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Satomi K, Ichimura K, Shibahara J. Decoding the DNA methylome of central nervous system tumors: An emerging modality for integrated diagnosis. Pathol Int 2024; 74:51-67. [PMID: 38224248 DOI: 10.1111/pin.13402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/16/2023] [Accepted: 12/18/2023] [Indexed: 01/16/2024]
Abstract
The definitive diagnosis and classification of individual cancers are crucial for patient care and cancer research. To achieve a robust diagnosis of central nervous system (CNS) tumors, a genotype-phenotype integrated diagnostic approach was introduced in recent versions of the World Health Organization classification, followed by the incorporation of a genome-wide DNA methylome-based classification. Microarray-based platforms are widely used to obtain DNA methylome data, and the German Cancer Research Center (Deutsches Krebsforschungszentrum [DKFZ]) has a webtool for a DNA methylation-based classifier (DKFZ classifier). Integration of DNA methylome will further enhance the precision of CNS tumor classification, especially in diagnostically challenging cases. However, in the clinical application of DNA methylome-based classification, challenges related to data interpretation persist, in addition to technical caveats, regulations, and limited accessibility. Dimensionality reduction (DMR) can complement integrated diagnosis by visualizing a profile and comparing it with other known samples. Therefore, DNA methylome-based classification is a highly useful research tool for auxiliary analysis in challenging diagnostic and rare disease cases, and for establishing novel tumor concepts. Decoding the DNA methylome, especially by DMR in addition to DKFZ classifier, emphasizes the capability of grasping the fundamental biological principles that provide new perspectives on CNS tumors.
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Affiliation(s)
- Kaishi Satomi
- Department of Pathology, Kyorin University Faculty of Medicine, Tokyo, Japan
| | - Koichi Ichimura
- Department of Brain Disease Translational Research, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Junji Shibahara
- Department of Pathology, Kyorin University Faculty of Medicine, Tokyo, Japan
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Yang Y, Zeng Q, Liu G, Zheng S, Luo T, Guo Y, Tang J, Huang Y. Hierarchical classification-based pan-cancer methylation analysis to classify primary cancer. BMC Bioinformatics 2023; 24:465. [PMID: 38066424 PMCID: PMC10709847 DOI: 10.1186/s12859-023-05529-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 10/12/2023] [Indexed: 12/18/2023] Open
Abstract
Hierarchical classification offers a more specific categorization of data and breaks down large classification problems into subproblems, providing improved prediction accuracy and predictive power for undefined categories, while also mitigating the impact of poor-quality data. Despite these advantages, its application in predicting primary cancer is rare. To leverage the similarity of cancers and the specificity of methylation patterns among them, we developed the Cancer Hierarchy Classification Tool (CHCT) using the idea of hierarchical classification, with methylation data from 30 cancer types and 8239 methylome samples downloaded from publicly available databases (The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO)). We used unsupervised clustering to divide the classification subproblems and screened differentially methylated sites using Analysis of variance (ANOVA) test, Tukey-kramer test, and Boruta algorithms to construct models for each classifier module. After validation, CHCT accurately classified 1568 out of 1660 cases in the test set, with an average accuracy of 94.46%. We further curated an independent validation cohort of 677 cancer samples from GEO and assigned a diagnosis using CHCT, which showed high diagnostic potential with generally high accuracies (an average accuracy of 91.40%). Moreover, CHCT demonstrates predictive capability for additional cancer types beyond its original classifier scope as demonstrated in the medulloblastoma and pituitary tumor datasets. In summary, CHCT can hierarchically classify primary cancer by methylation profile, by splitting a large-scale classification of 30 cancer types into ten smaller classification problems. These results indicate that cancer hierarchical classification has the potential to be an accurate and robust cancer classification method.
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Affiliation(s)
- Youpeng Yang
- Medicine School, Sun Yat-sen University, Shenzhen, 518107, China
| | - Qiuhong Zeng
- Geneplus-Shenzhen Institute, Shenzhen, 518118, China
| | - Gaotong Liu
- Geneplus-Shenzhen Institute, Shenzhen, 518118, China
| | - Shiyao Zheng
- Medicine School, Sun Yat-sen University, Shenzhen, 518107, China
| | - Tianyang Luo
- Medicine School, Sun Yat-sen University, Shenzhen, 518107, China
| | - Yibin Guo
- Medicine School, Sun Yat-sen University, Shenzhen, 518107, China.
| | - Jia Tang
- NHC Key Laboratory of Male Reproduction and Genetics, Guangdong Provincial Reproductive Science Institute (Guangdong Provincial Fertility Hospital), Guangzhou, 510062, China.
- School of Medicine, Jinan University, Guangzhou, 510632, China.
| | - Yi Huang
- Geneplus-Shenzhen Institute, Shenzhen, 518118, China.
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Lockwood CM, Borsu L, Cankovic M, Earle JSL, Gocke CD, Hameed M, Jordan D, Lopategui JR, Pullambhatla M, Reuther J, Rumilla KM, Tafe LJ, Temple-Smolkin RL, Terraf P, Tsimberidou AM. Recommendations for Cell-Free DNA Assay Validations: A Joint Consensus Recommendation of the Association for Molecular Pathology and College of American Pathologists. J Mol Diagn 2023; 25:876-897. [PMID: 37806433 DOI: 10.1016/j.jmoldx.2023.09.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 08/22/2023] [Accepted: 09/14/2023] [Indexed: 10/10/2023] Open
Abstract
Diagnosing, selecting therapy for, and monitoring cancer in patients using a minimally invasive blood test represents a significant advance in precision medicine. Wide variability exists in how circulating tumor DNA (ctDNA) assays are developed, validated, and reported in the literature, which hinders clinical adoption and may negatively impact patient care. Standardization is needed for factors affecting ctDNA assay performance and reporting, including pre-analytical variables, analytical considerations, and elements of laboratory assay reporting. The Association for Molecular Pathology Clinical Practice Committee's Liquid Biopsy Working Group (LBxWG), including organizational representation from the American Society of Clinical Oncology and the College of American Pathologists, has undertaken a full-text data extraction of 1228 ctDNA publications that describe assays performed in patients with lymphoma and solid tumor malignancies. With an emphasis on clinical assay validation, the LBxWG has developed a set of 13 best practice consensus recommendations for validating, reporting, and publishing clinical ctDNA assays. Recommendations include reporting key pre-analytical considerations and assay performance metrics; this analysis demonstrates these elements are inconsistently included in publications. The LBxWG recommendations are intended to assist clinical laboratories with validating and reporting ctDNA assays and to ensure high-quality data are included in publications. It is expected that these recommendations will need to be updated as the body of literature continues to mature.
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Affiliation(s)
- Christina M Lockwood
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington; Brotman Baty Institute for Precision Medicine, Seattle, Washington.
| | - Laetitia Borsu
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Milena Cankovic
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Henry Ford Hospital, Detroit, Michigan
| | - Jonathan S L Earle
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Hartford Hospital, Hartford, Connecticut; Hartford Pathology Associates, Hartford, Connecticut
| | - Christopher D Gocke
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Meera Hameed
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Jean R Lopategui
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | | | - Jacquelyn Reuther
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Invitae, San Francisco, California
| | - Kandelaria M Rumilla
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Laura J Tafe
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire
| | | | - Panieh Terraf
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Apostolia M Tsimberidou
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Investigational Cancer Therapeutics, Unit 455, The University of Texas MD Anderson Cancer Center, Houston, Texas
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Takahashi K, Takeda Y, Ono Y, Isomoto H, Mizukami Y. Current status of molecular diagnostic approaches using liquid biopsy. J Gastroenterol 2023; 58:834-847. [PMID: 37470859 PMCID: PMC10423147 DOI: 10.1007/s00535-023-02024-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 07/08/2023] [Indexed: 07/21/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the most aggressive and lethal cancers, and developing an efficient and reliable approach for its early-stage diagnosis is urgently needed. Precancerous lesions of PDAC, such as pancreatic intraepithelial neoplasia (PanIN) and intraductal papillary mucinous neoplasms (IPMN), arise through multiple steps of driver gene alterations in KRAS, TP53, CDKN2A, SMAD4, or GNAS. Hallmark mutations play a role in tumor initiation and progression, and their detection in bodily fluids is crucial for diagnosis. Recently, liquid biopsy has gained attention as an approach to complement pathological diagnosis, and in addition to mutation signatures in cell-free DNA, cell-free RNA, and extracellular vesicles have been investigated as potential diagnostic and prognostic markers. Integrating such molecular information to revise the diagnostic criteria for pancreatic cancer can enable a better understanding of the pathogenesis underlying inter-patient heterogeneity, such as sensitivity to chemotherapy and disease outcomes. This review discusses the current diagnostic approaches and clinical applications of genetic analysis in pancreatic cancer and diagnostic attempts by liquid biopsy and molecular analyses using pancreatic juice, duodenal fluid, and blood samples. Emerging knowledge in the rapidly advancing liquid biopsy field is promising for molecular profiling and diagnosing pancreatic diseases with significant diversity.
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Affiliation(s)
- Kenji Takahashi
- Division of Metabolism and Biosystemic Science, Gastroenterology, and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, 2-1 Midorigaoka Higashi, Asahikawa, Hokkaido, 078-8510, Japan.
| | - Yohei Takeda
- Division of Medicine and Clinical Science, Department of Multidisciplinary Internal Medicine, Faculty of Medicine, Tottori University, Tottori, Japan
| | - Yusuke Ono
- Division of Metabolism and Biosystemic Science, Gastroenterology, and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, 2-1 Midorigaoka Higashi, Asahikawa, Hokkaido, 078-8510, Japan
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Japan
| | - Hajime Isomoto
- Division of Medicine and Clinical Science, Department of Multidisciplinary Internal Medicine, Faculty of Medicine, Tottori University, Tottori, Japan
| | - Yusuke Mizukami
- Division of Metabolism and Biosystemic Science, Gastroenterology, and Hematology/Oncology, Department of Medicine, Asahikawa Medical University, 2-1 Midorigaoka Higashi, Asahikawa, Hokkaido, 078-8510, Japan
- Institute of Biomedical Research, Sapporo Higashi Tokushukai Hospital, Sapporo, Japan
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Shinozuka T, Kanda M, Kodera Y. Site-specific protein biomarkers in gastric cancer: a comprehensive review of novel biomarkers and clinical applications. Expert Rev Mol Diagn 2023; 23:701-712. [PMID: 37395000 DOI: 10.1080/14737159.2023.2232298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 06/29/2023] [Indexed: 07/04/2023]
Abstract
INTRODUCTION Gastric cancer (GC) is the fifth most common cancer and the fourth leading cause of cancer-related death worldwide, thus representing a significant global health burden. Early detection and monitoring of GC are essential to improve patient outcomes. While traditional cancer biomarkers such as carcinoembryonic antigen, carbohydrate antigen (CA) 19-9, and CA 72-4 are widely used, their limited sensitivity and specificity necessitate the exploration of alternative biomarkers. AREAS COVERED This review comprehensively analyzes the landscape of GC protein biomarkers identified from 2019 to 2022, with a focus on tissue, blood, urine, saliva, gastric juice, ascites, and exhaled breath as sample sources. We address the potential clinical applications of these biomarkers in early diagnosis, monitoring recurrence, and predicting survival and therapeutic response of GC patients. EXPERT OPINION The discovery of novel protein biomarkers holds great promise for improving the clinical management of GC. However, further validation in large, diverse cohorts is needed to establish the clinical utility of these biomarkers. Integrating these biomarkers with existing diagnostic and monitoring approaches will likely lead to improved personalized treatment plans and patient outcomes.
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Affiliation(s)
- Takahiro Shinozuka
- Department of Gastroenterological Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Mitsuro Kanda
- Department of Gastroenterological Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yasuhiro Kodera
- Department of Gastroenterological Surgery, Nagoya University Graduate School of Medicine, Nagoya, Japan
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Ruan Y, Tang Q, Qiao J, Wang J, Li H, Yue X, Sun Y, Wang P, Yang H, Liu Z. Identification of a novel glycolysis-related prognosis risk signature in triple-negative breast cancer. Front Oncol 2023; 13:1171496. [PMID: 37274269 PMCID: PMC10233057 DOI: 10.3389/fonc.2023.1171496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 05/05/2023] [Indexed: 06/06/2023] Open
Abstract
Introduction Triple-negative breast cancer (TNBC) is a particularly aggressive cluster of breast cancer characterized by significant molecular heterogeneity. Glycolysis is a metabolic pathway that is significantly associated with cancer progression, metastasis, recurrence and chemoresistance. However, the potential roles of glycolysis-related genes in TNBC remain unclear. Methods In the present study, we identified 108 glycolysis-related differentially expressed genes (DEGs) between breast cancer (BRCA) tumor tissues and normal tissues, and we divided patients into two different clusters with significantly distinct molecular characteristics, clinicopathological features, prognosis, immune cell infiltration and mutation burden. We then constructed a 10-gene signature that classified all TNBCs into low- and high-risk groups. Results The high-risk group had significantly lower survival than the low-risk group, which implied that the risk score was an independent prognostic indicator for TNBC patients. Consequently, we constructed and validated a prognostic nomogram, which accurately predicted individual overall survival (OS) of TNBC. Moreover, the risk score predicted the drug sensitivity of chemotherapeutic agents and immunotherapy for TNBC patients. Discussion The present comprehensive analysis of glycolysis-related DEGs in TNBC provides new methods for prognosis prediction and more effective treatment strategies.
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Affiliation(s)
- Yuxia Ruan
- Department of Breast Surgery, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Qiang Tang
- The Second Affiliated Hospital of Zhejiang University School Medicine, Hangzhou, China
| | - Jianghua Qiao
- Department of Breast Surgery, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Jiabin Wang
- Department of Breast Surgery, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Huimin Li
- Department of Cancer Cell Biology, Tianjin’s Key Laboratory of Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Xiayu Yue
- Department of Breast Surgery, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Yadong Sun
- Department of Breast Surgery, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Peili Wang
- Department of Breast Surgery, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Hanzhao Yang
- Department of Breast Surgery, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Zhenzhen Liu
- Department of Breast Surgery, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
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Brito-Rocha T, Constâncio V, Henrique R, Jerónimo C. Shifting the Cancer Screening Paradigm: The Rising Potential of Blood-Based Multi-Cancer Early Detection Tests. Cells 2023; 12:cells12060935. [PMID: 36980276 PMCID: PMC10047029 DOI: 10.3390/cells12060935] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/14/2023] [Accepted: 03/15/2023] [Indexed: 03/30/2023] Open
Abstract
Cancer remains a leading cause of death worldwide, partly owing to late detection which entails limited and often ineffective therapeutic options. Most cancers lack validated screening procedures, and the ones available disclose several drawbacks, leading to low patient compliance and unnecessary workups, adding up the costs to healthcare systems. Hence, there is a great need for innovative, accurate, and minimally invasive tools for early cancer detection. In recent years, multi-cancer early detection (MCED) tests emerged as a promising screening tool, combining molecular analysis of tumor-related markers present in body fluids with artificial intelligence to simultaneously detect a variety of cancers and further discriminate the underlying cancer type. Herein, we aim to provide a highlight of the variety of strategies currently under development concerning MCED, as well as the major factors which are preventing clinical implementation. Although MCED tests depict great potential for clinical application, large-scale clinical validation studies are still lacking.
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Affiliation(s)
- Tiago Brito-Rocha
- Cancer Biology and Epigenetics Group, Research Center (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (P.CCC), Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Master Program in Oncology, School of Medicine & Biomedical Sciences, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal
| | - Vera Constâncio
- Cancer Biology and Epigenetics Group, Research Center (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (P.CCC), Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Doctoral Program in Biomedical Sciences, School of Medicine & Biomedical Sciences, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal
| | - Rui Henrique
- Cancer Biology and Epigenetics Group, Research Center (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (P.CCC), Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Department of Pathology, Portuguese Oncology Institute of Porto (IPO-Porto), Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Department of Pathology and Molecular Immunology, School of Medicine & Biomedical Sciences, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology and Epigenetics Group, Research Center (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center Raquel Seruca (P.CCC), Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Department of Pathology and Molecular Immunology, School of Medicine & Biomedical Sciences, University of Porto (ICBAS-UP), Rua Jorge Viterbo Ferreira 228, 4050-513 Porto, Portugal
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Cell-of-Origin Targeted Drug Repurposing for Triple-Negative and Inflammatory Breast Carcinoma with HDAC and HSP90 Inhibitors Combined with Niclosamide. Cancers (Basel) 2023; 15:cancers15020332. [PMID: 36672285 PMCID: PMC9856736 DOI: 10.3390/cancers15020332] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/15/2022] [Accepted: 12/20/2022] [Indexed: 01/06/2023] Open
Abstract
We recently identified a cell-of-origin-specific mRNA signature associated with metastasis and poor outcome in triple-negative carcinoma (TNBC). This TNBC cell-of-origin signature is associated with the over-expression of histone deacetylases and zinc finger protein HDAC1, HDAC7, and ZNF92, respectively. Based on this signature, we discovered that the combination of three drugs (an HDAC inhibitor, an anti-helminthic Niclosamide, and an antibiotic Tanespimycin that inhibits HSP90) synergistically reduces the proliferation of the twelve tested TNBC cell lines. Additionally, we discovered that four out of five inflammatory breast carcinoma cell lines are sensitive to this combination. Significantly, the concentration of the drugs that are used in these experiments are within or below clinically achievable dose, and the synergistic activity only emerged when all three drugs were combined. Our results suggest that HDAC and HSP90 inhibitors combined with the tapeworm drug Niclosamide can achieve remarkably synergistic inhibition of TNBC and IBC. Since Niclosamide, HDAC, and HSP90 inhibitors were approved for clinical use for other cancer types, it may be possible to repurpose their combination for TNBC and IBC.
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Kamran M, Bhattacharya U, Omar M, Marchionni L, Ince TA. ZNF92, an unexplored transcription factor with remarkably distinct breast cancer over-expression associated with prognosis and cell-of-origin. NPJ Breast Cancer 2022; 8:99. [PMID: 36038558 PMCID: PMC9424319 DOI: 10.1038/s41523-022-00474-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 08/09/2022] [Indexed: 11/10/2022] Open
Abstract
Tumor phenotype is shaped both by transforming genomic alterations and the normal cell-of-origin. We identified a cell-of-origin associated prognostic gene expression signature, ET-9, that correlates with remarkably shorter overall and relapse free breast cancer survival, 8.7 and 6.2 years respectively. The genes associated with the ET-9 signature are regulated by histone deacetylase 7 (HDAC7) partly through ZNF92, a previously unexplored transcription factor with a single PubMed citation since its cloning in 1990s. Remarkably, ZNF92 is distinctively over-expressed in breast cancer compared to other tumor types, on a par with the breast cancer specificity of the estrogen receptor. Importantly, ET-9 signature appears to be independent of proliferation, and correlates with outcome in lymph-node positive, HER2+, post-chemotherapy and triple-negative breast cancers. These features distinguish ET-9 from existing breast cancer prognostic signatures that are generally related to proliferation and correlate with outcome in lymph-node negative, ER-positive, HER2-negative breast cancers. Our results suggest that ET-9 could be also utilized as a predictive signature to select patients for HDAC inhibitor treatment.
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Cardio-onco-metabolism: metabolic remodelling in cardiovascular disease and cancer. Nat Rev Cardiol 2022; 19:414-425. [PMID: 35440740 PMCID: PMC10112835 DOI: 10.1038/s41569-022-00698-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/17/2022] [Indexed: 02/07/2023]
Abstract
Cardiovascular disease and cancer are the two leading causes of morbidity and mortality in the world. The emerging field of cardio-oncology has revealed that these seemingly disparate disease processes are intertwined, owing to the cardiovascular sequelae of anticancer therapies, shared risk factors that predispose individuals to both cardiovascular disease and cancer, as well the possible potentiation of cancer growth by cardiac dysfunction. As a result, interest has increased in understanding the fundamental biological mechanisms that are central to the relationship between cardiovascular disease and cancer. Metabolism, appropriate regulation of energy, energy substrate utilization, and macromolecular synthesis and breakdown are fundamental processes for cellular and organismal survival. In this Review, we explore the emerging data identifying metabolic dysregulation as an important theme in cardio-oncology. We discuss the growing recognition of metabolic reprogramming in cardiovascular disease and cancer and view the novel area of cardio-oncology through the lens of metabolism.
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