-17411, Iran
| | - Enrico Mini
- Department of Health Sciences, University of Florence, Viale Pieraccini, 6, 50139 Firenze, Italy
| | - Stefania Nobili
- Department of Neuroscience, Psychology, Drug Research and Child Health-NEUROFARBA-Pharmacology and Toxicology Section, University of Florence, Viale Pieraccini, 6, 50139 Firenze, Italy
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Shin HJ, Hua JT, Li H. Recent advances in understanding DNA methylation of prostate cancer. Front Oncol 2023; 13:1182727. [PMID: 37234978 PMCID: PMC10206257 DOI: 10.3389/fonc.2023.1182727] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 04/24/2023] [Indexed: 05/28/2023] Open
Abstract
Epigenetic modifications, such as DNA methylation, is widely studied in cancer. DNA methylation patterns have been shown to distinguish between benign and malignant tumors in various cancers, including prostate cancer. It may also contribute to oncogenesis, as it is frequently associated with downregulation of tumor suppressor genes. Aberrant patterns of DNA methylation, in particular the CpG island hypermethylator phenotype (CIMP), have shown associative evidence with distinct clinical features and outcomes, such as aggressive subtypes, higher Gleason score, prostate-specific antigen (PSA), and overall tumor stage, overall worse prognosis, as well as reduced survival. In prostate cancer, hypermethylation of specific genes is significantly different between tumor and normal tissues. Methylation patterns could distinguish between aggressive subtypes of prostate cancer, including neuroendocrine prostate cancer (NEPC) and castration resistant prostate adenocarcinoma. Further, DNA methylation is detectable in cell-free DNA (cfDNA) and is reflective of clinical outcome, making it a potential biomarker for prostate cancer. This review summarizes recent advances in understanding DNA methylation alterations in cancers with the focus on prostate cancer. We discuss the advanced methodology used for evaluating DNA methylation changes and the molecular regulators behind these changes. We also explore the clinical potential of DNA methylation as prostate cancer biomarkers and its potential for developing targeted treatment of CIMP subtype of prostate cancer.
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Affiliation(s)
- Hyun Jin Shin
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, United States
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, United States
| | - Junjie T Hua
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, United States
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, United States
| | - Haolong Li
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, United States
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, United States
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Li M, Zhu C, Xue Y, Miao C, He R, Li W, Zhang B, Yu W, Huang X, Lv M, Xu Y, Huang Q. A DNA methylation signature for the prediction of tumour recurrence in stage II colorectal cancer. Br J Cancer 2023; 128:1681-1689. [PMID: 36828869 PMCID: PMC10133253 DOI: 10.1038/s41416-023-02155-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 01/05/2023] [Accepted: 01/11/2023] [Indexed: 02/26/2023] Open
Abstract
BACKGROUND A major challenge in stage II colorectal carcinoma is to identify patients with increased risk of recurrence. Biomarkers that distinguish patients with poor prognosis from patients without recurrence are currently lacking. This study aims to develop a robust DNA methylation classifier that allows the prediction of recurrence and chemotherapy benefit in patients with stage II colorectal cancer. We performed a genome-wide DNA methylation capture sequencing in 243 stage II colorectal carcinoma samples and identified a relapse-specific DNA methylation signature consisting of eight CpG sites. METHODS Two hundred and forty-three patients with stage II CRC were enrolled in this study. In order to select differential methylation sites among recurrence and non-recurrence stage II CRC samples, DNA methylation profiles of 62 tumour samples including 31 recurrence and 31 nonrecurrence samples were analysed using the Agilent SureSelectXT Human Methyl-Seq, a comprehensive target enrichment system to analyse CpG methylation. Pyrosequencing was applied to quantify the methylation level of candidate DNA methylation sites in 243 patients. Least absolute shrinkage and selection operator (LASSO) method was employed to build the disease recurrence prediction classifier. RESULTS We identified a relapse-related DNA methylation signature consisting of eight CpG sites in stage II CRC by DNA methylation capture sequencing. The classifier showed significantly higher prognostic accuracy than any clinicopathological risk factors. The Kaplan-Meier survival curve showed an association of high-risk score with poor prognosis. In multivariate analysis, the signature was the most significant prognosis factor, with an HR of 2.80 (95% CI, 1.71-4.58, P < 0.001). The signature could identify patients who are suitable candidates for adjuvant chemotherapy. CONCLUSIONS An eight-CpG DNA methylation signature is a reliable prognostic and predictive tool for disease recurrence in patients with stage II CRC.
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Affiliation(s)
- Min Li
- Cancer Center, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China
- Institute of Clinical Sciences, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China
| | - Congcong Zhu
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, 270 Dong'An Road, 200032, Shanghai, P. R. China
- Department of Oncology, Shanghai Medical College, Fudan University, 270 Dong'An Road, 200032, Shanghai, P. R. China
| | - Ying Xue
- Cancer Center, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China
- Institute of Clinical Sciences, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China
| | - Changhong Miao
- Cancer Center, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China
- Department of Anesthesiology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China
| | - Ruiping He
- Cancer Center, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China
- Institute of Clinical Sciences, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China
| | - Wei Li
- Laboratory of RNA Epigenetics, Institute of Biomedical Sciences, Fudan University, 130 Dong'An Road, 200032, Shanghai, P. R. China
| | - Baolong Zhang
- Laboratory of RNA Epigenetics, Institute of Biomedical Sciences, Fudan University, 130 Dong'An Road, 200032, Shanghai, P. R. China
| | - Wenqiang Yu
- Laboratory of RNA Epigenetics, Institute of Biomedical Sciences, Fudan University, 130 Dong'An Road, 200032, Shanghai, P. R. China
| | - Xingxu Huang
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, P. R. China
| | - Minzhi Lv
- Institute of Clinical Sciences, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China.
- Department of Biostatistics, Clinical Research Unit, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China.
| | - Ye Xu
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, 270 Dong'An Road, 200032, Shanghai, P. R. China.
- Department of Oncology, Shanghai Medical College, Fudan University, 270 Dong'An Road, 200032, Shanghai, P. R. China.
| | - Qihong Huang
- Cancer Center, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China.
- Institute of Clinical Sciences, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China.
- Shanghai Respiratory Research Institute, 180 Fenglin Road, 200032, Shanghai, P. R. China.
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Zhang Y, Wang Y, Zhang B, Li P, Zhao Y. Methods and biomarkers for early detection, prediction, and diagnosis of colorectal cancer. Biomed Pharmacother 2023; 163:114786. [PMID: 37119736 DOI: 10.1016/j.biopha.2023.114786] [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: 02/22/2023] [Revised: 04/17/2023] [Accepted: 04/24/2023] [Indexed: 05/01/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most common digestive diseases worldwide. It has steadily ascended to the top three cancers in terms of incidence and mortality. The primary cause is the inability to diagnose it at an early stage. Therefore, early detection and diagnosis are essential for colorectal cancer prevention. Although there are now various methods for CRC early detection, in addition to recent developments in surgical and multimodal therapy, the poor prognosis and late detection of CRC still remain significant. Thus, it is important to investigate novel technologies and biomarkers to improve the sensitization and specification of CRC diagnosis. Here, we present some common methods and biomarkers for early detection and diagnosis of CRC, we hope this review will encourage the adoption of screening programs and the clinical use of these potential molecules as biomarkers for CRC early detection and prognosis.
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Affiliation(s)
- Yue Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Yin Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China; Key Laboratory of Birth Regulation and Control Technology of National Health Commission of China, Maternal and Child Health Care Hospital of Shandong Province affiliated to Qingdao University, Shandong Province, China
| | - Bingqiang Zhang
- Key Laboratory of Cancer and Immune Cells of Qingdao, Qingdao 266021, China
| | - Peifeng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China.
| | - Yi Zhao
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China.
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