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Yang JH, Hansen AS. Enhancer selectivity in space and time: from enhancer-promoter interactions to promoter activation. Nat Rev Mol Cell Biol 2024; 25:574-591. [PMID: 38413840 DOI: 10.1038/s41580-024-00710-6] [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] [Accepted: 01/30/2024] [Indexed: 02/29/2024]
Abstract
The primary regulators of metazoan gene expression are enhancers, originally functionally defined as DNA sequences that can activate transcription at promoters in an orientation-independent and distance-independent manner. Despite being crucial for gene regulation in animals, what mechanisms underlie enhancer selectivity for promoters, and more fundamentally, how enhancers interact with promoters and activate transcription, remain poorly understood. In this Review, we first discuss current models of enhancer-promoter interactions in space and time and how enhancers affect transcription activation. Next, we discuss different mechanisms that mediate enhancer selectivity, including repression, biochemical compatibility and regulation of 3D genome structure. Through 3D polymer simulations, we illustrate how the ability of 3D genome folding mechanisms to mediate enhancer selectivity strongly varies for different enhancer-promoter interaction mechanisms. Finally, we discuss how recent technical advances may provide new insights into mechanisms of enhancer-promoter interactions and how technical biases in methods such as Hi-C and Micro-C and imaging techniques may affect their interpretation.
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Affiliation(s)
- Jin H Yang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA
| | - Anders S Hansen
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Koch Institute for Integrative Cancer Research, Cambridge, MA, USA.
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2
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Liu Z, Hu Y, Xie H, Chen K, Wen L, Fu W, Zhou X, Tang F. Single-Cell Chromatin Accessibility Analysis Reveals the Epigenetic Basis and Signature Transcription Factors for the Molecular Subtypes of Colorectal Cancers. Cancer Discov 2024; 14:1082-1105. [PMID: 38445965 DOI: 10.1158/2159-8290.cd-23-1445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 02/06/2024] [Accepted: 03/04/2024] [Indexed: 03/07/2024]
Abstract
Colorectal cancer is a highly heterogeneous disease, with well-characterized subtypes based on genome, DNA methylome, and transcriptome signatures. To chart the epigenetic landscape of colorectal cancers, we generated a high-quality single-cell chromatin accessibility atlas of epithelial cells for 29 patients. Abnormal chromatin states acquired in adenomas were largely retained in colorectal cancers, which were tightly accompanied by opposite changes of DNA methylation. Unsupervised analysis on malignant cells revealed two epigenetic subtypes, exactly matching the iCMS classification, and key iCMS-specific transcription factors (TFs) were identified, including HNF4A and PPARA for iCMS2 tumors and FOXA3 and MAFK for iCMS3 tumors. Notably, subtype-specific TFs bind to distinct target gene sets and contribute to both interpatient similarities and diversities for both chromatin accessibilities and RNA expressions. Moreover, we identified CpG-island methylator phenotypes and pinpointed chromatin state signatures and TF regulators for the CIMP-high subtype. Our work systematically revealed the epigenetic basis of the well-known iCMS and CIMP classifications of colorectal cancers. SIGNIFICANCE Our work revealed the epigenetic basis of the well-known iCMS and CIMP classifications of colorectal cancers. Moreover, interpatient minor similarities and major diversities of chromatin accessibility signatures of TF target genes can faithfully explain the corresponding interpatient minor similarities and major diversities of RNA expression signatures of colorectal cancers, respectively. This article is featured in Selected Articles from This Issue, p. 897.
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Affiliation(s)
- Zhenyu Liu
- School of Life Sciences, Biomedical Pioneering Innovation Center, Department of General Surgery, Third Hospital, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
| | - Yuqiong Hu
- School of Life Sciences, Biomedical Pioneering Innovation Center, Department of General Surgery, Third Hospital, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
- Key Laboratory of Organ Regeneration and Reconstruction, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, China
| | - Haoling Xie
- School of Life Sciences, Biomedical Pioneering Innovation Center, Department of General Surgery, Third Hospital, Peking University, Beijing, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Kexuan Chen
- School of Life Sciences, Biomedical Pioneering Innovation Center, Department of General Surgery, Third Hospital, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
| | - Lu Wen
- School of Life Sciences, Biomedical Pioneering Innovation Center, Department of General Surgery, Third Hospital, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
| | - Wei Fu
- School of Life Sciences, Biomedical Pioneering Innovation Center, Department of General Surgery, Third Hospital, Peking University, Beijing, China
- Peking University Third Hospital Cancer Center, Beijing, China
| | - Xin Zhou
- School of Life Sciences, Biomedical Pioneering Innovation Center, Department of General Surgery, Third Hospital, Peking University, Beijing, China
- Peking University Third Hospital Cancer Center, Beijing, China
| | - Fuchou Tang
- School of Life Sciences, Biomedical Pioneering Innovation Center, Department of General Surgery, Third Hospital, Peking University, Beijing, China
- Beijing Advanced Innovation Center for Genomics (ICG), Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
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3
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Shu J, Jelinek J, Chen H, Zhang Y, Qin T, Li M, Liu L, Issa JPJ. Genome-wide screening and functional validation of methylation barriers near promoters. Nucleic Acids Res 2024; 52:4857-4871. [PMID: 38647050 PMCID: PMC11109949 DOI: 10.1093/nar/gkae302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 03/13/2024] [Accepted: 04/09/2024] [Indexed: 04/25/2024] Open
Abstract
CpG islands near promoters are normally unmethylated despite being surrounded by densely methylated regions. Aberrant hypermethylation of these CpG islands has been associated with the development of various human diseases. Although local genetic elements have been speculated to play a role in protecting promoters from methylation, only a limited number of methylation barriers have been identified. In this study, we conducted an integrated computational and experimental investigation of colorectal cancer methylomes. Our study revealed 610 genes with disrupted methylation barriers. Genomic sequences of these barriers shared a common 41-bp sequence motif (MB-41) that displayed homology to the chicken HS4 methylation barrier. Using the CDKN2A (P16) tumor suppressor gene promoter, we validated the protective function of MB-41 and showed that loss of such protection led to aberrant hypermethylation. Our findings highlight a novel sequence signature of cis-acting methylation barriers in the human genome that safeguard promoters from silencing.
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Affiliation(s)
- Jingmin Shu
- College of Health Solutions, Arizona State University, Phoenix, AZ, USA
- Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Jaroslav Jelinek
- Fels Institute for Cancer Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
- Cooper Medical School at Rowan University, Camden, NJ 08103, USA
- Coriell Institute for Medical Research, Camden, NJ 08103, USA
| | - Hai Chen
- College of Health Solutions, Arizona State University, Phoenix, AZ, USA
- Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Yan Zhang
- Fels Institute for Cancer Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
| | - Taichun Qin
- Fels Institute for Cancer Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
| | - Ming Li
- Phoenix VA Health Care System, Phoenix, AZ 85012, USA
- University of Arizona College of Medicine, Phoenix, AZ 85004, USA
| | - Li Liu
- College of Health Solutions, Arizona State University, Phoenix, AZ, USA
- Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Jean-Pierre J Issa
- Fels Institute for Cancer Research, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140, USA
- Cooper Medical School at Rowan University, Camden, NJ 08103, USA
- Coriell Institute for Medical Research, Camden, NJ 08103, USA
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4
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Weng YY, Huang MY. The CpG Island Methylator Phenotype Status in Synchronous and Solitary Primary Colorectal Cancers: Prognosis and Effective Therapeutic Drug Prediction. Int J Mol Sci 2024; 25:5243. [PMID: 38791280 PMCID: PMC11121449 DOI: 10.3390/ijms25105243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 05/08/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024] Open
Abstract
Synchronous colorectal cancer (sCRC) is characterized by the occurrence of more than one tumor within six months of detecting the first tumor. Evidence suggests that sCRC might be more common in the serrated neoplasia pathway, marked by the CpG island methylator phenotype (CIMP), than in the chromosomal instability pathway (CIN). An increasing number of studies propose that CIMP could serve as a potential epigenetic predictor or prognostic biomarker of sCRC. Therapeutic drugs already used for treating CIMP-positive colorectal cancers (CRCs) are reviewed and drug selections for sCRC patients are discussed.
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Affiliation(s)
- Yun-Yun Weng
- Department of Radiation Oncology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
| | - Ming-Yii Huang
- Department of Radiation Oncology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan;
- Department of Radiation Oncology, School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
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5
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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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6
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Gretarsson KH, Abini-Agbomson S, Gloor SL, Weinberg DN, McCuiston JL, Kumary VUS, Hickman AR, Sahu V, Lee R, Xu X, Lipieta N, Flashner S, Adeleke OA, Popova IK, Taylor HF, Noll K, Windham CL, Maryanski DN, Venters BJ, Nakagawa H, Keogh MC, Armache KJ, Lu C. Cancer-associated DNA Hypermethylation of Polycomb Targets Requires DNMT3A Dual Recognition of Histone H2AK119 Ubiquitination and the Nucleosome Acidic Patch. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.18.585588. [PMID: 38562823 PMCID: PMC10983913 DOI: 10.1101/2024.03.18.585588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
During tumor development, promoter CpG islands (CGIs) that are normally silenced by Polycomb repressive complexes (PRCs) become DNA hypermethylated. The molecular mechanism by which de novo DNA methyltransferase(s) catalyze CpG methylation at PRC-regulated regions remains unclear. Here we report a cryo-EM structure of the DNMT3A long isoform (DNMT3A1) N-terminal region in complex with a nucleosome carrying PRC1-mediated histone H2A lysine 119 monoubiquitination (H2AK119Ub). We identify regions within the DNMT3A1 N-terminus that bind H2AK119Ub and the nucleosome acidic patch. This bidentate interaction is required for effective DNMT3A1 engagement with H2AK119Ub-modified chromatin in cells. Furthermore, aberrant redistribution of DNMT3A1 to Polycomb target genes inhibits their transcriptional activation during cell differentiation and recapitulates the cancer-associated DNA hypermethylation signature. This effect is rescued by disruption of the DNMT3A1-acidic patch interaction. Together, our analyses reveal a binding interface critical for countering promoter CGI DNA hypermethylation, a major molecular hallmark of cancer.
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7
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Linowiecka K, Guz J, Dziaman T, Urbanowska-Domańska O, Zarakowska E, Szpila A, Szpotan J, Skalska-Bugała A, Mijewski P, Siomek-Górecka A, Różalski R, Gackowski D, Oliński R, Foksiński M. The level of active DNA demethylation compounds in leukocytes and urine samples as potential epigenetic biomarkers in breast cancer patients. Sci Rep 2024; 14:6481. [PMID: 38499584 PMCID: PMC10948817 DOI: 10.1038/s41598-024-56326-5] [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: 08/07/2023] [Accepted: 03/05/2024] [Indexed: 03/20/2024] Open
Abstract
The active DNA demethylation process, which involves TET proteins, can affect DNA methylation pattern. TET dependent demethylation results in DNA hypomethylation by oxidation 5-methylcytosine (5-mC) to 5-hydroxymethylcytosine (5-hmC) and its derivatives. Moreover, TETs' activity may be upregulated by ascorbate. Given that aberrant DNA methylation of genes implicated in breast carcinogenesis may be involved in tumor progression, we wanted to determine whether breast cancer patients exert changes in the active DNA demethylation process. The study included blood samples from breast cancer patients (n = 74) and healthy subjects (n = 71). We analyzed the expression of genes involved in the active demethylation process (qRT-PCR), and 5-mC and its derivatives level (2D-UPLC MS/MS). The ascorbate level was determined using UPLC-MS. Breast cancer patients had significantly higher TET3 expression level, lower 5-mC and 5-hmC DNA levels. TET3 was significantly increased in luminal B breast cancer patients with expression of hormone receptors. Moreover, the ascorbate level in the plasma of breast cancer patients was decreased with the accompanying increase of sodium-dependent vitamin C transporters (SLC23A1 and SLC23A2). The presented study indicates the role of TET3 in DNA demethylation in breast carcinogenesis.
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Affiliation(s)
- Kinga Linowiecka
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Karlowicza 24, 85‑092, Bydgoszcz, Poland.
- Department of Human Biology, Institute of Biology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University in Toruń, Lwowska 1, 87-100, Toruń, Poland.
| | - Jolanta Guz
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Karlowicza 24, 85‑092, Bydgoszcz, Poland
| | - Tomasz Dziaman
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Karlowicza 24, 85‑092, Bydgoszcz, Poland
| | - Olga Urbanowska-Domańska
- Department of Oncology, Professor Franciszek Lukaszczyk Oncology Centre, Romanowskiej 2, 85-796, Bydgoszcz, Poland
| | - Ewelina Zarakowska
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Karlowicza 24, 85‑092, Bydgoszcz, Poland
| | - Anna Szpila
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Karlowicza 24, 85‑092, Bydgoszcz, Poland
| | - Justyna Szpotan
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Karlowicza 24, 85‑092, Bydgoszcz, Poland
- Department of Human Biology, Institute of Biology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University in Toruń, Lwowska 1, 87-100, Toruń, Poland
| | - Aleksandra Skalska-Bugała
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Karlowicza 24, 85‑092, Bydgoszcz, Poland
| | - Paweł Mijewski
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Karlowicza 24, 85‑092, Bydgoszcz, Poland
| | - Agnieszka Siomek-Górecka
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Karlowicza 24, 85‑092, Bydgoszcz, Poland
| | - Rafał Różalski
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Karlowicza 24, 85‑092, Bydgoszcz, Poland
| | - Daniel Gackowski
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Karlowicza 24, 85‑092, Bydgoszcz, Poland
| | - Ryszard Oliński
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Karlowicza 24, 85‑092, Bydgoszcz, Poland
| | - Marek Foksiński
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Karlowicza 24, 85‑092, Bydgoszcz, Poland.
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8
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Shim H, Jang K, Bang YH, Chu HBK, Kang J, Lee JY, Cho S, Lee HS, Jeon J, Hwang T, Joe S, Lim J, Choi JH, Joo EH, Park K, Moon JH, Han KY, Hong Y, Lee WY, Kim HC, Yun SH, Cho YB, Park YA, Huh JW, Shin JK, Pyo DH, Hong H, Lee HO, Park WY, Yang JO, Kim YJ. Comprehensive profiling of DNA methylation in Korean patients with colorectal cancer. BMB Rep 2024; 57:110-115. [PMID: 37605617 PMCID: PMC10910091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 06/27/2023] [Accepted: 08/21/2023] [Indexed: 08/23/2023] Open
Abstract
Alterations in DNA methylation play an important pathophysiological role in the development and progression of colorectal cancer. We comprehensively profiled DNA methylation alterations in 165 Korean patients with colorectal cancer (CRC), and conducted an in-depth investigation of cancer-specific methylation patterns. Our analysis of the tumor samples revealed a significant presence of hypomethylated probes, primarily within the gene body regions; few hypermethylated sites were observed, which were mostly enriched in promoter-like and CpG island regions. The CpG Island Methylator PhenotypeHigh (CIMP-H) exhibited notable enrichment of microsatellite instability-high (MSI-H). Additionally, our findings indicated a significant correlation between methylation of the MLH1 gene and MSI-H status. Furthermore, we found that the CIMP-H had a higher tendency to affect the right-side of the colon tissues and was slightly more prevalent among older patients. Through our methylome profile analysis, we successfully verified the thylation patterns and clinical characteristics of Korean patients with CRC. This valuable dataset lays a strong foundation for exploring novel molecular insights and potential therapeutic targets for the treatment of CRC. [BMB Reports 2024; 57(2): 110-115].
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Affiliation(s)
- Hyeran Shim
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Kiwon Jang
- Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
| | - Yeong Hak Bang
- Department of Digital Health, Samsung Advanced Institute for Health Science & Technology (SAIHST), Sungkyunkwan University, Seoul 06355, Korea
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea
| | - Hoang Bao Khanh Chu
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Jisun Kang
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Jin-Young Lee
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Sheehyun Cho
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Hong Seok Lee
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Jongbum Jeon
- Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
| | - Taeyeon Hwang
- Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
| | - Soobok Joe
- Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
| | - Jinyeong Lim
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul 06355, Korea
| | - Ji-Hye Choi
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul 06355, Korea
| | - Eun Hye Joo
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul 06355, Korea
| | - Kyunghee Park
- Samsung Genome Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea, Seoul 04779, Korea
| | - Ji Hwan Moon
- Samsung Genome Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea, Seoul 04779, Korea
| | - Kyung Yeon Han
- Samsung Genome Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea, Seoul 04779, Korea
| | - Yourae Hong
- Department of Oncology, Katholieke Universiteit Leuven, B-3000 Leuven, Belgium, Seoul 04779, Korea
| | - Woo Yong Lee
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea
| | - Hee Cheol Kim
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea
| | - Seong Hyeon Yun
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea
| | - Yong Beom Cho
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea
| | - Yoon Ah Park
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea
| | - Jung Wook Huh
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea
| | - Jung Kyong Shin
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea
| | - Dae Hee Pyo
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea
| | - Hyekyung Hong
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea
| | - Hae-Ock Lee
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
- Department of Biomedicine and Health Sciences, Graduate School, The Catholic University of Korea, Seoul 06591, Korea
| | - Woong-Yang Park
- Department of Digital Health, Samsung Advanced Institute for Health Science & Technology (SAIHST), Sungkyunkwan University, Seoul 06355, Korea
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul 06355, Korea
- Samsung Genome Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea, Seoul 04779, Korea
| | - Jin Ok Yang
- Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
| | - Young-Joon Kim
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
- LepiDyne Co., Ltd., Seoul 04779, Korea
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9
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Satomi K, Ichimura K, Shibahara J. Decoding the DNA methylome of central nervous system tumors: An emerging modality for integrated diagnosis. Pathol Int 2024; 74:51-67. [PMID: 38224248 DOI: 10.1111/pin.13402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/16/2023] [Accepted: 12/18/2023] [Indexed: 01/16/2024]
Abstract
The definitive diagnosis and classification of individual cancers are crucial for patient care and cancer research. To achieve a robust diagnosis of central nervous system (CNS) tumors, a genotype-phenotype integrated diagnostic approach was introduced in recent versions of the World Health Organization classification, followed by the incorporation of a genome-wide DNA methylome-based classification. Microarray-based platforms are widely used to obtain DNA methylome data, and the German Cancer Research Center (Deutsches Krebsforschungszentrum [DKFZ]) has a webtool for a DNA methylation-based classifier (DKFZ classifier). Integration of DNA methylome will further enhance the precision of CNS tumor classification, especially in diagnostically challenging cases. However, in the clinical application of DNA methylome-based classification, challenges related to data interpretation persist, in addition to technical caveats, regulations, and limited accessibility. Dimensionality reduction (DMR) can complement integrated diagnosis by visualizing a profile and comparing it with other known samples. Therefore, DNA methylome-based classification is a highly useful research tool for auxiliary analysis in challenging diagnostic and rare disease cases, and for establishing novel tumor concepts. Decoding the DNA methylome, especially by DMR in addition to DKFZ classifier, emphasizes the capability of grasping the fundamental biological principles that provide new perspectives on CNS tumors.
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Affiliation(s)
- Kaishi Satomi
- Department of Pathology, Kyorin University Faculty of Medicine, Tokyo, Japan
| | - Koichi Ichimura
- Department of Brain Disease Translational Research, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Junji Shibahara
- Department of Pathology, Kyorin University Faculty of Medicine, Tokyo, Japan
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10
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Geissler F, Nesic K, Kondrashova O, Dobrovic A, Swisher EM, Scott CL, J. Wakefield M. The role of aberrant DNA methylation in cancer initiation and clinical impacts. Ther Adv Med Oncol 2024; 16:17588359231220511. [PMID: 38293277 PMCID: PMC10826407 DOI: 10.1177/17588359231220511] [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: 08/02/2023] [Accepted: 11/21/2023] [Indexed: 02/01/2024] Open
Abstract
Epigenetic alterations, including aberrant DNA methylation, are now recognized as bone fide hallmarks of cancer, which can contribute to cancer initiation, progression, therapy responses and therapy resistance. Methylation of gene promoters can have a range of impacts on cancer risk, clinical stratification and therapeutic outcomes. We provide several important examples of genes, which can be silenced or activated by promoter methylation and highlight their clinical implications. These include the mismatch DNA repair genes MLH1 and MSH2, homologous recombination DNA repair genes BRCA1 and RAD51C, the TERT oncogene and genes within the P15/P16/RB1/E2F tumour suppressor axis. We also discuss how these methylation changes might occur in the first place - whether in the context of the CpG island methylator phenotype or constitutional DNA methylation. The choice of assay used to measure methylation can have a significant impact on interpretation of methylation states, and some examples where this can influence clinical decision-making are presented. Aberrant DNA methylation patterns in circulating tumour DNA (ctDNA) are also showing great promise in the context of non-invasive cancer detection and monitoring using liquid biopsies; however, caution must be taken in interpreting these results in cases where constitutional methylation may be present. Thus, this review aims to provide researchers and clinicians with a comprehensive summary of this broad, but important subject, illustrating the potentials and pitfalls of assessing aberrant DNA methylation in cancer.
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Affiliation(s)
- Franziska Geissler
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Ksenija Nesic
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Olga Kondrashova
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Alexander Dobrovic
- University of Melbourne Department of Surgery, Austin Health, Heidelberg, VIC, Australia
| | | | - Clare L. Scott
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
- Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, VIC, Australia
- Peter MacCallum Cancer Centre and Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
- Royal Women’s Hospital, Parkville, VIC, Australia
- Royal Melbourne Hospital, Parkville, VIC, Australia
| | - Matthew J. Wakefield
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, VIC, Australia
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11
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Xu Q, del Mundo IMA, Zewail-Foote M, Luke BT, Vasquez KM, Kowalski J. MoCoLo: a testing framework for motif co-localization. Brief Bioinform 2024; 25:bbae019. [PMID: 38521050 PMCID: PMC10960634 DOI: 10.1093/bib/bbae019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 01/08/2024] [Accepted: 01/09/2024] [Indexed: 03/25/2024] Open
Abstract
Sequence-level data offers insights into biological processes through the interaction of two or more genomic features from the same or different molecular data types. Within motifs, this interaction is often explored via the co-occurrence of feature genomic tracks using fixed-segments or analytical tests that respectively require window size determination and risk of false positives from over-simplified models. Moreover, methods for robustly examining the co-localization of genomic features, and thereby understanding their spatial interaction, have been elusive. We present a new analytical method for examining feature interaction by introducing the notion of reciprocal co-occurrence, define statistics to estimate it and hypotheses to test for it. Our approach leverages conditional motif co-occurrence events between features to infer their co-localization. Using reverse conditional probabilities and introducing a novel simulation approach that retains motif properties (e.g. length, guanine-content), our method further accounts for potential confounders in testing. As a proof-of-concept, motif co-localization (MoCoLo) confirmed the co-occurrence of histone markers in a breast cancer cell line. As a novel analysis, MoCoLo identified significant co-localization of oxidative DNA damage within non-B DNA-forming regions that significantly differed between non-B DNA structures. Altogether, these findings demonstrate the potential utility of MoCoLo for testing spatial interactions between genomic features via their co-localization.
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Affiliation(s)
- Qi Xu
- Department of Molecular Biosciences, College of Natural Sciences, The University of Texas at Austin, Austin, TX, 78712, USA
- Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Imee M A del Mundo
- Dell Pediatric Research Institute, Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Austin, Texas, 78723, USA
| | - Maha Zewail-Foote
- Department of Chemistry and Biochemistry, Southwestern University, Georgetown, TX, 78626, USA
| | - Brian T Luke
- Bioinformatics and Computational Science, Frederick National Laboratory for Cancer Research, Frederick, Maryland, 21701, USA
| | - Karen M Vasquez
- Dell Pediatric Research Institute, Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Austin, Texas, 78723, USA
| | - Jeanne Kowalski
- Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX, 78712, USA
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12
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Chakraborty B, Agarwal S, Kori S, Das R, Kashaw V, Iyer AK, Kashaw SK. Multiple Protein Biomarkers and Different Treatment Strategies for Colorectal Carcinoma: A Comprehensive Prospective. Curr Med Chem 2024; 31:3286-3326. [PMID: 37151060 DOI: 10.2174/0929867330666230505165031] [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: 11/12/2022] [Revised: 02/20/2023] [Accepted: 02/24/2023] [Indexed: 05/09/2023]
Abstract
In this review, we emphasized important biomarkers, pathogenesis, and newly developed therapeutic approaches in the treatment of colorectal cancer (CRC). This includes a complete description of small-molecule inhibitors, phytopharmaceuticals with antiproliferative potential, monoclonal antibodies for targeted therapy, vaccinations as immunotherapeutic agents, and many innovative strategies to intervene in the interaction of oncogenic proteins. Many factors combine to determine the clinical behavior of colorectal cancer and it is still difficult to comprehend the molecular causes of a person's vulnerability to CRC. It is also challenging to identify the causes of the tumor's onset, progression, and responsiveness or resistance to antitumor treatment. Current recommendations for targeted medications are being updated by guidelines throughout the world in light of the growing number of high-quality clinical studies. So, being concerned about the aforementioned aspects, we have tried to present a summarized pathogenic view, including a brief description of biomarkers and an update of compounds with their underlying mechanisms that are currently under various stages of clinical testing. This will help to identify gaps or shortfalls that can be addressed in upcoming colorectal cancer research.
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Affiliation(s)
- Biswadip Chakraborty
- Integrated Drug Discovery Research Laboratory, Department of Pharmaceutical Sciences, Dr. Harisingh Gour University (A Central University), Sagar (MP), India
| | - Shivangi Agarwal
- Integrated Drug Discovery Research Laboratory, Department of Pharmaceutical Sciences, Dr. Harisingh Gour University (A Central University), Sagar (MP), India
| | - Shivam Kori
- Integrated Drug Discovery Research Laboratory, Department of Pharmaceutical Sciences, Dr. Harisingh Gour University (A Central University), Sagar (MP), India
| | - Ratnesh Das
- Department of Chemistry, ISF College of Pharmacy, Moga-Punjab, India
| | - Varsha Kashaw
- Sagar Institute of Pharmaceutical Sciences, Sagar (M.P.), India
| | - Arun K Iyer
- Use-inspired Biomaterials & Integrated Nano Delivery (U-BiND) Systems Laboratory, Department of Pharmaceutical Sciences, Wayne State University, Detroit, Michigan, USA
- Molecular Imaging Program, Karmanos Cancer Institute, Detroit, Michigan, USA
| | - Sushil Kumar Kashaw
- Integrated Drug Discovery Research Laboratory, Department of Pharmaceutical Sciences, Dr. Harisingh Gour University (A Central University), Sagar (MP), India
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13
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Hosseini ST, Nemati F. Identification of GUCA2A and COL3A1 as prognostic biomarkers in colorectal cancer by integrating analysis of RNA-Seq data and qRT-PCR validation. Sci Rep 2023; 13:17086. [PMID: 37816854 PMCID: PMC10564945 DOI: 10.1038/s41598-023-44459-y] [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: 01/23/2023] [Accepted: 10/09/2023] [Indexed: 10/12/2023] Open
Abstract
By 2030, it is anticipated that there will be 2.2 million new instances of colorectal cancer worldwide, along with 1.1 million yearly deaths. Therefore, it is critical to develop novel biomarkers that could help in CRC early detection. We performed an integrated analysis of four RNA-Seq data sets and TCGA datasets in this study to find novel biomarkers for diagnostic, prediction, and as potential therapeutic for this malignancy, as well as to determine the molecular mechanisms of CRC carcinogenesis. Four RNA-Seq datasets of colorectal cancer were downloaded from the Sequence Read Archive (SRA) database. The metaSeq package was used to integrate differentially expressed genes (DEGs). The protein-protein interaction (PPI) network of the DEGs was constructed using the string platform, and hub genes were identified using the cytoscape software. The gene ontology and KEGG pathway enrichment analysis were performed using enrichR package. Gene diagnostic sensitivity and its association to clinicopathological characteristics were demonstrated by statistical approaches. By using qRT-PCR, GUCA2A and COL3A1 were examined in colon cancer and rectal cancer. We identified 5037 differentially expressed genes, including (4752 upregulated, 285 downregulated) across the studies between CRC and normal tissues. Gene ontology and KEGG pathway analyses showed that the highest proportion of up-regulated DEGs was involved in RNA binding and RNA transport. Integral component of plasma membrane and mineral absorption pathways were identified as containing down-regulated DEGs. Similar expression patterns for GUCA2A and COL3A1 were seen in qRT-PCR and integrated RNA-Seq analysis. Additionally, this study demonstrated that GUCA2A and COL3A1 may play a significant role in the development of CRC.
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Affiliation(s)
- Seyed Taleb Hosseini
- Department of Biology, Faculty of Basic Sciences, Qaemshahr Branch, Islamic Azad University, Mazandaran, Iran
- Young Researchers and Elite Club, Qaemshahr Branch, Islamic Azad University, Mazandaran, Iran
| | - Farkhondeh Nemati
- Department of Biology, Faculty of Basic Sciences, Qaemshahr Branch, Islamic Azad University, Mazandaran, Iran.
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14
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Chen YT, Yang H, Chu JW. Mechanical codes of chemical-scale specificity in DNA motifs. Chem Sci 2023; 14:10155-10166. [PMID: 37772098 PMCID: PMC10529945 DOI: 10.1039/d3sc01671d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 08/28/2023] [Indexed: 09/30/2023] Open
Abstract
In gene transcription, certain sequences of double-stranded (ds)DNA play a vital role in nucleosome positioning and expression initiation. That dsDNA is deformed to various extents in these processes leads us to ask: Could the genomic DNA also have sequence specificity in its chemical-scale mechanical properties? We approach this question using statistical machine learning to determine the rigidity between DNA chemical moieties. What emerges for the polyA, polyG, TpA, and CpG sequences studied here is a unique trigram that contains the quantitative mechanical strengths between bases and along the backbone. In a way, such a sequence-dependent trigram could be viewed as a DNA mechanical code. Interestingly, we discover a compensatory competition between the axial base-stacking interaction and the transverse base-pairing interaction, and such a reciprocal relationship constitutes the most discriminating feature of the mechanical code. Our results also provide chemical-scale understanding for experimental observables. For example, the long polyA persistence length is shown to have strong base stacking while its complement (polyAc) exhibits high backbone rigidity. The mechanical code concept enables a direct reading of the physical interactions encoded in the sequence which, with further development, is expected to shed new light on DNA allostery and DNA-binding drugs.
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Affiliation(s)
- Yi-Tsao Chen
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University Hsinchu 30010 Taiwan Republic of China
| | - Haw Yang
- Department of Chemistry, Princeton University Princeton NJ 08544 USA
| | - Jhih-Wei Chu
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University Hsinchu 30010 Taiwan Republic of China
- Department of Biological Science and Technology, Institute of Molecular Medicine and Bioengineering, Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Yang Ming Chiao Tung University Hsinchu 30010 Taiwan Republic of China
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15
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Wakayama S, Ouchi K, Takahashi S, Yamada Y, Komatsu Y, Shimada K, Yamaguchi T, Shirota H, Takahashi M, Ishioka C. TP53 Gain-of-Function Mutation is a Poor Prognostic Factor in High-Methylated Metastatic Colorectal Cancer. Clin Colorectal Cancer 2023; 22:327-338. [PMID: 37355363 DOI: 10.1016/j.clcc.2023.06.001] [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: 03/30/2023] [Revised: 05/26/2023] [Accepted: 06/02/2023] [Indexed: 06/26/2023]
Abstract
BACKGROUND Neither TP53 mutation nor DNA methylation status has been established as a biomarker alone of metastatic colorectal cancer. We analyzed the association between TP53 mutation functional subtypes and genome-wide DNA methylation status (GWMS) as combined prognostic markers. METHODS Patient clinical data were obtained from the TRICOLORE study, a randomized phase III trial. The TP53 mutations were classified into wild-type, gain-of-function (GOF) mutations, and non-gain-of-function (non-GOF) mutations. GWMS of the tumor tissues classified them into high-methylated colorectal cancer (HMCC) and low-methylated colorectal cancer (LMCC). Overall survival (OS) was compared based on these subgroups. RESULTS Of the 209 patients, 60 (28.7%) were HMCC and 149 (71.3%) were LMCC, 35 (16.7%) were TP53 wild-type and 174 (83.3%) were TP53 mutants including 79 (45.4%) GOF mutations and 95 (54.6%) non-GOF mutations. The OS of the HMCC group was shorter than that of the LMCC group (median 25.3 vs. 40.3 months, P < .001, hazard ratio 1.87) in the total cohort. The combined subgroup analyses of GWMS and TP53 mutation subtypes showed that the HMCC/GOF group had significantly shorter OS than the HMCC/non-GOF group, the LMCC/GOF group, and the LMCC/non-GOF group (median 17.7; 35.3, 40.3, and 41.2 months, P = .007, P < .001, and P < .001, respectively), regardless of the primary tumor location. By the multivariate analysis, only HMCC (P = .009) was a poor prognostic factor in the GOF mutation group. CONCLUSIONS TP53 GOF with HMCC is a newly identified poorest prognostic molecular subset in metastatic colorectal cancer.
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Affiliation(s)
- Shonosuke Wakayama
- Department of Medical Oncology, Tohoku University Hospital, Sendai, Miyagi, Japan; Department of Clinical Oncology, Graduate School of Medicine, Tohoku University, Sendai, Miyagi, Japan
| | - Kota Ouchi
- Department of Medical Oncology, Tohoku University Hospital, Sendai, Miyagi, Japan; Department of Clinical Oncology, Graduate School of Medicine, Tohoku University, Sendai, Miyagi, Japan
| | - Shin Takahashi
- Department of Medical Oncology, Tohoku University Hospital, Sendai, Miyagi, Japan; Department of Clinical Oncology, Graduate School of Medicine, Tohoku University, Sendai, Miyagi, Japan
| | - Yasuhide Yamada
- Comprehensive Cancer Center, National Center for Global Health and Medicine, Shinjuku-ku, Tokyo, Japan
| | - Yoshito Komatsu
- Department of Cancer Chemotherapy, Hokkaido University Hospital Cancer Center, Sapporo, Hokkaido, Japan
| | - Ken Shimada
- Department of Internal Medicine, Division of Medical Oncology, Showa University Koto Toyosu Hospital, Koto-ku, Tokyo, Japan
| | - Tatsuro Yamaguchi
- Department of Clinical Genetics, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Bunkyo-ku, Tokyo, Japan
| | - Hidekazu Shirota
- Department of Medical Oncology, Tohoku University Hospital, Sendai, Miyagi, Japan; Department of Clinical Oncology, Graduate School of Medicine, Tohoku University, Sendai, Miyagi, Japan
| | - Masanobu Takahashi
- Department of Medical Oncology, Tohoku University Hospital, Sendai, Miyagi, Japan; Department of Clinical Oncology, Graduate School of Medicine, Tohoku University, Sendai, Miyagi, Japan; Department of Clinical Oncology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Miyagi, Japan
| | - Chikashi Ishioka
- Department of Medical Oncology, Tohoku University Hospital, Sendai, Miyagi, Japan; Department of Clinical Oncology, Graduate School of Medicine, Tohoku University, Sendai, Miyagi, Japan; Department of Clinical Oncology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Miyagi, Japan.
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16
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Wie M, Khim K, Groehler IV A, Heo S, Woo J, Son K, Lee E, Ra J, Hong S, Schärer O, Choi J, Myung K. Alkylation of nucleobases by 2-chloro- N,N-diethylethanamine hydrochloride (CDEAH) sensitizes PARP1-deficient tumors. NAR Cancer 2023; 5:zcad042. [PMID: 37554969 PMCID: PMC10405566 DOI: 10.1093/narcan/zcad042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 06/16/2023] [Accepted: 07/26/2023] [Indexed: 08/10/2023] Open
Abstract
Targeting BRCA1- and BRCA2-deficient tumors through synthetic lethality using poly(ADP-ribose) polymerase inhibitors (PARPi) has emerged as a successful strategy for cancer therapy. PARPi monotherapy has shown excellent efficacy and safety profiles in clinical practice but is limited by the need for tumor genome mutations in BRCA or other homologous recombination genes as well as the rapid emergence of resistance. In this study, we identified 2-chloro-N,N-diethylethanamine hydrochloride (CDEAH) as a small molecule that selectively kills PARP1- and xeroderma pigmentosum A-deficient cells. CDEAH is a monofunctional alkylating agent that preferentially alkylates guanine nucleobases, forming DNA adducts that can be removed from DNA by either a PARP1-dependent base excision repair or nucleotide excision repair. Treatment of PARP1-deficient cells leads to the formation of strand breaks, an accumulation of cells in S phase and activation of the DNA damage response. Furthermore, CDEAH selectively inhibits PARP1-deficient xenograft tumor growth compared to isogenic PARP1-proficient tumors. Collectively, we report the discovery of an alkylating agent inducing DNA damage that requires PARP1 activity for repair and acts synergistically with PARPi.
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Affiliation(s)
- Minwoo Wie
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Keon Woo Khim
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Arnold S Groehler IV
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
| | - Soomin Heo
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Junhyeok Woo
- Department of Chemistry, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Kook Son
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
| | - Eun A Lee
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
| | - Jae Sun Ra
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
| | - Sung You Hong
- Department of Chemistry, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Orlando D Schärer
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Jang Hyun Choi
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
- Department of Biological Sciences, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Kyungjae Myung
- Center for Genomic Integrity, Institute for Basic Science, Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
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17
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Jevšinek Skok D, Hauptman N. In Silico Gene Prioritization Highlights the Significance of Bone Morphogenetic Protein 4 ( BMP4) Promoter Methylation across All Methylation Clusters in Colorectal Cancer. Int J Mol Sci 2023; 24:12692. [PMID: 37628872 PMCID: PMC10454928 DOI: 10.3390/ijms241612692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 08/03/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023] Open
Abstract
The cytosine-phosphate-guanine (CpG) island methylator phenotype (CIMP) represents one of the pathways involved in the development of colorectal cancer, characterized by genome-wide hypermethylation. To identify samples exhibiting hypermethylation, we used unsupervised hierarchical clustering on genome-wide methylation data. This clustering analysis revealed the presence of four distinct subtypes within the tumor samples, namely, CIMP-H, CIMP-L, cluster 3, and cluster 4. These subtypes demonstrated varying levels of methylation, categorized as high, intermediate, and very low. To gain further insights, we mapped significant probes from all clusters to Ensembl Regulatory build 89, with a specific focus on those located within promoter regions or bound regions. By intersecting the methylated promoter and bound regions across all methylation subtypes, we identified a total of 253 genes exhibiting aberrant methylation patterns in the promoter regions across all four subtypes of colorectal cancer. Among these genes, our comprehensive genome-wide analysis highlights bone morphogenic protein 4 (BMP4) as the most prominent candidate. This significant finding was derived through the utilization of various bioinformatics tools, emphasizing the potential role of BMP4 in colorectal cancer development and progression.
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Affiliation(s)
- Daša Jevšinek Skok
- Agricultural Institute of Slovenia, Hacquetova ulica 17, SI-1000 Ljubljana, Slovenia;
| | - Nina Hauptman
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, Korytkova 2, SI-1000 Ljubljana, Slovenia
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18
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Ohnmacht AJ, Rajamani A, Avar G, Kutkaite G, Gonçalves E, Saur D, Menden MP. The pharmacoepigenomic landscape of cancer cell lines reveals the epigenetic component of drug sensitivity. Commun Biol 2023; 6:825. [PMID: 37558831 PMCID: PMC10412573 DOI: 10.1038/s42003-023-05198-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: 01/14/2023] [Accepted: 08/01/2023] [Indexed: 08/11/2023] Open
Abstract
Aberrant DNA methylation accompanies genetic alterations during oncogenesis and tumour homeostasis and contributes to the transcriptional deregulation of key signalling pathways in cancer. Despite increasing efforts in DNA methylation profiling of cancer patients, there is still a lack of epigenetic biomarkers to predict treatment efficacy. To address this, we analyse 721 cancer cell lines across 22 cancer types treated with 453 anti-cancer compounds. We systematically detect the predictive component of DNA methylation in the context of transcriptional and mutational patterns, i.e., in total 19 DNA methylation biomarkers across 17 drugs and five cancer types. DNA methylation constitutes drug sensitivity biomarkers by mediating the expression of proximal genes, thereby enhancing biological signals across multi-omics data modalities. Our method reproduces anticipated associations, and in addition, we find that the NEK9 promoter hypermethylation may confer sensitivity to the NEDD8-activating enzyme (NAE) inhibitor pevonedistat in melanoma through downregulation of NEK9. In summary, we envision that epigenomics will refine existing patient stratification, thus empowering the next generation of precision oncology.
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Affiliation(s)
- Alexander Joschua Ohnmacht
- Computational Health Center, Helmholtz Munich, 85764, Neuherberg, Germany
- Department of Biology, Ludwig-Maximilians University Munich, 82152, Martinsried, Germany
| | - Anantharamanan Rajamani
- Division of Translational Cancer Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Chair of Translational Cancer Research and Institute of Experimental Cancer Therapy, Klinikum rechts der Isar, School of Medicine, Technische Universität München, Ismaninger Str. 22, 81675, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Ismaninger Str. 22, 81675, Munich, Germany
| | - Göksu Avar
- Computational Health Center, Helmholtz Munich, 85764, Neuherberg, Germany
- Department of Biology, Ludwig-Maximilians University Munich, 82152, Martinsried, Germany
| | - Ginte Kutkaite
- Computational Health Center, Helmholtz Munich, 85764, Neuherberg, Germany
- Department of Biology, Ludwig-Maximilians University Munich, 82152, Martinsried, Germany
| | - Emanuel Gonçalves
- Instituto Superior Técnico (IST), Universidade de Lisboa, 1049-001, Lisbon, Portugal
- INESC-ID, 1000-029, Lisbon, Portugal
| | - Dieter Saur
- Division of Translational Cancer Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Chair of Translational Cancer Research and Institute of Experimental Cancer Therapy, Klinikum rechts der Isar, School of Medicine, Technische Universität München, Ismaninger Str. 22, 81675, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technical University of Munich, Ismaninger Str. 22, 81675, Munich, Germany
| | - Michael Patrick Menden
- Computational Health Center, Helmholtz Munich, 85764, Neuherberg, Germany.
- Department of Biology, Ludwig-Maximilians University Munich, 82152, Martinsried, Germany.
- Department of Biochemistry and Pharmacology, University of Melbourne, Victoria, VIC, 3010, Australia.
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19
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Kerdivel G, Amrouche F, Calmejane MA, Carallis F, Hamroune J, Hantel C, Bertherat J, Assié G, Boeva V. DNA hypermethylation driven by DNMT1 and DNMT3A favors tumor immune escape contributing to the aggressiveness of adrenocortical carcinoma. Clin Epigenetics 2023; 15:121. [PMID: 37528470 PMCID: PMC10394822 DOI: 10.1186/s13148-023-01534-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 07/16/2023] [Indexed: 08/03/2023] Open
Abstract
BACKGROUND Adrenocortical carcinoma is rare and aggressive endocrine cancer of the adrenal gland. Within adrenocortical carcinoma, a recently described subtype characterized by a CpG island methylator phenotype (CIMP) has been associated with an especially poor prognosis. However, the drivers of CIMP remain unknown. Furthermore, the functional relation between CIMP and poor clinical outcomes of patients with adrenocortical carcinoma stays elusive. RESULTS Here, we show that CIMP in adrenocortical carcinoma is linked to the increased expression of DNA methyltransferases DNMT1 and DNMT3A driven by a gain of gene copy number and cell hyperproliferation. Importantly, we demonstrate that CIMP contributes to tumor aggressiveness by favoring tumor immune escape. This effect could be at least partially reversed by treatment with the demethylating agent 5-azacytidine. CONCLUSIONS In sum, our findings suggest that co-treatment with demethylating agents might enhance the efficacy of immunotherapy and could represent a novel therapeutic approach for patients with high CIMP adrenocortical carcinoma.
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Affiliation(s)
- Gwenneg Kerdivel
- INSERM, U1016, Cochin Institute, CNRS UMR8104, University of Paris, 24 rue du Faubourg Saint-Jacques, Paris, France
| | - Floriane Amrouche
- INSERM, U1016, Cochin Institute, CNRS UMR8104, University of Paris, 24 rue du Faubourg Saint-Jacques, Paris, France
| | - Marie-Ange Calmejane
- INSERM, U1016, Cochin Institute, CNRS UMR8104, University of Paris, 24 rue du Faubourg Saint-Jacques, Paris, France
| | | | - Juliette Hamroune
- INSERM, U1016, Cochin Institute, CNRS UMR8104, University of Paris, 24 rue du Faubourg Saint-Jacques, Paris, France
| | - Constanze Hantel
- Department of Endocrinology, Diabetology and Clinical Nutrition, University Hospital Zurich (USZ) and University of Zurich (UZH), Zurich, Switzerland
- Medizinische Klinik und Poliklinik III, University Hospital Carl Gustav Carus Dresden, Dresden, Germany
| | - Jérôme Bertherat
- INSERM, U1016, Cochin Institute, CNRS UMR8104, University of Paris, 24 rue du Faubourg Saint-Jacques, Paris, France
| | - Guillaume Assié
- INSERM, U1016, Cochin Institute, CNRS UMR8104, University of Paris, 24 rue du Faubourg Saint-Jacques, Paris, France
| | - Valentina Boeva
- INSERM, U1016, Cochin Institute, CNRS UMR8104, University of Paris, 24 rue du Faubourg Saint-Jacques, Paris, France.
- Department of Computer Science, Institute for Machine Learning, ETH Zurich, Universitätstrasse 6, 8092, Zurich, Switzerland.
- Swiss Institute of Bioinformatics (SIB), Zurich, Switzerland.
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20
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Cui W, Huang Z, Jin SG, Johnson J, Lau KH, Hostetter G, Pfeifer GP. Deficiency of the Polycomb Protein RYBP and TET Methylcytosine Oxidases Promotes Extensive CpG Island Hypermethylation and Malignant Transformation. Cancer Res 2023; 83:2480-2495. [PMID: 37272752 PMCID: PMC10391329 DOI: 10.1158/0008-5472.can-23-0269] [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: 01/24/2023] [Revised: 04/24/2023] [Accepted: 05/31/2023] [Indexed: 06/06/2023]
Abstract
Hypermethylation of CpG islands (CGI) is a common feature of cancer cells and predominantly affects Polycomb-associated genomic regions. Elucidating the underlying mechanisms leading to DNA hypermethylation in human cancer could help identify chemoprevention strategies. Here, we evaluated the role of Polycomb complexes and 5-methylcytosine (5mC) oxidases in protecting CGIs from DNA methylation and observed that four genes coding for components of Polycomb repressive complex 1 (PRC1) are downregulated in tumors. Inactivation of RYBP, a key activator of variant PRC1 complexes, in combination with all three 5mC oxidases (TET proteins) in nontumorigenic bronchial epithelial cells led to widespread hypermethylation of Polycomb-marked CGIs affecting almost 4,000 target genes, which closely resembled the DNA hypermethylation landscape observed in human squamous cell lung tumors. The RYBP- and TET-deficient cells showed methylation-associated aberrant regulation of cancer-relevant pathways, including defects in the Hippo tumor suppressor network. Notably, the quadruple knockout cells acquired a transformed phenotype, including anchorage-independent growth and formation of squamous cell carcinomas in mice. This work provides a mechanism promoting hypermethylation of CGIs and shows that such hypermethylation can lead to cell transformation. The breakdown of a two-pronged protection mechanism can be a route towards genome-wide hypermethylation of CGIs in tumors. SIGNIFICANCE Dysfunction of the Polycomb component RYBP in combination with loss of 5-methylcytosine oxidases promotes widespread hypermethylation of CpG islands in bronchial cells and induces tumorigenesis, resembling changes seen in human lung tumors.
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Affiliation(s)
- Wei Cui
- Department of Epigenetics, Van Andel Institute, Grand Rapids, Michigan
| | - Zhijun Huang
- Department of Epigenetics, Van Andel Institute, Grand Rapids, Michigan
| | - Seung-Gi Jin
- Department of Epigenetics, Van Andel Institute, Grand Rapids, Michigan
| | - Jennifer Johnson
- Department of Epigenetics, Van Andel Institute, Grand Rapids, Michigan
| | - Kin H. Lau
- Bioinformatics and Biostatistics Core, Van Andel Institute, Grand Rapids, Michigan
| | - Galen Hostetter
- Pathology and Biorepository Core, Van Andel Institute, Grand Rapids, Michigan
| | - Gerd P. Pfeifer
- Department of Epigenetics, Van Andel Institute, Grand Rapids, Michigan
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21
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Bhandari YR, Krishna V, Powers R, Parmar S, Thursby SJ, Gupta E, Kulak O, Gokare P, Reumers J, Van Wesenbeeck L, Bachman KE, Baylin SB, Easwaran H. Transcription factor expression repertoire basis for epigenetic and transcriptional subtypes of colorectal cancers. Proc Natl Acad Sci U S A 2023; 120:e2301536120. [PMID: 37487069 PMCID: PMC10401032 DOI: 10.1073/pnas.2301536120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 06/15/2023] [Indexed: 07/26/2023] Open
Abstract
Colorectal cancers (CRCs) form a heterogenous group classified into epigenetic and transcriptional subtypes. The basis for the epigenetic subtypes, exemplified by varying degrees of promoter DNA hypermethylation, and its relation to the transcriptional subtypes is not well understood. We link cancer-specific transcription factor (TF) expression alterations to methylation alterations near TF-binding sites at promoter and enhancer regions in CRCs and their premalignant precursor lesions to provide mechanistic insights into the origins and evolution of the CRC molecular subtypes. A gradient of TF expression changes forms a basis for the subtypes of abnormal DNA methylation, termed CpG-island promoter DNA methylation phenotypes (CIMPs), in CRCs and other cancers. CIMP is tightly correlated with cancer-specific hypermethylation at enhancers, which we term CpG-enhancer methylation phenotype (CEMP). Coordinated promoter and enhancer methylation appears to be driven by downregulation of TFs with common binding sites at the hypermethylated enhancers and promoters. The altered expression of TFs related to hypermethylator subtypes occurs early during CRC development, detectable in premalignant adenomas. TF-based profiling further identifies patients with worse overall survival. Importantly, altered expression of these TFs discriminates the transcriptome-based consensus molecular subtypes (CMS), thus providing a common basis for CIMP and CMS subtypes.
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Affiliation(s)
- Yuba R. Bhandari
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD21287
| | - Vinod Krishna
- Infectious Diseases and Vaccines Therapeutic Area, Janssen Research and Development, Spring House, PA19477
| | - Rachael Powers
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD21287
| | - Sehej Parmar
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD21287
| | - Sara-Jayne Thursby
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD21287
| | - Ekta Gupta
- Division of Gastroenterology and Hepatology, The Johns Hopkins University School of Medicine, Baltimore, MD21287
| | - Ozlem Kulak
- Division of Gastrointestinal and Liver Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD21287
| | - Prashanth Gokare
- Oncology Therapeutic Area, Janssen Research and Development, Spring House, PA19477
| | - Joke Reumers
- Discovery Technologies and Molecular Pharmacology, Therapeutics Discovery, Janssen Research and Development, Turnhoutseweg 30, 2340Beerse, Belgiumg
| | - Liesbeth Van Wesenbeeck
- Infectious Diseases and Vaccines Therapeutic Area, Janssen Research and Development, Turnhoutseweg 30, 2340Beerse, Belgium
| | - Kurtis E. Bachman
- Oncology Therapeutic Area, Janssen Research and Development, Spring House, PA19477
| | - Stephen B. Baylin
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD21287
| | - Hariharan Easwaran
- CRB1, Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University School of Medicine, Baltimore, MD21287
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22
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Tran TO, Lam LHT, Le NQK. Hyper-methylation of ABCG1 as an epigenetics biomarker in non-small cell lung cancer. Funct Integr Genomics 2023; 23:256. [PMID: 37523012 DOI: 10.1007/s10142-023-01185-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 07/22/2023] [Accepted: 07/24/2023] [Indexed: 08/01/2023]
Abstract
Non-small cell lung cancer (NSCLC) is the most prevalent histological type of lung cancer and the leading cause of death globally. Patients with NSCLC have a poor prognosis for various factors, and a late diagnosis is one of them. The DNA methylation of CpG island sequences found in the promoter regions of tumor suppressor genes has recently received attention as a potential biomarker of human cancer. In this study, we report DNA methylation changes of the adenosine triphosphate (ATP)-binding cassette transporter G1 (ABCG1), which belongs to the ATP cassette transporter family in NSCLC patients. Our results demonstrate that ABCG1 is hyper-methylation in NSCLC samples, and these changes are negatively correlated to gene and protein expression. Furthermore, the expression of the ABCG1 gene is significantly associated with the survival time of lung adenocarcinoma (LUAD) patients; however, it did not show a correlation to overall survival (OS) of lung squamous cell carcinoma (LUSC) patients. Notably, we found ABCG1 methylation status at locus cg20214535 is strongly associated with the survival time and consistently observed hyper-methylation in LUAD samples. This novel finding suggests ABCG1 is a potential candidate for targeted therapy in lung cancer via this specific probe. In addition, we illustrate the protein-protein interaction (PPI) of ABCG1 with other proteins and the strong communication of ABCG1 with immune cells.
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Affiliation(s)
- Thi-Oanh Tran
- International Ph.D. Program in Cell Therapy and Regenerative Medicine, College of Medicine, Taipei Medical University, 110, Taipei, Taiwan
- AIBioMed Research Group, Taipei Medical University, Taipei, 110, Taiwan
- Hematology and Blood Transfusion Center, Bach Mai Hospital, No. 78, Giai Phong street, Hanoi, Vietnam
| | - Luu Ho Thanh Lam
- Department of Pediatrics, Pham Ngoc Thach University of Medicine, Ho Chi Minh City, Vietnam
- Children's Hospital 1, Ho Chi Minh City, Vietnam
| | - Nguyen Quoc Khanh Le
- AIBioMed Research Group, Taipei Medical University, Taipei, 110, Taiwan.
- Professional Master Program in Artificial Intelligence in Medicine, College of Medicine, Taipei Medical University, Taipei, 110, Taiwan.
- Research Center for Artificial Intelligence in Medicine, Taipei Medical University, Taipei, 110, Taiwan.
- Translational Imaging Research Center, Taipei Medical University Hospital, Taipei, 110, Taiwan.
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23
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Shin HJ, Hua JT, Li H. Recent advances in understanding DNA methylation of prostate cancer. Front Oncol 2023; 13:1182727. [PMID: 37234978 PMCID: PMC10206257 DOI: 10.3389/fonc.2023.1182727] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 04/24/2023] [Indexed: 05/28/2023] Open
Abstract
Epigenetic modifications, such as DNA methylation, is widely studied in cancer. DNA methylation patterns have been shown to distinguish between benign and malignant tumors in various cancers, including prostate cancer. It may also contribute to oncogenesis, as it is frequently associated with downregulation of tumor suppressor genes. Aberrant patterns of DNA methylation, in particular the CpG island hypermethylator phenotype (CIMP), have shown associative evidence with distinct clinical features and outcomes, such as aggressive subtypes, higher Gleason score, prostate-specific antigen (PSA), and overall tumor stage, overall worse prognosis, as well as reduced survival. In prostate cancer, hypermethylation of specific genes is significantly different between tumor and normal tissues. Methylation patterns could distinguish between aggressive subtypes of prostate cancer, including neuroendocrine prostate cancer (NEPC) and castration resistant prostate adenocarcinoma. Further, DNA methylation is detectable in cell-free DNA (cfDNA) and is reflective of clinical outcome, making it a potential biomarker for prostate cancer. This review summarizes recent advances in understanding DNA methylation alterations in cancers with the focus on prostate cancer. We discuss the advanced methodology used for evaluating DNA methylation changes and the molecular regulators behind these changes. We also explore the clinical potential of DNA methylation as prostate cancer biomarkers and its potential for developing targeted treatment of CIMP subtype of prostate cancer.
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Affiliation(s)
- Hyun Jin Shin
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, United States
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, United States
| | - Junjie T Hua
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, United States
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, United States
| | - Haolong Li
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, United States
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, United States
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24
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Li M, Zhu C, Xue Y, Miao C, He R, Li W, Zhang B, Yu W, Huang X, Lv M, Xu Y, Huang Q. A DNA methylation signature for the prediction of tumour recurrence in stage II colorectal cancer. Br J Cancer 2023; 128:1681-1689. [PMID: 36828869 PMCID: PMC10133253 DOI: 10.1038/s41416-023-02155-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 01/05/2023] [Accepted: 01/11/2023] [Indexed: 02/26/2023] Open
Abstract
BACKGROUND A major challenge in stage II colorectal carcinoma is to identify patients with increased risk of recurrence. Biomarkers that distinguish patients with poor prognosis from patients without recurrence are currently lacking. This study aims to develop a robust DNA methylation classifier that allows the prediction of recurrence and chemotherapy benefit in patients with stage II colorectal cancer. We performed a genome-wide DNA methylation capture sequencing in 243 stage II colorectal carcinoma samples and identified a relapse-specific DNA methylation signature consisting of eight CpG sites. METHODS Two hundred and forty-three patients with stage II CRC were enrolled in this study. In order to select differential methylation sites among recurrence and non-recurrence stage II CRC samples, DNA methylation profiles of 62 tumour samples including 31 recurrence and 31 nonrecurrence samples were analysed using the Agilent SureSelectXT Human Methyl-Seq, a comprehensive target enrichment system to analyse CpG methylation. Pyrosequencing was applied to quantify the methylation level of candidate DNA methylation sites in 243 patients. Least absolute shrinkage and selection operator (LASSO) method was employed to build the disease recurrence prediction classifier. RESULTS We identified a relapse-related DNA methylation signature consisting of eight CpG sites in stage II CRC by DNA methylation capture sequencing. The classifier showed significantly higher prognostic accuracy than any clinicopathological risk factors. The Kaplan-Meier survival curve showed an association of high-risk score with poor prognosis. In multivariate analysis, the signature was the most significant prognosis factor, with an HR of 2.80 (95% CI, 1.71-4.58, P < 0.001). The signature could identify patients who are suitable candidates for adjuvant chemotherapy. CONCLUSIONS An eight-CpG DNA methylation signature is a reliable prognostic and predictive tool for disease recurrence in patients with stage II CRC.
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Affiliation(s)
- Min Li
- Cancer Center, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China
- Institute of Clinical Sciences, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China
| | - Congcong Zhu
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, 270 Dong'An Road, 200032, Shanghai, P. R. China
- Department of Oncology, Shanghai Medical College, Fudan University, 270 Dong'An Road, 200032, Shanghai, P. R. China
| | - Ying Xue
- Cancer Center, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China
- Institute of Clinical Sciences, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China
| | - Changhong Miao
- Cancer Center, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China
- Department of Anesthesiology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China
| | - Ruiping He
- Cancer Center, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China
- Institute of Clinical Sciences, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China
| | - Wei Li
- Laboratory of RNA Epigenetics, Institute of Biomedical Sciences, Fudan University, 130 Dong'An Road, 200032, Shanghai, P. R. China
| | - Baolong Zhang
- Laboratory of RNA Epigenetics, Institute of Biomedical Sciences, Fudan University, 130 Dong'An Road, 200032, Shanghai, P. R. China
| | - Wenqiang Yu
- Laboratory of RNA Epigenetics, Institute of Biomedical Sciences, Fudan University, 130 Dong'An Road, 200032, Shanghai, P. R. China
| | - Xingxu Huang
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, P. R. China
| | - Minzhi Lv
- Institute of Clinical Sciences, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China.
- Department of Biostatistics, Clinical Research Unit, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China.
| | - Ye Xu
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, 270 Dong'An Road, 200032, Shanghai, P. R. China.
- Department of Oncology, Shanghai Medical College, Fudan University, 270 Dong'An Road, 200032, Shanghai, P. R. China.
| | - Qihong Huang
- Cancer Center, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China.
- Institute of Clinical Sciences, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China.
- Shanghai Respiratory Research Institute, 180 Fenglin Road, 200032, Shanghai, P. R. China.
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25
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Tricarico R, Madzo J, Scher G, Cohen M, Jelinek J, Maegawa S, Nagarathinam R, Scher C, Chang WC, Nicolas E, Slifker M, Zhou Y, Devarajan K, Cai KQ, Kwok T, Nakajima P, Xu J, Mancuso P, Doneddu V, Bagella L, Williams R, Balachandran S, Maskalenko N, Campbell K, Ma X, Cañadas I, Viana-Errasti J, Moreno V, Valle L, Grivennikov S, Peshkova I, Kurilenko N, Mazitova A, Koltsova E, Lee H, Walsh M, Duttweiler R, Whetstine JR, Yen TJ, Issa JP, Bellacosa A. TET1 and TDG Suppress Inflammatory Response in Intestinal Tumorigenesis: Implications for Colorectal Tumors With the CpG Island Methylator Phenotype. Gastroenterology 2023; 164:921-936.e1. [PMID: 36764492 PMCID: PMC10586516 DOI: 10.1053/j.gastro.2023.01.039] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 12/28/2022] [Accepted: 01/14/2023] [Indexed: 02/12/2023]
Abstract
BACKGROUND & AIMS Aberrant DNA methylation is frequent in colorectal cancer (CRC), but underlying mechanisms and pathologic consequences are poorly understood. METHODS We disrupted active DNA demethylation genes Tet1 and/or Tdg from ApcMin mice and characterized the methylome and transcriptome of colonic adenomas. Data were compared to human colonic adenocarcinomas (COAD) in The Cancer Genome Atlas. RESULTS There were increased numbers of small intestinal adenomas in ApcMin mice expressing the TdgN151A allele, whereas Tet1-deficient and Tet1/TdgN151A-double heterozygous ApcMin colonic adenomas were larger with features of erosion and invasion. We detected reduction in global DNA hypomethylation in colonic adenomas from Tet1- and Tdg-mutant ApcMin mice and hypermethylation of CpG islands in Tet1-mutant ApcMin adenomas. Up-regulation of inflammatory, immune, and interferon response genes was present in Tet1- and Tdg-mutant colonic adenomas compared to control ApcMin adenomas. This up-regulation was also seen in murine colonic organoids and human CRC lines infected with lentiviruses expressing TET1 or TDG short hairpin RNA. A 127-gene inflammatory signature separated colonic adenocarcinomas into 4 groups, closely aligned with their microsatellite or chromosomal instability and characterized by different levels of DNA methylation and DNMT1 expression that anticorrelated with TET1 expression. Tumors with the CpG island methylator phenotype (CIMP) had concerted high DNMT1/low TET1 expression. TET1 or TDG knockdown in CRC lines enhanced killing by natural killer cells. CONCLUSIONS Our findings reveal a novel epigenetic regulation, linked to the type of genomic instability, by which TET1/TDG-mediated DNA demethylation decreases methylation levels and inflammatory/interferon/immune responses. CIMP in CRC is triggered by an imbalance of methylating activities over demethylating activities. These mice represent a model of CIMP CRC.
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Affiliation(s)
- Rossella Tricarico
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania; Nuclear Dynamics and Cancer Program, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Jozef Madzo
- Coriell Institute for Medical Research, Camden, New Jersey
| | - Gabrielle Scher
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania; Nuclear Dynamics and Cancer Program, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Maya Cohen
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania; Nuclear Dynamics and Cancer Program, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | | | - Shinji Maegawa
- University of Texas M.D. Anderson Cancer Center, Houston, Texas
| | | | - Carly Scher
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania; Nuclear Dynamics and Cancer Program, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Wen-Chi Chang
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Emmanuelle Nicolas
- Cancer Signaling and Microenvironment Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Michael Slifker
- Department of Biostatistics, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Yan Zhou
- Department of Biostatistics, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Karthik Devarajan
- Department of Biostatistics, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Kathy Q Cai
- Experimental Histopathology, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Tim Kwok
- Cell Culture Facility, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Pamela Nakajima
- Cell Culture Facility, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Jinfei Xu
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania; Nuclear Dynamics and Cancer Program, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Pietro Mancuso
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania; Nuclear Dynamics and Cancer Program, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Valentina Doneddu
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania; Nuclear Dynamics and Cancer Program, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Luigi Bagella
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy; Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, Pennsylvania
| | - Riley Williams
- Cancer Signaling and Microenvironment Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Siddharth Balachandran
- Cancer Signaling and Microenvironment Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Nicholas Maskalenko
- Cancer Signaling and Microenvironment Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Kerry Campbell
- Cancer Signaling and Microenvironment Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Xueying Ma
- Nuclear Dynamics and Cancer Program, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Israel Cañadas
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania; Nuclear Dynamics and Cancer Program, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Julen Viana-Errasti
- Hereditary Cancer Program Catalan Institute of Oncology, Oncobell Program, Investigación Biomédica de Bellvitge, Hospitalet de Llobregat, Barcelona, Spain
| | - Victor Moreno
- Oncology Data Analytics Program, Catalan Institute of Oncology, Oncobell Program, Investigación Biomédica de Bellvitge, Hospitalet de Llobregat, Barcelona, Spain; Consorcio de Investigación Biomédica en Red de Epidemiología y Salud Pública, Madrid, Spain; Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Laura Valle
- Hereditary Cancer Program Catalan Institute of Oncology, Oncobell Program, Investigación Biomédica de Bellvitge, Hospitalet de Llobregat, Barcelona, Spain; Centro de Investigación Biomédica en Red de Cáncer, Madrid, Spain
| | - Sergei Grivennikov
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania; Department of Medicine and Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California
| | - Iuliia Peshkova
- Cancer Signaling and Microenvironment Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania; Department of Medicine and Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California
| | - Natalia Kurilenko
- Cancer Signaling and Microenvironment Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania; Department of Medicine and Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California
| | - Aleksandra Mazitova
- Cancer Signaling and Microenvironment Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania; Department of Medicine and Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California
| | - Ekaterina Koltsova
- Cancer Signaling and Microenvironment Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania; Department of Medicine and Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California
| | - Hayan Lee
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania; Nuclear Dynamics and Cancer Program, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Martin Walsh
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania; Nuclear Dynamics and Cancer Program, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Reuben Duttweiler
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania; Nuclear Dynamics and Cancer Program, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Johnathan R Whetstine
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania; Nuclear Dynamics and Cancer Program, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Timothy J Yen
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania; Nuclear Dynamics and Cancer Program, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | | | - Alfonso Bellacosa
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania; Nuclear Dynamics and Cancer Program, Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania.
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26
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Methylation-sensitive transcription-enhanced single-molecule biosensing of DNA methylation in cancer cells and tissues. Anal Chim Acta 2023; 1251:340996. [PMID: 36925287 DOI: 10.1016/j.aca.2023.340996] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 02/21/2023] [Indexed: 02/24/2023]
Abstract
As a major epigenetic modification, DNA methylation participates in diverse cellular functions and emerges as a promising biomarker for disease diagnosis and monitoring. Herein, we developed a methylation-sensitive transcription-enhanced single-molecule biosensor to detect DNA methylation in human cells and tissues. In this biosensor, a rationally designed transcription machine is split into two parts including a promoter sequence (probe-P) for initiating transcription and a template sequence (probe-T) for RNA synthesis. The presence of specific DNA methylation leads to the formation of full-length transcription machine through sequence-specific ligation of probe-P and probe-T, initiating the synthesis of abundant ssRNA transcripts. The resultant ssRNAs can activate CRISPR/Cas12a to catalyze cyclic cleavage of fluorophore- and quencher-dual labeled signal probes, resulting in the recovery of the fluorophore signal that can be quantified by single-molecule detection. Taking advantages of the high-fidelity ligation of split transcription machine and the high efficiency of transcription- and CRISPR/Cas12a cleavage-mediated dual signal amplification, this single-molecule biosensor achieves a low detection limit of 337 aM and high selectivity. Moreover, it can distinguish 0.01% methylation level, and even accurately detect genomic DNA methylation in single cell and clinical samples, providing a powerful tool for epigenetic researches and clinical diagnostics.
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27
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Perez-Mayoral J, Gonzalez-Pons M, Centeno-Girona H, Montes-Rodríguez IM, Soto-Salgado M, Suárez B, Rodríguez N, Colón G, Sevilla J, Jorge D, Llor X, Xicola RM, Toro DH, Tous-López L, Torres-Torres M, Reyes JS, López-Acevedo N, Goel A, Rodríguez-Quilichini S, Cruz-Correa M. Molecular and Sociodemographic Colorectal Cancer Disparities in Latinos Living in Puerto Rico. Genes (Basel) 2023; 14:894. [PMID: 37107652 PMCID: PMC10138302 DOI: 10.3390/genes14040894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 04/05/2023] [Accepted: 04/07/2023] [Indexed: 04/29/2023] Open
Abstract
BACKGROUND The incidence of sporadic colorectal cancer (CRC) among individuals <50 years (early-onset CRC) has been increasing in the United States (U.S.) and Puerto Rico. CRC is currently the leading cause of cancer death among Hispanic men and women living in Puerto Rico (PRH). The objective of this study was to characterize the molecular markers and clinicopathologic features of colorectal tumors from PRH to better understand the molecular pathways leading to CRC in this Hispanic subpopulation. METHODS Microsatellite instability (MSI), CpG island methylator phenotype (CIMP), and KRAS and BRAF mutation status were analyzed. Sociodemographic and clinicopathological characteristics were evaluated using Chi-squared and Fisher's exact tests. RESULTS Of the 718 tumors analyzed, 34.2% (n = 245) were early-onset CRC, and 51.7% were males. Among the tumors with molecular data available (n = 192), 3.2% had MSI, 9.7% had BRAF, and 31.9% had KRAS mutations. The most common KRAS mutations observed were G12D (26.6%) and G13D (20.0%); G12C was present in 4.4% of tumors. A higher percentage of Amerindian admixture was significantly associated with early-onset CRC. CONCLUSIONS The differences observed in the prevalence of the molecular markers among PRH tumors compared to other racial/ethnic groups suggest a distinct molecular carcinogenic pathway among Hispanics. Additional studies are warranted.
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Affiliation(s)
| | - Maria Gonzalez-Pons
- University of Puerto Rico Comprehensive Cancer Center, San Juan, PR 00936, USA
| | | | | | | | - Belisa Suárez
- University of Puerto Rico Comprehensive Cancer Center, San Juan, PR 00936, USA
| | - Natalia Rodríguez
- School of Medicine, Universidad Central del Caribe, Bayamon, PR 00956, USA
| | - Giancarlo Colón
- School of Medicine, Universidad Central del Caribe, Bayamon, PR 00956, USA
| | - Javier Sevilla
- School of Medicine, Universidad Central del Caribe, Bayamon, PR 00956, USA
| | - Daphne Jorge
- School of Medicine, Ponce Health Sciences University, Ponce, PR 00716, USA
| | - Xavier Llor
- Department of Internal Medicine and Digestive Diseases, School of Medicine, Yale University, New Haven, CT 06520, USA
| | - Rosa M. Xicola
- Department of Internal Medicine and Digestive Diseases, School of Medicine, Yale University, New Haven, CT 06520, USA
| | - Doris H. Toro
- VA Caribbean Healthcare System, San Juan, PR 00921, USA
| | - Luis Tous-López
- Ashford Presbyterian Community Hospital, San Juan, PR 00907, USA
| | | | - José S. Reyes
- Ashford Presbyterian Community Hospital, San Juan, PR 00907, USA
| | | | - Ajay Goel
- Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA
| | | | - Marcia Cruz-Correa
- University of Puerto Rico Comprehensive Cancer Center, San Juan, PR 00936, USA
- Department of Medicine, Medical Sciences Campus, University of Puerto Rico, San Juan, PR 00935, USA
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Guo Q, Zhao L, Yan N, Li Y, Guo C, Dang S, Shen X, Han J, Luo Y. Integrated pan-cancer analysis and experimental verification of the roles of tropomyosin 4 in gastric cancer. Front Immunol 2023; 14:1148056. [PMID: 36993958 PMCID: PMC10041708 DOI: 10.3389/fimmu.2023.1148056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 02/27/2023] [Indexed: 03/14/2023] Open
Abstract
ObjectiveTo investigate the function of tropomyosin 4 (TPM4) using pan-cancer data, especially in gastric cancer (GC), using comprehensive bioinformatics analysis and molecular experiments.MethodsWe used UCSC Xena, The Cancer Genome Atlas (TCGA), Genotype-Tissue Expression Project (GTEx), TIMER2.0, GEPIA, cBioPortal, Xiantao tool, and UALCAN websites and databases for the extraction of pan-cancer data on TPM4. TPM4 expression was investigated with respect to prognosis, genetic alterations, epigenetic alterations, and immune infiltration. RNA22, miRWalk, miRDB, Starbase 2.0, and Cytoscape were used for identifying and constructing the regulatory networks of lncRNAs, miRNAs, and TPM4 in GC. Data from GSCALite, drug bank databases, and Connectivity Map (CMap) were used to analyze the sensitivity of drugs dependent on TPM4 expression. Gene Ontology (GO), enrichment analyses of the Kyoto Encyclopedia of Genes and Genomes (KEGG), wound healing assays, and (Matrigel) transwell experiments were used to investigate the biological functions of TPM4 in GC.ResultThe findings of the comprehensive pan-cancer analysis revealed that TPM4 has a certain diagnostic and prognosis value in most cancers. Alterations in the expression of TPM4, including duplications and deep mutations, and epigenetic alterations revealed that TPM4 expression is related to the expression of DNA methylation inhibitors and RNA methylation regulators at high concentrations. Besides, TPM4 expression was found to correlate with immune cell infiltration, immune checkpoint (ICP) gene expression, the tumor mutational burden (TMB), and microsatellite instability (MSI). Neoantigens (NEO) were also found to influence its response to immunotherapy. A lncRNA-miRNA -TPM4 network was found to regulate GC development and progression. TPM4 expression was related to docetaxel,5-fluorouracil, and eight small molecular targeted drugs sensitivity. Gene function enrichment analyses revealed that genes that were co-expressed with TPM4 were enriched within the extracellular matrix (ECM)-related pathways. Wound-healing and (Matrigel) transwell assays revealed that TPM4 promotes cell migration and invasion. TPM4, as an oncogene, plays a biological role, perhaps via ECM remodeling in GC.ConclusionsTPM4 is a prospective marker for the diagnosis, treatment outcome, immunology, chemotherapy, and small molecular drugs targeted for pan-cancer treatment, including GC treatment. The lncRNA-miRNA-TPM4network regulates the mechanism underlying GC progression. TPM4 may facilitate the invasion and migration of GC cells, possibly through ECM remodeling.
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Affiliation(s)
- Qijing Guo
- Research Center for High Altitude Medicine, Key Laboratory of High Altitude Medicine (Ministry of Education), Key Laboratory of Application and Foundation for High Altitude Medicine Research in Qinhai Province (Qinghai-Utah Joint Research Key Lab for High Altitude Medicine), Laboratory for High Altitude Medicine of Qinghai Province, Qinghai University, Xining, China
- Department of Oncology, Affiliated Hospital of Qinghai University, Xining, China
| | - Linglin Zhao
- Research Center for High Altitude Medicine, Key Laboratory of High Altitude Medicine (Ministry of Education), Key Laboratory of Application and Foundation for High Altitude Medicine Research in Qinhai Province (Qinghai-Utah Joint Research Key Lab for High Altitude Medicine), Laboratory for High Altitude Medicine of Qinghai Province, Qinghai University, Xining, China
| | - Nan Yan
- Research Center for High Altitude Medicine, Key Laboratory of High Altitude Medicine (Ministry of Education), Key Laboratory of Application and Foundation for High Altitude Medicine Research in Qinhai Province (Qinghai-Utah Joint Research Key Lab for High Altitude Medicine), Laboratory for High Altitude Medicine of Qinghai Province, Qinghai University, Xining, China
| | - Yan Li
- Department of Oncology, Affiliated Hospital of Qinghai University, Xining, China
| | - Cuiping Guo
- Department of Oncology, Affiliated Hospital of Qinghai University, Xining, China
| | - Shengyan Dang
- Department of Oncology, Affiliated Hospital of Qinghai University, Xining, China
| | - Xianliang Shen
- Department of Oncology, Affiliated Hospital of Qinghai University, Xining, China
| | - Jianfang Han
- Department of Oncology, Affiliated Hospital of Qinghai University, Xining, China
| | - Yushuang Luo
- Research Center for High Altitude Medicine, Key Laboratory of High Altitude Medicine (Ministry of Education), Key Laboratory of Application and Foundation for High Altitude Medicine Research in Qinhai Province (Qinghai-Utah Joint Research Key Lab for High Altitude Medicine), Laboratory for High Altitude Medicine of Qinghai Province, Qinghai University, Xining, China
- Department of Oncology, Affiliated Hospital of Qinghai University, Xining, China
- *Correspondence: Yushuang Luo,
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Yuan M, Xu J, Cao S, Sun S. DDX1 is a prognostic biomarker and correlates with immune infiltrations in hepatocellular carcinoma. BMC Immunol 2022; 23:59. [PMID: 36451087 PMCID: PMC9710136 DOI: 10.1186/s12865-022-00533-0] [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: 08/03/2022] [Accepted: 11/14/2022] [Indexed: 12/05/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the leading lethal malignant tumors worldwide. DEAD-box (DDX) family helicases are implicated in numerous human cancers. However, the role of DDX1 in HCC has not yet been fully elucidated. We downloaded gene expression data and clinical information data of HCC from The Cancer Genome Atlas and International Cancer Genome Consortium (ICGC) database and conducted subsequent analyses using the R package and online portal. The results revealed that HCC tissues had higher DDX1 expression compared with either paired or unpaired normal tissues. The increased DDX1 expression was closely related to the advanced pathological grade and histologic grade of HCC. Further analysis suggested that patients with high DDX1 expression contributed to poor prognosis The Cox regression analysis revealed that the expression level of DDX1 was an independent prognostic factor for HCC. In addition, an ICGC cohort was used for external validation. The cBio-Portal, MethSurv, and UALCAN database were used for evaluating the genomic mechanism. Moreover, the Tumor Immune Estimation Resource dataset and QUANTISEQ algorithm revealed that DDX1 expression positively correlates with immune infiltrating cells. We also identified the DDX1-related differentially expressed genes (DEGs) and explored their biological functions by GO, KEGG, and GSEA analyses, which indicated that DDX1 may regulate the progression of HCC. In general, increased DDX1 expression predicts a poor prognosis and drives the progression of HCC.
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Affiliation(s)
- Mengping Yuan
- grid.417384.d0000 0004 1764 2632Department of Gastroenterology, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, 325000 People’s Republic of China
| | - Jinyong Xu
- Department of Pathology, Shenzhen Hyzen Hospital, Shenzhen, 518038 People’s Republic of China
| | - Shuguang Cao
- grid.417384.d0000 0004 1764 2632Department of Gastroenterology, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, 325000 People’s Republic of China
| | - Shuangshuang Sun
- grid.417384.d0000 0004 1764 2632Department of Oncology, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, 325000 People’s Republic of China
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30
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Wang P, Song Q, Ren J, Zhang W, Wang Y, Zhou L, Wang D, Chen K, Jiang L, Zhang B, Chen W, Qu C, Zhao H, Jiao Y. Simultaneous analysis of mutations and methylations in circulating cell-free DNA for hepatocellular carcinoma detection. Sci Transl Med 2022; 14:eabp8704. [PMID: 36417488 DOI: 10.1126/scitranslmed.abp8704] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Cell-free DNA (cfDNA)-based liquid biopsy is a promising approach for the early detection of cancer. A major hurdle is the limited yield of cfDNA from one blood draw, limiting the use of most samples to one test of either mutation or methylation. Here, we develop a technology, Mutation Capsule Plus (MCP), which enables multiplex profiling of one cfDNA sample, including simultaneous detection of genetic and epigenetic alterations and genome-wide discovery of methylation markers. With this technology, we performed de novo screening of methylation markers on cfDNA samples from 30 hepatocellular carcinoma (HCC) cases and 30 non-HCC controls. The methylation markers enriched in HCC cfDNA were further profiled in parallel with a panel of mutations on a training cohort of 60 HCC and 60 non-HCC cases, resulting in an HCC detection model. We validated the model in an independent retrospective cohort with 58 HCC and 198 non-HCC cases and got 90% sensitivity with 94% specificity. Furthermore, we applied the model to a prospective cohort of 311 asymptomatic hepatitis B virus carriers with normal liver ultrasonography and serum AFP concentration. The model detected four of the five HCC cases in the cohort, showing 80% sensitivity and 94% specificity. These findings demonstrate that the MCP technology has potential for the discovery and validation of multiomics biomarkers for the noninvasive detection of cancer. This study also provides a comprehensive database of genetic and epigenetic alterations in the cfDNA of a large cohort of HCC cases and high-risk non-HCC individuals.
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Affiliation(s)
- Pei Wang
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Qianqian Song
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Jie Ren
- Fanshengzi Clinical Laboratory, Beijing 102206, China
| | - Weilong Zhang
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China.,Department of Hematology, Lymphoma Research Center, Peking University Third Hospital, Beijing 100191, China
| | - Yuting Wang
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China.,Immunology Department, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical Colleges, Beijing 100021, China
| | - Lin Zhou
- Fanshengzi Clinical Laboratory, Beijing 102206, China
| | - Dongmei Wang
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China.,Immunology Department, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical Colleges, Beijing 100021, China
| | - Kun Chen
- Immunology Department, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical Colleges, Beijing 100021, China
| | - Liping Jiang
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Bochao Zhang
- Fanshengzi Clinical Laboratory, Beijing 102206, China
| | - Wanqing Chen
- Office of Cancer Screening, National Cancer Center/ National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, No.17 Pan-jia-yuan South Lane, Chaoyang District, Beijing 100021, China
| | - Chunfeng Qu
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China.,Immunology Department, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical Colleges, Beijing 100021, China
| | - Hong Zhao
- Department of Hepatobiliary Surgery, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Yuchen Jiao
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
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31
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Bridging the Scientific Gaps to Identify Effective Treatments in Adrenocortical Cancer. Cancers (Basel) 2022; 14:cancers14215245. [DOI: 10.3390/cancers14215245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/20/2022] [Accepted: 10/25/2022] [Indexed: 11/17/2022] Open
Abstract
Adrenocortical cancer (ACC) typically presents in advanced stages of disease and has a dismal prognosis. One of the foremost reasons for this is the lack of available systemic therapies, with mitotane remaining the backbone of treatment since its discovery in the 1960s, despite underwhelming efficacy. Surgery remains the only potentially curative option, but about half of patients will recur post-operatively, often with metastatic disease. Other local treatment options have been attempted but are only used practically on a case-by-case basis. Over the past few decades there have been significant advances in understanding the molecular background of ACC, but this has not yet translated to better treatment options. Attempts at novel treatment strategies have not provided significant clinical benefit. This paper reviews our current treatment options and molecular understanding of ACC and the reasons why a successful treatment has remained elusive. Additionally, we discuss the knowledge gaps that need to be overcome to bring us closer to successful treatment and ways to bridge them.
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32
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Kim H, Sim M, Park N, Kwon K, Kim J, Kim J. msPIPE: a pipeline for the analysis and visualization of whole-genome bisulfite sequencing data. BMC Bioinformatics 2022; 23:383. [PMID: 36123620 PMCID: PMC9487059 DOI: 10.1186/s12859-022-04925-2] [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: 02/03/2022] [Accepted: 09/13/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND DNA methylation is an important epigenetic modification that is known to regulate gene expression. Whole-genome bisulfite sequencing (WGBS) is a powerful method for studying cytosine methylation in a whole genome. However, it is difficult to obtain methylation profiles using the WGBS raw reads and is necessary to be proficient in all types of bioinformatic tools for the study of DNA methylation. In addition, recent end-to-end pipelines for DNA methylation analyses are not sufficient for addressing those difficulties. RESULTS Here we present msPIPE, a pipeline for DNA methylation analyses with WGBS data seamlessly connecting all the required tasks ranging from data pre-processing to multiple downstream DNA methylation analyses. The msPIPE can generate various methylation profiles to analyze methylation patterns in the given sample, including statistical summaries and methylation levels. Also, the methylation levels in the functional regions of a genome are computed with proper annotation. The results of methylation profiles, hypomethylation, and differential methylation analysis are plotted in publication-quality figures. The msPIPE can be easily and conveniently used with a Docker image, which includes all dependent packages and software related to DNA methylation analyses. CONCLUSION msPIPE is a new end-to-end pipeline designed for methylation calling, profiling, and various types of downstream DNA methylation analyses, leading to the creation of publication-quality figures. msPIPE allows researchers to process and analyze the WGBS data in an easy and convenient way. It is available at https://github.com/jkimlab/msPIPE and https://hub.docker.com/r/jkimlab/mspipe .
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Affiliation(s)
- Heesun Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Mikang Sim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Nayoung Park
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Kisang Kwon
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Junyoung Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Jaebum Kim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, 05029, Republic of Korea.
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Wu BK, Mei SC, Chen EH, Zheng Y, Pan D. YAP induces an oncogenic transcriptional program through TET1-mediated epigenetic remodeling in liver growth and tumorigenesis. Nat Genet 2022; 54:1202-1213. [PMID: 35835915 PMCID: PMC9357225 DOI: 10.1038/s41588-022-01119-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 06/02/2022] [Indexed: 02/03/2023]
Abstract
Epigenetic remodeling is essential for oncogene-induced cellular transformation and malignancy. In contrast to histone post-translational modifications, how DNA methylation is remodeled by oncogenic signaling remains poorly understood. The oncoprotein YAP, a coactivator of the TEAD transcription factors mediating Hippo signaling, is widely activated in human cancers. Here, we identify the 5-methylcytosine dioxygenase TET1 as a direct YAP target and a master regulator that coordinates the genome-wide epigenetic and transcriptional reprogramming of YAP target genes in the liver. YAP activation induces the expression of TET1, which physically interacts with TEAD to cause regional DNA demethylation, histone H3K27 acetylation and chromatin opening in YAP target genes to facilitate transcriptional activation. Loss of TET1 not only reverses YAP-induced epigenetic and transcriptional changes but also suppresses YAP-induced hepatomegaly and tumorigenesis. These findings exemplify how oncogenic signaling regulates the site specificity of DNA demethylation to promote tumorigenesis and implicate TET1 as a potential target for modulating YAP signaling in physiology and disease.
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Affiliation(s)
- Bo-Kuan Wu
- Department of Physiology, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Szu-Chieh Mei
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Elizabeth H Chen
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yonggang Zheng
- Department of Physiology, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Duojia Pan
- Department of Physiology, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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Reale A, Tagliatesta S, Zardo G, Zampieri M. Counteracting aged DNA methylation states to combat ageing and age-related diseases. Mech Ageing Dev 2022; 206:111695. [PMID: 35760211 DOI: 10.1016/j.mad.2022.111695] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 06/09/2022] [Accepted: 06/22/2022] [Indexed: 12/18/2022]
Abstract
DNA methylation (DNAm) overwrites information about multiple extrinsic factors on the genome. Age is one of these factors. Age causes characteristic DNAm changes that are thought to be not only major drivers of normal ageing but also precursors to diseases, cancer being one of these. Although there is still much to learn about the relationship between ageing, age-related diseases and DNAm, we now know how to interpret some of the effects caused by age in the form of changes in methylation marks at specific loci. In fact, these changes form the basis of the so called "epigenetic clocks", which translate the genomic methylation profile into an "epigenetic age". Epigenetic age does not only estimate chronological age but can also predict the risk of chronic diseases and mortality. Epigenetic age is believed to be one of the most accurate metrics of biological age. Initial evidence has recently been gathered pointing to the possibility that the rate of epigenetic ageing can be slowed down or even reversed. In this review, we discuss some of the most relevant advances in this field. Expected outcome is that this approach can provide insights into how to preserve health and reduce the impact of ageing diseases in humans.
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Affiliation(s)
- Anna Reale
- Department of Experimental Medicine, Sapienza University of Rome, 00161 Rome, Italy.
| | - Stefano Tagliatesta
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, 00161 Rome, Italy.
| | - Giuseppe Zardo
- Department of Experimental Medicine, Sapienza University of Rome, 00161 Rome, Italy.
| | - Michele Zampieri
- Department of Experimental Medicine, Sapienza University of Rome, 00161 Rome, Italy.
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35
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Target-Based Small Molecule Drug Discovery for Colorectal Cancer: A Review of Molecular Pathways and In Silico Studies. Biomolecules 2022; 12:biom12070878. [PMID: 35883434 PMCID: PMC9312989 DOI: 10.3390/biom12070878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 06/05/2022] [Accepted: 06/17/2022] [Indexed: 01/27/2023] Open
Abstract
Colorectal cancer is one of the most prevalent cancer types. Although there have been breakthroughs in its treatments, a better understanding of the molecular mechanisms and genetic involvement in colorectal cancer will have a substantial role in producing novel and targeted treatments with better safety profiles. In this review, the main molecular pathways and driver genes that are responsible for initiating and propagating the cascade of signaling molecules reaching carcinoma and the aggressive metastatic stages of colorectal cancer were presented. Protein kinases involved in colorectal cancer, as much as other cancers, have seen much focus and committed efforts due to their crucial role in subsidizing, inhibiting, or changing the disease course. Moreover, notable improvements in colorectal cancer treatments with in silico studies and the enhanced selectivity on specific macromolecular targets were discussed. Besides, the selective multi-target agents have been made easier by employing in silico methods in molecular de novo synthesis or target identification and drug repurposing.
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36
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Effect of DNA methylation status on first-line anti-epidermal growth factor receptor treatment in patients with metastatic colorectal cancer. Int J Colorectal Dis 2022; 37:1439-1447. [PMID: 35612620 DOI: 10.1007/s00384-022-04177-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/01/2022] [Indexed: 02/04/2023]
Abstract
PURPOSE The CpG island methylator phenotype (CIMP), important for carcinogenesis, is a predictor of prognosis and chemotherapy sensitivity in colorectal cancer (CRC). However, there is a lack of consensus on CIMP markers, and thus, more comprehensive methylation markers are required to reliably predict the clinical outcomes. This study aimed to clarify the effects of genome-wide DNA methylation status on clinical outcomes in patients with metastatic CRC (mCRC) treated with epidermal growth factor receptor (EGFR) inhibitors. METHODS We enrolled 241 patients with mCRC, who received chemotherapy plus EGFR inhibitors as a first-line treatment. We analyzed the incidence and clinicopathological characteristics of highly methylated CRC (HMCC) and associations between genome-wide DNA methylation status and response rate (RR), progression-free survival (PFS), and overall survival (OS). RESULTS In total, 169 patients were included in the final analyses. The frequency of HMCC was 8.9% (15/169). The characteristics of patients with HMCC included right-sided primary tumor location (P = 0.042), undifferentiated histology (P = 0.047), and BRAF V600E mutation (P < 0.0001). Patients with HMCC showed worse clinical outcomes than those with low-methylated CRC in terms of RR (P = 0.017), PFS (P = 0.004), and OS (P = 0.019). In the multivariate analysis, peritoneal metastasis (P = 0.017), methylation status (P = 0.037), and BRAF V600E mutations (P = 0.0001) were independent factors for shorter PFS. CONCLUSIONS Genome-wide DNA methylation status is an independent factor associated with PFS in patients with mCRC treated with first-line EGFR inhibitors.
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Yang F, Shi J, Zhang L, Wang H, Li Y. Role of fibulin-1 gene promoter methylation in the carcinogenesis and development of tongue squamous cell carcinoma. Oral Surg Oral Med Oral Pathol Oral Radiol 2022; 133:432-440. [PMID: 35153187 DOI: 10.1016/j.oooo.2021.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 09/26/2021] [Accepted: 10/06/2021] [Indexed: 11/30/2022]
Abstract
OBJECTIVE Recently, fibulin-1 (FBLN1) has been shown to be downregulated in various cancers via promoter hypermethylation. Our study aimed to determine the expression and methylation status of FBLN1 in tongue squamous cell carcinoma (TSCC) tissues and cells. METHODS Methylation-specific polymerase chain reaction was implemented to detect the methylation status of the FBLN1 gene in TSCC tissues and Western blot analysis was used to detect the expression of FBLN1 protein. The human TSCC cell lines CAL27 and SCC9 were cultured in vitro and treated with 5-aza-deoxycytidine (5-Aza-dC). CCK-8, colony formation, and Transwell assays were performed to test TSCC cell proliferation, migration, and invasion following 5-Aza-dC treatment or overexpression of FBLN1, which was further verified in in vivo experiments. RESULTS FBLN1 was hypermethylated and the protein expression was reduced in TSCC tissues. After human TSCC cell lines (CAL27 and SCC9) were treated with 5-Aza-dC or overexpressed FBLN1, FBLN1 expression was upregulated and the TSCC cell proliferation, migration, and invasion abilities were suppressed. In vivo experiments further showed that demethylation or overexpression of FBLN1 slowed tumor growth in nude mice. CONCLUSION This study demonstrated that 5-Aza-dC treatment or overexpression of FBLN1 inhibited the growth of human TSCC.
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Affiliation(s)
- Fang Yang
- Department of Oncology, Daqing Oilfield General Hospital, Daqing, China
| | - Jing Shi
- Department of Stomatology, Daqing Oilfield General Hospital, Daqing, China
| | - Liangyu Zhang
- Department of Oncology, Daqing Oilfield General Hospital, Daqing, China.
| | - Hongyan Wang
- Department of Stomatology, Daqing Oilfield General Hospital, Daqing, China
| | - Yang Li
- Department of Stomatology, Daqing Oilfield General Hospital, Daqing, China
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Abstract
The landmark paper by Kane and colleagues was the first report of DNA methylation in the promoter of the human MLH1 gene in sporadic colon cancers with mismatch repair (MMR) deficiency. In both cell lines and primary tumors, promoter methylation was associated with loss of MLH1 protein expression and with a lack of mutations in the MLH1 coding region. Together with subsequent papers that showed that this methylation was directly responsible for loss of MLH1 expression and MMR deficiency, the observation expanded the two-hit hypothesis of tumor suppressor gene loss in cancer to include both genetic and epigenetic mechanisms of gene inactivation. More broadly, the paper contributed to normalization of the hypothesis of an epigenetic basis for cancer development. See related article by Kane and colleagues, Cancer Res 1997;57:808-11.
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Laurent A, Madigou T, Bizot M, Turpin M, Palierne G, Mahé E, Guimard S, Métivier R, Avner S, Le Péron C, Salbert G. TET2-mediated epigenetic reprogramming of breast cancer cells impairs lysosome biogenesis. Life Sci Alliance 2022; 5:5/7/e202101283. [PMID: 35351824 PMCID: PMC8963717 DOI: 10.26508/lsa.202101283] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 03/11/2022] [Accepted: 03/14/2022] [Indexed: 11/24/2022] Open
Abstract
TET2-mediated oxidation of 5-methylcytosine establishes an antiviral state and contributes to MYC-dependent down-regulation of genes involved in lysosome biogenesis and function in breast cancer cells. Methylation and demethylation of cytosines in DNA are believed to act as keystones of cell-specific gene expression by controlling the chromatin structure and accessibility to transcription factors. Cancer cells have their own transcriptional programs, and we sought to alter such a cancer-specific program by enforcing expression of the catalytic domain (CD) of the methylcytosine dioxygenase TET2 in breast cancer cells. The TET2 CD decreased the tumorigenic potential of cancer cells through both activation and repression of a repertoire of genes that, interestingly, differed in part from the one observed upon treatment with the hypomethylating agent decitabine. In addition to promoting the establishment of an antiviral state, TET2 activated 5mC turnover at thousands of MYC-binding motifs and down-regulated a panel of known MYC-repressed genes involved in lysosome biogenesis and function. Thus, an extensive cross-talk between TET2 and the oncogenic transcription factor MYC establishes a lysosomal storage disease–like state that contributes to an exacerbated sensitivity to autophagy inducers.
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Affiliation(s)
- Audrey Laurent
- Université Rennes 1, CNRS UMR6290, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes, France
| | - Thierry Madigou
- Université Rennes 1, CNRS UMR6290, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes, France
| | - Maud Bizot
- Université Rennes 1, CNRS UMR6290, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes, France
| | - Marion Turpin
- Université Rennes 1, CNRS UMR6290, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes, France
| | - Gaëlle Palierne
- Université Rennes 1, CNRS UMR6290, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes, France
| | - Elise Mahé
- Université Rennes 1, CNRS UMR6290, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes, France
| | - Sarah Guimard
- Université Rennes 1, CNRS UMR6290, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes, France
| | - Raphaël Métivier
- Université Rennes 1, CNRS UMR6290, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes, France
| | - Stéphane Avner
- Université Rennes 1, CNRS UMR6290, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes, France
| | - Christine Le Péron
- Université Rennes 1, CNRS UMR6290, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes, France
| | - Gilles Salbert
- Université Rennes 1, CNRS UMR6290, Institut de Génétique et Développement de Rennes, Campus de Beaulieu, Rennes, France
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Rodríguez-Mejía LC, Romero-Estudillo I, Rivillas-Acevedo LA, French-Pacheco L, Silva-Martínez GA, Alvarado-Caudillo Y, Colín-Castelán D, Rodríguez-Ríos D, Wrobel K, Wrobel K, Lund G, Zaina S. The DNA Methyltransferase Inhibitor RG108 is Converted to Activator Following Conjugation with Short Peptides. Int J Pept Res Ther 2022. [DOI: 10.1007/s10989-022-10390-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Muthamilselvan S, Raghavendran A, Palaniappan A. Stage-differentiated ensemble modeling of DNA methylation landscapes uncovers salient biomarkers and prognostic signatures in colorectal cancer progression. PLoS One 2022; 17:e0249151. [PMID: 35202405 PMCID: PMC8870460 DOI: 10.1371/journal.pone.0249151] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 02/01/2022] [Indexed: 12/15/2022] Open
Abstract
Background Aberrant DNA methylation acts epigenetically to skew the gene transcription rate up or down, contributing to cancer etiology. A gap in our understanding concerns the epigenomics of stagewise cancer progression. In this study, we have developed a comprehensive computational framework for the stage-differentiated modelling of DNA methylation landscapes in colorectal cancer (CRC). Methods The methylation β-matrix was derived from the public-domain TCGA data, converted into M-value matrix, annotated with AJCC stages, and analysed for stage-salient genes using an ensemble of approaches involving stage-differentiated modelling of methylation patterns and/or expression patterns. Differentially methylated genes (DMGs) were identified using a contrast against controls (adjusted p-value <0.001 and |log fold-change of M-value| >2), and then filtered using a series of all possible pairwise stage contrasts (p-value <0.05) to obtain stage-salient DMGs. These were then subjected to a consensus analysis, followed by matching with clinical data and performing Kaplan–Meier survival analysis to evaluate the impact of methylation patterns of consensus stage-salient biomarkers on disease prognosis. Results We found significant genome-wide changes in methylation patterns in cancer cases relative to controls agnostic of stage. The stage-differentiated models yielded the following consensus salient genes: one stage-I gene (FBN1), one stage-II gene (FOXG1), one stage-III gene (HCN1) and four stage-IV genes (NELL1, ZNF135, FAM123A, LAMA1). All the biomarkers were significantly hypermethylated in the promoter regions, indicating down-regulation of expression and implying a putative CpG island Methylator Phenotype (CIMP) manifestation. A prognostic signature consisting of FBN1 and FOXG1 survived all the analytical filters, and represents a novel early-stage epigenetic biomarker / target. Conclusions We have designed and executed a workflow for stage-differentiated epigenomic analysis of colorectal cancer progression, and identified several stage-salient diagnostic biomarkers, and an early-stage prognostic biomarker panel. The study has led to the discovery of an alternative CIMP-like signature in colorectal cancer, reinforcing the role of CIMP drivers in tumor pathophysiology.
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Affiliation(s)
- Sangeetha Muthamilselvan
- Department of Bioinformatics, School of Chemical and BioTechnology, SASTRA Deemed University, Thanjavur, India
| | - Abirami Raghavendran
- Department of Bioinformatics, School of Chemical and BioTechnology, SASTRA Deemed University, Thanjavur, India
| | - Ashok Palaniappan
- Department of Bioinformatics, School of Chemical and BioTechnology, SASTRA Deemed University, Thanjavur, India
- * E-mail:
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Li M, Xiao Q, Venkatachalam N, Hofheinz RD, Veldwijk MR, Herskind C, Ebert MP, Zhan T. Predicting response to neoadjuvant chemoradiotherapy in rectal cancer: from biomarkers to tumor models. Ther Adv Med Oncol 2022; 14:17588359221077972. [PMID: 35222695 PMCID: PMC8864271 DOI: 10.1177/17588359221077972] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 01/14/2022] [Indexed: 12/24/2022] Open
Abstract
Colorectal cancer (CRC) is a major contributor to cancer-associated morbidity worldwide and over one-third of CRC is located in the rectum. Neoadjuvant chemoradiotherapy (nCRT) followed by surgical resection is commonly applied to treat locally advanced rectal cancer (LARC). In this review, we summarize current and novel concepts of neoadjuvant therapy for LARC such as total neoadjuvant therapy and describe how these developments impact treatment response. Moreover, as response to nCRT is highly divergent in rectal cancers, we discuss the role of potential predictive biomarkers. We review recent advances in biomarker discovery, from a clinical as well as a histopathological and molecular perspective. Furthermore, the role of emerging predictive biomarkers derived from the tumor environment such as immune cell composition and gut microbiome is presented. Finally, we describe how different tumor models such as patient-derived cancer organoids are used to identify novel predictive biomarkers for chemoradiotherapy (CRT) in rectal cancer.
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Affiliation(s)
- Moying Li
- Medical Faculty Mannheim, Heidelberg University, Mannheim
| | - Qiyun Xiao
- Department of Medicine II, Mannheim University Hospital, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Nachiyappan Venkatachalam
- Department of Medicine II, Mannheim University Hospital, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Ralf-Dieter Hofheinz
- Department of Medicine III, Mannheim University Hospital, Medical Faculty Mannheim, Heidelberg University, Mannheim, GermanyMannheim Cancer Center, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Marlon R. Veldwijk
- Department of Radiation Oncology, Mannheim University Hospital, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Carsten Herskind
- Department of Radiation Oncology, Mannheim University Hospital, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Matthias P. Ebert
- Department of Medicine II, Mannheim University Hospital, Medical Faculty Mannheim, Heidelberg University, Mannheim, GermanyMannheim Cancer Center, Medical Faculty Mannheim, Heidelberg University, Mannheim, GermanyDKFZ-Hector Cancer Institute, University Medical Center Mannheim, Mannheim, Germany
| | - Tianzuo Zhan
- Department of Internal Medicine II, Mannheim University Hospital, Medical Faculty Mannheim, Heidelberg University, Theodor-Kutzer-Ufer 1-3, D-68167 Mannheim, GermanyMannheim Cancer Center, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
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Zhuang X, Chen B, Huang S, Han J, Zhou G, Xu S, Chen M, Zeng Z, Zhang S. Hypermethylation of miR-145 promoter-mediated SOX9-CLDN8 pathway regulates intestinal mucosal barrier in Crohn's disease. EBioMedicine 2022; 76:103846. [PMID: 35124427 PMCID: PMC8829091 DOI: 10.1016/j.ebiom.2022.103846] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/12/2022] [Accepted: 01/13/2022] [Indexed: 12/20/2022] Open
Abstract
Background Intestinal barrier impairment plays an essential role in the pathogenesis of Crohn's disease (CD), and claudins (CLDNs) dysfunction contributes to intestinal mucosa injury. SOX9, an important transcription factor, is upregulated in the disease-affected colon of patients with CD; however, its precise role in CD remains largely unknown. Our aim was to explore the interaction between SOX9 and CLDNs, and further elucidate the underlying mechanisms in CD. Methods SOX9 expression in patients with CD was evaluated using quantitative polymerase chain reaction, immunoblotting, and immunohistochemistry. The regulatory relationship between SOX9 and CLDNs was analyzed via a dual-luciferase reporter assay, chromatin immunoprecipitation, overexpression, and RNA interference methods. MicroRNAs (miRNAs) involved in the SOX9-CLDN pathway were predicted with bioinformatics analysis, and the upstream molecular mechanism was interpreted using MassARRAY methylation detection. Findings Upregulated expression of SOX9 in the disease-affected intestine mucosa was identified in both patients with CD and mice challenged with trinitrobenzene sulfonic acid (TNBS). SOX9 negatively regulated the expression of CLDN8, accompanying reduced intestinal permeability. MiR-145-5p downregulation was found in patients with CD and TNBS-induced colitis mice owing to an aberrant miR-145 promoter hypermethylation, which subsequently interfered the SOX9-CLDN8 pathway. MiR-145-5p agomir treatment alleviated TNBS-induced colitis in wild-type mice by inhibiting Sox9 expression and restoring Cldn8 expression, whereas similar findings were not apparent in the Cldn8−/− mice. Interpretation SOX9 mediates the crosstalk between upstream miR-145-5p and downstream CLDN8, and further impairs intestinal mucosal barrier homeostasis in CD. Targeting the miR-145-5p/SOX9/CLDN8 pathway represents a promising therapeutic strategy for CD. Funding The National Natural Science Foundation of China (#81870374, #81670498, #81630018, #82070538, #8210031148), the Guangdong Science and Technology (#2017A030306021, #2020A1515111087), the Guangzhou Science and Technology Department (#202002030041), and the Fundamental Research Funds for the Central Universities (#19ykzd11).
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Affiliation(s)
- Xiaojun Zhuang
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Baili Chen
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Shanshan Huang
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jing Han
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Gaoshi Zhou
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Shu Xu
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Minhu Chen
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Zhirong Zeng
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China.
| | - Shenghong Zhang
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China.
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ARID1A loss-of-function induces CpG island methylator phenotype. Cancer Lett 2022; 532:215587. [DOI: 10.1016/j.canlet.2022.215587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 11/26/2021] [Accepted: 02/03/2022] [Indexed: 11/22/2022]
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Mundy-Bosse BL, Weigel C, Wu YZ, Abdelbaky S, Youssef Y, Casas SB, Polley N, Ernst G, Young KA, McConnell KK, Nalin AP, Wu KG, Broughton M, Lordo MR, Altynova E, Hegewisch-Solloa E, Enriquez-Vera DY, Dueñas D, Barrionuevo C, Yu SC, Saleem A, Suarez CJ, Briercheck EL, Molina-Kirsch H, Loughran TP, Weichenhan D, Plass C, Reneau JC, Mace EM, Gamboa FV, Weinstock DM, Natkunam Y, Caligiuri MA, Mishra A, Porcu P, Baiocchi RA, Brammer JE, Freud AG, Oakes CC. Identification and targeting of the developmental blockade in extranodal natural killer/T cell lymphoma. Blood Cancer Discov 2022; 3:154-169. [PMID: 35247900 PMCID: PMC9414823 DOI: 10.1158/2643-3230.bcd-21-0098] [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: 06/15/2021] [Revised: 12/01/2021] [Accepted: 01/24/2022] [Indexed: 11/16/2022] Open
Abstract
Extranodal natural killer/T-cell lymphoma (ENKTL) is an aggressive, rare lymphoma of natural killer (NK) cell origin with poor clinical outcomes. Here we used phenotypic and molecular profiling, including epigenetic analyses, to investigate how ENKTL ontogeny relates to normal NK-cell development. We demonstrate that neoplastic NK cells are stably, but reversibly, arrested at earlier stages of NK-cell maturation. Genes downregulated in the most epigenetic immature tumors were associated with polycomb silencing along with genomic gain and overexpression of EZH2. ENKTL cells exhibited genome-wide DNA hypermethylation. Tumor-specific DNA methylation gains were associated with polycomb-marked regions, involving extensive gene silencing and loss of transcription factor binding. To investigate therapeutic targeting, we treated novel patient-derived xenograft (PDX) models of ENKTL with the DNA hypomethylating agent, 5-azacytidine. Treatment led to reexpression of NK-cell developmental genes, phenotypic NK-cell differentiation, and prolongation of survival. These studies lay the foundation for epigenetic-directed therapy in ENKTL. SIGNIFICANCE Through epigenetic and transcriptomic analyses of ENKTL, a rare, aggressive malignancy, along with normal NK-cell developmental intermediates, we identified that extreme DNA hypermethylation targets genes required for NK-cell development. Disrupting this epigenetic blockade in novel PDX models led to ENKTL differentiation and improved survival. This article is highlighted in the In This Issue feature, p. 85.
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Affiliation(s)
- Bethany L. Mundy-Bosse
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio
- The Comprehensive Cancer Center, The James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, Ohio
- Corresponding Authors: Bethany L. Mundy-Bosse, The Ohio State University James Comprehensive Cancer Center, 882 Biomedical Research Tower, 460 West 12th Avenue, Columbus, OH 43210. Phone: 614-688-6564; E-mail: ; Aharon G. Freud, The Ohio State University James Comprehensive Cancer Center, 892 Biomedical Research Tower, 460 West 12th Avenue, Columbus, OH 43210. Phone: 614-293-7904; E-mail: ; and Christopher C. Oakes, The Ohio State University James Comprehensive Cancer Center, 455 OSU CCC/Wiseman Hall, 410 West 12th Avenue, Columbus, OH 43210. Phone: 614-685-9284; E-mail:
| | - Christoph Weigel
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio
- The Comprehensive Cancer Center, The James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, Ohio
| | - Yue-Zhong Wu
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio
- The Comprehensive Cancer Center, The James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, Ohio
| | - Salma Abdelbaky
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio
- The Comprehensive Cancer Center, The James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, Ohio
| | - Youssef Youssef
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio
| | - Susana Beceiro Casas
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio
| | - Nicholas Polley
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio
| | - Gabrielle Ernst
- The Comprehensive Cancer Center, The James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, Ohio
| | - Karen A. Young
- The Comprehensive Cancer Center, The James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, Ohio
| | - Kathleen K. McConnell
- The Comprehensive Cancer Center, The James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, Ohio
| | - Ansel P. Nalin
- Medical Scientist Training Program, The Ohio State University, Columbus, Ohio
| | - Kevin G. Wu
- The Comprehensive Cancer Center, The James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, Ohio
| | - Megan Broughton
- The Comprehensive Cancer Center, The James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, Ohio
| | - Matthew R. Lordo
- Medical Scientist Training Program, The Ohio State University, Columbus, Ohio
| | - Ekaterina Altynova
- The Comprehensive Cancer Center, The James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, Ohio
| | - Everardo Hegewisch-Solloa
- Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York
| | | | - Daniela Dueñas
- Instituto Nacional de Enfermedades Neoplasticas, Lima, Peru
| | | | - Shan-Chi Yu
- Department of Pathology, National Taiwan University Hospital, Taipei, Taiwan
| | - Atif Saleem
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Carlos J. Suarez
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Edward L. Briercheck
- Department of Medicine, Division of Hematology and Medical Oncology, Fred Hutchinson Cancer Research Institute and the University of Washington, Seattle, Washington
| | | | - Thomas P. Loughran
- Division of Hematology, Department of Medicine, University of Virginia Cancer Center, Charlottesville, Virginia
| | - Dieter Weichenhan
- Division of Epigenomics, The German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christoph Plass
- Division of Epigenomics, The German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - John C. Reneau
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio
- The Comprehensive Cancer Center, The James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, Ohio
| | - Emily M. Mace
- Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York
| | - Fabiola Valvert Gamboa
- Department of Medical Oncology, Liga Nacional Contra el Cáncer, Guatemala City, Guatemala
| | - David M. Weinstock
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Yasodha Natkunam
- Department of Pathology, Stanford University School of Medicine, Stanford, California
| | - Michael A. Caligiuri
- Department of Hematology and Hematopoietic Cell Transplantation, City of Hope National Medical Center, Los Angeles, California
| | - Anjali Mishra
- Division of Hematologic Malignancies and Hematopoietic Stem Cell Transplantation, Department of Medical Oncology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Pierluigi Porcu
- Division of Hematologic Malignancies and Hematopoietic Stem Cell Transplantation, Department of Medical Oncology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Robert A. Baiocchi
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio
- The Comprehensive Cancer Center, The James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, Ohio
| | - Jonathan E. Brammer
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio
- The Comprehensive Cancer Center, The James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, Ohio
| | - Aharon G. Freud
- The Comprehensive Cancer Center, The James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, Ohio
- Department of Pathology, The Ohio State University, Columbus, Ohio
- Corresponding Authors: Bethany L. Mundy-Bosse, The Ohio State University James Comprehensive Cancer Center, 882 Biomedical Research Tower, 460 West 12th Avenue, Columbus, OH 43210. Phone: 614-688-6564; E-mail: ; Aharon G. Freud, The Ohio State University James Comprehensive Cancer Center, 892 Biomedical Research Tower, 460 West 12th Avenue, Columbus, OH 43210. Phone: 614-293-7904; E-mail: ; and Christopher C. Oakes, The Ohio State University James Comprehensive Cancer Center, 455 OSU CCC/Wiseman Hall, 410 West 12th Avenue, Columbus, OH 43210. Phone: 614-685-9284; E-mail:
| | - Christopher C. Oakes
- Division of Hematology, Department of Internal Medicine, The Ohio State University, Columbus, Ohio
- The Comprehensive Cancer Center, The James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, Ohio
- Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio
- Corresponding Authors: Bethany L. Mundy-Bosse, The Ohio State University James Comprehensive Cancer Center, 882 Biomedical Research Tower, 460 West 12th Avenue, Columbus, OH 43210. Phone: 614-688-6564; E-mail: ; Aharon G. Freud, The Ohio State University James Comprehensive Cancer Center, 892 Biomedical Research Tower, 460 West 12th Avenue, Columbus, OH 43210. Phone: 614-293-7904; E-mail: ; and Christopher C. Oakes, The Ohio State University James Comprehensive Cancer Center, 455 OSU CCC/Wiseman Hall, 410 West 12th Avenue, Columbus, OH 43210. Phone: 614-685-9284; E-mail:
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Paweł K, Maria Małgorzata S. CpG Island Methylator Phenotype-A Hope for the Future or a Road to Nowhere? Int J Mol Sci 2022; 23:ijms23020830. [PMID: 35055016 PMCID: PMC8777692 DOI: 10.3390/ijms23020830] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 12/01/2021] [Accepted: 12/07/2021] [Indexed: 02/06/2023] Open
Abstract
The CpG island methylator phenotype (CIMP) can be regarded as the most notable emanation of epigenetic instability in cancer. Since its discovery in the late 1990s, CIMP has been extensively studied, mainly in colorectal cancers (CRC) and gliomas. Consequently, knowledge on molecular and pathological characteristics of CIMP in CRC and other tumour types has rapidly expanded. Concordant and widespread hypermethylation of multiple CpG islands observed in CIMP in multiple cancers raised hopes for future epigenetically based diagnostics and treatments of solid tumours. However, studies on CIMP in solid tumours were hampered by a lack of generalisability and reproducibility of epigenetic markers. Moreover, CIMP was not a satisfactory marker in predicting clinical outcomes. The idea of targeting epigenetic abnormalities such as CIMP for cancer therapy has not been implemented for solid tumours, either. Twenty-one years after its discovery, we aim to cover both the fundamental and new aspects of CIMP and its future application as a diagnostic marker and target in anticancer therapies.
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Complete pathological response of colorectal peritoneal metastases in Lynch syndrome after immunotherapy case report: is a paradigm shift in cytoreductive surgery needed? BMC Gastroenterol 2022; 22:17. [PMID: 35012456 PMCID: PMC8751316 DOI: 10.1186/s12876-021-02084-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Accepted: 12/24/2021] [Indexed: 11/30/2022] Open
Abstract
Background We report the first case of a patient affected by peritoneal metastases from colon cancer, arising in the context of Lynch syndrome with pathological complete response. The patient was treated with immunotherapy and cytoreductive surgery. This paper discusses the implications of these novel therapies for the management of PM. Case presentation A 50-year-old man affected by Lynch syndrome was referred to our institution for metachronous peritoneal recurrence of ascending colon adenocarcinoma. As a second-line treatment, he received Nivolumab therapy with stable disease. Patient underwent cytoreductive surgery with residual disease and a pathological complete response. Flow cytometry described a particular immune sub-population response. There was no evidence of disease progression after nine months. Conclusion This is the first report of a Lynch patient affected by peritoneal metastases of colorectal cancer, treated with cytoreductive surgery (CRS) and resulting in a pathological complete response after immune checkpoint inhibitors treatment (ICIs). This case report may suggest that patients with peculiar immunological features could benefit from a tailored approach, since “classical” CRS paradigms may not effectively predict the clinical outcome. Further large-scale studies are needed to determine the correct operative management of such patients (tailored or “standard” CRS), defining the correct surgical timing and eventual discontinuation of ICI therapy after surgery. Supplementary Information The online version contains supplementary material available at 10.1186/s12876-021-02084-x.
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Gu P, Zeng Y, Ma W, Zhang W, Liu Y, Guo F, Ruan X, Chi J, Zheng X, Gao M. Characterization of the CpG island methylator phenotype subclass in papillary thyroid carcinoma. Front Endocrinol (Lausanne) 2022; 13:1008301. [PMID: 36353231 PMCID: PMC9637834 DOI: 10.3389/fendo.2022.1008301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 10/04/2022] [Indexed: 11/28/2022] Open
Abstract
CpG island methylator phenotype (CIMP), characterized by the concurrent and widespread hypermethylation of a cluster of CpGs, has been reported to play an important role in carcinogenesis. Limited studies have explored the role of CIMP in papillary thyroid carcinomas (PTCs). Here, in genome-wide DNA methylation analysis of 350 primary PTCs from the Cancer Genome Atlas database that were assessed using the Illumina HumanMethylation450K platform, our study helps to identify two subtypes displayed markedly distinct DNA methylation levels, termed CIMP (high levels of DNA methylation) and nCIMP subgroup (low levels of DNA methylation). Interestingly, PTCs with CIMP tend to have a higher degree of malignancy, since this subtype was tightly associated with older age, advanced pathological stage, and lymph node metastasis (all P < 0.05). Differential methylation analysis showed a broad methylation gain in CIMP and subsequent generalized gene set testing analysis based on the significantly methylated probes in CIMP showed remarkable enrichment in epithelial mesenchymal transition and angiogenesis hallmark pathways, confirming that the CIMP phenotype may promote the tumor progression from another perspective. Analysis of tumor microenvironment showed that CIMP PTCs are in an immune-depletion status, which may affect the effectiveness of immunotherapy. Genetically, the significantly higher tumor mutation burden and copy number alteration both at the genome and focal level confirmed the genomic heterogeneity and chromosomal instability of CIMP. tumor Corresponding to the above findings, PTC patients with CIMP showed remarkable poor clinical outcome as compared to nCIMP regarding overall survival and progression-free survival. More importantly, CIMP was associated with worse survival independent of known prognostic factors.
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Affiliation(s)
- Pengfei Gu
- Department of Thyroid and Neck Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin, China
| | - Yu Zeng
- Department of Thyroid and Neck Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin, China
| | - Weike Ma
- Department of Thyroid and Neck Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin, China
| | - Wei Zhang
- Department of Thyroid and Neck Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin, China
| | - Yu Liu
- Department of Thyroid and Neck Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin, China
| | - Fengli Guo
- Department of Thyroid and Neck Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin, China
| | - Xianhui Ruan
- Department of Thyroid and Neck Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin, China
| | - Jiadong Chi
- Department of Thyroid and Neck Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin, China
- *Correspondence: Jiadong Chi, ; Xiangqian Zheng, ; Ming Gao,
| | - Xiangqian Zheng
- Department of Thyroid and Neck Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin, China
- *Correspondence: Jiadong Chi, ; Xiangqian Zheng, ; Ming Gao,
| | - Ming Gao
- Department of Thyroid and Neck Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin, China
- Department of Thyroid and Breast Surgery, Tianjin Union Medical Center, Tianjin, China
- Tianjin Key Laboratory of General Surgery in Construction, Tianjin Union Medical Center, Tianjin, China
- *Correspondence: Jiadong Chi, ; Xiangqian Zheng, ; Ming Gao,
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Harada H, Nie Y, Araki I, Soeno T, Chuman M, Washio M, Sakuraya M, Ushiku H, Niihara M, Hosoda K, Kumamoto Y, Naitoh T, Sangai T, Hiki N, Yamashita K. Haploinsufficiency by minute MutL homolog 1 promoter DNA methylation may represent unique phenotypes of microsatellite instability-gastric carcinogenesis. PLoS One 2021; 16:e0260303. [PMID: 34936649 PMCID: PMC8694418 DOI: 10.1371/journal.pone.0260303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 11/06/2021] [Indexed: 11/19/2022] Open
Abstract
Promoter DNA methylation of MutL homolog 1 (MLH1) is considered to play a causative role in microsatellite instability (MSI) carcinogenesis in primary gastric cancer, and a high MSI status is associated with treatment sensitivity to human cancers. Nevertheless, clinicopathological analysis is defective for MLH1 methylation status in a quantitative manner. We newly developed quantitative methylation specific PCR using a TaqMan probe and applied it to 138 patients with primary gastric cancer who underwent gastrectomy in addition to basic molecular features such as MSI, Epstein Barr virus, and other DNA methylation status. (1) In primary gastric cancer, median methylation value was 0.055, ranging from 0 to 124.3. First, MLH1 hypermethylation was strongly correlated with MSI-High/MSI-Low status and suppressed immunostaining (P < 0.0001). (2) The MLH1 hypermethylation was associated with advanced age (P = 0.0048), antral location (P = 0.0486), synchronous multiple gastric cancer (P = 0.0001), and differentiated histology (P = 0.028). (3) Log-rank plot analysis identified the most relevant cut-off value (0.23) to reflect gentle phenotypes in MLH1 hypermethylation cases (P = 0.0019), especially in advanced gastric cancer (P = 0.0132), which are designated as haploinsufficiency of MSI (MSI-haplo) phenotype in this study. (4) In synchronous multiple gastric cancer, MLH1 hypermethylation was not necessarily confirmed as field cancerization. (5) MSI-haplo defined by MLH1 methylation status represented distinct prognostic phenotype even after molecular classifications. MLH1 hypermethylation designated as MSI-haplo may represent unique prognostic phenotype during gastric carcinogenesis.
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Affiliation(s)
- Hiroki Harada
- Department of Upper-gastrointestinal Surgery, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Yusuke Nie
- Department of General, Pediatric and Hepatobiliary-Pancreatic Surgery, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Ippeita Araki
- Department of Upper-gastrointestinal Surgery, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Takafumi Soeno
- Department of Upper-gastrointestinal Surgery, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Motohiro Chuman
- Department of Upper-gastrointestinal Surgery, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Marie Washio
- Department of Upper-gastrointestinal Surgery, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Mikiko Sakuraya
- Department of Upper-gastrointestinal Surgery, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Hideki Ushiku
- Department of Upper-gastrointestinal Surgery, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Masahiro Niihara
- Department of Upper-gastrointestinal Surgery, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Kei Hosoda
- Department of Upper-gastrointestinal Surgery, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Yusuke Kumamoto
- Department of General, Pediatric and Hepatobiliary-Pancreatic Surgery, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Takeshi Naitoh
- Department of Lower Gastrointestinal Surgery, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Takafumi Sangai
- Department of Breast and Thyroid Surgery, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Naoki Hiki
- Department of Upper-gastrointestinal Surgery, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Keishi Yamashita
- Department of Upper-gastrointestinal Surgery, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
- Division of Advanced Surgical Oncology, Department of Research and Development Center for New Medical Frontiers, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
- * E-mail:
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50
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Lee JY, Park JW. Modified cytosines versus cytosine in a DNA polymerase: retrieving thermodynamic and kinetic constants at the single molecule level. Analyst 2021; 147:341-348. [PMID: 34935781 DOI: 10.1039/d1an02108g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNA methylation plays key roles in various areas, such as gene expression, regulation, epigenetics, and cancers. Since 5-methylcytosine (5mC) is commonly present in methylated DNA, characterizing the binding kinetics and thermodynamics of the nucleotide to the enzymatic pocket can help to understand the DNA replication process. Furthermore, 5-carboxycytosine (5caC) is a form that appears through the iterative oxidation of 5mC, and its effect on the DNA replication process is still not well known. Here, we immobilized a DNA polymerase (DNAP) with an orientation control on a tip of an atomic force microscope (AFM), and observed the interaction between the immobilized deoxyguanosine triphosphate (dGTP) on the surface and the DNAP in the presence of a DNA duplex. The interaction probability increased as the concentration of the DNA strand, and the affinity constant between the DNAP and DNA was obtained by fitting the change. Increasing the concentration of dGTP in solution diminished the interaction probability, and a fitting allowed us to retrieve the affinity constant between dGTP and the DNAP holding the DNA in the reaction pocket. Because the dissociation constant could be obtained through the loading rate dependence of the unbinding force value, both affinity and kinetic constants for cytosine (C), 5mC, and 5caC in the DNAP were compared in the light of the steric and electronic effect of the substituents at 5-position of cytosine.
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Affiliation(s)
- Ji Yoon Lee
- Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea.
| | - Joon Won Park
- Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea. .,Institute of Convergence Science, Yonsei University, 50 Yonsei-ro Seodaemun-gu, Seoul, 03722, Republic of Korea
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