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Chaudhary U, Banerjee S. Decoding the Non-coding: Tools and Databases Unveiling the Hidden World of "Junk" RNAs for Innovative Therapeutic Exploration. ACS Pharmacol Transl Sci 2024; 7:1901-1915. [PMID: 39022352 PMCID: PMC11249652 DOI: 10.1021/acsptsci.3c00388] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 05/15/2024] [Accepted: 05/27/2024] [Indexed: 07/20/2024]
Abstract
Non-coding RNAs are pivotal regulators of gene and protein expression, exerting crucial influences on diverse biological processes. Their dysregulation is frequently implicated in the onset and progression of diseases, notably cancer. A profound comprehension of the intricate mechanisms governing ncRNAs is imperative for devising innovative therapeutic interventions against these debilitating conditions. Significantly, nearly 80% of our genome comprises ncRNAs, underscoring their centrality in cellular processes. The elucidation of ncRNA functions is pivotal for grasping the complexities of gene regulation and its implications for human health. Modern genome sequencing techniques yield vast datasets, stored in specialized databases. To harness this wealth of information and to understand the crosstalk of non-coding RNAs, knowledge of available databases is required, and many new sophisticated computational tools have emerged. These tools play a pivotal role in the identification, prediction, and annotation of ncRNAs, thereby facilitating their experimental validation. This Review succinctly outlines the current understanding of ncRNAs, emphasizing their involvement in disease development. It also highlights the databases and tools instrumental in classifying, annotating, and evaluating ncRNAs. By extracting meaningful biological insights from seemingly "junk" data, these tools empower scientists to unravel the intricate roles of ncRNAs in shaping human health.
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Affiliation(s)
- Uma Chaudhary
- Department of Biotechnology,
School of Biosciences and Technology, Vellore
Institute of Technology (VIT), Vellore, Tamil Nadu 632014, India
| | - Satarupa Banerjee
- Department of Biotechnology,
School of Biosciences and Technology, Vellore
Institute of Technology (VIT), Vellore, Tamil Nadu 632014, India
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2
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Piao YJ, Kim HS, Kim H, Shen J, Moon WK. SerpinB2 deficiency is associated with delayed mammary tumor development and decreased pro-tumorigenic macrophage polarization. BMC Cancer 2024; 24:792. [PMID: 38956496 PMCID: PMC11221169 DOI: 10.1186/s12885-024-12473-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 06/04/2024] [Indexed: 07/04/2024] Open
Abstract
The in vivo functions of SerpinB2 in tumor cells and tumor-associated macrophages (TAMs) during breast cancer development and metastasis remain elusive. SerpinB2-deficient MMTV-PyMT mice (PyMTSB2-/-) were previously produced to explore the biological roles of SerpinB2 in breast cancer. Compared with MMTV-PyMT wild-type (PyMTWT) mice, PyMTSB2-/- mice showed delayed tumor progression and reduced CK8 + tumor cell dissemination to lymph nodes. RNA-Seq data revealed significantly enriched genes associated with inflammatory responses, especially upregulated M1 and downregulated M2 macrophage marker genes in PyMTSB2-/- tumors. Decreased CD206+M2 and increased NOS2+M1 markers were detected in the primary tumors and metastatic lymph nodes of PyMTSB2-/- mice. In an in vitro study, SerpinB2 knockdown decreased the sphere formation and migration of MDA-MB-231 cells and suppressed protumorigenic M2 polarization of RAW264.7 cells. The combination of low SerpinB2, high NOS2, and low CD206 expression was favorable for survival in patients with breast cancer, as assessed in the BreastMark dataset. Our study demonstrates that SerpinB2 deficiency delays mammary tumor development and metastasis in PyMTWT mice, along with reduced sphere formation and migration abilities of tumor cells and decreased macrophage protumorigenic polarization.
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Affiliation(s)
- Yin Ji Piao
- Department of Radiology, Sun Yat-Sen Memorial Hospital and Sun Yat-Sen University, No. 107 Yanjiang Road West, Guangzhou, 510120, China
- Department of Biomedical Sciences, Seoul National University College of Medicine, 103 Daehak-Ro, Jongno-Gu, Seoul, 03080, Korea
| | - Hoe Suk Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, 103 Daehak-Ro, Jongno-Gu, Seoul, 03080, Korea
- Department of Pharmaceutical Sciences, College of Pharmacy & Allied Health Professions, South Dakota State University, SAV# 255, Box 2202C, Brookings, SD, 57007, USA
| | - Hyelim Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, 103 Daehak-Ro, Jongno-Gu, Seoul, 03080, Korea
| | - Jun Shen
- Department of Radiology, Sun Yat-Sen Memorial Hospital and Sun Yat-Sen University, No. 107 Yanjiang Road West, Guangzhou, 510120, China.
| | - Woo Kyung Moon
- Department of Biomedical Sciences, Seoul National University College of Medicine, 103 Daehak-Ro, Jongno-Gu, Seoul, 03080, Korea.
- Department of Radiology, Seoul National University Hospital and Seoul National University College of Medicine, 101 Daehak-Ro, Jongno-Gu, Seoul, 03080, Korea.
- Biomedical Research Institute, Seoul National University Hospital, 101 Daehak-Ro, Jongno-Gu, Seoul, 03080, Korea.
- Integrated Major in Innovative Medical Science, Seoul National University Graduate School, 103 Daehak-Ro, Jongno-Gu, Seoul, 03080, Korea.
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3
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Liu J, Yu Y, Li M, Wu Y, Chen W, Liu G, Liu L, Lin J, Peng C, Sun W, Wu X, Chen X. PMBC: a manually curated database for prognostic markers of breast cancer. Database (Oxford) 2024; 2024:baae033. [PMID: 38748636 PMCID: PMC11095525 DOI: 10.1093/database/baae033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 02/21/2024] [Accepted: 05/07/2024] [Indexed: 05/19/2024]
Abstract
Breast cancer is notorious for its high mortality and heterogeneity, resulting in different therapeutic responses. Classical biomarkers have been identified and successfully commercially applied to predict the outcome of breast cancer patients. Accumulating biomarkers, including non-coding RNAs, have been reported as prognostic markers for breast cancer with the development of sequencing techniques. However, there are currently no databases dedicated to the curation and characterization of prognostic markers for breast cancer. Therefore, we constructed a curated database for prognostic markers of breast cancer (PMBC). PMBC consists of 1070 markers covering mRNAs, lncRNAs, miRNAs and circRNAs. These markers are enriched in various cancer- and epithelial-related functions including mitogen-activated protein kinases signaling. We mapped the prognostic markers into the ceRNA network from starBase. The lncRNA NEAT1 competes with 11 RNAs, including lncRNAs and mRNAs. The majority of the ceRNAs in ABAT belong to pseudogenes. The topology analysis of the ceRNA network reveals that known prognostic RNAs have higher closeness than random. Among all the biomarkers, prognostic lncRNAs have a higher degree, while prognostic mRNAs have significantly higher closeness than random RNAs. These results indicate that the lncRNAs play important roles in maintaining the interactions between lncRNAs and their ceRNAs, which might be used as a characteristic to prioritize prognostic lncRNAs based on the ceRNA network. PMBC renders a user-friendly interface and provides detailed information about individual prognostic markers, which will facilitate the precision treatment of breast cancer. PMBC is available at the following URL: http://www.pmbreastcancer.com/.
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Affiliation(s)
- Jiabei Liu
- School of Automation, Guangdong University of Technology, 100 Outer Ring West Road, Guangzhou University City, Panyu District, Guangzhou 510006, China
| | - Yiyi Yu
- School of Automation, Guangdong University of Technology, 100 Outer Ring West Road, Guangzhou University City, Panyu District, Guangzhou 510006, China
| | - Mingyue Li
- School of Automation, Guangdong University of Technology, 100 Outer Ring West Road, Guangzhou University City, Panyu District, Guangzhou 510006, China
| | - Yixuan Wu
- School of Automation, Guangdong University of Technology, 100 Outer Ring West Road, Guangzhou University City, Panyu District, Guangzhou 510006, China
| | - Weijun Chen
- School of Automation, Guangdong University of Technology, 100 Outer Ring West Road, Guangzhou University City, Panyu District, Guangzhou 510006, China
| | - Guanru Liu
- School of Automation, Guangdong University of Technology, 100 Outer Ring West Road, Guangzhou University City, Panyu District, Guangzhou 510006, China
| | - Lingxian Liu
- School of Automation, Guangdong University of Technology, 100 Outer Ring West Road, Guangzhou University City, Panyu District, Guangzhou 510006, China
| | - Jiechun Lin
- School of Automation, Guangdong University of Technology, 100 Outer Ring West Road, Guangzhou University City, Panyu District, Guangzhou 510006, China
| | - Chujun Peng
- School of Automation, Guangdong University of Technology, 100 Outer Ring West Road, Guangzhou University City, Panyu District, Guangzhou 510006, China
| | - Weijun Sun
- School of Automation, Guangdong University of Technology, 100 Outer Ring West Road, Guangzhou University City, Panyu District, Guangzhou 510006, China
- Guangdong Key Laboratory of IoT Information Technology, Guangdong University of Technology, 100 Outer Ring West Road, Guangzhou University City, Panyu District, Guangzhou 510006, China
| | - Xiaoli Wu
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, 100 Outer Ring West Road, Guangzhou University City, Panyu District, Guangzhou 510006, China
| | - Xin Chen
- School of Automation, Guangdong University of Technology, 100 Outer Ring West Road, Guangzhou University City, Panyu District, Guangzhou 510006, China
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4
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Thompson EJ, Escarbe S, Tvorogov D, Farshid G, Gregory PA, Khew-Goodall Y, Madden S, Ingman WV, Lindeman GJ, Lim E, Lopez AF, Bonder CS. Interleukin-3 production by basal-like breast cancer cells is associated with poor prognosis. Growth Factors 2024; 42:49-61. [PMID: 38299881 DOI: 10.1080/08977194.2023.2297693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 12/07/2023] [Indexed: 02/02/2024]
Abstract
Breast cancer represents a collection of pathologies with different molecular subtypes, histopathology, risk factors, clinical behavior, and responses to treatment. "Basal-like" breast cancers predominantly lack the receptors for estrogen and progesterone (ER/PR), lack amplification of human epidermal growth factor receptor 2 (HER2) but account for 10-15% of all breast cancers, are largely insensitive to targeted treatment and represent a disproportionate number of metastatic cases and deaths. Analysis of interleukin (IL)-3 and the IL-3 receptor subunits (IL-3RA + CSF2RB) reveals elevated expression in predominantly the basal-like group. Further analysis suggests that IL-3 itself, but not the IL-3 receptor subunits, associates with poor patient outcome. Histology on patient-derived xenografts supports the notion that breast cancer cells are a significant source of IL-3 that may promote disease progression. Taken together, these observations suggest that IL-3 may be a useful marker in solid tumors, particularly triple negative breast cancer, and warrants further investigation into its contribution to disease pathogenesis.
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Affiliation(s)
- Emma J Thompson
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, Australia
| | - Samantha Escarbe
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, Australia
| | - Denis Tvorogov
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, Australia
| | - Gelareh Farshid
- BreastScreen SA and SA Pathology, Adelaide, Australia
- Adelaide Medical School, University of Adelaide, Adelaide, Australia
| | - Philip A Gregory
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, Australia
- Adelaide Medical School, University of Adelaide, Adelaide, Australia
| | - Yeesim Khew-Goodall
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, Australia
- Adelaide Medical School, University of Adelaide, Adelaide, Australia
- School of Biological Sciences, University of Adelaide, Australia
| | | | - Wendy V Ingman
- Adelaide Medical School, University of Adelaide, Adelaide, Australia
- The Robinson Research Institute, University of Adelaide, Adelaide, Australia
| | - Geoffrey J Lindeman
- Cancer Biology and Stem Cells Division, Walter, Eliza Hall Institute of Medical Research, Melbourne, Australia
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Australia
- Department of Medicine, Royal Melbourne Hospital, University of Melbourne, Melbourne, Australia
| | - Elgene Lim
- Garvan Institute of Medical Research and St. Vincent"s Clinical School, University of New South Wales, Darlinghurst,Australia
| | - Angel F Lopez
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, Australia
- Adelaide Medical School, University of Adelaide, Adelaide, Australia
| | - Claudine S Bonder
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, Australia
- Adelaide Medical School, University of Adelaide, Adelaide, Australia
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5
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Orsini A, Diquigiovanni C, Bonora E. Omics Technologies Improving Breast Cancer Research and Diagnostics. Int J Mol Sci 2023; 24:12690. [PMID: 37628869 PMCID: PMC10454385 DOI: 10.3390/ijms241612690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 08/09/2023] [Accepted: 08/10/2023] [Indexed: 08/27/2023] Open
Abstract
Breast cancer (BC) has yielded approximately 2.26 million new cases and has caused nearly 685,000 deaths worldwide in the last two years, making it the most common diagnosed cancer type in the world. BC is an intricate ecosystem formed by both the tumor microenvironment and malignant cells, and its heterogeneity impacts the response to treatment. Biomedical research has entered the era of massive omics data thanks to the high-throughput sequencing revolution, quick progress and widespread adoption. These technologies-liquid biopsy, transcriptomics, epigenomics, proteomics, metabolomics, pharmaco-omics and artificial intelligence imaging-could help researchers and clinicians to better understand the formation and evolution of BC. This review focuses on the findings of recent multi-omics-based research that has been applied to BC research, with an introduction to every omics technique and their applications for the different BC phenotypes, biomarkers, target therapies, diagnosis, treatment and prognosis, to provide a comprehensive overview of the possibilities of BC research.
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Affiliation(s)
| | - Chiara Diquigiovanni
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40131 Bologna, Italy; (A.O.); (E.B.)
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6
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Han X, Liu T, Zhai J, Liu C, Wang W, Nie C, Wang Q, Zhu X, Zhou H, Tian W. Association between EPHA5 methylation status in peripheral blood leukocytes and the risk and prognosis of gastric cancer. PeerJ 2022; 10:e13774. [PMID: 36164608 PMCID: PMC9508887 DOI: 10.7717/peerj.13774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 07/01/2022] [Indexed: 01/19/2023] Open
Abstract
Purpose Altered DNA methylation, genetic alterations, and environmental factors are involved in tumorigenesis. As a tumor suppressor gene, abnormal EPHA5 methylation was found in gastric cancer (GC) tissues and was linked to the initiation, progression and prognosis of GC. In this study, the EPHA5 methylation level in peripheral blood leukocytes (PBLs) was detected to explore its relationship with GC risk and prognosis. Methods A total of 366 GC cases and 374 controls were selected as the subjects of this study to collect their environmental factors, and the EPHA5 methylation status was detected through the methylation-sensitive high-resolution melting method. Logistic regression analysis was utilized to evaluate the associations among EPHA5 methylation, environmental factors and GC risk. Meanwhile, the propensity score (PS) was used to adjust the imbalance of some independent variables. Results After PS adjustment, EPHA5 Pm (positive methylation) was more likely to increase the GC risk than EPHA5 Nm (negative methylation) (ORb = 1.827, 95% CI [1.202-2.777], P = 0.005). EPHA5 Pm had a more significant association with GC risk in the elderly (ORa = 2.785, 95% CI [1.563-4.961], P = 0.001) and H. pylori-negative groups (ORa = 2.758, 95% CI [1.369-5.555], P = 0.005). Moreover, the combined effects of EPHA5 Pm and H. pylori infection (ORc a = 3.543, 95% CI [2.233-5.621], P < 0.001), consumption of alcohol (ORc a = 2.893, 95% CI [1.844-4.539], P < 0.001), and salty food intake (ORc a = 4.018, 95% CI [2.538-6.362], P < 0.001) on increasing the GC risk were observed. In addition, no convincing association was found between EPHA5 Pm and the GC prognosis. Conclusions EPHA5 methylation in PBLs and its combined effects with environmental risk factors are related to the GC risk.
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Cerqueira OLD, Botelho MCS, Fiore APZP, Osório CABDT, Tomasin R, Morais MCC, López RVM, Cardoso EC, Vilella-Arias SA, Reis EM, Bruni-Cardoso A. Prognostic value of integrin αV expression and localization pattern in invasive breast carcinomas. Neoplasia 2022; 30:100803. [PMID: 35526305 PMCID: PMC9092997 DOI: 10.1016/j.neo.2022.100803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 04/18/2022] [Indexed: 10/25/2022]
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Wolowczyk C, Neckmann U, Aure MR, Hall M, Johannessen B, Zhao S, Skotheim RI, Andersen SB, Zwiggelaar R, Steigedal TS, Lingjærde OC, Sahlberg KK, Almaas E, Bjørkøy G. NRF2 drives an oxidative stress response predictive of breast cancer. Free Radic Biol Med 2022; 184:170-184. [PMID: 35381325 DOI: 10.1016/j.freeradbiomed.2022.03.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/29/2022] [Accepted: 03/30/2022] [Indexed: 12/12/2022]
Abstract
Many breast cancer patients are diagnosed with small, well-differentiated, hormone receptor-positive tumors. Risk of relapse is not easily identified in these patients, resulting in overtreatment. To identify metastasis-related gene expression patterns, we compared the transcriptomes of the non-metastatic 67NR and metastatic 66cl4 cell lines from the murine 4T1 mammary tumor model. The transcription factor nuclear factor, erythroid 2-like 2 (NRF2, encoded by NFE2L2) was constitutively activated in the metastatic cells and tumors, and correspondingly a subset of established NRF2-regulated genes was also upregulated. Depletion of NRF2 increased basal levels of reactive oxygen species (ROS) and severely reduced ability to form primary tumors and lung metastases. Consistently, a set of NRF2-controlled genes was elevated in breast cancer biopsies. Sixteen of these were combined into a gene expression signature that significantly improves the PAM50 ROR score, and is an independent, strong predictor of prognosis, even in hormone receptor-positive tumors.
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Affiliation(s)
- Camilla Wolowczyk
- Centre of Molecular Inflammation Research and Department of Cancer Research and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway; Department of Biomedical Laboratory Science, Faculty of Natural Sciences, Norwegian University of Science and Technology, Trondheim, Norway; Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim, Norway.
| | - Ulrike Neckmann
- Centre of Molecular Inflammation Research and Department of Cancer Research and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway; Department of Biomedical Laboratory Science, Faculty of Natural Sciences, Norwegian University of Science and Technology, Trondheim, Norway; Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim, Norway
| | - Miriam Ragle Aure
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway; Department of Medical Genetics, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Martina Hall
- Department of Biotechnology and Food Science, Faculty of Natural Sciences, Norwegian University of Science and Technology, Trondheim, Norway; K.G.Jebsen Center for Genetic Epidemiology, Department of Public Health and General Practice, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Norway
| | - Bjarne Johannessen
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital-Radiumhospitalet, Oslo, Norway; Norwegian Cancer Genomics Consortium, Oslo, Norway
| | - Sen Zhao
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital-Radiumhospitalet, Oslo, Norway; Norwegian Cancer Genomics Consortium, Oslo, Norway
| | - Rolf I Skotheim
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital-Radiumhospitalet, Oslo, Norway; Norwegian Cancer Genomics Consortium, Oslo, Norway
| | - Sonja B Andersen
- Centre of Molecular Inflammation Research and Department of Cancer Research and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway; Department of Biomedical Laboratory Science, Faculty of Natural Sciences, Norwegian University of Science and Technology, Trondheim, Norway
| | - Rosalie Zwiggelaar
- Centre of Molecular Inflammation Research and Department of Cancer Research and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
| | - Tonje S Steigedal
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | | | - Kristine Kleivi Sahlberg
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway; Department of Research, Vestre Viken Hospital Trust, Drammen, Norway
| | - Eivind Almaas
- Department of Biotechnology and Food Science, Faculty of Natural Sciences, Norwegian University of Science and Technology, Trondheim, Norway; K.G.Jebsen Center for Genetic Epidemiology, Department of Public Health and General Practice, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Norway
| | - Geir Bjørkøy
- Centre of Molecular Inflammation Research and Department of Cancer Research and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway; Department of Biomedical Laboratory Science, Faculty of Natural Sciences, Norwegian University of Science and Technology, Trondheim, Norway
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9
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Tsao LC, Crosby EJ, Trotter TN, Wei J, Wang T, Yang X, Summers AN, Lei G, Rabiola CA, Chodosh LA, Muller WJ, Lyerly HK, Hartman ZC. Trastuzumab/Pertuzumab combination therapy stimulates anti-tumor responses through complement-dependent cytotoxicity and phagocytosis. JCI Insight 2022; 7:155636. [PMID: 35167491 PMCID: PMC8986081 DOI: 10.1172/jci.insight.155636] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 02/09/2022] [Indexed: 11/17/2022] Open
Abstract
Standard-of-care treatment for advanced HER2+ breast cancers (BC) is comprised of two HER2-specific monoclonal antibodies (mAb), Trastuzumab (T) and Pertuzumab (P) with chemotherapy. While this combination (T+P) is highly effective, its synergistic mechanism of action (MOA) is not completely known. Initial studies had demonstrated that Pertuzumab suppressed HER2 hetero-dimerization as the potential therapeutic MOA, thus the improved outcome associated with the T+P combination MOA compared to Trastuzumab alone has been widely reported as being due to Pertuzumab-mediated suppression of HER2 signaling in combination with Trastuzumab-mediated induction of anti-tumor immunity. Unraveling this MOA may be critical to extend this combination strategy to other antigens or other cancers, as well as improving this current treatment modality. Using novel murine and human versions of Pertuzumab, we found it induced both Antibody-Dependent-Cellular-Phagocytosis (ADCP) by tumor-associated macrophages and suppression of HER2 oncogenic signaling. Most significantly, we identified that only T+P combination therapy, but not when either antibody used in isolation, allows for the activation of the classical complement pathway, resulting in both direct complement-dependent cytotoxicity (CDC) as well as complement-dependent cellular phagocytosis (CDCP) of HER2+ BC cells. Notably, we show that tumor expression of C1q was positively associated with survival outcome in HER2+ BC patients, whereas expression of complement regulators CD55 and CD59 were inversely correlated, suggesting the importance of complement activity in clinical outcomes. Accordingly, inhibition of C1 activity in mice abolished the synergistic therapeutic activity of T+P therapy, whereas knockdown of CD55 and CD59 expression enhanced T+P efficacy. In summary, our study identifies classical complement activation as a significant anti-tumor MOA for T+P therapy that may be functionally enhanced to augment therapeutic efficacy in the clinic.
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Affiliation(s)
- Li-Chung Tsao
- Department of Surgery, Duke University, Durham, United States of America
| | - Erika J Crosby
- Department of Surgery, Duke University, Durham, United States of America
| | - Timothy N Trotter
- Department of Surgery, Duke University, Durham, United States of America
| | - Junping Wei
- Department of Surgery, Duke University, Durham, United States of America
| | - Tao Wang
- Department of Surgery, Duke University, Durham, United States of America
| | - Xiao Yang
- Department of Surgery, Duke University, Durham, United States of America
| | - Amanda N Summers
- Department of Surgery, Duke University, Durham, United States of America
| | - Gangjun Lei
- Department of Surgery, Duke University, Durham, United States of America
| | | | - Lewis A Chodosh
- Department of Cancer Biology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, United States of America
| | | | - Herbert Kim Lyerly
- Department of Surgery, Duke University, Durham, United States of America
| | - Zachary C Hartman
- Department of Surgery, Duke University, Durham, United States of America
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10
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Sommerville L, Howard J, Evans S, Kelly P, McCann A. Comparative gene expression study highlights molecular similarities between triple negative breast cancer tumours and feline mammary carcinomas. Vet Comp Oncol 2022; 20:535-538. [PMID: 35006637 PMCID: PMC9303714 DOI: 10.1111/vco.12800] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 01/07/2022] [Indexed: 01/26/2023]
Abstract
Triple negative breast cancer (TNBC) is a rare, highly metastatic subtype of breast cancer that typically develops tumours of a high histological grade. As TNBC is negative for the oestrogen, progesterone and HER2 receptors it is also not eligible for targeted hormonal therapies. Therefore, those diagnosed with TNBC are faced with a very poor prognosis. Feline mammary carcinomas (FMCs) have been shown to share key characteristics of TNBC and are being investigated as novel animal models of this disease. A study by Granados‐Soler et al., investigating prognostic markers of FMCs provided the basis of this research, and their prognostic value in TNBC was evaluated using a ‘data‐mining’ research approach. Overall, the comparative genomic aspect of this research identified several potential prognostic markers translatable across TNBC and FMCs. These prognostic markers warrant further investigation in comparative oncology studies.
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Affiliation(s)
- Lara Sommerville
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland.,UCD School of Medicine, College of Health and Agricultural Sciences (CHAS), University College Dublin, Dublin, Ireland
| | - Jane Howard
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland.,UCD School of Medicine, College of Health and Agricultural Sciences (CHAS), University College Dublin, Dublin, Ireland
| | - Shane Evans
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland.,UCD School of Medicine, College of Health and Agricultural Sciences (CHAS), University College Dublin, Dublin, Ireland
| | - Pamela Kelly
- UCD School of Veterinary Medicine, Veterinary Sciences Centre, University College Dublin, Dublin, Ireland
| | - Amanda McCann
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland.,UCD School of Medicine, College of Health and Agricultural Sciences (CHAS), University College Dublin, Dublin, Ireland
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11
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Bolado-Carrancio A, Lee M, Ewing A, Muir M, Macleod KG, Gallagher WM, Nguyen LK, Carragher NO, Semple CA, Brunton VG, Caswell PT, von Kriegsheim A. ISGylation drives basal breast tumour progression by promoting EGFR recycling and Akt signalling. Oncogene 2021; 40:6235-6247. [PMID: 34556814 PMCID: PMC8566238 DOI: 10.1038/s41388-021-02017-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 08/29/2021] [Accepted: 09/10/2021] [Indexed: 02/08/2023]
Abstract
ISG15 is an ubiquitin-like modifier that is associated with reduced survival rates in breast cancer patients. The mechanism by which ISG15 achieves this however remains elusive. We demonstrate that modification of Rab GDP-Dissociation Inhibitor Beta (GDI2) by ISG15 (ISGylation) alters endocytic recycling of the EGF receptor (EGFR) in non-interferon stimulated cells using CRISPR-knock out models for ISGylation. By regulating EGFR trafficking, ISGylation enhances EGFR recycling and sustains Akt-signalling. We further show that Akt signalling positively correlates with levels of ISG15 and its E2-ligase in basal breast cancer cohorts, confirming the link between ISGylation and Akt signalling in human tumours. Persistent and enhanced Akt activation explains the more aggressive tumour behaviour observed in human breast cancers. We show that ISGylation can act as a driver of tumour progression rather than merely being a bystander.
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Affiliation(s)
- Alfonso Bolado-Carrancio
- Edinburgh Cancer Research Centre, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XU, UK
| | - Martin Lee
- Edinburgh Cancer Research Centre, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XU, UK
| | - Ailith Ewing
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XU, UK
| | - Morwenna Muir
- Edinburgh Cancer Research Centre, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XU, UK
| | - Kenneth G Macleod
- Edinburgh Cancer Research Centre, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XU, UK
| | - William M Gallagher
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Dublin, D4, Republic of Ireland
| | - Lan K Nguyen
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, 3800, Australia
| | - Neil O Carragher
- Edinburgh Cancer Research Centre, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XU, UK
| | - Colin A Semple
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XU, UK
| | - Valerie G Brunton
- Edinburgh Cancer Research Centre, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XU, UK
| | - Patrick T Caswell
- Wellcome Trust Centre for Cell-Matrix Research, School of Biological Sciences, Faculty of Biology Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Manchester, UK
| | - Alex von Kriegsheim
- Edinburgh Cancer Research Centre, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XU, UK.
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12
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Zhang K, Wang YY, Xu Y, Zhang L, Zhu J, Si PC, Wang YW, Ma R. A two-miRNA signature of upregulated miR-185-5p and miR-362-5p as a blood biomarker for breast cancer. Pathol Res Pract 2021; 222:153458. [PMID: 33962174 DOI: 10.1016/j.prp.2021.153458] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 04/24/2021] [Accepted: 04/24/2021] [Indexed: 12/24/2022]
Abstract
BACKGROUND Differentially expressed microRNAs (miRNAs) in the blood of breast cancer patients may serve as diagnostic biomarkers. METHODS In this study, miRNA microarray of the blood of breast cancer patients and healthy controls was performed. Candidate differentially expressed miRNAs were further verified by real-time polymerase chain reaction in 68 breast cancer patients and 13 healthy controls. RESULTS Six upregulated blood miRNAs (miR-26b-5p, miR-106b-5p, miR-142-3p, miR-142-5p, miR-185-5p, and miR-362-5p) were identified in breast cancer patients. These six miRNAs could discriminate breast cancer patients from healthy controls, with areas under the receiver operating characteristic curve (AUCs) of 0.8891, 0.8158, 0.8529, 0.8507, 0.9050, and 0.9333, respectively. Bioinformatic analysis showed that the six miRNAs were potentially involved in numerous cancer-related pathways, including the mitogen-activated protein kinase signaling pathway, nuclear factor-kappa B signaling pathway, and the transforming growth factor-beta signaling pathway. Importantly, two miRNAs (miR-185-5p and miR-362-5p) were used to construct a two-miRNA panel by logistic regression. The two-miRNA panel displayed a better diagnostic performance than each of the miRNAs alone, with a higher AUC (0.957), sensitivity (92.65 %), and specificity (92.31 %). Additionally, the high expression of the six miRNAs or the two-miRNA panel was associated with poor prognosis of breast cancer. CONCLUSIONS We identified six upregulated miRNAs and a two-miRNA panel in the blood as potential biomarkers for the diagnosis and prognosis of breast cancer.
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Affiliation(s)
- Kai Zhang
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, 107 West Wenhua Road, Jinan, 250012, Shandong, People's Republic of China
| | - Yan-Yan Wang
- Health Management Center, Qilu Hospital of Shandong University, 107 West Wenhua Road, Jinan, 250012, Shandong, People's Republic of China
| | - Yao Xu
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, 107 West Wenhua Road, Jinan, 250012, Shandong, People's Republic of China
| | - Li Zhang
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, 107 West Wenhua Road, Jinan, 250012, Shandong, People's Republic of China
| | - Jiang Zhu
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, 107 West Wenhua Road, Jinan, 250012, Shandong, People's Republic of China
| | - Peng-Chao Si
- Key Laboratory for Liquid-Solid Structural Evolution and Processing of Materials (Ministry of Education), Research Center for Carbon Nanomaterials, School of Materials Science and Engineering, Shandong University, Jinan, 250061, Shandong, People's Republic of China
| | - Ya-Wen Wang
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, 107 West Wenhua Road, Jinan, 250012, Shandong, People's Republic of China.
| | - Rong Ma
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, 107 West Wenhua Road, Jinan, 250012, Shandong, People's Republic of China.
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13
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Kim NI, Park MH, Kweon SS, Cho N, Lee JS. Squalene epoxidase expression is associated with breast tumor progression and with a poor prognosis in breast cancer. Oncol Lett 2021; 21:259. [PMID: 33664822 PMCID: PMC7882892 DOI: 10.3892/ol.2021.12520] [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: 10/15/2020] [Accepted: 01/18/2021] [Indexed: 12/28/2022] Open
Abstract
Differentially expressed genes (DEGs) have been previously identified using massive parallel RNA sequencing in matched normal, breast cancer (BC) and nodal metastatic tissues. Squalene epoxidase (SQLE), one of these DEGs, is a key enzyme in cholesterol synthesis. The aim of the present study was to investigate the potential involvement of SQLE in the tumorigenic process of BC and to determine its association with the clinical outcome of BC. SQLE mRNA expression was measured using reverse transcription-quantitative PCR in 10 pairs of ductal carcinoma in situ (DCIS) and BC tissues and their adjacent normal tissues. Immunohistochemical staining of SQLE on tissue microarray was performed in 26 normal breast, 79 DCIS and 198 BC samples. The role of SQLE as a prognostic biomarker in patients with BC has been verified using BreastMark. SQLE mRNA expression was significantly increased in DCIS and BC tissues compared with that in their adjacent normal tissues. High SQLE expression was detected in 0, 48.1 and 40.4% of normal breast, DCIS and BC tissues, respectively. SQLE expression in DCIS and BC tissues was significantly higher than that in normal breast tissues. High SQLE expression was observed in DCIS with higher nuclear grade, comedo-type necrosis and HER2 positivity. High SQLE expression in BC was associated with larger tumor size, nodal metastases, higher stage, HER2 subtype and distant metastatic relapse. High SQLE expression was associated with poor disease-free and overall survival, and independently predicted poor disease-free survival in patients with BC. Following BreastMark analysis, high SQLE mRNA expression in BC was significantly associated with a poor prognosis in the ‘all’, lymph node negative, lymph node positive, luminal A subtype and luminal B subtype groups. Therefore, SQLE expression may be upregulated during the tumorigenic process of BC, and high SQLE expression may be a useful biomarker for predicting a poor prognosis in patients with BC.
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Affiliation(s)
- Nah Ihm Kim
- Department of Pathology, Chonnam National University Medical School, Gwangju 61469, Republic of Korea
| | - Min Ho Park
- Department of Surgery, Chonnam National University Medical School, Gwangju 61469, Republic of Korea
| | - Sun-Seog Kweon
- Department of Preventive Medicine, Chonnam National University Medical School, Gwangju 61469, Republic of Korea
| | - Namki Cho
- College of Pharmacy, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Ji Shin Lee
- Department of Pathology, Chonnam National University Medical School, Gwangju 61469, Republic of Korea
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14
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Patel KD, Vora HH, Patel PS. Transcriptional Biomarkers in Oral Cancer: An Integrative Analysis and the Cancer Genome Atlas Validation. Asian Pac J Cancer Prev 2021; 22:371-380. [PMID: 33639650 PMCID: PMC8190349 DOI: 10.31557/apjcp.2021.22.2.371] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 01/20/2021] [Indexed: 12/24/2022] Open
Abstract
OBJECTIVE An impervious mortality rate in oral cancer (OC) to a certain extent explains the exigencies of precise biomarkers. Therefore, the study was intended to identify OC candidate biomarkers using samples of healthy normal tissues (N=335), adjacent normal tissues (N=93) and OC tissues (N=533) from online microarray data. METHODS Differentially expressed genes (DEGs) were recognised through GeneSpring software (Fold change >4.0 and 'p' value.
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Affiliation(s)
| | | | - Prabhudas S Patel
- The Gujarat Cancer & Research Institute, Civil Hospital Campus, Asarwa, Ahmedabad-380 016, Gujarat, India.
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15
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Akhand SS, Chen H, Purdy SC, Liu Z, Anderson JC, Willey CD, Wendt MK. Fibroblast growth factor receptor facilitates recurrence of minimal residual disease following trastuzumab emtansine therapy. NPJ Breast Cancer 2021; 7:5. [PMID: 33479246 PMCID: PMC7820437 DOI: 10.1038/s41523-020-00213-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 10/29/2020] [Indexed: 12/28/2022] Open
Abstract
Trastuzumab-emtansine (T-DM1) is an antibody-drug conjugate (ADC) that efficiently delivers a highly potent microtubule inhibitor to HER2 overexpressing cells. Herein, we utilize HER2 transformed human mammary epithelial cells (HME2) to demonstrate in vitro and in vivo response and recurrence upon T-DM1 treatment. Continuous in vitro dosing of HME2 cells with T-DM1 failed to produce a spontaneously resistant cell line. However, induction of epithelial-mesenchymal transition (EMT) via pretreatment with TGF-β1 was capable of promoting emergence of T-DM1-resistant (TDM1R) cells. Flow cytometric analyses indicated that induction of EMT decreased trastuzumab binding, prior to overt loss of HER2 expression in TDM1R cells. Kinome analyses of TDM1R cells indicated increased phosphorylation of ErbB1, ErbB4, and FGFR1. TDM1R cells failed to respond to the ErbB kinase inhibitors lapatinib and afatinib, but they acquired sensitivity to FIIN4, a covalent FGFR kinase inhibitor. In vivo, minimal residual disease (MRD) remained detectable via bioluminescent imaging following T-DM1-induced tumor regression. Upon cessation of the ADC, relapse occurred and secondary tumors were resistant to additional rounds of T-DM1. These recurrent tumors could be inhibited by FIIN4. Moreover, ectopic overexpression of FGFR1 was sufficient to enhance tumor growth, diminish trastuzumab binding, and promote recurrence following T-DM1-induced MRD. Finally, patient-derived xenografts from a HER2+ breast cancer patient who had progressed on trastuzumab failed to respond to T-DM1, but tumor growth was significantly inhibited by FIIN4. Overall, our studies strongly support therapeutic combination of TDM1 with FGFR-targeted agents in HER2+ breast cancer.
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Affiliation(s)
- Saeed S Akhand
- Purdue University Center for Cancer Research, Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, 47907, USA
| | - Hao Chen
- Purdue University Center for Cancer Research, Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, 47907, USA
| | - Stephen Connor Purdy
- Purdue University Center for Cancer Research, Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, 47907, USA
| | - Zian Liu
- Purdue University Center for Cancer Research, Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, 47907, USA
| | - Joshua C Anderson
- Department of Radiation Oncology, University of Alabama at Birmingham, Birmingham, AL, 35244, USA
| | - Christopher D Willey
- Department of Radiation Oncology, University of Alabama at Birmingham, Birmingham, AL, 35244, USA
| | - Michael K Wendt
- Purdue University Center for Cancer Research, Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, 47907, USA.
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16
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Abdullah A, Akhand SS, Paez JSP, Brown W, Pan L, Libring S, Badamy M, Dykuizen E, Solorio L, Andy Tao W, Wendt MK. Epigenetic targeting of neuropilin-1 prevents bypass signaling in drug-resistant breast cancer. Oncogene 2021; 40:322-333. [PMID: 33128042 PMCID: PMC7808937 DOI: 10.1038/s41388-020-01530-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 10/13/2020] [Accepted: 10/15/2020] [Indexed: 12/18/2022]
Abstract
Human epidermal growth factor receptor 2 (HER2)-amplified breast cancers are treated using targeted antibodies and kinase inhibitors, but resistance to these therapies leads to systemic tumor recurrence of metastatic disease. Herein, we conducted gene expression analyses of HER2 kinase inhibitor-resistant cell lines as compared to their drug-sensitive counterparts. These data demonstrate the induction of epithelial-mesenchymal transition (EMT), which included enhanced expression of fibroblast growth factor receptor 1 (FGFR1) and axonal guidance molecules known as neuropilins (NRPs). Immunoprecipitation of FGFR1 coupled with mass spectroscopy indicated that FGFR1 forms a physical complex with NRPs, which is enhanced upon induction of EMT. Confocal imaging revealed that FGFR1 and NRP1 predominantly interact throughout the cytoplasm. Along these lines, short hairpin RNA-mediated depletion of NRP1, but not the use of NRP1-blocking antibodies, inhibited FGFR signaling and reduced tumor cell growth in vitro and in vivo. Our results further indicate that NRP1 upregulation during EMT is mediated via binding of the chromatin reader protein, bromodomain containing 4 (BRD4) in the NRP1 proximal promoter region. Pharmacological inhibition of BRD4 decreased NRP1 expression and ablated FGF-mediated tumor cell growth. Overall, our studies indicate that NRPs facilitate aberrant growth factor signaling during EMT-associated drug resistance and metastasis. Pharmacological combination of epigenetic modulators with FGFR-targeted kinase inhibitors may provide improved outcomes for breast cancer patients with drug-resistant metastatic disease.
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MESH Headings
- Animals
- Apoptosis
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Breast Neoplasms/drug therapy
- Breast Neoplasms/genetics
- Breast Neoplasms/pathology
- Cell Proliferation
- Drug Resistance, Neoplasm/genetics
- Epigenesis, Genetic
- Epithelial-Mesenchymal Transition
- Female
- Gene Expression Regulation, Neoplastic/drug effects
- Humans
- Mice
- Mice, Inbred BALB C
- Mice, Nude
- Neuropilin-1/genetics
- Neuropilin-1/metabolism
- Protein Kinase Inhibitors/pharmacology
- Receptor, Fibroblast Growth Factor, Type 1/genetics
- Receptor, Fibroblast Growth Factor, Type 1/metabolism
- Tumor Cells, Cultured
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Ammara Abdullah
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, 47907, USA
| | - Saeed Salehin Akhand
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, 47907, USA
| | - Juan Sebastian Paez Paez
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, 47907, USA
| | - Wells Brown
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, 47907, USA
| | - Li Pan
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, 47907, USA
| | - Sarah Libring
- Department of Biomedical Engineering, Purdue University, West Lafayette, IN, 47907, USA
| | - Michael Badamy
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, 47907, USA
| | - Emily Dykuizen
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, 47907, USA
- Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN, 47907, USA
| | - Luis Solorio
- Department of Biomedical Engineering, Purdue University, West Lafayette, IN, 47907, USA
- Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN, 47907, USA
| | - W Andy Tao
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, 47907, USA
- Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN, 47907, USA
| | - Michael K Wendt
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, 47907, USA.
- Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN, 47907, USA.
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17
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Voutsadakis IA. Vitamin D receptor (VDR) and metabolizing enzymes CYP27B1 and CYP24A1 in breast cancer. Mol Biol Rep 2020; 47:9821-9830. [PMID: 33259013 DOI: 10.1007/s11033-020-05780-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 08/28/2020] [Indexed: 01/05/2023]
Abstract
Vitamin D Receptor (VDR), a nuclear steroid receptor, is a transcription factor with a primary physiologic role in calcium metabolism. It has also a physiologic role in breast tissues during development of the gland and postpartum. In addition, it is commonly expressed in breast cancer and has tumor suppressive effects. Cytochrome enzymes CYP27B1 and CYP24A1 that perform the final conversion of the circulating form of vitamin D, 25-hydroxyvitamin D (25-OHD) to the active VDR ligand, 1a,25-dihydroxyvitamin D and the catabolism of it to inactive 24,25-dihydroxyvitamin D, respectively, are also expressed in breast cancer tissues. Defective regulation of the receptor and the metabolic enzymes of VDR ligand is prevalent in breast cancer and leads to decreased VDR signaling. The expression and molecular defects of VDR, CYP27B1 and CYP24A1 that perturb physiologic function, the implications for breast cancer progression and therapeutic opportunities are discussed in this paper.
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Affiliation(s)
- Ioannis A Voutsadakis
- Algoma District Cancer Program, Sault Area Hospital, 750 Great Northern Road, Sault Ste. Marie, ON, P6B 0A8, Canada. .,Section of Internal Medicine, Division of Clinical Sciences, Northern Ontario School of Medicine, Sudbury, ON, Canada.
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18
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Dong G, Ma G, Wu R, Liu J, Liu M, Gao A, Li X, A J, Liu X, Zhang Z, Zhang B, Fu L, Dong JT. ZFHX3 Promotes the Proliferation and Tumor Growth of ER-Positive Breast Cancer Cells Likely by Enhancing Stem-Like Features and MYC and TBX3 Transcription. Cancers (Basel) 2020; 12:cancers12113415. [PMID: 33217982 PMCID: PMC7698617 DOI: 10.3390/cancers12113415] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/10/2020] [Accepted: 11/12/2020] [Indexed: 12/23/2022] Open
Abstract
Simple Summary Breast cancer is a common malignancy, but the understanding of its cellular and molecular mechanisms is limited. The ZFHX3 transcription factor regulates mammary epithelial cells’ proliferation and differentiation by interacting with estrogen and progesterone receptors. Both these receptors play crucial roles in breast cancer development, but whether ZFHX3 also impacts breast cancer is unknown. In this study, the authors aim to determine if ZFHX3 promotes breast cancer cells’ proliferation and tumor growth and explore the underlying cellular and molecular mechanisms. Higher ZFHX3 expression is associated with worse patient survival in breast cancer, ZFHX3 promotes the proliferation and tumor growth of breast cancer cells, and several breast cancer stem cell factors appear to be involved in the role of ZFHX3 in breast cancer growth. The findings suggest that ZFHX3 is a novel oncogenic molecule promoting breast cancer development. Such a molecule could provide novel opportunities for the treatment of breast cancer. Abstract Breast cancer is a common malignancy, but the understanding of its cellular and molecular mechanisms is limited. ZFHX3, a transcription factor with many homeodomains and zinc fingers, suppresses prostatic carcinogenesis but promotes tumor growth of liver cancer cells. ZFHX3 regulates mammary epithelial cells’ proliferation and differentiation by interacting with estrogen and progesterone receptors, potent breast cancer regulators. However, whether ZFHX3 plays a role in breast carcinogenesis is unknown. Here, we found that ZFHX3 promoted the proliferation and tumor growth of breast cancer cells in culture and nude mice; and higher expression of ZFHX3 in human breast cancer specimens was associated with poorer prognosis. The knockdown of ZFHX3 in ZFHX3-high MCF-7 cells decreased, and ZFHX3 overexpression in ZFHX3-low T-47D cells increased the proportion of breast cancer stem cells (BCSCs) defined by mammosphere formation and the expression of CD44, CD24, and/or aldehyde dehydrogenase 1. Among several transcription factors that have been implicated in BCSCs, MYC and TBX3 were transcriptionally activated by ZFHX3 via promoter binding, as demonstrated by luciferase-reporter and ChIP assays. These findings suggest that ZFHX3 promotes breast cancer cells’ proliferation and tumor growth likely by enhancing BCSC features and upregulating MYC, TBX3, and others.
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Affiliation(s)
- Ge Dong
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China; (G.D.); (G.M.); (J.L.); (M.L.); (A.G.); (X.L.); (J.A.); (L.F.)
| | - Gui Ma
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China; (G.D.); (G.M.); (J.L.); (M.L.); (A.G.); (X.L.); (J.A.); (L.F.)
| | - Rui Wu
- Department of Human Cell Biology and Genetics, School of Medicine, Southern University of Science and Technology, 1088 Xueyuan Blvd, Shenzhen 518055, China; (R.W.); (X.L.); (Z.Z.)
| | - Jinming Liu
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China; (G.D.); (G.M.); (J.L.); (M.L.); (A.G.); (X.L.); (J.A.); (L.F.)
| | - Mingcheng Liu
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China; (G.D.); (G.M.); (J.L.); (M.L.); (A.G.); (X.L.); (J.A.); (L.F.)
- Department of Human Cell Biology and Genetics, School of Medicine, Southern University of Science and Technology, 1088 Xueyuan Blvd, Shenzhen 518055, China; (R.W.); (X.L.); (Z.Z.)
| | - Ang Gao
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China; (G.D.); (G.M.); (J.L.); (M.L.); (A.G.); (X.L.); (J.A.); (L.F.)
| | - Xiawei Li
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China; (G.D.); (G.M.); (J.L.); (M.L.); (A.G.); (X.L.); (J.A.); (L.F.)
- Department of Human Cell Biology and Genetics, School of Medicine, Southern University of Science and Technology, 1088 Xueyuan Blvd, Shenzhen 518055, China; (R.W.); (X.L.); (Z.Z.)
| | - Jun A
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China; (G.D.); (G.M.); (J.L.); (M.L.); (A.G.); (X.L.); (J.A.); (L.F.)
- Department of Human Cell Biology and Genetics, School of Medicine, Southern University of Science and Technology, 1088 Xueyuan Blvd, Shenzhen 518055, China; (R.W.); (X.L.); (Z.Z.)
| | - Xiaoyu Liu
- Department of Human Cell Biology and Genetics, School of Medicine, Southern University of Science and Technology, 1088 Xueyuan Blvd, Shenzhen 518055, China; (R.W.); (X.L.); (Z.Z.)
| | - Zhiqian Zhang
- Department of Human Cell Biology and Genetics, School of Medicine, Southern University of Science and Technology, 1088 Xueyuan Blvd, Shenzhen 518055, China; (R.W.); (X.L.); (Z.Z.)
| | - Baotong Zhang
- Emory Winship Cancer Institute, Department of Hematology and Medical Oncology, Emory University School of Medicine, 1365-C Clifton Road, Atlanta, GA 30322, USA;
| | - Liya Fu
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin 300071, China; (G.D.); (G.M.); (J.L.); (M.L.); (A.G.); (X.L.); (J.A.); (L.F.)
| | - Jin-Tang Dong
- Department of Human Cell Biology and Genetics, School of Medicine, Southern University of Science and Technology, 1088 Xueyuan Blvd, Shenzhen 518055, China; (R.W.); (X.L.); (Z.Z.)
- Correspondence:
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19
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Schroth W, Büttner FA, Kandabarau S, Hoppe R, Fritz P, Kumbrink J, Kirchner T, Brauer HA, Ren Y, Henderson D, Madden SF, Sauer G, Fehm T, Wallwiener D, Fasching PA, Mürdter T, Schwab M, Brauch H. Gene Expression Signatures of BRCAness and Tumor Inflammation Define Subgroups of Early-Stage Hormone Receptor-Positive Breast Cancer Patients. Clin Cancer Res 2020; 26:6523-6534. [PMID: 33008814 DOI: 10.1158/1078-0432.ccr-20-1923] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 08/07/2020] [Accepted: 09/28/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE Patients with estrogen receptor- and/or progesterone receptor-positive, early breast cancer benefit from hormonal treatment, yet high global death burdens due to high prevalence and long-term recurrence risk call for biomarkers to guide additional treatment approaches. EXPERIMENTAL DESIGN From a prospective, observational study of postmenopausal early breast cancer patients treated with tamoxifen or aromatase inhibitors, gene expression analyses of 612 tumors was performed using the NanoString Breast Cancer 360 panel to interrogate 23 breast cancer pathways. Candidate signatures associated with disease subtype and event-free survival (EFS) were obtained by cluster analysis, Cox modeling, and conditional inference trees, and were independently tested in 613 patients from BreastMark. Tumor-infiltrating lymphocytes (TIL) were assessed on tissue sections, and mutational burden was assessed in 36 tumors by whole-exome sequencing. RESULTS PAM50-derived classification distinguished lower-risk (Luminal A) from higher-risk subtypes (Luminal B, P = 0.04; HER2, P = 0.006; Basal, P = 0.008). In higher-risk patients, shorter EFS was associated with low androgen receptor [HR = 3.61; 95% confidence interval (CI), 1.72-7.56; P = 0.001] or high BRCAness signature expression (HR = 3.58; 95% CI, 1.19-10.7; P = 0.023). BRCAness was independently confirmed as a predictor of shorter EFS (HR = 2.64; 95% CI, 1.31-5.34; P = 0.007). About 13%-15% of patients, enriched for high-grade, higher-risk subtypes (P ≤ 0.0001), had strong expression of the Tumor Inflammation Signature (TIS) suggestive of an inhibited antitumor immune response. TIS scores were strongly associated with TIL numbers (P < 1e-30) but not with tumor mutation status. CONCLUSIONS BRCA-related DNA repair deficiency and suppressed tumor immune responses may be clinically relevant predictors of endocrine therapy complementing treatment options in subgroups of hormone-sensitive early breast cancer.
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Affiliation(s)
- Werner Schroth
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany. .,University of Tübingen, Tübingen, Germany
| | - Florian A Büttner
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany.,University of Tübingen, Tübingen, Germany
| | - Siarhei Kandabarau
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany.,University of Tübingen, Tübingen, Germany
| | - Reiner Hoppe
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany.,University of Tübingen, Tübingen, Germany
| | - Peter Fritz
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany.,Institute of Pathology, Robert-Bosch Hospital, Stuttgart, Germany
| | - Jörg Kumbrink
- Institute of Pathology, Faculty of Medicine, Ludwig Maximilian University, Munich, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Munich, Munich Germany
| | - Thomas Kirchner
- Institute of Pathology, Faculty of Medicine, Ludwig Maximilian University, Munich, Germany.,German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Partner Site Munich, Munich Germany
| | | | - Yuqi Ren
- NanoString Technologies Inc., Seattle, Washington
| | | | - Stephen F Madden
- Data Science Center, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Georg Sauer
- Department of Obstetrics and Gynecology, Robert-Bosch Hospital, Stuttgart, Germany
| | - Tanja Fehm
- Department of Gynecology and Obstetrics, University of Düsseldorf, Düsseldorf, Germany
| | - Diethelm Wallwiener
- Department of Obstetrics and Gynecology, University Hospital of Tübingen, Tübingen, Germany
| | - Peter A Fasching
- Department of Gynecology and Obstetrics, University Hospital Erlangen and Comprehensive Cancer Center Erlangen-EMN, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Thomas Mürdter
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany.,University of Tübingen, Tübingen, Germany
| | | | - Hiltrud Brauch
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart, Germany.,University of Tübingen, Tübingen, Germany.,Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen, Germany.,German Cancer Consortium (DKTK), Partner Site Tübingen, German Cancer Research Center (DKFZ), Heidelberg, Germany
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20
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Kiely M, Tse LA, Koka H, Wang D, Lee P, Wang F, Wu C, Tsang KH, Chan WC, Law SH, Zhang H, Karlins E, Zhu B, Hutchinson A, Hicks B, Zhu B, Yang XR. Age-related DNA methylation in paired normal and tumour breast tissue in Chinese breast cancer patients. Epigenetics 2020; 16:677-691. [PMID: 32970968 PMCID: PMC8143246 DOI: 10.1080/15592294.2020.1819661] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Age-related DNA methylation is a potential mechanism contributing to breast cancer development. Studies of primarily Caucasian women have identified many CpG sites of age-related methylation in non-diseased breast tissue possibly driving cancer development over time. There is a paucity of studies involving Asian women whose ages at breast cancer onset are usually younger than Caucasians. We identified the 181 most consistent age-related methylation events in non-diseased breast tissue across published studies. Age-related methylation events were measured in adjacent normal and breast tumour tissue in an exclusively Asian population at the previously identified age-related methylation sites. Age-related methylation was found in 118 probes in adjacent normal breast tissue. Methylation of 99% of these sites was increased with age and predominantly located on CpG islands in promoter regions. To ascertain biological relevance to breast cancer, we focused on the 37 sites with overall higher methylation in tumour compared to adjacent normal samples. Some sites positively related to age, including AQP5 and CORO6, inversely correlated with gene expression. Several others have known involvement in suppression of carcinogenesis including GPC5 and SST, suggesting that perturbation of epigenetic regulation at these sites due to ageing may contribute to the progression of carcinogenesis. This study highlights an age-related methylation landscape in non-tumour tissue, consistent not just across studies, but also across different populations. We present candidate age-related methylation sites warranting further investigation as potential epigenetic drivers of breast cancer. They may serve as potential targets of site-specific demethylation intervention strategies for the prevention of age-related breast cancer.
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Affiliation(s)
- Maeve Kiely
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Lap Ah Tse
- Jockey Club School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong, China
| | - Hela Koka
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Difei Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA.,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Priscilla Lee
- Jockey Club School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong, China
| | - Feng Wang
- Jockey Club School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong, China
| | - Cherry Wu
- North District Hospital, Hong Kong, China
| | | | | | | | - Han Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Eric Karlins
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA.,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA.,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Amy Hutchinson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA.,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Belynda Hicks
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA.,Cancer Genomics Research Laboratory, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
| | - Xiaohong R Yang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD, USA
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21
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Nephronectin promotes breast cancer brain metastatic colonization via its integrin-binding domains. Sci Rep 2020; 10:12237. [PMID: 32699247 PMCID: PMC7376038 DOI: 10.1038/s41598-020-69242-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 07/07/2020] [Indexed: 12/18/2022] Open
Abstract
This study demonstrates a role for the extracellular matrix protein nephronectin (NPNT) in promoting experimental breast cancer brain metastasis, possibly through enhanced binding to- and migration through brain endothelial cells. With the introduction of more targeted breast cancer treatments, a prolonged survival has resulted during the last decade. Consequently, an increased number of patients develop metastasis in the brain, a challenging organ to treat. We recently reported that NPNT was highly expressed in primary breast cancer and associated with unfavourable prognosis. The current study addresses our hypothesis that NPNT promotes brain metastases through its integrin-binding motifs. SAGE-sequencing revealed that NPNT was significantly up-regulated in human breast cancer tissue compared to pair-matched normal breast tissue. Human brain metastatic breast cancers expressed both NPNT and its receptor, integrin α8β1. Using an open access repository; BreastMark, we found a correlation between high NPNT mRNA levels and poor prognosis for patients with the luminal B subtype. The 66cl4 mouse cell line was used for expression of wild-type and mutant NPNT, which is unable to bind α8β1. Using an in vivo model of brain metastatic colonization, 66cl4-NPNT cells showed an increased ability to form metastatic lesions compared to cells with mutant NPNT, possibly through reduced endothelial adhesion and transmigration.
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22
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Mohr CJ, Schroth W, Mürdter TE, Gross D, Maier S, Stegen B, Dragoi A, Steudel FA, Stehling S, Hoppe R, Madden S, Ruth P, Huber SM, Brauch H, Lukowski R. Subunits of BK channels promote breast cancer development and modulate responses to endocrine treatment in preclinical models. Br J Pharmacol 2020; 179:2906-2924. [PMID: 32468618 DOI: 10.1111/bph.15147] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 03/20/2020] [Accepted: 05/13/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND AND PURPOSE Pore-forming α subunits of the voltage- and Ca2+ -activated K+ channel with large conductance (BKα) promote malignant phenotypes of breast tumour cells. Auxiliary subunits such as the leucine-rich repeat containing 26 (LRRC26) protein, also termed BKγ1, may be required to permit activation of BK currents at a depolarized resting membrane potential that frequently occur in non-excitable tumour cells. EXPERIMENTAL APPROACH Anti-tumour effects of BKα loss were investigated in breast tumour-bearing MMTV-PyMT transgenic BKα knockout (KO) mice, primary MMTV-PyMT cell cultures, and in a syngeneic transplantation model of breast cancer derived from these cells. The therapeutic relevance of BK channels in the context of endocrine treatment was assessed in human breast cancer cell lines expressing either low (MCF-7) or high (MDA-MB-453) levels of BKα and BKγ1, as well as in BKα-negative MDA-MB-157. KEY RESULTS BKα promoted breast cancer onset and overall survival in preclinical models. Conversely, lack of BKα and/or knockdown of BKγ1 attenuated proliferation of murine and human breast cancer cells in vitro. At low concentrations, tamoxifen and its major active metabolites stimulated proliferation of BKα/γ1-positive breast cancer cells, independent of the genomic signalling controlled by the oestrogen receptor. Finally, tamoxifen increased the relative survival time of BKα KO but not of wild-type tumour cell recipient mice. CONCLUSION AND IMPLICATIONS Breast cancer initiation, progression, and tamoxifen sensitivity depend on functional BK channels thereby providing a rationale for the future exploration of the oncogenic actions of BK channels in clinical outcomes with anti-oestrogen therapy.
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Affiliation(s)
- Corinna J Mohr
- Department of Pharmacology, Toxicology and Clinical Pharmacy, Institute of Pharmacy, University of Tuebingen, Tuebingen, Germany.,Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart and University of Tuebingen, Germany
| | - Werner Schroth
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart and University of Tuebingen, Germany
| | - Thomas E Mürdter
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart and University of Tuebingen, Germany
| | - Dominic Gross
- Department of Pharmacology, Toxicology and Clinical Pharmacy, Institute of Pharmacy, University of Tuebingen, Tuebingen, Germany
| | - Selina Maier
- Department of Pharmacology, Toxicology and Clinical Pharmacy, Institute of Pharmacy, University of Tuebingen, Tuebingen, Germany.,Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart and University of Tuebingen, Germany
| | - Benjamin Stegen
- Department of Radiation Oncology, University of Tuebingen, Tuebingen, Germany
| | - Alice Dragoi
- Department of Pharmacology, Toxicology and Clinical Pharmacy, Institute of Pharmacy, University of Tuebingen, Tuebingen, Germany
| | - Friederike A Steudel
- Department of Pharmacology, Toxicology and Clinical Pharmacy, Institute of Pharmacy, University of Tuebingen, Tuebingen, Germany
| | - Severine Stehling
- Department of Pharmacology, Toxicology and Clinical Pharmacy, Institute of Pharmacy, University of Tuebingen, Tuebingen, Germany
| | - Reiner Hoppe
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart and University of Tuebingen, Germany
| | - Stephen Madden
- RCSI Division of Population Health Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Peter Ruth
- Department of Pharmacology, Toxicology and Clinical Pharmacy, Institute of Pharmacy, University of Tuebingen, Tuebingen, Germany
| | - Stephan M Huber
- Department of Radiation Oncology, University of Tuebingen, Tuebingen, Germany
| | - Hiltrud Brauch
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, Stuttgart and University of Tuebingen, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.,iFIT-Cluster of Excellence, University of Tuebingen, Tuebingen, Germany
| | - Robert Lukowski
- Department of Pharmacology, Toxicology and Clinical Pharmacy, Institute of Pharmacy, University of Tuebingen, Tuebingen, Germany
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23
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Abstract
Over sixty percent of all mammalian protein-coding genes are estimated to be regulated by microRNAs (miRNAs), and unsurprisingly miRNA dysregulation has been linked with cancer. Aberrant miRNA expression in cancer cells has been linked with tumourigenesis and drug resistance. In the past decade, increasing number of studies have demonstrated that cholesterol accumulation fuels tumour growth and contributes to drug resistance, therefore, miRNAs controlling cholesterol metabolism and homeostasis are obvious hypothetical targets for investigating their role in cholesterol-mediated drug resistance in cancer. In this review, we have collated published evidences to consolidate this hypothesis and have scrutinized it by utilizing computational tools to explore the role of miRNAs in cholesterol-mediated drug resistance in breast cancer cells. We found that hsa-miR-128 and hsa-miR-223 regulate genes mediating lipid signalling and cholesterol metabolism, cancer drug resistance and breast cancer genes. The analysis demonstrates that targeting these miRNAs in cancer cells presents an opportunity for developing new strategies to combat anticancer drug resistance.
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24
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Zhou Z, Wu B, Tang X, Ke R, Zou Q. Comprehensive Analysis of Fibroblast Growth Factor Receptor (FGFR) Family Genes in Breast Cancer by Integrating Online Databases and Bioinformatics. Med Sci Monit 2020; 26:e923517. [PMID: 32381997 PMCID: PMC7236589 DOI: 10.12659/msm.923517] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Fibroblast growth factor receptors (FGFRs) play vital roles in the development and progression of human cancers. This study aimed to comprehensively understand the prognostic performances of FGFR1-4 expression in breast cancer (BC) by mining databases. MATERIAL AND METHODS The levels of FGFR1-4 expression in BC were analyzed by online databases, GEPIA (Gene Expression Profiling Interactive Analysis) and UALCAN. Survival analysis of FGFR1-4 was carried out by Kaplan-Meier plotter. GSE74146 was downloaded from Gene Expression Omnibus (GEO) and analyzed by GEO2R to screen the differentially expressed genes (DEGs) between FGFR2-silenced BC cells and control. Over-presentation for DEGs were done by Enrichr tool. Networks of DEGs were obtained by using Search Tool for the Retrieval of Interacting Genes (STRING) and Cytoscape software. Hub genes were identified by cytoHubba Cytoscape plugin. RESULTS The online databases showed that FGFR1 was significantly downregulated whereas FGFR3 was upregulated in BC. Kaplan-Meier plotter demonstrated the upregulation of both FGFR1 and FGFR3 indicated favorable relapse free survival (RFS) whereas FGFR4 overexpression predicted unfavorable overall survival (OS) in BC patients. Importantly, our results showed FGFR2 overexpression robustly predicted favorable OS and RFS in BC. Further bioinformatics analysis of GSE74146 suggested FGFR2 mainly participated in regulating degradation and organization of the extracellular matrix and signaling of retinoic acid. Moreover, CXCL8, CD44, MMP9, and BMP7 were identified as crucial FGFR2-related hub genes. CONCLUSIONS Our study comprehensively analyzed the prognostic values of FGFR1-4 expression in BC and proposed FGFR2 might serve as a promising biomarker. However, the underlying mechanisms remain to be elucidated.
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Affiliation(s)
- Zhaoping Zhou
- Department of Plastic and Reconstructive Surgery, Huashan Hospital, Fudan University, Shanghai, China (mainland)
| | - Baojin Wu
- Department of Plastic Surgery, Huashan Hospital, Fudan University, Shanghai, China (mainland)
| | - Xinjie Tang
- Department of Plastic and Reconstructive Surgery, Huashan Hospital, Fudan University, Shanghai, China (mainland)
| | - Ronghu Ke
- Department of Plastic Surgery, Huashan Hospital, Fudan University, Shanghai, China (mainland)
| | - Qiang Zou
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai, China (mainland)
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25
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Lin Q, He Y, Wang X, Zhang Y, Hu M, Guo W, He Y, Zhang T, Lai L, Sun Z, Yi Z, Liu M, Chen Y. Targeting Pyruvate Carboxylase by a Small Molecule Suppresses Breast Cancer Progression. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:1903483. [PMID: 32382484 PMCID: PMC7201266 DOI: 10.1002/advs.201903483] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 02/14/2020] [Accepted: 02/24/2020] [Indexed: 05/29/2023]
Abstract
Rapid metabolism differentiates cancer cells from normal cells and relies on anaplerotic pathways. However, the mechanisms of anaplerosis-associated enzymes are rarely understood. The lack of potent and selective antimetabolism drugs restrains further clinical investigations. A small molecule ZY-444 ((N 4-((5-(4-(benzyloxy)phenyl)-2-thiophenyl)methyl)-N 2-isobutyl-2,4-pyrimidinediamine) is discovered to inhibit cancer cell proliferation specifically, having potent efficacies against tumor growth, metastasis, and recurrence. ZY-444 binds to cellular pyruvate carboxylase (PC), a key anaplerotic enzyme of the tricarboxylic acid cycle, and inactivates its catalytic activity. PC inhibition suppresses breast cancer growth and metastasis through inhibiting the Wnt/β-catenin/Snail signaling pathway. Lower PC expression in patient tumors is correlated with significant survival benefits. Comparative profiles of PC expression in cancer versus normal tissues implicate the tumor selectivity of ZY-444. Overall, ZY-444 holds promise therapeutically as an anti-cancer metabolism agent.
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Affiliation(s)
- Qingxiang Lin
- East China Normal University and Shanghai Fengxian District Central Hospital Joint Center for Translational MedicineShanghai Key Laboratory of Regulatory BiologyInstitute of Biomedical Sciences and School of Life SciencesEast China Normal UniversityShanghai200241P. R. China
| | - Yuan He
- East China Normal University and Shanghai Fengxian District Central Hospital Joint Center for Translational MedicineShanghai Key Laboratory of Regulatory BiologyInstitute of Biomedical Sciences and School of Life SciencesEast China Normal UniversityShanghai200241P. R. China
- Joint Center for Translational MedicineSouthern Medical University Affiliated Fengxian HospitalShanghai201499P. R. China
| | - Xue Wang
- East China Normal University and Shanghai Fengxian District Central Hospital Joint Center for Translational MedicineShanghai Key Laboratory of Regulatory BiologyInstitute of Biomedical Sciences and School of Life SciencesEast China Normal UniversityShanghai200241P. R. China
| | - Yong Zhang
- East China Normal University and Shanghai Fengxian District Central Hospital Joint Center for Translational MedicineShanghai Key Laboratory of Regulatory BiologyInstitute of Biomedical Sciences and School of Life SciencesEast China Normal UniversityShanghai200241P. R. China
| | - Meichun Hu
- East China Normal University and Shanghai Fengxian District Central Hospital Joint Center for Translational MedicineShanghai Key Laboratory of Regulatory BiologyInstitute of Biomedical Sciences and School of Life SciencesEast China Normal UniversityShanghai200241P. R. China
| | - Weikai Guo
- East China Normal University and Shanghai Fengxian District Central Hospital Joint Center for Translational MedicineShanghai Key Laboratory of Regulatory BiologyInstitute of Biomedical Sciences and School of Life SciencesEast China Normal UniversityShanghai200241P. R. China
| | - Yundong He
- East China Normal University and Shanghai Fengxian District Central Hospital Joint Center for Translational MedicineShanghai Key Laboratory of Regulatory BiologyInstitute of Biomedical Sciences and School of Life SciencesEast China Normal UniversityShanghai200241P. R. China
| | - Tao Zhang
- East China Normal University and Shanghai Fengxian District Central Hospital Joint Center for Translational MedicineShanghai Key Laboratory of Regulatory BiologyInstitute of Biomedical Sciences and School of Life SciencesEast China Normal UniversityShanghai200241P. R. China
| | - Li Lai
- East China Normal University and Shanghai Fengxian District Central Hospital Joint Center for Translational MedicineShanghai Key Laboratory of Regulatory BiologyInstitute of Biomedical Sciences and School of Life SciencesEast China Normal UniversityShanghai200241P. R. China
| | - Zhenliang Sun
- Joint Center for Translational MedicineSouthern Medical University Affiliated Fengxian HospitalShanghai201499P. R. China
| | - Zhengfang Yi
- East China Normal University and Shanghai Fengxian District Central Hospital Joint Center for Translational MedicineShanghai Key Laboratory of Regulatory BiologyInstitute of Biomedical Sciences and School of Life SciencesEast China Normal UniversityShanghai200241P. R. China
- Joint Center for Translational MedicineSouthern Medical University Affiliated Fengxian HospitalShanghai201499P. R. China
| | - Mingyao Liu
- East China Normal University and Shanghai Fengxian District Central Hospital Joint Center for Translational MedicineShanghai Key Laboratory of Regulatory BiologyInstitute of Biomedical Sciences and School of Life SciencesEast China Normal UniversityShanghai200241P. R. China
| | - Yihua Chen
- East China Normal University and Shanghai Fengxian District Central Hospital Joint Center for Translational MedicineShanghai Key Laboratory of Regulatory BiologyInstitute of Biomedical Sciences and School of Life SciencesEast China Normal UniversityShanghai200241P. R. China
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26
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Wu Z, Tang H, Xiong Q, Liu D, Xia T, Liang H, Ye Q. Prognostic Role of microRNA-205 in Human Gynecological Cancer: A Meta-Analysis of Fourteen Studies. DNA Cell Biol 2020; 39:875-889. [PMID: 32354230 DOI: 10.1089/dna.2019.5316] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Several studies have revealed that miR-205 plays important roles in the development of gynecological cancers and thus may serve as a potential prognostic biomarker, but the current conclusions remain controversial. Therefore, the goal of this study was to explore the prognostic significance and functional mechanisms of miR-205 based on a meta-analysis and bioinformatics investigation. A total of 14 published studies containing 5835 patients were enrolled by searching the PubMed, EMBASE, and Cochrane library databases, 13 (14 datasets) and 5 (6 datasets) of which evaluated the correlations between the expression level of miR-205 and overall survival (OS) or disease-free survival (DFS)/disease-specific survival (DSS)/progression-free survival (PFS)/distant metastasis-free survival (DMFS), respectively. Furthermore, the use of online Kaplan-Meier plotter database analysis supplemented another seven results for OS. Then, a meta-analysis using these 21 and 6 datasets was performed. As a result, the overall analysis failed to demonstrate any significant associations between miR-205 expression and OS (p = 0.267) or DSS/DFS/DMFS/PFS (p = 0.457), but the subgroup analysis suggested that elevated miR-205 predicted a reduced OS for breast cancer (BC) patients (hazard ratio [HR] = 0.84, 95% confidence interval [CI] = 0.72-0.98; p = 0.022), while higher miR-205 was associated with a poor DSS for endometrial cancer (EC) patients (HR = 2.19, 95% CI = 1.45-3.32; p < 0.001). Function prediction analysis indicated that miR-205 may be involved in BC by negatively influencing hub genes, SMARCA5 and SIAH1, whereas miR-205 may participate in EC by negatively modulating BMPR1B because of the presence of interactions of miR-205 with them at 3'-untranslated region and their opposite prognosis outcomes with miR-205. In conclusion, our findings suggest miR-205 may be a promising prognostic biomarker and therapeutic target for BC and EC patients.
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Affiliation(s)
- Zhixi Wu
- Department of Obstetrics and Gynecology, Dongguan People's Hospital (Affiliated Dongguan Hospital, South Medical University), Dongguan, China
| | - Hong Tang
- Department of Gynecology, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Qian Xiong
- Department of Gynecology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Dong Liu
- Department of Gynecology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Tingting Xia
- Center for Reproductive Medicine, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Huichao Liang
- Department of Obstetrics and Gynecology, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Qingjian Ye
- Department of Gynecology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
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27
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Kim NI, Park MH, Kweon SS, Lee JS. B7-H3 and B7-H4 Expression in Breast Cancer and Their Association with Clinicopathological Variables and T Cell Infiltration. Pathobiology 2020; 87:179-192. [PMID: 32088722 DOI: 10.1159/000505756] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 12/29/2019] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVES B7-H3 and B7-H4 proteins are expressed in breast cancer tissues, but their relationships with respect to tumor immune surveillance and outcomes in breast cancer are not conclusive. METHODS We first examined B7-H3 and B7-H4 mRNA expression in the Genotype-Tissue Expression (GTEx) and The Cancer Genome Atlas (TCGA) datasets. Next, mRNA and protein expression were assessed by RNAscope in situ hybridization (ISH) and immunohistochemistry in 10 pairs of breast cancer and matched normal tissues. Immunohistochemical staining of B7-H3, B7-H4, CD3, and CD8 was performed in tissue microarray slides containing 198 breast cancer samples. Association of B7-H3 and B7-H4 expression with survival was verified using the publicly accessible BreastMark tool. RESULTS B7-H3 and B7-H4 mRNA expression were significantly higher in breast cancer samples in the TCGA dataset than in normal breast tissues in the GTEx dataset. RNAscope ISH and immunohistochemistry showed that B7-H3 and B7-H4 mRNA and protein appeared to be mainly expressed in cancer cells. Expression of B7-H3 and B7-H4 tended to be associated with low-density scores of stromal tumor-infiltrating lymphocytes (TILs) as well as molecular subtypes. Expressions of B7-H3 and B7-H4 were negatively correlated with stromal CD3+ and CD8+ T cell infiltration density. B7-H3 and B7-H4 expression was not associated with survival, which was verified by BreastMark analysis. CONCLUSION Expression levels of B7-H3 and B7-H4 were independent of clinical outcomes of breast cancer. There was an inverse relationship between the expression of B7-H3 and B7-H4 in breast cancer and the density of stromal TILs and CD8+ T lymphocytes. This inverse relationship may represent a promising target in the field of breast cancer immunotherapy.
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Affiliation(s)
- Nah Ihm Kim
- Department of Pathology, Chonnam National University Medical School, Gwangju, Republic of Korea
| | - Min Ho Park
- Department of Surgery, Chonnam National University Medical School, Gwangju, Republic of Korea
| | - Sun-Seog Kweon
- Department of Preventive Medicine, Chonnam National University Medical School, Gwangju, Republic of Korea
| | - Ji Shin Lee
- Department of Pathology, Chonnam National University Medical School, Gwangju, Republic of Korea,
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28
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Zheng H, Zhang G, Zhang L, Wang Q, Li H, Han Y, Xie L, Yan Z, Li Y, An Y, Dong H, Zhu W, Guo X. Comprehensive Review of Web Servers and Bioinformatics Tools for Cancer Prognosis Analysis. Front Oncol 2020; 10:68. [PMID: 32117725 PMCID: PMC7013087 DOI: 10.3389/fonc.2020.00068] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 01/15/2020] [Indexed: 01/10/2023] Open
Abstract
Prognostic biomarkers are of great significance to predict the outcome of patients with cancer, to guide the clinical treatments, to elucidate tumorigenesis mechanisms, and offer the opportunity of identifying therapeutic targets. To screen and develop prognostic biomarkers, high throughput profiling methods including gene microarray and next-generation sequencing have been widely applied and shown great success. However, due to the lack of independent validation, only very few prognostic biomarkers have been applied for clinical practice. In order to cross-validate the reliability of potential prognostic biomarkers, some groups have collected the omics datasets (i.e., epigenetics/transcriptome/proteome) with relative follow-up data (such as OS/DSS/PFS) of clinical samples from different cohorts, and developed the easy-to-use online bioinformatics tools and web servers to assist the biomarker screening and validation. These tools and web servers provide great convenience for the development of prognostic biomarkers, for the study of molecular mechanisms of tumorigenesis and progression, and even for the discovery of important therapeutic targets. Aim to help researchers to get a quick learning and understand the function of these tools, the current review delves into the introduction of the usage, characteristics and algorithms of tools, and web servers, such as LOGpc, KM plotter, GEPIA, TCPA, OncoLnc, PrognoScan, MethSurv, SurvExpress, UALCAN, etc., and further help researchers to select more suitable tools for their own research. In addition, all the tools introduced in this review can be reached at http://bioinfo.henu.edu.cn/WebServiceList.html.
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Affiliation(s)
- Hong Zheng
- Cell Signal Transduction Laboratory, Bioinformatics Center, School of Basic Medical Sciences, School of Software, Institute of Biomedical Informatics, Henan University, Kaifeng, China
| | - Guosen Zhang
- Cell Signal Transduction Laboratory, Bioinformatics Center, School of Basic Medical Sciences, School of Software, Institute of Biomedical Informatics, Henan University, Kaifeng, China
| | - Lu Zhang
- Cell Signal Transduction Laboratory, Bioinformatics Center, School of Basic Medical Sciences, School of Software, Institute of Biomedical Informatics, Henan University, Kaifeng, China
| | - Qiang Wang
- Cell Signal Transduction Laboratory, Bioinformatics Center, School of Basic Medical Sciences, School of Software, Institute of Biomedical Informatics, Henan University, Kaifeng, China
| | - Huimin Li
- Cell Signal Transduction Laboratory, Bioinformatics Center, School of Basic Medical Sciences, School of Software, Institute of Biomedical Informatics, Henan University, Kaifeng, China
| | - Yali Han
- Cell Signal Transduction Laboratory, Bioinformatics Center, School of Basic Medical Sciences, School of Software, Institute of Biomedical Informatics, Henan University, Kaifeng, China
| | - Longxiang Xie
- Cell Signal Transduction Laboratory, Bioinformatics Center, School of Basic Medical Sciences, School of Software, Institute of Biomedical Informatics, Henan University, Kaifeng, China
| | - Zhongyi Yan
- Cell Signal Transduction Laboratory, Bioinformatics Center, School of Basic Medical Sciences, School of Software, Institute of Biomedical Informatics, Henan University, Kaifeng, China
| | - Yongqiang Li
- Cell Signal Transduction Laboratory, Bioinformatics Center, School of Basic Medical Sciences, School of Software, Institute of Biomedical Informatics, Henan University, Kaifeng, China
| | - Yang An
- Cell Signal Transduction Laboratory, Bioinformatics Center, School of Basic Medical Sciences, School of Software, Institute of Biomedical Informatics, Henan University, Kaifeng, China
| | - Huan Dong
- Cell Signal Transduction Laboratory, Bioinformatics Center, School of Basic Medical Sciences, School of Software, Institute of Biomedical Informatics, Henan University, Kaifeng, China
| | - Wan Zhu
- Department of Anesthesia, Stanford University, Stanford, CA, United States
| | - Xiangqian Guo
- Cell Signal Transduction Laboratory, Bioinformatics Center, School of Basic Medical Sciences, School of Software, Institute of Biomedical Informatics, Henan University, Kaifeng, China
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29
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Bar HY, Booth JG, Wells MT. A Scalable Empirical Bayes Approach to Variable Selection in Generalized Linear Models. J Comput Graph Stat 2020; 29:535-546. [PMID: 38919169 PMCID: PMC11198964 DOI: 10.1080/10618600.2019.1706542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 04/20/2019] [Accepted: 12/11/2019] [Indexed: 10/25/2022]
Abstract
A new empirical Bayes approach to variable selection in the context of generalized linear models is developed. The proposed algorithm scales to situations in which the number of putative explanatory variables is very large, possibly much larger than the number of responses. The coefficients in the linear predictor are modeled as a three-component mixture allowing the explanatory variables to have a random positive effect on the response, a random negative effect, or no effect. A key assumption is that only a small (but unknown) fraction of the candidate variables have a non-zero effect. This assumption, in addition to treating the coefficients as random effects facilitates an approach that is computationally efficient. In particular, the number of parameters that have to be estimated is small, and remains constant regardless of the number of explanatory variables. The model parameters are estimated using a Generalized Alternating Maximization algorithm which is scalable, and leads to significantly faster convergence compared with simulation-based fully Bayesian methods.
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Affiliation(s)
- Haim Y Bar
- Department of Statistics University of Connecticut, Storrs CT, 06269, USA
| | - James G Booth
- Department of Statistics and Data Science, Cornell University, Ithaca NY, 14853, USA
| | - Martin T Wells
- Department of Statistics and Data Science, Cornell University, Ithaca NY, 14853, USA
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30
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Kim GE, Kim NI, Lee JS, Park MH, Kang K. Differentially Expressed Genes in Matched Normal, Cancer, and Lymph Node Metastases Predict Clinical Outcomes in Patients With Breast Cancer. Appl Immunohistochem Mol Morphol 2020; 28:111-122. [PMID: 32044879 PMCID: PMC7028469 DOI: 10.1097/pai.0000000000000717] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Accepted: 09/27/2018] [Indexed: 01/27/2023]
Abstract
Genome-wide screening of transcriptional changes among normal, cancer, and nodal metastases provides insights into the molecular basis of breast cancer (BC) progression and metastasis. To identify transcriptional changes and differentially expressed genes (DEGs) in the metastatic progression of BC and to determine the prognostic role of these DEGs in clinical outcome, we compared transcriptome profiling in matched normal, cancer, and lymph node metastatic tissues of 7 patients with estrogen receptor-positive, HER2-negative BC by using massive parallel RNA sequencing. The global profiles of gene expression in cancer and nodal metastases were highly correlated (r=0.962, P<0.001). In 6 (85.8%) patients, cancer and corresponding nodal metastases from the same patient clustered together. We identified 1522 and 664 DEGs between normal and cancer and between cancer and nodal metastases, respectively. The DEGs in normal versus cancer and cancer versus nodal metastases were significantly clustered in 1 and 8 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, respectively. The chemokine signaling pathway was the most significant pathway in the cancer-to-nodal metastasis transition (false discovery rate=2.15E-13). The expression of 2 dysregulated RAC2 and PTGDS genes was confirmed by quantitative real-time polymerase chain reaction and immunohistochemistry. Interestingly, the lower RAC2 and PTGDS expression were associated with significantly worse disease-free survival in patients with BC. Our results show a high concordance of gene expression in BC and their nodal metastases, and identify DEGs associated with the metastatic progression of BC. The DEGs identified in this study represent novel biomarkers for predicting the prognosis of patients with BC.
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Affiliation(s)
| | | | | | - Min Ho Park
- Surgery, Chonnam National University Medical School, Gwangju
| | - Keunsoo Kang
- Department of Microbiology, College of Natural Sciences, Dankook University, Cheonan, Republic of Korea
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31
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Eckhardt BL, Cao Y, Redfern AD, Chi LH, Burrows AD, Roslan S, Sloan EK, Parker BS, Loi S, Ueno NT, Lau PKH, Latham B, Anderson RL. Activation of Canonical BMP4-SMAD7 Signaling Suppresses Breast Cancer Metastasis. Cancer Res 2020; 80:1304-1315. [PMID: 31941699 DOI: 10.1158/0008-5472.can-19-0743] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 10/30/2019] [Accepted: 01/02/2020] [Indexed: 11/16/2022]
Abstract
Metastasis is the major cause of death in patients with cancer; with no therapeutic cure, treatments remain largely palliative. As such, new targets and therapeutic strategies are urgently required. Here, we show that bone morphogenetic protein-4 (BMP4) blocks metastasis in animal models of breast cancer and predicts improved survival in patients. In preclinical models of spontaneous metastasis, BMP4 acted as an autocrine mediator to modulate a range of known metastasis-regulating genes, including Smad7, via activation of canonical BMP-SMAD signaling. Restored BMP4 expression or therapeutically administered BMP4 protein, blocked metastasis and increased survival by sensitizing cancer cells to anoikis, thereby reducing the number of circulating tumor cells. Gene silencing of Bmp4 or its downstream mediator Smad7, reversed this phenotype. Administration of recombinant BMP4 markedly reduced spontaneous metastasis to lung and bone. Elevated levels of BMP4 and SMAD7 were prognostic for improved recurrence-free survival and overall survival in patients with breast cancer, indicating the importance of canonical BMP4 signaling in the suppression of metastasis and highlighting new avenues for therapy against metastatic disease. SIGNIFICANCE: Targeting the BMP4-SMAD7 signaling axis presents a novel therapeutic strategy to combat metastatic breast cancer, a disease that has had no reduction in patient mortality over 20 years. GRAPHICAL ABSTRACT: http://cancerres.aacrjournals.org/content/canres/80/6/1304/F1.large.jpg.
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Affiliation(s)
- Bedrich L Eckhardt
- Morgan Welch Inflammatory Breast Cancer Research and Clinic, Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas. .,Olivia Newton-John Cancer Research Institute, Heidelberg, Australia
| | - Yuan Cao
- Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia
| | - Andrew D Redfern
- School of Medicine, University of Western Australia, Perth, Australia
| | - Lap Hing Chi
- Olivia Newton-John Cancer Research Institute, Heidelberg, Australia.,School of Cancer Medicine, La Trobe University, Bundoora, Victoria, Australia
| | - Allan D Burrows
- Olivia Newton-John Cancer Research Institute, Heidelberg, Australia.,School of Cancer Medicine, La Trobe University, Bundoora, Victoria, Australia
| | - Suraya Roslan
- Olivia Newton-John Cancer Research Institute, Heidelberg, Australia
| | - Erica K Sloan
- Monash Institute of Pharmaceutical Sciences, Drug Discovery Biology Theme, Monash University, Parkville, Victoria, Australia
| | - Belinda S Parker
- La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, Australia
| | - Sherene Loi
- Research Division, Peter MacCallum Cancer Centre, Parkville, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Naoto T Ueno
- Morgan Welch Inflammatory Breast Cancer Research and Clinic, Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Peter K H Lau
- Department of Health Western Australia, Perth, Australia.,Cancer Medicine, Peter MacCallum Cancer Centre, Parkville, Australia
| | - Bruce Latham
- Department of Anatomical Pathology, Fiona Stanley Hospital, Perth, Australia
| | - Robin L Anderson
- Olivia Newton-John Cancer Research Institute, Heidelberg, Australia. .,School of Cancer Medicine, La Trobe University, Bundoora, Victoria, Australia.,Research Division, Peter MacCallum Cancer Centre, Parkville, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
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32
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Kim H, Kim HS, Moon WK. Comparison of transcriptome expression alterations by chronic exposure to low-dose bisphenol A in different subtypes of breast cancer cells. Toxicol Appl Pharmacol 2019; 385:114814. [PMID: 31715268 DOI: 10.1016/j.taap.2019.114814] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 10/22/2019] [Accepted: 11/08/2019] [Indexed: 12/25/2022]
Abstract
The impacts of chronic bisphenol A (BPA) exposure suspected to be a potential risk factor for breast cancer progression are not thoroughly understood in different subtypes of breast cancer cells (BCCs). This study aimed to compare the differentially expressed genes (DEGs) and biological functions in MCF-7 (luminal A), SK-BR3 (HER2-enriched) and MDA-MB-231 (triple-negative) cells exposed to BPA at an environmentally human-relevant low dose (10-8 M) for 30 days, by using the approach of RNA sequencing and online informatics tools. BPA-exposure resulted in 172, 137, and 139 DEGs in MCF-7/BPA, SK-BR3/BPA, and MDA-MB-231/BPA, respectively. The significantly enriched gene ontology terms of DEGs in each cell were different: cellular response to gonadotropin-releasing hormone, negative regulation of fibrinolysis, choline metabolism, glutamate signaling pathways and coagulation pathway in MCF-7/BPA; positive regulation of inflammatory response and VEGF/VEGFR signaling pathways in SK-BR3/BPA; negative regulation of keratinocyte proliferation and HIF signaling pathways in MDA-MB-231/BPA cells. The immune network analysis of DEGs across the breast cancer cells indicated NKT, NK and T cell activation and dendritic cell migration by regulating the expression of immunomodulatory genes. High expression of IL19, CA9 and SPARC identified in MCF-7/BPA, SK-BR3/BPA, and MDA-MB-231/BPA are detrimental gene signatures to predict poor overall survival in luminal A, HER2-enriched and triple-negative breast cancer patients, respectively. These findings indicate chronic BPA exposure has dissimilar impacts on the regulation of gene expression and diverse biological functions, including immune modulation, in different subtypes of BCCs.
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Affiliation(s)
- Hyelim Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea
| | - Hoe Suk Kim
- Department of Radiology, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea
| | - Woo Kyung Moon
- Department of Radiology, Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea; Department of Biomedical Sciences, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea; Department of Radiology, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu, Seoul 03080, Republic of Korea.
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33
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Denkiewicz M, Saha I, Rakshit S, Sarkar JP, Plewczynski D. Identification of Breast Cancer Subtype Specific MicroRNAs Using Survival Analysis to Find Their Role in Transcriptomic Regulation. Front Genet 2019; 10:1047. [PMID: 31798622 PMCID: PMC6837165 DOI: 10.3389/fgene.2019.01047] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 09/30/2019] [Indexed: 01/19/2023] Open
Abstract
The microRNA (miRNA) biomolecules have a significant role in the development of breast cancer, and their expression profiles are different in each subtype of breast cancer. Thus, our goal is to use the Next Generation Sequencing provided high-throughput miRNA expression and clinical data in an integrated fashion to perform survival analysis in order to identify breast cancer subtype specific miRNAs, and analyze associated genes and transcription factors. We select top 100 miRNAs for each of the four subtypes, based on the value of hazard ratio and p-value, thereafter, identify 44 miRNAs that are related to all four subtypes, which we call as four-star miRNAs. Moreover, 12, 14, 9, and 15 subtype specific, viz. one-star miRNAs, are also identified. The resulting miRNAs are validated by using machine learning methods to differentiate tumor cases from controls (for four-star miRNAs), and subtypes (for one-star miRNAs). The four-star miRNAs provide 95% average accuracy, while in case of one-star miRNAs 81% accuracy is achieved for HER2-Enriched. Differences in expression of miRNAs between cancer stages is also analyzed, and a subset of eight miRNAs is found, for which expression is increased in stage II relative to stage I, including hsa-miR-10b-5p, which contributes to breast cancer metastasis. Subsequently we prepare regulatory networks in order to identify the interactions among miRNAs, their targeted genes and transcription factors (TFs), that are targeting those miRNAs. In this way, key regulatory circuits are identified, where genes such as TP53, ESR1, BRCA1, MYC, and others, that are known to be important genetic factors for the cause of breast cancer, produce transcription factors that target the same genes as well as interact with the selected miRNAs. To provide further biological validation the Protein-Protein Interaction (PPI) networks are prepared and Kyoto Encyclopedia of Genes and Genomes pathway and gene ontology (GO) enrichment analysis are performed. Among the enriched pathways many are breast cancer-related, such as PI3K-Akt or p53 signaling pathways, and contain proteins such as TP53, also present in the regulatory networks. Moreover, we find that the genes are enriched in GO terms associated with breast cancer. Our results provide detailed analysis of selected miRNAs and their regulatory networks.
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Affiliation(s)
- Michał Denkiewicz
- Laboratory of Functional and Structural Genomics, Center of New Technologies, University of Warsaw, Warsaw, Poland
- College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Warsaw, Poland
- Faculty of Mathematics and Information Science, Warsaw University of Technology Warsaw, Poland
| | - Indrajit Saha
- Department of Computer Science and Engineering, National Institute of Technical Teachers’ Training and Research, Kolkata, India
| | - Somnath Rakshit
- Laboratory of Functional and Structural Genomics, Center of New Technologies, University of Warsaw, Warsaw, Poland
- Department of Computer Science and Engineering, National Institute of Technical Teachers’ Training and Research, Kolkata, India
| | - Jnanendra Prasad Sarkar
- Cognitive and Analytics, Larsen & Toubro Infotech Ltd., Pune, India
- Department of Computer Science & Engineering, Jadavpur University, Kolkata, India
| | - Dariusz Plewczynski
- Laboratory of Functional and Structural Genomics, Center of New Technologies, University of Warsaw, Warsaw, Poland
- Faculty of Mathematics and Information Science, Warsaw University of Technology Warsaw, Poland
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34
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Leslie PL, Chao YL, Tsai YH, Ghosh SK, Porrello A, Van Swearingen AED, Harrison EB, Cooley BC, Parker JS, Carey LA, Pecot CV. Histone deacetylase 11 inhibition promotes breast cancer metastasis from lymph nodes. Nat Commun 2019; 10:4192. [PMID: 31519896 PMCID: PMC6744422 DOI: 10.1038/s41467-019-12222-5] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 08/27/2019] [Indexed: 01/28/2023] Open
Abstract
Lymph node (LN) metastases correspond with a worse prognosis in nearly all cancers, yet the occurrence of cancer spreading from LNs remains controversial. Additionally, the mechanisms explaining how cancers survive and exit LNs are largely unknown. Here, we show that breast cancer patients frequently have LN metastases that closely resemble distant metastases. In addition, using a microsurgical model, we show how LN metastasis development and dissemination is regulated by the expression of a chromatin modifier, histone deacetylase 11 (HDAC11). Genetic and pharmacologic blockade of HDAC11 decreases LN tumor growth, yet substantially increases migration and distant metastasis formation. Collectively, we reveal a mechanism explaining how HDAC11 plasticity promotes breast cancer growth as well as dissemination from LNs and suggest caution with the use of HDAC inhibitors. The prognosis of cancer patients with lymph node (LN) metastasis is worse than those without. Here, the authors report that while histone deacetylase 11 (HDAC11) inhibition suppresses tumor growth within the LN, it also promotes cancer cell migration out of the LN to form distant metastasis, and therefore suggest caution with HDAC inhibitors.
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Affiliation(s)
- Patrick L Leslie
- UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Yvonne L Chao
- UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Yi-Hsuan Tsai
- UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Subrata K Ghosh
- UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Alessandro Porrello
- UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Amanda E D Van Swearingen
- UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Emily B Harrison
- UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Brian C Cooley
- UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.,Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Joel S Parker
- UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Lisa A Carey
- UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.,Division of Hematology and Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Chad V Pecot
- UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA. .,Division of Hematology and Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
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35
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YKL-40/CHI3L1 facilitates migration and invasion in HER2 overexpressing breast epithelial progenitor cells and generates a niche for capillary-like network formation. In Vitro Cell Dev Biol Anim 2019; 55:838-853. [PMID: 31482369 PMCID: PMC6881255 DOI: 10.1007/s11626-019-00403-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 08/13/2019] [Indexed: 12/17/2022]
Abstract
Epithelial to mesenchymal transition (EMT) is a developmental event that is hijacked in some diseases such as fibrosis and cancer. In cancer, EMT has been linked to increased invasion and metastasis and is generally associated with a poor prognosis. In this study, we have compared phenotypic and functional differences between two isogenic cell lines with an EMT profile: D492M and D492HER2 that are both derived from D492, a breast epithelial cell line with stem cell properties. D492M is non-tumorigenic while D492HER2 is tumorigenic. Thus, the aim of this study was to analyze the expression profile of these cell lines, identify potential oncogenes, and evaluate their effects on cellular phenotype. We performed transcriptome and secretome analyses of D492M and D492HER2 and verified expression of selected genes at the RNA and protein level. One candidate, YKL-40 (also known as CHI3L1), was selected for further studies due to its differential expression between D492M and D492HER2, being considerably higher in D492HER2. YKL-40 has been linked to chronic inflammation diseases and cancer, yet its function is not fully understood. Knock-down experiments of YKL-40 in D492HER2 resulted in reduced migration and invasion as well as reduced ability to induce angiogenesis in an in vitro assay, plus changes in the EMT-phenotype. In summary, our data suggest that YKL-40 may provide D492HER2 with increased aggressiveness, supporting cancer progression and facilitating angiogenesis.
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36
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Creevey L, Bleach R, Madden SF, Toomey S, Bane FT, Varešlija D, Hill AD, Young LS, McIlroy M. Altered Steroid Milieu in AI-Resistant Breast Cancer Facilitates AR Mediated Gene-Expression Associated with Poor Response to Therapy. Mol Cancer Ther 2019; 18:1731-1743. [PMID: 31289138 DOI: 10.1158/1535-7163.mct-18-0791] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 10/23/2018] [Accepted: 07/03/2019] [Indexed: 11/16/2022]
Abstract
Divergent roles for androgen receptor (AR) in breast cancer have been reported. Following aromatase inhibitor (AI) treatment, the conversion of circulating androgens into estrogens can be diminished by >99%. We wished to establish whether the steroid environment can dictate the role of AR and the implications of this for subsequent therapy. This study utilizes models of AI resistance to explore responsiveness to PI3K/mTOR and anti-AR therapy when cells are exposed to unconverted weak androgens. Transcriptomic alterations driven by androstenedione (4AD) were assessed by RNA-sequencing. AR and estrogen receptor (ER) recruitment to target gene promoters was evaluated using ChIP, and relevance to patient profiles was performed using publicly available data sets. Although BEZ235 showed decreased viability across AI-sensitive and -resistant cell lines, anti-AR treatment elicited a decrease in cell viability only in the AI-resistant model. Serum and glucocorticoid-regulated kinase 3 (SGK3) and cAMP-dependent protein kinase inhibitor β (PKIB) were confirmed to be regulated by 4AD and shown to be mediated by AR; crucially, reexposure to estradiol suppressed expression of these genes. Meta-analysis of transcript levels showed high expression of SGK3 and PKIB to be associated with poor response to endocrine therapy (HR = 2.551, P = 0.003). Furthermore, this study found levels of SGK3 to be sustained in patients who do not respond to AI therapy. This study highlights the importance of the tumor steroid environment. SGK3 and PKIB are associated with poor response to endocrine therapy and could have utility in tailoring therapeutic approaches.
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Affiliation(s)
- Laura Creevey
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland (RCSI), Dublin, Ireland
| | - Rachel Bleach
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland (RCSI), Dublin, Ireland
| | - Stephen F Madden
- Data Science Centre, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Sinead Toomey
- Department of Oncology, Royal College of Surgeons in Ireland, Beaumont Hospital, Dublin, Ireland
| | - Fiona T Bane
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland (RCSI), Dublin, Ireland
| | - Damir Varešlija
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland (RCSI), Dublin, Ireland
| | - Arnold D Hill
- Department of Surgery, Royal College of Surgeons in Ireland, Beaumont Hospital, Dublin, Ireland
| | - Leonie S Young
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland (RCSI), Dublin, Ireland
| | - Marie McIlroy
- Endocrine Oncology Research Group, Department of Surgery, Royal College of Surgeons in Ireland (RCSI), Dublin, Ireland.
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37
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Gendoo DMA, Zon M, Sandhu V, Manem VSK, Ratanasirigulchai N, Chen GM, Waldron L, Haibe-Kains B. MetaGxData: Clinically Annotated Breast, Ovarian and Pancreatic Cancer Datasets and their Use in Generating a Multi-Cancer Gene Signature. Sci Rep 2019; 9:8770. [PMID: 31217513 PMCID: PMC6584731 DOI: 10.1038/s41598-019-45165-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 05/31/2019] [Indexed: 12/13/2022] Open
Abstract
A wealth of transcriptomic and clinical data on solid tumours are under-utilized due to unharmonized data storage and format. We have developed the MetaGxData package compendium, which includes manually-curated and standardized clinical, pathological, survival, and treatment metadata across breast, ovarian, and pancreatic cancer data. MetaGxData is the largest compendium of curated transcriptomic data for these cancer types to date, spanning 86 datasets and encompassing 15,249 samples. Open access to standardized metadata across cancer types promotes use of their transcriptomic and clinical data in a variety of cross-tumour analyses, including identification of common biomarkers, and assessing the validity of prognostic signatures. Here, we demonstrate that MetaGxData is a flexible framework that facilitates meta-analyses by using it to identify common prognostic genes in ovarian and breast cancer. Furthermore, we use the data compendium to create the first gene signature that is prognostic in a meta-analysis across 3 cancer types. These findings demonstrate the potential of MetaGxData to serve as an important resource in oncology research, and provide a foundation for future development of cancer-specific compendia.
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Affiliation(s)
- Deena M A Gendoo
- Centre for Computational Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, B15 2TT, United Kingdom.
| | - Michael Zon
- Princess Margaret Cancer Center, University Health Network, Toronto, M5G 2C1, Canada.,Department of Biomedical Engineering, McMaster University, Toronto, L8S 4L8, Canada
| | - Vandana Sandhu
- Princess Margaret Cancer Center, University Health Network, Toronto, M5G 2C1, Canada
| | - Venkata S K Manem
- Princess Margaret Cancer Center, University Health Network, Toronto, M5G 2C1, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, M5S 3H7, Canada.,Institut Universitaire de Cardiologie et de Pneumologie de Québec, Université Laval, Québec City, G1V 4G5, Canada
| | | | - Gregory M Chen
- Princess Margaret Cancer Center, University Health Network, Toronto, M5G 2C1, Canada
| | - Levi Waldron
- Graduate School of Public Health and Health Policy, Institute of Implementation Science in Population Health, City University of New York School, New York, 11101, USA.
| | - Benjamin Haibe-Kains
- Princess Margaret Cancer Center, University Health Network, Toronto, M5G 2C1, Canada. .,Department of Medical Biophysics, University of Toronto, Toronto, M5S 3H7, Canada. .,Department of Computer Science, University of Toronto, Toronto, M5T 3A1, Canada. .,Ontario Institute of Cancer Research, Toronto, M5G 0A3, Canada. .,Vector Institute, Toronto, M5G 1M1, Canada.
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38
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Irey EA, Lassiter CM, Brady NJ, Chuntova P, Wang Y, Knutson TP, Henzler C, Chaffee TS, Vogel RI, Nelson AC, Farrar MA, Schwertfeger KL. JAK/STAT inhibition in macrophages promotes therapeutic resistance by inducing expression of protumorigenic factors. Proc Natl Acad Sci U S A 2019; 116:12442-12451. [PMID: 31147469 PMCID: PMC7056941 DOI: 10.1073/pnas.1816410116] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Tumor-associated macrophages contribute to tumor progression and therapeutic resistance in breast cancer. Within the tumor microenvironment, tumor-derived factors activate pathways that modulate macrophage function. Using in vitro and in vivo models, we find that tumor-derived factors induce activation of the Janus kinase (JAK)/signal transducer and activator of transcription 3 (STAT3) pathway in macrophages. We also demonstrate that loss of STAT3 in myeloid cells leads to enhanced mammary tumorigenesis. Further studies show that macrophages contribute to resistance of mammary tumors to the JAK/STAT inhibitor ruxolitinib in vivo and that ruxolitinib-treated macrophages produce soluble factors that promote resistance of tumor cells to JAK inhibition in vitro. Finally, we demonstrate that STAT3 deletion and JAK/STAT inhibition in macrophages increases expression of the protumorigenic factor cyclooxygenase-2 (COX-2), and that COX-2 inhibition enhances responsiveness of tumors to ruxolitinib. These findings define a mechanism through which macrophages promote therapeutic resistance and highlight the importance of understanding the impact of targeted therapies on the tumor microenvironment.
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Affiliation(s)
- Emily A Irey
- Microbiology, Immunology and Cancer Biology Graduate Program, University of Minnesota, Minneapolis, MN 55455
| | - Chelsea M Lassiter
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455
| | - Nicholas J Brady
- Microbiology, Immunology and Cancer Biology Graduate Program, University of Minnesota, Minneapolis, MN 55455
| | - Pavlina Chuntova
- Microbiology, Immunology and Cancer Biology Graduate Program, University of Minnesota, Minneapolis, MN 55455
| | - Ying Wang
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455
| | - Todd P Knutson
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455
- University of Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455
| | - Christine Henzler
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455
- University of Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN 55455
| | - Thomas S Chaffee
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455
| | - Rachel I Vogel
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455
- Department of Obstetrics, Gynecology and Women's Health, Division of Gynecologic Oncology, University of Minnesota, Minneapolis, MN 55455
| | - Andrew C Nelson
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455
| | - Michael A Farrar
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455
- Center for Immunology, University of Minnesota, Minneapolis, MN 55455
| | - Kathryn L Schwertfeger
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455;
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455
- Center for Immunology, University of Minnesota, Minneapolis, MN 55455
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39
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Linares A, Assou S, Lapierre M, Thouennon E, Duraffourd C, Fromaget C, Boulahtouf A, Tian G, Ji J, Sahin O, Badia E, Boulle N, Cavaillès V. Increased expression of the HDAC9 gene is associated with antiestrogen resistance of breast cancers. Mol Oncol 2019; 13:1534-1547. [PMID: 31099456 PMCID: PMC6599838 DOI: 10.1002/1878-0261.12505] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 04/26/2019] [Accepted: 05/15/2019] [Indexed: 12/19/2022] Open
Abstract
Estrogens play a pivotal role in breast cancer etiology, and endocrine therapy remains the main first line treatment for estrogen receptor‐alpha (ERα)‐positive breast cancer. ER are transcription factors whose activity is finely regulated by various regulatory complexes, including histone deacetylases (HDACs). Here, we investigated the role of HDAC9 in ERα signaling and response to antiestrogens in breast cancer cells. Various Michigan Cancer Foundation‐7 (MCF7) breast cancer cell lines that overexpress class IIa HDAC9 or that are resistant to the partial antiestrogen 4‐hydroxy‐tamoxifen (OHTam) were used to study phenotypic changes in response to ER ligands by using transcriptomic and gene set enrichment analyses. Kaplan–Meier survival analyses were performed using public transcriptomic datasets from human breast cancer biopsies. In MCF7 breast cancer cells, HDAC9 decreased ERα mRNA and protein expression and inhibited its transcriptional activity. Conversely, HDAC9 mRNA was strongly overexpressed in OHTam‐resistant MCF7 cells and in ERα‐negative breast tumor cell lines. Moreover, HDAC9‐overexpressing cells were less sensitive to OHTam antiproliferative effects compared with parental MCF7 cells. Several genes (including MUC1, SMC3 and S100P) were similarly deregulated in OHTam‐resistant and in HDAC9‐overexpressing MCF7 cells. Finally, HDAC9 expression was positively associated with genes upregulated in endocrine therapy‐resistant breast cancers and high HDAC9 levels were associated with worse prognosis in patients treated with OHTam. These results demonstrate the complex interactions of class IIa HDAC9 with ERα signaling in breast cancer cells and its effect on the response to hormone therapy.
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Affiliation(s)
- Aurélien Linares
- IRCM, Institut de Recherche en Cancérologie de Montpellier, France.,INSERM, U1194, Montpellier, France.,Université Montpellier, France.,ICM, Montpellier, France
| | - Said Assou
- Université Montpellier, France.,IRMB, Institute for Regenerative Medicine & Biotherapy, Montpellier, France.,INSERM, U1183, Montpellier, France
| | - Marion Lapierre
- IRCM, Institut de Recherche en Cancérologie de Montpellier, France.,INSERM, U1194, Montpellier, France.,Université Montpellier, France.,ICM, Montpellier, France
| | - Erwan Thouennon
- IRCM, Institut de Recherche en Cancérologie de Montpellier, France.,INSERM, U1194, Montpellier, France.,Université Montpellier, France.,ICM, Montpellier, France
| | - Céline Duraffourd
- Laboratoire de Biopathologie des Tumeurs, CHU Arnaud de Villeneuve, Montpellier, France
| | - Carole Fromaget
- Laboratoire de Biopathologie des Tumeurs, CHU Arnaud de Villeneuve, Montpellier, France
| | - Abdelhay Boulahtouf
- IRCM, Institut de Recherche en Cancérologie de Montpellier, France.,INSERM, U1194, Montpellier, France.,Université Montpellier, France.,ICM, Montpellier, France
| | - Gao Tian
- Key Laboratory of Carcinogenesis and Translational Research Ministry of Education, Department of Gastrointestinal Surgery, Peking University Cancer Hospital & Institute, Beijing, China
| | - Jiafu Ji
- Key Laboratory of Carcinogenesis and Translational Research Ministry of Education, Department of Gastrointestinal Surgery, Peking University Cancer Hospital & Institute, Beijing, China
| | - Ozgur Sahin
- Department of Drug Discovery and Biomedical Sciences, University of South Carolina, Columbia, SC, USA
| | - Eric Badia
- IRCM, Institut de Recherche en Cancérologie de Montpellier, France.,INSERM, U1194, Montpellier, France.,Université Montpellier, France.,ICM, Montpellier, France
| | - Nathalie Boulle
- IRCM, Institut de Recherche en Cancérologie de Montpellier, France.,INSERM, U1194, Montpellier, France.,Université Montpellier, France.,ICM, Montpellier, France.,Laboratoire de Biopathologie des Tumeurs, CHU Arnaud de Villeneuve, Montpellier, France
| | - Vincent Cavaillès
- IRCM, Institut de Recherche en Cancérologie de Montpellier, France.,INSERM, U1194, Montpellier, France.,Université Montpellier, France.,ICM, Montpellier, France
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40
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Fekete JT, Győrffy B. ROCplot.org: Validating predictive biomarkers of chemotherapy/hormonal therapy/anti-HER2 therapy using transcriptomic data of 3,104 breast cancer patients. Int J Cancer 2019; 145:3140-3151. [PMID: 31020993 DOI: 10.1002/ijc.32369] [Citation(s) in RCA: 160] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Revised: 04/02/2019] [Accepted: 04/17/2019] [Indexed: 11/10/2022]
Abstract
Systemic therapy of breast cancer can include chemotherapy, hormonal therapy and targeted therapy. Prognostic biomarkers are able to predict survival and predictive biomarkers are able to predict therapy response. In this report, we describe the initial release of the first available online tool able to identify gene expression-based predictive biomarkers using transcriptomic data of a large set of breast cancer patients. Published gene expression data of 36 publicly available datasets were integrated with treatment data into a unified database. Response to therapy was determined using either author-reported pathological complete response data (n = 1,775) or relapse-free survival status at 5 years (n = 1,329). Treatment data includes chemotherapy (n = 2,108), endocrine therapy (n = 971) and anti-human epidermal growth factor receptor 2 (HER2) therapy (n = 267). The transcriptomic database includes 20,089 unique genes and 54,675 probe sets. Gene expression and therapy response are compared using receiver operating characteristics and Mann-Whitney tests. We demonstrate the utility of the pipeline by cross-validating 23 paclitaxel resistance-associated genes in different molecular subtypes of breast cancer. An additional set of established biomarkers including TP53 for chemotherapy in Luminal breast cancer (p = 1.01E-19, AUC = 0.769), HER2 for trastuzumab therapy (p = 8.4E-04, AUC = 0.629) and PGR for hormonal therapy (p = 8.6E-05, AUC = 0.7), are also endorsed. The tool is designed to validate and rank new predictive biomarker candidates in real time. By analyzing the selected genes in a large set of independent patients, one can select the most robust candidates and quickly eliminate those that are most likely to fail in a clinical setting. The analysis tool is accessible at www.rocplot.org.
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Affiliation(s)
- János T Fekete
- 2nd Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Balázs Győrffy
- 2nd Department of Pediatrics, Semmelweis University, Budapest, Hungary.,MTA TTK Lendület Cancer Biomarker Research Group, Institute of Enzymology, Hungarian Academy of Sciences, Budapest, Hungary
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41
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Hong R, Zhang W, Xia X, Zhang K, Wang Y, Wu M, Fan J, Li J, Xia W, Xu F, Chen J, Wang S, Zhan Q. Preventing BRCA1/ZBRK1 repressor complex binding to the GOT2 promoter results in accelerated aspartate biosynthesis and promotion of cell proliferation. Mol Oncol 2019; 13:959-977. [PMID: 30714292 PMCID: PMC6441895 DOI: 10.1002/1878-0261.12466] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 12/27/2018] [Accepted: 01/24/2019] [Indexed: 02/06/2023] Open
Abstract
Breast cancer susceptibility gene 1 (BRCA1) has been implicated in modulating metabolism via transcriptional regulation. However, direct metabolic targets of BRCA1 and the underlying regulatory mechanisms are still unknown. Here, we identified several metabolic genes, including the gene which encodes glutamate‐oxaloacetate transaminase 2 (GOT2), a key enzyme for aspartate biosynthesis, which are repressed by BRCA1. We report that BRCA1 forms a co‐repressor complex with ZBRK1 that coordinately represses GOT2 expression via a ZBRK1 recognition element in the promoter of GOT2. Impairment of this complex results in upregulation of GOT2, which in turn increases aspartate and alpha ketoglutarate production, leading to rapid cell proliferation of breast cancer cells. Importantly, we found that GOT2 can serve as an independent prognostic factor for overall survival and disease‐free survival of patients with breast cancer, especially triple‐negative breast cancer. Interestingly, we also demonstrated that GOT2 overexpression sensitized breast cancer cells to methotrexate, suggesting a promising precision therapeutic strategy for breast cancer treatment. In summary, our findings reveal that BRCA1 modulates aspartate biosynthesis through transcriptional repression of GOT2, and provides a biological basis for treatment choices in breast cancer.
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Affiliation(s)
- Ruoxi Hong
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Weimin Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Xi Xia
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, China.,Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety and Beijing Laboratory for Food Quality and Safety, China Agricultural University, Beijing, China
| | - Kai Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yan Wang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Mengjiao Wu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Jiawen Fan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Jinting Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Wen Xia
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Fei Xu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jie Chen
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Shusen Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Qimin Zhan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Molecular Oncology, Peking University Cancer Hospital & Institute, Beijing, China.,State Key Laboratory of Molecular Oncology, National Cancer Institute and Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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42
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Jeschke U, Zhang X, Kuhn C, Jalaguier S, Colinge J, Pfender K, Mayr D, Ditsch N, Harbeck N, Mahner S, Sixou S, Cavaillès V. The Prognostic Impact of the Aryl Hydrocarbon Receptor (AhR) in Primary Breast Cancer Depends on the Lymph Node Status. Int J Mol Sci 2019; 20:ijms20051016. [PMID: 30813617 PMCID: PMC6429124 DOI: 10.3390/ijms20051016] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 02/20/2019] [Accepted: 02/20/2019] [Indexed: 01/04/2023] Open
Abstract
Increasing evidence implicates the aryl hydrocarbon receptor (AhR) as a possible regulator of mammary carcinogenesis. This study aims to clarify its prognostic impact in breast cancer (BC). Meta-analyses performed at the mRNA level demonstrated that the predictive value of AhR expression in BC depends on the lymph node (LN) status. AhR expression and sub-cellular location were then analyzed by immunohistochemistry in 302 primary BC samples. AhR was expressed in almost 90% of cases with a predominant nuclear location. Nuclear and cytoplasmic AhR levels were significantly correlated and associated with the expression of RIP140 (receptor-interacting protein of 140 kDa), an AhR transcriptional coregulator and target gene. Interestingly, total and nuclear AhR levels were only significantly correlated with short overall survival in node-negative patients. In this sub-group, total and nuclear AhR expression had an even stronger prognostic impact in patients with low RIP140-expressing tumors. Very interestingly, the total AhR prognostic value was also significant in luminal-like BCs and was an independent prognostic marker for LN-negative patients. Altogether, this study suggests that AhR is a marker of poor prognosis for patients with LN-negative luminal-like BCs, which warrants further evaluation.
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Affiliation(s)
- Udo Jeschke
- LMU Munich, University Hospital, Department of Obstetrics and Gynecology, 81377 Munich, Germany.
| | - Xi Zhang
- LMU Munich, University Hospital, Department of Obstetrics and Gynecology, 81377 Munich, Germany.
- Tsinghua Berkeley Shenzhen Institute, Tsinghua University, Shenzhen 518055, China.
| | - Christina Kuhn
- LMU Munich, University Hospital, Department of Obstetrics and Gynecology, 81377 Munich, Germany.
| | - Stéphan Jalaguier
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, 34298 Montpellier, France.
- Université de Montpellier, 34000 Montpellier, France.
- Institut régional du Cancer de Montpellier, 34298 Montpellier, France.
| | - Jacques Colinge
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, 34298 Montpellier, France.
- Université de Montpellier, 34000 Montpellier, France.
- Institut régional du Cancer de Montpellier, 34298 Montpellier, France.
| | - Kristina Pfender
- LMU Munich, University Hospital, Department of Obstetrics and Gynecology, 81377 Munich, Germany.
| | - Doris Mayr
- LMU Munich, Department of Pathology, 80337 Munich, Germany.
| | - Nina Ditsch
- LMU Munich, University Hospital, Department of Obstetrics and Gynecology, 81377 Munich, Germany.
| | - Nadia Harbeck
- LMU Munich, University Hospital, Department of Obstetrics and Gynecology, 81377 Munich, Germany.
| | - Sven Mahner
- LMU Munich, University Hospital, Department of Obstetrics and Gynecology, 81377 Munich, Germany.
| | - Sophie Sixou
- LMU Munich, University Hospital, Department of Obstetrics and Gynecology, 81377 Munich, Germany.
- Faculté des Sciences Pharmaceutiques, Université Paul Sabatier Toulouse III, 31062 Toulouse CEDEX 09, France.
- Cholesterol Metabolism and Therapeutic Innovations, Cancer Research Center of Toulouse (CRCT), UMR 1037, Université de Toulouse, CNRS, Inserm, UPS, 31037 Toulouse, France.
| | - Vincent Cavaillès
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, 34298 Montpellier, France.
- Université de Montpellier, 34000 Montpellier, France.
- Institut régional du Cancer de Montpellier, 34298 Montpellier, France.
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43
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Gökmen-Polar Y, Neelamraju Y, Goswami CP, Gu Y, Gu X, Nallamothu G, Vieth E, Janga SC, Ryan M, Badve SS. Splicing factor ESRP1 controls ER-positive breast cancer by altering metabolic pathways. EMBO Rep 2019; 20:embr.201846078. [PMID: 30665944 DOI: 10.15252/embr.201846078] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 12/04/2018] [Accepted: 12/11/2018] [Indexed: 12/12/2022] Open
Abstract
The epithelial splicing regulatory proteins 1 and 2 (ESRP1 and ESRP2) control the epithelial-to-mesenchymal transition (EMT) splicing program in cancer. However, their role in breast cancer recurrence is unclear. In this study, we report that high levels of ESRP1, but not ESRP2, are associated with poor prognosis in estrogen receptor positive (ER+) breast tumors. Knockdown of ESRP1 in endocrine-resistant breast cancer models decreases growth significantly and alters the EMT splicing signature, which we confirm using TCGA SpliceSeq data of ER+ BRCA tumors. However, these changes are not accompanied by the development of a mesenchymal phenotype or a change in key EMT-transcription factors. In tamoxifen-resistant cells, knockdown of ESRP1 affects lipid metabolism and oxidoreductase processes, resulting in the decreased expression of fatty acid synthase (FASN), stearoyl-CoA desaturase 1 (SCD1), and phosphoglycerate dehydrogenase (PHGDH) at both the mRNA and protein levels. Furthermore, ESRP1 knockdown increases the basal respiration and spare respiration capacity. This study reports a novel role for ESRP1 that could form the basis for the prevention of tamoxifen resistance in ER+ breast cancer.
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Affiliation(s)
- Yesim Gökmen-Polar
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Yaseswini Neelamraju
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Chirayu P Goswami
- Department of Bioinformatics, Thomas Jefferson University Hospitals, Philadelphia, PA, USA
| | - Yuan Gu
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Xiaoping Gu
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Gouthami Nallamothu
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Edyta Vieth
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Sarath C Janga
- Department of BioHealth Informatics, School of Informatics and Computing, IUPUI, Indianapolis, IN, USA.,Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA.,Centre for Computational Biology and Bioinformatics Indiana University School of Medicine, Indianapolis, IN, USA
| | - Michael Ryan
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,In Silico Solutions, Falls Church, VA, USA
| | - Sunil S Badve
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA .,Indiana University Melvin and Bren Simon Cancer Center, Indianapolis, IN, USA.,Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
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44
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Jayanthi VSPKSA, Das AB, Saxena U. Fabrication of an immunosensor for quantitative detection of breast cancer biomarker UBE2C. RSC Adv 2019; 9:16738-16745. [PMID: 35516403 PMCID: PMC9064433 DOI: 10.1039/c8ra10245g] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 05/12/2019] [Indexed: 11/21/2022] Open
Abstract
Antibodies crosslinking on PANI modified electrode to design a highly selective immunosensor to detect UBE2C.
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Affiliation(s)
| | - Asim Bikas Das
- Department of Biotechnology
- National Institute of Technology Warangal
- Warangal-506004
- India
| | - Urmila Saxena
- Department of Biotechnology
- National Institute of Technology Warangal
- Warangal-506004
- India
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45
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Torres-Adorno AM, Vitrac H, Qi Y, Tan L, Levental KR, Fan YY, Yang P, Chapkin RS, Eckhardt BL, Ueno NT. Eicosapentaenoic acid in combination with EPHA2 inhibition shows efficacy in preclinical models of triple-negative breast cancer by disrupting cellular cholesterol efflux. Oncogene 2018; 38:2135-2150. [PMID: 30459358 PMCID: PMC6430703 DOI: 10.1038/s41388-018-0569-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 09/26/2018] [Accepted: 10/17/2018] [Indexed: 01/06/2023]
Abstract
Triple-negative breast cancer (TNBC), the most aggressive breast cancer subtype, currently lacks effective targeted therapy options. Eicosapentaenoic acid (EPA), an omega-3 fatty acid and constituent of fish oil, is a common supplement with anti-inflammatory properties. Although it is not a mainstream treatment, several preclinical studies have demonstrated that EPA exerts anti-tumor activity in breast cancer. However, against solid tumors, EPA as a monotherapy is clinically ineffective; thus, we sought to develop a novel targeted drug combination to bolster its therapeutic action against TNBC. Using a high-throughput functional siRNA screen, we identified Ephrin type-A receptor 2 (EPHA2), an oncogenic cell-surface receptor tyrosine kinase, as a therapeutic target that sensitizes TNBC cells to EPA. EPHA2 expression was uniquely elevated in TNBC cell lines and patient tumors. In independent functional expression studies in TNBC models, EPHA2 gene-silencing combined with EPA significantly reduced cell growth and enhanced apoptosis compared with monotherapies, both in vitro and in vivo. EPHA2 specific inhibitors similarly enhanced the therapeutic action of EPA. Finally, we identified that therapy-mediated apoptosis was attributed to a lethal increase in cancer cell membrane polarity due to ABCA1 inhibition and subsequent dysregulation of cholesterol homeostasis. This study provides new molecular and pre-clinical evidence to support a clinical evaluation of EPA combined with EPHA2 inhibition in patients with TNBC.
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Affiliation(s)
- Angie M Torres-Adorno
- The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA.,Section of Translational Breast Cancer Research and Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Heidi Vitrac
- Department of Biochemistry and Molecular Biology, UTHealth McGovern Medical School, Houston, TX, USA
| | - Yuan Qi
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lin Tan
- Department of Palliative, Rehabilitation and Integrative Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kandice R Levental
- Department of Integrative Biology and Pharmacology, UTHealth McGovern Medical School, Houston, TX, USA
| | - Yang-Yi Fan
- Program in Integrative Nutrition & Complex Diseases, Department of Nutrition and Food Science, Texas A&M University, College Station, TX, USA
| | - Peiying Yang
- Department of Palliative, Rehabilitation and Integrative Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Robert S Chapkin
- Program in Integrative Nutrition & Complex Diseases, Department of Nutrition and Food Science, Texas A&M University, College Station, TX, USA
| | - Bedrich L Eckhardt
- Section of Translational Breast Cancer Research and Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Naoto T Ueno
- Section of Translational Breast Cancer Research and Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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46
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Chen X, Miao Z, Divate M, Zhao Z, Cheung E. KM-express: an integrated online patient survival and gene expression analysis tool for the identification and functional characterization of prognostic markers in breast and prostate cancers. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2018; 2018:5051102. [PMID: 29992322 PMCID: PMC6041744 DOI: 10.1093/database/bay069] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 06/13/2018] [Indexed: 12/26/2022]
Abstract
The identification and functional characterization of novel biomarkers in cancer requires survival analysis and gene expression analysis of both patient samples and cell line models. To help facilitate this process, we have developed KM-Express. KM-Express holds an extensive manually curated transcriptomic profile of 45 different datasets for prostate and breast cancer with phenotype and pathoclinical information, spanning from clinical samples to cell lines. KM-Express also contains The Cancer Genome Atlas datasets for 30 other cancer types with matching cell line expression data for 23 of them. We present KM-Express as a hypothesis generation tool for researchers to identify potential new prognostic RNA biomarkers as well as targets for further downstream functional cell-based studies. Specifically, KM-Express allows users to compare the expression level of genes in different groups of patients based on molecular, genetic, clinical and pathological status. Moreover, KM-Express aids the design of biological experiments based on the expression profile of the genes in different cell lines. Thus, KM-Express provides a one-stop analysis from bench work to clinical prospects. We have used this tool to successfully evaluate the prognostic potential of previously published biomarkers for prostate cancer and breast cancer. We believe KM-Express will accelerate the translation of biomedical research from bench to bed. Database URL: http://ec2-52-201-246-161.compute-1.amazonaws.com/kmexpress/index.php
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Affiliation(s)
- Xin Chen
- Guangdong Key Laboratory of IoT Information Technology, School of Automation, Guangdong University of Technology, No. 100 Waihuan Xi Road, Guangzhou Higher Education Mega Center, Panyu District, Guangzhou 510006, PR China.,Faculty of Health Sciences (E12), University of Macau, Avenida da Universidade, Room 4045, Taipa, Macau, China
| | - Zhengqiang Miao
- Faculty of Health Sciences (E12), University of Macau, Avenida da Universidade, Room 4045, Taipa, Macau, China
| | - Mayur Divate
- Faculty of Health Sciences (E12), University of Macau, Avenida da Universidade, Room 4045, Taipa, Macau, China
| | - Zuxianglan Zhao
- Faculty of Health Sciences (E12), University of Macau, Avenida da Universidade, Room 4045, Taipa, Macau, China
| | - Edwin Cheung
- Faculty of Health Sciences (E12), University of Macau, Avenida da Universidade, Room 4045, Taipa, Macau, China
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Zhang H, Zhang Y, Chen C, Zhu X, Zhang C, Xia Y, Zhao Y, Andrisani OM, Kong L. A double-negative feedback loop between DEAD-box protein DDX21 and Snail regulates epithelial-mesenchymal transition and metastasis in breast cancer. Cancer Lett 2018; 437:67-78. [DOI: 10.1016/j.canlet.2018.08.021] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 08/21/2018] [Accepted: 08/22/2018] [Indexed: 01/19/2023]
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48
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Park J, Jang JH, Park GS, Chung Y, You HJ, Kim JH. BLT2, a leukotriene B4 receptor 2, as a novel prognostic biomarker of triple-negative breast cancer. BMB Rep 2018; 51:373-377. [PMID: 29898809 PMCID: PMC6130834 DOI: 10.5483/bmbrep.2018.51.8.127] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Indexed: 12/18/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is considered to be a notorious type of cancer due to its aggressive metastatic potential and poor prognosis. Recent evidence suggests that BLT2, a low-affinity LTB4 receptor is critically associated with the phenotypes of TNBC cells, including invasion, metastasis, and survival. Furthermore, in a group of 545 breast cancer patients with metastasis, we observed that the high-BLT2 subgroup had a lower disease-free-survival rate than the low-BLT2 subgroup. Thus, we theorized that anti-BLT2 strategies could facilitate the development of new therapies used for TNBC. This review focuses on recent discoveries regarding BLT2 and its roles in as a novel prognostic biomarker in TNBC.
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Affiliation(s)
- JaeIn Park
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Korea
| | - Jae-Hyun Jang
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Korea
| | - Geun-Soo Park
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Korea
| | - Yunro Chung
- Department of Biomedical Informatics, Arizona State University, Scottsdale, AZ 85259, USA
| | - Hye Jin You
- Translational Research Branch, Division of Translational Science, National Cancer Center, Goyang 10408, Korea
| | - Jae-Hong Kim
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Korea
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49
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TTK promotes mesenchymal signaling via multiple mechanisms in triple negative breast cancer. Oncogenesis 2018; 7:69. [PMID: 30206215 PMCID: PMC6133923 DOI: 10.1038/s41389-018-0077-z] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 05/16/2018] [Accepted: 06/15/2018] [Indexed: 02/06/2023] Open
Abstract
Abnormal expression of TTK kinase has been associated with the initiation, progression, and therapeutic resistance of breast and other cancers, but its roles remain to be clarified. In this study, we examined the role of TTK in triple negative breast cancer (TNBC), and found that higher TTK expression correlated with mesenchymal and proliferative phenotypes in TNBC cells. Pharmacologic inhibition and genomic silencing of TTK not only reversed the epithelial-to-mesenchymal transition (EMT) in TNBC cells, but also increased the expression of KLF5, an effector of TGF-β signaling and inhibitor of EMT. In addition, TTK inhibition decreased the expression of EMT-associated micro-RNA miR-21 but increased the expression of miR-200 family members and suppressed TGF-β signaling. To test if upregulation of KLF5 plays a role in TTK-induced EMT, TTK and KLF5 were silenced simultaneously, which reversed the decreased EMT caused by loss of TTK. Consistently, the decrease in miR-21 expression and increase in miR-200 expression caused by TTK silencing were rescued by loss of KLF5. Altogether, this study highlights a novel role and signaling pathway for TTK in regulating EMT of TN breast cancer cells through TGF-β and KLF5 signaling, highlighting targetable signaling pathways for TTK inhibitors in aggressive breast cancer.
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50
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Shinde A, Wilmanski T, Chen H, Teegarden D, Wendt MK. Pyruvate carboxylase supports the pulmonary tropism of metastatic breast cancer. Breast Cancer Res 2018; 20:76. [PMID: 30005601 PMCID: PMC6045837 DOI: 10.1186/s13058-018-1008-9] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 06/25/2018] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Overcoming systemic dormancy and initiating secondary tumor grow under unique microenvironmental conditions is a major rate-limiting step in metastatic progression. Disseminated tumor cells encounter major changes in nutrient supplies and oxidative stresses compared to the primary tumor and must demonstrate significant metabolic plasticity to adapt to specific metastatic sites. Recent studies suggest that differential utilization of pyruvate sits as a critical node in determining the organotropism of metastatic breast cancer. Pyruvate carboxylase (PC) is key enzyme that converts pyruvate into oxaloacetate for utilization in gluconeogenesis and replenishment of the TCA cycle. METHODS Patient survival was analyzed with respect to gene copy number alterations and differential mRNA expression levels of PC. Expression of PC was analyzed in the MCF-10A, D2-HAN and the 4 T1 breast cancer progression series under in vitro and in vivo growth conditions. PC expression was depleted via shRNAs and the impact on in vitro cell growth, mammary fat pad tumor growth, and pulmonary and non-pulmonary metastasis was assessed by bioluminescent imaging. Changes in glycolytic capacity, oxygen consumption, and response to oxidative stress were quantified upon PC depletion. RESULTS Genomic copy number increases in PC were observed in 16-30% of metastatic breast cancer patients. High expression of PC mRNA was associated with decreased patient survival in the MCTI and METABRIC patient datasets. Enhanced expression of PC was not recapitulated in breast cancer progression models when analyzed under glucose-rich in vitro culture conditions. In contrast, PC expression was dramatically enhanced upon glucose deprivation and in vivo in pulmonary metastases. Depletion of PC led to a dramatic decrease in 4 T1 pulmonary metastasis, but did not affect orthotopic primary tumor growth. Tail vein inoculations confirmed the role of PC in facilitating pulmonary, but not extrapulmonary tumor initiation. PC-depleted cells demonstrated a decrease in glycolytic capacity and oxygen consumption rates and an enhanced sensitivity to oxidative stress. CONCLUSIONS Our studies indicate that PC is specifically required for the growth of breast cancer that has disseminated to the lungs. Overall, these findings point to the potential of targeting PC for the treatment of pulmonary metastatic breast cancer.
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Affiliation(s)
- Aparna Shinde
- Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN, 47907, USA.,Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, 47907, USA
| | - Tomasz Wilmanski
- Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN, 47907, USA.,Department of Nutrition Science, West Lafayette, IN, 47907, USA
| | - Hao Chen
- Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN, 47907, USA.,Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, 47907, USA
| | - Dorothy Teegarden
- Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN, 47907, USA.,Department of Nutrition Science, West Lafayette, IN, 47907, USA
| | - Michael K Wendt
- Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN, 47907, USA. .,Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, 47907, USA.
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