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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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2
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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. [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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3
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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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4
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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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5
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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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6
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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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7
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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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8
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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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9
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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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10
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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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11
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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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12
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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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13
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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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14
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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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15
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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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17
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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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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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19
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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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20
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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] [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% versus 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 versus 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% versus 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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21
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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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22
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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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23
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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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24
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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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25
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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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26
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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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27
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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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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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29
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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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30
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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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31
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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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32
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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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Ocaña-Paredes B, Rivera-Orellana S, Ramírez-Sánchez D, Montalvo-Guerrero J, Freire MP, Espinoza-Ferrao S, Altamirano-Colina A, Echeverría-Espinoza P, Ramos-Medina MJ, Echeverría-Garcés G, Granda-Moncayo D, Jácome-Alvarado A, Andrade MG, López-Cortés A. The pharmacoepigenetic paradigm in cancer treatment. Front Pharmacol 2024; 15:1381168. [PMID: 38720770 PMCID: PMC11076712 DOI: 10.3389/fphar.2024.1381168] [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: 02/02/2024] [Accepted: 04/11/2024] [Indexed: 05/12/2024] Open
Abstract
Epigenetic modifications, characterized by changes in gene expression without altering the DNA sequence, play a crucial role in the development and progression of cancer by significantly influencing gene activity and cellular function. This insight has led to the development of a novel class of therapeutic agents, known as epigenetic drugs. These drugs, including histone deacetylase inhibitors, histone acetyltransferase inhibitors, histone methyltransferase inhibitors, and DNA methyltransferase inhibitors, aim to modulate gene expression to curb cancer growth by uniquely altering the epigenetic landscape of cancer cells. Ongoing research and clinical trials are rigorously evaluating the efficacy of these drugs, particularly their ability to improve therapeutic outcomes when used in combination with other treatments. Such combination therapies may more effectively target cancer and potentially overcome the challenge of drug resistance, a significant hurdle in cancer therapy. Additionally, the importance of nutrition, inflammation control, and circadian rhythm regulation in modulating drug responses has been increasingly recognized, highlighting their role as critical modifiers of the epigenetic landscape and thereby influencing the effectiveness of pharmacological interventions and patient outcomes. Epigenetic drugs represent a paradigm shift in cancer treatment, offering targeted therapies that promise a more precise approach to treating a wide spectrum of tumors, potentially with fewer side effects compared to traditional chemotherapy. This progress marks a step towards more personalized and precise interventions, leveraging the unique epigenetic profiles of individual tumors to optimize treatment strategies.
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Affiliation(s)
- Belén Ocaña-Paredes
- Cancer Research Group (CRG), Faculty of Medicine, Universidad de Las Américas, Quito, Ecuador
| | | | - David Ramírez-Sánchez
- Cancer Research Group (CRG), Faculty of Medicine, Universidad de Las Américas, Quito, Ecuador
| | | | - María Paula Freire
- Cancer Research Group (CRG), Faculty of Medicine, Universidad de Las Américas, Quito, Ecuador
| | | | | | | | - María José Ramos-Medina
- German Cancer Research Center (DKFZ), Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Gabriela Echeverría-Garcés
- Centro de Referencia Nacional de Genómica, Secuenciación y Bioinformática, Instituto Nacional de Investigación en Salud Pública “Leopoldo Izquieta Pérez”, Quito, Ecuador
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), Santiago, Chile
| | | | - Andrea Jácome-Alvarado
- Cancer Research Group (CRG), Faculty of Medicine, Universidad de Las Américas, Quito, Ecuador
| | - María Gabriela Andrade
- Cancer Research Group (CRG), Faculty of Medicine, Universidad de Las Américas, Quito, Ecuador
| | - Andrés López-Cortés
- Cancer Research Group (CRG), Faculty of Medicine, Universidad de Las Américas, Quito, Ecuador
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34
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Adampourezare M, Nikzad B, Amini M, Sheibani N. Fluorimetric detection of DNA methylation by cerium oxide nanoparticles for early cancer diagnosis. Heliyon 2024; 10:e28695. [PMID: 38586346 PMCID: PMC10998132 DOI: 10.1016/j.heliyon.2024.e28695] [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: 03/30/2023] [Revised: 03/21/2024] [Accepted: 03/22/2024] [Indexed: 04/09/2024] Open
Abstract
In this study, a very sensitive fluorescence nano-biosensor was developed using CeO2 nanoparticles for the rapid detection of DNA methylation. The characteristics of CeO2 nanoparticles were determined by transmission electron microscopy (TEM), scanning electron microscopy (SEM), energy dispersive spectroscopy (EDS), X-ray diffraction (XRD) spectroscopy, UV-visible spectroscopy, and fluorescence spectroscopy. The CeO2 nanoparticles were reacted with a single-stranded DNA (ssDNA) probe, and then methylated and unmethylated target DNAs hybridized with an ssDNA probe, and the fluorescence emission was measured. Upon adding the target unmethylated and methylated ssDNA, the fluorescence intensity increased in the linear range of concentration from 2 × 10-13 - 10-18 M. The limit of detection (LOD) was 1.597 × 10-6 M for methylated DNA and 1.043 × 10-6 M for unmethylated DNA. The fluorescence emission intensity of methylated sequences was higher than of that unmethylated sequences. The fabricated DNA nanobiosensor showed a fluorescence emission at 420 nm with an excitation wavelength of 280 nm. The impact of CeO2 binding on methylated and unmethylated DNA was further demonstrated by agarose gel electrophoresis. Finally, the actual sample analysis suggested that the nanobiosensor could have practical applications for detecting methylation in the human plasma samples.
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Affiliation(s)
- Mina Adampourezare
- Research Center of Bioscience and Biotechnology, University of Tabriz, Tabriz, Iran
| | - Behzad Nikzad
- Research Center of Bioscience and Biotechnology, University of Tabriz, Tabriz, Iran
| | - Mojtaba Amini
- Department of Inorganic Chemistry, Faculty of Chemistry, University of Tabriz, Tabriz, Iran
| | - Nader Sheibani
- Department of Ophthalmology and Visual Sciences, University of Wisconsin School of Medicine and Public Health, Madison WI 53705, USA
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35
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Li H, Li C, Zhang Y, Jiang W, Zhang F, Tang X, Sun G, Xu S, Dong X, Shou J, Yang Y, Chen M. Comprehensive analysis of m 6 A methylome and transcriptome by Nanopore sequencing in clear cell renal carcinoma. Mol Carcinog 2024; 63:677-687. [PMID: 38362848 DOI: 10.1002/mc.23680] [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: 09/04/2023] [Revised: 12/01/2023] [Accepted: 01/02/2024] [Indexed: 02/17/2024]
Abstract
N6 -methyladenosine (m6 A) is the most prevalent epigenetic modification on eukaryotic messenger RNAs. Recent studies have focused on elucidating the key role of m6 A modification patterns in tumor progression. However, the relationship between m6 A and transcriptional regulation remains elusive. Nanopore technology enables the quantification of m6 A levels at each genomic site. In this study, a pair of tumor tissues and adjacent normal tissues from clear cell renal cell carcinoma (ccRCC) surgical samples were collected for Nanopore direct RNA sequencing. We identified 9644 genes displaying anomalous m6 A modifications, with 5343 genes upregulated and 4301 genes downregulated. Among these, 5224 genes were regarded as dysregulated genes, encompassing abnormal regulation of both m6 A modification and RNA expression. Gene Set Enrichment Analysis revealed an enrichment of these genes in pathways related to renal system progress and fatty acid metabolic progress. Furthermore, the χ2 test demonstrated a significant association between the levels of m6 A in dysregulated genes and their transcriptional expression levels. Additionally, we identified four obesity-associated genes (FTO, LEPR, ADIPOR2, and NPY5R) among the dysregulated genes. Further analyses using public databases revealed that these four genes were all related to the prognosis and diagnosis of ccRCC. This study introduced the novel approach of employing conjoint analysis of m6 A modification and RNA expression based on Nanopore sequencing to explore potential disease-related genes. Our work demonstrates the feasibility of the application of Nanopore sequencing technology in RNA epigenetic regulation research and identifies new potential therapeutic targets for ccRCC.
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Affiliation(s)
- Hexin Li
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Chang Li
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Yuxiang Zhang
- Cancer Data Center, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Weixing Jiang
- Cancer Data Center, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Fubo Zhang
- Cancer Data Center, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiaokun Tang
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Gaoyuan Sun
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Siyuan Xu
- Clinical Biobank, Beijing Hospital, National Center of Gerontology, National Health Commission, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Xin Dong
- Cancer Data Center, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jianzhong Shou
- Cancer Data Center, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yong Yang
- Department of Oncology, Huai'an TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Jiangsu, China
| | - Meng Chen
- Cancer Data Center, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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36
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Kaur H, Kaur G, Ali SA. Postbiotics Implication in the Microbiota-Host Intestinal Epithelial Cells Mutualism. Probiotics Antimicrob Proteins 2024; 16:443-458. [PMID: 36933160 DOI: 10.1007/s12602-023-10062-w] [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: 03/08/2023] [Indexed: 03/19/2023]
Abstract
To sustain host health and provide the microbial community with a nutrient-rich environment, the host and gut microbiota must interact with one another. These interactions between commensal bacterial and intestinal epithelial cells (IECs) serve as the first line of defense against gut microbiota in preserving intestinal homeostasis. In this microenvironment, the post-biotics and similar molecules such as p40 exert several beneficial effects through regulation of IECs. Importantly, post-biotics were discovered to be transactivators of the EGF receptor (EGFR) in IECs, inducing protective cellular responses and alleviating colitis. The transient exposure to post-biotics such as p40 during the neonatal period reprograms IECs by upregulation of a methyltransferase, Setd1β, leading to a sustained increase in TGF- β release for the expansion of regulatory T cells (Tregs) in the intestinal lamina propria and durable protection against colitis in adulthood. This crosstalk between the IECs and post-biotic secreted factors was not reviewed previously. Therefore, this review describes the role of probiotic-derived factors in the sustainability of intestinal health and improving gut homeostasis via certain signaling pathways. In the era of precision medicine and targeted therapies, more basic, preclinical, and clinical evidence is needed to clarify the efficacy of probiotics released as functional factors in maintaining intestinal health and preventing and treating disease.
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Affiliation(s)
- Harpreet Kaur
- Animal Biochemistry Division, ICAR-NDRI, Karnal, 132001, India
| | - Gurjeet Kaur
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, NSW, 2052, Australia
- Mark Wainwright Analytical Centre, Bioanalytical Mass Spectrometry Facility, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Syed Azmal Ali
- Cell Biology and Proteomics Lab, Animal Biotechnology Center, ICAR-NDRI, Karnal, 132001, India.
- Division Proteomics of Stem Cells and Cancer, German Cancer Research Center, Heidelberg, 69120, Germany.
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37
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Zhu L, Tang N, Hang H, Zhou Y, Dong J, Yang Y, Mao L, Qiu Y, Fu X, Cao W. Loss of Claudin-1 incurred by DNMT aberration promotes pancreatic cancer progression. Cancer Lett 2024; 586:216611. [PMID: 38309617 DOI: 10.1016/j.canlet.2024.216611] [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: 10/10/2023] [Revised: 11/30/2023] [Accepted: 12/23/2023] [Indexed: 02/05/2024]
Abstract
Pancreatic cancer (PC) is one of the most malignant and deadly tumors of digestive system with complex etiology and pathogenesis. Dysregulations of oncogenes and tumor suppressors due to epigenetic modifications causally affect tumorogenesis; however the key tumor suppressors and their regulations in PC are only partially defined. In this study, we found that Claudin-1 (encoded by CLDN1 gene) was significantly suppressed in PC that correlated with a poor clinical prognosis. Claudin-1 knockdown enhanced PC cell proliferation, migration, and stemness. Pancreatic specific Cldn1 knockout in KPC (LSLKrasG12D/Pdx1-Cre/Trp53R172H+) and KC (LSLKrasG12D/Pdx1-Cre) mice reduced mouse survival, promoted acinar-to-ductal metaplasia (ADM) process, and accelerated the development of pancreatic intraepithelial neoplasia (PanIN) and PC. Further investigation revealed that Claudin-1 suppression was mainly caused by aberrant DNA methylatransferase 1 (DNMT1) and DNMT3A elevations and the resultant CLDN1 promoter hypermethylation, as a DNMT specific inhibitor SGI-1027 effectively reversed the Claudin-1 suppression and inhibited PC progression both in vitro and in vivo in a Claudin-1 preservation-dependent manner. Together, our data suggest that Claudin-1 functions as a tumor suppressor in PC and its epigenetic suppression due to DNMT aberrations is a crucial event that promotes PC development and progression.
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Affiliation(s)
- Linxi Zhu
- Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, 321 Zhongshan Road, Nanjing, 210008, China
| | - Neng Tang
- Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, 321 Zhongshan Road, Nanjing, 210008, China
| | - Hexing Hang
- Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, 321 Zhongshan Road, Nanjing, 210008, China
| | - Yan Zhou
- Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, 321 Zhongshan Road, Nanjing, 210008, China
| | - Jian Dong
- Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, 321 Zhongshan Road, Nanjing, 210008, China
| | - Yifei Yang
- Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, 321 Zhongshan Road, Nanjing, 210008, China
| | - Liang Mao
- Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, 321 Zhongshan Road, Nanjing, 210008, China
| | - Yudong Qiu
- Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, 321 Zhongshan Road, Nanjing, 210008, China.
| | - Xu Fu
- Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, 321 Zhongshan Road, Nanjing, 210008, China.
| | - Wangsen Cao
- Nanjing University Medical School, Jiangsu Key Lab of Molecular Medicine, 22 Hankou Road, Nanjing, 210093, China; Yancheng Medical Research Center of Nanjing University Medical School, Yancheng First Hospital, Affiliated Hospital of Nanjing University Medical School, The First People's Hospital of Yancheng, 66 Southern People Road, Yancheng, 224008, China.
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Meevassana J, Varophas S, Prabsattru P, Kamolratanakul S, Ruangritchankul K, Kitkumthorn N. 5-Methylcytosine immunohistochemistry for predicting cutaneous melanoma prognosis. Sci Rep 2024; 14:7554. [PMID: 38555324 PMCID: PMC10981665 DOI: 10.1038/s41598-024-58011-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 03/25/2024] [Indexed: 04/02/2024] Open
Abstract
There is a correlation between DNA methylation and the diseased stage and poor survival. 5-methylcytosine (5-mC) is one of the epigenetic modifications of bases that researchers focus on. Staining with 5-mC immunohistochemistry was used to examine pathological samples taken from individuals diagnosed with cutaneous melanoma. Between Breslow levels 2 and 4, there was a significant difference in the H-score of 5-mC expression (p = 0.046). A significant reduction in 5-mC expression H-scores was seen in patients who were diagnosed with ulcers (p = 0.039). It was shown that patients with low 5-mC had a significantly worse overall survival rate (p = 0.027).
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Affiliation(s)
- Jiraroch Meevassana
- Center of Excellence in Burn and Wound Care, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Shananya Varophas
- Department of Surgery, Division of Plastic and Reconstructive Surgery, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Piyawan Prabsattru
- Center of Excellence in Burn and Wound Care, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Supitcha Kamolratanakul
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | | | - Nakarin Kitkumthorn
- Department of Oral Biology, Faculty of Dentistry, Mahidol University, No. 6, Yothi Road, Ratchathewi District, Bangkok, 10400, Thailand.
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Carrillo-Perez F, Pizurica M, Zheng Y, Nandi TN, Madduri R, Shen J, Gevaert O. Generation of synthetic whole-slide image tiles of tumours from RNA-sequencing data via cascaded diffusion models. Nat Biomed Eng 2024:10.1038/s41551-024-01193-8. [PMID: 38514775 DOI: 10.1038/s41551-024-01193-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 02/29/2024] [Indexed: 03/23/2024]
Abstract
Training machine-learning models with synthetically generated data can alleviate the problem of data scarcity when acquiring diverse and sufficiently large datasets is costly and challenging. Here we show that cascaded diffusion models can be used to synthesize realistic whole-slide image tiles from latent representations of RNA-sequencing data from human tumours. Alterations in gene expression affected the composition of cell types in the generated synthetic image tiles, which accurately preserved the distribution of cell types and maintained the cell fraction observed in bulk RNA-sequencing data, as we show for lung adenocarcinoma, kidney renal papillary cell carcinoma, cervical squamous cell carcinoma, colon adenocarcinoma and glioblastoma. Machine-learning models pretrained with the generated synthetic data performed better than models trained from scratch. Synthetic data may accelerate the development of machine-learning models in scarce-data settings and allow for the imputation of missing data modalities.
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Affiliation(s)
- Francisco Carrillo-Perez
- Stanford Center for Biomedical Informatics Research (BMIR), Stanford University, School of Medicine, Stanford, CA, USA
| | - Marija Pizurica
- Stanford Center for Biomedical Informatics Research (BMIR), Stanford University, School of Medicine, Stanford, CA, USA
- Internet technology and Data science Lab (IDLab), Ghent University, Ghent, Belgium
| | - Yuanning Zheng
- Stanford Center for Biomedical Informatics Research (BMIR), Stanford University, School of Medicine, Stanford, CA, USA
| | - Tarak Nath Nandi
- Data Science and Learning Division, Argonne National Laboratory, Lemont, IL, USA
| | - Ravi Madduri
- Data Science and Learning Division, Argonne National Laboratory, Lemont, IL, USA
| | - Jeanne Shen
- Department of Pathology, Stanford University, School of Medicine, Palo Alto, CA, USA
| | - Olivier Gevaert
- Stanford Center for Biomedical Informatics Research (BMIR), Stanford University, School of Medicine, Stanford, CA, USA.
- Department of Biomedical Data Science, Stanford University, School of Medicine, Stanford, CA, USA.
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40
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Wang Y, Situ X, Cardenas H, Siu E, Alhunayan SA, Keathley R, Tanner E, Wei JJ, Tan Y, Prabhu Dessai CV, Cheng JX, Matei D. Preclinical Evaluation of NTX-301, a Novel DNA Hypomethylating Agent in Ovarian Cancer. Clin Cancer Res 2024; 30:1175-1188. [PMID: 38231483 PMCID: PMC10947827 DOI: 10.1158/1078-0432.ccr-23-2368] [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: 08/07/2023] [Revised: 11/27/2023] [Accepted: 01/12/2024] [Indexed: 01/18/2024]
Abstract
PURPOSE DNA methylation causes silencing of tumor-suppressor and differentiation-associated genes, being linked to chemoresistance. Previous studies demonstrated that hypomethylating agents (HMA) resensitize ovarian cancer to chemotherapy. NTX-301 is a highly potent and orally bioavailable HMA, in early clinical development. EXPERIMENTAL DESIGN The antitumor effects of NTX-301 were studied in ovarian cancer models by using cell viability, stemness and ferroptosis assays, RNA sequencing, lipidomic analyses, and stimulated Raman spectroscopy. RESULTS Ovarian cancer cells (SKOV3, IC50 = 5.08 nmol/L; OVCAR5 IC50 = 3.66 nmol/L) were highly sensitive to NTX-301 compared with fallopian tube epithelial cells. NTX-301 downregulated expression of DNA methyltransferases 1-3 and induced transcriptomic reprogramming with 15,000 differentially expressed genes (DEG, P < 0.05). Among them, Gene Ontology enrichment analysis identified regulation of fatty acid biosynthesis and molecular functions related to aldehyde dehydrogenase (ALDH) and oxidoreductase, known features of cancer stem cells. Low-dose NTX-301 reduced the ALDH(+) cell population and expression of stemness-associated transcription factors. Stearoyl-coenzyme A desaturase 1 (SCD), which regulates production of unsaturated fatty acids (UFA), was among the top DEG downregulated by NTX-301. NTX-301 treatment decreased levels of UFA and increased oxidized lipids, and this was blunted by deferoxamine, indicating cell death via ferroptosis. NTX-301-induced ferroptosis was rescued by oleic acid. In vivo, monotherapy with NTX-301 significantly inhibited ovarian cancer and patient-derived xenograft growth (P < 0.05). Decreased SCD levels and increased oxidized lipids were detected in NTX-301-treated xenografts. CONCLUSIONS NTX-301 is active in ovarian cancer models. Our findings point to a new mechanism by which epigenetic blockade disrupts lipid homeostasis and promotes cancer cell death.
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Affiliation(s)
- Yinu Wang
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Xiaolei Situ
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Horacio Cardenas
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Ellie Siu
- Department of Biological Sciences, Weinberg College of Arts and Sciences, Northwestern University, Chicago, Illinois
| | - Sayedabdulrazzaq A Alhunayan
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Russell Keathley
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
- Driskill Graduate Program in Life Sciences, Northwestern University, Chicago, Illinois
| | - Edward Tanner
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Jian-Jun Wei
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
- Robert H. Lurie Comprehensive Cancer Center, Chicago, Illinois
| | - Yuying Tan
- Department of Physics, Boston University, Boston, Massachusetts
| | | | - Ji-Xin Cheng
- Department of Physics, Boston University, Boston, Massachusetts
| | - Daniela Matei
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
- Robert H. Lurie Comprehensive Cancer Center, Chicago, Illinois
- Jesse Brown Veteran Affairs Medical Center, Chicago, Illinois
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Fietz S, Diekmann E, de Vos L, Zarbl R, Hunecke A, Glosch AK, Färber M, Sirokay J, Hoffmann F, Fröhlich A, Franzen A, Strieth S, Landsberg J, Dietrich D. Circulating Cell-Free SHOX2 DNA Methylation Is a Predictive, Prognostic, and Monitoring Biomarker in Adjuvant and Palliative Anti-PD-1-Treated Melanoma. Clin Chem 2024; 70:516-527. [PMID: 38300881 DOI: 10.1093/clinchem/hvad230] [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: 07/26/2023] [Accepted: 12/13/2023] [Indexed: 02/03/2024]
Abstract
BACKGROUND The majority of metastatic melanoma patients initially do not respond or acquire resistance to anti-programmed cell death 1 (PD-1) immunotherapy. Liquid biopsy biomarkers might provide useful early response information and allow for personalized treatment decisions. METHODS We prospectively assessed circulating cell-free SHOX2 DNA methylation (SHOX2 ccfDNAm) levels and their dynamic changes in blood plasma of melanoma patients by quantitative methylation-specific polymerase chain reaction. Patients were treated with either palliative (n = 42) or adjuvant (n = 55) anti-PD-1 immunotherapy. Moreover, we included n = 126 control patients without evidence of malignant disease. We analyzed SHOX2 ccfDNAm status prior to and 4 weeks after palliative treatment initiation with regard to outcome [objective response, progression-free survival (PFS), and overall survival (OS)]. In the adjuvant setting, we associated longitudinal SHOX2 ccfDNAm status with disease recurrence. RESULTS Sensitivity was 60% with 25/42 melanoma patients showing increased SHOX2 ccfDNAm levels, whereas specificity was 98% with 123/126 (P < 0.001) control patients having SHOX2 ccfDNAm levels below cut-off. Pretreatment SHOX2 ccfDNAm status did not correlate with outcome; however, SHOX2 ccfDNAm negativity 4 weeks after palliative treatment initiation was strongly associated with improved survival [PFS: hazard ratio (HR) = 0.25, P = 0.002; OS: HR = 0.12, P = 0.007]. Pretreatment positive patients who reached SHOX2 ccfDNAm clearance after 4 weeks of immunotherapy showed an exceptionally beneficial outcome. SHOX2 ccfDNAm testing allowed for an early detection of distant metastases in adjuvant-treated melanoma patients. CONCLUSIONS Our study suggests SHOX2 ccfDNAm to be an early predictor of outcome in anti-PD-1 treated melanoma patients. SHOX2 ccfDNAm testing may aid individualized treatment decision-making.
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Affiliation(s)
- Simon Fietz
- Department of Dermatology and Allergology, University Hospital Bonn, Bonn, Germany
- Department of Otorhinolaryngology, Head and Neck Surgery, University Hospital Bonn, Bonn, Germany
| | - Eric Diekmann
- Department of Otorhinolaryngology, Head and Neck Surgery, University Hospital Bonn, Bonn, Germany
| | - Luka de Vos
- Department of Dermatology and Allergology, University Hospital Bonn, Bonn, Germany
- Department of Otorhinolaryngology, Head and Neck Surgery, University Hospital Bonn, Bonn, Germany
| | - Romina Zarbl
- Department of Otorhinolaryngology, Head and Neck Surgery, University Hospital Bonn, Bonn, Germany
| | - Alina Hunecke
- Department of Otorhinolaryngology, Head and Neck Surgery, University Hospital Bonn, Bonn, Germany
| | - Ann-Kathrin Glosch
- Department of Otorhinolaryngology, Head and Neck Surgery, University Hospital Bonn, Bonn, Germany
| | - Moritz Färber
- Department of Otorhinolaryngology, Head and Neck Surgery, University Hospital Bonn, Bonn, Germany
| | - Judith Sirokay
- Department of Dermatology and Allergology, University Hospital Bonn, Bonn, Germany
| | - Friederike Hoffmann
- Department of Dermatology and Allergology, University Hospital Bonn, Bonn, Germany
| | - Anne Fröhlich
- Department of Dermatology and Allergology, University Hospital Bonn, Bonn, Germany
| | - Alina Franzen
- Department of Otorhinolaryngology, Head and Neck Surgery, University Hospital Bonn, Bonn, Germany
| | - Sebastian Strieth
- Department of Otorhinolaryngology, Head and Neck Surgery, University Hospital Bonn, Bonn, Germany
| | - Jennifer Landsberg
- Department of Dermatology and Allergology, University Hospital Bonn, Bonn, Germany
| | - Dimo Dietrich
- Department of Otorhinolaryngology, Head and Neck Surgery, University Hospital Bonn, Bonn, Germany
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Bagheri M, Lee MK, Muller KE, Miller TW, Pattabiraman DR, Christensen BC. Alteration of DNA methyltransferases by eribulin elicits broad DNA methylation changes with potential therapeutic implications for triple-negative breast cancer. Epigenomics 2024; 16:293-308. [PMID: 38356412 PMCID: PMC10910603 DOI: 10.2217/epi-2023-0339] [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: 09/26/2023] [Accepted: 01/23/2024] [Indexed: 02/16/2024] Open
Abstract
Background: Triple-negative breast cancer (TNBC) is an aggressive disease with limited treatment options. Eribulin, a chemotherapeutic drug, induces epigenetic changes in cancer cells, suggesting a unique mechanism of action. Materials & methods: MDA-MB 231 cells were treated with eribulin and paclitaxel, and the samples from 53 patients treated with neoadjuvant eribulin were compared with those from 14 patients who received the standard-of-care treatment using immunohistochemistry. Results: Eribulin treatment caused significant DNA methylation changes in drug-tolerant persister TNBC cells, and it also elicited changes in the expression levels of epigenetic modifiers (DNMT1, TET1, DNMT3A/B) in vitro and in primary TNBC tumors. Conclusion: These findings provide new insights into eribulin's mechanism of action and potential biomarkers for predicting TNBC treatment response.
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Affiliation(s)
- Meisam Bagheri
- Department of Molecular & Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
- Dartmouth Cancer Center, Lebanon, NH 03756, USA
| | - Min Kyung Lee
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - Kristen E Muller
- Dartmouth Cancer Center, Lebanon, NH 03756, USA
- Department of Pathology, Geisel School of Medicine at Dartmouth, Lebanon NH 03756, USA
| | - Todd W Miller
- Department of Molecular & Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
- Dartmouth Cancer Center, Lebanon, NH 03756, USA
- Department of Pharmacology & Toxicology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Diwakar R Pattabiraman
- Department of Molecular & Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
- Dartmouth Cancer Center, Lebanon, NH 03756, USA
| | - Brock C Christensen
- Department of Molecular & Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
- Department of Community & Family Medicine, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
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Wang H, Yang S, Chen L, Li Y, He P, Wang G, Dong H, Ma P, Ding G. Tumor diagnosis using carbon-based quantum dots: Detection based on the hallmarks of cancer. Bioact Mater 2024; 33:174-222. [PMID: 38034499 PMCID: PMC10684566 DOI: 10.1016/j.bioactmat.2023.10.004] [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: 06/28/2023] [Revised: 09/15/2023] [Accepted: 10/05/2023] [Indexed: 12/02/2023] Open
Abstract
Carbon-based quantum dots (CQDs) have been shown to have promising application value in tumor diagnosis. Their use, however, is severely hindered by the complicated nature of the nanostructures in the CQDs. Furthermore, it seems impossible to formulate the mechanisms involved using the inadequate theoretical frameworks that are currently available for CQDs. In this review, we re-consider the structure-property relationships of CQDs and summarize the current state of development of CQDs-based tumor diagnosis based on biological theories that are fully developed. The advantages and deficiencies of recent research on CQDs-based tumor diagnosis are thus explained in terms of the manifestation of nine essential changes in cell physiology. This review makes significant progress in addressing related problems encountered with other nanomaterials.
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Affiliation(s)
- Hang Wang
- National Key Laboratory of Materials for Integrated Circuit, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, PR China
- CAS Center for Excellence in Superconducting Electronics (CENSE), Chinese Academy of Sciences, Shanghai, 200050, PR China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, PR China
| | - Siwei Yang
- National Key Laboratory of Materials for Integrated Circuit, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, PR China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, PR China
| | - Liangfeng Chen
- National Key Laboratory of Materials for Integrated Circuit, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, PR China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, PR China
| | - Yongqiang Li
- National Key Laboratory of Materials for Integrated Circuit, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, PR China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, PR China
| | - Peng He
- National Key Laboratory of Materials for Integrated Circuit, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, PR China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, PR China
| | - Gang Wang
- Department of Microelectronic Science and Engineering, School of Physical Science and Technology, Ningbo University, Ningbo, 315211, PR China
| | - Hui Dong
- National Key Laboratory of Materials for Integrated Circuit, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, PR China
- CAS Center for Excellence in Superconducting Electronics (CENSE), Chinese Academy of Sciences, Shanghai, 200050, PR China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, PR China
| | - Peixiang Ma
- Shanghai Key Laboratory of Orthopedic Implants, Department of Orthopedic Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, PR China
| | - Guqiao Ding
- National Key Laboratory of Materials for Integrated Circuit, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, PR China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, PR China
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Wang J, Zhang C, Zhang L, Yao HJ, Liu X, Shi Y, Zhao J, Bo X, Chen H, Li L. Comparative study on genomic and epigenomic profiles of retinoblastoma or tuberous sclerosis complex via nanopore sequencing and a joint screening framework. Cancer Gene Ther 2024; 31:439-453. [PMID: 38146007 DOI: 10.1038/s41417-023-00714-y] [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: 08/09/2023] [Revised: 11/23/2023] [Accepted: 11/29/2023] [Indexed: 12/27/2023]
Abstract
Recurrence and extraocular metastasis in advanced intraocular retinoblastoma (RB) are still major obstacles for successful treatment of Chinese children. Tuberous sclerosis complex (TSC) is a very rare, multisystemic genetic disorder characterized by hamartomatous growth. In this study, we aimed to compare genomic and epigenomic profiles with human RB or TSC using recently developed nanopore sequencing, and to identify disease-associated variations or genes. Peripheral blood samples were collected from either RB or RB/TSC patients plus their normal siblings, followed by nanopore sequencing and identification of disease-specific structural variations (SVs) and differentially methylated regions (DMRs) by a systematic biology strategy named as multiomics-based joint screening framework. In total, 316 RB- and 1295 TSC-unique SVs were identified, as well as 1072 RB- and 1114 TSC-associated DMRs, respectively. We eventually identified 6 key genes for RB for further functional validation. Knockdown of CDK19 with specific siRNAs significantly inhibited Y79 cellular proliferation and increased sensitivity to carboplatin, whereas downregulation of AHNAK2 promoted the cell growth as well as drug resistance. Those two genes might serve as potential diagnostic markers or therapeutic targets of RB. The systematic biology strategy combined with functional validation might be an effective approach for rare pediatric malignances with limited samples and challenging collection process.
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Affiliation(s)
- Junting Wang
- State Key Laboratory of Respiratory Health and Multimorbidity, NHC Key Laboratory of Biotechnology for Microbial Drugs, Department of Oncology, Institute of Medicinal Biotechnology (IMB), Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), NO.1 Tiantan Xili, Beijing, 100050, China
- Institute of Health Service and Transfusion Medicine, Beijing, 100850, P.R. China
| | - Chengyue Zhang
- Department of Ophthalmology, Beijing Children's Hospital affiliated with Capital Medical University, National Center for Children's Health, Beijing, 100045, China.
| | - Li Zhang
- State Key Laboratory of Respiratory Health and Multimorbidity, NHC Key Laboratory of Biotechnology for Microbial Drugs, Department of Oncology, Institute of Medicinal Biotechnology (IMB), Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), NO.1 Tiantan Xili, Beijing, 100050, China
| | - Hong-Juan Yao
- State Key Laboratory of Respiratory Health and Multimorbidity, NHC Key Laboratory of Biotechnology for Microbial Drugs, Department of Oncology, Institute of Medicinal Biotechnology (IMB), Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), NO.1 Tiantan Xili, Beijing, 100050, China
| | - Xiaohong Liu
- Guang'anmen Hospital, Chinese Academy of Chinese Medical Sciences, No.5 BeiXianGe St., Beijing, 100053, China
| | - Yuchen Shi
- Dongzhimen Hospital, Beijing University of Chinese Medicine, No.5 Haiyuncang, Beijing, 100700, China
| | - Junyang Zhao
- Department of Ophthalmology, Beijing Children's Hospital affiliated with Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Xiaochen Bo
- Institute of Health Service and Transfusion Medicine, Beijing, 100850, P.R. China
| | - Hebing Chen
- Institute of Health Service and Transfusion Medicine, Beijing, 100850, P.R. China.
| | - Liang Li
- State Key Laboratory of Respiratory Health and Multimorbidity, NHC Key Laboratory of Biotechnology for Microbial Drugs, Department of Oncology, Institute of Medicinal Biotechnology (IMB), Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), NO.1 Tiantan Xili, Beijing, 100050, China.
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Song Y, Shen T, Sun H, Wang X. Genome-wide analyses reveal the regulatory roles of DNA methylation-regulated alternative promoter transcripts in breast cancer. Hum Genet 2024; 143:385-399. [PMID: 38502355 DOI: 10.1007/s00439-024-02653-6] [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: 08/07/2023] [Accepted: 02/06/2024] [Indexed: 03/21/2024]
Abstract
A certain proportion of genes are regulated by multiple, distinct promoters, revealing a dynamic landscape of the cancer transcriptome. However, the contribution of alternative promoters (APs) in breast cancer (BRCA) remains largely unexplored. Here, we identified 3654 genes with multiple promoters in BRCA patients, and 53 of them could generate distinct AP transcripts that are dysregulated and prognosis-related in BRCA, namely prognosis-related dysregulated AP (prdeAP) transcripts. Interestingly, when we searched for the genomic signatures of these prdeAP genes, we found that the promoter regions of 92% of the prdeAP genes were enriched with abundant DNA methylation signals. Through further bioinformatic analysis and experimental validation, we showed that AP selections of TANK, UNKL, CCL28, and MAP1LC3A were regulated by DNA methylation upon their corresponding promoter regions. Functionally, by overexpressing AP variants of TANK, we found that TANK|55731 could dramatically suppress MDA-MB-231 cell proliferation and migration. Meanwhile, pan-cancer survival analyses suggested that AP variants of TANK provided more accurate prognostic predictive ability than TANK gene in a variety of tumor types, including BRCA. Together, by uncovering the DNA methylation-regulated AP transcripts with tumor prognostic features, our work revealed a novel layer of regulators in BRCA progression and provided potential targets that served as effective biomarkers for anti-BRCA treatment.
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Affiliation(s)
- Yingdong Song
- Department of Geriatrics, Gerontology Institute of Anhui Province, Centre for Leading Medicine and Advanced Technologies of IHM, The First Affiliated Hospital, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Tao Shen
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Metabolic Diseases, Anhui Provincial Engineering Research Centre for Molecular Detection and Diagnostics, College of Life Sciences, Anhui Normal University, Wuhu, China.
| | - Huihui Sun
- Department of Geriatrics, Gerontology Institute of Anhui Province, Centre for Leading Medicine and Advanced Technologies of IHM, The First Affiliated Hospital, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Xiangting Wang
- Department of Geriatrics, Gerontology Institute of Anhui Province, Centre for Leading Medicine and Advanced Technologies of IHM, The First Affiliated Hospital, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
- Anhui Province Key Laboratory of Geriatric Immunology and Nutrition Therapy, Hefei, China.
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Long X, Wang Y, Jian ZQ, He Q. Comparison of clinical features and prognosis of early- and late-onset colorectal cancer. WORLD CHINESE JOURNAL OF DIGESTOLOGY 2024; 32:116-122. [DOI: 10.11569/wcjd.v32.i2.116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]
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47
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Maurya SK, Rehman AU, Zaidi MAA, Khan P, Gautam SK, Santamaria-Barria JA, Siddiqui JA, Batra SK, Nasser MW. Epigenetic alterations fuel brain metastasis via regulating inflammatory cascade. Semin Cell Dev Biol 2024; 154:261-274. [PMID: 36379848 PMCID: PMC10198579 DOI: 10.1016/j.semcdb.2022.11.001] [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: 09/09/2022] [Revised: 10/28/2022] [Accepted: 11/02/2022] [Indexed: 11/13/2022]
Abstract
Brain metastasis (BrM) is a major threat to the survival of melanoma, breast, and lung cancer patients. Circulating tumor cells (CTCs) cross the blood-brain barrier (BBB) and sustain in the brain microenvironment. Genetic mutations and epigenetic modifications have been found to be critical in controlling key aspects of cancer metastasis. Metastasizing cells confront inflammation and gradually adapt in the unique brain microenvironment. Currently, it is one of the major areas that has gained momentum. Researchers are interested in the factors that modulate neuroinflammation during BrM. We review here various epigenetic factors and mechanisms modulating neuroinflammation and how this helps CTCs to adapt and survive in the brain microenvironment. Since epigenetic changes could be modulated by targeting enzymes such as histone/DNA methyltransferase, deacetylases, acetyltransferases, and demethylases, we also summarize our current understanding of potential drugs targeting various aspects of epigenetic regulation in BrM.
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Affiliation(s)
- Shailendra Kumar Maurya
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68108, USA
| | - Asad Ur Rehman
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68108, USA
| | - Mohd Ali Abbas Zaidi
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68108, USA
| | - Parvez Khan
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68108, USA
| | - Shailendra K Gautam
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68108, USA
| | | | - Jawed Akhtar Siddiqui
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68108, USA; Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68108, USA
| | - Surinder K Batra
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68108, USA; Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68108, USA; Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Mohd Wasim Nasser
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68108, USA; Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68108, USA.
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Tahara S, Tahara T, Yamazaki J, Shijimaya T, Horiguchi N, Funasaka K, Fukui T, Nakagawa Y, Shibata T, Naganuma M, Tsukamoto T, Ohmiya N. Helicobacter pylori infection associated DNA methylation in primary gastric cancer significantly correlates with specific molecular and clinicopathological features. Mol Carcinog 2024; 63:266-274. [PMID: 37846801 DOI: 10.1002/mc.23650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 08/23/2023] [Accepted: 10/01/2023] [Indexed: 10/18/2023]
Abstract
Helicobacter pylori induces DNA methylation in gastric mucosa, which links to gastric cancer (GC) risk. In contrast, CpG island methylator phenotype (CIMP) is defined as high levels of cancer-specific methylation and provides distinct molecular and clinicopathological features of GC. The association between those two types of methylation in GC remains unclear. We examined DNA methylation of well-validated H. pylori infection associated genes in GC and its adjacent mucosa and investigated its association with CIMP, various molecular subtypes and clinical features. We studied 50 candidate loci in 24 gastric samples to identify H. pylori infection associated genes. Identified loci were further examined in 624 gastric tissue from 217 primary GC, 217 adjacent mucosa, and 190 mucosae from cancer-free subjects. We identified five genes (IGF2, SLC16A2, SOX11, P2RX7, and MYOD1) as hypermethylated in H. pylori infected gastric mucosa. In non-neoplastic mucosa, methylation of H. pylori infection associated genes was higher in patients with GC than those without. In primary GC tissues, higher methylation of H. pylori infection associated genes correlated with CIMP-positive and its related features, such as MLH1 methylated cases. On the other hand, GC with lower methylation of these genes presented aggressive clinicopathological features including undifferentiated histopathology, advanced stage at diagnosis. H. pylori infection associated DNA methylation is correlated with CIMP, specific molecular and clinicopathological features in GC, supporting its utility as promising biomarker in this tumor type.
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Affiliation(s)
- Sayumi Tahara
- Department of Diagnostic Pathology I, Fujita Health University School of Medicine, Toyoake, Japan
| | - Tomomitsu Tahara
- Department of Gastroenterology, Fujita Health University School of Medicine, Toyoake, Japan
- Third Department of Internal Medicine, Kansai Medical University, Hirakata, Japan
| | - Jumpei Yamazaki
- Translational Research Unit, Veterinary Teaching Hospital, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
| | - Takuya Shijimaya
- Third Department of Internal Medicine, Kansai Medical University, Hirakata, Japan
| | - Noriyuki Horiguchi
- Department of Gastroenterology, Fujita Health University School of Medicine, Toyoake, Japan
| | - Kohei Funasaka
- Department of Gastroenterology, Fujita Health University School of Medicine, Toyoake, Japan
| | - Toshiro Fukui
- Third Department of Internal Medicine, Kansai Medical University, Hirakata, Japan
| | - Yoshihito Nakagawa
- Department of Gastroenterology, Fujita Health University School of Medicine, Toyoake, Japan
| | - Tomoyuki Shibata
- Department of Gastroenterology, Fujita Health University School of Medicine, Toyoake, Japan
| | - Makoto Naganuma
- Third Department of Internal Medicine, Kansai Medical University, Hirakata, Japan
| | - Tetsuya Tsukamoto
- Department of Diagnostic Pathology I, Fujita Health University School of Medicine, Toyoake, Japan
| | - Naoki Ohmiya
- Department of Advanced Endoscopy, Fujita Health University, Toyoake, Aichi, Japan
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Long Y, Mao C, Liu S, Tao Y, Xiao D. Epigenetic modifications in obesity-associated diseases. MedComm (Beijing) 2024; 5:e496. [PMID: 38405061 PMCID: PMC10893559 DOI: 10.1002/mco2.496] [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: 08/03/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/27/2024] Open
Abstract
The global prevalence of obesity has reached epidemic levels, significantly elevating the susceptibility to various cardiometabolic conditions and certain types of cancer. In addition to causing metabolic abnormalities such as insulin resistance (IR), elevated blood glucose and lipids, and ectopic fat deposition, obesity can also damage pancreatic islet cells, endothelial cells, and cardiomyocytes through chronic inflammation, and even promote the development of a microenvironment conducive to cancer initiation. Improper dietary habits and lack of physical exercise are important behavioral factors that increase the risk of obesity, which can affect gene expression through epigenetic modifications. Epigenetic alterations can occur in early stage of obesity, some of which are reversible, while others persist over time and lead to obesity-related complications. Therefore, the dynamic adjustability of epigenetic modifications can be leveraged to reverse the development of obesity-associated diseases through behavioral interventions, drugs, and bariatric surgery. This review provides a comprehensive summary of the impact of epigenetic regulation on the initiation and development of obesity-associated cancers, type 2 diabetes, and cardiovascular diseases, establishing a theoretical basis for prevention, diagnosis, and treatment of these conditions.
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Affiliation(s)
- Yiqian Long
- Department of Pathology, Xiangya HospitalCentral South UniversityChangshaHunanChina
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Department of Pathology, School of Basic MedicineCentral South UniversityChangshaHunanChina
| | - Chao Mao
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Department of Pathology, School of Basic MedicineCentral South UniversityChangshaHunanChina
- NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic MedicineCentral South UniversityChangshaChina
| | - Shuang Liu
- Department of Pathology, Xiangya HospitalCentral South UniversityChangshaHunanChina
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Department of Pathology, School of Basic MedicineCentral South UniversityChangshaHunanChina
- Department of Oncology, Institute of Medical Sciences, National Clinical Research Center for Geriatric DisordersXiangya HospitalCentral South UniversityChangshaHunanChina
| | - Yongguang Tao
- Department of Pathology, Xiangya HospitalCentral South UniversityChangshaHunanChina
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Department of Pathology, School of Basic MedicineCentral South UniversityChangshaHunanChina
- NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic MedicineCentral South UniversityChangshaChina
- Hunan Key Laboratory of Early Diagnosis and Precision Therapy in Lung Cancer, Department of Thoracic SurgerySecond Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Desheng Xiao
- Department of Pathology, Xiangya HospitalCentral South UniversityChangshaHunanChina
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Department of Pathology, School of Basic MedicineCentral South UniversityChangshaHunanChina
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50
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Daenekas B, Pérez E, Boniolo F, Stefan S, Benfatto S, Sill M, Sturm D, Jones DTW, Capper D, Zapatka M, Hovestadt V. Conumee 2.0: enhanced copy-number variation analysis from DNA methylation arrays for humans and mice. Bioinformatics 2024; 40:btae029. [PMID: 38244574 PMCID: PMC10868300 DOI: 10.1093/bioinformatics/btae029] [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: 06/30/2023] [Revised: 12/14/2023] [Accepted: 01/16/2024] [Indexed: 01/22/2024] Open
Abstract
MOTIVATION Copy-number variations (CNVs) are common genetic alterations in cancer and their detection may impact tumor classification and therapeutic decisions. However, detection of clinically relevant large and focal CNVs remains challenging when sample material or resources are limited. This has motivated us to create a software tool to infer CNVs from DNA methylation arrays which are often generated as part of clinical routines and in research settings. RESULTS We present our R package, conumee 2.0, that combines tangent normalization, an adjustable genomic binning heuristic, and weighted circular binary segmentation to utilize DNA methylation arrays for CNV analysis and mitigate technical biases and batch effects. Segmentation results were validated in a lung squamous cell carcinoma dataset from TCGA (n = 367 samples) by comparison to segmentations derived from genotyping arrays (Pearson's correlation coefficient of 0.91). We further introduce a segmented block bootstrapping approach to detect focal alternations that achieved 60.9% sensitivity and 98.6% specificity for deletions affecting CDKN2A/B (60.0% and 96.9% for RB1, respectively) in a low-grade glioma cohort from TCGA (n = 239 samples). Finally, our tool provides functionality to detect and summarize CNVs across large sample cohorts. AVAILABILITY AND IMPLEMENTATION Conumee 2.0 is available under open-source license at: https://github.com/hovestadtlab/conumee2.
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Affiliation(s)
- Bjarne Daenekas
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, United States
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, United States
- Department of Neuropathology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Eilís Pérez
- Department of Neuropathology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Fabio Boniolo
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, United States
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, United States
| | - Sabina Stefan
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, United States
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, United States
| | - Salvatore Benfatto
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, United States
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, United States
| | - Martin Sill
- Hopp Children’s Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Dominik Sturm
- Hopp Children’s Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
- Department of Pediatric Oncology, Hematology & Immunology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - David T W Jones
- Hopp Children’s Cancer Center Heidelberg (KiTZ), 69120 Heidelberg, Germany
- Division of Pediatric Glioma Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - David Capper
- Department of Neuropathology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Marc Zapatka
- Division of Molecular Genetics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Volker Hovestadt
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, United States
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, United States
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