1
|
Ma Y, Huang X, Wang Y, Lei Y, Yu J, Yu S, Gao Y, Yang J, Zhao F, Yu H, Zeng J, Chu Y, Yang M, Li G, Xie X, Zhang J. NNMT/1-MNA Promote Cell-Cycle Progression of Breast Cancer by Targeting UBC12/Cullin-1-Mediated Degradation of P27 Proteins. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2305907. [PMID: 38126621 PMCID: PMC10916551 DOI: 10.1002/advs.202305907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 11/17/2023] [Indexed: 12/23/2023]
Abstract
Cell cycle dysregulation is a defining feature of breast cancer. Here, 1-methyl-nicotinamide (1-MNA), metabolite of nicotinamide N-methyltransferase(NNMT) is identified, as a novel driver of cell-cycle progression in breast cancer. NNMT, highly expressed in breast cancer tissues, positively correlates with tumor grade, TNM stage, Ki-67 index, and tumor size. Ablation of NNMT expression dramatically suppresses cell proliferation and causes cell-cycle arrest in G0/G1 phase. This phenomenon predominantly stems from the targeted action of 1-MNA, resulting in a specific down-regulation of p27 protein expression. Mechanistically, 1-MNA expedites the degradation of p27 proteins by enhancing cullin-1 neddylation, crucial for the activation of Cullin-1-RING E3 ubiquitin ligase(CRL1)-an E3 ubiquitin ligase targeting p27 proteins. NNMT/1-MNA specifically up-regulates the expression of UBC12, an E2 NEDD8-conjugating enzyme required for cullin-1 neddylation. 1-MNA showes high binding affinity to UBC12, extending the half-life of UBC12 proteins via preventing their localization to lysosome for degradation. Therefore, 1-MNA is a bioactive metabolite that promotes breast cancer progression by reinforcing neddylation pathway-mediated p27 degradation. The study unveils the link between NNMT enzymatic activity with cell-cycle progression, indicating that 1-MNA may be involved in the remodeling of tumor microenvironment.
Collapse
Affiliation(s)
- Yilei Ma
- Department of Clinical LaboratorySir Run Run Shaw HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiang310016P. R. China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang ProvinceHangzhouZhejiang310016P. R. China
| | - Xucheng Huang
- Department of Clinical LaboratorySir Run Run Shaw HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiang310016P. R. China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang ProvinceHangzhouZhejiang310016P. R. China
| | - Yanzhong Wang
- Department of Clinical LaboratorySir Run Run Shaw HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiang310016P. R. China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang ProvinceHangzhouZhejiang310016P. R. China
| | - Yinjiao Lei
- Department of Clinical LaboratorySir Run Run Shaw HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiang310016P. R. China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang ProvinceHangzhouZhejiang310016P. R. China
- Department of PathologySir Run Run Shaw HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiang310016P. R. China
| | - Jinwei Yu
- Department of Clinical LaboratorySir Run Run Shaw HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiang310016P. R. China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang ProvinceHangzhouZhejiang310016P. R. China
| | - Shaobo Yu
- Department of Clinical LaboratorySir Run Run Shaw HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiang310016P. R. China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang ProvinceHangzhouZhejiang310016P. R. China
| | - Yuzhen Gao
- Department of Clinical LaboratorySir Run Run Shaw HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiang310016P. R. China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang ProvinceHangzhouZhejiang310016P. R. China
| | - Jun Yang
- Department of Clinical LaboratorySir Run Run Shaw HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiang310016P. R. China
- Department of CytopathologyNingbo Diagnostic Pathology CenterNingboZhejiang315046P. R. China
| | - Feng Zhao
- Department of Clinical LaboratorySir Run Run Shaw HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiang310016P. R. China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang ProvinceHangzhouZhejiang310016P. R. China
| | - Haitao Yu
- Department of Clinical LaboratorySir Run Run Shaw HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiang310016P. R. China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang ProvinceHangzhouZhejiang310016P. R. China
| | - Jin Zeng
- Department of Clinical LaboratorySir Run Run Shaw HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiang310016P. R. China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang ProvinceHangzhouZhejiang310016P. R. China
| | - Yadong Chu
- Department of Clinical LaboratorySir Run Run Shaw HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiang310016P. R. China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang ProvinceHangzhouZhejiang310016P. R. China
- Department of Clinical LaboratoryZhejiang Armed Police Corps HospitalHangzhouZhejiang310051P. R. China
| | - Min Yang
- Department of Clinical LaboratorySir Run Run Shaw HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiang310016P. R. China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang ProvinceHangzhouZhejiang310016P. R. China
| | - Guoli Li
- Department of Clinical LaboratorySir Run Run Shaw HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiang310016P. R. China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang ProvinceHangzhouZhejiang310016P. R. China
| | - Xinyou Xie
- Department of Clinical LaboratorySir Run Run Shaw HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiang310016P. R. China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang ProvinceHangzhouZhejiang310016P. R. China
| | - Jun Zhang
- Department of Clinical LaboratorySir Run Run Shaw HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiang310016P. R. China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang ProvinceHangzhouZhejiang310016P. R. China
| |
Collapse
|
2
|
Zhong L, Wang F, Liu D, Kuang W, Ji N, Li J, Zeng X, Li T, Dan H, Chen Q. Single-cell transcriptomics dissects premalignant progression in proliferative verrucous leukoplakia. Oral Dis 2024; 30:172-186. [PMID: 35950708 DOI: 10.1111/odi.14347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 07/19/2022] [Accepted: 08/05/2022] [Indexed: 11/28/2022]
Abstract
OBJECTIVE Proliferative verrucous leukoplakia (PVL) is characterized by a spectrum of clinicopathological features and a high risk of malignant transformation. In this study, we aimed to delineate the dynamic changes in molecular signature during PVL progression and identify the potential cell subtypes that play a key role in the premalignant evolution of PVL. METHODS We performed single-cell RNA sequencing on three biopsy samples from a large PVL lesion. These samples exhibited a histopathological continuum of PVL progression. RESULTS By analyzing the transcriptome profiles of 27,611 cells from these samples, we identified ten major cell lineages and revealed that cellular remodeling occurred during the progression of PVL lesions, including epithelial, stromal, and immune cells. Epithelial cells are shifted to tumorigenic states and secretory patterns at the premalignant stage. Immune cells showed growing immunosuppressive phenotypes during PVL progression. Remarkably, two novel cell subtypes INSR+ endothelial cells and ASPN+ fibroblasts, were discovered and may play vital roles in microenvironment remodeling, such as angiogenesis and stromal fibrosis, which are closely involved in malignant transformation. CONCLUSION Our work is the first to depict the cellular landscape of PVL and speculate that disease progression may be driven by functional remodeling of multiple cell subtypes.
Collapse
Affiliation(s)
- Liang Zhong
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Fei Wang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Dan Liu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Wenjing Kuang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Ning Ji
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jing Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xin Zeng
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Taiwen Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Hongxia Dan
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Qianming Chen
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| |
Collapse
|
3
|
Soliman TN, Keifenheim D, Parker PJ, Clarke DJ. Cell cycle responses to Topoisomerase II inhibition: Molecular mechanisms and clinical implications. J Cell Biol 2023; 222:e202209125. [PMID: 37955972 PMCID: PMC10641588 DOI: 10.1083/jcb.202209125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023] Open
Abstract
DNA Topoisomerase IIA (Topo IIA) is an enzyme that alters the topological state of DNA and is essential for the separation of replicated sister chromatids and the integrity of cell division. Topo IIA dysfunction activates cell cycle checkpoints, resulting in arrest in either the G2-phase or metaphase of mitosis, ultimately triggering the abscission checkpoint if non-disjunction persists. These events, which directly or indirectly monitor the activity of Topo IIA, have become of major interest as many cancers have deficiencies in Topoisomerase checkpoints, leading to genome instability. Recent studies into how cells sense Topo IIA dysfunction and respond by regulating cell cycle progression demonstrate that the Topo IIA G2 checkpoint is distinct from the G2-DNA damage checkpoint. Likewise, in mitosis, the metaphase Topo IIA checkpoint is separate from the spindle assembly checkpoint. Here, we integrate mechanistic knowledge of Topo IIA checkpoints with the current understanding of how cells regulate progression through the cell cycle to accomplish faithful genome transmission and discuss the opportunities this offers for therapy.
Collapse
Affiliation(s)
- Tanya N. Soliman
- Barts Cancer Institute, Queen Mary University London, London, UK
| | - Daniel Keifenheim
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | | | - Duncan J. Clarke
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| |
Collapse
|
4
|
Sawant M, Wilson A, Sridaran D, Mahajan K, O'Conor CJ, Hagemann IS, Luo J, Weimholt C, Li T, Roa JC, Pandey A, Wu X, Mahajan NP. Epigenetic reprogramming of cell cycle genes by ACK1 promotes breast cancer resistance to CDK4/6 inhibitor. Oncogene 2023; 42:2263-2277. [PMID: 37330596 PMCID: PMC10348910 DOI: 10.1038/s41388-023-02747-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 05/16/2023] [Accepted: 06/08/2023] [Indexed: 06/19/2023]
Abstract
Hormone receptor-positive, HER2-negative advanced breast cancers exhibit high sensitivity to CDK4/6 inhibitors such as palbociclib. However, most patients inevitably develop resistance, thus identification of new actionable therapeutic targets to overcome the recurrent disease is an urgent need. Immunohistochemical studies of tissue microarray revealed increased activation of non-receptor tyrosine kinase, ACK1 (also known as TNK2) in most of the breast cancer subtypes, independent of their hormone receptor status. Chromatin immunoprecipitation studies demonstrated that the nuclear target of activated ACK1, pY88-H4 epigenetic marks, were deposited at cell cycle genes, CCNB1, CCNB2 and CDC20, which in turn initiated their efficient transcription. Pharmacological inhibition of ACK1 using its inhibitor, (R)-9b dampened CCNB1, CCNB2 and CDC20 expression, caused G2/M arrest, culminating in regression of palbociclib-resistant breast tumor growth. Further, (R)-9b suppressed expression of CXCR4 receptor, which resulted in significant impairment of metastasis of breast cancer cells to lung. Overall, our pre-clinical data identifies activated ACK1 as an oncogene that epigenetically controls the cell cycle genes governing the G2/M transition in breast cancer cells. ACK1 inhibitor, (R)-9b could be a novel therapeutic option for the breast cancer patients that have developed resistance to CDK4/6 inhibitors.
Collapse
Affiliation(s)
- Mithila Sawant
- Department of Surgery, Washington University in St. Louis, Cancer Research Building, 660 Euclid Ave., St. Louis, MO, 63110, USA
- Division of Urologic Surgery, Washington University in St. Louis, Cancer Research Building, 660 Euclid Ave., St. Louis, MO, 63110, USA
| | - Audrey Wilson
- Department of Surgery, Washington University in St. Louis, Cancer Research Building, 660 Euclid Ave., St. Louis, MO, 63110, USA
- Division of Urologic Surgery, Washington University in St. Louis, Cancer Research Building, 660 Euclid Ave., St. Louis, MO, 63110, USA
| | - Dhivya Sridaran
- Department of Surgery, Washington University in St. Louis, Cancer Research Building, 660 Euclid Ave., St. Louis, MO, 63110, USA
- Division of Urologic Surgery, Washington University in St. Louis, Cancer Research Building, 660 Euclid Ave., St. Louis, MO, 63110, USA
| | - Kiran Mahajan
- Department of Surgery, Washington University in St. Louis, Cancer Research Building, 660 Euclid Ave., St. Louis, MO, 63110, USA
- Division of Urologic Surgery, Washington University in St. Louis, Cancer Research Building, 660 Euclid Ave., St. Louis, MO, 63110, USA
| | - Christopher J O'Conor
- Department of Pathology and Immunology, Washington University in St. Louis, Cancer Research Building, 660 Euclid Ave., St. Louis, MO, 63110, USA
| | - Ian S Hagemann
- Department of Pathology and Immunology, Washington University in St. Louis, Cancer Research Building, 660 Euclid Ave., St. Louis, MO, 63110, USA
| | - Jingqin Luo
- Siteman Cancer Center, Washington University in St. Louis, Cancer Research Building, 660 Euclid Ave., St. Louis, MO, 63110, USA
| | - Cody Weimholt
- Department of Pathology and Immunology, Washington University in St. Louis, Cancer Research Building, 660 Euclid Ave., St. Louis, MO, 63110, USA
- Siteman Cancer Center, Washington University in St. Louis, Cancer Research Building, 660 Euclid Ave., St. Louis, MO, 63110, USA
| | - Tiandao Li
- Bioinformatics Research Core, Center of Regenerative Medicine, Department of Developmental Biology, Washington University in St. Louis, St. Louis, MO, 63110, USA
| | - Juan Carlos Roa
- Department of Pathology, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Akhilesh Pandey
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA
- Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA
| | - Xinyan Wu
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA
- Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA
| | - Nupam P Mahajan
- Department of Surgery, Washington University in St. Louis, Cancer Research Building, 660 Euclid Ave., St. Louis, MO, 63110, USA.
- Division of Urologic Surgery, Washington University in St. Louis, Cancer Research Building, 660 Euclid Ave., St. Louis, MO, 63110, USA.
- Siteman Cancer Center, Washington University in St. Louis, Cancer Research Building, 660 Euclid Ave., St. Louis, MO, 63110, USA.
| |
Collapse
|
5
|
Shabana SM, Gad NS, Othman AI, Mohamed AF, El-Missiry MA. β-caryophyllene oxide induces apoptosis and inhibits proliferation of A549 lung cancer cells. Med Oncol 2023; 40:189. [PMID: 37233859 DOI: 10.1007/s12032-023-02022-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 04/02/2023] [Indexed: 05/27/2023]
Abstract
One of the most common cancers that result in death is lung cancer. There is new hope in the fight against lung cancer thanks to the chemopreventive properties of natural dietary substances like β-caryophyllene oxide (CPO), and research is currently being done to test this theory. CPO, a sesquiterpene isolated from medicinal plant essential oils, inhibits carcinogenesis and has been effective in treating many cancers. This study examined how CPO affected proliferation of human lung cancer A549 cells. CPO was found to have an inhibitory concentration (IC50) of 124.1 g/ml. The proliferative markers Ki67 and PCNA were significantly inhibited after cells were treated with CPO at a concentration of 50 g/ml compared to controls. CPO-treated cells expressed more P21, P53, and DNA strand breaks than controls. This was accompanied by a significant cell cycle arrest in the S and G2/M phases. In treated A549 cells, this was also associated with a significant induction of apoptosis, as shown by the upregulation of the expression of caspases 3, 7, and 9, as well as Bax, and the downregulation of Bcl-2. Furthermore, the redox status of treated A549 cells revealed a marked rise in GSH and GPx activity levels and a decline in 4-HNE levels, indicating low oxidative stress following CPO treatment of A549 cells. In conclusion, cell cycle arrest and apoptosis, which are unrelated to oxidative stress, were the mechanisms by which CPO reduced cancer lung cell growth. This finding might be a potential therapeutic target for the treatment of lung cancer. Hypothetical scheme of CPO anticancer effects (mechanism of signaling) in A549 cells; in vitro. CPO treatment increases expression of p21, p53 and DNA fragmentation. These events cause arrest of cell cycle which was associated with significant induction in apoptosis via increase expression of caspases (-3,-7,-9), and Bax and downregulation of Bcl-2.
Collapse
Affiliation(s)
- Sameh M Shabana
- Department of Zoology, Faculty of Science, Mansoura University, Mansoura, 35516, Egypt.
| | - Nahla S Gad
- Department of Zoology, Faculty of Science, Mansoura University, Mansoura, 35516, Egypt
| | - Azza I Othman
- Department of Zoology, Faculty of Science, Mansoura University, Mansoura, 35516, Egypt
| | - Aly Fahmy Mohamed
- The International Center for Advanced Researches (ICTAR-Egypt), Al-Azhar University, Cairo, 307422, Egypt
| | | |
Collapse
|
6
|
ASGARD is A Single-cell Guided Pipeline to Aid Repurposing of Drugs. Nat Commun 2023; 14:993. [PMID: 36813801 PMCID: PMC9945835 DOI: 10.1038/s41467-023-36637-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 02/10/2023] [Indexed: 02/24/2023] Open
Abstract
Single-cell RNA sequencing technology has enabled in-depth analysis of intercellular heterogeneity in various diseases. However, its full potential for precision medicine has yet to be reached. Towards this, we propose A Single-cell Guided Pipeline to Aid Repurposing of Drugs (ASGARD) that defines a drug score to recommend drugs by considering all cell clusters to address the intercellular heterogeneity within each patient. ASGARD shows significantly better average accuracy on single-drug therapy compared to two bulk-cell-based drug repurposing methods. We also demonstrated that it performs considerably better than other cell cluster-level predicting methods. In addition, we validate ASGARD using the drug response prediction method TRANSACT with Triple-Negative-Breast-Cancer patient samples. We find that many top-ranked drugs are either approved by the Food and Drug Administration or in clinical trials treating corresponding diseases. In conclusion, ASGARD is a promising drug repurposing recommendation tool guided by single-cell RNA-seq for personalized medicine. ASGARD is free for educational use at https://github.com/lanagarmire/ASGARD .
Collapse
|
7
|
Wu J, Wang W, Shao X, Lin G, Wang X. Facing the CDK4/6i resistance dilemma in patients with breast cancer, exploration of the resistance mechanism and possible reverse strategy: A narrative review. Medicine (Baltimore) 2022; 101:e32238. [PMID: 36595763 PMCID: PMC9794308 DOI: 10.1097/md.0000000000032238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Breast cancer is one of the highest rates of malignancy of women, approximate 70% metastatic breast cancer are hormone receptor positive (HR+) and human epidermal growth factor receptor 2 negative (HER2-). Hormone therapy is the primary strategy of HR+/HER2- metastatic breast cancer. With the permission of cyclin-dependent kinase 4 and 6 inhibitors (CDK4/6i), progress free survival and overall survival were significantly licensed. However, inevitable outcome of CDK4/6i resistance has become the main reason that restricts the clinical benefit of patients. In recent years, the research on dealing with drug resistance has become a hot topic, a large number of molecular mechanisms have been focused, and a lot of experiments have been carried out at the preclinical level. This review summarizes the current knowledge of CDK4/6i resistance mechanism, systematically expounds the signaling pathways and targets leading to CDK4/6i resistance, analyzes different ways and mechanisms, and provides theoretical guidance for the clinical reversal of endocrine therapy resistance.
Collapse
Affiliation(s)
- Jiayi Wu
- Department of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, China
| | - Wei Wang
- Department of Clinical Medicine, Wenzhou Medical University, Wenzhou, China
| | - Xiying Shao
- Department of Breast Medicine, Zhejiang Cancer Hospital, Hangzhou, China
- *Correspondence: Xiaojia Wang, Department of Breast Medicine, Zhejiang Cancer Hospital, Hangzhou, China (e-mail: ) and Xiying Shao, Department of Breast Medicine, Zhejiang Cancer Hospital, Hangzhou, China (e-mail: )
| | - Guang Lin
- Department of Clinical Medicine, Wenzhou Medical University, Wenzhou, China
| | - Xiaojia Wang
- Department of Breast Medicine, Zhejiang Cancer Hospital, Hangzhou, China
- *Correspondence: Xiaojia Wang, Department of Breast Medicine, Zhejiang Cancer Hospital, Hangzhou, China (e-mail: ) and Xiying Shao, Department of Breast Medicine, Zhejiang Cancer Hospital, Hangzhou, China (e-mail: )
| |
Collapse
|
8
|
Tufail M, Cui J, Wu C. Breast cancer: molecular mechanisms of underlying resistance and therapeutic approaches. Am J Cancer Res 2022; 12:2920-2949. [PMID: 35968356 PMCID: PMC9360230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 06/11/2022] [Indexed: 06/15/2023] Open
Abstract
Breast cancer (BC) affects over 250,000 women in the US each year. Drug-resistant cancer cells are responsible for most breast cancer fatalities. Scientists are developing novel chemotherapeutic drugs and targeted therapy combinations to overcome cancer cell resistance. Combining drugs can reduce the chances of a tumor developing resistance to treatment. Clinical research has shown that combination chemotherapy enhances or improves survival, depending on the patient's response to treatment. Combination therapy is a highly successful supplemental cancer treatment. This review sheds light on intrinsic resistance to BC drugs and the importance of combination therapy for BC treatment. In addition to recurrence and metastasis of BC, the article discussed biomarkers for BC.
Collapse
Affiliation(s)
- Muhammad Tufail
- Institute of Biomedical Sciences, Shanxi UniversityTaiyuan 030006, Shanxi, China
| | - Jia Cui
- Department of Microbiology, Changzhi Medical CollegeChangzhi 046000, Shanxi, China
| | - Changxin Wu
- Institute of Biomedical Sciences, Shanxi UniversityTaiyuan 030006, Shanxi, China
| |
Collapse
|
9
|
Waszczykowska K, Prażanowska K, Kałuzińska Ż, Kołat D, Płuciennik E. Discovering biomarkers for hormone-dependent tumors: in silico study on signaling pathways implicated in cell cycle and cytoskeleton regulation. Mol Genet Genomics 2022; 297:947-963. [PMID: 35532795 DOI: 10.1007/s00438-022-01900-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 04/16/2022] [Indexed: 02/07/2023]
Abstract
Malignancies dependent on hormone homeostasis include breast, ovary, cervical, prostate, testis and uterine tumors. Hormones are involved in signal transduction which orchestrate processes, such as apoptosis, proliferation, cell cycle or cytoskeleton organization. Currently, there is a need for novel biomarkers which would help to diagnose cancers efficiently. In this study, the genes implicated in signaling that is important in hormone-sensitive carcinogenesis were investigated regarding their prognostic significance. Data of seven cancer cohorts were collected from FireBrowse. 54 gene sets implicated in specific pathways were browsed through MSig database. Profiling was assessed via Monocle3, while gene ontology through PANTHER. For confirmation, correlation analysis was performed using WGCNA. Protein-protein networks were visualized via Cytoscape and impact of genes on survival, as well as cell cycle or cytoskeleton-related prognostic signatures, was tested. Several differences in expression profile were identified, some of them allowed to distinguish histology. Functional annotation revealed that various regulation of cell cycle, adhesion, migration, apoptosis and angiogenesis underlie these differences. Clinical traits, such as histological type or cancer staging, were found during evaluation of module-trait relationships. Of modules, the TopHubs (COL6A3, TNR, GTF2A1, NKX3-1) interacted directly with, e.g., PDGFB, ITGA10, SP1 or AKT3. Among TopHubs and interacting proteins, many showed an impact on hazard ratio and affected the cell cycle or cytoskeleton-related prognostic signatures, e.g., COL1A1 or PDGFB. In conclusion, this study laid the foundation for further hormone-sensitive carcinogenesis research through identification of genes which prove that crosstalk between cell cycle and cytoskeleton exists, opening avenues for future therapeutic strategies.
Collapse
Affiliation(s)
| | - Karolina Prażanowska
- Faculty of Biomedical Sciences, Medical University of Lodz, 90-752, Lodz, Poland
| | - Żaneta Kałuzińska
- Department of Molecular Carcinogenesis, Medical University of Lodz, 90-752, Lodz, Poland.
| | - Damian Kołat
- Department of Molecular Carcinogenesis, Medical University of Lodz, 90-752, Lodz, Poland
| | - Elżbieta Płuciennik
- Department of Molecular Carcinogenesis, Medical University of Lodz, 90-752, Lodz, Poland
| |
Collapse
|
10
|
Golestaneh M, Firoozrai M, Javid H, Hashemy SI. The substance P/ neurokinin-1 receptor signaling pathway mediates metastasis in human colorectal SW480 cancer cells. Mol Biol Rep 2022; 49:4893-4900. [DOI: 10.1007/s11033-022-07348-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 03/03/2022] [Accepted: 03/08/2022] [Indexed: 12/17/2022]
|
11
|
Abstract
The Covid-19 pandemic has spread rapidly across the globe, resulting in more than 3 million deaths worldwide. The symptoms of Covid-19 are usually mild and non-specific, however in some cases patients may develop acute respiratory distress syndrome (ARDS) and systemic inflammation. Individuals with inflammatory or immunocompromising illnesses, such as cancer, are more susceptible to develop ARDS and have higher rates of mortality. This is mediated through an initial hyperstimulated immune response which results in elevated levels of pro-inflammatory cytokines and a subsequent cytokine storm. This potentiates positive feedback loops which are unable to be balanced by anti-inflammatory mediators. Therefore, elevated levels of IL-1β, as a result of NLRP3 inflammasome activation, as well as IL-6 and TNF-α amongst many others, contribute to the progression of various cancer types. Furthermore, Covid-19 progression is associated with the depletion of CD8+ and CD4+ T cells, B cell and natural killer cell numbers. Collectively, a Covid-19-dependent pro-inflammatory profile and immune suppression promotes the optimal microenvironment for tumourigenesis, initiation and immune evasion of malignant cells, tumour progression and metastasis as well as cancer recurrence. There are, however, therapeutic windows of opportunity that may combat both Covid-19 and cancer to improve patient outcomes.
Collapse
|
12
|
Baur B, Lee DI, Haag J, Chasman D, Gould M, Roy S. Deciphering the Role of 3D Genome Organization in Breast Cancer Susceptibility. Front Genet 2022; 12:788318. [PMID: 35087569 PMCID: PMC8787344 DOI: 10.3389/fgene.2021.788318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 12/21/2021] [Indexed: 11/25/2022] Open
Abstract
Cancer risk by environmental exposure is modulated by an individual's genetics and age at exposure. This age-specific period of susceptibility is referred to as the "Window of Susceptibility" (WOS). Rats have a similar WOS for developing breast cancer. A previous study in rat identified an age-specific long-range regulatory interaction for the cancer gene, Pappa, that is associated with breast cancer susceptibility. However, the global role of three-dimensional genome organization and downstream gene expression programs in the WOS is not known. Therefore, we generated Hi-C and RNA-seq data in rat mammary epithelial cells within and outside the WOS. To systematically identify higher-order changes in 3D genome organization, we developed NE-MVNMF that combines network enhancement followed by multitask non-negative matrix factorization. We examined three-dimensional genome organization dynamics at the level of individual loops as well as higher-order domains. Differential chromatin interactions tend to be associated with differentially up-regulated genes with the WOS and recapitulate several human SNP-gene interactions associated with breast cancer susceptibility. Our approach identified genomic blocks of regions with greater overall differences in contact count between the two time points when the cluster assignments change and identified genes and pathways implicated in early carcinogenesis and cancer treatment. Our results suggest that WOS-specific changes in 3D genome organization are linked to transcriptional changes that may influence susceptibility to breast cancer.
Collapse
Affiliation(s)
- Brittany Baur
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, United States
| | - Da-Inn Lee
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, United States
| | - Jill Haag
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI, United States
| | - Deborah Chasman
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, United States
| | - Michael Gould
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI, United States
| | - Sushmita Roy
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, United States
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, United States
| |
Collapse
|
13
|
Anuraga G, Wang WJ, Phan NN, An Ton NT, Ta HDK, Berenice Prayugo F, Minh Xuan DT, Ku SC, Wu YF, Andriani V, Athoillah M, Lee KH, Wang CY. Potential Prognostic Biomarkers of NIMA (Never in Mitosis, Gene A)-Related Kinase (NEK) Family Members in Breast Cancer. J Pers Med 2021; 11:1089. [PMID: 34834441 PMCID: PMC8625415 DOI: 10.3390/jpm11111089] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/18/2021] [Accepted: 10/19/2021] [Indexed: 02/06/2023] Open
Abstract
Breast cancer remains the most common malignant cancer in women, with a staggering incidence of two million cases annually worldwide; therefore, it is crucial to explore novel biomarkers to assess the diagnosis and prognosis of breast cancer patients. NIMA-related kinase (NEK) protein kinase contains 11 family members named NEK1-NEK11, which were discovered from Aspergillus Nidulans; however, the role of NEK family genes for tumor development remains unclear and requires additional study. In the present study, we investigate the prognosis relationships of NEK family genes for breast cancer development, as well as the gene expression signature via the bioinformatics approach. The results of several integrative analyses revealed that most of the NEK family genes are overexpressed in breast cancer. Among these family genes, NEK2/6/8 overexpression had poor prognostic significance in distant metastasis-free survival (DMFS) in breast cancer patients. Meanwhile, NEK2/6 had the highest level of DNA methylation, and the functional enrichment analysis from MetaCore and Gene Set Enrichment Analysis (GSEA) suggested that NEK2 was associated with the cell cycle, G2M checkpoint, DNA repair, E2F, MYC, MTORC1, and interferon-related signaling. Moreover, Tumor Immune Estimation Resource (TIMER) results showed that the transcriptional levels of NEK2 were positively correlated with immune infiltration of B cells and CD4+ T Cell. Collectively, the current study indicated that NEK family genes, especially NEK2 which is involved in immune infiltration, and may serve as prognosis biomarkers for breast cancer progression.
Collapse
Affiliation(s)
- Gangga Anuraga
- PhD Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan; (G.A.); (H.D.K.T.); (K.-H.L.)
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; (F.B.P.); (D.T.M.X.); (S.-C.K.)
- Department of Statistics, Faculty of Science and Technology, Universitas PGRI Adi Buana, Surabaya 60234, Indonesia;
| | - Wei-Jan Wang
- Research Center for Cancer Biology, Department of Biological Science and Technology, China Medical University, Taichung 40604, Taiwan;
| | - Nam Nhut Phan
- Institute for Environmental Science, Nguyen Tat Thanh University, Ho Chi Minh City 700000, Vietnam; (N.N.P.); (N.T.A.T.)
| | - Nu Thuy An Ton
- Institute for Environmental Science, Nguyen Tat Thanh University, Ho Chi Minh City 700000, Vietnam; (N.N.P.); (N.T.A.T.)
| | - Hoang Dang Khoa Ta
- PhD Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan; (G.A.); (H.D.K.T.); (K.-H.L.)
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; (F.B.P.); (D.T.M.X.); (S.-C.K.)
| | - Fidelia Berenice Prayugo
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; (F.B.P.); (D.T.M.X.); (S.-C.K.)
| | - Do Thi Minh Xuan
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; (F.B.P.); (D.T.M.X.); (S.-C.K.)
| | - Su-Chi Ku
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; (F.B.P.); (D.T.M.X.); (S.-C.K.)
| | - Yung-Fu Wu
- Department of Medical Research, Tri-Service General Hospital, School of Medicine, National Defense Medical Center, Taipei 11490, Taiwan;
| | - Vivin Andriani
- Department of Biological Science, Faculty of Science and Technology, Universitas PGRI Adi Buana, Surabaya 60234, Indonesia;
| | - Muhammad Athoillah
- Department of Statistics, Faculty of Science and Technology, Universitas PGRI Adi Buana, Surabaya 60234, Indonesia;
| | - Kuen-Haur Lee
- PhD Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan; (G.A.); (H.D.K.T.); (K.-H.L.)
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; (F.B.P.); (D.T.M.X.); (S.-C.K.)
- Cancer Center, Wan Fang Hospital, Taipei Medical University, Taipei 11031, Taiwan
| | - Chih-Yang Wang
- PhD Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan; (G.A.); (H.D.K.T.); (K.-H.L.)
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; (F.B.P.); (D.T.M.X.); (S.-C.K.)
| |
Collapse
|
14
|
Strengths and Weaknesses of Cell Synchronization Protocols Based on Inhibition of DNA Synthesis. Int J Mol Sci 2021; 22:ijms221910759. [PMID: 34639098 PMCID: PMC8509769 DOI: 10.3390/ijms221910759] [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: 09/07/2021] [Revised: 10/01/2021] [Accepted: 10/02/2021] [Indexed: 01/01/2023] Open
Abstract
Synchronous cell populations are commonly used for the analysis of various aspects of cellular metabolism at specific stages of the cell cycle. Cell synchronization at a chosen cell cycle stage is most frequently achieved by inhibition of specific metabolic pathway(s). In this respect, various protocols have been developed to synchronize cells in particular cell cycle stages. In this review, we provide an overview of the protocols for cell synchronization of mammalian cells based on the inhibition of synthesis of DNA building blocks-deoxynucleotides and/or inhibition of DNA synthesis. The mechanism of action, examples of their use, and advantages and disadvantages are described with the aim of providing a guide for the selection of suitable protocol for different studied situations.
Collapse
|
15
|
Vetrichelvan O, Gorjala P, Goodman O, Mitra R. Bergamottin a CYP3A inhibitor found in grapefruit juice inhibits prostate cancer cell growth by downregulating androgen receptor signaling and promoting G0/G1 cell cycle block and apoptosis. PLoS One 2021; 16:e0257984. [PMID: 34570813 PMCID: PMC8476002 DOI: 10.1371/journal.pone.0257984] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 09/14/2021] [Indexed: 01/05/2023] Open
Abstract
Prostate cancer is the second leading cause of cancer related death in American men. Several therapies have been developed to treat advanced prostate cancer, but these therapies often have severe side effects. To improve the outcome with fewer side effects we focused on the furanocoumarin bergamottin, a natural product found in grapefruit juice and a potent CYP3A inhibitor. Our recent studies have shown that CYP3A5 inhibition can block androgen receptor (AR) signaling, critical for prostate cancer growth. We observed that bergamottin reduces prostate cancer (PC) cell growth by decreasing both total and nuclear AR (AR activation) reducing downstream AR signaling. Bergamottin’s role in reducing AR activation was confirmed by confocal microscopy studies and reduction in prostate specific antigen (PSA) levels, which is a marker for prostate cancer. Further studies revealed that bergamottin promotes cell cycle block and accumulates G0/G1 cells. The cell cycle block was accompanied with reduction in cyclin D, cyclin B, CDK4, P-cdc2 (Y15) and P-wee1 (S642). We also observed that bergamottin triggers apoptosis in prostate cancer cell lines as evident by TUNEL staining and PARP cleavage. Our data suggests that bergamottin may suppress prostate cancer growth, especially in African American (AA) patients carrying wild type CYP3A5 often presenting aggressive disease.
Collapse
Affiliation(s)
- Opalina Vetrichelvan
- Department of Biomedical Sciences, College of Medicine, Roseman University of Health Sciences, Las Vegas, Nevada, United States of America
| | - Priyatham Gorjala
- Department of Biomedical Sciences, College of Medicine, Roseman University of Health Sciences, Las Vegas, Nevada, United States of America
| | - Oscar Goodman
- Department of Biomedical Sciences, College of Medicine, Roseman University of Health Sciences, Las Vegas, Nevada, United States of America.,Comprehensive Cancer Centers of Nevada, Las Vegas, Nevada, United States of America
| | - Ranjana Mitra
- Department of Biomedical Sciences, College of Medicine, Roseman University of Health Sciences, Las Vegas, Nevada, United States of America
| |
Collapse
|
16
|
He B, Xiao Y, Liang H, Huang Q, Du Y, Li Y, Garmire D, Sun D, Garmire LX. ASGARD: A Single-cell Guided pipeline to Aid Repurposing of Drugs. ARXIV 2021:2109.06377. [PMID: 34545335 PMCID: PMC8452105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Revised: 12/22/2022] [Indexed: 01/04/2023]
Abstract
Intercellular heterogeneity is a major obstacle to successful precision medicine. Single-cell RNA sequencing (scRNA-seq) technology has enabled in-depth analysis of intercellular heterogeneity in various diseases. However, its full potential for precision medicine has yet to be reached. Towards this, we propose a new drug recommendation system called: A Single-cell Guided Pipeline to Aid Repurposing of Drugs (ASGARD). ASGARD defines a novel drug score predicting drugs by considering all cell clusters to address the intercellular heterogeneity within each patient. We tested ASGARD on multiple diseases, including breast cancer, acute lymphoblastic leukemia, and coronavirus disease 2019 (COVID-19). On single-drug therapy, ASGARD shows significantly better average accuracy (AUC of 0.92) compared to two other bulk-cell-based drug repurposing methods (AUC of 0.80 and 0.76). It is also considerably better (AUC of 0.82) than other cell cluster level predicting methods (AUC of 0.67 and 0.55). In addition, ASGARD is also validated by the drug response prediction method TRANSACT with Triple-Negative-Breast-Cancer patient samples. Many top-ranked drugs are either approved by FDA or in clinical trials treating corresponding diseases. In silico cell-type specific drop-out experiments using triple-negative breast cancers show the importance of T cells in the tumor microenvironment in affecting drug predictions. In conclusion, ASGARD is a promising drug repurposing recommendation tool guided by single-cell RNA-seq for personalized medicine. ASGARD is free for educational use at https://github.com/lanagarmire/ASGARD.
Collapse
Affiliation(s)
- Bing He
- Department of Computational Medicine and Bioinformatics, Medical School, University of Michigan, Ann Arbor, MI, USA
| | - Yao Xiao
- Department of Computational Medicine and Bioinformatics, Medical School, University of Michigan, Ann Arbor, MI, USA
| | - Haodong Liang
- Department of Statistics, College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI, USA
| | - Qianhui Huang
- Department of Computational Medicine and Bioinformatics, Medical School, University of Michigan, Ann Arbor, MI, USA
| | - Yuheng Du
- Department of Computational Medicine and Bioinformatics, Medical School, University of Michigan, Ann Arbor, MI, USA
| | - Yijun Li
- Department of Computational Medicine and Bioinformatics, Medical School, University of Michigan, Ann Arbor, MI, USA
| | - David Garmire
- Department of Electrical Engineering and Computer Science, College of Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Duxin Sun
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, MI, USA
| | - Lana X Garmire
- Department of Computational Medicine and Bioinformatics, Medical School, University of Michigan, Ann Arbor, MI, USA
| |
Collapse
|
17
|
Alanazi MM, Elkady H, Alsaif NA, Obaidullah AJ, Alkahtani HM, Alanazi MM, Alharbi MA, Eissa IH, Dahab MA. New quinoxaline-based VEGFR-2 inhibitors: design, synthesis, and antiproliferative evaluation with in silico docking, ADMET, toxicity, and DFT studies. RSC Adv 2021; 11:30315-30328. [PMID: 35493991 PMCID: PMC9044819 DOI: 10.1039/d1ra05925d] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 08/30/2021] [Indexed: 01/26/2023] Open
Abstract
A new series of 3-methylquinoxaline-based derivatives having the same essential pharmacophoric features as VEGFR-2 inhibitors have been synthesized and evaluated for their antiproliferative activities against two human cancer cell lines, MCF-7 and HepG-2. Compounds 15b and 17b demonstrated a significant antiproliferative effect with IC50 ranging from 2.3 to 5.8 μM. An enzymatic assay was carried out for all the tested candidates against VEGFR-2. Compound 17b was the most potent VEGFR-2 inhibitor (IC50 = 2.7 nM). Mechanistic investigation including cell cycle arrest and apoptosis was performed for compound 17b against HepG-2 cells, and the results revealed that 17b induced cell apoptosis and arrested cell cycle in the G2/M phase. Moreover, apoptosis analyses were conducted for compound 17b to evaluate its apoptotic potential. The results showed upregulation in caspase-3 and caspase-9 levels, and improving the Bax/Bcl-2 ratio by more than 10-fold. Docking studies were performed to determine the possible interaction with the VEGFR-2 active site. Further docking studies were carried out for compound 17b against cytochrome P450 to present such compounds as non-inhibitors. In silico ADMET, toxicity, and physico-chemical properties revealed that most of the synthesized members have acceptable values of drug-likeness. Finally, DFT studies were carried out to calculate the thermodynamic, molecular orbital and electrostatic potential properties.
Collapse
Affiliation(s)
- Mohammed M Alanazi
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University P.O. Box 2457 Riyadh 11541 Saudi Arabia
| | - Hazem Elkady
- Pharmaceutical Medicinal Chemistry & Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University Cairo 11884 Egypt
| | - Nawaf A Alsaif
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University P.O. Box 2457 Riyadh 11541 Saudi Arabia
| | - Ahmad J Obaidullah
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University P.O. Box 2457 Riyadh 11541 Saudi Arabia
| | - Hamad M Alkahtani
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University P.O. Box 2457 Riyadh 11541 Saudi Arabia
| | - Manal M Alanazi
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University P.O. Box 2457 Riyadh 11541 Saudi Arabia
| | - Madhawi A Alharbi
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University P.O. Box 2457 Riyadh 11541 Saudi Arabia
| | - Ibrahim H Eissa
- Pharmaceutical Medicinal Chemistry & Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University Cairo 11884 Egypt
| | - Mohammed A Dahab
- Pharmaceutical Medicinal Chemistry & Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University Cairo 11884 Egypt
| |
Collapse
|
18
|
Azwar S, Seow HF, Abdullah M, Faisal Jabar M, Mohtarrudin N. Recent Updates on Mechanisms of Resistance to 5-Fluorouracil and Reversal Strategies in Colon Cancer Treatment. BIOLOGY 2021; 10:854. [PMID: 34571731 PMCID: PMC8466833 DOI: 10.3390/biology10090854] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 08/04/2020] [Accepted: 08/11/2020] [Indexed: 02/06/2023]
Abstract
5-Fluorouracil (5-FU) plus leucovorin (LV) remain as the mainstay standard adjuvant chemotherapy treatment for early stage colon cancer, and the preferred first-line option for metastatic colon cancer patients in combination with oxaliplatin in FOLFOX, or irinotecan in FOLFIRI regimens. Despite treatment success to a certain extent, the incidence of chemotherapy failure attributed to chemotherapy resistance is still reported in many patients. This resistance, which can be defined by tumor tolerance against chemotherapy, either intrinsic or acquired, is primarily driven by the dysregulation of various components in distinct pathways. In recent years, it has been established that the incidence of 5-FU resistance, akin to multidrug resistance, can be attributed to the alterations in drug transport, evasion of apoptosis, changes in the cell cycle and DNA-damage repair machinery, regulation of autophagy, epithelial-to-mesenchymal transition, cancer stem cell involvement, tumor microenvironment interactions, miRNA dysregulations, epigenetic alterations, as well as redox imbalances. Certain resistance mechanisms that are 5-FU-specific have also been ascertained to include the upregulation of thymidylate synthase, dihydropyrimidine dehydrogenase, methylenetetrahydrofolate reductase, and the downregulation of thymidine phosphorylase. Indeed, the successful modulation of these mechanisms have been the game plan of numerous studies that had employed small molecule inhibitors, plant-based small molecules, and non-coding RNA regulators to effectively reverse 5-FU resistance in colon cancer cells. It is hoped that these studies would provide fundamental knowledge to further our understanding prior developing novel drugs in the near future that would synergistically work with 5-FU to potentiate its antitumor effects and improve the patient's overall survival.
Collapse
Affiliation(s)
- Shamin Azwar
- Department of Pathology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia; (S.A.); (H.F.S.); (M.A.)
| | - Heng Fong Seow
- Department of Pathology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia; (S.A.); (H.F.S.); (M.A.)
| | - Maha Abdullah
- Department of Pathology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia; (S.A.); (H.F.S.); (M.A.)
| | - Mohd Faisal Jabar
- Department of Surgery, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia;
| | - Norhafizah Mohtarrudin
- Department of Pathology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang 43400, Malaysia; (S.A.); (H.F.S.); (M.A.)
| |
Collapse
|
19
|
Chota A, George BP, Abrahamse H. Interactions of multidomain pro-apoptotic and anti-apoptotic proteins in cancer cell death. Oncotarget 2021; 12:1615-1626. [PMID: 34381566 PMCID: PMC8351602 DOI: 10.18632/oncotarget.28031] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 07/13/2021] [Indexed: 12/15/2022] Open
Abstract
Cancer is a global public health concern that is characterized by the uncontrolled growth of tumor cells. It is regarded as the subsequent cause of death after cardiovascular disease. The most common types of cancer include breast, colorectal, lung, and prostate. The risk factors attributed to the development of common types of cancer are tobacco smoking, excessive alcohol consumption, dietary factors, ultraviolet radiation (UV), and lack of physical activities. Two major cellular apoptotic pathways targeted in cancer therapies are intrinsic and extrinsic. These two pathways are regulated by different types of proteins, the multidomain pro-apoptotic proteins (Bak, Bax, and Bok), BH3-only pro-apoptotic proteins (Bid, Bim, Bad, Noxa, and Puma), and the anti-apoptotic proteins (Mcl-1, Bfl-1, Bcl-XL, Bcl-2, Bcl-w, and Bcl-B). Other significant molecules/factors that are known to execute cellular apoptotic pathways include bioactive compounds, and reactive oxygen species (ROS). Proteolytic caspases are known to play a vital role in the initiation of apoptotic activities in cancerous cells. Based on their functions, they are categorized into initiators and executioners. Nanotechnology has produced novel outcomes in modern medicine. The green synthesis of nanoparticles has demonstrated prospective improvements in cancer therapies in combination with the existing therapies including photodynamic therapy. This review aims at highlighting the association between pro-apoptotic and anti-apoptotic proteins, and their significance in cancer therapy.
Collapse
Affiliation(s)
- Alexander Chota
- Laser Research Centre, Faculty of Health Sciences, University of Johannesburg, Doornfontein 2028, South Africa
| | - Blassan P. George
- Laser Research Centre, Faculty of Health Sciences, University of Johannesburg, Doornfontein 2028, South Africa
| | - Heidi Abrahamse
- Laser Research Centre, Faculty of Health Sciences, University of Johannesburg, Doornfontein 2028, South Africa
| |
Collapse
|
20
|
Local ablation of gastric cancer by reconstituted apolipoprotein B lipoparticles carrying epigenetic drugs. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2021; 37:102450. [PMID: 34332115 DOI: 10.1016/j.nano.2021.102450] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 04/28/2021] [Accepted: 07/10/2021] [Indexed: 11/21/2022]
Abstract
Epigenetic inhibitors have shown anticancer effects. Combination chemotherapy with epigenetic inhibitors has shown high effectiveness in gastric cancer clinical trials, but severe side effect and local progression are the causes of treatment failure. Therefore, we sought to develop an acidity-sensitive drug delivery system to release drugs locally to diminish unfavorable outcome of gastric cancer. In this study, we showed that, as compared with single agents, combination treatment with the demethylating agent 5'-aza-2'-deoxycytidine and HDAC inhibitors Trichostatin A or LBH589 decreased cell survival, blocked cell cycle by reducing number of S-phase cells and expression of cyclins, increased cell apoptosis by inducing expression of Bim and cleaved Caspase 3, and reexpressed tumor suppressor genes more effectively in MGCC3I cells. As a carrier, reconstituted apolipoprotein B lipoparticles (rABLs) could release drugs in acidic environments. Orally administrated embedded drugs not only showed inhibitory effects on gastric tumor growth in a syngeneic orthotopic mouse model, but also reduced the hepatic and renal toxicity. In conclusion, we have established rABL-based nanoparticles embedded epigenetic inhibitors for local treatment of gastric cancer, which have good therapeutic effects but do not cause severe side effects.
Collapse
|
21
|
Farghadani R, Naidu R. Curcumin: Modulator of Key Molecular Signaling Pathways in Hormone-Independent Breast Cancer. Cancers (Basel) 2021; 13:cancers13143427. [PMID: 34298639 PMCID: PMC8307022 DOI: 10.3390/cancers13143427] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 06/27/2021] [Accepted: 06/30/2021] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Breast cancer remains the most commonly diagnosed cancer and the leading cause of cancer death among females worldwide. It is a highly heterogeneous disease, classified according to hormone and growth factor receptor expression. Patients with triple negative breast cancer (TNBC) (estrogen receptor-negative/progesterone receptor-negative/human epidermal growth factor receptor (HER2)-negative) and hormone-independent HER2 overexpressing subtypes still represent highly aggressive behavior, metastasis, poor prognosis, and drug resistance. Thus, new alternative anticancer agents based on the use of natural products have been receiving enormous attention. In this regard, curcumin is a promising lead in cancer drug discovery due its ability to modulate a diverse range of molecular targets and signaling pathways. The current review has emphasized the underlying mechanism of curcumin anticancer action mediated through the modulation of PI3K/Akt/mTOR, JAK/STAT, MAPK, NF-ĸB, p53, Wnt/β-catenin, apoptosis, and cell cycle pathways in hormone-independent breast cancer, providing frameworks for future studies and insights to improve its efficiency in clinical practice. Abstract Breast cancer is the most frequently diagnosed cancer and the leading cause of cancer death among women worldwide. Despite the overall successes in breast cancer therapy, hormone-independent HER2 negative breast cancer, also known as triple negative breast cancer (TNBC), lacking estrogens and progesterone receptors and with an excessive expression of human epidermal growth factor receptor 2 (HER2), along with the hormone-independent HER2 positive subtype, still remain major challenges in breast cancer treatment. Due to their poor prognoses, aggressive phenotype, and highly metastasis features, new alternative therapies have become an urgent clinical need. One of the most noteworthy phytochemicals, curcumin, has attracted enormous attention as a promising drug candidate in breast cancer prevention and treatment due to its multi-targeting effect. Curcumin interrupts major stages of tumorigenesis including cell proliferation, survival, angiogenesis, and metastasis in hormone-independent breast cancer through the modulation of multiple signaling pathways. The current review has highlighted the anticancer activity of curcumin in hormone-independent breast cancer via focusing on its impact on key signaling pathways including the PI3K/Akt/mTOR pathway, JAK/STAT pathway, MAPK pathway, NF-ĸB pathway, p53 pathway, and Wnt/β-catenin, as well as apoptotic and cell cycle pathways. Besides, its therapeutic implications in clinical trials are here presented.
Collapse
|
22
|
Pandey P, Khan F, Maurya P. Targeting Jab1 using hesperidin (dietary phytocompound) for inducing apoptosis in HeLa cervical cancer cells. J Food Biochem 2021; 45:e13800. [PMID: 34047379 DOI: 10.1111/jfbc.13800] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 05/06/2021] [Accepted: 05/10/2021] [Indexed: 12/11/2022]
Abstract
Plant flavonoids have been emerged as a potent anticancerous agent by exhibiting significant growth inhibitory potential and apoptotic induction in several carcinomas via targeting several oncoproteins. However, inverse association of hesperidin with Jab1 oncoprotein in cervical cancer has rarely been reported. Thus, we have intended our research study towards establishing this unexplored inverse correlation of hesperidin with Jab1 which could further prevent cervical cancer progression. Our research findings clearly demonstrated that hesperidin treatment resulted in Jab1 gene down-regulation and p27 up-regulation in a dose-dependent manner in HeLa cancer cells. These gene modulations might occur via excessive reactive oxygen species (ROS) generation and caspase-3 activation which further resulted in apoptotic induction. Increase in apoptotic cells was confirmed through Hoechst staining and cell cycle analysis. Thus, these results strongly suggested that Jab1 is a potent therapeutic target of hesperidin to suppress cell growth and trigger apoptosis in HeLa cells. PRACTICAL APPLICATIONS: Dietary flavonoids play a crucial role in the management of numerous malignancies via targeting several mutated oncogenes. Our study strongly exhibited that hesperidin treatment suppressed the HeLa cancer cell proliferation via increased ROS generation and reduced Jab1 mRNA expression. Thus, the inference of Jab1-mediated intracellular signals by hesperidin might be a novel approach to control cervical cancer.
Collapse
Affiliation(s)
- Pratibha Pandey
- Department of Biotechnology, Noida Institute of Engineering and Technology, Greater Noida, India
| | - Fahad Khan
- Department of Biotechnology, Noida Institute of Engineering and Technology, Greater Noida, India
| | - Pooja Maurya
- Department of Biotechnology, Noida Institute of Engineering and Technology, Greater Noida, India
| |
Collapse
|
23
|
Jiménez-Salazar JE, Damian-Ferrara R, Arteaga M, Batina N, Damián-Matsumura P. Non-Genomic Actions of Estrogens on the DNA Repair Pathways Are Associated With Chemotherapy Resistance in Breast Cancer. Front Oncol 2021; 11:631007. [PMID: 33869016 PMCID: PMC8044931 DOI: 10.3389/fonc.2021.631007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 01/27/2021] [Indexed: 12/12/2022] Open
Abstract
Estrogens have been implicated in the etiology of breast cancer for a long time. It has been stated that long-term exposure to estrogens is associated with a higher incidence of breast cancer, since estradiol (E2) stimulates breast cell growth; however, its effect on DNA damage/repair is only starting to be investigated. Recent studies have documented that estrogens are able to modify the DNA damage response (DDR) and DNA repair mechanisms. On the other hand, it has been proposed that DDR machinery can be altered by estrogen signaling pathways, that can be related to cancer progression and chemoresistance. We have demonstrated that E2 promotes c-Src activation and breast cancer cell motility, through a non-genomic pathway. This review discusses scientific evidence supporting this non-genomic mechanism where estrogen modifies the DNA repair pathways, and its relationship to potential causes of chemoresistance.
Collapse
Affiliation(s)
- Javier E Jiménez-Salazar
- Department of Biology of Reproduction, Division of Biological Sciences and Health (DCBS), Autonomous Metropolitan University (UAM), Mexico City, Mexico.,School of Medicine, National Autonomous University of Mexico (UNAM), Mexico City, Mexico
| | - Rebeca Damian-Ferrara
- Monterrey Institute of Technology and Higher Education (ITESM), School of Engineering and Sciences, Monterrey, Mexico
| | - Marcela Arteaga
- Department of Biology of Reproduction, Division of Biological Sciences and Health (DCBS), Autonomous Metropolitan University (UAM), Mexico City, Mexico
| | - Nikola Batina
- Nanotechnology and Molecular Engineering Laboratory, Department of Chemistry, Division of Basic Science and Engineering (DCBI), Autonomous Metropolitan University (UAM), Mexico City, Mexico
| | - Pablo Damián-Matsumura
- Department of Biology of Reproduction, Division of Biological Sciences and Health (DCBS), Autonomous Metropolitan University (UAM), Mexico City, Mexico
| |
Collapse
|
24
|
Khatamian N, Soltani M, Shadan B, Neamati A, Tabrizi MH, Hormozi B. Pinus morrisonicola needles essential oil nanoemulsions as a novel strong antioxidant and anticancer agent. INORG NANO-MET CHEM 2021. [DOI: 10.1080/24701556.2021.1892760] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
| | - Mozhgan Soltani
- Department of Biology, Islamic Azad University, Mashhad, Iran
| | - Behnaz Shadan
- Faculty of Basic Sciences, Department of Biochemistry, Islamic Azad University, Shahrekord, Iran
| | - Ali Neamati
- Department of Biology, Islamic Azad University, Mashhad, Iran
| | | | - Bahareh Hormozi
- Department of Biology, Islamic Azad University, Mashhad, Iran
| |
Collapse
|
25
|
Maan M, Agrawal NJ, Padmanabhan J, Leitzinger CC, Rivera-Rivera Y, Saavedra HI, Chellappan SP. Tank Binding Kinase 1 modulates spindle assembly checkpoint components to regulate mitosis in breast and lung cancer cells. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1868:118929. [PMID: 33310066 DOI: 10.1016/j.bbamcr.2020.118929] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 11/17/2020] [Accepted: 12/07/2020] [Indexed: 11/25/2022]
Abstract
Error-free progression through mitosis is critical for proper cell division and accurate distribution of the genetic material. The anaphase-promoting complex/cyclosome (APC/C) ubiquitin ligase regulates the progression from metaphase to anaphase and its activation is controlled by the cofactors Cdc20 and Cdh1. Additionally, genome stability is maintained by the spindle assembly checkpoint (SAC), which monitors proper attachment of chromosomes to spindle microtubules prior to cell division. We had shown a role for Tank Binding Kinase 1 (TBK1) in microtubule dynamics and mitosis and here we describe a novel role of TBK1 in regulating SAC in breast and lung cancer cells. TBK1 interacts with and phosphorylates Cdc20 and Cdh1 and depletion of TBK1 elevates SAC components. TBK1 inhibition increases the association of Cdc20 with APC/C and BubR1 indicating inactivation of APC/C; similarly, interaction of Cdh1 with APC/C is also enhanced. TBK1 and TTK inhibition reduces cell viability and enhances centrosome amplification and micronucleation. These results indicate that alterations in TBK1 will impede mitotic progression and combining TBK1 inhibitors with other regulators of mitosis might be effective in eliminating cancer cells.
Collapse
Affiliation(s)
- Meenu Maan
- Department of Tumor Biology, H, Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Drive, Tampa, FL 33612, United States of America
| | - Neha Jaiswal Agrawal
- Department of Tumor Biology, H, Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Drive, Tampa, FL 33612, United States of America
| | - Jaya Padmanabhan
- Department of Tumor Biology, H, Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Drive, Tampa, FL 33612, United States of America
| | - Christelle Colin Leitzinger
- Department of Tumor Biology, H, Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Drive, Tampa, FL 33612, United States of America
| | - Yainyrette Rivera-Rivera
- Department of Basic Sciences, Division of Pharmacology and Cancer Biology, Ponce Health Sciences University/Ponce Research Institute, Ponce 00716-2348, Puerto Rico
| | - Harold I Saavedra
- Department of Basic Sciences, Division of Pharmacology and Cancer Biology, Ponce Health Sciences University/Ponce Research Institute, Ponce 00716-2348, Puerto Rico
| | - Srikumar P Chellappan
- Department of Tumor Biology, H, Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Drive, Tampa, FL 33612, United States of America.
| |
Collapse
|
26
|
Arroyo M, Cañuelo A, Calahorra J, Hastert F, Sánchez A, Clarke DJ, Marchal J. Mitotic entry upon Topo II catalytic inhibition is controlled by Chk1 and Plk1. FEBS J 2020; 287:4933-4951. [PMID: 32144855 PMCID: PMC7483426 DOI: 10.1111/febs.15280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 01/13/2020] [Accepted: 03/03/2020] [Indexed: 12/11/2022]
Abstract
Catalytic inhibition of topoisomerase II during G2 phase delays onset of mitosis due to the activation of the so-called decatenation checkpoint. This checkpoint is less known compared with the extensively studied G2 DNA damage checkpoint and is partially compromised in many tumor cells. We recently identified MCPH1 as a key regulator that confers cells with the capacity to adapt to the decatenation checkpoint. In the present work, we have explored the contributions of checkpoint kinase 1 (Chk1) and polo-like kinase 1 (Plk1), in order to better understand the molecular basis of decatenation checkpoint. Our results demonstrate that Chk1 function is required to sustain the G2 arrest induced by catalytic inhibition of Topo II. Interestingly, Chk1 loss of function restores adaptation in cells lacking MCPH1. Furthermore, we demonstrate that Plk1 function is required to bypass the decatenation checkpoint arrest in cells following Chk1 inhibition. Taken together, our data suggest that MCPH1 is critical to allow checkpoint adaptation by counteracting Chk1-mediated inactivation of Plk1. Importantly, we also provide evidence that MCPH1 function is not required to allow recovery from this checkpoint, which lends support to the notion that checkpoint adaptation and recovery are different mechanisms distinguished in part by specific effectors.
Collapse
Affiliation(s)
- M. Arroyo
- Departamento de Biología ExperimentalUniversidad de Jaén, Spain
| | - A. Cañuelo
- Departamento de Biología ExperimentalUniversidad de Jaén, Spain
| | - J. Calahorra
- Departamento de Biología ExperimentalUniversidad de Jaén, Spain
| | - F.D. Hastert
- Department of Biology, Technische Universität Darmstadt, Germany
| | - A. Sánchez
- Departamento de Biología ExperimentalUniversidad de Jaén, Spain
| | - D. J. Clarke
- Department of Genetics, Cell Biology and Development, University of Minnesota, US
| | - J.A. Marchal
- Departamento de Biología ExperimentalUniversidad de Jaén, Spain
| |
Collapse
|
27
|
Auria-Luna F, Fernández-Moreira V, Marqués-López E, Gimeno MC, Herrera RP. Ultrasound-assisted multicomponent synthesis of 4H-pyrans in water and DNA binding studies. Sci Rep 2020; 10:11594. [PMID: 32665694 PMCID: PMC7360557 DOI: 10.1038/s41598-020-68076-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 06/18/2020] [Indexed: 12/21/2022] Open
Abstract
A simple approach to synthesize new highly substituted 4H-pyran derivatives is described. Efficient Et3N acts as a readily accessible catalyst of this process performed in pure water and with only a 20 mol% of catalyst loading. The extremely simple operational methodology, short reaction times, clean procedure and excellent product yields render this new approach extremely appealing for the synthesis of 4H-pyrans, as potentially biological scaffolds. Additionally, DNA interaction analysis reveals that 4H-pyran derivatives behave preferably as minor groove binders over major groove or intercalators. Therefore, this is one of the scarce examples where pyrans have resulted to be interesting DNA binders with high binding constants (Kb ranges from 1.53 × 104 M-1 to 2.05 × 106 M-1).
Collapse
Affiliation(s)
- Fernando Auria-Luna
- Departamento de Química Orgánica, Laboratorio de Organocatálisis Asimétrica, Instituto de Síntesis Química y Catálisis Homogénea (ISQCH), CSIC-Universidad de Zaragoza, C/ Pedro Cerbuna, Nº12, 50009, Zaragoza, Spain
| | - Vanesa Fernández-Moreira
- Departamento de Química Inorgánica, Instituto de Síntesis Química y Catálisis Homogénea (ISQCH), CSIC-Universidad de Zaragoza, C/ Pedro Cerbuna, Nº12, 50009, Zaragoza, Spain
| | - Eugenia Marqués-López
- Departamento de Química Orgánica, Laboratorio de Organocatálisis Asimétrica, Instituto de Síntesis Química y Catálisis Homogénea (ISQCH), CSIC-Universidad de Zaragoza, C/ Pedro Cerbuna, Nº12, 50009, Zaragoza, Spain
| | - M Concepción Gimeno
- Departamento de Química Inorgánica, Instituto de Síntesis Química y Catálisis Homogénea (ISQCH), CSIC-Universidad de Zaragoza, C/ Pedro Cerbuna, Nº12, 50009, Zaragoza, Spain
| | - Raquel P Herrera
- Departamento de Química Orgánica, Laboratorio de Organocatálisis Asimétrica, Instituto de Síntesis Química y Catálisis Homogénea (ISQCH), CSIC-Universidad de Zaragoza, C/ Pedro Cerbuna, Nº12, 50009, Zaragoza, Spain.
| |
Collapse
|
28
|
Olivares-Urbano MA, Griñán-Lisón C, Marchal JA, Núñez MI. CSC Radioresistance: A Therapeutic Challenge to Improve Radiotherapy Effectiveness in Cancer. Cells 2020; 9:cells9071651. [PMID: 32660072 PMCID: PMC7407195 DOI: 10.3390/cells9071651] [Citation(s) in RCA: 103] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 07/03/2020] [Accepted: 07/07/2020] [Indexed: 12/12/2022] Open
Abstract
Radiotherapy (RT) is a modality of oncologic treatment that can be used to treat approximately 50% of all cancer patients either alone or in combination with other treatment modalities such as surgery, chemotherapy, immunotherapy, and therapeutic targeting. Despite the technological advances in RT, which allow a more precise delivery of radiation while progressively minimizing the impact on normal tissues, issues like radioresistance and tumor recurrence remain important challenges. Tumor heterogeneity is responsible for the variation in the radiation response of the different tumor subpopulations. A main factor related to radioresistance is the presence of cancer stem cells (CSC) inside tumors, which are responsible for metastases, relapses, RT failure, and a poor prognosis in cancer patients. The plasticity of CSCs, a process highly dependent on the epithelial–mesenchymal transition (EMT) and associated to cell dedifferentiation, complicates the identification and eradication of CSCs and it might be involved in disease relapse and progression after irradiation. The tumor microenvironment and the interactions of CSCs with their niches also play an important role in the response to RT. This review provides a deep insight into the characteristics and radioresistance mechanisms of CSCs and into the role of CSCs and tumor microenvironment in both the primary tumor and metastasis in response to radiation, and the radiobiological principles related to the CSC response to RT. Finally, we summarize the major advances and clinical trials on the development of CSC-based therapies combined with RT to overcome radioresistance. A better understanding of the potential therapeutic targets for CSC radiosensitization will provide safer and more efficient combination strategies, which in turn will improve the live expectancy and curability of cancer patients.
Collapse
Affiliation(s)
| | - Carmen Griñán-Lisón
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research, University of Granada, 18100 Granada, Spain;
- Department of Human Anatomy and Embryology, Faculty of Medicine, University of Granada, 18016 Granada, Spain
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), 18012 Granada, Spain
- Excellence Research Unit “Modeling Nature” (MNat), University of Granada, 18016 Granada, Spain
| | - Juan Antonio Marchal
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research, University of Granada, 18100 Granada, Spain;
- Department of Human Anatomy and Embryology, Faculty of Medicine, University of Granada, 18016 Granada, Spain
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), 18012 Granada, Spain
- Excellence Research Unit “Modeling Nature” (MNat), University of Granada, 18016 Granada, Spain
- Correspondence: (J.A.M.); (M.I.N.); Tel.: +34-958-249321 (J.A.M.); +34-958-242077 (M.I.N.)
| | - María Isabel Núñez
- Department of Radiology and Physical Medicine, University of Granada, 18016 Granada, Spain;
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research, University of Granada, 18100 Granada, Spain;
- Instituto de Investigación Biosanitaria de Granada (ibs.GRANADA), 18012 Granada, Spain
- Correspondence: (J.A.M.); (M.I.N.); Tel.: +34-958-249321 (J.A.M.); +34-958-242077 (M.I.N.)
| |
Collapse
|
29
|
Network modeling of patients' biomolecular profiles for clinical phenotype/outcome prediction. Sci Rep 2020; 10:3612. [PMID: 32107391 PMCID: PMC7046773 DOI: 10.1038/s41598-020-60235-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 11/05/2019] [Indexed: 12/15/2022] Open
Abstract
Methods for phenotype and outcome prediction are largely based on inductive supervised models that use selected biomarkers to make predictions, without explicitly considering the functional relationships between individuals. We introduce a novel network-based approach named Patient-Net (P-Net) in which biomolecular profiles of patients are modeled in a graph-structured space that represents gene expression relationships between patients. Then a kernel-based semi-supervised transductive algorithm is applied to the graph to explore the overall topology of the graph and to predict the phenotype/clinical outcome of patients. Experimental tests involving several publicly available datasets of patients afflicted with pancreatic, breast, colon and colorectal cancer show that our proposed method is competitive with state-of-the-art supervised and semi-supervised predictive systems. Importantly, P-Net also provides interpretable models that can be easily visualized to gain clues about the relationships between patients, and to formulate hypotheses about their stratification.
Collapse
|
30
|
Javanshir A, Karimi E, Maragheh AD, Tabrizi MH. The antioxidant and anticancer potential of Ricinus communis L. essential oil nanoemulsions. JOURNAL OF FOOD MEASUREMENT AND CHARACTERIZATION 2020. [DOI: 10.1007/s11694-020-00385-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
|
31
|
Pennock ND, Jindal S, Horton W, Sun D, Narasimhan J, Carbone L, Fei SS, Searles R, Harrington CA, Burchard J, Weinmann S, Schedin P, Xia Z. RNA-seq from archival FFPE breast cancer samples: molecular pathway fidelity and novel discovery. BMC Med Genomics 2019; 12:195. [PMID: 31856832 PMCID: PMC6924022 DOI: 10.1186/s12920-019-0643-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 12/08/2019] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Formalin-fixed, paraffin-embedded (FFPE) tissues for RNA-seq have advantages over fresh frozen tissue including abundance and availability, connection to rich clinical data, and association with patient outcomes. However, FFPE-derived RNA is highly degraded and chemically modified, which impacts its utility as a faithful source for biological inquiry. METHODS True archival FFPE breast cancer cases (n = 58), stored at room temperature for 2-23 years, were utilized to identify key steps in tissue selection, RNA isolation, and library choice. Gene expression fidelity was evaluated by comparing FFPE data to public data obtained from fresh tissues, and by employing single-gene, gene set and transcription network-based regulon analyses. RESULTS We report a single 10 μm section of breast tissue yields sufficient RNA for RNA-seq, and a relationship between RNA quality and block age that was not linear. We find single-gene analysis is limiting with FFPE tissues, while targeted gene set approaches effectively distinguish ER+ from ER- breast cancers. Novel utilization of regulon analysis identified the transcription factor KDM4B to associate with ER+ disease, with KDM4B regulon activity and gene expression having prognostic significance in an independent cohort of ER+ cases. CONCLUSION Our results, which outline a robust FFPE-RNA-seq pipeline for broad use, support utilizing FFPE tissues to address key questions in the breast cancer field, including the delineation between indolent and life-threatening disease, biological stratification and molecular mechanisms of treatment resistance.
Collapse
Affiliation(s)
- Nathan D Pennock
- Department of Cell, Developmental and Cancer Biology, Oregon Health & Science University, 2720 SW Moody Ave, Portland, OR, 97201, USA
| | - Sonali Jindal
- Department of Cell, Developmental and Cancer Biology, Oregon Health & Science University, 2720 SW Moody Ave, Portland, OR, 97201, USA
- Knight Cancer Institute, Oregon Health & Science University, 2720 SW Moody Ave, Portland, OR, 97201, USA
| | - Wesley Horton
- Department of Cell, Developmental and Cancer Biology, Oregon Health & Science University, 2720 SW Moody Ave, Portland, OR, 97201, USA
- Computational Biology Program, Oregon Health & Science University, Portland, OR, 97201, USA
| | - Duanchen Sun
- Computational Biology Program, Oregon Health & Science University, Portland, OR, 97201, USA
| | - Jayasri Narasimhan
- Department of Cell, Developmental and Cancer Biology, Oregon Health & Science University, 2720 SW Moody Ave, Portland, OR, 97201, USA
| | - Lucia Carbone
- Division of Genetics, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, 97006, USA
- Department of Medicine, Knight Cardiovascular Institute, Oregon Health & Science University, 3303 SW Bond Ave, Portland, OR, 97239, USA
| | - Suzanne S Fei
- Bioinformatics & Biostatistics Core, Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, 97006, USA
| | - Robert Searles
- Integrated Genomics Laboratory, Knight Cancer Institute, Oregon Health & Science University Knight Cancer Institute, Portland, OR, 97239, USA
| | - Christina A Harrington
- Integrated Genomics Laboratory, Knight Cancer Institute, Oregon Health & Science University Knight Cancer Institute, Portland, OR, 97239, USA
| | - Julja Burchard
- Computational Biology Program, Oregon Health & Science University, Portland, OR, 97201, USA
| | - Sheila Weinmann
- Center for Health Research, Kaiser Permanente Northwest, Portland, OR, 97278, USA
| | - Pepper Schedin
- Department of Cell, Developmental and Cancer Biology, Oregon Health & Science University, 2720 SW Moody Ave, Portland, OR, 97201, USA.
- Knight Cancer Institute, Oregon Health & Science University, 2720 SW Moody Ave, Portland, OR, 97201, USA.
- Young Women's Breast Cancer Translational Program, University of Colorado Anschutz Medical Campus, 1665 Aurora Court, USA, Aurora, CO, 80045, USA.
| | - Zheng Xia
- Computational Biology Program, Oregon Health & Science University, Portland, OR, 97201, USA.
- Department of Molecular Microbiology and Immunology Oregon Health & Science University, Portland, OR, 97273, USA.
| |
Collapse
|
32
|
Fleck JL, Pavel AB, Cassandras CG. A pan-cancer analysis of progression mechanisms and drug sensitivity in cancer cell lines. Mol Omics 2019; 15:399-405. [PMID: 31570905 DOI: 10.1039/c9mo00119k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Biomarker discovery involves identifying genetic abnormalities within a tumor. However, one of the main challenges in defining such therapeutic targets is accounting for the molecular heterogeneity of cancer. By integrating somatic mutation and gene expression data from hundreds of heterogeneous cell lines from the Cancer Cell Line Encyclopedia (CCLE), we identify sequences of genetic events that may help explain common patterns of oncogenesis across 22 tumor types, and evaluate the general effect of late-stage mutations on drug sensitivity and resistance mechanisms. Through gene enrichment analysis, we find several cancer-specific and immune pathways that are significantly enriched in each of our three proposed phases of cancer progression. By further analyzing the drug activity area associated with compounds that target the BRAF oncogene, a known predictor of drug sensitivity for several compounds used in cancer treatment, we verify that the acquisition of new driver mutations interferes with the targeted drug mechanism, meaning that cells without late-stage mutations generally respond better to drugs.
Collapse
Affiliation(s)
- Julia L Fleck
- Department of Industrial Engineering, Pontifical Catholic University of Rio de Janeiro, Rua Marques de Sao Vicente, 225, Rio de Janeiro, Brazil.
| | | | | |
Collapse
|
33
|
Presti D, Quaquarini E. The PI3K/AKT/mTOR and CDK4/6 Pathways in Endocrine Resistant HR+/HER2- Metastatic Breast Cancer: Biological Mechanisms and New Treatments. Cancers (Basel) 2019; 11:E1242. [PMID: 31450618 PMCID: PMC6770492 DOI: 10.3390/cancers11091242] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 08/17/2019] [Accepted: 08/20/2019] [Indexed: 12/30/2022] Open
Abstract
Endocrine-based treatments are the normal standard-of-care in women with hormone receptor-positive/Human Epidermal growth factor Receptor 2-negative metastatic breast cancer. Despite the well-known efficacy of these drugs as first-line therapies, about 50% of women develop endocrine resistance and disease progression. The treatment of these patients has represented one of the most important research fields in the last few years, with several multicenter phase II/III trials published or still ongoing. Novel therapies, such as cyclin-dependent kinase (CDK)4/6 and phosphatidylinositol 3-kinase (PI3K)/protein kinase B (AKT)/mammalian target of rapamycin (mTOR) inhibitors, have significantly changed the prognosis of patients progressing to a previous endocrine treatment, allowing a great benefit in terms of progression-free survival and, in some cases, of overall survival. However, identifying response predictors is essential for the rational use of these drugs to avoid unnecessary toxicity and costs, and to ensure the optimal therapeutic sequence is used. In this review, we analyze the PI3K/AKT/mTOR and CDK4/6 pathways and their roles in endocrine resistant metastatic breast cancer. We then focus on the new treatments developed and the roles of these drugs in overcoming endocrine resistance, describing the latest clinical trials that led to the approval of the drugs in clinical practice.
Collapse
Affiliation(s)
- Daniele Presti
- Department of Internal Medicine and Therapeutics, University of Pavia, 27100 Pavia, Italy
- Medical Oncology Unit, IRCCS ICS Maugeri SpA SB, 27100 Pavia, Italy
| | - Erica Quaquarini
- Medical Oncology Unit, IRCCS ICS Maugeri SpA SB, 27100 Pavia, Italy.
- Experimental Medicine, University of Pavia, 27100 Pavia, Italy.
| |
Collapse
|
34
|
Zahid KR, Su M, Khan ARR, Han S, Deming G, Raza U. Systems biology based meth-miRNA-mRNA regulatory network identifies metabolic imbalance and hyperactive cell cycle signaling involved in hepatocellular carcinoma onset and progression. Cancer Cell Int 2019; 19:89. [PMID: 31007607 PMCID: PMC6454777 DOI: 10.1186/s12935-019-0804-3] [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: 12/16/2018] [Accepted: 03/27/2019] [Indexed: 12/12/2022] Open
Abstract
Background Hepatocellular carcinoma (HCC) is one of the leading cause of cancer associated deaths worldwide. Independent studies have proposed altered DNA methylation pattern and aberrant microRNA (miRNA) levels leading to abnormal expression of different genes as important regulators of disease onset and progression in HCC. Here, using systems biology approaches, we aimed to integrate methylation, miRNA profiling and gene expression data into a regulatory methylation-miRNA–mRNA (meth-miRNA–mRNA) network to better understand the onset and progression of the disease. Methods Patients’ gene methylation, miRNA expression and gene expression data were retrieved from the NCBI GEO and TCGA databases. Differentially methylated genes, and differentially expressed miRNAs and genes were identified by comparing respective patients’ data using two tailed Student’s t-test. Functional annotation and pathway enrichment, miRNA–mRNA inverse pairing and gene set enrichment analyses (GSEA) were performed using DAVID, miRDIP v4.1 and GSEA tools respectively. meth-miRNA–mRNA network was constructed using Cytoscape v3.5.1. Kaplan–Meier survival analyses were performed using R script and significance was calculated by Log-rank (Mantel-Cox) test. Results We identified differentially expressed mRNAs, miRNAs, and differentially methylated genes in HCC as compared to normal adjacent tissues by analyzing gene expression, miRNA expression, and methylation profiling data of HCC patients and integrated top miRNAs along with their mRNA targets and their methylation profile into a regulatory meth-miRNA–mRNA network using systems biology approach. Pathway enrichment analyses of identified genes revealed suppressed metabolic pathways and hyperactive cell cycle signaling as key features of HCC onset and progression which we validated in 10 different HCC patients’ datasets. Next, we confirmed the inverse correlation between gene methylation and its expression, and between miRNA and its targets’ expression in various datasets. Furthermore, we validated the clinical significance of identified methylation, miRNA and mRNA signatures by checking their association with clinical features and survival of HCC patients. Conclusions Overall, we suggest that simultaneous (1) reversal of hyper-methylation and/or oncogenic miRNA driven suppression of genes involved in metabolic pathways, and (2) induction of hyper-methylation and/or tumor suppressor miRNA driven suppression of genes involved in cell cycle signaling have potential of inhibiting disease aggressiveness, and predicting good survival in HCC. Electronic supplementary material The online version of this article (10.1186/s12935-019-0804-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Kashif Rafiq Zahid
- 1Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Carson International Cancer Center, Shenzhen University, Shenzhen, 518060 Guangdong China
| | - Mingyang Su
- 1Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Carson International Cancer Center, Shenzhen University, Shenzhen, 518060 Guangdong China
| | - Abdur Rehman Raza Khan
- 2Military College of Signals, National University of Science and Technology (NUST), Khadim Hussain Rd, Rawalpindi, Pakistan
| | - Shiming Han
- 3School of Biological Sciences and Technology, Liupanshui Normal University, Liupanshui, 553004 China
| | - Gou Deming
- 1Shenzhen Key Laboratory of Microbial Genetic Engineering, College of Life Sciences and Oceanography, Carson International Cancer Center, Shenzhen University, Shenzhen, 518060 Guangdong China
| | - Umar Raza
- Department of Biological Sciences, National University of Medical Sciences (NUMS), Abid Majeed Road, Rawalpindi, Pakistan
| |
Collapse
|
35
|
Tiong KL, Yeang CH. MGSEA - a multivariate Gene set enrichment analysis. BMC Bioinformatics 2019; 20:145. [PMID: 30885118 PMCID: PMC6421703 DOI: 10.1186/s12859-019-2716-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 03/06/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Gene Set Enrichment Analysis (GSEA) is a powerful tool to identify enriched functional categories of informative biomarkers. Canonical GSEA takes one-dimensional feature scores derived from the data of one platform as inputs. Numerous extensions of GSEA handling multimodal OMIC data are proposed, yet none of them explicitly captures combinatorial relations of feature scores from multiple platforms. RESULTS We propose multivariate GSEA (MGSEA) to capture combinatorial relations of gene set enrichment among multiple platform features. MGSEA successfully captures designed feature relations from simulated data. By applying it to the scores of delineating breast cancer and glioblastoma multiforme (GBM) subtypes from The Cancer Genome Atlas (TCGA) datasets of CNV, DNA methylation and mRNA expressions, we find that breast cancer and GBM data yield both similar and distinct outcomes. Among the enriched functional categories, subtype-specific biomarkers are dominated by mRNA expression in many functional categories in both cancer types and also by CNV in many functional categories in breast cancer. The enriched functional categories belonging to distinct combinatorial patterns are involved different oncogenic processes: cell proliferation (such as cell cycle control, estrogen responses, MYC and E2F targets) for mRNA expression in breast cancer, invasion and metastasis (such as cell adhesion and epithelial-mesenchymal transition (EMT)) for CNV in breast cancer, and diverse processes (such as immune and inflammatory responses, cell adhesion, angiogenesis, and EMT) for mRNA expression in GBM. These observations persist in two external datasets (Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) for breast cancer and Repository for Molecular Brain Neoplasia Data (REMBRANDT) for GBM) and are consistent with knowledge of cancer subtypes. We further compare the characteristics of MGSEA with several extensions of GSEA and point out the pros and cons of each method. CONCLUSIONS We demonstrated the utility of MGSEA by inferring the combinatorial relations of multiple platforms for cancer subtype delineation in three multi-OMIC datasets: TCGA, METABRIC and REMBRANDT. The inferred combinatorial patterns are consistent with the current knowledge and also reveal novel insights about cancer subtypes. MGSEA can be further applied to any genotype-phenotype association problems with multimodal OMIC data.
Collapse
Affiliation(s)
- Khong-Loon Tiong
- Institute of Statistical Science, Academia Sinica, Taipei, Taiwan
| | | |
Collapse
|
36
|
Jiang L, Yu X, Ma X, Liu H, Zhou S, Zhou X, Meng Q, Wang L, Jiang W. Identification of transcription factor-miRNA-lncRNA feed-forward loops in breast cancer subtypes. Comput Biol Chem 2018; 78:1-7. [PMID: 30476706 DOI: 10.1016/j.compbiolchem.2018.11.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 10/18/2018] [Accepted: 11/14/2018] [Indexed: 12/21/2022]
Abstract
Previous studies have demonstrated that transcription factor-miRNA-gene feed-forward loops (FFLs) played important roles in tumorigenesis. However, the lncRNA-involved FFLs have not been explored very well. Understanding the characteristics of lncRNA-involved FFLs in breast cancer subtypes may be a key question with clinical implications. In this study, we firstly constructed an integrated background regulatory network. Then, based on mRNA, miRNA, and lncRNA differential expression, we identified 147, 140, 284, 1031 dysregulated FFLs for luminal A, luminal B, HER2+ and basal-like subtype of breast cancer, respectively. Importantly, the known breast cancer-associated lncRNAs and miRNAs were enriched in the identified dysregulated FFLs. Through merging the dysregulated FFLs, we constructed the regulatory sub-network for each subtype. We found that all sub-networks were enriched in the well-known cancer-related pathways, such as cell cycle, pathways in cancer. Next, we also identified potential prognostic FFLs for subtypes of breast cancer, such as the hsa-miR-182-5p_JUN_XIST in basal-like subtype. Finally, we also discussed the potential application of inferring the candidate drugs for breast cancer treatment through modulating the lncRNA expression in the dysregulated FFLs. Collectively, this study elucidated the roles of lncRNA-involved FFLs in breast cancer subtypes, which could contribute to understanding breast cancer pathogenesis and improving the treatment.
Collapse
Affiliation(s)
- Leiming Jiang
- College of Automation Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, 21106, China; College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Xuexin Yu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Xueyan Ma
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Haizhou Liu
- College of Automation Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, 21106, China
| | - Shunheng Zhou
- College of Automation Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, 21106, China
| | - Xu Zhou
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Qianqian Meng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China
| | - Lihong Wang
- Department of Pathophysiology, School of Medicine, Southeast University, Nanjing, 210009, China.
| | - Wei Jiang
- College of Automation Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing, 21106, China; College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China.
| |
Collapse
|
37
|
Teng Y, Zhu K, Xiong C, Huang J. Electrodeformation-Based Biomechanical Chip for Quantifying Global Viscoelasticity of Cancer Cells Regulated by Cell Cycle. Anal Chem 2018; 90:8370-8378. [DOI: 10.1021/acs.analchem.8b00584] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
| | - Kui Zhu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | | | | |
Collapse
|
38
|
Mboge MY, Mahon BP, McKenna R, Frost SC. Carbonic Anhydrases: Role in pH Control and Cancer. Metabolites 2018; 8:E19. [PMID: 29495652 PMCID: PMC5876008 DOI: 10.3390/metabo8010019] [Citation(s) in RCA: 157] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 02/08/2018] [Accepted: 02/22/2018] [Indexed: 02/07/2023] Open
Abstract
The pH of the tumor microenvironment drives the metastatic phenotype and chemotherapeutic resistance of tumors. Understanding the mechanisms underlying this pH-dependent phenomenon will lead to improved drug delivery and allow the identification of new therapeutic targets. This includes an understanding of the role pH plays in primary tumor cells, and the regulatory factors that permit cancer cells to thrive. Over the last decade, carbonic anhydrases (CAs) have been shown to be important mediators of tumor cell pH by modulating the bicarbonate and proton concentrations for cell survival and proliferation. This has prompted an effort to inhibit specific CA isoforms, as an anti-cancer therapeutic strategy. Of the 12 active CA isoforms, two, CA IX and XII, have been considered anti-cancer targets. However, other CA isoforms also show similar activity and tissue distribution in cancers and have not been considered as therapeutic targets for cancer treatment. In this review, we consider all the CA isoforms and their possible role in tumors and their potential as targets for cancer therapy.
Collapse
Affiliation(s)
- Mam Y Mboge
- University of Florida, College of Medicine, Department of Biochemistry and Molecular Biology, P.O. Box 100245, Gainesville, FL 32610, USA.
| | - Brian P Mahon
- University of Florida, College of Medicine, Department of Biochemistry and Molecular Biology, P.O. Box 100245, Gainesville, FL 32610, USA.
| | - Robert McKenna
- University of Florida, College of Medicine, Department of Biochemistry and Molecular Biology, P.O. Box 100245, Gainesville, FL 32610, USA.
| | - Susan C Frost
- University of Florida, College of Medicine, Department of Biochemistry and Molecular Biology, P.O. Box 100245, Gainesville, FL 32610, USA.
| |
Collapse
|
39
|
Meksiarun P, Aoki PHB, Van Nest SJ, Sobral-Filho RG, Lum JJ, Brolo AG, Jirasek A. Breast cancer subtype specific biochemical responses to radiation. Analyst 2018; 143:3850-3858. [DOI: 10.1039/c8an00345a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
External beam radiotherapy is a common form of treatment for breast cancer.
Collapse
Affiliation(s)
- Phiranuphon Meksiarun
- Department of Physics
- I.K. Barber School of Arts and Sciences
- University of British Columbia – Okanagan
- Kelowna
- Canada
| | - Pedro H. B. Aoki
- São Paulo State University (UNESP)
- School of Sciences
- Humanities and Languages
- Campus Assis
- Brazil
| | | | | | - Julian J. Lum
- University of Victoria
- Department of Biochemistry and Microbiology
- Victoria
- Canada
- Trev and Joyce Deeley Research Centre
| | | | - Andrew Jirasek
- Department of Physics
- I.K. Barber School of Arts and Sciences
- University of British Columbia – Okanagan
- Kelowna
- Canada
| |
Collapse
|
40
|
Losada-Echeberría M, Herranz-López M, Micol V, Barrajón-Catalán E. Polyphenols as Promising Drugs against Main Breast Cancer Signatures. Antioxidants (Basel) 2017; 6:E88. [PMID: 29112149 PMCID: PMC5745498 DOI: 10.3390/antiox6040088] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 10/30/2017] [Accepted: 11/03/2017] [Indexed: 12/19/2022] Open
Abstract
Breast cancer is one of the most common neoplasms worldwide, and in spite of clinical and pharmacological advances, it is still a clinical problem, causing morbidity and mortality. On the one hand, breast cancer shares with other neoplasms some molecular signatures such as an imbalanced redox state, cell cycle alterations, increased proliferation and an inflammatory status. On the other hand, breast cancer shows differential molecular subtypes that determine its prognosis and treatment. These are characterized mainly by hormone receptors especially estrogen receptors (ERs) and epidermal growth factor receptor 2 (HER2). Tumors with none of these receptors are classified as triple negative breast cancer (TNBC) and are associated with a worse prognosis. The success of treatments partially depends on their specificity and the adequate molecular classification of tumors. New advances in anticancer drug discovery using natural compounds have been made in the last few decades, and polyphenols have emerged as promising molecules. They may act on various molecular targets because of their promiscuous behavior, presenting several physiological effects, some of which confer antitumor activity. This review analyzes the accumulated evidence of the antitumor effects of plant polyphenols on breast cancer, with special attention to their activity on ERs and HER2 targets and also covering different aspects such as redox balance, uncontrolled proliferation and chronic inflammation.
Collapse
Affiliation(s)
- María Losada-Echeberría
- Institute of Molecular and Cell Biology (IBMC), Miguel Hernández University (UMH), Avda. Universidad s/n, Elche 03202, Spain.
| | - María Herranz-López
- Institute of Molecular and Cell Biology (IBMC), Miguel Hernández University (UMH), Avda. Universidad s/n, Elche 03202, Spain.
| | - Vicente Micol
- Institute of Molecular and Cell Biology (IBMC), Miguel Hernández University (UMH), Avda. Universidad s/n, Elche 03202, Spain.
- CIBER, Fisiopatología de la Obesidad y la Nutrición, CIBERobn, Instituto de Salud Carlos III (CB12/03/30038), Palma de Mallorca 07122, Spain.
| | - Enrique Barrajón-Catalán
- Institute of Molecular and Cell Biology (IBMC), Miguel Hernández University (UMH), Avda. Universidad s/n, Elche 03202, Spain.
| |
Collapse
|