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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] [Grants] [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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Oliveira DVNP, Biskup E, O'Rourke CJ, Hentze JL, Andersen JB, Høgdall C, Høgdall EV. Developing a DNA Methylation Signature to Differentiate High-Grade Serous Ovarian Carcinomas from Benign Ovarian Tumors. Mol Diagn Ther 2024:10.1007/s40291-024-00740-y. [PMID: 39414761 DOI: 10.1007/s40291-024-00740-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/08/2024] [Indexed: 10/18/2024]
Abstract
INTRODUCTION Epithelial ovarian cancer (EOC) represents a significant health challenge, with high-grade serous ovarian cancer (HGSOC) being the most common subtype. Early detection is hindered by nonspecific symptoms, leading to late-stage diagnoses and poor survival rates. Biomarkers are crucial for early diagnosis and personalized treatment OBJECTIVE: Our goal was to develop a robust statistical procedure to identify a set of differentially methylated probes (DMPs) that would allow differentiation between HGSOC and benign ovarian tumors. METHODOLOGY Using the Infinium EPIC Methylation array, we analyzed the methylation profiles of 48 ovarian samples diagnosed with HGSOC, borderline ovarian tumors, or benign ovarian disease. Through a multi-step statistical procedure combining univariate and multivariate logistic regression models, we aimed to identify CpG sites of interest. RESULTS AND CONCLUSIONS We discovered 21 DMPs and developed a predictive model validated in two independent cohorts. Our model, using a distance-to-centroid approach, accurately distinguished between benign and malignant disease. This model can potentially be used in other types of sample material. Moreover, the strategy of the model development and validation can also be used in other disease contexts for diagnostic purposes.
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Affiliation(s)
| | - Edyta Biskup
- Department of Pathology, Herlev Hospital, University of Copenhagen, Herlev, Denmark
| | - Colm J O'Rourke
- Biotech Research & Innovation Centre, Department of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Julie L Hentze
- Department of Pathology, Herlev Hospital, University of Copenhagen, Herlev, Denmark
| | - Jesper B Andersen
- Biotech Research & Innovation Centre, Department of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Claus Høgdall
- Department of Gynecology, Juliane Marie Centre, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Estrid V Høgdall
- Department of Pathology, Herlev Hospital, University of Copenhagen, Herlev, Denmark.
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Li Q, Geng S, Luo H, Wang W, Mo YQ, Luo Q, Wang L, Song GB, Sheng JP, Xu B. Signaling pathways involved in colorectal cancer: pathogenesis and targeted therapy. Signal Transduct Target Ther 2024; 9:266. [PMID: 39370455 PMCID: PMC11456611 DOI: 10.1038/s41392-024-01953-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 07/25/2024] [Accepted: 08/16/2024] [Indexed: 10/08/2024] Open
Abstract
Colorectal cancer (CRC) remains one of the leading causes of cancer-related mortality worldwide. Its complexity is influenced by various signal transduction networks that govern cellular proliferation, survival, differentiation, and apoptosis. The pathogenesis of CRC is a testament to the dysregulation of these signaling cascades, which culminates in the malignant transformation of colonic epithelium. This review aims to dissect the foundational signaling mechanisms implicated in CRC, to elucidate the generalized principles underpinning neoplastic evolution and progression. We discuss the molecular hallmarks of CRC, including the genomic, epigenomic and microbial features of CRC to highlight the role of signal transduction in the orchestration of the tumorigenic process. Concurrently, we review the advent of targeted and immune therapies in CRC, assessing their impact on the current clinical landscape. The development of these therapies has been informed by a deepening understanding of oncogenic signaling, leading to the identification of key nodes within these networks that can be exploited pharmacologically. Furthermore, we explore the potential of integrating AI to enhance the precision of therapeutic targeting and patient stratification, emphasizing their role in personalized medicine. In summary, our review captures the dynamic interplay between aberrant signaling in CRC pathogenesis and the concerted efforts to counteract these changes through targeted therapeutic strategies, ultimately aiming to pave the way for improved prognosis and personalized treatment modalities in colorectal cancer.
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Affiliation(s)
- Qing Li
- The Shapingba Hospital, Chongqing University, Chongqing, China
- Chongqing Key Laboratory of Intelligent Oncology for Breast Cancer, Chongqing University Cancer Hospital and School of Medicine, Chongqing University, Chongqing, China
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
| | - Shan Geng
- Central Laboratory, The Affiliated Dazu Hospital of Chongqing Medical University, Chongqing, China
| | - Hao Luo
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
- Cancer Center, Daping Hospital, Army Medical University, Chongqing, China
| | - Wei Wang
- Chongqing Municipal Health and Health Committee, Chongqing, China
| | - Ya-Qi Mo
- Chongqing Key Laboratory of Intelligent Oncology for Breast Cancer, Chongqing University Cancer Hospital and School of Medicine, Chongqing University, Chongqing, China
| | - Qing Luo
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
| | - Lu Wang
- Chongqing Key Laboratory of Intelligent Oncology for Breast Cancer, Chongqing University Cancer Hospital and School of Medicine, Chongqing University, Chongqing, China
| | - Guan-Bin Song
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China.
| | - Jian-Peng Sheng
- College of Artificial Intelligence, Nanjing University of Aeronautics and Astronautics, Nanjing, China.
| | - Bo Xu
- Chongqing Key Laboratory of Intelligent Oncology for Breast Cancer, Chongqing University Cancer Hospital and School of Medicine, Chongqing University, Chongqing, China.
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Chang Y, Guo H, Li X, Zong L, Wei J, Li Z, Luo C, Yang X, Fang H, Kong X, Hou X. Development of a First-in-Class DNMT1/HDAC Inhibitor with Improved Therapeutic Potential and Potentiated Antitumor Immunity. J Med Chem 2024; 67:16480-16504. [PMID: 39264152 DOI: 10.1021/acs.jmedchem.4c01310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2024]
Abstract
Epigenetic therapies have emerged as a key paradigm for treating malignancies. In this study, a series of DNMT1/HDAC dual inhibitors were obtained by fusing the key pharmacophores from DNMT1 inhibitors (DNMT1i) and HDAC inhibitors (HDACi). Among them, compound (R)-23a demonstrated significant DNMT1 and HDAC inhibition both in vitro and in cells and largely phenocopied the synergistic effects of combined DNMT1i and HDACi in reactivating epigenetically silenced tumor suppressor genes (TSGs). This translated into a profound tumor growth inhibition (TGI = 98%) of (R)-23a in an MV-4-11 xenograft model, while displaying improved tolerability compared with single agent combination. Moreover, in a syngeneic MC38 mouse colorectal tumor model, (R)-23a outperformed the combinatory treatment in reshaping the tumor immune microenvironment and inducing tumor regression. Collectively, the novel DNMT1/HDAC dual inhibitor (R)-23a effectively reverses the cancer-specific epigenetic abnormalities and holds great potential for further development into cancer therapeutic agents.
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Affiliation(s)
- Yingjie Chang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 Wenhuaxi Road, Jinan 250012, China
| | - Huahui Guo
- State Key Laboratory of Respiratory Disease, China-New Zealand Joint Laboratory on Biomedicine and Health, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- University of Chinese Academy of Sciences (UCAS), 19 Yuquan Road, Beijing 100049, China
| | - Xue Li
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 Wenhuaxi Road, Jinan 250012, China
| | - Liangyi Zong
- State Key Laboratory of Respiratory Disease, China-New Zealand Joint Laboratory on Biomedicine and Health, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- University of Chinese Academy of Sciences (UCAS), 19 Yuquan Road, Beijing 100049, China
| | - Jiale Wei
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Zhihai Li
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Cheng Luo
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Xinying Yang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 Wenhuaxi Road, Jinan 250012, China
| | - Hao Fang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 Wenhuaxi Road, Jinan 250012, China
| | - Xiangqian Kong
- State Key Laboratory of Respiratory Disease, China-New Zealand Joint Laboratory on Biomedicine and Health, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
- University of Chinese Academy of Sciences (UCAS), 19 Yuquan Road, Beijing 100049, China
| | - Xuben Hou
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 Wenhuaxi Road, Jinan 250012, China
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Jaikaria A, Kumar R, Asrani RK, Jamwal S, Verma A, Santoshrao JG, Bisen HK, Patial V, Sharma D, Kumar R, Kumar A, Patil RD. Unveiling the Anticarcinogenic Potential of Inula racemosa Hook. f. Root Extract Against DMBA-Induced Mammary Tumour in Sprague Dawley Rats. ENVIRONMENTAL TOXICOLOGY 2024. [PMID: 39301821 DOI: 10.1002/tox.24419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 07/16/2024] [Accepted: 08/31/2024] [Indexed: 09/22/2024]
Abstract
The Himalayan plant Inula racemosa has medicinal properties and can be used to prevent or treat cancer. This is because it contains certain chemicals that are known to fight cancer cells with few or no side effects. I. racemosa has been used for this purpose for many years in traditional medicine and has shown promising results. The present study was crafted to explore the suppressive impacts on cellular proliferation of the root extract derived from I. racemosa via in vivo experimentation. I. racemosa (IR) root extract was tested at three different doses (100, 250, and 500 mg/Kg BW) for 18 weeks to assess its anti-neoplastic activity against mammary tumors in female rats. The assessment included various parameters such as hematological and biochemical indices, tumor parameters, oxidative stress analysis, gross and histopathological lesion determination, Masson's trichrome staining, immunohistochemical expression of Ki-67, MMP-9, and VEGF in mammary gland tissues, and molecular docking. The chemopreventive action of IR root extract was demonstrated by the inhibition of tumor parameters (tumor size and tumor volume), minimum changes in the liver (ALT, AST, and ALP) and kidney enzymes (BUN and creatinine), declined lipid peroxidation activity, decline gross, and histological changes in mammary gland tumors, reduced expression of KI-67, MMP-9, and VEGF and maximum binding affinity of isoalantolactone with VEGF through molecular docking. The study suggests that the active constituents (isoalantolactone and alantolactone) of I. racemosa roots have anti-neoplastic activity against mammary tumors, making them a valuable therapeutic regimen for the future.
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Affiliation(s)
- Ankita Jaikaria
- Department of Veterinary Pathology, Dr. G.C Negi College of Veterinary and Animal Sciences, CSK Himachal Pradesh Agricultural University, Palampur, Himachal Pradesh, India
| | - Rakesh Kumar
- Department of Veterinary Pathology, Dr. G.C Negi College of Veterinary and Animal Sciences, CSK Himachal Pradesh Agricultural University, Palampur, Himachal Pradesh, India
| | - R K Asrani
- Department of Veterinary Pathology, Dr. G.C Negi College of Veterinary and Animal Sciences, CSK Himachal Pradesh Agricultural University, Palampur, Himachal Pradesh, India
| | - Smriti Jamwal
- Department of Veterinary Pathology, Dr. G.C Negi College of Veterinary and Animal Sciences, CSK Himachal Pradesh Agricultural University, Palampur, Himachal Pradesh, India
| | - Abhishek Verma
- Department of Veterinary Pathology, Dr. G.C Negi College of Veterinary and Animal Sciences, CSK Himachal Pradesh Agricultural University, Palampur, Himachal Pradesh, India
| | - Joshi Gaurav Santoshrao
- Department of Veterinary Pathology, Dr. G.C Negi College of Veterinary and Animal Sciences, CSK Himachal Pradesh Agricultural University, Palampur, Himachal Pradesh, India
| | - Harsh Krishnakumar Bisen
- Department of Veterinary Pathology, Dr. G.C Negi College of Veterinary and Animal Sciences, CSK Himachal Pradesh Agricultural University, Palampur, Himachal Pradesh, India
| | - Vikram Patial
- Division of Dietetics and Nutrition Technology, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Dixit Sharma
- Department of Animal Sciences, Central University of Himachal Pradesh, Kangra, Himachal Pradesh, India
| | - Rohit Kumar
- Department of Surgery and Radiology, Dr. G.C. Negi College of Veterinary and Animal Sciences, CSK Himachal Pradesh Agricultural University, Palampur, Himachal Pradesh, India
| | - Adarsh Kumar
- Department of Surgery and Radiology, Dr. G.C. Negi College of Veterinary and Animal Sciences, CSK Himachal Pradesh Agricultural University, Palampur, Himachal Pradesh, India
| | - R D Patil
- Department of Veterinary Pathology, Dr. G.C Negi College of Veterinary and Animal Sciences, CSK Himachal Pradesh Agricultural University, Palampur, Himachal Pradesh, India
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6
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Rajanathadurai J, Perumal E, Sindya J. Advances in targeting cancer epigenetics using CRISPR-dCas9 technology: A comprehensive review and future prospects. Funct Integr Genomics 2024; 24:164. [PMID: 39292321 DOI: 10.1007/s10142-024-01455-3] [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: 07/09/2024] [Revised: 08/30/2024] [Accepted: 09/11/2024] [Indexed: 09/19/2024]
Abstract
Cancer, a complex and multifaceted group of diseases, continues to challenge the boundaries of medical science and healthcare. Its relentless impact on global health, both in terms of prevalence and mortality, underscores the urgent need for a comprehensive understanding of its underlying mechanisms and innovative therapeutic approaches. In recent years, significant progress has been achieved in identifying the genetic and epigenetic mechanisms that cause cancer development and treatment resistance. Researchers are currently investigating the possibility of epigenetic editing such as CRISPR-dCas9 (Clustered Regularly Interspaced Short Palindromic Repeats/deactivated CRISPR-associated protein 9) technologies, for targeting and modifying cancer related epigenetic alterations. A revolutionary form of precision cancer treatment called CRISPR-dCas9 is derived from the bacterial CRISPR-Cas (CRISPR-associated nuclease) system. CRISPR-dCas9 can be combined with epigenetic effectors (EE) to alter malignant epigenetic characteristics associated with cancer. The purpose of this review article is to provide a thorough analysis of recent advancements in utilizing CRISPR-dCas9 technology to target and modify epigenetic changes associated with cancer. This review aims to summarize the latest research developments, evaluate the effectiveness and limitations of CRISPR-dCas9 applications in cancer therapy, identify key challenges such as delivery methods and explore future directions for improving and expanding these technologies. Here, we address the various obstacles that may arise in clinical applications while showcasing the latest advancements and potential future uses of CRISPR-Cas9 in cancer therapy.
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Affiliation(s)
- Jeevitha Rajanathadurai
- Cancer Genomics Lab, Center for Global Health Research, Saveetha Medical College and Hospital, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, 602105, India
| | - Elumalai Perumal
- Cancer Genomics Lab, Center for Global Health Research, Saveetha Medical College and Hospital, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, 602105, India.
| | - Jospin Sindya
- Cancer Genomics Lab, Center for Global Health Research, Saveetha Medical College and Hospital, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, 602105, India
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7
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Li S, Liang X, Shao Q, Wang G, Huang Y, Wen P, Jiang D, Zeng X. Research hotspots and trends of epigenetic therapy in oncology: a bibliometric analysis from 2004 to 2023. Front Pharmacol 2024; 15:1465954. [PMID: 39329125 PMCID: PMC11424529 DOI: 10.3389/fphar.2024.1465954] [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: 07/17/2024] [Accepted: 08/30/2024] [Indexed: 09/28/2024] Open
Abstract
Background Epigenetics denotes heritable alterations in gene expression patterns independent of changes in DNA sequence. Epigenetic therapy seeks to reprogram malignant cells to a normal phenotype and has been extensively investigated in oncology. This study conducts a bibliometric analysis of epigenetic therapy in cancer, providing a comprehensive overview of current research, identifying trends, and highlighting key areas of investigation. Methods Publications concerning epigenetic inhibitors in cancer spanning 2004 to 2023 were retrieved from the Web of Science Core Collection (WoSCC). Co-occurrence analysis using VOSviewer assessed current status and focal points. Evolutionary trends and bursts in the knowledge domain were analyzed using CiteSpace. Bibliometrix facilitated topic evolution and revealed trends in keywords. National, institutional, and author affiliations and collaborations were also examined. Results A total of 2,153 articles and reviews on epigenetic therapy in oncology were identified, demonstrating a consistent upward trend over time. The United States (745 papers), University of Texas MD Anderson Cancer Center (57 papers), and Stephen B. Baylin (27 papers) emerged as the most productive country, institution, and author, respectively. Keyword co-occurrence analysis identified five primary clusters: tumor, DNA methylation, epigenetic therapy, expression, and immunotherapy. In the past 5 years, newly emerging themes with increased centrality and density include "drug resistance," "immunotherapy," and "combination therapy." The most cited publication reviewed current understanding of potential causes of epigenetic diseases and proposed future therapeutic strategies. Conclusion In the past two decades, the importance of epigenetic therapy in cancer research has become increasingly prominent. The United States occupies a key position in this field, while China, despite having published a large number of related papers, still has relatively limited influence. Current research focuses on the "combination therapy" of epigenetic drugs. Future studies should further explore the sequencing and scheduling of combination therapies, optimize trial designs and dosing regimens to improve clinical efficacy.
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Affiliation(s)
- Sisi Li
- Department of Breast Cancer Center, Chongqing University Cancer Hospital, Chongqing, China
- Chongqing Key Laboratory for Intelligent Oncology in Breast Cancer (iCQBC), Chongqing University Cancer Hospital, Chongqing, China
| | - Xinrui Liang
- Department of Breast Cancer Center, Chongqing University Cancer Hospital, Chongqing, China
| | - Qing Shao
- Department of Breast Cancer Center, Chongqing University Cancer Hospital, Chongqing, China
- Chongqing Key Laboratory for Intelligent Oncology in Breast Cancer (iCQBC), Chongqing University Cancer Hospital, Chongqing, China
| | - Guanwen Wang
- Department of Breast Cancer Center, Chongqing University Cancer Hospital, Chongqing, China
- Chongqing Key Laboratory for Intelligent Oncology in Breast Cancer (iCQBC), Chongqing University Cancer Hospital, Chongqing, China
| | - Yuxin Huang
- School of Medicine, Chongqing University, Chongqing, China
| | - Ping Wen
- School of Medicine, Chongqing University, Chongqing, China
| | - Dongping Jiang
- School of Medicine, Chongqing University, Chongqing, China
| | - Xiaohua Zeng
- Department of Breast Cancer Center, Chongqing University Cancer Hospital, Chongqing, China
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Cheng G, Xu J, Wang H, Chen J, Huang L, Qian ZR, Fan Y. mtPCDI: a machine learning-based prognostic model for prostate cancer recurrence. Front Genet 2024; 15:1430565. [PMID: 39296545 PMCID: PMC11408181 DOI: 10.3389/fgene.2024.1430565] [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: 05/10/2024] [Accepted: 08/22/2024] [Indexed: 09/21/2024] Open
Abstract
Background This research seeks to formulate a prognostic model for forecasting prostate cancer recurrence by examining the interaction between mitochondrial function and programmed cell death (PCD). Methods The research involved analyzing four gene expression datasets from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) using univariate Cox regression. These analyses identified genes linked with mitochondrial function and PCD that correlate with recurrence prognosis. Various machine learning algorithms were then employed to construct an optimal predictive model. Results A key outcome was the creation of a mitochondrial-related programmed cell death index (mtPCDI), which effectively predicts the prognosis of prostate cancer patients. It was observed that individuals with lower mtPCDI exhibited higher immune activity, correlating with better recurrence outcomes. Conclusion The study demonstrates that mtPCDI can be used for personalized risk assessment and therapeutic decision-making, highlighting its clinical significance and providing insights into the biological processes affecting prostate cancer recurrence.
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Affiliation(s)
- Guoliang Cheng
- Department of Urology Surgery, The Fourth People's Hospital of Jinan, Jinan, Shandong, China
| | - Junrong Xu
- Department of Urology Surgery, The Fourth People's Hospital of Jinan, Jinan, Shandong, China
| | - Honghua Wang
- Department of Urology Surgery, The Fourth People's Hospital of Jinan, Jinan, Shandong, China
| | - Jingzhao Chen
- Beidou Precision Medicine Institute, Guangzhou, China
| | - Liwei Huang
- Beidou Precision Medicine Institute, Guangzhou, China
| | - Zhi Rong Qian
- Beidou Precision Medicine Institute, Guangzhou, China
| | - Yong Fan
- Department of Urology Surgery, The Fourth People's Hospital of Jinan, Jinan, Shandong, China
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9
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Low JT, Chan MWY, Shen CH, Wei KL. Immunological hide-and-seek: epigenetically reprogrammed cancer cells and the dynamics of CD8 + T cells. Mol Biol Rep 2024; 51:959. [PMID: 39230620 DOI: 10.1007/s11033-024-09882-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: 06/13/2024] [Accepted: 08/22/2024] [Indexed: 09/05/2024]
Abstract
Cancer remains a global health burden, shaped by both genetic mutations and epigenetic dysregulation. Epigenetic alteration plays a pivotal role in tumorigenesis, immune response modulation, and the emergence of treatment resistance. This review emphasizes the intricate interplay between epigenetically reprogrammed cancer cells and the tumor microenvironment (TME), a relationship central to the immunoediting concept, which encompasses elimination, equilibrium, and escape phases. This review highlights the significance of CD8+ T cells as potent anticancer agents and discusses the mechanisms by which tumor cells evade immune surveillance and evolve resistance to immunotherapy. Such evasion entails the regulation of inhibitory molecules, antigen presentation machinery, and cytokine milieu. Furthermore, this review explores the complex dynamics culminating in CD8+ T cell dysfunction within the TME. In summary, this work offers insights into the indispensable role of epigenetic mechanisms in bolstering cancer cell survival amidst immunological challenges within the TME.
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Affiliation(s)
- Jie-Ting Low
- Department of Biomedical Sciences, National Chung Cheng University, Min-Hsiung, Chiayi, Taiwan
- Epigenomics and Human Diseases Research Center, National Chung Cheng University, Min-Hsiung, Chiayi, Taiwan
- Center for Innovative Research on Aging Society (CIRAS), National Chung Cheng University, Min-Hsiung, Chiayi, Taiwan
| | - Michael W Y Chan
- Department of Biomedical Sciences, National Chung Cheng University, Min-Hsiung, Chiayi, Taiwan.
- Epigenomics and Human Diseases Research Center, National Chung Cheng University, Min-Hsiung, Chiayi, Taiwan.
- Center for Innovative Research on Aging Society (CIRAS), National Chung Cheng University, Min-Hsiung, Chiayi, Taiwan.
- Research Center for Precision Environmental Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.
| | - Cheng-Huang Shen
- Department of Urology, Ditmanson Medical Foundation Chiayi Christian Hospital, Chiayi, Taiwan.
| | - Kuo-Liang Wei
- Division of Gastroenterology, Chang Gung Memorial Hospital, Chiayi, Taiwan.
- College of Medicine, Chang Gung University, Taoyuan, Taiwan.
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10
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Voss FO, Berkhof J, Duin S, Fons G, van Beurden M, Steenbergen RDM, Bleeker MCG. DNA Methylation and p53 Immunohistochemistry as Prognostic Biomarkers for Vulvar Lichen Sclerosus. Mod Pathol 2024; 37:100553. [PMID: 38925253 DOI: 10.1016/j.modpat.2024.100553] [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: 12/01/2023] [Revised: 06/18/2024] [Accepted: 06/20/2024] [Indexed: 06/28/2024]
Abstract
Vulvar lichen sclerosus (LS) is an inflammatory dermatosis that can progress to human papillomavirus (HPV)-independent vulvar intraepithelial neoplasia (HPVi VIN) and vulvar squamous cell carcinoma (VSCC). Although LS has a much lower cancer risk compared with HPVi VIN (5% vs 50%, respectively), its incidence is significantly higher. Therefore, there is a clinical need to identify LS patients with an increased cancer risk. Our objective was to study the value of DNA methylation and p53 immunohistochemistry (IHC) as prognostic biomarkers for progression to cancer in patients with LS. Vulvar tissues from 236 patients were selected, including 75 LS and 68 HPVi VIN, both with and without cancer development, 32 VSCC, and 61 healthy vulvar controls. Samples were subjected to p53 IHC and DNA methylation analysis of a 3-gene marker panel containing ZNF582, SST, and miR124-2. Methylation levels and p53 IHC status (mutant or wild-type) were assessed and compared among all disease categories. Odds ratios were determined to identify whether the biomarkers were associated with progression to cancer in patients with LS. The highest methylation levels were found in HPVi VIN and VSCC, followed by LS and healthy vulvar controls. The largest heterogeneity in methylation levels was observed in LS cases. In fact, the 3-marker panel tested positive in 70% of LS, which progressed to VSCC vs only 17% of LS in patients without cancer development (P = .002). Also, mutant p53 IHC was observed more frequently in LS with progression to VSCC compared with nonprogressive LS cases (42% vs 3%, respectively, P = .001). Multivariable analysis identified a mutant p53 status as the only independent risk factor for cancer development in LS (odds ratio: 34.0, 95% CI: 1.4-807.4). In conclusion, DNA methylation testing and p53 IHC show strong potential as prognostic biomarkers for the identification of LS patients at high risk of progression to cancer.
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Affiliation(s)
- Féline O Voss
- Amsterdam UMC location Vrije Universiteit Amsterdam, Pathology, Amsterdam, The Netherlands; Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Johannes Berkhof
- Amsterdam UMC location Vrije Universiteit Amsterdam, Epidemiology and Data Science, Amsterdam, The Netherlands
| | - Sylvia Duin
- Amsterdam UMC location Vrije Universiteit Amsterdam, Pathology, Amsterdam, The Netherlands; Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Guus Fons
- Amsterdam UMC location Vrije Universiteit Amsterdam, Gynecology, Amsterdam, The Netherlands
| | - Marc van Beurden
- Netherlands Cancer Institute/Antoni Van Leeuwenhoek Hospital, Gynecology, Amsterdam, The Netherlands
| | - Renske D M Steenbergen
- Amsterdam UMC location Vrije Universiteit Amsterdam, Pathology, Amsterdam, The Netherlands; Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Maaike C G Bleeker
- Amsterdam UMC location Vrije Universiteit Amsterdam, Pathology, Amsterdam, The Netherlands; Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands.
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11
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Tian S, Chen M. The mechanisms and drug therapies of colorectal cancer and epigenetics: bibliometrics and visualized analysis. Front Pharmacol 2024; 15:1466156. [PMID: 39268463 PMCID: PMC11391208 DOI: 10.3389/fphar.2024.1466156] [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: 07/17/2024] [Accepted: 08/19/2024] [Indexed: 09/15/2024] Open
Abstract
Background Numerous studies have demonstrated a link between epigenetics and CRC. However, there has been no systematic analysis or visualization of relevant publications using bibliometrics. Methods 839 publications obtained from the Web of Science Core (WoSCC) were systematically analyzed using CiteSpace and VOSviewer software. Results The results show that the countries, institutions, and authors with the most published articles are the United States, Harvard University, and Ogino and Shuji, respectively. SEPT9 is a blood test for the early detection of colorectal cancer. Vitamin D and gut microbiota mediate colorectal cancer and epigenetics, and probiotics may reduce colorectal cancer-related symptoms. We summarize the specific epigenetic mechanisms of CRC and the current existence and potential epigenetic drugs associated with these mechanisms. It is closely integrated with clinical practice, and the possible research directions and challenges in the future are proposed. Conclusion This study reviews the current research trends and hotspots in CRC and epigenetics, which can promote the development of this field and provide references for researchers in this field.
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Affiliation(s)
- Siyu Tian
- School of Clinical Medicine, Chengdu University of TCM, Chengdu, China
| | - Min Chen
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
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12
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Dakal TC, Kakde GS, Maurya PK. Genomic, epigenomic and transcriptomic landscape of glioblastoma. Metab Brain Dis 2024:10.1007/s11011-024-01414-8. [PMID: 39180605 DOI: 10.1007/s11011-024-01414-8] [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: 05/23/2024] [Accepted: 08/13/2024] [Indexed: 08/26/2024]
Abstract
The mostly aggressive and extremely malignant type of central nervous system is Glioblastoma (GBM), which is characterized by an extremely short average survival time of lesser than 16 months. The primary cause of this phenomenon can be attributed to the extensively altered genome of GBM, which is characterized by the dysregulation of numerous critical signaling pathways and epigenetics regulations associated with proliferation, cellular growth, survival, and apoptosis. In light of this, different genetic alterations in critical signaling pathways and various epigenetics regulation mechanisms are associated with GBM and identified as distinguishing markers. Such GBM prognostic alterations are identified in PI3K/AKT, p53, RTK, RAS, RB, STAT3 and ZIP4 signaling pathways, metabolic pathway (IDH1/2), as well as alterations in epigenetic regulation genes (MGMT, CDKN2A-p16INK4aCDKN2B-p15INK4b). The exploration of innovative diagnostic and therapeutic approaches that specifically target these pathways is utmost importance to enhance the future medication for GBM. This study provides a comprehensive overview of dysregulated epigenetic mechanisms and signaling pathways due to mutations, methylation, and copy number alterations of in critical genes in GBM with prevalence and emphasizing their significance.
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Affiliation(s)
- Tikam Chand Dakal
- Genome and Computational Biology Lab, Mohanlal Sukhadia, University, Udaipur, Rajasthan, 313001, India.
| | - Ganesh S Kakde
- Department of Biochemistry, Central University of Haryana, Mahendergarh, 123031, Haryana, India
| | - Pawan Kumar Maurya
- Department of Biochemistry, Central University of Haryana, Mahendergarh, 123031, Haryana, India.
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13
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Sharma V, Chaudhary AA, Bawari S, Gupta S, Mishra R, Khan SUD, Ali MAM, Shahid M, Srivastava S, Verma D, Gupta A, Kumar S, Kumar S. Unraveling cancer progression pathways and phytochemical therapeutic strategies for its management. Front Pharmacol 2024; 15:1414790. [PMID: 39246660 PMCID: PMC11377287 DOI: 10.3389/fphar.2024.1414790] [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: 04/09/2024] [Accepted: 05/09/2024] [Indexed: 09/10/2024] Open
Abstract
Cancer prevention is currently envisioned as a molecular-based approach to prevent carcinogenesis in pre-cancerous stages, i.e., dysplasia and carcinoma in situ. Cancer is the second-leading cause of mortality worldwide, and a more than 61% increase is expected by 2040. A detailed exploration of cancer progression pathways, including the NF-kβ signaling pathway, Wnt-B catenin signaling pathway, JAK-STAT pathway, TNF-α-mediated pathway, MAPK/mTOR pathway, and apoptotic and angiogenic pathways and effector molecules involved in cancer development, has been discussed in the manuscript. Critical evaluation of these effector molecules through molecular approaches using phytomolecules can intersect cancer formation and its metastasis. Manipulation of effector molecules like NF-kβ, SOCS, β-catenin, BAX, BAK, VEGF, STAT, Bcl2, p53, caspases, and CDKs has played an important role in inhibiting tumor growth and its spread. Plant-derived secondary metabolites obtained from natural sources have been extensively studied for their cancer-preventing potential in the last few decades. Eugenol, anethole, capsaicin, sanguinarine, EGCG, 6-gingerol, and resveratrol are some examples of such interesting lead molecules and are mentioned in the manuscript. This work is an attempt to put forward a comprehensive approach to understanding cancer progression pathways and their management using effector herbal molecules. The role of different plant metabolites and their chronic toxicity profiling in modulating cancer development pathways has also been highlighted.
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Affiliation(s)
- Vikas Sharma
- Metro College of Health Sciences and Research, Greater Noida, India
- School of Pharmacy, Sharda University, Greater Noida, India
| | - Anis Ahmad Chaudhary
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Sweta Bawari
- Amity Institute of Pharmacy, Amity University, Noida, India
| | - Saurabh Gupta
- Department of Biotechnology, GLA University, Mathura, India
| | - Richa Mishra
- Department of Computer Engineering, Parul University, Vadodara, India
| | - Salah-Ud-Din Khan
- Department of Biochemistry, College of Medicine, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Mohamed A M Ali
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University, Riyadh, Saudi Arabia
- Department of Biochemistry, Faculty of Science, Ain Shams University, Cairo, Egypt
| | - Mohammad Shahid
- Department of Basic Medical Sciences, College of Medicine, Prince Sattam bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | | | - Devvrat Verma
- Department of Biotechnology, Graphic Era (Deemed to be University), Dehradun, Uttarakhand, India
| | - Arti Gupta
- Lloyd School of Pharmacy, Greater Noida, India
| | - Sanjay Kumar
- Biological and Bio-computational Laboratory, Department of Life Science, Sharda School of Basic Sciences and Research, Sharda University, Greater Noida, India
| | - Sandeep Kumar
- School of Pharmacy, Sharda University, Greater Noida, India
- DST-FIST Laboratory, Department of Life Sciences, School of Basic Sciences and Research, Sharda University, Greater Noida, India
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14
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Mundhara N, Sadhukhan P. Cracking the Codes behind Cancer Cells' Immune Evasion. Int J Mol Sci 2024; 25:8899. [PMID: 39201585 PMCID: PMC11354234 DOI: 10.3390/ijms25168899] [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: 07/12/2024] [Revised: 08/03/2024] [Accepted: 08/09/2024] [Indexed: 09/02/2024] Open
Abstract
Immune evasion is a key phenomenon in understanding tumor recurrence, metastasis, and other critical steps in tumor progression. The tumor microenvironment (TME) is in constant flux due to the tumor's ability to release signals that affect it, while immune cells within it can impact cancer cell behavior. Cancer cells undergo several changes, which can change the enrichment of different immune cells and modulate the activity of existing immune cells in the tumor microenvironment. Cancer cells can evade immune surveillance by downregulating antigen presentation or expressing immune checkpoint molecules. High levels of tumor-infiltrating lymphocytes (TILs) correlate with better outcomes, and robust immune responses can control tumor growth. On the contrary, increased enrichment of Tregs, myeloid-derived suppressor cells, and M2-like anti-inflammatory macrophages can hinder effective immune surveillance and predict poor prognosis. Overall, understanding these immune evasion mechanisms guides therapeutic strategies. Researchers aim to modulate the TME to enhance immune surveillance and improve patient outcomes. In this review article, we strive to summarize the composition of the tumor immune microenvironment, factors affecting the tumor immune microenvironment (TIME), and different therapeutic modalities targeting the immune cells. This review is a first-hand reference to understand the basics of immune surveillance and immune evasion.
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Affiliation(s)
| | - Pritam Sadhukhan
- Department of Oncology, Johns Hopkins University, Baltimore, MD 21287, USA
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15
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Li Y, Jiang LN, Zhao BK, Li ML, Jiang YY, Liu YS, Liu SH, Zhu L, Ye X, Zhao JM. Lecithin-cholesterol acyltransferase is a potential tumor suppressor and predictive marker for hepatocellular carcinoma metastasis. World J Gastrointest Oncol 2024; 16:3651-3671. [PMID: 39171187 PMCID: PMC11334038 DOI: 10.4251/wjgo.v16.i8.3651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 05/27/2024] [Accepted: 06/18/2024] [Indexed: 08/07/2024] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is a major cause of cancer mortality worldwide, and metastasis is the main cause of early recurrence and poor prognosis. However, the mechanism of metastasis remains poorly understood. AIM To determine the possible mechanism affecting HCC metastasis and provide a possible theoretical basis for HCC treatment. METHODS The candidate molecule lecithin-cholesterol acyltransferase (LCAT) was screened by gene microarray and bioinformatics analysis. The expression levels of LCAT in clinical cohort samples was detected by quantitative real-time polymerase chain reaction and western blotting. The proliferation, migration, invasion and tumor-forming ability were measured by Cell Counting Kit-8, Transwell cell migration, invasion, and clonal formation assays, respectively. Tumor formation was detected in nude mice after LCAT gene knockdown or overexpression. The immunohistochemistry for Ki67, E-cadherin, N-cadherin, matrix metalloproteinase 9 and vascular endothelial growth factor were performed in liver tissues to assess the effect of LCAT on HCC. Gene set enrichment analysis (GSEA) on various gene signatures were analyzed with GSEA version 3.0. Three machine-learning algorithms (random forest, support vector machine, and logistic regression) were applied to predict HCC metastasis in The Cancer Genome Atlas and GEO databases. RESULTS LCAT was identified as a novel gene relating to HCC metastasis by using gene microarray in HCC tissues. LCAT was significantly downregulated in HCC tissues, which is correlated with recurrence, metastasis and poor outcome of HCC patients. Functional analysis indicated that LCAT inhibited HCC cell proliferation, migration and invasion both in vitro and in vivo. Clinicopathological data showed that LCAT was negatively associated with HCC size and metastasis (HCC size ≤ 3 cm vs 3-9 cm, P < 0.001; 3-9 cm vs > 9 cm, P < 0.01; metastatic-free HCC vs extrahepatic metastatic HCC, P < 0.05). LCAT suppressed the growth, migration and invasion of HCC cell lines via PI3K/AKT/mTOR signaling. Our results indicated that the logistic regression model based on LCAT, TNM stage and the serum level of α-fetoprotein in HCC patients could effectively predict high metastatic risk HCC patients. CONCLUSION LCAT is downregulated at translational and protein levels in HCC and might inhibit tumor metastasis via attenuating PI3K/AKT/mTOR signaling. LCAT is a prognostic marker and potential therapeutic target for HCC.
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Affiliation(s)
- Yan Li
- Department of Pathology and Hepatology, The Fifth Medical Center of Chinese PLA General Hospital, Beijing 100039, China
| | - Li-Na Jiang
- Department of Pathology and Hepatology, The Fifth Medical Center of Chinese PLA General Hospital, Beijing 100039, China
| | - Bo-Kang Zhao
- Department of Hepatology, Center of Infectious Diseases and Pathogen Biology, The First Hospital of Jilin University, Changchun 130061, Jilin Province, China
| | - Mei-Ling Li
- Department of Pathology and Hepatology, The Fifth Medical Center of Chinese PLA General Hospital, Beijing 100039, China
| | - Yi-Yun Jiang
- Department of Pathology and Hepatology, The Fifth Medical Center of Chinese PLA General Hospital, Beijing 100039, China
| | - Yi-Si Liu
- First Department of Liver Disease Center, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
| | - Shu-Hong Liu
- Department of Pathology and Hepatology, The Fifth Medical Center of Chinese PLA General Hospital, Beijing 100039, China
| | - Li Zhu
- Department of Pathology and Hepatology, The Fifth Medical Center of Chinese PLA General Hospital, Beijing 100039, China
| | - Xin Ye
- Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Jing-Min Zhao
- Department of Pathology, The Fifth Medical Center of Chinese PLA General Hospital, Beijing 100039, China
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16
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Mohan N, Johnson GS, Tovar Perez JE, Dashwood WM, Rajendran P, Dashwood RH. Alternative splicing of BAZ1A in colorectal cancer disrupts the DNA damage response and increases chemosensitization. Cell Death Dis 2024; 15:570. [PMID: 39112459 PMCID: PMC11306231 DOI: 10.1038/s41419-024-06954-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 07/23/2024] [Accepted: 07/25/2024] [Indexed: 08/10/2024]
Abstract
Bromodomain Adjacent to Zinc Finger Domain 1A (BAZ1A) is a critical regulator of chromatin remodeling. We sought to clarify the roles of BAZ1A in the etiology of colorectal cancer, including the mechanisms of its alternatively spliced variants. Public databases were examined and revealed high BAZ1A expression in the majority of colorectal cancer patients, which was corroborated in a panel of human colon cancer cell lines. BAZ1A silencing reduced cell viability and increased markers of DNA damage, apoptosis, and senescence, along with the downregulation of Wnt/β-catenin signaling. The corresponding molecular changes resulted in tumor growth inhibition when BAZ1A-knockout cells were implanted into nude mice. In rescue experiments, a short isoform of BAZ1A that was associated with alternative splicing by the DBIRD complex failed to restore DNA repair activity in colon cancer cells and maintained chemosensitivity to phleomycin treatment, unlike the full-length BAZ1A. A working model proposes that a buried domain in the N-terminus of the BAZ1A short isoform lacks the ability to access linker DNA, thereby disrupting the activity of the associated chromatin remodeling complexes. Given the current interest in RNA splicing deregulation and cancer etiology, additional mechanistic studies are warranted with new lead compounds targeting BAZ1A, and other members of the BAZ family, with a view to improved therapeutic interventions.
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Affiliation(s)
- Nivedhitha Mohan
- Center for Epigenetics & Disease Prevention, Texas A&M Health, Houston, TX, USA
| | - Gavin S Johnson
- Center for Epigenetics & Disease Prevention, Texas A&M Health, Houston, TX, USA
- CRISPR Therapeutics, South Boston, MA, USA
| | | | | | - Praveen Rajendran
- Center for Epigenetics & Disease Prevention, Texas A&M Health, Houston, TX, USA.
- Department of Translational Medical Sciences, Texas A&M College of Medicine, Houston, TX, USA.
| | - Roderick H Dashwood
- Center for Epigenetics & Disease Prevention, Texas A&M Health, Houston, TX, USA.
- Department of Translational Medical Sciences, Texas A&M College of Medicine, Houston, TX, USA.
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17
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Dong Q, Gong C, Jiang Q, Liu Y, Hu Y, Wang D, Liu H, Zheng T, Song C, Wang T, Ju R, Wang C, Song D, Liu Z, Liu Y, Lu Y, Fan J, Liu M, Gao T, An Z, Zhang J, Li P, Cao C, Liu X. Identification of differentially expressed tumour-related genes regulated by UHRF1-driven DNA methylation. Sci Rep 2024; 14:18371. [PMID: 39112494 PMCID: PMC11306747 DOI: 10.1038/s41598-024-69110-2] [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: 11/14/2023] [Accepted: 07/31/2024] [Indexed: 08/10/2024] Open
Abstract
Ubiquitin-like with PHD and RING finger domains 1 (UHRF1) is an epigenetic regulator that plays critical roles in tumours. However, the DNA methylation alteration patterns driven by UHRF1 and the related differentially expressed tumour-related genes remain unclear. In this study, a UHRF1-shRNA MCF-7 cell line was constructed, and whole-genome bisulfite sequencing and RNA sequencing were performed. The DNA methylation alteration landscape was elucidated, and DNA methylation-altered regions (DMRs) were found to be distributed in both gene bodies and adjacent regions. The DMRs were annotated and categorized into 488 hypermethylated/1696 hypomethylated promoters and 1149 hypermethylated/5501 hypomethylated gene bodies. Through an integrated analysis with the RNA sequencing data, 217 methylation-regulated upregulated genes and 288 downregulated genes were identified, and these genes were primarily enriched in nervous system development and cancer signalling pathways. Further analysis revealed 21 downregulated oncogenes and 15 upregulated TSGs. We also showed that UHRF1 silencing inhibited cell proliferation and migration and suppressed tumour growth in vivo. Our study suggested that UHRF1 and the oncogenes or TSGs it regulates might serve as biomarkers and targets for breast cancer treatment.
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Affiliation(s)
- Qincai Dong
- Beijing Institute of Biotechnology, Beijing, 100850, China
| | - Chunxue Gong
- Institute of Health Sciences, Anhui University, Hefei, 230601, China
| | - Qian Jiang
- Institute of Health Sciences, Anhui University, Hefei, 230601, China
| | - Yue Liu
- Beijing Institute of Biotechnology, Beijing, 100850, China
| | - Yong Hu
- Beijing Institute of Biotechnology, Beijing, 100850, China
| | - Di Wang
- Beijing Institute of Biotechnology, Beijing, 100850, China
| | - Hainan Liu
- Beijing Institute of Biotechnology, Beijing, 100850, China
| | - Tong Zheng
- Beijing Institute of Biotechnology, Beijing, 100850, China
| | - Caiwei Song
- Beijing Institute of Biotechnology, Beijing, 100850, China
| | - Tingting Wang
- Institute of Health Sciences, Anhui University, Hefei, 230601, China
| | - Ruixia Ju
- Beijing Institute of Biotechnology, Beijing, 100850, China
| | - Chen Wang
- Institute of Health Sciences, Anhui University, Hefei, 230601, China
| | - Dengcen Song
- Beijing Institute of Biotechnology, Beijing, 100850, China
| | - Zijing Liu
- Beijing Institute of Biotechnology, Beijing, 100850, China
| | - Yuting Liu
- Beijing Institute of Biotechnology, Beijing, 100850, China
| | - Yuwei Lu
- Beijing Institute of Biotechnology, Beijing, 100850, China
| | - Jinlian Fan
- Beijing Institute of Biotechnology, Beijing, 100850, China
| | - Mengzi Liu
- Beijing Institute of Biotechnology, Beijing, 100850, China
| | - Ting Gao
- Beijing Institute of Biotechnology, Beijing, 100850, China
| | - Ziqian An
- Beijing Institute of Biotechnology, Beijing, 100850, China
| | - Jiaxin Zhang
- Beijing Institute of Biotechnology, Beijing, 100850, China
| | - Ping Li
- Beijing Institute of Biotechnology, Beijing, 100850, China
| | - Cheng Cao
- Beijing Institute of Biotechnology, Beijing, 100850, China.
| | - Xuan Liu
- Beijing Institute of Biotechnology, Beijing, 100850, China.
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18
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Yi JM. Epigenetic regulation of HERVs: Implications for cancer immunotherapy. Genes Genomics 2024:10.1007/s13258-024-01546-2. [PMID: 39088189 DOI: 10.1007/s13258-024-01546-2] [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: 05/21/2024] [Accepted: 07/07/2024] [Indexed: 08/02/2024]
Abstract
BACKGROUND Human endogenous retroviruses (HERVs), integrated into the human genome during primate evolution, constitute approximately 8% of the human genome. Although most HERVs are non-protein-coding owing to mutations, insertions, deletions, and truncations, recent research has revealed their diverse roles in biological processes, including disease pathogenesis. OBJECTIVE Although many HERVs remain inactive, they have been implicated in various diseases, particularly cancer, prompting an increased interest in harnessing HERVs for therapeutic purposes. This review explores the recent advancements in our understanding of the biological roles of HERVs, emphasizing their clinical relevance in cancer treatment. METHODS Here, we discuss how the detection of transposable elements (TEs), including HERVs, by the immune system triggers innate immune responses in human cancers. CONCLUSION Additionally, we outline recent progress in elucidating the implications of HERV activation in cancer and how targeting HERVs holds promise for anti-cancer treatments by modulating epigenetic plasticity and disrupting cancer initiation and progression.
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Affiliation(s)
- Joo Mi Yi
- Department of Microbiology and Immunology, College of Medicine, Inje University, Busan, 47392, South Korea.
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Bloomington, IN, 47405, USA.
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19
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Pîslaru AI, Albișteanu SM, Ilie AC, Ștefaniu R, Mârza A, Moscaliuc Ș, Nicoară M, Turcu AM, Grigoraș G, Alexa ID. Lung Cancer: New Directions in Senior Patients Assessment. Geriatrics (Basel) 2024; 9:101. [PMID: 39195131 DOI: 10.3390/geriatrics9040101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 07/10/2024] [Accepted: 07/30/2024] [Indexed: 08/29/2024] Open
Abstract
Age is but one significant prognostic factor in lung cancer, influencing survival, treatment response, and outcomes. This narrative review synthesizes findings from searches of 11 leading databases of research studies, systematic reviews, book chapters, and clinical trial reports on lung cancer in senior patients, with a focus on geriatric assessment as well as biomarkers. Key prognostic factors for lung cancer in seniors include biological age, functional capability, physical and psychological comorbidities, frailty, nutrition, status, and biomarkers like DNA methylation age. We identified the most valuable assessments that balance efficacy with quality of life. Optimizing care and improving outcomes with senior lung cancer patients benefits from a tailored therapeutic approach incorporating a complex geriatric assessment. A multidisciplinary collaboration between geriatricians, oncologists, and pulmonologists is crucial.
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Affiliation(s)
- Anca Iuliana Pîslaru
- Department of Medical Specialties II, Faculty of Medicine, "Grigore T. Popa" University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Sabinne-Marie Albișteanu
- Department of Medical Specialties II, Faculty of Medicine, "Grigore T. Popa" University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Adina Carmen Ilie
- Department of Medical Specialties II, Faculty of Medicine, "Grigore T. Popa" University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Ramona Ștefaniu
- Department of Medical Specialties II, Faculty of Medicine, "Grigore T. Popa" University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Aurelia Mârza
- Department of Medical Specialties II, Faculty of Medicine, "Grigore T. Popa" University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Ștefan Moscaliuc
- Department of Oncology, Faculty of Medicine, "Grigore T. Popa" University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Mălina Nicoară
- Department of Oncology, Faculty of Medicine, "Grigore T. Popa" University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Ana-Maria Turcu
- Department of Medical Specialties II, Faculty of Medicine, "Grigore T. Popa" University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Gabriela Grigoraș
- Department of Medical Specialties II, Faculty of Medicine, "Grigore T. Popa" University of Medicine and Pharmacy, 700115 Iasi, Romania
| | - Ioana Dana Alexa
- Department of Medical Specialties II, Faculty of Medicine, "Grigore T. Popa" University of Medicine and Pharmacy, 700115 Iasi, Romania
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20
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Al-Ruwishan A, Amer B, Salem A, Abdi A, Chimpandu N, Esa A, Melemenis A, Saleem MZ, Mathew R, Gamallat Y. Advancements in Understanding the Hide-and-Seek Strategy of Hibernating Breast Cancer Cells and Their Implications in Oncology from a Broader Perspective: A Comprehensive Overview. Curr Issues Mol Biol 2024; 46:8340-8367. [PMID: 39194709 DOI: 10.3390/cimb46080492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Revised: 07/27/2024] [Accepted: 07/29/2024] [Indexed: 08/29/2024] Open
Abstract
Despite recent advancements in technology, breast cancer still poses a significant threat, often resulting in fatal consequences. While early detection and treatments have shown some promise, many breast cancer patients continue to struggle with the persistent fear of the disease returning. This fear is valid, as breast cancer cells can lay dormant for years before remerging, evading traditional treatments like a game of hide and seek. The biology of these dormant breast cancer cells presents a crucial yet poorly understood challenge in clinical settings. In this review, we aim to explore the mysterious world of dormant breast cancer cells and their significant impact on patient outcomes and prognosis. We shed light on the elusive role of the G9a enzyme and many other epigenetic factors in breast cancer recurrence, highlighting its potential as a target for eliminating dormant cancer cells and preventing disease relapse. Through this comprehensive review, we not only emphasise the urgency of unravelling the dynamics of dormant breast cancer cells to improve patient outcomes and advance personalised oncology but also provide a guide for fellow researchers. By clearly outlining the clinical and research gaps surrounding dormant breast cancer cells from a molecular perspective, we aim to inspire further exploration of this critical area, ultimately leading to improved patient care and treatment strategies.
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Affiliation(s)
- Aiman Al-Ruwishan
- Space for Research Initiative, Research Horizons, London NW10 2PU, UK
| | - Bushra Amer
- Department of Family Medicine, College of Human Medicine, Michigan State University, East Lansing, MI 48824, USA
| | - Ahmed Salem
- Department of Biological and Biochemical Sciences, Faculty of Chemical Technology, University of Pardubice, 53210 Pardubice, Czech Republic
| | - Ahmed Abdi
- Independent Researcher, Uxbridge UB9 6JH, UK
| | | | | | | | - Muhammad Zubair Saleem
- Department of Pharmacology and Systems Physiology, College of Medicine, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Roselit Mathew
- Department of Oncology, Biochemistry and Molecular Biology, and Laboratory Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Yaser Gamallat
- Department of Oncology, Biochemistry and Molecular Biology, and Laboratory Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
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21
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Pedersen EA, Verhaegen ME, Joseph MK, Harms KL, Harms PW. Merkel cell carcinoma: updates in tumor biology, emerging therapies, and preclinical models. Front Oncol 2024; 14:1413793. [PMID: 39136002 PMCID: PMC11317257 DOI: 10.3389/fonc.2024.1413793] [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: 04/07/2024] [Accepted: 07/08/2024] [Indexed: 08/15/2024] Open
Abstract
Merkel cell carcinoma (MCC) is an aggressive cutaneous neuroendocrine carcinoma thought to arise via either viral (Merkel cell polyomavirus) or ultraviolet-associated pathways. Surgery and radiotherapy have historically been mainstays of management, and immunotherapy has improved outcomes for advanced disease. However, there remains a lack of effective therapy for those patients who fail to respond to these established approaches, underscoring a critical need to better understand MCC biology for more effective prognosis and treatment. Here, we review the fundamental aspects of MCC biology and the recent advances which have had profound impact on management. The first genetically-engineered mouse models for MCC tumorigenesis provide opportunities to understand the potential MCC cell of origin and may prove useful for preclinical investigation of novel therapeutics. The MCC cell of origin debate has also been advanced by recent observations of MCC arising in association with a clonally related hair follicle tumor or squamous cell carcinoma in situ. These studies also suggested a role for epigenetics in the origin of MCC, highlighting a potential utility for this therapeutic avenue in MCC. These and other therapeutic targets form the basis for a wealth of ongoing clinical trials to improve MCC management. Here, we review these recent advances in the context of the existing literature and implications for future investigations.
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Affiliation(s)
| | | | - Mallory K. Joseph
- Department of Dermatology, University of Michigan, Ann Arbor, MI, United States
| | - Kelly L. Harms
- Department of Dermatology, University of Michigan, Ann Arbor, MI, United States
| | - Paul W. Harms
- Department of Dermatology, University of Michigan, Ann Arbor, MI, United States
- Department of Pathology, University of Michigan, Ann Arbor, MI, United States
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22
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Yan B, Wang D, Ettwiller L. Simultaneous assessment of human genome and methylome data in a single experiment using limited deamination of methylated cytosine. Genome Res 2024; 34:904-913. [PMID: 38858087 PMCID: PMC11293541 DOI: 10.1101/gr.278294.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 06/04/2024] [Indexed: 06/12/2024]
Abstract
Multiomics require concerted recording of independent information, ideally from a single experiment. In this study, we introduce RIMS-seq2, a high-throughput technique to simultaneously sequence genomes and overlay methylation information while requiring only a small modification of the experimental protocol for high-throughput DNA sequencing to include a controlled deamination step. Importantly, the rate of deamination of 5-methylcytosine is negligible and thus does not interfere with standard DNA sequencing and data processing. Thus, RIMS-seq2 libraries from whole- or targeted-genome sequencing show the same germline variation calling accuracy and sensitivity compared with standard DNA-seq. Additionally, regional methylation levels provide an accurate map of the human methylome.
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Affiliation(s)
- Bo Yan
- New England Biolabs Incorporated, Ipswich, Massachusetts 01938, USA
| | - Duan Wang
- SLC Management, Wellesley Hills, Massachusetts 02481, USA
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23
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Honer MA, Ferman BI, Gray ZH, Bondarenko EA, Whetstine JR. Epigenetic modulators provide a path to understanding disease and therapeutic opportunity. Genes Dev 2024; 38:473-503. [PMID: 38914477 PMCID: PMC11293403 DOI: 10.1101/gad.351444.123] [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] [Indexed: 06/26/2024]
Abstract
The discovery of epigenetic modulators (writers, erasers, readers, and remodelers) has shed light on previously underappreciated biological mechanisms that promote diseases. With these insights, novel biomarkers and innovative combination therapies can be used to address challenging and difficult to treat disease states. This review highlights key mechanisms that epigenetic writers, erasers, readers, and remodelers control, as well as their connection with disease states and recent advances in associated epigenetic therapies.
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Affiliation(s)
- Madison A Honer
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Biomedical Sciences Program, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania 19140, USA
| | - Benjamin I Ferman
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Biomedical Sciences Program, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania 19140, USA
| | - Zach H Gray
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Biomedical Sciences Program, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania 19140, USA
| | - Elena A Bondarenko
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
| | - Johnathan R Whetstine
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA;
- Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
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24
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Laranjeira ABA, Nguyen D, Pelosof LC, Doroshow JH, Yang SX. Upregulation of TET2 and Resistance to DNA Methyltransferase (DNMT) Inhibitors in DNMT1-Deleted Cancer Cells. Diseases 2024; 12:163. [PMID: 39057134 PMCID: PMC11276550 DOI: 10.3390/diseases12070163] [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: 05/16/2024] [Revised: 07/11/2024] [Accepted: 07/16/2024] [Indexed: 07/28/2024] Open
Abstract
BACKGROUND Ten-eleven-translocation (TET) 2 is a member of the TET family of proteins (TET1-3). DNMT1 gene deletion confers resistance to DNA methyltransferase (DNMT) inhibitors in colorectal, breast, and ovarian cancer cells. Currently, the effect of DNMT1 gene status on TET2 phenotype following DNMT inhibitor treatment is unclear in human malignancies. METHODS Human colorectal carcinoma HCT116 cells (DNMT+/+) and their isogenic DNMT1 knockout (DNMT1-/-) counterpart were treated with DNMT inhibitors. Expression of TET2 and tumor suppressor (p16ink4A and p15ink4B) proteins were examined by Western blot. Apoptosis and CDKN2A promoter demethylation following drug treatment were detected by Annexin-V apoptosis assay and methylation-specific PCR. RESULTS TET2 expression was robustly increased in DNMT1-/- cells by 0.5 µM and 5 µM decitabine and azacitidine treatment. Augmentation of TET2 expression was accompanied by re-expression of p16ink4A and p15ink4B proteins and CDKN2A promoter demethylation. TET2 upregulation and tumor suppressor re-expression were associated with resistance conferred by DNMT1 deletion. Treatment with 5-aza-4'-thio-2'-deoxycytidine at a low 0.5 µM dose only upregulated TET2 and reduced CDKN2A promoter methylation, and re-expression of p16ink4A in DNMT1-/- cells. DNMT inhibitors showed minimal effects on TET2 upregulation and re-expression of tumor suppressor proteins in cells with intact DNMT1. CONCLUSIONS DNMT1 gene deletion made cancer cells prone to TET2 upregulation and activation of tumor suppressor expression upon DNMT inhibitor challenge. TET2 augmentation is concomitant with resistance to DNMT inhibitors in a DNMT1-deleted state.
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Affiliation(s)
| | | | | | | | - Sherry X. Yang
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (A.B.A.L.); (D.N.); (L.C.P.); (J.H.D.)
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25
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KAŠTELAN SNJEŽANA, PAVIČIĆ ANADIDOVIĆ, PAŠALIĆ DARIA, NIKUŠEVA-MARTIĆ TAMARA, ČANOVIĆ SAMIR, KOVAČEVIĆ PETRA, KONJEVODA SUZANA. Biological characteristics and clinical management of uveal and conjunctival melanoma. Oncol Res 2024; 32:1265-1285. [PMID: 39055896 PMCID: PMC11267116 DOI: 10.32604/or.2024.048437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 04/23/2024] [Indexed: 07/28/2024] Open
Abstract
Uveal and conjunctival melanomas are relatively rare tumors; nonetheless, they pose a significant risk of mortality for a large number of affected individuals. The pathogenesis of melanoma at different sites is very similar, however, the prognosis for patients with ocular melanoma remains unfavourable, primarily due to its distinctive genetic profile and tumor microenvironment. Regardless of considerable advances in understanding the genetic characteristics and biological behaviour, the treatment of uveal and conjunctival melanoma remains a formidable challenge. To enhance the prospect of success, collaborative efforts involving medical professionals and researchers in the fields of ocular biology and oncology are essential. Current data show a lack of well-designed randomized clinical trials and limited benefits in current forms of treatment for these tumors. Despite advancements in the development of effective melanoma therapeutic strategies, all current treatments for uveal melanoma (UM) and conjunctival melanoma (CoM) remain unsatisfactory, resulting in a poor long-term prognosis. Ongoing trials offer hope for positive outcomes in advanced and metastatic tumors. A more comprehensive understanding of the genetic and molecular abnormalities involved in the development and progression of ocular melanomas opens the way for the development of personalized therapy, with various potential therapeutic targets currently under consideration. Increased comprehension of the molecular pathogenesis of UM and CoM and their specificities may aid in the development of new and more effective systemic therapeutic agents, with the hope of improving the prognosis for patients with metastatic disease.
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Affiliation(s)
- SNJEŽANA KAŠTELAN
- School of Medicine, University of Zagreb, Zagreb, 10000, Croatia
- Department of Ophthalmology, Clinical Hospital Dubrava, Zagreb, 10000, Croatia
| | | | - DARIA PAŠALIĆ
- Department of Medical Chemistry, Biochemistry and Clinical Chemistry, School of Medicine, University of Zagreb, Zagreb, 10000, Croatia
| | - TAMARA NIKUŠEVA-MARTIĆ
- Department of Biology and Genetics, School of Medicine, University of Zagreb, Zagreb, 10000, Croatia
| | - SAMIR ČANOVIĆ
- Department of Ophthalmology, Zadar General Hospital, Zadar, 23000, Croatia
- Department of Health Studies, University of Zadar, Zadar, 23000, Croatia
| | - PETRA KOVAČEVIĆ
- School of Medicine, University of Zagreb, Zagreb, 10000, Croatia
- School of Medicine, University of Split, Split, 21000, Croatia
| | - SUZANA KONJEVODA
- Department of Ophthalmology, Zadar General Hospital, Zadar, 23000, Croatia
- Department of Health Studies, University of Zadar, Zadar, 23000, Croatia
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26
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Zahraeifard S, Xiao Z, So JY, Ahad A, Montoya S, Park WY, Sornapudi T, Andohkow T, Read A, Kedei N, Koparde V, Yang H, Lee M, Wong N, Cam M, Wang K, Ruppin E, Luo J, Hollander C, Yang L. Loss of tumor suppressors promotes inflammatory tumor microenvironment and enhances LAG3+T cell mediated immune suppression. Nat Commun 2024; 15:5873. [PMID: 38997291 PMCID: PMC11245525 DOI: 10.1038/s41467-024-50262-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 07/02/2024] [Indexed: 07/14/2024] Open
Abstract
Low response rate, treatment relapse, and resistance remain key challenges for cancer treatment with immune checkpoint blockade (ICB). Here we report that loss of specific tumor suppressors (TS) induces an inflammatory response and promotes an immune suppressive tumor microenvironment. Importantly, low expression of these TSs is associated with a higher expression of immune checkpoint inhibitory mediators. Here we identify, by using in vivo CRISPR/Cas9 based loss-of-function screening, that NF1, TSC1, and TGF-β RII as TSs regulating immune composition. Loss of each of these three TSs leads to alterations in chromatin accessibility and enhances IL6-JAK3-STAT3/6 inflammatory pathways. This results in an immune suppressive landscape, characterized by increased numbers of LAG3+ CD8 and CD4 T cells. ICB targeting LAG3 and PD-L1 simultaneously inhibits metastatic progression in preclinical triple negative breast cancer (TNBC) mouse models of NF1-, TSC1- or TGF-β RII- deficient tumors. Our study thus reveals a role of TSs in regulating metastasis via non-cell-autonomous modulation of the immune compartment and provides proof-of-principle for ICB targeting LAG3 for patients with NF1-, TSC1- or TGF-β RII-inactivated cancers.
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Affiliation(s)
- Sara Zahraeifard
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Zhiguang Xiao
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Jae Young So
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Abdul Ahad
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Selina Montoya
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Woo Yong Park
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Trinadharao Sornapudi
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Tiffany Andohkow
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Abigail Read
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Noemi Kedei
- Collaborative Protein Technology Resource, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Vishal Koparde
- Collaborative Bioinformatics Resource, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
- Advanced Biomedical Computational Sciences, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21701, USA
| | - Howard Yang
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Maxwell Lee
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Nathan Wong
- Collaborative Bioinformatics Resource, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
- Advanced Biomedical Computational Sciences, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, 21701, USA
| | - Maggie Cam
- Collaborative Bioinformatics Resource, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Kun Wang
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Eytan Ruppin
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Ji Luo
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Christine Hollander
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Li Yang
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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27
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Ma Y, Li Y, Wen Z, Lai Y, Kamila K, Gao J, Xu WY, Gong C, Chen F, Shi L, Zhang Y, Chen H, Zhu M. Genome wide identification of novel DNA methylation driven prognostic markers in colorectal cancer. Sci Rep 2024; 14:15654. [PMID: 38977698 PMCID: PMC11231291 DOI: 10.1038/s41598-024-60351-9] [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: 01/12/2024] [Accepted: 04/22/2024] [Indexed: 07/10/2024] Open
Abstract
Colorectal cancer (CRC) stands as a major contributor to cancer-related fatalities within China. There is an urgent need to identify accurate biomarkers for recurrence predicting in CRC. Reduced representation bisulfite sequencing was used to perform a comparative analysis of methylation profiles in tissue samples from 30 recurrence to 30 non-recurrence patients with CRC. Least absolute shrinkage and selection operator method was performed to select the differential methylation regions (DMRs) and built a DNA methylation classifier for predicting recurrence. Based on the identified top DMRs, a methylation classifier was built and consisted of eight hypermethylated DMRs in CRC. The DNA methylation classifier showed high accuracy for predicting recurrence with an area under the receiver operator characteristic curve of 0.825 (95% CI 0.680-0.970). The Kaplan-Meier survival analysis demonstrated that CRC patients with high methylation risk score, evaluated by the DNA methylation classifier, had poorer survival than low risk score (Hazard Ratio 4.349; 95% CI 1.783-10.61, P = 0.002). And only CRC patients with low methylation risk score could acquire benefit from adjuvant therapy. The DNA methylation classifier has been proved as crucial biomarkers for predicting recurrence and exhibited promising prognostic value after curative surgery in patients with CRC.
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Affiliation(s)
- Yuhua Ma
- Xinjiang Key Laboratory of Clinical Genetic Testing and Biomedical Information, Karamay Central Hospital, Karamay, 834099, Xin Jiang, China
- Department of Pathology, Karamay Central Hospital, No. 67, Junggar Road, Karamay, 834099, Xin Jiang, China
| | - Yuanxin Li
- Xinjiang Key Laboratory of Clinical Genetic Testing and Biomedical Information, Karamay Central Hospital, Karamay, 834099, Xin Jiang, China
- Department of Pathology, Karamay Central Hospital, No. 67, Junggar Road, Karamay, 834099, Xin Jiang, China
| | - Zhahong Wen
- Singlera Genomics (Shanghai) Ltd., Shanghai, 201318, China
| | - Yining Lai
- Xinjiang Key Laboratory of Clinical Genetic Testing and Biomedical Information, Karamay Central Hospital, Karamay, 834099, Xin Jiang, China
- Department of Pathology, Karamay Central Hospital, No. 67, Junggar Road, Karamay, 834099, Xin Jiang, China
| | - Kulaixijiang Kamila
- Xinjiang Key Laboratory of Clinical Genetic Testing and Biomedical Information, Karamay Central Hospital, Karamay, 834099, Xin Jiang, China
- Department of Pathology, Karamay Central Hospital, No. 67, Junggar Road, Karamay, 834099, Xin Jiang, China
| | - Jing Gao
- Xinjiang Key Laboratory of Clinical Genetic Testing and Biomedical Information, Karamay Central Hospital, Karamay, 834099, Xin Jiang, China
- Department of Pathology, Karamay Central Hospital, No. 67, Junggar Road, Karamay, 834099, Xin Jiang, China
| | - Wang-Yang Xu
- Singlera Genomics (Shanghai) Ltd., Shanghai, 201318, China
| | | | - Feifan Chen
- Singlera Genomics (Shanghai) Ltd., Shanghai, 201318, China
| | - Liuqing Shi
- Singlera Genomics (Shanghai) Ltd., Shanghai, 201318, China
| | - Yunzhi Zhang
- Singlera Genomics (Shanghai) Ltd., Shanghai, 201318, China
| | - Hanzhang Chen
- Department of Pathology, Zhabei Central Hospital of Shanghai, No. 619, Zhonghua New Road, Jing'an District, Shanghai, 200070, China.
| | - Min Zhu
- Xinjiang Key Laboratory of Clinical Genetic Testing and Biomedical Information, Karamay Central Hospital, Karamay, 834099, Xin Jiang, China.
- Department of Pathology, Karamay Central Hospital, No. 67, Junggar Road, Karamay, 834099, Xin Jiang, China.
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28
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Mulet-Lazaro R, van Herk S, Nuetzel M, Sijs-Szabo A, Díaz N, Kelly K, Erpelinck-Verschueren C, Schwarzfischer-Pfeilschifter L, Stanewsky H, Ackermann U, Glatz D, Raithel J, Fischer A, Pohl S, Rijneveld A, Vaquerizas JM, Thiede C, Plass C, Wouters BJ, Delwel R, Rehli M, Gebhard C. Epigenetic alterations affecting hematopoietic regulatory networks as drivers of mixed myeloid/lymphoid leukemia. Nat Commun 2024; 15:5693. [PMID: 38972954 PMCID: PMC11228033 DOI: 10.1038/s41467-024-49811-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: 08/11/2023] [Accepted: 06/19/2024] [Indexed: 07/09/2024] Open
Abstract
Leukemias with ambiguous lineage comprise several loosely defined entities, often without a clear mechanistic basis. Here, we extensively profile the epigenome and transcriptome of a subgroup of such leukemias with CpG Island Methylator Phenotype. These leukemias exhibit comparable hybrid myeloid/lymphoid epigenetic landscapes, yet heterogeneous genetic alterations, suggesting they are defined by their shared epigenetic profile rather than common genetic lesions. Gene expression enrichment reveals similarity with early T-cell precursor acute lymphoblastic leukemia and a lymphoid progenitor cell of origin. In line with this, integration of differential DNA methylation and gene expression shows widespread silencing of myeloid transcription factors. Moreover, binding sites for hematopoietic transcription factors, including CEBPA, SPI1 and LEF1, are uniquely inaccessible in these leukemias. Hypermethylation also results in loss of CTCF binding, accompanied by changes in chromatin interactions involving key transcription factors. In conclusion, epigenetic dysregulation, and not genetic lesions, explains the mixed phenotype of this group of leukemias with ambiguous lineage. The data collected here constitute a useful and comprehensive epigenomic reference for subsequent studies of acute myeloid leukemias, T-cell acute lymphoblastic leukemias and mixed-phenotype leukemias.
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Affiliation(s)
- Roger Mulet-Lazaro
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Stanley van Herk
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | - Margit Nuetzel
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Aniko Sijs-Szabo
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Noelia Díaz
- Max Planck Institute for Molecular Biomedicine, Muenster, Germany
- Renewable Marine Resources Department, Institute of Marine Sciences (ICM-CSIC), Barcelona, Spain
| | - Katherine Kelly
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Claudia Erpelinck-Verschueren
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
- Oncode Institute, Utrecht, the Netherlands
| | | | - Hanna Stanewsky
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Ute Ackermann
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Dagmar Glatz
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Johanna Raithel
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Alexander Fischer
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
| | - Sandra Pohl
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany
- Department of Conservative Dentistry and Periodontology, University Hospital Regensburg, Regensburg, Germany
| | - Anita Rijneveld
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands
| | - Juan M Vaquerizas
- Max Planck Institute for Molecular Biomedicine, Muenster, Germany
- MRC London Institute of Medical Sciences, London, United Kingdom
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, Hammersmith Hospital 8 Campus, London, United Kingdom
| | - Christian Thiede
- Medizinische Klinik und Poliklinik I, Universitätsklinikum Carl Gustav Carus, Dresden, Germany
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Bas J Wouters
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands.
- Oncode Institute, Utrecht, the Netherlands.
| | - Ruud Delwel
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, the Netherlands.
- Oncode Institute, Utrecht, the Netherlands.
| | - Michael Rehli
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany.
- Leibniz Institute for Immunotherapy (LIT), Regensburg, Germany.
| | - Claudia Gebhard
- Department of Internal Medicine III, University Hospital Regensburg, Regensburg, Germany.
- Leibniz Institute for Immunotherapy (LIT), Regensburg, Germany.
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Seo SY, Youn SH, Bae JH, Lee SH, Lee SY. Detection and Characterization of Methylated Circulating Tumor DNA in Gastric Cancer. Int J Mol Sci 2024; 25:7377. [PMID: 39000483 PMCID: PMC11242052 DOI: 10.3390/ijms25137377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 06/17/2024] [Accepted: 06/18/2024] [Indexed: 07/16/2024] Open
Abstract
Gastric cancer is the fifth most common disease in the world and the fourth most common cause of death. It is diagnosed through esophagogastroduodenoscopy with biopsy; however, there are limitations in finding lesions in the early stages. Recently, research has been actively conducted to use liquid biopsy to diagnose various cancers, including gastric cancer. Various substances derived from cancer are reflected in the blood. By analyzing these substances, it was expected that not only the presence or absence of cancer but also the type of cancer can be diagnosed. However, the amount of these substances is extremely small, and even these have various variables depending on the characteristics of the individual or the characteristics of the cancer. To overcome these, we collected methylated DNA fragments using MeDIP and compared them with normal plasma to characterize gastric cancer tissue or patients' plasma. We attempted to diagnose gastric cancer using the characteristics of cancer reflected in the blood through the cancer tissue and patients' plasma. As a result, we confirmed that the consistency of common methylated fragments between tissue and plasma was approximately 41.2% and we found the possibility of diagnosing and characterizing cancer using the characteristics of the fragments through SFR and 5'end-motif analysis.
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Affiliation(s)
- Seung Young Seo
- Department of Internal Medicine, Jeonbuk National University Medical School, Jeonju-si 54907, Republic of Korea
- Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute, Jeonbuk National University Hospital, 634-18 Keuman-dong, Dukjin-gu, Jeonju-si 54907, Republic of Korea
| | - Sang Hee Youn
- Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute, Jeonbuk National University Hospital, 634-18 Keuman-dong, Dukjin-gu, Jeonju-si 54907, Republic of Korea
- Department of Radiation Oncology, Jeonbuk National University Medical School, Jeonju-si 54907, Republic of Korea
| | - Jin-Han Bae
- Research Center, Cancer Breaker, Yongin-si 16942, Republic of Korea
- Cancer Genomic Research Institute, Clinomics, Chungju-si 28161, Republic of Korea
| | - Sung-Hun Lee
- Cancer Genomic Research Institute, Clinomics, Chungju-si 28161, Republic of Korea
| | - Sun Young Lee
- Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute, Jeonbuk National University Hospital, 634-18 Keuman-dong, Dukjin-gu, Jeonju-si 54907, Republic of Korea
- Department of Radiation Oncology, Jeonbuk National University Medical School, Jeonju-si 54907, Republic of Korea
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Geiger C, Needhamsen M, Emanuelsson EB, Norrbom J, Steindorf K, Sundberg CJ, Reitzner SM, Lindholm ME. DNA methylation of exercise-responsive genes differs between trained and untrained men. BMC Biol 2024; 22:147. [PMID: 38965555 PMCID: PMC11225400 DOI: 10.1186/s12915-024-01938-6] [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: 11/15/2023] [Accepted: 06/14/2024] [Indexed: 07/06/2024] Open
Abstract
BACKGROUND Physical activity is well known for its multiple health benefits and although the knowledge of the underlying molecular mechanisms is increasing, our understanding of the role of epigenetics in long-term training adaptation remains incomplete. In this intervention study, we included individuals with a history of > 15 years of regular endurance or resistance training compared to age-matched untrained controls performing endurance or resistance exercise. We examined skeletal muscle DNA methylation of genes involved in key adaptation processes, including myogenesis, gene regulation, angiogenesis and metabolism. RESULTS A greater number of differentially methylated regions and differentially expressed genes were identified when comparing the endurance group with the control group than in the comparison between the strength group and the control group at baseline. Although the cellular composition of skeletal muscle samples was generally consistent across groups, variations were observed in the distribution of muscle fiber types. Slow-twitch fiber type genes MYH7 and MYL3 exhibited lower promoter methylation and elevated expression in endurance-trained athletes, while the same group showed higher methylation in transcription factors such as FOXO3, CREB5, and PGC-1α. The baseline DNA methylation state of those genes was associated with the transcriptional response to an acute bout of exercise. Acute exercise altered very few of the investigated CpG sites. CONCLUSIONS Endurance- compared to resistance-trained athletes and untrained individuals demonstrated a different DNA methylation signature of selected skeletal muscle genes, which may influence transcriptional dynamics following a bout of acute exercise. Skeletal muscle fiber type distribution is associated with methylation of fiber type specific genes. Our results suggest that the baseline DNA methylation landscape in skeletal muscle influences the transcription of regulatory genes in response to an acute exercise bout.
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Affiliation(s)
- Carla Geiger
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
- Division of Physical Activity, Prevention and Cancer, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
- Medical School, Heidelberg University, Heidelberg, Germany
| | - Maria Needhamsen
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Eric B Emanuelsson
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Jessica Norrbom
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Karen Steindorf
- Division of Physical Activity, Prevention and Cancer, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Carl Johan Sundberg
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
- Department of Learning, Informatics, Management and Ethics, Karolinska Institutet, Stockholm, Sweden
- Department of Laboratory Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Stefan M Reitzner
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
- Department for Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Malene E Lindholm
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden.
- Center for Inherited Cardiovascular Disease, School of Medicine, Stanford University, 870 Quarry Rd, Stanford, CA, 94305, USA.
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Upadhaya PG, Nabar SJ. Direct radiolabeling of methotrexate and methotrexate micelles with Tc-99m using QbD approach. Appl Radiat Isot 2024; 209:111313. [PMID: 38603864 DOI: 10.1016/j.apradiso.2024.111313] [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: 12/23/2023] [Revised: 03/24/2024] [Accepted: 04/04/2024] [Indexed: 04/13/2024]
Abstract
The aim of the work presented in this manuscript was to radiolabel methotrexate and prepare radiolabeled methotrexate micelles, an antifolate drug with Tc-99m using QbD approach. The radiolabeling was executed using the experimental design and the radiolabeled drug was further encapsulated in micelles. The authors are of the view that the radiolabeled MTX could be used to target the folate receptor overexpressing cancers such as the kidney, colorectal, breast, brain etc thereby opening newer possibilities to the theranostic applications of the formed conjugate.
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Affiliation(s)
- Prashant G Upadhaya
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Mumbai, Maharashtra, 400019, India
| | - Swapna J Nabar
- Radiation Medicine Centre, Bhabha Atomic Research Centre, Annex Building, Tata Memorial Hospital Campus, JerbaiWadia Road, Dadar East, Mumbai, 400012, India.
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Talukder P, Chanda S, Chaudhuri B, Choudhury SR, Saha D, Dash S, Banerjee A, Chatterjee B. CRISPR-Based Gene Editing: a Modern Approach for Study and Treatment of Cancer. Appl Biochem Biotechnol 2024; 196:4439-4456. [PMID: 37737443 DOI: 10.1007/s12010-023-04708-2] [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] [Accepted: 08/16/2023] [Indexed: 09/23/2023]
Abstract
The development and emergence of clustered regularly interspaced short palindromic repeats (CRISPR) as a genome-editing technology have created a plethora of opportunities in genetic engineering. The ability of sequence-specific addition or removal of DNA in an efficient and cost-effective manner has revolutionized modern research in the field of life science and healthcare. CRISPR is widely used as a genome engineering tool in clinical studies for observing gene expression and metabolic pathway regulations in detail. Even in the case of transgenic research and personalized gene manipulation studies, CRISPR-based technology is used extensively. To understand and even to correct the underlying genetic problem is of cancer, CRISPR-based technology can be used. Various kinds of work is going on throughout the world which are attempting to target different genes in order to discover novel and effective methodologies for the treatment of cancer. In this review, we provide a brief overview on the application of CRISPR gene editing technology in cancer treatment focusing on the key aspects of cancer screening, modelling and therapy techniques.
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Affiliation(s)
- Pratik Talukder
- Department of Biotechnology, University of Engineering and Management, Kolkata, West Bengal, 700156, India.
| | - Sounak Chanda
- Department of Biotechnology, University of Engineering and Management, Kolkata, West Bengal, 700156, India
| | - Biswadeep Chaudhuri
- Department of Biotechnology, University of Engineering and Management, Kolkata, West Bengal, 700156, India
| | | | - Debanjan Saha
- School of Biosciences and Technology, VIT, Vellore, Tamil Nadu, 632014, India
| | - Sudipta Dash
- Department of Biotechnology, IIT, Kharagpur, West Bengal, 721302, India
| | - Abhineet Banerjee
- Department of Biotechnology, NIT, Durgapur, West Bengal, 713209, India
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Sandhu APS, Tanvir, Singh K, Singh S, Antaal H, Luthra S, Singla A, Nijjar GS, Aulakh SK, Kaur Y. Decoding Cancer Risk: Understanding Gene-Environment Interactions in Cancer Development. Cureus 2024; 16:e64936. [PMID: 39165474 PMCID: PMC11335134 DOI: 10.7759/cureus.64936] [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: 07/17/2024] [Indexed: 08/22/2024] Open
Abstract
While lifestyle choices or behavioral patterns remain the most significant factors influencing cancer risk, environmental exposure to certain chemicals, both manufactured and natural, may also contribute to an individual's likelihood of developing cancer. This interplay of factors, coupled with an aging demographic and shifting lifestyle patterns, has led to an increasing prevalence of cancer in recent years. This study examines the environmental and behavioral factors that contribute to anomalies in the immune system and increase the risk of developing cancer. Significant environmental and occupational factors include the contamination of air and water, exposure to radiation, contact with harmful microorganisms and pathogens, and workplace exposure to carcinogens such as asbestos, certain chemicals, and industrial pollutants. Behavioral factors, such as food, physical activity, stress, substance misuse, and sleep patterns, have a substantial impact on immunological function and the likelihood of developing cancer. For example, pollutants like benzene and arsenic can disrupt immune function and raise the risk of developing cancer. Similarly, lifestyle variables such as inactivity and poor nutrition have been linked to an increased risk of cancer. Long-term stress and substance abuse can also decrease immunological responses, increasing the risk of developing cancer. The review underlines the complexities of examining gene-environment interactions, as well as the importance of using several perspectives to fully comprehend these pathways. Future investigations should emphasize improved methodology and larger sample sizes. Public health campaigns should aim to reduce human exposure to cancer-causing compounds known as carcinogens while also encouraging the adoption of healthy behaviors and habits. Tailored preventive approaches that account for individual genetic vulnerabilities have the potential to improve cancer prevention and treatment.
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Affiliation(s)
- Ajay Pal Singh Sandhu
- Internal Medicine, Sri Guru Ram Das University of Health Sciences and Research, Amritsar, IND
| | - Tanvir
- Medicine, Government Medical College Amritsar, Amritsar, IND
| | | | - Sumerjit Singh
- Internal Medicine, Government Medical College Amritsar, Amritsar, IND
| | - Harman Antaal
- Internal Medicine, Government Medical College Patiala, Patiala, IND
| | - Shivansh Luthra
- Medicine, Government Medical College Amritsar, Amritsar, IND
| | | | | | - Smriti K Aulakh
- Internal Medicine, Sri Guru Ram Das University of Health Sciences and Research, Amritsar, IND
| | - Yasmeen Kaur
- Medicine, Government Medical College Amritsar, Amritsar, IND
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Razavinia A, Razavinia A, Jamshidi Khalife Lou R, Ghavami M, Shahri F, Tafazoli A, Khalesi B, Hashemi ZS, Khalili S. Exosomes as novel tools for renal cell carcinoma therapy, diagnosis, and prognosis. Heliyon 2024; 10:e32875. [PMID: 38948044 PMCID: PMC11211897 DOI: 10.1016/j.heliyon.2024.e32875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 03/06/2024] [Accepted: 06/11/2024] [Indexed: 07/02/2024] Open
Abstract
Background Renal Cell Carcinoma (RCC) stands as a formidable challenge within the field of oncology, despite considerable research endeavors. The advanced stages of this malignancy present formidable barriers to effective treatment and management. Objective This review aims to explore the potential of exosomes in addressing the diagnostic and therapeutic challenges associated with RCC. Specifically, it investigates the role of exosomes as biomarkers and therapeutic vehicles in the context of RCC management. Methods For this review article, a comprehensive literature search was conducted using databases such as PubMed, employing relevant keywords to identify research articles pertinent to the objectives of the review. Initially, 200 articles were identified, which underwent screening to remove duplicates and assess relevance based on titles and abstracts, followed by a detailed examination of full texts. From the selected articles, relevant data were extracted and synthesized to address the review's objectives. The conclusions were drawn based on a thorough analysis of the findings. The quality was ensured through independent review and resolution of discrepancies among multiple reviewers. Results Exosomes demonstrate potential as diagnostic tools for early detection, prognosis, and treatment monitoring in RCC. Their ability to deliver various therapeutic agents, such as small interfering RNAs, lncRNAs, chemotherapeutic drugs, and immune-stimulating agents, allows for a personalized approach to RCC management. By leveraging exosome-based technologies, precision and efficacy in treatment strategies can be significantly enhanced. Conclusion Despite the promising advancements enabled by exosomes in the management of RCC, further research is necessary to refine exosome-based technologies and validate their efficacy, safety, and long-term benefits through rigorous clinical trials. Embracing exosomes as integral components of RCC diagnosis and treatment represents a significant step towards improving patient outcomes and addressing the persistent challenges posed by this malignancy in the field of oncology.
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Affiliation(s)
- Amir Razavinia
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Abazar Razavinia
- Genetics Department, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Roya Jamshidi Khalife Lou
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Mahlegha Ghavami
- Department of Pathology, Dalhousie University, Halifax, NS, Canada
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada
| | - Forouzan Shahri
- Department of Chemistry, Faculty of Sciences, University of Guilan, Iran
| | - Aida Tafazoli
- Department of Bacterial and Virology, Shiraz medical school, Shiraz, Iran
| | - Bahman Khalesi
- Department of Research and Production of Poultry Viral Vaccine, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization, Karaj 3197619751, Iran
| | - Zahra Sadat Hashemi
- ATMP Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Saeed Khalili
- Department of Biology Sciences, Shahid Rajaee Teacher Training University, Tehran, Iran
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Chowdhury R, Bhuia MS, Wilairatana P, Afroz M, Hasan R, Ferdous J, Rakib AI, Sheikh S, Mubarak MS, Islam MT. An insight into the anticancer potentials of lignan arctiin: A comprehensive review of molecular mechanisms. Heliyon 2024; 10:e32899. [PMID: 38988539 PMCID: PMC11234030 DOI: 10.1016/j.heliyon.2024.e32899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 05/10/2024] [Accepted: 05/22/2024] [Indexed: 07/12/2024] Open
Abstract
Natural products are being developed as possible treatment options due to the rising prevalence of cancer and the harmful side effects of synthetic medications. Arctiin is a naturally occurring lignan found in numerous plants and exhibits different pharmacological activities, along with cancer. To elucidate the anticancer properties and underlying mechanisms of action, a comprehensive search of various electronic databases was conducted using appropriate keywords to identify relevant publications. The findings suggest that arctiin exhibits anticancer properties against tumor formation and various cancers such as cervical, myeloma, prostate, endothelial, gastric, and colon cancers in several preclinical pharmacological investigations. This naturally occurring compound exerts its anticancer effect through different cellular mechanisms, including mitochondrial dysfunction, cell cycle at different phases (G2/M), inhibition of cell proliferation, apoptotic cell death, and cytotoxic effects, as well as inhibition of migration and invasion of various malignant cells. Moreover, the study also revealed that, among the various cellular pathways, arctiin was shown to be more potent in terms of the PI3K/AKT and JAK/STAT signaling pathways. However, pharmacokinetic investigation indicated the compound's poor oral bioavailability. Because of these findings, arctiin might be considered a promising chemotherapeutic drug candidate.
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Affiliation(s)
- Raihan Chowdhury
- Department of Pharmacy, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj 8100, Bangladesh
- Phytochemistry and Biodiversity Research Laboratory, BioLuster Research Center, Gopalganj 8100, Dhaka, Bangladesh
| | - Md. Shimul Bhuia
- Department of Pharmacy, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj 8100, Bangladesh
- Phytochemistry and Biodiversity Research Laboratory, BioLuster Research Center, Gopalganj 8100, Dhaka, Bangladesh
| | - Polrat Wilairatana
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | - Meher Afroz
- Department of Pharmacy, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj 8100, Bangladesh
- Phytochemistry and Biodiversity Research Laboratory, BioLuster Research Center, Gopalganj 8100, Dhaka, Bangladesh
| | - Rubel Hasan
- Department of Pharmacy, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj 8100, Bangladesh
- Phytochemistry and Biodiversity Research Laboratory, BioLuster Research Center, Gopalganj 8100, Dhaka, Bangladesh
| | - Jannatul Ferdous
- Phytochemistry and Biodiversity Research Laboratory, BioLuster Research Center, Gopalganj 8100, Dhaka, Bangladesh
- Department of Biotechnology and Genetic Engineering, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj 8100, Bangladesh
| | - Asraful Islam Rakib
- Department of Pharmacy, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj 8100, Bangladesh
- Phytochemistry and Biodiversity Research Laboratory, BioLuster Research Center, Gopalganj 8100, Dhaka, Bangladesh
| | - Salehin Sheikh
- Department of Pharmacy, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj 8100, Bangladesh
- Phytochemistry and Biodiversity Research Laboratory, BioLuster Research Center, Gopalganj 8100, Dhaka, Bangladesh
| | | | - Muhammad Torequl Islam
- Department of Pharmacy, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj 8100, Bangladesh
- Phytochemistry and Biodiversity Research Laboratory, BioLuster Research Center, Gopalganj 8100, Dhaka, Bangladesh
- Pharmacy Discipline, Khulna University, Khulna 9208, Bangladesh
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Quan S, Huang H. Epigenetic contribution to cancer. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2024; 387:1-25. [PMID: 39179345 DOI: 10.1016/bs.ircmb.2024.05.003] [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: 08/26/2024]
Abstract
Epigenetics has transformed our understanding of cancer by revealing how changes in gene activity, which do not alter the DNA itself, can initiate and progress the disease. These changes include adjustments in DNA methylation, histone configuration, and non-coding RNA activity. For instance, DNA methylation can inactivate genes that typically protect against cancer, leading to broader genomic instability. Histone modifications can alter how tightly DNA is wound, influencing which genes are active or silenced; while non-coding RNAs can interfere with the messages that direct protein production, impacting cancer-related processes. Unlike genetic mutations, which are permanent and irreversible, epigenetic changes provide a malleable target for therapeutic intervention, allowing potentially reversible adjustments to gene expression patterns. This flexibility is essential in the complex landscape of cancer where static genetic solutions may be insufficient. Additionally, epigenetics bridges the gap between genetic predispositions and environmental influences on cancer, offering a comprehensive framework for understanding how lifestyle factors and external exposures impact cancer risk and progression. The integration of epigenetics into cancer research not only enhances our understanding of the disease but also opens innovative avenues for intervention that were previously unexplored in traditional genetic-focused studies. Technologies like advanced sequencing and precise epigenetic modification are paving the way for early cancer detection and more personalized treatment approaches, highlighting the critical role of epigenetics in modern cancer care.
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Affiliation(s)
- Songhua Quan
- Department of Urology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Hao Huang
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States.
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Yan W, Rao D, Fan F, Liang H, Zhang Z, Dong H. Hepatitis B virus X protein and TGF-β: partners in the carcinogenic journey of hepatocellular carcinoma. Front Oncol 2024; 14:1407434. [PMID: 38962270 PMCID: PMC11220127 DOI: 10.3389/fonc.2024.1407434] [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: 03/26/2024] [Accepted: 05/21/2024] [Indexed: 07/05/2024] Open
Abstract
Hepatitis B infection is substantially associated with the development of liver cancer globally, with the prevalence of hepatocellular carcinoma (HCC) cases exceeding 50%. Hepatitis B virus (HBV) encodes the Hepatitis B virus X (HBx) protein, a pleiotropic regulatory protein necessary for the transcription of the HBV covalently closed circular DNA (cccDNA) microchromosome. In previous studies, HBV-associated HCC was revealed to be affected by HBx in multiple signaling pathways, resulting in genetic mutations and epigenetic modifications in proto-oncogenes and tumor suppressor genes. In addition, transforming growth factor-β (TGF-β) has dichotomous potentials at various phases of malignancy as it is a crucial signaling pathway that regulates multiple cellular and physiological processes. In early HCC, TGF-β has a significant antitumor effect, whereas in advanced HCC, it promotes malignant progression. TGF-β interacts with the HBx protein in HCC, regulating the pathogenesis of HCC. This review summarizes the respective and combined functions of HBx and TGB-β in HCC occurrence and development.
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Affiliation(s)
- Wei Yan
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, Hubei, China
- Hubei Province for the Clinical Medicine Research Center of Hepatic Surgery, Wuhan, Hubei, China
| | - Dean Rao
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, Hubei, China
- Hubei Province for the Clinical Medicine Research Center of Hepatic Surgery, Wuhan, Hubei, China
| | - Feimu Fan
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, Hubei, China
- Hubei Province for the Clinical Medicine Research Center of Hepatic Surgery, Wuhan, Hubei, China
| | - Huifang Liang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, Hubei, China
- Hubei Province for the Clinical Medicine Research Center of Hepatic Surgery, Wuhan, Hubei, China
- Key Laboratory of Organ Transplantation, Ministry of Education, National Health Commission (NHC), Chinese Academy of Medical Sciences, Wuhan, China
| | - Zunyi Zhang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, Hubei, China
- Hubei Province for the Clinical Medicine Research Center of Hepatic Surgery, Wuhan, Hubei, China
| | - Hanhua Dong
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, Hubei, China
- Hubei Province for the Clinical Medicine Research Center of Hepatic Surgery, Wuhan, Hubei, China
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Wang J, Gao W, Yu H, Xu Y, Bai C, Cong Q, Zhu Y. Research Progress on the Role of Epigenetic Methylation Modification in Hepatocellular Carcinoma. J Hepatocell Carcinoma 2024; 11:1143-1156. [PMID: 38911291 PMCID: PMC11192199 DOI: 10.2147/jhc.s458734] [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: 01/09/2024] [Accepted: 05/30/2024] [Indexed: 06/25/2024] Open
Abstract
Hepatocellular carcinoma (HCC) stands as the prevailing form of primary liver cancer, characterized by a poor prognosis and high mortality rate. A pivotal factor in HCC tumorigenesis is epigenetics, specifically the regulation of gene expression through methylation. This process relies significantly on the action of proteins that modify methylation, including methyltransferases, their associated binding proteins, and demethylases. These proteins are crucial regulators, orchestrating the methylation process by regulating enzymes and their corresponding binding proteins. This orchestration facilitates the reading, binding, detection, and catalysis of gene methylation sites. Methylation ences the development, prolisignificantly influferation, invasion, and prognosis of HCC. Furthermore, methylation modification and its regulatory mechanisms activate distinct biological characteristics in HCC cancer stem cells, such as inducing cancer-like differentiation of stem cells. They also influence the tumor microenvironment (TME) in HCC, modulate immune responses, affect chemotherapy resistance in HCC patients, and contribute to HCC progression through signaling pathway feedback. Given the essential role of methylation in genetic information, it holds promise as a potential tool for the early detection of HCC and as a target to improve drug resistance and promote apoptosis in HCC cells.
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Affiliation(s)
- Jing Wang
- Infectious Department, the First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, 116000, People’s Republic of China
| | - Wenyue Gao
- Infectious Department, the First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, 116000, People’s Republic of China
| | - Hongbo Yu
- Infectious Department, the First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, 116000, People’s Republic of China
| | - Yuting Xu
- Infectious Department, the First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, 116000, People’s Republic of China
| | - Changchuan Bai
- Internal Department of Chinese Medicine, Dalian Hospital of Traditional Chinese Medicine, Dalian, Liaoning, 116013, People’s Republic of China
| | - Qingwei Cong
- Infectious Department, the First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, 116000, People’s Republic of China
| | - Ying Zhu
- Infectious Department, the First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, 116000, People’s Republic of China
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Miranda-Roblero HO, Saavedra-Salazar LF, Galicia-Moreno M, Arceo-Orozco S, Caloca-Camarena F, Sandoval-Rodriguez A, García-Bañuelos J, Frias-Gonzalez C, Almeida-López M, Martínez-López E, Armendariz-Borunda J, Monroy-Ramirez HC. Pirfenidone Reverts Global DNA Hypomethylation, Promoting DNMT1/UHRF/PCNA Coupling Complex in Experimental Hepatocarcinoma. Cells 2024; 13:1013. [PMID: 38920644 PMCID: PMC11201610 DOI: 10.3390/cells13121013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 06/03/2024] [Accepted: 06/04/2024] [Indexed: 06/27/2024] Open
Abstract
Hepatocellular carcinoma (HCC) development is associated with altered modifications in DNA methylation, changing transcriptional regulation. Emerging evidence indicates that DNA methyltransferase 1 (DNMT1) plays a key role in the carcinogenesis process. This study aimed to investigate how pirfenidone (PFD) modifies this pathway and the effect generated by the association between c-Myc expression and DNMT1 activation. Rats F344 were used for HCC development using 50 mg/kg of diethylnitrosamine (DEN) and 25 mg/kg of 2-Acetylaminofluorene (2-AAF). The HCC/PFD group received simultaneous doses of 300 mg/kg of PFD. All treatments lasted 12 weeks. On the other hand, HepG2 cells were used to evaluate the effects of PFD in restoring DNA methylation in the presence of the inhibitor 5-Aza. Histopathological, biochemical, immunohistochemical, and western blot analysis were carried out and our findings showed that PFD treatment reduced the amount and size of tumors along with decreased Glipican-3, β-catenin, and c-Myc expression in nuclear fractions. Also, this treatment improved lipid metabolism by modulating PPARγ and SREBP1 signaling. Interestingly, PFD augmented DNMT1 and DNMT3a protein expression, which restores global methylation, both in our in vivo and in vitro models. In conclusion, our results suggest that PFD could slow down HCC development by controlling DNA methylation.
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MESH Headings
- Animals
- DNA (Cytosine-5-)-Methyltransferase 1/metabolism
- DNA (Cytosine-5-)-Methyltransferase 1/genetics
- DNA Methylation/drug effects
- DNA Methylation/genetics
- Pyridones/pharmacology
- Rats
- Carcinoma, Hepatocellular/drug therapy
- Carcinoma, Hepatocellular/pathology
- Carcinoma, Hepatocellular/genetics
- Carcinoma, Hepatocellular/metabolism
- Humans
- Hep G2 Cells
- Proliferating Cell Nuclear Antigen/metabolism
- Male
- Rats, Inbred F344
- Liver Neoplasms/drug therapy
- Liver Neoplasms/pathology
- Liver Neoplasms/genetics
- Gene Expression Regulation, Neoplastic/drug effects
- Diethylnitrosamine
- Liver Neoplasms, Experimental/drug therapy
- Liver Neoplasms, Experimental/pathology
- Liver Neoplasms, Experimental/metabolism
- Liver Neoplasms, Experimental/genetics
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Affiliation(s)
- Hipolito Otoniel Miranda-Roblero
- Programa de Doctorado en Ciencias en Biología Molecular en Medicina, CUCS, University of Guadalajara, Guadalajara 44340, Mexico; (H.O.M.-R.); (L.F.S.-S.)
- Institute of Molecular Biology in Medicine and Gene Therapy, Department of Molecular Biology and Genomics, University Center of Health Sciences, University of Guadalajara, Guadalajara 44100, Mexico; (M.G.-M.); (S.A.-O.); (F.C.-C.); (A.S.-R.); (J.G.-B.)
| | - Liliana Faridi Saavedra-Salazar
- Programa de Doctorado en Ciencias en Biología Molecular en Medicina, CUCS, University of Guadalajara, Guadalajara 44340, Mexico; (H.O.M.-R.); (L.F.S.-S.)
- Institute of Molecular Biology in Medicine and Gene Therapy, Department of Molecular Biology and Genomics, University Center of Health Sciences, University of Guadalajara, Guadalajara 44100, Mexico; (M.G.-M.); (S.A.-O.); (F.C.-C.); (A.S.-R.); (J.G.-B.)
| | - Marina Galicia-Moreno
- Institute of Molecular Biology in Medicine and Gene Therapy, Department of Molecular Biology and Genomics, University Center of Health Sciences, University of Guadalajara, Guadalajara 44100, Mexico; (M.G.-M.); (S.A.-O.); (F.C.-C.); (A.S.-R.); (J.G.-B.)
| | - Scarlet Arceo-Orozco
- Institute of Molecular Biology in Medicine and Gene Therapy, Department of Molecular Biology and Genomics, University Center of Health Sciences, University of Guadalajara, Guadalajara 44100, Mexico; (M.G.-M.); (S.A.-O.); (F.C.-C.); (A.S.-R.); (J.G.-B.)
| | - Fernando Caloca-Camarena
- Institute of Molecular Biology in Medicine and Gene Therapy, Department of Molecular Biology and Genomics, University Center of Health Sciences, University of Guadalajara, Guadalajara 44100, Mexico; (M.G.-M.); (S.A.-O.); (F.C.-C.); (A.S.-R.); (J.G.-B.)
| | - Ana Sandoval-Rodriguez
- Institute of Molecular Biology in Medicine and Gene Therapy, Department of Molecular Biology and Genomics, University Center of Health Sciences, University of Guadalajara, Guadalajara 44100, Mexico; (M.G.-M.); (S.A.-O.); (F.C.-C.); (A.S.-R.); (J.G.-B.)
| | - Jesús García-Bañuelos
- Institute of Molecular Biology in Medicine and Gene Therapy, Department of Molecular Biology and Genomics, University Center of Health Sciences, University of Guadalajara, Guadalajara 44100, Mexico; (M.G.-M.); (S.A.-O.); (F.C.-C.); (A.S.-R.); (J.G.-B.)
| | - Claudia Frias-Gonzalez
- Programa de Doctorado en Ciencias en Biología Molecular en Medicina, CUCS, University of Guadalajara, Guadalajara 44340, Mexico; (H.O.M.-R.); (L.F.S.-S.)
- Institute of Molecular Biology in Medicine and Gene Therapy, Department of Molecular Biology and Genomics, University Center of Health Sciences, University of Guadalajara, Guadalajara 44100, Mexico; (M.G.-M.); (S.A.-O.); (F.C.-C.); (A.S.-R.); (J.G.-B.)
| | - Mónica Almeida-López
- University Center of Health Sciences, University of Guadalajara, Guadalajara 44340, Mexico
| | - Erika Martínez-López
- Institute of Translational Nutrigenetics and Nutrigenomics, Department of Molecular Biology and Genomics, University Center of Health Sciences, University of Guadalajara, Guadalajara 44100, Mexico
| | - Juan Armendariz-Borunda
- Institute of Molecular Biology in Medicine and Gene Therapy, Department of Molecular Biology and Genomics, University Center of Health Sciences, University of Guadalajara, Guadalajara 44100, Mexico; (M.G.-M.); (S.A.-O.); (F.C.-C.); (A.S.-R.); (J.G.-B.)
- Tecnologico de Monterrey, School of Medicine and Health Sciences, Zapopan 45138, Mexico
| | - Hugo Christian Monroy-Ramirez
- Institute of Molecular Biology in Medicine and Gene Therapy, Department of Molecular Biology and Genomics, University Center of Health Sciences, University of Guadalajara, Guadalajara 44100, Mexico; (M.G.-M.); (S.A.-O.); (F.C.-C.); (A.S.-R.); (J.G.-B.)
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40
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Yates J, Schaufelberger H, Steinacher R, Schär P, Truninger K, Boeva V. DNA-methylation variability in normal mucosa: a field cancerization marker in patients with adenomatous polyps. J Natl Cancer Inst 2024; 116:974-982. [PMID: 38273663 PMCID: PMC11160500 DOI: 10.1093/jnci/djae016] [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: 09/30/2023] [Revised: 12/13/2023] [Accepted: 01/12/2024] [Indexed: 01/27/2024] Open
Abstract
BACKGROUND The phenomenon of field cancerization reflects the transition of normal cells into those predisposed to cancer. Assessing the scope and intensity of this process in the colon may support risk prediction and colorectal cancer prevention. METHODS The Swiss Epigenetic Colorectal Cancer Study (SWEPIC) study, encompassing 1111 participants for DNA methylation analysis and a subset of 84 for RNA sequencing, was employed to detect field cancerization in individuals with adenomatous polyps (AP). Methylation variations were evaluated for their discriminative capability, including in external cohorts, genomic localization, clinical correlations, and associated RNA expression patterns. RESULTS Normal cecal tissue of individuals harboring an AP in the proximal colon manifested dysregulated DNA methylation compared to tissue from healthy individuals at 558 unique loci. Leveraging these adenoma-related differentially variable and methylated CpGs (aDVMCs), our classifier discerned between healthy and AP-adjacent tissues across SWEPIC datasets (cross-validated area under the receiver operating characteristic curve [ROC AUC] = 0.63-0.81), including within age-stratified cohorts. This discriminative capacity was validated in 3 external sets, differentiating healthy from cancer-adjacent tissue (ROC AUC = 0.82-0.88). Notably, aDVMC dysregulation correlated with polyp multiplicity. More than 50% of aDVMCs were significantly associated with age. These aDVMCs were enriched in active regions of the genome (P < .001), and associated genes exhibited altered expression in AP-adjacent tissues. CONCLUSIONS Our findings underscore the early onset of field cancerization in the right colon during the neoplastic transformation process. A more extensive validation of aDVMC dysregulation as a stratification tool could pave the way for enhanced surveillance approaches, especially given its linkage to adenoma emergence.
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Affiliation(s)
- Josephine Yates
- Department of Computer Science, Institute for Machine Learning, ETH Zürich, Zurich, Switzerland
- ETH AI Center, ETH Zürich, Zurich, Switzerland
- Swiss Institute for Bioinformatics (SIB), Lausanne, Switzerland
| | | | | | - Primo Schär
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Kaspar Truninger
- Department of Biomedicine, University of Basel, Basel, Switzerland
- Department of Gastroenterology and Hepatology, University Hospital Zurich, Zurich, Switzerland
| | - Valentina Boeva
- Department of Computer Science, Institute for Machine Learning, ETH Zürich, Zurich, Switzerland
- ETH AI Center, ETH Zürich, Zurich, Switzerland
- Swiss Institute for Bioinformatics (SIB), Lausanne, Switzerland
- Cochin Institute, Inserm U1016, National Centre for Scientific Research (CNRS) UMR 8104, Paris Descartes University UMR-S1016, Paris, France
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41
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Kulac I, Roudier MP, Haffner MC. Molecular Pathology of Prostate Cancer. Clin Lab Med 2024; 44:161-180. [PMID: 38821639 DOI: 10.1016/j.cll.2023.08.003] [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: 06/02/2024]
Abstract
Molecular profiling studies have shed new light on the complex biology of prostate cancer. Genomic studies have highlighted that structural rearrangements are among the most common recurrent alterations. In addition, both germline and somatic mutations in DNA repair genes are enriched in patients with advanced disease. Primary prostate cancer has long been known to be multifocal, but recent studies demonstrate that a large fraction of prostate cancer shows evidence of multiclonality, suggesting that genetically distinct, independently arising tumor clones coexist. Metastatic prostate cancer shows a high level of morphologic and molecular diversity, which is associated with resistance to systemic therapies. The resulting high level of intratumoral heterogeneity has important implications for diagnosis and poses major challenges for the implementation of molecular studies. Here we provide a concise review of the molecular pathology of prostate cancer, highlight clinically relevant alterations, and discuss opportunities for molecular testing.
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Affiliation(s)
- Ibrahim Kulac
- Department of Pathology, Koç University School of Medicine, Davutpasa Caddesi No:4, Istanbul 34010, Turkey
| | - Martine P Roudier
- Department of Urology, University of Washington, Northeast Pacific Street, Seattle, WA 98195, USA
| | - Michael C Haffner
- Division of Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue, Seattle, WA 98109, USA; Division of Clinical Research, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue, Seattle, WA 98109, USA; Department of Pathology, University of Washington, Seattle, WA, USA; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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42
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Walke V, Das S, Mittal A, Agrawal A. Tumor Educated Platelets as a Biomarker for Diagnosis of Lung cancer: A Systematic Review. Asian Pac J Cancer Prev 2024; 25:1911-1920. [PMID: 38918651 PMCID: PMC11382850 DOI: 10.31557/apjcp.2024.25.6.1911] [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: 02/01/2024] [Indexed: 06/27/2024] Open
Abstract
INTRODUCTION Lung cancer is one of the commonest cause of cancer associated mortality worldwide. Platelets have emerged as key players in cancer development and progression by supporting tumor growth, and dissemination. In the present systematic review, we analyzed RNA transfer between cancer cells and platelets and explored potential role of different platelet RNA profiles as onco-signature in diagnosis, subtyping, disease progression and treatment monitoring in carcinoma lung carcinoma. MATERIALS AND METHODS The study followed Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines and Cochrane Manual of Systematic Reviews and Meta-analysis that included seven studies on patients with lung cancer, with data on tumor-educated platelets, and control group. The outcome measured was based on sensitivity, specificity, and ROC. PUBMED, SCOPUS, Central Cochrane Registry of Controlled Trials and Science Direct databases were searched using specific search terms until October 2023. QUADAS - 2 tool was used to assess quality, risk of bias and applicability concerns. RESULTS The analysis revealed AUC > 70% for different platelet mRNAs, with sensitivity and specificity of more than 60 %. AUC and sensitivity were highest for ITGA2B (AUC 0.922; sensitivity 92.8%). lncRNA GTF2H2-1 was the most specific platelet RNA. On QUADAS-2 tool, 3/7 articles were unclear in reference standards, patient flow timing, and 1/7 had high bias in both aspects. For applicability, 1/7 studies were unclear in reference standards, and 2/7 in index tests. CONCLUSION TEP RNA can aid in early diagnosis of lung cancer and of proven utility in its early-stage detection. TEP RNA can also monitor disease progression and treatment response.
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Affiliation(s)
- Vaishali Walke
- Pathology and Lab Medicine, All India Institute of Medical Sciences, Bhopal, India
| | - Saikat Das
- Radiation Oncology, All India Institute of Medical Sciences, Bhopal, India
| | - Amol Mittal
- Neurosurgery, All India Institute of Medical Sciences, Bhopal, India
| | - Amit Agrawal
- Neurosurgery, All India Institute of Medical Sciences, Bhopal, India
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43
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Tabatabaei T, Rezvany MR, Ghasemi B, Vafaei F, Zadeh MK, Zaker F, Salmaninejad A. Effect of DNMT3A R882H Hot Spot Mutations on DDX43 Promoter Methylation in Acute Myeloid Leukemia. BIOMED RESEARCH INTERNATIONAL 2024; 2024:9625043. [PMID: 38807916 PMCID: PMC11132831 DOI: 10.1155/2024/9625043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 04/21/2024] [Accepted: 05/06/2024] [Indexed: 05/30/2024]
Abstract
Epigenetic alterations have been observed in many hematological malignancies, including acute myeloid leukemia (AML). Many of these alterations result from mutations in DNA methyl transferase (DNMT) enzymes, disabling them to methylate target genes in a proper way. In this case-control study, we investigated the association between R882H mutation in DNMT3A gene and DDX43 gene methylation in patients with AML. 47 AML patients and 6 controls were included in this study. After DNA extraction, amplification refractory mutation system (ARMS)-PCR was used to evaluate R882H mutations in DNMT3A gene. The high-resolution melting (HRM) method was used to determine the methylation changes of the DDX43 gene promoter. R882H mutation was only found in 10.6% (5 out of 47) of AML patients. The frequency of DDX43 gene methylation was significantly higher in patients without R882H mutations compared to patients with R882H mutations (P < 0.05). The DNMT3A R882H mutation is typically present in a minority of AML patients. Nevertheless, this mutation is associated with a reduced frequency of methylation in the DDX43 promoter region.
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Affiliation(s)
- Tahere Tabatabaei
- Department of Hematology and Blood Transfusion, School of Allied Medical Sciences, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Rezvany
- Department of Hematology and Blood Transfusion, School of Allied Medical Sciences, Iran University of Medical Sciences, Tehran, Iran
| | - Bahare Ghasemi
- Department of Hematology and Blood Transfusion, School of Allied Medical Sciences, Iran University of Medical Sciences, Tehran, Iran
| | - Farzane Vafaei
- Blood Transfusion Research Center, High Institute for Research and Education in Transfusion Medicine, Isfahan, Iran
| | - Masoumeh Kiani Zadeh
- Blood Transfusion Research Center, High Institute for Research and Education in Transfusion Medicine, Tehran, Iran
| | - Farhad Zaker
- Department of Hematology and Blood Transfusion, School of Allied Medical Sciences, Iran University of Medical Sciences, Tehran, Iran
| | - Arash Salmaninejad
- Regenerative Medicine, Organ Procurement and Transplantation Multi-Disciplinary Center, Razi Hospital, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran
- Department of Medical Genetics, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
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44
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Lao Z, Ding LW, Sun QY, Jia L, Yan B, Ng AYJ, Capinpin SM, Wang R, Ying L, Chng WJ, Phillip Koeffler H, Koh WP, Yuan JM, Yang H, Goh YT, Grigoropoulos N. A Pre-Leukemic DNA Methylation Signature in Healthy Individuals at Higher Risk for Developing Myeloid Malignancy. Clin Cancer Res 2024; 30:2170-2180. [PMID: 38437679 PMCID: PMC11096012 DOI: 10.1158/1078-0432.ccr-22-3804] [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: 12/28/2022] [Revised: 10/23/2023] [Accepted: 02/29/2024] [Indexed: 03/06/2024]
Abstract
PURPOSE DNA methylation alterations are widespread in acute myelogenous leukemia (AML) and myelodysplastic syndrome (MDS), some of which appear to have evolved independently of somatic mutations in epigenetic regulators. Although the presence of somatic mutations in peripheral blood can predict the risk of development of AML and MDS, its accuracy remains unsatisfactory. EXPERIMENTAL DESIGN We performed global DNA methylation profiling in a case control study nested within the Singapore Chinese Health Study to evaluate whether DNA methylation alterations were associated with AML/MDS development. Targeted deep sequencing and methylated DNA immunoprecipitation sequencing (MeDIP-seq) were performed on peripheral blood collected a median of 9.9 years before diagnosis of AML or MDS, together with age-matched still-healthy individuals as controls. RESULTS Sixty-six individuals who developed AML or MDS displayed significant DNA methylation changes in the peripheral blood compared with 167 age- and gender-matched controls who did not develop AML/MDS during the follow-up period. Alterations in methylation in the differentially methylation regions were associated with increased odds of developing AML/MDS. CONCLUSIONS The epigenetic changes may be acquired independently and before somatic mutations that are relevant for AML/MDS development. The association between methylation changes and the risk of pre-AML/MDS in these individuals was considerably stronger than somatic mutations, suggesting that methylation changes could be used as biomarkers for pre-AML/MDS screening.
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Affiliation(s)
- Zhentang Lao
- Department of Haematology, Singapore General Hospital, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Ling-Wen Ding
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
- Department of Pathology, National University of Singapore; Nanomedicine Translational Research Programme, Yong Yoo Lin School of Medicine, National University of Singapore. Singapore
| | - Qiao-Yang Sun
- Department of Haematology, Singapore General Hospital, Singapore
- Department of Neurology, Singapore General Hospital, National Neuroscience Institute, Singapore
| | - Li Jia
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Benedict Yan
- Department of Laboratory Medicine, National University Hospital, Singapore
| | | | - Sharah Mae Capinpin
- Healthy Longitudinal Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, National University of Singapore, Singapore
| | - Renwei Wang
- Division of Cancer Control and Population Sciences, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Li Ying
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Wee Joo Chng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
- NUS Center for Cancer Research and Dept of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- National University Cancer Institute, National University Health System, Singapore
| | - H Phillip Koeffler
- National University Cancer Institute, National University Health System, Singapore
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Woon-Puay Koh
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Jian-Min Yuan
- Division of Cancer Control and Population Sciences, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania. USA
| | - Henry Yang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
- Department of Biomedical Informatics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Yeow Tee Goh
- Department of Haematology, Singapore General Hospital, Singapore
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Thi HV, Ngo AD, Chu DT. Epigenetic regulation in ovarian cancer. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2024; 387:77-98. [PMID: 39179349 DOI: 10.1016/bs.ircmb.2024.03.006] [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: 08/26/2024]
Abstract
Ovarian cancer is one of the diseases that have the highest mortality rate for women, especially women over 50 years old. In the future, incidence and mortality rates are predicted to extend in countries with low HDI. Instability in the structure and function of genetic factors has long been known as a cause of cancer, including ovarian cancer. Besides understanding gene mutations, epigenetic alterations have emerged as another aspect leading to the pathogenesis of ovarian neoplasm. The development and progression of this fatal disease have been found to be associated with abnormalities of epigenetic regulation. DNA methylation, histone modification, and non-coding RNAs-based gene silencing are processes of interest in developing ovarian carcinoma and are also new targets for cancer detection or treatment.
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Affiliation(s)
- Hue Vu Thi
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam; Faculty of Applied Sciences, International School, Vietnam National University, Hanoi, Vietnam
| | - Anh-Dao Ngo
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam
| | - Dinh-Toi Chu
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam; Faculty of Applied Sciences, International School, Vietnam National University, Hanoi, Vietnam.
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Ishidoya M, Fujita T, Tasaka S, Fujii H. Real-time MBDi-RPA using methyl-CpG binding protein 2: A real-time detection method for simple and rapid estimation of CpG methylation status. Anal Chim Acta 2024; 1302:342486. [PMID: 38580404 DOI: 10.1016/j.aca.2024.342486] [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: 11/17/2023] [Revised: 02/21/2024] [Accepted: 03/14/2024] [Indexed: 04/07/2024]
Abstract
BACKGROUND Analysis of CpG methylation is informative for cancer diagnosis. Previously, we developed a novel method to discriminate CpG methylation status in target DNA by blocking recombinase polymerase amplification (RPA), an isothermal DNA amplification technique, using methyl-CpG binding domain (MBD) protein 2 (MBD2). The method was named MBD protein interference-RPA (MBDi-RPA). In this study, MBDi-RPA was performed using methyl-CpG binding protein 2 (MeCP2), another MBD family protein, as the blocking agent. RESULTS MBDi-RPA using MeCP2 detected low levels of CpG methylation, showing that it had higher sensitivity than MBDi-RPA using MBD2. We also developed real-time RPA, which enabled rapid analysis of DNA amplification without the need for laborious agarose gel electrophoresis and used it in combination with MBDi-RPA. We termed this method real-time MBDi-RPA. The method using MeCP2 could determine the abundance ratio of CpG-methylated target DNA simply and rapidly, although highly sensitive detection was challenging. SIGNIFICANCE AND NOVELTY Real-time MBDi-RPA using MeCP2 could be potentially useful for estimating CpG methylation status in target DNA prior to more detailed analyses.
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Affiliation(s)
- Mina Ishidoya
- Department of Respiratory Medicine, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki, Aomori, 036-8562, Japan
| | - Toshitsugu Fujita
- Department of Biochemistry and Genome Biology, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki, Aomori, 036-8562, Japan.
| | - Sadatomo Tasaka
- Department of Respiratory Medicine, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki, Aomori, 036-8562, Japan
| | - Hodaka Fujii
- Department of Biochemistry and Genome Biology, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki, Aomori, 036-8562, Japan
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47
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Damare R, Engle K, Kumar G. Targeting epidermal growth factor receptor and its downstream signaling pathways by natural products: A mechanistic insight. Phytother Res 2024; 38:2406-2447. [PMID: 38433568 DOI: 10.1002/ptr.8166] [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: 08/02/2023] [Revised: 01/30/2024] [Accepted: 02/03/2024] [Indexed: 03/05/2024]
Abstract
The epidermal growth factor receptor (EGFR) is a transmembrane receptor tyrosine kinase (RTK) that maintains normal tissues and cell signaling pathways. EGFR is overactivated and overexpressed in many malignancies, including breast, lung, pancreatic, and kidney. Further, the EGFR gene mutations and protein overexpression activate downstream signaling pathways in cancerous cells, stimulating the growth, survival, resistance to apoptosis, and progression of tumors. Anti-EGFR therapy is the potential approach for treating malignancies and has demonstrated clinical success in treating specific cancers. The recent report suggests most of the clinically used EGFR tyrosine kinase inhibitors developed resistance to the cancer cells. This perspective provides a brief overview of EGFR and its implications in cancer. We have summarized natural products-derived anticancer compounds with the mechanistic basis of tumor inhibition via the EGFR pathway. We propose that developing natural lead molecules into new anticancer agents has a bright future after clinical investigation.
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Affiliation(s)
- Rutuja Damare
- Department of Natural Products, Chemical Sciences, National Institute of Pharmaceutical Education and Research-Hyderabad, Hyderabad, India
| | - Kritika Engle
- Department of Natural Products, Chemical Sciences, National Institute of Pharmaceutical Education and Research-Hyderabad, Hyderabad, India
| | - Gautam Kumar
- Department of Natural Products, Chemical Sciences, National Institute of Pharmaceutical Education and Research-Hyderabad, Hyderabad, India
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48
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Enikeeva K, Rafikova G, Sharifyanova Y, Mulyukova D, Vanzin A, Pavlov V. Epigenetics as a Key Factor in Prostate Cancer. Adv Biol (Weinh) 2024; 8:e2300520. [PMID: 38379272 DOI: 10.1002/adbi.202300520] [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: 09/27/2023] [Revised: 01/01/2024] [Indexed: 02/22/2024]
Abstract
Nowadays, prostate cancer is one of the most common forms of malignant neoplasms in men all over the world. Against the background of increasing incidence, there is a high mortality rate from prostate cancer, which is associated with an inadequate treatment strategy. Such a high prevalence of prostate cancer requires the development of methods that can ensure early detection of the disease, improve the effectiveness of treatment, and predict the therapeutic effect. Under these circumstances, it becomes crucial to focus on the development of effective diagnostic and therapeutic approaches. Due to the development of molecular genetic methods, a large number of studies have been accumulated on the role of epigenetic regulation of gene activity in cancer development, since it is epigenetic changes that can be detected at the earliest stages of cancer development. The presence of epigenetic aberrations in tumor tissue and correlations with drug resistance suggest new therapeutic approaches. Detection of epigenetic alterations such as CpG island methylation, histone modification, and microRNAs as biomarkers will improve the diagnosis of the disease, and the use of these strategies as targets for therapy will allow for greater personalization of prostate cancer treatment.
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Affiliation(s)
- Kadriia Enikeeva
- Institute of Urology and Clinical Oncology, Bashkir State Medical University, Ufa, 450008, Russia
| | - Guzel Rafikova
- Institute of Urology and Clinical Oncology, Bashkir State Medical University, Ufa, 450008, Russia
| | - Yuliya Sharifyanova
- Institute of Urology and Clinical Oncology, Bashkir State Medical University, Ufa, 450008, Russia
| | - Diana Mulyukova
- Institute of Urology and Clinical Oncology, Bashkir State Medical University, Ufa, 450008, Russia
| | - Alexandr Vanzin
- Institute of Urology and Clinical Oncology, Bashkir State Medical University, Ufa, 450008, Russia
| | - Valentin Pavlov
- Institute of Urology and Clinical Oncology, Bashkir State Medical University, Ufa, 450008, Russia
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49
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Zhao N, Lai C, Wang Y, Dai S, Gu H. Understanding the role of DNA methylation in colorectal cancer: Mechanisms, detection, and clinical significance. Biochim Biophys Acta Rev Cancer 2024; 1879:189096. [PMID: 38499079 DOI: 10.1016/j.bbcan.2024.189096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 02/18/2024] [Accepted: 03/13/2024] [Indexed: 03/20/2024]
Abstract
Colorectal cancer (CRC) is one of the deadliest malignancies worldwide, ranking third in incidence and second in mortality. Remarkably, early stage localized CRC has a 5-year survival rate of over 90%; in stark contrast, the corresponding 5-year survival rate for metastatic CRC (mCRC) is only 14%. Compounding this problem is the staggering lack of effective therapeutic strategies. Beyond genetic mutations, which have been identified as critical instigators of CRC initiation and progression, the importance of epigenetic modifications, particularly DNA methylation (DNAm), cannot be underestimated, given that DNAm can be used for diagnosis, treatment monitoring and prognostic evaluation. This review addresses the intricate mechanisms governing aberrant DNAm in CRC and its profound impact on critical oncogenic pathways. In addition, a comprehensive review of the various techniques used to detect DNAm alterations in CRC is provided, along with an exploration of the clinical utility of cancer-specific DNAm alterations.
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Affiliation(s)
- Ningning Zhao
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China; Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei 230031, China
| | - Chuanxi Lai
- Division of Colorectal Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China
| | - Yunfei Wang
- Zhejiang ShengTing Biotech. Ltd, Hangzhou 310000, China
| | - Sheng Dai
- Division of Colorectal Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310016, China.
| | - Hongcang Gu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China; Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei 230031, China.
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50
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Kim Y, Ko JY, Kong HK, Lee M, Chung W, Lim S, Son D, Oh S, Park JW, Kim DY, Lee M, Han W, Park WY, Yoo KH, Park JH. Hypomethylation of ATP1A1 Is Associated with Poor Prognosis and Cancer Progression in Triple-Negative Breast Cancer. Cancers (Basel) 2024; 16:1666. [PMID: 38730618 PMCID: PMC11083557 DOI: 10.3390/cancers16091666] [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: 03/22/2024] [Revised: 04/15/2024] [Accepted: 04/24/2024] [Indexed: 05/13/2024] Open
Abstract
Dysregulated DNA methylation in cancer is critical in the transcription machinery associated with cancer progression. Triple-negative breast cancer (TNBC) is the most aggressive breast cancer subtype, but no treatment targeting TNBC biomarkers has yet been developed. To identify specific DNA methylation patterns in TNBC, methyl-binding domain protein 2 (MBD) sequencing data were compared in TNBC and the three other major breast cancer subtypes. Integrated analysis of DNA methylation and gene expression identified a gene set showing a correlation between DNA methylation and gene expression. ATPase Na+/K+-transporting subunit alpha 1 (ATP1A1) was found to be specifically hypomethylated in the coding sequence (CDS) region and to show increased expression in TNBC. The Cancer Genome Atlas (TCGA) database also showed that hypomethylation and high expression of ATP1A1 were strongly associated with poor survival in patients with TNBC. Furthermore, ATP1A1 knockdown significantly reduced the viability and tumor-sphere formation of TNBC cells. These results suggest that the hypomethylation and overexpression of ATP1A1 could be a prognostic marker in TNBC and that the manipulation of ATP1A1 expression could be a therapeutic target in this disease.
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Affiliation(s)
- Yesol Kim
- Department of Biological Science, Research Institute of Women’s Health, Sookmyung Women’s University, Seoul 04310, Republic of Korea; (Y.K.); (J.Y.K.)
| | - Je Yeong Ko
- Department of Biological Science, Research Institute of Women’s Health, Sookmyung Women’s University, Seoul 04310, Republic of Korea; (Y.K.); (J.Y.K.)
| | - Hyun Kyung Kong
- Department of Biological Science, Research Institute of Women’s Health, Sookmyung Women’s University, Seoul 04310, Republic of Korea; (Y.K.); (J.Y.K.)
| | - Minyoung Lee
- Department of Biological Science, Research Institute of Women’s Health, Sookmyung Women’s University, Seoul 04310, Republic of Korea; (Y.K.); (J.Y.K.)
| | - Woosung Chung
- Samsung Genome Institute, Samsung Medical Center, Seoul 06351, Republic of Korea
| | - Sera Lim
- Department of Biological Science, Research Institute of Women’s Health, Sookmyung Women’s University, Seoul 04310, Republic of Korea; (Y.K.); (J.Y.K.)
| | - Dasom Son
- Department of Biological Science, Research Institute of Women’s Health, Sookmyung Women’s University, Seoul 04310, Republic of Korea; (Y.K.); (J.Y.K.)
| | - Sumin Oh
- Department of Biological Science, Research Institute of Women’s Health, Sookmyung Women’s University, Seoul 04310, Republic of Korea; (Y.K.); (J.Y.K.)
| | - Jee Won Park
- Department of Biological Science, Research Institute of Women’s Health, Sookmyung Women’s University, Seoul 04310, Republic of Korea; (Y.K.); (J.Y.K.)
| | - Do Yeon Kim
- Department of Biological Science, Research Institute of Women’s Health, Sookmyung Women’s University, Seoul 04310, Republic of Korea; (Y.K.); (J.Y.K.)
| | - Minju Lee
- Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Wonshik Han
- Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
- Department of Surgery, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Woong-Yang Park
- Samsung Genome Institute, Samsung Medical Center, Seoul 06351, Republic of Korea
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences & Technology, Sungkyunkwan University, Seoul 06355, Republic of Korea
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Kyung Hyun Yoo
- Department of Biological Science, Research Institute of Women’s Health, Sookmyung Women’s University, Seoul 04310, Republic of Korea; (Y.K.); (J.Y.K.)
| | - Jong Hoon Park
- Department of Biological Science, Research Institute of Women’s Health, Sookmyung Women’s University, Seoul 04310, Republic of Korea; (Y.K.); (J.Y.K.)
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