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Ye Q, Wang J, Ducatman B, Raese RA, Rogers JL, Wan YW, Dong C, Padden L, Pugacheva EN, Qian Y, Guo NL. Expression-Based Diagnosis, Treatment Selection, and Drug Development for Breast Cancer. Int J Mol Sci 2023; 24:10561. [PMID: 37445737 DOI: 10.3390/ijms241310561] [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: 04/28/2023] [Revised: 06/06/2023] [Accepted: 06/21/2023] [Indexed: 07/15/2023] Open
Abstract
There is currently no gene expression assay that can assess if premalignant lesions will develop into invasive breast cancer. This study sought to identify biomarkers for selecting patients with a high potential for developing invasive carcinoma in the breast with normal histology, benign lesions, or premalignant lesions. A set of 26-gene mRNA expression profiles were used to identify invasive ductal carcinomas from histologically normal tissue and benign lesions and to select those with a higher potential for future cancer development (ADHC) in the breast associated with atypical ductal hyperplasia (ADH). The expression-defined model achieved an overall accuracy of 94.05% (AUC = 0.96) in classifying invasive ductal carcinomas from histologically normal tissue and benign lesions (n = 185). This gene signature classified cancer development in ADH tissues with an overall accuracy of 100% (n = 8). The mRNA expression patterns of these 26 genes were validated using RT-PCR analyses of independent tissue samples (n = 77) and blood samples (n = 48). The protein expression of PBX2 and RAD52 assessed with immunohistochemistry were prognostic of breast cancer survival outcomes. This signature provided significant prognostic stratification in The Cancer Genome Atlas breast cancer patients (n = 1100), as well as basal-like and luminal A subtypes, and was associated with distinct immune infiltration and activities. The mRNA and protein expression of the 26 genes was associated with sensitivity or resistance to 18 NCCN-recommended drugs for treating breast cancer. Eleven genes had significant proliferative potential in CRISPR-Cas9/RNAi screening. Based on this gene expression signature, the VEGFR inhibitor ZM-306416 was discovered as a new drug for treating breast cancer.
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Affiliation(s)
- Qing Ye
- West Virginia University Cancer Institute/Mary Babb Randolph Cancer Center, West Virginia University, Morgantown, WV 26506, USA
| | - Jiajia Wang
- West Virginia University Cancer Institute/Mary Babb Randolph Cancer Center, West Virginia University, Morgantown, WV 26506, USA
| | - Barbara Ducatman
- Department of Pathology, West Virginia University, Morgantown, WV 26506, USA
| | - Rebecca A Raese
- West Virginia University Cancer Institute/Mary Babb Randolph Cancer Center, West Virginia University, Morgantown, WV 26506, USA
| | - Jillian L Rogers
- West Virginia University Cancer Institute/Mary Babb Randolph Cancer Center, West Virginia University, Morgantown, WV 26506, USA
| | - Ying-Wooi Wan
- West Virginia University Cancer Institute/Mary Babb Randolph Cancer Center, West Virginia University, Morgantown, WV 26506, USA
| | - Chunlin Dong
- West Virginia University Cancer Institute/Mary Babb Randolph Cancer Center, West Virginia University, Morgantown, WV 26506, USA
| | - Lindsay Padden
- West Virginia University Cancer Institute/Mary Babb Randolph Cancer Center, West Virginia University, Morgantown, WV 26506, USA
| | - Elena N Pugacheva
- West Virginia University Cancer Institute/Mary Babb Randolph Cancer Center, West Virginia University, Morgantown, WV 26506, USA
- Department of Biochemistry and Molecular Medicine, School of Medicine, West Virginia University, Morgantown, WV 26506, USA
- Department of Radiation Oncology, School of Medicine, West Virginia University, Morgantown, WV 26506, USA
| | - Yong Qian
- Pathology and Physiology Research Branch, National Institute for Occupational Safety and Health, Morgantown, WV 26505, USA
| | - Nancy Lan Guo
- West Virginia University Cancer Institute/Mary Babb Randolph Cancer Center, West Virginia University, Morgantown, WV 26506, USA
- Department of Occupational and Environmental Health Sciences, School of Public Health, West Virginia University, Morgantown, WV 26506, USA
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Du T, Han J. Arginine Metabolism and Its Potential in Treatment of Colorectal Cancer. Front Cell Dev Biol 2021; 9:658861. [PMID: 34095122 PMCID: PMC8172978 DOI: 10.3389/fcell.2021.658861] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/26/2021] [Indexed: 12/29/2022] Open
Abstract
Colorectal cancer is the leading cause of death from cancer globally. The current treatment protocol still heavily relies on early detection and surgery. The molecular mechanisms underlying development of colorectal cancer are clinically important and determine the prognosis and treatment response. The arginine metabolism pathway is hyperactive in colorectal cancer and several molecules involved in the pathway are potential targets for chemoprevention and targeted colorectal cancer therapy. Endothelial nitric oxide synthase (eNOS), argininosuccinate synthetase and ornithine decarboxylase (ODC) are the main enzymes for arginine metabolism. Limiting arginine-rich meat consumption and inhibiting ODC activity largely reduces polyamine synthesis and the incidence of colorectal cancer. Arginine transporter CAT-1 and Human member 14 of the solute carrier family 6 (SLC6A14) are overexpressed in colorectal cancer cells and contributes to intracellular arginine levels. Human member 9 of the solute carrier family 38 (SLC38A9) serves as a component of the lysosomal arginine-sensing machinery. Pharmaceutical inhibition of single enzyme or arginine transporter is hard to meet requirement of restoring of abnormal arginine metabolic network. Apart from application in early screening for colorectal cancer, microRNA-based therapeutic strategy that simultaneously manipulating multiple targets involved in arginine metabolism brings promising future in the treatment of colorectal cancer.
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Affiliation(s)
- Tao Du
- Department of Colorectal Surgery, East Hospital, Tongji University School of Medicine, Pudong, China
| | - Junyi Han
- Department of Colorectal Surgery, East Hospital, Tongji University School of Medicine, Pudong, China
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Bojarska J, New R, Borowiecki P, Remko M, Breza M, Madura ID, Fruziński A, Pietrzak A, Wolf WM. The First Insight Into the Supramolecular System of D,L-α-Difluoromethylornithine: A New Antiviral Perspective. Front Chem 2021; 9:679776. [PMID: 34055746 PMCID: PMC8155678 DOI: 10.3389/fchem.2021.679776] [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: 03/12/2021] [Accepted: 04/26/2021] [Indexed: 12/28/2022] Open
Abstract
Targeting the polyamine biosynthetic pathway by inhibiting ornithine decarboxylase (ODC) is a powerful approach in the fight against diverse viruses, including SARS-CoV-2. Difluoromethylornithine (DFMO, eflornithine) is the best-known inhibitor of ODC and a broad-spectrum, unique therapeutical agent. Nevertheless, its pharmacokinetic profile is not perfect, especially when large doses are required in antiviral treatment. This article presents a holistic study focusing on the molecular and supramolecular structure of DFMO and the design of its analogues toward the development of safer and more effective formulations. In this context, we provide the first deep insight into the supramolecular system of DFMO supplemented by a comprehensive, qualitative and quantitative survey of non-covalent interactions via Hirshfeld surface, molecular electrostatic potential, enrichment ratio and energy frameworks analysis visualizing 3-D topology of interactions in order to understand the differences in the cooperativity of interactions involved in the formation of either basic or large synthons (Long-range Synthon Aufbau Modules, LSAM) at the subsequent levels of well-organized supramolecular self-assembly, in comparison with the ornithine structure. In the light of the drug discovery, supramolecular studies of amino acids, essential constituents of proteins, are of prime importance. In brief, the same amino-carboxy synthons are observed in the bio-system containing DFMO. DFT calculations revealed that the biological environment changes the molecular structure of DFMO only slightly. The ADMET profile of structural modifications of DFMO and optimization of its analogue as a new promising drug via molecular docking are discussed in detail.
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Affiliation(s)
- Joanna Bojarska
- Chemistry Department, Institute of Ecological and Inorganic Chemistry, Technical University of Lodz, Lodz, Poland
| | - Roger New
- Faculty of Science & Technology, Middlesex University, London, United Kingdom
| | - Paweł Borowiecki
- Faculty of Chemistry, Department of Drugs Technology and Biotechnology, Laboratory of Biocatalysis and Biotransformation, Warsaw University of Technology, Warsaw, Poland
| | | | - Martin Breza
- Department of Physical Chemistry, Slovak Technical University, Bratislava, Slovakia
| | - Izabela D. Madura
- Faculty of Chemistry, Warsaw University of Technology, Warsaw, Poland
| | - Andrzej Fruziński
- Chemistry Department, Institute of Ecological and Inorganic Chemistry, Technical University of Lodz, Lodz, Poland
| | - Anna Pietrzak
- Chemistry Department, Institute of Ecological and Inorganic Chemistry, Technical University of Lodz, Lodz, Poland
| | - Wojciech M. Wolf
- Chemistry Department, Institute of Ecological and Inorganic Chemistry, Technical University of Lodz, Lodz, Poland
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Qin Y, Deng J, Zhang L, Yuan J, Yang H, Li Q. Tumor microenvironment characterization in triple-negative breast cancer identifies prognostic gene signature. Aging (Albany NY) 2021; 13:5485-5505. [PMID: 33536349 PMCID: PMC7950290 DOI: 10.18632/aging.202478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 10/31/2020] [Indexed: 04/15/2023]
Abstract
We aimed to elucidate the landscape of tumor microenvironment (TME) in triple-negative breast cancer (TNBC). Cohorts from Gene Expression Omnibus database (N = 107) and METABRIC (N = 299) were used as the training set and validation set, respectively. TME was evaluated via single-sample gene set enrichment analysis, and unsupervised clustering was used for cluster identification. Consequently, TNBC was classified into two distinct TME clusters (Cluster 1 and Cluster 2) according to predefined immune-related terms. Cluster 1 was characterized by low immune infiltration with poor prognosis; whereas, Cluster 2 was characterized by high immune infiltration with better survival probability. Further, Cluster 1 had larger tumor volumes, while Cluster 2 had smaller tumor volumes. Finally, a TME signature for prognosis stratification in TNBC was developed and validated. In summary, we comprehensively evaluated the TME of TNBC and constructed a TME signature that correlated with prognosis. Our results provide new insights for the immunotherapy of TNBC.
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Affiliation(s)
- Yan Qin
- Department of Breast Surgery, Guangxi Medical University Cancer Hospital, Nanning 530021, Guangxi, People's Republic of China
| | - Jiehua Deng
- Department of Breast Surgery, Guangxi Medical University Cancer Hospital, Nanning 530021, Guangxi, People's Republic of China
| | - Lihua Zhang
- Department of Breast Surgery, Guangxi Medical University Cancer Hospital, Nanning 530021, Guangxi, People's Republic of China
| | - Jiaxing Yuan
- Department of Breast Surgery, Guangxi Medical University Cancer Hospital, Nanning 530021, Guangxi, People's Republic of China
| | - Huawei Yang
- Department of Breast Surgery, Guangxi Medical University Cancer Hospital, Nanning 530021, Guangxi, People's Republic of China
| | - Qiuyun Li
- Department of Breast Surgery, Guangxi Medical University Cancer Hospital, Nanning 530021, Guangxi, People's Republic of China
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Alhosin M, Razvi SSI, Sheikh RA, Khan JA, Zamzami MA, Choudhry H. Thymoquinone and Difluoromethylornithine (DFMO) Synergistically Induce Apoptosis of Human Acute T Lymphoblastic Leukemia Jurkat Cells Through the Modulation of Epigenetic Pathways. Technol Cancer Res Treat 2020; 19:1533033820947489. [PMID: 32912061 PMCID: PMC7488875 DOI: 10.1177/1533033820947489] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Thymoquinone (TQ), a natural anticancer agent exerts cytotoxic effects on several tumors by targeting multiple pathways, including apoptosis. Difluoromethylornithine (DFMO), an irreversible inhibitor of the ornithine decarboxylase (ODC) enzyme, has shown promising inhibitory activities in many cancers including leukemia by decreasing the biosynthesis of the intracellular polyamines. The present study aimed to investigate the combinatorial cytotoxic effects of TQ and DFMO on human acute T lymphoblastic leukemia Jurkat cells and to determine the underlying mechanisms. Here, we show that the combination of DFMO and TQ significantly reduced cell viability and resulted in significant synergistic effects on apoptosis when compared to either DFMO or TQ alone. RNA-sequencing showed that many key epigenetic players including Ubiquitin-like containing PHD and Ring finger 1 (UHRF1) and its 2 partners DNA methyltransferase 1 (DNMT1) and histone deacetylase 1 (HDAC1) were down-regulated in DFMO-treated Jurkat cells. The combination of DFMO and TQ dramatically decreased the expression of UHRF1, DNMT1 and HDAC1 genes compared to either DFMO or TQ alone. UHRF1 knockdown led to a decrease in Jurkat cell viability. In conclusion, these results suggest that the combination of DFMO and TQ could be a promising new strategy for the treatment of human acute T lymphoblastic leukemia by targeting the epigenetic code.
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Affiliation(s)
- Mahmoud Alhosin
- Department of Biochemistry, Faculty of Science, 37848King Abdulaziz University, Jeddah, Saudi Arabia.,Cancer Metabolism and Epigenetic Unit, Faculty of Science, 37848King Abdulaziz University, Jeddah, Saudi Arabia
| | - Syed Shoeb I Razvi
- Department of Biochemistry, Faculty of Science, 37848King Abdulaziz University, Jeddah, Saudi Arabia.,Math and Science Department, 441417Community College of Qatar, Doha, Qatar
| | - Ryan A Sheikh
- Department of Biochemistry, Faculty of Science, 37848King Abdulaziz University, Jeddah, Saudi Arabia
| | - Jalaluddin A Khan
- Department of Biochemistry, Faculty of Science, 37848King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mazin A Zamzami
- Department of Biochemistry, Faculty of Science, 37848King Abdulaziz University, Jeddah, Saudi Arabia.,Cancer Metabolism and Epigenetic Unit, Faculty of Science, 37848King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hani Choudhry
- Department of Biochemistry, Faculty of Science, 37848King Abdulaziz University, Jeddah, Saudi Arabia.,Cancer Metabolism and Epigenetic Unit, Faculty of Science, 37848King Abdulaziz University, Jeddah, Saudi Arabia
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Abstract
Increased polyamine synthesis and inflammation have long been associated with intraepithelial neoplasia, which are risk factors for cancer development in humans. Targeting polyamine metabolism (by use of polyamine synthesis inhibitors or polyamine catabolism activators) and inflammation (by use of nonsteroidal anti-inflammatory drugs) has been studied for many cancers, including colon, prostate, and skin. Genetic epidemiology results indicate that a genetic variant associated with the expression of a polyamine biosynthetic gene is associated with risk of colon and prostate cancers. A clinical trial of difluoromethylornithine (DFMO), a selective inhibitor of polyamine synthesis, showed that the 1 year treatment duration reduced prostate volume and serum prostate-specific antigen doubling time in men with a family history of prostate cancer. A second, clinical trial of DFMO in combination with sulindac, a NSAID in patients with prior colon polyps found that the 3-year treatment was associated with a 70% reduction of all, and over a 90% reduction of advanced and/or multiple metachronous colon adenomas. In this chapter, we discuss that similar combination prevention strategies of targeting polyamines and inflammation can be effective in reducing risk factors associated with the development of human cancers.
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