1
|
Hsu YC, Chiu YC, Lu TP, Hsiao TH, Chen Y. Predicting drug response through tumor deconvolution by cancer cell lines. PATTERNS (NEW YORK, N.Y.) 2024; 5:100949. [PMID: 38645769 PMCID: PMC11026976 DOI: 10.1016/j.patter.2024.100949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 02/07/2024] [Accepted: 02/12/2024] [Indexed: 04/23/2024]
Abstract
Large-scale cancer drug sensitivity data have become available for a collection of cancer cell lines, but only limited drug response data from patients are available. Bridging the gap in pharmacogenomics knowledge between in vitro and in vivo datasets remains challenging. In this study, we trained a deep learning model, Scaden-CA, for deconvoluting tumor data into proportions of cancer-type-specific cell lines. Then, we developed a drug response prediction method using the deconvoluted proportions and the drug sensitivity data from cell lines. The Scaden-CA model showed excellent performance in terms of concordance correlation coefficients (>0.9 for model testing) and the correctly deconvoluted rate (>70% across most cancers) for model validation using Cancer Cell Line Encyclopedia (CCLE) bulk RNA data. We applied the model to tumors in The Cancer Genome Atlas (TCGA) dataset and examined associations between predicted cell viability and mutation status or gene expression levels to understand underlying mechanisms of potential value for drug repurposing.
Collapse
Affiliation(s)
- Yu-Ching Hsu
- Bioinformatics Program, Taiwan International Graduate Program, National Taiwan University, Taipei 115, Taiwan
- Bioinformatics Program, Institute of Statistical Science, Taiwan International Graduate Program, Academia Sinica, Taipei 115, Taiwan
- Institute of Health Data Analytics and Statistics, Department of Public Health, College of Public Health, National Taiwan University, Taipei 100, Taiwan
- Greehey Children’s Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Yu-Chiao Chiu
- Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15232, USA
| | - Tzu-Pin Lu
- Institute of Health Data Analytics and Statistics, Department of Public Health, College of Public Health, National Taiwan University, Taipei 100, Taiwan
| | - Tzu-Hung Hsiao
- Department of Medical Research, Taichung Veterans General Hospital, Taichung 40705, Taiwan
| | - Yidong Chen
- Greehey Children’s Cancer Research Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA
- Department of Population Health Sciences, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| |
Collapse
|
2
|
Thomas D, Palczewski M, Kuschman H, Hoffman B, Yang H, Glynn S, Wilson D, Kool E, Montfort W, Chang J, Petenkaya A, Chronis C, Cundari T, Sappa S, Islam K, McVicar D, Fan Y, Chen Q, Meerzaman D, Sierk M. Nitric oxide inhibits ten-eleven translocation DNA demethylases to regulate 5mC and 5hmC across the genome. RESEARCH SQUARE 2024:rs.3.rs-4131804. [PMID: 38645113 PMCID: PMC11030528 DOI: 10.21203/rs.3.rs-4131804/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
DNA methylation at cytosine bases of eukaryotic DNA (5-methylcytosine, 5mC) is a heritable epigenetic mark that can regulate gene expression in health and disease. Enzymes that metabolize 5mC have been well-characterized, yet the discovery of endogenously produced signaling molecules that regulate DNA methyl-modifying machinery have not been described. Herein, we report that the free radical signaling molecule nitric oxide (NO) can directly inhibit the Fe(II)/2-OG-dependent DNA demethylases ten-eleven translocation (TET) and human AlkB homolog 2 (ALKBH2). Physiologic NO concentrations reversibly inhibited TET and ALKBH2 demethylase activity by binding to the mononuclear non-heme iron atom which formed a dinitrosyliron complex (DNIC) preventing cosubstrates (2-OG and O2) from binding. In cancer cells treated with exogenous NO, or cells endogenously synthesizing NO, there was a global increase in 5mC and 5-hydroxymethylcytosine (5hmC) in DNA, the substrates for TET, that could not be attributed to increased DNA methyltransferase activity. 5mC was also elevated in NO-producing cell-line-derived mouse xenograft and patient-derived xenograft tumors. Genome-wide DNA methylome analysis of cells chronically treated with NO (10 days) demonstrated enrichment of 5mC and 5hmC at gene-regulatory loci which correlated to changes in the expression of NO-regulated tumor-associated genes. Regulation of DNA methylation is distinctly different from canonical NO signaling and represents a novel epigenetic role for NO.
Collapse
Affiliation(s)
| | - Marianne Palczewski
- University of Illinois Chicago, College of Pharmacy, Department of Pharmaceutical Sciences
| | - Hannah Kuschman
- University of Illinois Chicago, College of Pharmacy, Department of Pharmaceutical Sciences
| | | | - Hao Yang
- Weinberg College of Arts and Sciences, Northwestern University, Department of Chemistry
| | - Sharon Glynn
- University of Galway, College of Medicine, Nursing and Health Sciences, School of Medicine, D. of Pathology
| | | | - Eric Kool
- Stanford University, Department of Chemistry, School of Humanities and Sciences
| | | | - Jenny Chang
- Houston Methodist, Department of Medicine and Oncology, Weill Cornell Medical College
| | - Aydolun Petenkaya
- University of Illinois Chicago, College of Medicine, Biochemistry and Molecular Genetics
| | - Constantinos Chronis
- University of Illinois Chicago, College of Medicine, Biochemistry and Molecular Genetics
| | | | - Sushma Sappa
- University of Pittsburgh, Department of Chemistry
| | | | - Daniel McVicar
- National Institutes of Health, National Cancer Institute, Center for Cancer Research
| | - Yu Fan
- National Cancer Institute, Center for Biomedical Informatics and Information Technology
| | - Qingrong Chen
- National Cancer Institute, Center for Biomedical Informatics and Information Technology
| | - Daoud Meerzaman
- National Cancer Institute, Center for Biomedical Informatics and Information Technology
| | - Michael Sierk
- National Cancer Institute, Center for Biomedical Informatics and Information Technology
| |
Collapse
|
3
|
Bakshi HA, Mkhael M, Faruck HL, Khan AU, Aljabali AAA, Mishra V, El-Tanani M, Charbe NB, Tambuwala MM. Cellular signaling in the hypoxic cancer microenvironment: Implications for drug resistance and therapeutic targeting. Cell Signal 2024; 113:110911. [PMID: 37805102 DOI: 10.1016/j.cellsig.2023.110911] [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: 07/18/2023] [Revised: 09/18/2023] [Accepted: 10/02/2023] [Indexed: 10/09/2023]
Abstract
The rewiring of cellular metabolism is a defining characteristic of cancer, as tumor cells adapt to acquire essential nutrients from a nutrient-poor environment to sustain their viability and biomass. While hypoxia has been identified as a major factor depriving cancer cells of nutrients, recent studies have revealed that cancer cells distant from supporting blood vessels also face nutrient limitations. To overcome this challenge, hypoxic cancer cells, which heavily rely on glucose as an energy source, employ alternative pathways such as glycogen metabolism and reductive carboxylation of glutamine to meet their energy requirements for survival. Our preliminary studies, alongside others in the field, have shown that under glucose-deficient conditions, hypoxic cells can utilize mannose and maltose as alternative energy sources. This review aims to comprehensively examine the hypoxic cancer microenvironment, its association with drug resistance, and potential therapeutic strategies for targeting this unique niche. Furthermore, we will critically evaluate the current literature on hypoxic cancer microenvironments and explore state-of-the-art techniques used to analyze alternate carbohydrates, specifically mannose and maltose, in complex biological fluids. We will also propose the most effective analytical methods for quantifying mannose and maltose in such biological samples. By gaining a deeper understanding of the hypoxic cancer cell microenvironment and its role in drug resistance, novel therapeutic approaches can be developed to exploit this knowledge.
Collapse
Affiliation(s)
- Hamid A Bakshi
- Laboratory of Cancer Therapy Resistance and Drug Target Discovery, The Hormel Institute, University of Minnesota, Austin MN55912, USA; School of Pharmacy and Pharmaceutical Sciences, Ulster University, BT521SA, UK.
| | - Michella Mkhael
- School of Pharmacy and Pharmaceutical Sciences, Ulster University, BT521SA, UK
| | - Hakkim L Faruck
- Laboratory of Cell Signaling and Tumorigenesis, The Hormel Institute, University of Minnesota, Austin MN55912, USA
| | - Asad Ullah Khan
- Laboratory of Molecular Biology of Chronic Diseases, The Hormel Institute, University of Minnesota, Austin MN55912, USA
| | - Alaa A A Aljabali
- Faculty of Pharmacy, Department of Pharmaceutical Sciences, Yarmouk University Irbid, Jordan
| | - Vijay Mishra
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab 144411, India
| | - Mohamed El-Tanani
- RAK Medical and Health Sciences University, Ras al Khaimah, United Arab Emirates
| | - Nitin B Charbe
- Center for Pharmacometrics & Systems Pharmacology, Department of Pharmaceutics (Lake Nona), University of Florida, Orlando, FL, USA
| | - Murtaza M Tambuwala
- Lincoln Medical School, University of Lincoln, Brayford Pool Campus, Lincoln LN6 7TS, UK.
| |
Collapse
|
4
|
Lee RS, Sad K, Fawwal DV, Spangle JM. Emerging Role of Epigenetic Modifiers in Breast Cancer Pathogenesis and Therapeutic Response. Cancers (Basel) 2023; 15:4005. [PMID: 37568822 PMCID: PMC10417282 DOI: 10.3390/cancers15154005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 08/04/2023] [Accepted: 08/05/2023] [Indexed: 08/13/2023] Open
Abstract
Breast cancer pathogenesis, treatment, and patient outcomes are shaped by tumor-intrinsic genomic alterations that divide breast tumors into molecular subtypes. These molecular subtypes often dictate viable therapeutic interventions and, ultimately, patient outcomes. However, heterogeneity in therapeutic response may be a result of underlying epigenetic features that may further stratify breast cancer patient outcomes. In this review, we examine non-genetic mechanisms that drive functional changes to chromatin in breast cancer to contribute to cell and tumor fitness and highlight how epigenetic activity may inform the therapeutic response. We conclude by providing perspectives on the future of therapeutic targeting of epigenetic enzymes, an approach that holds untapped potential to improve breast cancer patient outcomes.
Collapse
Affiliation(s)
- Richard Sean Lee
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA; (R.S.L.); (K.S.); (D.V.F.)
- Department of Biology, Emory College, Atlanta, GA 30322, USA
| | - Kirti Sad
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA; (R.S.L.); (K.S.); (D.V.F.)
| | - Dorelle V. Fawwal
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA; (R.S.L.); (K.S.); (D.V.F.)
- Biochemistry, Cell & Developmental Biology Graduate Program, Emory University School of Medicine, Atlanta, GA 30311, USA
| | - Jennifer Marie Spangle
- Department of Radiation Oncology, Emory University School of Medicine, Atlanta, GA 30322, USA; (R.S.L.); (K.S.); (D.V.F.)
| |
Collapse
|
5
|
Ye M, Gao R, Chen S, Wei M, Wang J, Zhang B, Wu S, Xu Y, Wu P, Chen X, Ma J, Ma D, Dong K. Downregulation of MEG3 and upregulation of EZH2 cooperatively promote neuroblastoma progression. J Cell Mol Med 2022; 26:2377-2391. [PMID: 35257481 PMCID: PMC8995459 DOI: 10.1111/jcmm.17258] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 02/01/2022] [Accepted: 02/21/2022] [Indexed: 12/12/2022] Open
Abstract
Neuroblastoma (NB), an embryonic tumour originating from sympathetic crest cells, is the most common extracranial solid tumour type in children with poor overall prognosis. Accumulating evidence has demonstrated the involvement of long non‐coding RNA (lncRNA) in numerous biological processes and their associations with embryonic development and multiple diseases. Ectopic lncRNA expression is linked to malignant tumours. Previous studies by our team indicate that MEG3 attenuates NB autophagy through inhibition of FOXO1 and epithelial‐mesenchymal transition via the mTOR pathway in vitro. Moreover, MEG3 and EZH2 negatively regulate each other. In present study, we first collected 60 NB tissues and 20 adjacent tissues for Quantitative real‐time polymerase chain reaction (Q‐PCR) experiments and performed clinical correlation analysis of the results. At the same time, nude mice were used for subcutaneous tumour formation to detect the effect of MEG3 in vivo. Two NB cell lines, SK‐N‐AS and SK‐N‐BE(2)C, were overexpressed MEG3 and rescued with EZH2 and then were subjected to proliferation, migration, invasion, apoptosis and autophagy experiments. RNA‐binding protein immunoprecipitation (RIP) and Co‐Immunoprecipitation (Co‐IP) experiments were performed to explore the molecular mechanism of MEG3 and EZH2 interaction. Q‐PCR revealed that MEG3 expression was negatively correlated with INSS stage and risk grade of NB. Moreover, MEG3 overexpression was associated with inhibition of NB growth in vivo. MEG3 exerted an anti‐cancer effect via stimulatory effects on EZH2 ubiquitination leading to its degradation. Conversely, EZH2 interacted with DNMT1 and HDAC1 to induce silencing of MEG3. The EZH2 inhibitor, DZNep, and HDAC inhibitor, SAHA, displayed synergistic activity against NB. Combined treatment with DZNep and SAHA inhibited proliferation, migration and invasion of NB through suppression of the PI3K/AKT/mTOR/FOXO1 pathway. In conclusion, downregulation of MEG3 and upregulation of EZH2 forms a feedback loop that concertedly promotes the development of NB. Combined blockage of EZH2 and HDAC1 with the appropriate inhibitors may therefore present an effective treatment strategy for NB cases with low MEG3 and high EZH2 expression.
Collapse
Affiliation(s)
- Mujie Ye
- Department of Pediatric Surgery, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China.,Department of Geriatric Gastroenterology, Neuroendocrine Tumor Center, Jiangsu Province Hospital, The First Affiliated Hospital of Nanjing Medical University, Institute of Neuroendocrine Tumor, Nanjing Medical University, Nanjing, China
| | - Runnan Gao
- Department of Pediatric Surgery, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Shiyu Chen
- Department of Biochemistry and Molecular Biology, Research Center for Birth Defects, Institutes of Biomedical Sciences, Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Meng Wei
- Department of Pediatric Surgery, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Jing Wang
- Department of Pediatric Surgery, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Bowen Zhang
- Department of Biochemistry and Molecular Biology, Research Center for Birth Defects, Institutes of Biomedical Sciences, Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Suwen Wu
- Obstetrics and Gynaecology Hospital, Fudan University, Shanghai, China
| | - Yuexin Xu
- Department of Biochemistry and Molecular Biology, Research Center for Birth Defects, Institutes of Biomedical Sciences, Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Peixuan Wu
- Department of Biochemistry and Molecular Biology, Research Center for Birth Defects, Institutes of Biomedical Sciences, Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Xin Chen
- Department of Facial Plastic and Reconstructive Surgery, Eye and ENT Hospital, ENT Institute, Fudan University, Shanghai, China
| | - Jing Ma
- Department of Facial Plastic and Reconstructive Surgery, Eye and ENT Hospital, ENT Institute, Fudan University, Shanghai, China
| | - Duan Ma
- Department of Biochemistry and Molecular Biology, Research Center for Birth Defects, Institutes of Biomedical Sciences, Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Kuiran Dong
- Department of Pediatric Surgery, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| |
Collapse
|
6
|
Yang J, Song C, Zhan X. The role of protein acetylation in carcinogenesis and targeted drug discovery. Front Endocrinol (Lausanne) 2022; 13:972312. [PMID: 36171897 PMCID: PMC9510633 DOI: 10.3389/fendo.2022.972312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 08/23/2022] [Indexed: 12/01/2022] Open
Abstract
Protein acetylation is a reversible post-translational modification, and is involved in many biological processes in cells, such as transcriptional regulation, DNA damage repair, and energy metabolism, which is an important molecular event and is associated with a wide range of diseases such as cancers. Protein acetylation is dynamically regulated by histone acetyltransferases (HATs) and histone deacetylases (HDACs) in homeostasis. The abnormal acetylation level might lead to the occurrence and deterioration of a cancer, and is closely related to various pathophysiological characteristics of a cancer, such as malignant phenotypes, and promotes cancer cells to adapt to tumor microenvironment. Therapeutic modalities targeting protein acetylation are a potential therapeutic strategy. This article discussed the roles of protein acetylation in tumor pathology and therapeutic drugs targeting protein acetylation, which offers the contributions of protein acetylation in clarification of carcinogenesis, and discovery of therapeutic drugs for cancers, and lays the foundation for precision medicine in oncology.
Collapse
Affiliation(s)
- Jingru Yang
- Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
- Medical Science and Technology Innovation Center, Shandong First Medical University, Jinan, China
| | - Cong Song
- Medical Science and Technology Innovation Center, Shandong First Medical University, Jinan, China
| | - Xianquan Zhan
- Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
- Medical Science and Technology Innovation Center, Shandong First Medical University, Jinan, China
- *Correspondence: Xianquan Zhan,
| |
Collapse
|
7
|
Vorinostat (SAHA) and Breast Cancer: An Overview. Cancers (Basel) 2021; 13:cancers13184700. [PMID: 34572928 PMCID: PMC8468501 DOI: 10.3390/cancers13184700] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/12/2021] [Accepted: 09/15/2021] [Indexed: 02/07/2023] Open
Abstract
Vorinostat (SAHA), an inhibitor of class I and II of histone deacetylases, is the first histone deacetylase inhibitor (HDI) approved for the treatment of cutaneous T-cell lymphoma in 2006. HDIs are promising anticancer agents that inhibit the proliferation of many types of cancer cells including breast carcinoma (BC). BC is a heterogeneous disease with variable biological behavior, morphological features, and response to therapy. Although significant progress in the treatment of BC has been made, high toxicity to normal cells, serious side effects, and the occurrence of multi-drug resistance limit the effective therapy of BC patients. Therefore, new active agents which improve the effectiveness of currently used regimens are highly needed. This manuscript analyzes preclinical and clinical trials data of SAHA, applied individually or in combination with other anticancer agents, considering different histological subtypes of BC.
Collapse
|
8
|
Gonçalves DA, Jasiulionis MG, de Melo FHM. The Role of the BH4 Cofactor in Nitric Oxide Synthase Activity and Cancer Progression: Two Sides of the Same Coin. Int J Mol Sci 2021; 22:9546. [PMID: 34502450 PMCID: PMC8431490 DOI: 10.3390/ijms22179546] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 08/22/2021] [Accepted: 08/23/2021] [Indexed: 12/14/2022] Open
Abstract
Cancer development is associated with abnormal proliferation, genetic instability, cell death resistance, metabolic reprogramming, immunity evasion, and metastasis. These alterations are triggered by genetic and epigenetic alterations in genes that control cell homeostasis. Increased reactive oxygen and nitrogen species (ROS, RNS) induced by different enzymes and reactions with distinct molecules contribute to malignant transformation and tumor progression by modifying DNA, proteins, and lipids, altering their activities. Nitric oxide synthase plays a central role in oncogenic signaling modulation and redox landscape. Overexpression of the three NOS isoforms has been found in innumerous types of cancer contributing to tumor growth and development. Although the main function of NOS is the production of nitric oxide (NO), it can be a source of ROS in some pathological conditions. Decreased tetrahydrobiopterin (BH4) cofactor availability is involved in NOS dysfunction, leading to ROS production and reduced levels of NO. The regulation of NOSs by BH4 in cancer is controversial since BH4 has been reported as a pro-tumoral or an antitumoral molecule. Therefore, in this review, the role of BH4 in the control of NOS activity and its involvement in the capabilities acquired along tumor progression of different cancers was described.
Collapse
Affiliation(s)
- Diego Assis Gonçalves
- Micro-Imuno-Parasitology Department, Universidade Federal de São Paulo, São Paulo 04023-062, Brazil;
- Department of Parasitology, Microbiology and Immunology, Federal University of Juiz de Fora, Juiz de Fora 36036-900, Brazil
| | | | - Fabiana Henriques Machado de Melo
- Department of Pharmacology, Institute of Biomedical Science, University of São Paulo, São Paulo 05508-000, Brazil
- Institute of Medical Assistance to Public Servants of the State (IAMSPE), São Paulo 04039-000, Brazil
| |
Collapse
|