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Saleem MA, Mustafa MS. Promoter Hypermethylation of the BRCA1 Gene as a Novel Biomarker for Prostate Cancer. Cureus 2024; 16:e66467. [PMID: 39246954 PMCID: PMC11380563 DOI: 10.7759/cureus.66467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/07/2024] [Indexed: 09/10/2024] Open
Abstract
Prostate cancer (PCa) is recognized as one of the most common malignancies that greatly affects the male population globally. Breast cancer gene 1 (BRCA1) is an important tumor suppressor gene that plays a central role in the maintenance of genomic integrity by promoting the repair of double-strand breaks of DNA. Here, we present a pilot study to examine the promoter methylation and gene expression of the BRCA1 gene in patients with PCa in Erbil governorate, Iraq. The collection of samples took place in Erbil City, Iraq, specifically at Rizgary Hospital, PAR Hospital, and Al-Mufti's private laboratory. A total of 40 tissue samples were collected from age-matched individuals, comprising 30 pathologically confirmed PCa cases and 10 normal prostatic tissue taken from individuals who, during diagnosis, were found to be negative for PCa. Data on demographic and clinical information, such as pathological stage, age, and prostate-specific antigen (PSA) level, were gathered from the medical records. The impact of the promoter methylation was forecasted using the DNA bisulfite conversion technique and methyl-specific PCR (MSP) with specific primers for the BRCA1 promoter region. The assessment of BRCA1 expression was conducted using quantitative real-time PCR (qPCR). Among the 30 patients examined, 76.6% (23 cases) were found to have BRCA1 promoter methylation, and none of the normal tissues appeared to have DNA methylation. BRCA1 promoter methylation was positively associated with the advanced stage of disease (p=0.01) and Gleason score (p=0.007). The analysis revealed a significant downregulation of the BRCA1 gene expression in methylated tumor samples as compared to non-methylated tumors and normal tissues, suggesting the role of epigenetic silencing. To the best of our knowledge, this is the first study investigating methylation status and level of BRCA1 mRNA transcripts among PCa patients in Iraq. Our findings suggest that promoter hypermethylation of the BRCA1 gene could serve as a viable biomarker for PCa, marking a significant discovery.
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Affiliation(s)
- Mohammed A Saleem
- Department of Biology, College of Science, Salahaddin University-Erbil, Erbil, IRQ
| | - Mustafa S Mustafa
- Department of Biology, College of Science, Salahaddin University-Erbil, Erbil, IRQ
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Kim Y, Ko JY, Kong HK, Lee M, Chung W, Lim S, Son D, Oh S, Park JW, Kim DY, Lee M, Han W, Park WY, Yoo KH, Park JH. Hypomethylation of ATP1A1 Is Associated with Poor Prognosis and Cancer Progression in Triple-Negative Breast Cancer. Cancers (Basel) 2024; 16:1666. [PMID: 38730618 PMCID: PMC11083557 DOI: 10.3390/cancers16091666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 04/15/2024] [Accepted: 04/24/2024] [Indexed: 05/13/2024] Open
Abstract
Dysregulated DNA methylation in cancer is critical in the transcription machinery associated with cancer progression. Triple-negative breast cancer (TNBC) is the most aggressive breast cancer subtype, but no treatment targeting TNBC biomarkers has yet been developed. To identify specific DNA methylation patterns in TNBC, methyl-binding domain protein 2 (MBD) sequencing data were compared in TNBC and the three other major breast cancer subtypes. Integrated analysis of DNA methylation and gene expression identified a gene set showing a correlation between DNA methylation and gene expression. ATPase Na+/K+-transporting subunit alpha 1 (ATP1A1) was found to be specifically hypomethylated in the coding sequence (CDS) region and to show increased expression in TNBC. The Cancer Genome Atlas (TCGA) database also showed that hypomethylation and high expression of ATP1A1 were strongly associated with poor survival in patients with TNBC. Furthermore, ATP1A1 knockdown significantly reduced the viability and tumor-sphere formation of TNBC cells. These results suggest that the hypomethylation and overexpression of ATP1A1 could be a prognostic marker in TNBC and that the manipulation of ATP1A1 expression could be a therapeutic target in this disease.
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Affiliation(s)
- Yesol Kim
- Department of Biological Science, Research Institute of Women’s Health, Sookmyung Women’s University, Seoul 04310, Republic of Korea; (Y.K.); (J.Y.K.)
| | - Je Yeong Ko
- Department of Biological Science, Research Institute of Women’s Health, Sookmyung Women’s University, Seoul 04310, Republic of Korea; (Y.K.); (J.Y.K.)
| | - Hyun Kyung Kong
- Department of Biological Science, Research Institute of Women’s Health, Sookmyung Women’s University, Seoul 04310, Republic of Korea; (Y.K.); (J.Y.K.)
| | - Minyoung Lee
- Department of Biological Science, Research Institute of Women’s Health, Sookmyung Women’s University, Seoul 04310, Republic of Korea; (Y.K.); (J.Y.K.)
| | - Woosung Chung
- Samsung Genome Institute, Samsung Medical Center, Seoul 06351, Republic of Korea
| | - Sera Lim
- Department of Biological Science, Research Institute of Women’s Health, Sookmyung Women’s University, Seoul 04310, Republic of Korea; (Y.K.); (J.Y.K.)
| | - Dasom Son
- Department of Biological Science, Research Institute of Women’s Health, Sookmyung Women’s University, Seoul 04310, Republic of Korea; (Y.K.); (J.Y.K.)
| | - Sumin Oh
- Department of Biological Science, Research Institute of Women’s Health, Sookmyung Women’s University, Seoul 04310, Republic of Korea; (Y.K.); (J.Y.K.)
| | - Jee Won Park
- Department of Biological Science, Research Institute of Women’s Health, Sookmyung Women’s University, Seoul 04310, Republic of Korea; (Y.K.); (J.Y.K.)
| | - Do Yeon Kim
- Department of Biological Science, Research Institute of Women’s Health, Sookmyung Women’s University, Seoul 04310, Republic of Korea; (Y.K.); (J.Y.K.)
| | - Minju Lee
- Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Wonshik Han
- Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
- Department of Surgery, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Woong-Yang Park
- Samsung Genome Institute, Samsung Medical Center, Seoul 06351, Republic of Korea
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences & Technology, Sungkyunkwan University, Seoul 06355, Republic of Korea
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Kyung Hyun Yoo
- Department of Biological Science, Research Institute of Women’s Health, Sookmyung Women’s University, Seoul 04310, Republic of Korea; (Y.K.); (J.Y.K.)
| | - Jong Hoon Park
- Department of Biological Science, Research Institute of Women’s Health, Sookmyung Women’s University, Seoul 04310, Republic of Korea; (Y.K.); (J.Y.K.)
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Bagheri M, Lee MK, Muller KE, Miller TW, Pattabiraman DR, Christensen BC. Alteration of DNA methyltransferases by eribulin elicits broad DNA methylation changes with potential therapeutic implications for triple-negative breast cancer. Epigenomics 2024; 16:293-308. [PMID: 38356412 PMCID: PMC10910603 DOI: 10.2217/epi-2023-0339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 01/23/2024] [Indexed: 02/16/2024] Open
Abstract
Background: Triple-negative breast cancer (TNBC) is an aggressive disease with limited treatment options. Eribulin, a chemotherapeutic drug, induces epigenetic changes in cancer cells, suggesting a unique mechanism of action. Materials & methods: MDA-MB 231 cells were treated with eribulin and paclitaxel, and the samples from 53 patients treated with neoadjuvant eribulin were compared with those from 14 patients who received the standard-of-care treatment using immunohistochemistry. Results: Eribulin treatment caused significant DNA methylation changes in drug-tolerant persister TNBC cells, and it also elicited changes in the expression levels of epigenetic modifiers (DNMT1, TET1, DNMT3A/B) in vitro and in primary TNBC tumors. Conclusion: These findings provide new insights into eribulin's mechanism of action and potential biomarkers for predicting TNBC treatment response.
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Affiliation(s)
- Meisam Bagheri
- Department of Molecular & Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
- Dartmouth Cancer Center, Lebanon, NH 03756, USA
| | - Min Kyung Lee
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - Kristen E Muller
- Dartmouth Cancer Center, Lebanon, NH 03756, USA
- Department of Pathology, Geisel School of Medicine at Dartmouth, Lebanon NH 03756, USA
| | - Todd W Miller
- Department of Molecular & Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
- Dartmouth Cancer Center, Lebanon, NH 03756, USA
- Department of Pharmacology & Toxicology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Diwakar R Pattabiraman
- Department of Molecular & Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
- Dartmouth Cancer Center, Lebanon, NH 03756, USA
| | - Brock C Christensen
- Department of Molecular & Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
- Department of Community & Family Medicine, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
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Tahara S, Tahara T, Yamazaki J, Shijimaya T, Horiguchi N, Funasaka K, Fukui T, Nakagawa Y, Shibata T, Naganuma M, Tsukamoto T, Ohmiya N. Helicobacter pylori infection associated DNA methylation in primary gastric cancer significantly correlates with specific molecular and clinicopathological features. Mol Carcinog 2024; 63:266-274. [PMID: 37846801 DOI: 10.1002/mc.23650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 08/23/2023] [Accepted: 10/01/2023] [Indexed: 10/18/2023]
Abstract
Helicobacter pylori induces DNA methylation in gastric mucosa, which links to gastric cancer (GC) risk. In contrast, CpG island methylator phenotype (CIMP) is defined as high levels of cancer-specific methylation and provides distinct molecular and clinicopathological features of GC. The association between those two types of methylation in GC remains unclear. We examined DNA methylation of well-validated H. pylori infection associated genes in GC and its adjacent mucosa and investigated its association with CIMP, various molecular subtypes and clinical features. We studied 50 candidate loci in 24 gastric samples to identify H. pylori infection associated genes. Identified loci were further examined in 624 gastric tissue from 217 primary GC, 217 adjacent mucosa, and 190 mucosae from cancer-free subjects. We identified five genes (IGF2, SLC16A2, SOX11, P2RX7, and MYOD1) as hypermethylated in H. pylori infected gastric mucosa. In non-neoplastic mucosa, methylation of H. pylori infection associated genes was higher in patients with GC than those without. In primary GC tissues, higher methylation of H. pylori infection associated genes correlated with CIMP-positive and its related features, such as MLH1 methylated cases. On the other hand, GC with lower methylation of these genes presented aggressive clinicopathological features including undifferentiated histopathology, advanced stage at diagnosis. H. pylori infection associated DNA methylation is correlated with CIMP, specific molecular and clinicopathological features in GC, supporting its utility as promising biomarker in this tumor type.
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Affiliation(s)
- Sayumi Tahara
- Department of Diagnostic Pathology I, Fujita Health University School of Medicine, Toyoake, Japan
| | - Tomomitsu Tahara
- Department of Gastroenterology, Fujita Health University School of Medicine, Toyoake, Japan
- Third Department of Internal Medicine, Kansai Medical University, Hirakata, Japan
| | - Jumpei Yamazaki
- Translational Research Unit, Veterinary Teaching Hospital, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
| | - Takuya Shijimaya
- Third Department of Internal Medicine, Kansai Medical University, Hirakata, Japan
| | - Noriyuki Horiguchi
- Department of Gastroenterology, Fujita Health University School of Medicine, Toyoake, Japan
| | - Kohei Funasaka
- Department of Gastroenterology, Fujita Health University School of Medicine, Toyoake, Japan
| | - Toshiro Fukui
- Third Department of Internal Medicine, Kansai Medical University, Hirakata, Japan
| | - Yoshihito Nakagawa
- Department of Gastroenterology, Fujita Health University School of Medicine, Toyoake, Japan
| | - Tomoyuki Shibata
- Department of Gastroenterology, Fujita Health University School of Medicine, Toyoake, Japan
| | - Makoto Naganuma
- Third Department of Internal Medicine, Kansai Medical University, Hirakata, Japan
| | - Tetsuya Tsukamoto
- Department of Diagnostic Pathology I, Fujita Health University School of Medicine, Toyoake, Japan
| | - Naoki Ohmiya
- Department of Advanced Endoscopy, Fujita Health University, Toyoake, Aichi, Japan
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Ma JJ, Xiang C, Zhu HQ, Bai BL, Wang P, Zhao GA. Expression and prognosis analysis of integrin subunit α3 (ITGA3) in papillary thyroid cancer. Heliyon 2024; 10:e23163. [PMID: 38163190 PMCID: PMC10756987 DOI: 10.1016/j.heliyon.2023.e23163] [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: 01/30/2023] [Revised: 11/23/2023] [Accepted: 11/28/2023] [Indexed: 01/03/2024] Open
Abstract
Integrin subunit α3 (ITGA3) is a member of the integrin family and interacts with extracellular matrix proteins. However, there have been few reports regarding the role of ITGA3 in papillary thyroid cancer. The expression levels of ITGA3 were firstly analyzed by bioinformatics tools and in vitro experiments, followed by evaluating its prognostic significance in papillary thyroid cancer patients using Kaplan-Meier, receiver operating characteristic, and Cox regression analyses. Then, cBioportal and GSCA databases were applied to evaluate genetic alterations of ITGA3. Functional enrichment analysis was conducted and the upstream miRNAs of ITGA3 were determined. The results showed that the ITGA3 mRNA and protein levels were higher in the papillary thyroid cancer group than those in the normal group (all P < 0.05). Moreover, ITGA3 performed well in distinguishing the recurrence-free survival (RFS) status and served as an independent prognostic factor of papillary thyroid cancer patients (P < 0.01). Besides, significant relations between ITGA3 and genetic alterations were observed (FDR <0.01). Functional enrichment analysis indicated ECM-receptor interaction and cell adhesion molecules were the shared regulatory pathways. Moreover, ITGA3 might be the target gene of hsa-miR-3129, hsa-miR-181d, hsa-miR-181b, hsa-miR-199a, and hsa-miR-199b. Of note, the ITGA3 mRNA level was reduced after has-miR-199b-3p/5p was overexpressed. In conclusion, ITGA3 could be a reliable biomarker and have potential value in predicting the RFS status of papillary thyroid cancer patients.
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Affiliation(s)
- Jun-jie Ma
- Department of Thyroid Surgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310009, Zhejiang, China
| | - Cheng Xiang
- Department of Thyroid Surgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310009, Zhejiang, China
| | - Heng-qing Zhu
- Department of Thyroid Surgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310009, Zhejiang, China
| | - Bing-long Bai
- Department of Thyroid Surgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310009, Zhejiang, China
| | - Ping Wang
- Department of Thyroid Surgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310009, Zhejiang, China
| | - Guan-an Zhao
- Department of Urology, Lishui City People's Hospital, Lishui 323000, Zhejiang, China
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Alvarez-Frutos L, Barriuso D, Duran M, Infante M, Kroemer G, Palacios-Ramirez R, Senovilla L. Multiomics insights on the onset, progression, and metastatic evolution of breast cancer. Front Oncol 2023; 13:1292046. [PMID: 38169859 PMCID: PMC10758476 DOI: 10.3389/fonc.2023.1292046] [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: 09/10/2023] [Accepted: 11/23/2023] [Indexed: 01/05/2024] Open
Abstract
Breast cancer is the most common malignant neoplasm in women. Despite progress to date, 700,000 women worldwide died of this disease in 2020. Apparently, the prognostic markers currently used in the clinic are not sufficient to determine the most appropriate treatment. For this reason, great efforts have been made in recent years to identify new molecular biomarkers that will allow more precise and personalized therapeutic decisions in both primary and recurrent breast cancers. These molecular biomarkers include genetic and post-transcriptional alterations, changes in protein expression, as well as metabolic, immunological or microbial changes identified by multiple omics technologies (e.g., genomics, epigenomics, transcriptomics, proteomics, glycomics, metabolomics, lipidomics, immunomics and microbiomics). This review summarizes studies based on omics analysis that have identified new biomarkers for diagnosis, patient stratification, differentiation between stages of tumor development (initiation, progression, and metastasis/recurrence), and their relevance for treatment selection. Furthermore, this review highlights the importance of clinical trials based on multiomics studies and the need to advance in this direction in order to establish personalized therapies and prolong disease-free survival of these patients in the future.
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Affiliation(s)
- Lucia Alvarez-Frutos
- Laboratory of Cell Stress and Immunosurveillance, Unidad de Excelencia Instituto de Biomedicina y Genética Molecular (IBGM), Universidad de Valladolid – Centro Superior de Investigaciones Cientificas (CSIC), Valladolid, Spain
| | - Daniel Barriuso
- Laboratory of Cell Stress and Immunosurveillance, Unidad de Excelencia Instituto de Biomedicina y Genética Molecular (IBGM), Universidad de Valladolid – Centro Superior de Investigaciones Cientificas (CSIC), Valladolid, Spain
| | - Mercedes Duran
- Laboratory of Molecular Genetics of Hereditary Cancer, Unidad de Excelencia Instituto de Biomedicina y Genética Molecular (IBGM), Universidad de Valladolid – Centro Superior de Investigaciones Cientificas (CSIC), Valladolid, Spain
| | - Mar Infante
- Laboratory of Molecular Genetics of Hereditary Cancer, Unidad de Excelencia Instituto de Biomedicina y Genética Molecular (IBGM), Universidad de Valladolid – Centro Superior de Investigaciones Cientificas (CSIC), Valladolid, Spain
| | - Guido Kroemer
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Université Paris Cité, Sorbonne Université, Inserm U1138, Institut Universitaire de France, Paris, France
- Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, Villejuif, France
- Department of Biology, Institut du Cancer Paris CARPEM, Hôpital Européen Georges Pompidou, Paris, France
| | - Roberto Palacios-Ramirez
- Laboratory of Cell Stress and Immunosurveillance, Unidad de Excelencia Instituto de Biomedicina y Genética Molecular (IBGM), Universidad de Valladolid – Centro Superior de Investigaciones Cientificas (CSIC), Valladolid, Spain
| | - Laura Senovilla
- Laboratory of Cell Stress and Immunosurveillance, Unidad de Excelencia Instituto de Biomedicina y Genética Molecular (IBGM), Universidad de Valladolid – Centro Superior de Investigaciones Cientificas (CSIC), Valladolid, Spain
- Centre de Recherche des Cordeliers, Equipe labellisée par la Ligue contre le cancer, Université Paris Cité, Sorbonne Université, Inserm U1138, Institut Universitaire de France, Paris, France
- Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, Villejuif, France
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Janin M, Davalos V, Esteller M. Cancer metastasis under the magnifying glass of epigenetics and epitranscriptomics. Cancer Metastasis Rev 2023; 42:1071-1112. [PMID: 37369946 PMCID: PMC10713773 DOI: 10.1007/s10555-023-10120-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023]
Abstract
Most of the cancer-associated mortality and morbidity can be attributed to metastasis. The role of epigenetic and epitranscriptomic alterations in cancer origin and progression has been extensively demonstrated during the last years. Both regulations share similar mechanisms driven by DNA or RNA modifiers, namely writers, readers, and erasers; enzymes responsible of respectively introducing, recognizing, or removing the epigenetic or epitranscriptomic modifications. Epigenetic regulation is achieved by DNA methylation, histone modifications, non-coding RNAs, chromatin accessibility, and enhancer reprogramming. In parallel, regulation at RNA level, named epitranscriptomic, is driven by a wide diversity of chemical modifications in mostly all RNA molecules. These two-layer regulatory mechanisms are finely controlled in normal tissue, and dysregulations are associated with every hallmark of human cancer. In this review, we provide an overview of the current state of knowledge regarding epigenetic and epitranscriptomic alterations governing tumor metastasis, and compare pathways regulated at DNA or RNA levels to shed light on a possible epi-crosstalk in cancer metastasis. A deeper understanding on these mechanisms could have important clinical implications for the prevention of advanced malignancies and the management of the disseminated diseases. Additionally, as these epi-alterations can potentially be reversed by small molecules or inhibitors against epi-modifiers, novel therapeutic alternatives could be envisioned.
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Affiliation(s)
- Maxime Janin
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute (IJC), IJC Building, Germans Trias I Pujol, Ctra de Can Ruti, Cami de Les Escoles S/N, 08916 Badalona, Barcelona, Spain
- Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain
| | - Veronica Davalos
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute (IJC), IJC Building, Germans Trias I Pujol, Ctra de Can Ruti, Cami de Les Escoles S/N, 08916 Badalona, Barcelona, Spain
| | - Manel Esteller
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute (IJC), IJC Building, Germans Trias I Pujol, Ctra de Can Ruti, Cami de Les Escoles S/N, 08916 Badalona, Barcelona, Spain.
- Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain.
- Institucio Catalana de Recerca I Estudis Avançats (ICREA), Barcelona, Catalonia, Spain.
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Catalonia, Spain.
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Bagheri M, Lee MK, Muller KE, Miller TW, Pattabiraman DR, Christensen BC. Alteration of DNMT1/DNMT3A by eribulin elicits global DNA methylation changes with potential therapeutic implications for triple-negative breast cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.09.544426. [PMID: 37333096 PMCID: PMC10274899 DOI: 10.1101/2023.06.09.544426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Triple-negative breast cancer (TNBC) is an aggressive disease subtype with limited treatment options. Eribulin is a chemotherapeutic approved for the treatment of advanced breast cancer that has been shown to elicit epigenetic changes. We investigated the effect of eribulin treatment on genome-scale DNA methylation patterns in TNBC cells. Following repeated treatment, The results showed that eribulin-induced changes in DNA methylation patterns evident in persister cells. Eribulin also affected the binding of transcription factors to genomic ZEB1 binding sites and regulated several cellular pathways, including ERBB and VEGF signaling and cell adhesion. Eribulin also altered the expression of epigenetic modifiers including DNMT1, TET1, and DNMT3A/B in persister cells. Data from primary human TNBC tumors supported these findings: DNMT1 and DNMT3A levels were altered by eribulin treatment in human primary TNBC tumors. Our results suggest that eribulin modulates DNA methylation patterns in TNBC cells by altering the expression of epigenetic modifiers. These findings have clinical implications for using eribulin as a therapeutic agent.
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Affiliation(s)
- Meisam Bagheri
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03766
- Dartmouth Cancer Center, Lebanon, NH, 03756
| | - Min Kyung Lee
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, 03756
| | - Kristen E. Muller
- Dartmouth Cancer Center, Lebanon, NH, 03756
- Department of Pathology, Dartmouth-Hitchcock Medical Center, Lebanon NH 03756, USA
| | - Todd W. Miller
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03766
- Dartmouth Cancer Center, Lebanon, NH, 03756
| | - Diwakar R. Pattabiraman
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03766
- Dartmouth Cancer Center, Lebanon, NH, 03756
| | - Brock C. Christensen
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Lebanon, NH 03766
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Lebanon, NH, 03756
- Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth, Lebanon, NH, 03756
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9
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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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10
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Chu DT, Ngo AD, Wu CC. Epigenetics in cancer development, diagnosis and therapy. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 198:73-92. [PMID: 37225325 DOI: 10.1016/bs.pmbts.2023.01.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
Cancer is a dangerous disease and one of the leading causes of death in the world. In 2020, there were nearly 10 million cancer deaths and approximately 20 million new cases. New cases and deaths from cancer are expected to increase further in the coming years. To have a deeper insight into the mechanism of carcinogenesis, epigenetics studies have been published and received much attention from scientists, doctors, and patients. Among alterations in epigenetics, DNA methylation and histone modification are studied by many scientists. They have been reported to be a major contributor in tumor formation and are involved in metastasis. From the understanding of DNA methylation and histone modification, effective, accurate and cost-effective methods for diagnosis and screening of cancer patients have been introduced. Furthermore, therapeutic approaches and drugs targeting altered epigenetics have also been clinically studied and have shown positive results in combating tumor progression. Several cancer drugs that rely on DNA methylation inactivation or histone modification have been approved by the FDA for the treatment of cancer patients. In summary, epigenetics changes such as DNA methylation or histone modification are take part in tumor growth, and they also have great prospect to study diagnostic and therapeutic methods of this dangerous disease.
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Affiliation(s)
- Dinh-Toi Chu
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam; Faculty of Applied Sciences, International School, Vietnam National University, Hanoi, Vietnam.
| | - Anh-Dao Ngo
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam
| | - Chia-Ching Wu
- Department of Cell Biology and Anatomy, College of Medicine, National Cheng Kung University, Tainan, Taiwan; International Center for Wound Repair and Regeneration, National Cheng Kung University, Tainan, Taiwan; Department of Biomedical Engineering, National Cheng Kung University, Tainan, Taiwan
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Chromatin profile-based identification of a novel ER-positive breast cancer subgroup with reduced ER-responsive element accessibility. Br J Cancer 2023; 128:1208-1222. [PMID: 36725920 PMCID: PMC10050410 DOI: 10.1038/s41416-023-02178-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 01/19/2023] [Accepted: 01/23/2023] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Oestrogen receptor (ER) signalling-dependent cancer cell growth is one of the major features of ER-positive breast cancer (BC). Inhibition of ER function is a standard and effective treatment for ER-positive tumours; however, ~20% of patients with ER-positive BC experience early or late recurrence. In this study, we examined intertumour heterogeneity from an epigenetic perspective based on the hypothesis that the intrinsic difference in epigenetic states around ER signalling pathway underlies endocrine therapy resistance. METHODS We performed transposase-accessible chromatin sequencing (ATAC-seq) analysis of 42 BC samples, including 35 ER-positive(+) human epidermal growth factor receptor 2 (HER2)-negative(-) and 7 triple-negative tumours. We also reanalysed ATAC-seq data of 45 ER + /HER2 - tumours in the Cancer Genome Atlas (TCGA) BC cohort to validate our observations. RESULTS We conducted a comprehensive analysis of cis-regulatory elements (CREs) using ATAC-seq, identifying three subgroups based on chromatin accessibility profiles. We identified a subgroup of ER-positive BCs with a distinctive chromatin accessibility pattern including reduced accessibility to ER-responsive elements (EREs). The same subgroup was also observed in TCGA BC cohort. Despite the reduced accessibility to EREs, the expression of ER and potential ER target genes were not decreased in these tumours. CONCLUSION Our findings highlight the existence of a subset of ER-positive BCs with unchanged ER expression but reduced EREs accessibility that cannot be distinguished by conventional immunostaining for ER. Future studies should determine whether these tumours are associated with resistance to endocrine therapy.
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12
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Yang X, Zheng W, Li M, Zhang S. Somatic Super-Enhancer Epigenetic Signature for Overall Survival Prediction in Patients with Breast Invasive Carcinoma. Bioinform Biol Insights 2023; 17:11779322231162767. [PMID: 37020500 PMCID: PMC10068971 DOI: 10.1177/11779322231162767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 02/18/2023] [Indexed: 04/03/2023] Open
Abstract
To analyze genome-wide super-enhancers (SEs) methylation signature of breast invasive carcinoma (BRCA) and its clinical value. Differential methylation sites (DMS) between BRCA and adjacent tissues from The Cancer Genome Atlas (TCGA) database were identified by using ChAMP package in R software. Super-enhancers were identified sing ROSE software. Overlap analysis was used to assess the potential DMS in SEs region. Feature selection was performed by Cox regression and least absolute shrinkage and selection operator (LASSO) algorithm based on TCGA training cohort. Prognosis model validation was performed in TCGA training cohort, TCGA validation cohort, and gene expression omnibus (GEO) test cohort. The gene ontology and KEGG analysis revealed that SEs target genes were significantly enriched in cell-migration-associated processes and pathways. A total of 83 654 DMS were identified between BRCA and adjacent tissues. Around 2397 DMS in SEs region were identified by overlap study and used to feature selection. By using Cox regression and LASSO algorithm, 42 features were selected to develop a clinical prediction model (CPM). Both training (TCGA) and validation cohorts (TCGA and GEO) show that the CPM has ideal discrimination and calibration. The CPM based on DMS at SE regions has ideal discrimination and calibration, which combined with tumor node metastasis (TNM) stage could improve prognostication, and thus contribute to individualized medicine.
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Affiliation(s)
- Xu Yang
- Department of Urology, Fujian Medical
University Union Hospital, Fuzhou, P.R. China
| | - Wenzhong Zheng
- Department of Urology, Fujian Medical
University Union Hospital, Fuzhou, P.R. China
| | - Mengqiang Li
- Department of Urology, Fujian Medical
University Union Hospital, Fuzhou, P.R. China
| | - Shiqiang Zhang
- Department of Urology, Kidney and
Urology Center, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen,
P.R. China
- Shiqiang Zhang, Department of Urology,
Kidney and Urology Center, The Seventh Affiliated Hospital, Sun Yat-Sen
University, No.628, Zhenyuan Rd, Guangming (New) Dist., Shenzhen 518107, P.R.
China.
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Shoukat I, Mueller CR. Searching for DNA methylation in patients triple-negative breast cancer: a liquid biopsy approach. Expert Rev Mol Diagn 2023; 23:41-51. [PMID: 36715539 DOI: 10.1080/14737159.2023.2173579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
INTRODUCTION Liquid biopsies are proving to have diagnostic and prognostic value in many different cancers, and in breast cancer they have the potential to improve outcomes by providing valuable information throughout a patient's cancer journey. However, patients with triple negative breast cancer (TNBC) have received little benefit from such liquid biopsies due to underlying limitations in the discovery and utility of robust biomarkers. Here, we examine the development of DNA methylation-based liquid biopsy assays for breast cancer and how they pertain to TNBC. AREAS COVERED We conducted a systematic review of liquid biopsy assays for breast cancer and analyzed their relevance in TNBC. We show that the utility of DNA mutation-based assays is poor for TNBC due to the low mutational frequencies across the genome in this subtype. We offer a detailed review of mDETECT - a liquid biopsy specifically designed for assessing tumor burden in TNBC patients. EXPERT OPINION DNA methylation are foundational and robust events that occur in cancer evolution and may differentiate almost all forms of cancer, including TNBC. Longitudinal patient monitoring using DNA methylation-based liquid biopsies offers great potential for improving the detection and management of TNBC.
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Affiliation(s)
- Irsa Shoukat
- Queen's Cancer Research Institute, Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada
| | - Christopher R Mueller
- Queen's Cancer Research Institute, Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada
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Analysis of Intrinsic Breast Cancer Subtypes: The Clinical Utility of Epigenetic Biomarkers and TP53 Mutation Status in Triple-Negative Cases. Int J Mol Sci 2022; 23:ijms232315429. [PMID: 36499753 PMCID: PMC9741387 DOI: 10.3390/ijms232315429] [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: 10/06/2022] [Revised: 11/21/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
This study aimed at analyzing the DNA methylation pattern and TP53 mutation status of intrinsic breast cancer (BC) subtypes for improved characterization and survival prediction. DNA methylation of 17 genes was tested by methylation-specific PCR in 116 non-familial BRCA mutation-negative BC and 29 control noncancerous cases. At least one gene methylation was detected in all BC specimens and a 10-gene panel statistically significantly separated tumors from noncancerous breast tissues. Methylation of FILIP1L and MT1E was predominant in triple-negative (TN) BC, while other BC subtypes were characterized by RASSF1, PRKCB, MT1G, APC, and RUNX3 hypermethylation. TP53 mutation (TP53-mut) was found in 38% of sequenced samples and mainly affected TN BC cases (87%). Cox analysis revealed that TN status, age at diagnosis, and RUNX3 methylation are independent prognostic factors for overall survival (OS) in BC. The combinations of methylated biomarkers, RUNX3 with MT1E or FILIP1L, were also predictive for shorter OS, whereas methylated FILIP1L was predictive of a poor outcome in the TP53-mut subgroup. Therefore, DNA methylation patterns of specific genes significantly separate BC from noncancerous breast tissues and distinguishes TN cases from non-TN BC, whereas the combination of two-to-three epigenetic biomarkers can be an informative tool for BC outcome predictions.
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Yang G, Lu T, Weisenberger DJ, Liang G. The Multi-Omic Landscape of Primary Breast Tumors and Their Metastases: Expanding the Efficacy of Actionable Therapeutic Targets. Genes (Basel) 2022; 13:1555. [PMID: 36140723 PMCID: PMC9498783 DOI: 10.3390/genes13091555] [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] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/08/2022] [Accepted: 08/23/2022] [Indexed: 12/02/2022] Open
Abstract
Breast cancer (BC) mortality is almost exclusively due to metastasis, which is the least understood aspect of cancer biology and represents a significant clinical challenge. Although we have witnessed tremendous advancements in the treatment for metastatic breast cancer (mBC), treatment resistance inevitably occurs in most patients. Recently, efforts in characterizing mBC revealed distinctive genomic, epigenomic and transcriptomic (multi-omic) landscapes to that of the primary tumor. Understanding of the molecular underpinnings of mBC is key to understanding resistance to therapy and the development of novel treatment options. This review summarizes the differential molecular landscapes of BC and mBC, provides insights into the genomic heterogeneity of mBC and highlights the therapeutically relevant, multi-omic features that may serve as novel therapeutic targets for mBC patients.
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Affiliation(s)
- Guang Yang
- School of Sciences, China Pharmaceutical University, Nanjing 211121, China
- China Grand Enterprises, Beijing 100101, China
| | - Tao Lu
- School of Sciences, China Pharmaceutical University, Nanjing 211121, China
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 211121, China
| | - Daniel J. Weisenberger
- Department of Biochemistry and Molecular Medicine, University of Southern California, Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA
| | - Gangning Liang
- Department of Urology, University of Southern California, Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA
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Conway K, Tsai YS, Edmiston SN, Parker JS, Parrish EA, Hao H, Kuan PF, Scott GA, Frank JS, Googe P, Ollila DW, Thomas NE. Characterization of the CpG Island Hypermethylated Phenotype Subclass in Primary Melanomas. J Invest Dermatol 2022; 142:1869-1881.e10. [PMID: 34843679 PMCID: PMC9135958 DOI: 10.1016/j.jid.2021.11.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 10/28/2021] [Accepted: 11/08/2021] [Indexed: 12/26/2022]
Abstract
Cutaneous melanoma can be lethal even if detected at an early stage. Epigenetic profiling may facilitate the identification of aggressive primary melanomas with unfavorable outcomes. We performed clustering of whole-genome methylation data to identify subclasses that were then assessed for survival, clinical features, methylation patterns, and biological pathways. Among 89 cutaneous primary invasive melanomas, we identified three methylation subclasses exhibiting low methylation, intermediate methylation, or hypermethylation of CpG islands, known as the CpG island methylator phenotype (CIMP). CIMP melanomas occurred as early as tumor stage 1b and, compared with low-methylation melanomas, were associated with age at diagnosis ≥65 years, lentigo maligna melanoma histologic subtype, presence of ulceration, higher American Joint Committee on Cancer stage and tumor stage, and lower tumor-infiltrating lymphocyte grade (all P < 0.05). Patients with CIMP melanomas had worse melanoma-specific survival (hazard ratio = 11.84; confidence interval = 4.65‒30.20) than those with low-methylation melanomas, adjusted for age, sex, American Joint Committee on Cancer stage, and tumor-infiltrating lymphocyte grade. Genes hypermethylated in CIMP compared with those in low-methylation melanomas included PTEN, VDR, PD-L1, TET2, and gene sets related to development/differentiation, the extracellular matrix, and immunity. CIMP melanomas exhibited hypermethylation of genes important in melanoma progression and tumor immunity, and although present in some early melanomas, CIMP was associated with worse survival independent of known prognostic factors.
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Affiliation(s)
- Kathleen Conway
- Department of Epidemiology, UNC Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Department of Dermatology, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Lineberger Comprehensive Cancer Center, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
| | - Yihsuan S Tsai
- Lineberger Comprehensive Cancer Center, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Sharon N Edmiston
- Lineberger Comprehensive Cancer Center, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Joel S Parker
- Lineberger Comprehensive Cancer Center, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Department of Genetics, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Eloise A Parrish
- Lineberger Comprehensive Cancer Center, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Honglin Hao
- Department of Genetics, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Pei Fen Kuan
- Department of Applied Mathematics & Statistics, Stony Brook University, Stony Brook, New York, USA
| | - Glynis A Scott
- Department of Dermatology, University of Rochester Medical Center, Rochester, New York, USA; Department of Pathology & Laboratory Medicine, University of Rochester Medical Center, Rochester, New York, USA
| | - Jill S Frank
- Department of Surgery, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Paul Googe
- Department of Dermatology, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Department of Pathology and Lab Medicine, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - David W Ollila
- Lineberger Comprehensive Cancer Center, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Department of Surgery, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Nancy E Thomas
- Department of Dermatology, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Lineberger Comprehensive Cancer Center, UNC School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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O6-Methylguanine-DNA Methyltransferase and ATP-Binding Cassette Membrane Transporter G2 Promotor Methylation: Can Predict the Response to Chemotherapy in Advanced Breast Cancer? Rep Biochem Mol Biol 2022; 11:20-29. [PMID: 35765521 PMCID: PMC9208568 DOI: 10.52547/rbmb.11.1.20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 11/02/2021] [Indexed: 01/11/2023]
Abstract
Background ATP-binding cassette membrane transporter G2 (ABCG2) gene is one of transporter family and well characterized for their association with chemoresistance. Promoter methylation is a mechanism for regulation of gene expression. O6-Methyl guanine DNA methyl transferase (MGMT) gene plays a fundamental role in DNA repair. MGMT has the ability to remove alkyl adducts from DNA at the O6 position of guanine. Alkylating agents exert their function through adding these alkyls adducts to DNA leading to cell death unless it is repaired by MGMT. MGMT promoter was found to be methylated in several malignancies. The aim of the present work is to study the relation of MGMT and ABCG2 promoter methylation status in advanced breast cancer patients to response to cyclophosphamide-doxorubicin (AC) based therapeutic regime. Methods This retrospective study included Forty-two female patients with advanced breast cancer assessed before receiving chemotherapy and after the completion of regimens. They were grouped into responders and non-responders according to RECIST criteria. Methylation analysis of MGMT and ABCG2 genes were performed on breast cancer tissues. Results MGMT promoter was methylated in 40.5% of the cases. ABCG2 promoter was methylated in 14.3% of cases. There was no statistically significant association between MGMT and ABCG2 promoter methylation status and clinicopathological parameters. There was statistically significant association between methylation status of both promoters and response to AC when followed by Taxane. Conclusion Methylation of MGMT and ABCG2 promoters combined could be a potential predictive factor for response to cyclophosphamide-doxorubicin based therapeutic regime.
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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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Yates J, Boeva V. Deciphering the etiology and role in oncogenic transformation of the CpG island methylator phenotype: a pan-cancer analysis. Brief Bioinform 2022; 23:6520307. [PMID: 35134107 PMCID: PMC8921629 DOI: 10.1093/bib/bbab610] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/06/2021] [Accepted: 12/30/2021] [Indexed: 12/25/2022] Open
Abstract
Numerous cancer types have shown to present hypermethylation of CpG islands, also known as a CpG island methylator phenotype (CIMP), often associated with survival variation. Despite extensive research on CIMP, the etiology of this variability remains elusive, possibly due to lack of consistency in defining CIMP. In this work, we utilize a pan-cancer approach to further explore CIMP, focusing on 26 cancer types profiled in the Cancer Genome Atlas (TCGA). We defined CIMP systematically and agnostically, discarding any effects associated with age, gender or tumor purity. We then clustered samples based on their most variable DNA methylation values and analyzed resulting patient groups. Our results confirmed the existence of CIMP in 19 cancers, including gliomas and colorectal cancer. We further showed that CIMP was associated with survival differences in eight cancer types and, in five, represented a prognostic biomarker independent of clinical factors. By analyzing genetic and transcriptomic data, we further uncovered potential drivers of CIMP and classified them in four categories: mutations in genes directly involved in DNA demethylation; mutations in histone methyltransferases; mutations in genes not involved in methylation turnover, such as KRAS and BRAF; and microsatellite instability. Among the 19 CIMP-positive cancers, very few shared potential driver events, and those drivers were only IDH1 and SETD2 mutations. Finally, we found that CIMP was strongly correlated with tumor microenvironment characteristics, such as lymphocyte infiltration. Overall, our results indicate that CIMP does not exhibit a pan-cancer manifestation; rather, general dysregulation of CpG DNA methylation is caused by heterogeneous mechanisms.
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Affiliation(s)
- Josephine Yates
- Institute for Machine Learning, Department of Computer Science, ETH Zürich, Zurich 8092, Switzerland
| | - Valentina Boeva
- Institute for Machine Learning, Department of Computer Science, ETH Zürich, Zurich 8092, Switzerland.,Swiss Institute for Bioinformatics (SIB), Zürich, Switzerland.,Cochin Institute, Inserm U1016, CNRS UMR 8104, Paris Descartes University UMR-S1016, Paris 75014, France
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Lee M, Untch BR, Xu B, Ghossein R, Han C, Kuo F, Valero C, Nadeem Z, Patel N, Makarov V, Dogan S, Wong RJ, Sherman EJ, Ho AL, Chan TA, Fagin JA, Morris LGT. Genomic and Transcriptomic Correlates of Thyroid Carcinoma Evolution after BRAF Inhibitor Therapy. Mol Cancer Res 2022; 20:45-55. [PMID: 34635506 PMCID: PMC8738128 DOI: 10.1158/1541-7786.mcr-21-0442] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 08/12/2021] [Accepted: 10/04/2021] [Indexed: 12/16/2022]
Abstract
Targeted inhibition of BRAF V600E achieves tumor control in a subset of advanced thyroid tumors. Nearly all tumors develop resistance, and some have been observed to subsequently undergo dedifferentiation. The molecular alterations associated with thyroid cancer dedifferentiation in the setting of BRAF inhibition are unknown. We analyzed targeted next-generation sequencing data from 639 advanced, recurrent and/or metastatic thyroid carcinomas, including 15 tumors that were treated with BRAF inhibitor drugs and had tissue sampled during or posttreatment, 8 of which had matched pretherapy samples. Pre- and posttherapy tissues from one additional patient were profiled with whole-exome sequencing and RNA expression profiling. Mutations in genes comprising the SWI/SNF chromatin remodeling complex and the PI3K-AKT-mTOR, MAPK, and JAK-STAT pathways all increased in prevalence across more dedifferentiated thyroid cancer histologies. Of 7 thyroid cancers that dedifferentiated after BRAF inhibition, 6 had mutations in these pathways. These mutations were mostly absent from matched pretreatment samples and were rarely detected in tumors that did not dedifferentiate. Additional analyses in one of the vemurafenib-treated tumors before and after anaplastic transformation revealed the emergence of an oncogenic PIK3CA mutation, activation of ERK signaling, dedifferentiation, and development of an immunosuppressive tumor microenvironment. These findings validate earlier preclinical data implicating these genetic pathways in resistance to BRAF inhibitors, and suggest that genetic alterations mediating acquired drug resistance may also promote thyroid tumor dedifferentiation. IMPLICATIONS: The possibility that thyroid cancer dedifferentiation may be attributed to selective pressure applied by BRAF inhibitor-targeted therapy should be investigated further.
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Affiliation(s)
- Mark Lee
- Weill Cornell Medicine, New York, New York
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Brian R Untch
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Bin Xu
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ronald Ghossein
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Catherine Han
- Weill Cornell Medicine, New York, New York
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Fengshen Kuo
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Cristina Valero
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Zaineb Nadeem
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Neal Patel
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Vladimir Makarov
- Center for Immunotherapy and Precision Immuno-Oncology, Cleveland Clinic, Cleveland, Ohio
| | - Snjezana Dogan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Richard J Wong
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Eric J Sherman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Alan L Ho
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Timothy A Chan
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, New York
- Center for Immunotherapy and Precision Immuno-Oncology, Cleveland Clinic, Cleveland, Ohio
| | - James A Fagin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Luc G T Morris
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York.
- Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, New York
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The Role of DNA Methylation and DNA Methyltransferases in Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:317-348. [DOI: 10.1007/978-3-031-11454-0_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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22
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Ray SK, Mukherjee S. Epigenetic Reprogramming and Landscape of Transcriptomic Interactions: Impending Therapeutic Interference of Triple-Negative Breast Cancer in Molecular Medicine. Curr Mol Med 2021; 22:835-850. [PMID: 34872474 DOI: 10.2174/1566524021666211206092437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 10/18/2021] [Accepted: 10/25/2021] [Indexed: 11/22/2022]
Abstract
The mechanisms governing the development and progression of cancers are believed to be the consequence of hereditary deformities and epigenetic modifications. Accordingly, epigenetics has become an incredible and progressively explored field of research to discover better prevention and therapy for neoplasia, especially triple-negative breast cancer (TNBC). It represents 15-20% of all invasive breast cancers and will, in general, have bellicose histological highlights and poor clinical outcomes. In the early phases of triple-negative breast carcinogenesis, epigenetic deregulation modifies chromatin structure and influences the plasticity of cells. It up-keeps the oncogenic reprogramming of malignant progenitor cells with the acquisition of unrestrained selfrenewal capacities. Genomic impulsiveness in TNBC prompts mutations, copy number variations, as well as genetic rearrangements, while epigenetic remodeling includes an amendment by DNA methylation, histone modification, and noncoding RNAs of gene expression profiles. It is currently evident that epigenetic mechanisms assume a significant part in the pathogenesis, maintenance, and therapeutic resistance of TNBC. Although TNBC is a heterogeneous malaise that is perplexing to describe and treat, the ongoing explosion of genetic and epigenetic research will help to expand these endeavors. Latest developments in transcriptome analysis have reformed our understanding of human diseases, including TNBC at the molecular medicine level. It is appealing to envision transcriptomic biomarkers to comprehend tumor behavior more readily regarding its cellular microenvironment. Understanding these essential biomarkers and molecular changes will propel our capability to treat TNBC adequately. This review will depict the different aspects of epigenetics and the landscape of transcriptomics in triple-negative breast carcinogenesis and their impending application for diagnosis, prognosis, and treatment decision with the view of molecular medicine.
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Affiliation(s)
| | - Sukhes Mukherjee
- Department of Biochemistry All India Institute of Medical Sciences. Bhopal, Madhya pradesh-462020. India
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23
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Quintas-Granados LI, Cortés H, Carmen MGD, Leyva-Gómez G, Bustamante-Montes LP, Rodríguez-Morales M, Villegas-Vazquez EY, López-Reyes I, Alcaraz-Estrada SL, Sandoval-Basilio J, Soto-Reyes E, Sharifi-Rad J, Figueroa-González G, Reyes-Hernández OD. The high methylation level of a novel 151-bp CpG island in the ESR1 gene promoter is associated with a poor breast cancer prognosis. Cancer Cell Int 2021; 21:649. [PMID: 34863151 PMCID: PMC8645138 DOI: 10.1186/s12935-021-02343-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 11/15/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The ESR1 gene suffers methylation changes in many types of cancers, including breast cancer (BC), the most frequently diagnosed cancer in women that is also present in men. Methylation at promoter A of ESR1 is the worse prognosis in terms of overall survival; thus, the early detection, prognostic, and prediction of therapy involve some methylation biomarkers. METHODS Therefore, our study aimed to examine the methylation levels at the ESR1 gene in samples from Mexican BC patients and its possible association with menopausal status. RESULTS We identified a novel 151-bp CpG island in the promoter A of the ESR1 gene. Interestingly, methylation levels at this CpG island in positive ERα tumors were approximately 50% less than negative ERα or control samples. Furthermore, methylation levels at ESR1 were associated with menopausal status. In postmenopausal patients, the methylation levels were 1.5-fold higher than in premenopausal patients. Finally, according to tumor malignancy, triple-negative cancer subtypes had higher ESR1 methylation levels than luminal/HER2+ or luminal A subtypes. CONCLUSIONS Our findings suggest that methylation at this novel CpG island might be a promising prognosis marker.
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Affiliation(s)
| | - Hernán Cortés
- Laboratorio de Medicina Genómica, Departamento de Genómica, Instituto Nacional de Rehabilitación Luis Guillermo Ibarra Ibarra, 14389, Mexico City, Mexico
| | | | - Gerardo Leyva-Gómez
- Departamento de Farmacia, Facultad de Química, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | | | | | - Edgar Yebran Villegas-Vazquez
- Departamento de Biotecnología y Bioingeniería del Centro de Investigación y de Estudios Avanzados del IPN, Mexico City, Mexico
| | - Israel López-Reyes
- Colegio de Ciencias y Humanidades, Plantel Cuautepec, Universidad Autónoma de la Ciudad de México, Mexico City, Mexico
| | - Sofía Lizeth Alcaraz-Estrada
- División de Medicina Genomica, Centro Médico Nacional "20 de Noviembre"-ISSSTE, Mexico, 03100, Mexico City, Mexico
| | - Jorge Sandoval-Basilio
- Laboratorio de Biología Molecular, Universidad Hipócrates, Acapulco, Gro., México
- Laboratorio de Investigación Clínica, Facultad de Medicina, Universidad Autónoma de Guerrero, Acapulco, Gro., México
| | - Ernesto Soto-Reyes
- Departamento de Ciencias Naturales, Universidad Autónoma Metropolitana-Cuajimalpa (UAM-C), Mexico City, Mexico
| | | | - Gabriela Figueroa-González
- Laboratorio de Farmacogenética, UMIEZ, Facultad de Estudios Superiores Zaragoza, Universidad Nacional Autónoma de México, 09230, Mexico City, México.
| | - Octavio Daniel Reyes-Hernández
- Laboratorio de Biología Molecular del Cáncer, UMIEZ, Facultad de Estudios Superiores Zaragoza, Universidad Nacional Autónoma de México, 09230, Mexico City, México.
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24
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Khandker SS, Shakil MS, Hossen MS. Gold Nanoparticles; Potential Nanotheranostic Agent in Breast Cancer: A Comprehensive Review with Systematic Search Strategy. Curr Drug Metab 2021; 21:579-598. [PMID: 32520684 DOI: 10.2174/1389200221666200610173724] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 03/19/2020] [Accepted: 04/02/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND Breast cancer is a heterogeneous disease typically prevalent among women and is the second-largest cause of death worldwide. Early diagnosis is the key to minimize the cancer-induced complication, however, the conventional diagnostic strategies have been sluggish, complex, and, to some extent, non-specific. Therapeutic tools are not so convenient and side effects of current therapies offer the development of novel theranostic tool to combat this deadly disease. OBJECTIVE This article aims to summarize the advances in the diagnosis and treatment of breast cancer with gold nanoparticles (GNP or AuNP). METHODS A systematic search was conducted in the three popular electronic online databases including PubMed, Google Scholar, and Web of Science, regarding GNP as breast cancer theranostics. RESULTS Published literature demonstrated that GNPs tuned with photosensitive moieties, nanomaterials, drugs, peptides, nucleotide, peptides, antibodies, aptamer, and other biomolecules improve the conventional diagnostic and therapeutic strategies of breast cancer management with minimum cytotoxic effect. GNP derived diagnosis system assures reproducibility, reliability, and accuracy cost-effectively. Additionally, surface-modified GNP displayed theranostic potential even in the metastatic stage of breast cancer. CONCLUSION Divergent strategies have shown the theranostic potential of surface tuned GNPs against breast cancer even in the metastatic stage with minimum cytotoxic effects both in vitro and in vivo.
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Affiliation(s)
- Shahad Saif Khandker
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Md Salman Shakil
- Department of Pharmacology & Toxicology, University of Otago, 362 Leith St., North Dunedin, Dunedin 9016, New Zealand
| | - Md Sakib Hossen
- Department of Biochemistry, Primeasia University, Banani, Dhaka, Bangladesh
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25
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The Roles of DNA Demethylases in Triple-Negative Breast Cancer. Pharmaceuticals (Basel) 2021; 14:ph14070628. [PMID: 34209564 PMCID: PMC8308559 DOI: 10.3390/ph14070628] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/21/2021] [Accepted: 06/25/2021] [Indexed: 02/07/2023] Open
Abstract
Triple-negative breast cancers (TNBCs) are very heterogenous, molecularly diverse, and are characterized by a high propensity to relapse or metastasize. Clinically, TNBC remains a diagnosis of exclusion by the lack of hormone receptors (Estrogen Receptor (ER) and Progesterone Receptor (PR)) as well as the absence of overexpression and/or amplification of HER2. DNA methylation plays an important role in breast cancer carcinogenesis and TNBCs have a distinct DNA methylation profile characterized by marked hypomethylation and lower gains of methylations compared to all other subtypes. DNA methylation is regulated by the balance of DNA methylases (DNMTs) and DNA demethylases (TETs). Here, we review the roles of TETs as context-dependent tumor-suppressor genes and/or oncogenes in solid tumors, and we discuss the current understandings of the oncogenic role of TET1 and its therapeutic implications in TNBCs.
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26
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27
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Li Y, Li F, Bai X, Li Y, Ni C, Zhao X, Zhang D. ITGA3 Is Associated With Immune Cell Infiltration and Serves as a Favorable Prognostic Biomarker for Breast Cancer. Front Oncol 2021; 11:658547. [PMID: 34094951 PMCID: PMC8172804 DOI: 10.3389/fonc.2021.658547] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/21/2021] [Indexed: 12/11/2022] Open
Abstract
Background ITGA3 is a member of the integrin family, a cell surface adhesion molecule that can interact with extracellular matrix (ECM) proteins. The purpose of this study was to explore the significance of ITGA3 expression in the prognosis and clinical diagnosis of breast cancer patients. Methods Oncomine, the Human Protein Atlas (HPA) and UALCAN were used to analyze the expression of ITGA3 in various cancers. PrognoScan, GEPIA, Kaplan–Meier plotter and Easysurv were utilized to analyze the prognosis of ITGA3 in certain cancers. Based on TCGA data, a receiver operating characteristic (ROC) curve was used to evaluate the diagnostic performance of ITGA3 expression. cBio-Portal and MethSurv were used to evaluate the genomic mechanism. LinkedOmics, NetworkAnalyst and Metascape were used to build the signaling network. TIMER is a web server for comprehensive analysis of tumor infiltrating immune cells and tumor infiltrating lymphocytes (TILs). Results The expression of ITGA3 in normal breast tissues was greater than that in breast cancer tissues at both the mRNA and protein levels. High expression of ITGA3 was associated with better prognosis of breast cancer patients. ROC analysis indicated that ITGA3 had significant diagnostic value. Genomic analysis revealed that promoter methylation of ITGA3 leads to transcriptional silencing, which may be one of the mechanisms underlying ITGA3 downregulation in BRCA. Immune infiltration analysis showed that ITGA3 may be involved in the recruitment of immune cells. Conclusions This study identified ITGA3 as a novel biomarker to estimate the diagnosis and prognosis of breast cancer. In addition, ITGA3 is involved in ECM regulation and immune cell infiltration.
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Affiliation(s)
- Yue Li
- Department of Pathology, Tianjin Medical University, Tianjin, China
| | - Fan Li
- Department of Pathology, Tianjin Medical University, Tianjin, China
| | - Xiaoyu Bai
- Department of Pathology, Tianjin Medical University, Tianjin, China
| | - Yanlei Li
- Department of Pathology, Tianjin Medical University, Tianjin, China.,Department of Pathology, General Hospital of Tianjin Medical University, Tianjin, China
| | - Chunsheng Ni
- Department of Pathology, Tianjin Medical University, Tianjin, China.,Department of Pathology, General Hospital of Tianjin Medical University, Tianjin, China
| | - Xiulan Zhao
- Department of Pathology, Tianjin Medical University, Tianjin, China.,Department of Pathology, General Hospital of Tianjin Medical University, Tianjin, China
| | - Danfang Zhang
- Department of Pathology, Tianjin Medical University, Tianjin, China.,Department of Pathology, General Hospital of Tianjin Medical University, Tianjin, China
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28
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Sena IFG, Rocha BGS, Picoli CC, Santos GSP, Costa AC, Gonçalves BOP, Garcia APV, Soltani-Asl M, Coimbra-Campos LMC, Silva WN, Costa PAC, Pinto MCX, Amorim JH, Azevedo VAC, Resende RR, Heller D, Cassali GD, Mintz A, Birbrair A. C(3)1-TAg in C57BL/6 J background as a model to study mammary tumor development. Histochem Cell Biol 2021; 156:165-182. [PMID: 34003355 DOI: 10.1007/s00418-021-01995-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/09/2021] [Indexed: 02/06/2023]
Abstract
Diagnosis and prognosis of breast cancer is based on disease staging identified through histopathological and molecular biology techniques. Animal models are used to gain mechanistic insights into the development of breast cancer. C(3)1-TAg is a genetically engineered mouse model that develops mammary cancer. However, carcinogenesis caused by this transgene was characterized in the Friend Virus B (FVB) background. As most genetic studies are done in mice with C57BL/6 J background, we aimed to define the histological alterations in C3(1)-TAg C57BL/6 J animals. Our results showed that C3(1)-TAg animals with C57BL/6 J background develop solid-basaloid adenoid cystic carcinomas with increased fibrosis, decreased area of adipocytes, and a high proliferative index, which are triple-negative for progesterone, estrogen, and human epidermal growth factor receptor 2 (HER2) receptors. Our results also revealed that tumor development is slower in the C57BL/6 J background when compared with the FVB strain, providing a better model to study the different stages in breast cancer progression.
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Affiliation(s)
- Isadora F G Sena
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Beatriz G S Rocha
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Caroline C Picoli
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Gabryella S P Santos
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Alinne C Costa
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Bryan O P Gonçalves
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Ana Paula V Garcia
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Maryam Soltani-Asl
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | | | - Walison N Silva
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Pedro A C Costa
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Mauro C X Pinto
- Laboratory of Neuropharmacology and Neurochemistry, Institute of Biological Sciences, Federal University of Goiás, Goiânia, GO, Brazil
| | - Jaime H Amorim
- Center of Biological Sciences and Health, Federal University of West Bahia, Barreiras, BA, Brazil
| | - Vasco A C Azevedo
- Cellular and Molecular Genetics Laboratory, Department of Genetics, Ecology and Evolution, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Rodrigo R Resende
- Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Debora Heller
- Hospital Israelita Albert Einstein, São Paulo, Brazil.,Cruzeiro Do Sul University, São Paulo, Brazil
| | - Geovanni D Cassali
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Akiva Mintz
- Department of Radiology, Columbia University Medical Center, New York, NY, USA
| | - Alexander Birbrair
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil. .,Department of Radiology, Columbia University Medical Center, New York, NY, USA.
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29
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Integrative analysis of DNA methylation and gene expression profiles identified potential breast cancer-specific diagnostic markers. Biosci Rep 2021; 40:224161. [PMID: 32412047 PMCID: PMC7263199 DOI: 10.1042/bsr20201053] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/13/2020] [Accepted: 05/14/2020] [Indexed: 12/14/2022] Open
Abstract
Breast cancer is a common malignant tumor among women whose prognosis is largely determined by the period and accuracy of diagnosis. We here propose to identify a robust DNA methylation-based breast cancer-specific diagnostic signature. Genome-wide DNA methylation and gene expression profiles of breast cancer patients along with their adjacent normal tissues from the Cancer Genome Atlas (TCGA) were obtained as the training set. CpGs that with significantly elevated methylation level in breast cancer than not only their adjacent normal tissues and the other ten common cancers from TCGA but also the healthy breast tissues from the Gene Expression Omnibus (GEO) were finally remained for logistic regression analysis. Another independent breast cancer DNA methylation dataset from GEO was used as the testing set. Lots of CpGs were hyper-methylated in breast cancer samples compared with adjacent normal tissues, which tend to be negatively correlated with gene expressions. Eight CpGs located at RIIAD1, ENPP2, ESPN, and ETS1, were finally retained. The diagnostic model was reliable in separating BRCA from normal samples. Besides, chromatin accessibility status of RIIAD1, ENPP2, ESPN and ETS1 showed great differences between MCF-7 and MDA-MB-231 cell lines. In conclusion, the present study should be helpful for breast cancer early and accurate diagnosis.
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30
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Wu SL, Zhang X, Chang M, Huang C, Qian J, Li Q, Yuan F, Sun L, Yu X, Cui X, Jiang J, Cui M, Liu Y, Wu HW, Liang ZY, Wang X, Niu Y, Tong WM, Jin F. Genome-wide 5-hydroxymethylcytosine Profiling Analysis Identifies MAP7D1 as A Novel Regulator of Lymph Node Metastasis in Breast Cancer. GENOMICS PROTEOMICS & BIOINFORMATICS 2021; 19:64-79. [PMID: 33716151 PMCID: PMC8498923 DOI: 10.1016/j.gpb.2019.05.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Revised: 05/07/2019] [Accepted: 05/31/2019] [Indexed: 11/28/2022]
Abstract
Although DNA 5-hydroxymethylcytosine (5hmC) is recognized as an important epigenetic mark in cancer, its precise role in lymph node metastasis remains elusive. In this study, we investigated how 5hmC associates with lymph node metastasis in breast cancer. Accompanying with high expression of TET1 and TET2 proteins, large numbers of genes in the metastasis-positive primary tumors exhibit higher 5hmC levels than those in the metastasis-negative primary tumors. In contrast, the TET protein expression and DNA 5hmC decrease significantly within the metastatic lesions in the lymph nodes compared to those in their matched primary tumors. Through genome-wide analysis of 8 sets of primary tumors, we identified 100 high-confidence metastasis-associated 5hmC signatures, and it is found that increased levels of DNA 5hmC and gene expression of MAP7D1 associate with high risk of lymph node metastasis. Furthermore, we demonstrate that MAP7D1, regulated by TET1, promotes tumor growth and metastasis. In conclusion, the dynamic 5hmC profiles during lymph node metastasis suggest a link between DNA 5hmC and lymph node metastasis. Meanwhile, the role of MAP7D1 in breast cancer progression suggests that the metastasis-associated 5hmC signatures are potential biomarkers to predict the risk for lymph node metastasis, which may serve as diagnostic and therapeutic targets for metastatic breast cancer.
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Affiliation(s)
- Shuang-Ling Wu
- Department of Surgical Oncology and Breast Surgery, the First Affiliated Hospital of China Medical University, Shenyang 110000, China; Department of Pathology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Molecular Pathology Research Center, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Xiaoyi Zhang
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Center for Bioinformatics, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
| | - Mengqi Chang
- Department of Pathology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Molecular Pathology Research Center, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Changcai Huang
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Center for Bioinformatics, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
| | - Jun Qian
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Center for Bioinformatics, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
| | - Qing Li
- Department of Pathology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Molecular Pathology Research Center, Chinese Academy of Medical Sciences, Beijing 100005, China
| | - Fang Yuan
- Beijing National Laboratory for Molecular Sciences (BNLMS), MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry, Peking University, Beijing 100871, China
| | - Lihong Sun
- Center for Experimental Animal Research, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College. Beijing 100005, China
| | - Xinmiao Yu
- Department of Surgical Oncology and Breast Surgery, the First Affiliated Hospital of China Medical University, Shenyang 110000, China
| | - Xinmiao Cui
- Department of Surgical Oncology and Breast Surgery, the First Affiliated Hospital of China Medical University, Shenyang 110000, China
| | - Jiayi Jiang
- Department of Surgical Oncology and Breast Surgery, the First Affiliated Hospital of China Medical University, Shenyang 110000, China
| | - Mengyao Cui
- Department of Surgical Oncology and Breast Surgery, the First Affiliated Hospital of China Medical University, Shenyang 110000, China
| | - Ye Liu
- Department of Surgical Oncology and Breast Surgery, the First Affiliated Hospital of China Medical University, Shenyang 110000, China
| | - Huan-Wen Wu
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Molecular Pathology Research Center, Chinese Academy of Medical Sciences. Beijing 100005, China
| | - Zhi-Yong Liang
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Molecular Pathology Research Center, Chinese Academy of Medical Sciences. Beijing 100005, China
| | - Xiaoyue Wang
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Center for Bioinformatics, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, China
| | - Yamei Niu
- Department of Pathology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Molecular Pathology Research Center, Chinese Academy of Medical Sciences, Beijing 100005, China.
| | - Wei-Min Tong
- Department of Pathology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Molecular Pathology Research Center, Chinese Academy of Medical Sciences, Beijing 100005, China; Center for Experimental Animal Research, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College. Beijing 100005, China.
| | - Feng Jin
- Department of Surgical Oncology and Breast Surgery, the First Affiliated Hospital of China Medical University, Shenyang 110000, China.
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31
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Zhang W, Guan X, Tang J. The long non-coding RNA landscape in triple-negative breast cancer. Cell Prolif 2021; 54:e12966. [PMID: 33314471 PMCID: PMC7848969 DOI: 10.1111/cpr.12966] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 11/03/2020] [Accepted: 11/25/2020] [Indexed: 02/06/2023] Open
Abstract
Triple-negative breast cancer (TNBC) is a type of breast cancer that has a higher risk of distant recurrence and metastasis, leading to a relatively aggressive biological behaviour and poor outcome. So far, the clinical management of TNBC is challenging because of its heterogeneity and paucity of specific targeted therapy. Recently, various studies have identified a lot of differently expressed long non-coding RNAs (lncRNAs) in TNBC. Those lncRNAs have been reported to play important roles in the multistep process of TNBC tumorigenesis. Here, we review the biological characteristics of lncRNAs, and present the current state of knowledge concerning the expression, function and regulation of lncRNAs in TNBC. Accumulating studies explored the potential lncRNAs-based therapeutics in TNBC, including the techniques of genetic modification using antisense oligonucleotides, locked nucleic acid and RNA nanotechnology. In current review, we also discuss the future prospects of studies about lncRNAs in TNBC and development of lncRNA-based strategies for clinical TNBC patients.
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Affiliation(s)
- Wenwen Zhang
- Department of OncologyNanjing First Hospital, Nanjing Medical UniversityNanjingChina
| | - Xiaoxiang Guan
- Department of OncologyThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Jinhai Tang
- Department of General SurgeryThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
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32
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Liu XR, Zhang RY, Gong H, Rugo HS, Chen LB, Fu Y, Che JW, Tie J, Shao B, Wan FL, Kong WY, Song GH, Jiang HF, Xu GB, Li HP. Methylome Variation Predicts Exemestane Resistance in Advanced ER + Breast Cancer. Technol Cancer Res Treat 2020; 19:1533033819896331. [PMID: 32129154 PMCID: PMC7057408 DOI: 10.1177/1533033819896331] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Background: More than 30% of estrogen receptor-positive breast cancers are resistant to primary
hormone therapy, and about 40% that initially respond to hormone therapy eventually
acquire resistance. Although the mechanisms of hormone therapy resistance remain
unclear, aberrant DNA methylation has been implicated in oncogenesis and drug
resistance. Purpose: We investigated the relationship between methylome variations in circulating tumor DNA
and exemestane resistance, to track hormone therapy efficacy. Methods: We prospectively recruited 16 patients who were receiving first-line therapy in our
center. All patients received exemestane-based hormone therapy after enrollment. We
collected blood samples at baseline, first follow-up (after 2 therapeutic cycles) and at
detection of disease progression. Disease that progressed within 6 months under
exemestane treatment was considered exemestane resistance but was considered relatively
exemestane-sensitive otherwise. We obtained circulating tumor DNA-derived methylomes
using the whole-genome bisulfide sequencing method. Methylation calling was done by
BISMARK software; differentially methylated regions for exemestane resistance were
calculated afterward. Results: Median follow-up for the 16 patients was 19.0 months. We found 7 exemestane
resistance-related differentially methylated regions, located in different chromosomes,
with both significantly different methylation density and methylation ratio. Baseline
methylation density and methylation ratio of chromosome 6 [32400000-32599999] were both
high in exemestane resistance. High baseline methylation ratios of chromosome 3
[67800000-67999999] (P = .013), chromosome 3 [140200000-140399999]
(P = .037), and chromosome 12 [101200000-101399999]
(P = .026) could also predict exemestane resistance. During
exemestane treatment, synchronized changes in methylation density and methylation ratio
in chromosome 6 [32400000-32599999] could accurately stratify patients in terms of
progression-free survival (P = .000033). Cutoff values of methylation
density and methylation ratio for chromosome 6 [149600000-149799999] were 0.066 and
0.076, respectively. Conclusion: Methylation change in chromosome 6 [149600000-149799999] is an ideal predictor of
exemestane resistance with great clinical potential.
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Affiliation(s)
- Xiao-Ran Liu
- Department of Breast Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China.,The authors contributed eually to the article
| | - Ru-Yan Zhang
- Department of Breast Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China.,The authors contributed eually to the article
| | - Hao Gong
- M3 Genomics, Inc, Guangzhou, Guangdong, China.,The authors contributed eually to the article
| | - Hope S Rugo
- University of California San Francisco Helen Diller Family Comprehensive Cancer Center, CA, USA
| | | | - Yuan Fu
- M3 Genomics, Inc, Guangzhou, Guangdong, China
| | - Jian-Wei Che
- M3 Genomics, Inc, Guangzhou, Guangdong, China.,Life Healthcare Group Ltd, Beijing, China
| | - Jian Tie
- Department of Breast Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China
| | - Bin Shao
- Department of Breast Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China
| | - Feng-Ling Wan
- Department of Breast Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China
| | - Wei-Yao Kong
- Department of Breast Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China
| | - Guo-Hong Song
- Department of Breast Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China
| | - Han-Fang Jiang
- Department of Breast Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China
| | - Guo-Bing Xu
- Department of Breast Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China
| | - Hui-Ping Li
- Department of Breast Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China
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Pan Z, Tan C, Rao L, Zhang H, Zheng Y, Hao L, Ji L, Mao Z. Recoding the Cancer Epigenome by Intervening in Metabolism and Iron Homeostasis with Mitochondria‐Targeted Rhenium(I) Complexes. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202008624] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Zheng‐Yin Pan
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry School of Chemistry Sun Yat-Sen University Guangzhou 510275 P. R. China
| | - Cai‐Ping Tan
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry School of Chemistry Sun Yat-Sen University Guangzhou 510275 P. R. China
| | - Lu‐Si Rao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry School of Chemistry Sun Yat-Sen University Guangzhou 510275 P. R. China
| | - Hang Zhang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry School of Chemistry Sun Yat-Sen University Guangzhou 510275 P. R. China
| | - Yue Zheng
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry School of Chemistry Sun Yat-Sen University Guangzhou 510275 P. R. China
| | - Liang Hao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry School of Chemistry Sun Yat-Sen University Guangzhou 510275 P. R. China
| | - Liang‐Nian Ji
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry School of Chemistry Sun Yat-Sen University Guangzhou 510275 P. R. China
| | - Zong‐Wan Mao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry School of Chemistry Sun Yat-Sen University Guangzhou 510275 P. R. China
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Pan ZY, Tan CP, Rao LS, Zhang H, Zheng Y, Hao L, Ji LN, Mao ZW. Recoding the Cancer Epigenome by Intervening in Metabolism and Iron Homeostasis with Mitochondria-Targeted Rhenium(I) Complexes. Angew Chem Int Ed Engl 2020; 59:18755-18762. [PMID: 32634290 DOI: 10.1002/anie.202008624] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Indexed: 12/16/2022]
Abstract
The development and malignancy of cancer cells are closely related to the changes of the epigenome. In this work, a mitochondria-targeted rhenium(I) complex (DFX-Re3), integrating the clinical iron chelating agent deferasirox (DFX), has been designed. By relocating iron to the mitochondria and changing the key metabolic species related to epigenetic modifications, DFX-Re3 can elevate the methylation levels of histone, DNA, and RNA. As a consequence, DFX-Re3 affects the events related to apoptosis, RNA polymerases, and T-cell receptor signaling pathways. Finally, it is shown that DFX-Re3 induces immunogenic apoptotic cell death and exhibits potent antitumor activity in vivo. This study provides a new approach for the design of novel epigenetic drugs that can recode the cancer epigenome by intervening in mitochondrial metabolism and iron homeostasis.
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Affiliation(s)
- Zheng-Yin Pan
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, P. R. China
| | - Cai-Ping Tan
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, P. R. China
| | - Lu-Si Rao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, P. R. China
| | - Hang Zhang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, P. R. China
| | - Yue Zheng
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, P. R. China
| | - Liang Hao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, P. R. China
| | - Liang-Nian Ji
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, P. R. China
| | - Zong-Wan Mao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, P. R. China
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Leal A, Sidransky D, Brait M. Tissue and Cell-Free DNA-Based Epigenomic Approaches for Cancer Detection. Clin Chem 2020; 66:105-116. [PMID: 31843869 DOI: 10.1373/clinchem.2019.303594] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 11/01/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND Over 9 million people die of cancer each year worldwide, reflecting the unmet need for effective biomarkers for both cancer diagnosis and prognosis. Cancer diagnosis is complex because the majority of malignant tumors present with long periods of latency and lack of clinical presentation at early stages. During carcinogenesis, premalignant cells experience changes in their epigenetic landscapes, such as differential DNA methylation, histone modifications, nucleosome positioning, and higher orders of chromatin changes that confer growth advantage and contribute to determining the biologic phenotype of human cancers. CONTENT Recent progress in microarray platforms and next-generation sequencing approaches has allowed the characterization of abnormal epigenetic patterns genome wide in a large number of cancer cases. The sizable amount of processed data also comes with challenges regarding data management and assessment for effective biomarker exploration to be further applied in prospective clinical trials. Epigenetics-based single or panel tests of genes are being explored for clinical management to fulfill unmet needs in oncology. The advance of these tests to the clinical routine will depend on rigorous, extensive, and independent validation in well-annotated cohort of patients and commercial development of clinical routine-friendly and adequate procedures. SUMMARY In this review we discuss the analytic validation of tissue and cell-free DNA-based epigenomic approaches for early cancer detection, diagnosis, and treatment monitoring and the clinical utility of candidate epigenetic alterations applied to colorectal, glioblastoma, breast, prostate, bladder, and lung cancer management.
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Affiliation(s)
- Alessandro Leal
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - David Sidransky
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD.,Department of Otolaryngology and Head & Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Mariana Brait
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD.,Department of Otolaryngology and Head & Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD
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So JY, Skrypek N, Yang HH, Merchant AS, Nelson GW, Chen WD, Ishii H, Chen JM, Hu G, Achyut BR, Yoon EC, Han L, Huang C, Cam MC, Zhao K, Lee MP, Yang L. Induction of DNMT3B by PGE2 and IL6 at Distant Metastatic Sites Promotes Epigenetic Modification and Breast Cancer Colonization. Cancer Res 2020; 80:2612-2627. [PMID: 32265226 PMCID: PMC7299749 DOI: 10.1158/0008-5472.can-19-3339] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 02/26/2020] [Accepted: 03/27/2020] [Indexed: 11/16/2022]
Abstract
Current cancer treatments are largely based on the genetic characterization of primary tumors and are ineffective for metastatic disease. Here we report that DNA methyltransferase 3B (DNMT3B) is induced at distant metastatic sites and mediates epigenetic reprogramming of metastatic tumor cells. Multiomics analysis and spontaneous metastatic mouse models revealed that DNMT3B alters multiple pathways including STAT3, NFκB, PI3K/Akt, β-catenin, and Notch signaling, which are critical for cancer cell survival, apoptosis, proliferation, invasion, and colonization. PGE2 and IL6 were identified as critical inflammatory mediators in DNMT3B induction. DNMT3B expression levels positively correlated with human metastatic progression. Targeting IL6 or COX-2 reduced DNMT3B induction and improved chemo or PD1 therapy. We propose a novel mechanism linking the metastatic microenvironment with epigenetic alterations that occur at distant sites. These results caution against the "Achilles heel" in cancer therapies based on primary tumor characterization and suggests targeting DNMT3B induction as new option for treating metastatic disease. SIGNIFICANCE: These findings reveal that DNMT3B epigenetically regulates multiple pro-oncogenic signaling pathways via the inflammatory microenvironment at distant sites, cautioning the clinical approach basing current therapies on genetic characterization of primary tumors.
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Affiliation(s)
- Jae Young So
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Nicolas Skrypek
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Howard H Yang
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Anand S Merchant
- Collaborative Bioinformatics Resource, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - George W Nelson
- Collaborative Bioinformatics Resource, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Wei-Dong Chen
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
- Genetics Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Hiroki Ishii
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Jennifer M Chen
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Gangqing Hu
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Bhagelu R Achyut
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Esther C Yoon
- Department of Pathology, New York Medical College, Valhalla, New York
| | - Liying Han
- Department of Pathology, New York Medical College, Valhalla, New York
| | - Chuanshu Huang
- Department of Environmental Medicine and Biochemistry and Molecular Pharmacology, New York University School of Medicine, Tuxedo, New York
| | - Margaret C Cam
- Collaborative Bioinformatics Resource, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Keji Zhao
- Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Maxwell P Lee
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Li Yang
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, NCI, NIH, Bethesda, Maryland.
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Wong KK. DNMT1: A key drug target in triple-negative breast cancer. Semin Cancer Biol 2020; 72:198-213. [PMID: 32461152 DOI: 10.1016/j.semcancer.2020.05.010] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 05/04/2020] [Accepted: 05/18/2020] [Indexed: 02/06/2023]
Abstract
Triple-negative breast cancer (TNBC) is the most aggressive subtype of breast cancer. Altered epigenetics regulation including DNA hypermethylation by DNA methyltransferase 1 (DNMT1) has been implicated as one of the causes of TNBC tumorigenesis. In this review, the oncogenic functions rendered by DNMT1 in TNBCs, and DNMT1 inhibitors targeting TNBC cells are presented and discussed. In summary, DNMT1 expression is associated with poor breast cancer survival, and it is overexpressed in TNBC subtype. The oncogenic roles of DNMT1 in TNBCs include: (1) Repression of estrogen receptor (ER) expression; (2) Promotion of epithelial-mesenchymal transition (EMT) required for metastasis; (3) Induces cellular autophagy and; (4) Promotes the growth of cancer stem cells in TNBCs. DNMT1 confers these phenotypes by hypermethylating the promoter regions of ER, multiple tumor suppressor genes, microRNAs and epithelial markers involved in suppressing EMT. DNMT1 inhibitors exert anti-tumorigenic effects against TNBC cells. This includes the hypomethylating agents azacitidine, decitabine and guadecitabine that might sensitize TNBC patients to immune checkpoint blockade therapy. DNMT1 represents an epigenetic target for TNBC cells destruction as well as to derail their metastatic and aggressive phenotypes.
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Affiliation(s)
- Kah Keng Wong
- Department of Immunology, School of Medical Sciences, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia.
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Lu A, Wang W, Wang-Renault SF, Ring BZ, Tanaka Y, Weng J, Su L. 5-Aza-2'-deoxycytidine advances the epithelial-mesenchymal transition of breast cancer cells by demethylating Sipa1 promoter-proximal elements. J Cell Sci 2020; 133:jcs.236125. [PMID: 32193333 PMCID: PMC7240297 DOI: 10.1242/jcs.236125] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Accepted: 03/02/2020] [Indexed: 12/17/2022] Open
Abstract
Human breast cancer cells exhibit considerable diversity in the methylation status of genomic DNA CpGs that regulate metastatic transcriptome networks. In this study, we identified human Sipa1 promoter-proximal elements that contained a CpG island and demonstrated that the methylation status of the CpG island was inversely correlated with SIPA1 protein expression in cancer cells. 5-Aza-2′-deoxycytidine (5-Aza-CdR), a DNA methyltransferase inhibitor, promoted the expression of Sipa1 in the MCF7 breast cancer cells with a low level of SIPA1 expression. On the contrary, in MDA-MB-231 breast cancer cells with high SIPA1 expression levels, hypermethylation of the CpG island negatively regulated the transcription of Sipa1. In addition, the epithelial–mesenchymal transition (EMT) was reversed after knocking down Sipa1 in MDA-MB-231 cells. However, the EMT was promoted in MCF7 cells with over-expression of SIPA1 or treated with 5-Aza-CdR. Taken together, hypomethylation of the CpG island in Sipa1 promoter-proximal elements could enhance SIPA1 expression in breast cancer cells, which could facilitate EMT of cancer cells, possibly increasing a risk of cancer cell metastasis in individuals treated with 5-Aza-CdR. Summary: Hypomethylation by 5-Aza-CdR upregulates the SIPA1 expression and promotes epithelial–mesenchymal transition in breast cancer cells, possibly increasing the risk of cancer cell metastasis.
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Affiliation(s)
- Ang Lu
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Wei Wang
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Shu-Fang Wang-Renault
- INSERM UMR-S1147, CNRS SNC5014; Paris Descartes University, Equipe Labellisée Ligue Nationale Contre le Cancer, Paris 75006, France
| | - Brian Z Ring
- Institute of Genomic and Personalized Medicine, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Yoshimasa Tanaka
- Center for Medical Innovation, Nagasaki University, 1-7-1, Sakamoto, Nagasaki, 852-8588, Japan
| | - Jun Weng
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Li Su
- Key Laboratory of Molecular Biophysics of Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China .,Research Institute of Huazhong University of Science and Technology in Shenzhen, Shenzhen, 518063, China
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Coyne GO'S, Wang L, Zlott J, Juwara L, Covey JM, Beumer JH, Cristea MC, Newman EM, Koehler S, Nieva JJ, Garcia AA, Gandara DR, Miller B, Khin S, Miller SB, Steinberg SM, Rubinstein L, Parchment RE, Kinders RJ, Piekarz RL, Kummar S, Chen AP, Doroshow JH. Intravenous 5-fluoro-2'-deoxycytidine administered with tetrahydrouridine increases the proportion of p16-expressing circulating tumor cells in patients with advanced solid tumors. Cancer Chemother Pharmacol 2020; 85:979-993. [PMID: 32314030 PMCID: PMC7188725 DOI: 10.1007/s00280-020-04073-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 04/06/2020] [Indexed: 12/12/2022]
Abstract
PURPOSE Following promising responses to the DNA methyltransferase (DNMT) inhibitor 5-fluoro-2'-deoxycytidine (FdCyd) combined with tetrahydrouridine (THU) in phase 1 testing, we initiated a non-randomized phase 2 study to assess response to this combination in patients with advanced solid tumor types for which tumor suppressor gene methylation is potentially prognostic. To obtain pharmacodynamic evidence for DNMT inhibition by FdCyd, we developed a novel method for detecting expression of tumor suppressor protein p16/INK4A in circulating tumor cells (CTCs). METHODS Patients in histology-specific strata (breast, head and neck [H&N], or non-small cell lung cancers [NSCLC] or urothelial transitional cell carcinoma) were administered FdCyd (100 mg/m2) and THU (350 mg/m2) intravenously 5 days/week for 2 weeks, in 28-day cycles, and progression-free survival (PFS) rate and objective response rate (ORR) were evaluated. Blood specimens were collected for CTC analysis. RESULTS Ninety-three eligible patients were enrolled (29 breast, 21 H&N, 25 NSCLC, and 18 urothelial). There were three partial responses. All strata were terminated early due to insufficient responses (H&N, NSCLC) or slow accrual (breast, urothelial). However, the preliminary 4-month PFS rate (42%) in the urothelial stratum exceeded the predefined goal-though the ORR (5.6%) did not. An increase in the proportion of p16-expressing cytokeratin-positive CTCs was detected in 69% of patients evaluable for clinical and CTC response, but was not significantly associated with clinical response. CONCLUSION Further study of FdCyd + THU is potentially warranted in urothelial carcinoma but not NSCLC or breast or H&N cancer. Increase in the proportion of p16-expressing cytokeratin-positive CTCs is a pharmacodynamic marker of FdCyd target engagement.
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Affiliation(s)
- Geraldine O 'Sullivan Coyne
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, 31 Center Drive, Bldg. 31 Room 3A-44, Bethesda, MD, 20892, USA
| | - Lihua Wang
- Clinical Pharmacodynamic Biomarkers Program, Applied/Developmental Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Jennifer Zlott
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, 31 Center Drive, Bldg. 31 Room 3A-44, Bethesda, MD, 20892, USA
| | - Lamin Juwara
- Clinical Monitoring Research Program, Clinical Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Joseph M Covey
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, 31 Center Drive, Bldg. 31 Room 3A-44, Bethesda, MD, 20892, USA
| | - Jan H Beumer
- Department of Pharmaceutical Sciences, University of Pittsburgh School of Pharmacy, Pittsburgh, PA, USA
| | - Mihaela C Cristea
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA, USA
| | - Edward M Newman
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, CA, USA
| | | | - Jorge J Nieva
- University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Agustin A Garcia
- University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA, USA
- Louisiana State University, New Orleans, LA, 70112, USA
| | - David R Gandara
- University of California Davis Cancer Center, Sacramento, CA, USA
| | - Brandon Miller
- Clinical Pharmacodynamic Biomarkers Program, Applied/Developmental Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Sonny Khin
- Clinical Pharmacodynamic Biomarkers Program, Applied/Developmental Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Sarah B Miller
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, 31 Center Drive, Bldg. 31 Room 3A-44, Bethesda, MD, 20892, USA
| | - Seth M Steinberg
- Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Larry Rubinstein
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, 31 Center Drive, Bldg. 31 Room 3A-44, Bethesda, MD, 20892, USA
| | - Ralph E Parchment
- Clinical Pharmacodynamic Biomarkers Program, Applied/Developmental Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Robert J Kinders
- Clinical Pharmacodynamic Biomarkers Program, Applied/Developmental Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Richard L Piekarz
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, 31 Center Drive, Bldg. 31 Room 3A-44, Bethesda, MD, 20892, USA
| | - Shivaani Kummar
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, 31 Center Drive, Bldg. 31 Room 3A-44, Bethesda, MD, 20892, USA
| | - Alice P Chen
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, 31 Center Drive, Bldg. 31 Room 3A-44, Bethesda, MD, 20892, USA
| | - James H Doroshow
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, 31 Center Drive, Bldg. 31 Room 3A-44, Bethesda, MD, 20892, USA.
- Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.
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40
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Bao-Caamano A, Rodriguez-Casanova A, Diaz-Lagares A. Epigenetics of Circulating Tumor Cells in Breast Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1220:117-134. [PMID: 32304083 DOI: 10.1007/978-3-030-35805-1_8] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Liquid biopsy based on the analysis of circulating tumor cells (CTCs) has emerged as an important field of research. Molecular characterization of CTCs can provide insights into cancer biology and biomarkers for the clinic, representing a non-invasive powerful tool for monitoring breast cancer metastasis and predict the therapeutic response. Epigenetic mechanisms play a key role in the control of gene expression and their alteration contributes to cancer development and progression. These epigenetic modifications in CTCs have been described mainly related to modifications of the DNA methylation pattern and changes in the expression profile of noncoding RNAs. Here we summarize the recent findings on the epigenetic characterization of CTCs in breast cancer and their clinical value as tumor biomarkers, and discuss challenges and opportunities in this field.
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Affiliation(s)
- Aida Bao-Caamano
- Cancer Epigenomics, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, Spain
| | - Aitor Rodriguez-Casanova
- Cancer Epigenomics, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, Spain.,Roche-Chus Joint Unit, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago de Compostela, Santiago de Compostela, Spain
| | - Angel Diaz-Lagares
- Cancer Epigenomics, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, Spain. .,Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain.
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Güiza F, Vanhorebeek I, Verstraete S, Verlinden I, Derese I, Ingels C, Dulfer K, Verbruggen SC, Garcia Guerra G, Joosten KF, Wouters PJ, Van den Berghe G. Effect of early parenteral nutrition during paediatric critical illness on DNA methylation as a potential mediator of impaired neurocognitive development: a pre-planned secondary analysis of the PEPaNIC international randomised controlled trial. THE LANCET RESPIRATORY MEDICINE 2020; 8:288-303. [DOI: 10.1016/s2213-2600(20)30046-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 11/07/2019] [Accepted: 11/13/2019] [Indexed: 12/12/2022]
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42
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Kuehl PJ, Tellez CS, Grimes MJ, March TH, Tessema M, Revelli DA, Mallis LM, Dye WW, Sniegowski T, Badenoch A, Burke M, Dubose D, Vodak DT, Picchi MA, Belinsky SA. 5-Azacytidine inhaled dry powder formulation profoundly improves pharmacokinetics and efficacy for lung cancer therapy through genome reprogramming. Br J Cancer 2020; 122:1194-1204. [PMID: 32103148 PMCID: PMC7156464 DOI: 10.1038/s41416-020-0765-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 02/06/2020] [Indexed: 12/31/2022] Open
Abstract
Background Epigenetic therapy through demethylation of 5-methylcytosine has been largely ineffective in treating lung cancer, most likely due to poor tissue distribution with oral or subcutaneous delivery of drugs such as 5-azacytidine (5AZA). An inhalable, stable dry powder formulation of 5AZA was developed. Methods Pharmacokinetics of inhaled dry powder and aqueous formulations of 5AZA were compared to an injected formulation. Efficacy studies and effect of therapy on the epigenome were conducted in an orthotopic rat lung cancer model for inhaled formulations. Results Inhaled dry powder 5AZA showed superior pharmacokinetic properties in lung, liver, brain and blood compared to the injected formulation and for all tissues except lung compared to an inhaled aqueous formulation. Only dry powder 5AZA was detected in brain (~4-h half-life). Inhaled dry powder was superior to inhaled aqueous 5AZA in reducing tumour burden 70–95%. Superiority of inhaled 5AZA dry powder was linked to effectively reprogramming the cancer genome through demethylation and gene expression changes in cancer signalling and immune pathways. Conclusions These findings could lead to widespread use of this drug as the first inhaled dry powder therapeutic for treating local and metastatic lung cancer, for adjuvant therapy, and in combination with immunotherapy to improve patient survival.
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Affiliation(s)
- Philip J Kuehl
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM, USA
| | - Carmen S Tellez
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM, USA
| | - Marcie J Grimes
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM, USA
| | - Thomas H March
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM, USA
| | - Mathewos Tessema
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM, USA
| | - David A Revelli
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM, USA
| | - Larry M Mallis
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM, USA
| | - Wendy W Dye
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM, USA
| | - Tyler Sniegowski
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM, USA
| | | | | | | | | | - Maria A Picchi
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM, USA
| | - Steven A Belinsky
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, NM, USA.
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DNA sequence context as a marker of CpG methylation instability in normal and cancer tissues. Sci Rep 2020; 10:1721. [PMID: 32015379 PMCID: PMC6997448 DOI: 10.1038/s41598-020-58331-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 01/13/2020] [Indexed: 11/09/2022] Open
Abstract
DNA methylation alterations are related to multiple molecular mechanisms. The DNA context of CpG sites plays a crucial role in the maintenance and stability of methylation patterns. The quantitative relationship between DNA composition and DNA methylation has been studied in normal as well as pathological conditions, showing that DNA methylation status is highly dependent on the local sequence context. In this work, we describe this relationship by analyzing the DNA sequence context associated to methylation profiles in both physiological and pathological conditions. In particular, we used DNA motifs to describe methylation stability patterns in normal tissues and aberrant methylation events in cancer lesions. In this manuscript, we show how different groups of DNA sequences can be related to specific epigenetic events, across normal and cancer tissues, and provide a thorough structural and functional characterization of these sequences.
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44
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Jinesh GG, Brohl AS. The genetic script of metastasis. Biol Rev Camb Philos Soc 2020; 95:244-266. [PMID: 31663259 DOI: 10.1111/brv.12562] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 09/24/2019] [Accepted: 09/26/2019] [Indexed: 01/24/2023]
Abstract
Metastasis is a pivotal event that changes the course of cancers from benign and treatable to malignant and difficult to treat, resulting in the demise of patients. Understanding the genetic control of metastasis is thus crucial to develop efficient and sustainable targeted therapies. Here we discuss the alterations in epigenetic mechanisms, transcription, chromosomal instability, chromosome imprinting, non-coding RNAs, coding RNAs, mutant RNAs, enhancers, G-quadruplexes, and copy number variation to dissect the genetic control of metastasis. We conclude that the genetic control of metastasis is predominantly executed through epithelial to mesenchymal transition and evasion of cell death. We discuss how genetic regulatory mechanisms can be harnessed for therapeutic purposes to achieve sustainable control over cancer metastasis.
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Affiliation(s)
- Goodwin G Jinesh
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, 33612, U.S.A.,Sarcoma Department, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, 33612, U.S.A
| | - Andrew S Brohl
- Sarcoma Department, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, 33612, U.S.A.,Chemical Biology and Molecular Medicine Program, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, 33612, U.S.A
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45
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de Ruijter TC, van der Heide F, Smits KM, Aarts MJ, van Engeland M, Heijnen VCG. Prognostic DNA methylation markers for hormone receptor breast cancer: a systematic review. Breast Cancer Res 2020; 22:13. [PMID: 32005275 PMCID: PMC6993426 DOI: 10.1186/s13058-020-1250-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 01/15/2020] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND In patients with hormone receptor-positive breast cancer, differentiating between patients with a low and a high risk of recurrence is an ongoing challenge. In current practice, prognostic clinical parameters are used for risk prediction. DNA methylation markers have been proven to be of additional prognostic value in several cancer types. Numerous prognostic DNA methylation markers for breast cancer have been published in the literature. However, to date, none of these markers are used in clinical practice. METHODS We conducted a systematic review of PubMed and EMBASE to assess the number and level of evidence of published DNA methylation markers for hormone receptor-positive breast cancer. To obtain an overview of the reporting quality of the included studies, all were scored according to the REMARK criteria that were established as reporting guidelines for prognostic biomarker studies. RESULTS A total of 74 studies were identified reporting on 87 different DNA methylation markers. Assessment of the REMARK criteria showed variation in reporting quality of the studies. Eighteen single markers and one marker panel were studied in multiple independent populations. Hypermethylation of the markers RASSF1, BRCA, PITX2, CDH1, RARB, PCDH10 and PGR, and the marker panel GSTP1, RASSF1 and RARB showed a statistically significant correlation with poor disease outcome that was confirmed in at least one other, independent study. CONCLUSION This systematic review provides an overview on published prognostic DNA methylation markers for hormone receptor-positive breast cancer and identifies eight markers that have been independently validated. Analysis of the reporting quality of included studies suggests that future research on this topic would benefit from standardised reporting guidelines.
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Affiliation(s)
- Tim C. de Ruijter
- Division of Medical Oncology, Maastricht University Medical Center, PO Box 5800, 6202 AZ Maastricht, The Netherlands
- GROW – School for Oncology and Developmental Biology, Maastricht University Medical Center, 6200 MD Maastricht, The Netherlands
| | - Frank van der Heide
- Division of Medical Oncology, Maastricht University Medical Center, PO Box 5800, 6202 AZ Maastricht, The Netherlands
| | - Kim M. Smits
- Division of Medical Oncology, Maastricht University Medical Center, PO Box 5800, 6202 AZ Maastricht, The Netherlands
- GROW – School for Oncology and Developmental Biology, Maastricht University Medical Center, 6200 MD Maastricht, The Netherlands
- Department of Pathology, Maastricht University Medical Centre, 6202 AZ Maastricht, The Netherlands
| | - Maureen J. Aarts
- Division of Medical Oncology, Maastricht University Medical Center, PO Box 5800, 6202 AZ Maastricht, The Netherlands
- GROW – School for Oncology and Developmental Biology, Maastricht University Medical Center, 6200 MD Maastricht, The Netherlands
| | - Manon van Engeland
- GROW – School for Oncology and Developmental Biology, Maastricht University Medical Center, 6200 MD Maastricht, The Netherlands
- Department of Pathology, Maastricht University Medical Centre, 6202 AZ Maastricht, The Netherlands
| | - Vivianne C. G. Heijnen
- Division of Medical Oncology, Maastricht University Medical Center, PO Box 5800, 6202 AZ Maastricht, The Netherlands
- GROW – School for Oncology and Developmental Biology, Maastricht University Medical Center, 6200 MD Maastricht, The Netherlands
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46
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Court F, Le Boiteux E, Fogli A, Müller-Barthélémy M, Vaurs-Barrière C, Chautard E, Pereira B, Biau J, Kemeny JL, Khalil T, Karayan-Tapon L, Verrelle P, Arnaud P. Transcriptional alterations in glioma result primarily from DNA methylation-independent mechanisms. Genome Res 2019; 29:1605-1621. [PMID: 31533980 PMCID: PMC6771409 DOI: 10.1101/gr.249219.119] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 08/27/2019] [Indexed: 02/06/2023]
Abstract
In cancer cells, aberrant DNA methylation is commonly associated with transcriptional alterations, including silencing of tumor suppressor genes. However, multiple epigenetic mechanisms, including polycomb repressive marks, contribute to gene deregulation in cancer. To dissect the relative contribution of DNA methylation–dependent and –independent mechanisms to transcriptional alterations at CpG island/promoter-associated genes in cancer, we studied 70 samples of adult glioma, a widespread type of brain tumor, classified according to their isocitrate dehydrogenase (IDH1) mutation status. We found that most transcriptional alterations in tumor samples were DNA methylation–independent. Instead, altered histone H3 trimethylation at lysine 27 (H3K27me3) was the predominant molecular defect at deregulated genes. Our results also suggest that the presence of a bivalent chromatin signature at CpG island promoters in stem cells predisposes not only to hypermethylation, as widely documented, but more generally to all types of transcriptional alterations in transformed cells. In addition, the gene expression strength in healthy brain cells influences the choice between DNA methylation- and H3K27me3-associated silencing in glioma. Highly expressed genes were more likely to be repressed by H3K27me3 than by DNA methylation. Our findings support a model in which altered H3K27me3 dynamics, more specifically defects in the interplay between polycomb protein complexes and the brain-specific transcriptional machinery, is the main cause of transcriptional alteration in glioma cells. Our study provides the first comprehensive description of epigenetic changes in glioma and their relative contribution to transcriptional changes. It may be useful for the design of drugs targeting cancer-related epigenetic defects.
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Affiliation(s)
- Franck Court
- Laboratoire Génétique Reproduction et Développement (GReD), Université Clermont Auvergne, CNRS, INSERM, BP 38, Clermont-Ferrand 63001, France
| | - Elisa Le Boiteux
- Laboratoire Génétique Reproduction et Développement (GReD), Université Clermont Auvergne, CNRS, INSERM, BP 38, Clermont-Ferrand 63001, France
| | - Anne Fogli
- Laboratoire Génétique Reproduction et Développement (GReD), Université Clermont Auvergne, CNRS, INSERM, BP 38, Clermont-Ferrand 63001, France.,Biochemistry and Molecular Biology Department, Clermont-Ferrand Hospital, Clermont-Ferrand 63003, France
| | - Mélanie Müller-Barthélémy
- Laboratoire Génétique Reproduction et Développement (GReD), Université Clermont Auvergne, CNRS, INSERM, BP 38, Clermont-Ferrand 63001, France.,Pathology Department, Jean Perrin Center, Clermont-Ferrand 63011, France
| | - Catherine Vaurs-Barrière
- Laboratoire Génétique Reproduction et Développement (GReD), Université Clermont Auvergne, CNRS, INSERM, BP 38, Clermont-Ferrand 63001, France
| | - Emmanuel Chautard
- Pathology Department, Jean Perrin Center, Clermont-Ferrand 63011, France.,Université Clermont Auvergne, INSERM, U1240 IMoST, Clermont-Ferrand 63011, France
| | - Bruno Pereira
- Biostatistics Department, Délégation à la Recherche Clinique et à l'Innovation, Clermont-Ferrand Hospital, Clermont-Ferrand 63003, France
| | - Julian Biau
- Université Clermont Auvergne, INSERM, U1240 IMoST, Clermont-Ferrand 63011, France.,Radiotherapy Department, Jean Perrin Center, Clermont-Ferrand 63011, France
| | - Jean-Louis Kemeny
- Pathology Department, Université Clermont Auvergne and Clermont-Ferrand Hospital, Clermont-Ferrand 63003, France
| | - Toufic Khalil
- Department of Neurosurgery, Clermont-Ferrand Hospital, Clermont-Ferrand 63003, France
| | - Lucie Karayan-Tapon
- INSERM, U1084, Poitiers 86021, France.,Poitiers University, Poitiers 86000, France.,Department of Cancer Biology, Poitiers Hospital, Poitiers 86021, France
| | - Pierre Verrelle
- INSERM, U1196 CNRS UMR9187, Curie Institute, Orsay 91405, France.,Radiotherapy Department Curie Institute, Paris 75005, France.,Université Clermont Auvergne, Clermont-Ferrand 63000, France
| | - Philippe Arnaud
- Laboratoire Génétique Reproduction et Développement (GReD), Université Clermont Auvergne, CNRS, INSERM, BP 38, Clermont-Ferrand 63001, France
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Kumar R, Paul AM, Rameshwar P, Pillai MR. Epigenetic Dysregulation at the Crossroad of Women's Cancer. Cancers (Basel) 2019; 11:cancers11081193. [PMID: 31426393 PMCID: PMC6721458 DOI: 10.3390/cancers11081193] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 08/07/2019] [Accepted: 08/08/2019] [Indexed: 02/07/2023] Open
Abstract
An increasingly number of women of all age groups are affected by cancer, despite substantial progress in our understanding of cancer pathobiology, the underlying genomic alterations and signaling cascades, and cellular-environmental interactions. Though our understanding of women’s cancer is far more complete than ever before, there is no comprehensive model to explain the reasons behind the increased incidents of certain reproductive cancer among older as well as younger women. It is generally suspected that environmental and life-style factors affecting hormonal and growth control pathways might help account for the rise of women’s cancers in younger age, as well, via epigenetic mechanisms. Epigenetic regulators play an important role in orchestrating an orderly coordination of cellular signals in gene activity in response to upstream signaling and/or epigenetic modifiers present in a dynamic extracellular milieu. Here we will discuss the broad principles of epigenetic regulation of DNA methylation and demethylation, histone acetylation and deacetylation, and RNA methylation in women’s cancers in the context of gene expression, hormonal action, and the EGFR family of cell surface receptor tyrosine kinases. We anticipate that a better understanding of the epigenetics of women’s cancers may provide new regulatory leads and further fuel the development of new epigenetic biomarkers and therapeutic approaches.
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Affiliation(s)
- Rakesh Kumar
- Cancer Biology Program, Rajiv Gandhi Centre for Biotechnology, Trivandrum, Kerala 695014, India.
- Department of Medicine, Division of Hematology-Oncology, Rutgers New Jersey Medical School, Newark, NJ 07103, USA.
- Department of Human and Molecular Genetics, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, USA.
| | - Aswathy Mary Paul
- Cancer Biology Program, Rajiv Gandhi Centre for Biotechnology, Trivandrum, Kerala 695014, India
- Graduate Degree Program, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Pranela Rameshwar
- Department of Medicine, Division of Hematology-Oncology, Rutgers New Jersey Medical School, Newark, NJ 07103, USA
| | - M Radhakrishna Pillai
- Cancer Biology Program, Rajiv Gandhi Centre for Biotechnology, Trivandrum, Kerala 695014, India
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48
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Downs BM, Mercado-Rodriguez C, Cimino-Mathews A, Chen C, Yuan JP, Van Den Berg E, Cope LM, Schmitt F, Tse GM, Ali SZ, Meir-Levi D, Sood R, Li J, Richardson AL, Mosunjac MB, Rizzo M, Tulac S, Kocmond KJ, de Guzman T, Lai EW, Rhees B, Bates M, Wolff AC, Gabrielson E, Harvey SC, Umbricht CB, Visvanathan K, Fackler MJ, Sukumar S. DNA Methylation Markers for Breast Cancer Detection in the Developing World. Clin Cancer Res 2019; 25:6357-6367. [PMID: 31300453 DOI: 10.1158/1078-0432.ccr-18-3277] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 02/04/2019] [Accepted: 07/02/2019] [Indexed: 12/21/2022]
Abstract
PURPOSE An unmet need in low-resource countries is an automated breast cancer detection assay to prioritize women who should undergo core breast biopsy and pathologic review. Therefore, we sought to identify and validate a panel of methylated DNA markers to discriminate between cancer and benign breast lesions using cells obtained by fine-needle aspiration (FNA).Experimental Design: Two case-control studies were conducted comparing cancer and benign breast tissue identified from clinical repositories in the United States, China, and South Africa for marker selection/training (N = 226) and testing (N = 246). Twenty-five methylated markers were assayed by Quantitative Multiplex-Methylation-Specific PCR (QM-MSP) to select and test a cancer-specific panel. Next, a pilot study was conducted on archival FNAs (49 benign, 24 invasive) from women with mammographically suspicious lesions using a newly developed, 5-hour, quantitative, automated cartridge system. We calculated sensitivity, specificity, and area under the receiver-operating characteristic curve (AUC) compared with histopathology for the marker panel. RESULTS In the discovery cohort, 10 of 25 markers were selected that were highly methylated in breast cancer compared with benign tissues by QM-MSP. In the independent test cohort, this panel yielded an AUC of 0.937 (95% CI = 0.900-0.970). In the FNA pilot, we achieved an AUC of 0.960 (95% CI = 0.883-1.0) using the automated cartridge system. CONCLUSIONS We developed and piloted a fast and accurate methylation marker-based automated cartridge system to detect breast cancer in FNA samples. This quick ancillary test has the potential to prioritize cancer over benign tissues for expedited pathologic evaluation in poorly resourced countries.
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Affiliation(s)
- Bradley M Downs
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | - Ashley Cimino-Mathews
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Chuang Chen
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, Wuhan, P.R. China
| | - Jing-Ping Yuan
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan, P.R. China
| | - Eunice Van Den Berg
- Department of Anatomical Pathology, University of Witwaterstrand and National Health Laboratory Service, Johannesburg, South Africa
| | - Leslie M Cope
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Fernando Schmitt
- Medical Faculty of Porto University, Institute of Molecular Pathology and Immunology of Porto University, Porto, Portugal
| | - Gary M Tse
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong Special Administrative Region
| | - Syed Z Ali
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Danielle Meir-Levi
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Rupali Sood
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Juanjuan Li
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, Wuhan, P.R. China
| | - Andrea L Richardson
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Marina B Mosunjac
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia
| | - Monica Rizzo
- Department of Surgery, Emory University School of Medicine, Atlanta, Georgia
| | | | | | | | | | | | | | - Antonio C Wolff
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Edward Gabrielson
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Susan C Harvey
- Department of Radiology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Christopher B Umbricht
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Kala Visvanathan
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Bloomberg School of Public Health, Baltimore, Maryland
| | - Mary Jo Fackler
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
| | - Saraswati Sukumar
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland.
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Hata A, Nakajima T, Matsusaka K, Fukuyo M, Morimoto J, Yamamoto T, Sakairi Y, Rahmutulla B, Ota S, Wada H, Suzuki H, Matsubara H, Yoshino I, Kaneda A. A low DNA methylation epigenotype in lung squamous cell carcinoma and its association with idiopathic pulmonary fibrosis and poorer prognosis. Int J Cancer 2019; 146:388-399. [PMID: 31241180 DOI: 10.1002/ijc.32532] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Revised: 06/09/2019] [Accepted: 06/14/2019] [Indexed: 12/25/2022]
Abstract
Patients with idiopathic pulmonary fibrosis (IPF) have higher risk of developing lung cancer, for example, squamous cell carcinoma (SCC), and show poor prognosis, while the molecular basis has not been fully investigated. Here we conducted DNA methylome analysis of lung SCC using 20 SCC samples with/without IPF, and noncancerous lung tissue samples from smokers/nonsmokers, using Infinium HumanMethylation 450K array. SCC was clustered into low- and high-methylation epigenotypes by hierarchical clustering analysis. Genes hypermethylated in SCC significantly included genes targeted by polycomb repressive complex in embryonic stem cells, and genes associated with Gene Ontology terms, for example, "transcription" and "cell adhesion," while genes hypermethylated specifically in high-methylation subgroup significantly included genes associated with "negative regulation of growth." Low-methylation subgroup significantly correlated with IPF (78%, vs. 17% in high-methylation subgroup, p = 0.04), and the correlation was validated by additional Infinium analysis of SCC samples (n = 44 in total), and data from The Cancer Genome Atlas (n = 390). The correlation between low-methylation subgroup and IPF was further validated by quantitative methylation analysis of marker genes commonly hypermethylated in SCC (HOXA2, HOXA9 and PCDHGB6), and markers specifically hypermethylated in high-methylation subgroup (DLEC1, CFTR, MT1M, CRIP3 and ALDH7A1) in 77 SCC cases using pyrosequencing (p = 0.003). Furthermore, low-methylation epigenotype significantly correlated with poorer prognosis among all SCC patients, or among patients without IPF. Multivariate analysis showed that low-methylation epigenotype is an independent predictor of poor prognosis. These may suggest that lung SCC could be stratified into molecular subtypes with distinct prognosis, and low-methylation lung SCC that significantly correlates with IPF shows unfavorable outcome.
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Affiliation(s)
- Atsushi Hata
- Department of General Thoracic Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan.,Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Takahiro Nakajima
- Department of General Thoracic Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Keisuke Matsusaka
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Masaki Fukuyo
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan.,Department of Genome Research and Development, Kazusa DNA Research Institute, Chiba, Japan
| | - Junichi Morimoto
- Department of General Thoracic Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Takayoshi Yamamoto
- Department of General Thoracic Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Yuichi Sakairi
- Department of General Thoracic Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Bahityar Rahmutulla
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Satoshi Ota
- Department of Pathology, Chiba University Hospital, Chiba, Japan
| | - Hironobu Wada
- Department of General Thoracic Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Hidemi Suzuki
- Department of General Thoracic Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Hisahiro Matsubara
- Department of Frontier Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Ichiro Yoshino
- Department of General Thoracic Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Atsushi Kaneda
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
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50
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Humphries B, Wang Z, Yang C. MicroRNA Regulation of Epigenetic Modifiers in Breast Cancer. Cancers (Basel) 2019; 11:E897. [PMID: 31252590 PMCID: PMC6678197 DOI: 10.3390/cancers11070897] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 06/16/2019] [Accepted: 06/24/2019] [Indexed: 12/20/2022] Open
Abstract
Epigenetics refers to the heritable changes in gene expression without a change in the DNA sequence itself. Two of these major changes include aberrant DNA methylation as well as changes to histone modification patterns. Alterations to the epigenome can drive expression of oncogenes and suppression of tumor suppressors, resulting in tumorigenesis and cancer progression. In addition to modifications of the epigenome, microRNA (miRNA) dysregulation is also a hallmark for cancer initiation and metastasis. Advances in our understanding of cancer biology demonstrate that alterations in the epigenome are not only a major cause of miRNA dysregulation in cancer, but that miRNAs themselves also indirectly drive these DNA and histone modifications. More explicitly, recent work has shown that miRNAs can regulate chromatin structure and gene expression by directly targeting key enzymes involved in these processes. This review aims to summarize these research findings specifically in the context of breast cancer. This review also discusses miRNAs as epigenetic biomarkers and as therapeutics, and presents a comprehensive summary of currently validated epigenetic targets in breast cancer.
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Affiliation(s)
- Brock Humphries
- Center for Molecular Imaging, Department of Radiology, University of Michigan, Ann Arbor, MI 48109; USA.
| | - Zhishan Wang
- Department of Toxicology and Cancer Biology, College of Medicine, University of Kentucky, Lexington, KY 40536, USA
| | - Chengfeng Yang
- Department of Toxicology and Cancer Biology, College of Medicine, University of Kentucky, Lexington, KY 40536, USA.
- Center for Research on Environment Disease, College of Medicine, University of Kentucky, Lexington, KY 40536; USA.
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