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Ye Q, Raese R, Luo D, Cao S, Wan YW, Qian Y, Guo NL. MicroRNA, mRNA, and Proteomics Biomarkers and Therapeutic Targets for Improving Lung Cancer Treatment Outcomes. Cancers (Basel) 2023; 15:cancers15082294. [PMID: 37190222 DOI: 10.3390/cancers15082294] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 03/31/2023] [Accepted: 04/04/2023] [Indexed: 05/17/2023] Open
Abstract
The majority of lung cancer patients are diagnosed with metastatic disease. This study identified a set of 73 microRNAs (miRNAs) that classified lung cancer tumors from normal lung tissues with an overall accuracy of 96.3% in the training patient cohort (n = 109) and 91.7% in unsupervised classification and 92.3% in supervised classification in the validation set (n = 375). Based on association with patient survival (n = 1016), 10 miRNAs were identified as potential tumor suppressors (hsa-miR-144, hsa-miR-195, hsa-miR-223, hsa-miR-30a, hsa-miR-30b, hsa-miR-30d, hsa-miR-335, hsa-miR-363, hsa-miR-451, and hsa-miR-99a), and 4 were identified as potential oncogenes (hsa-miR-21, hsa-miR-31, hsa-miR-411, and hsa-miR-494) in lung cancer. Experimentally confirmed target genes were identified for the 73 diagnostic miRNAs, from which proliferation genes were selected from CRISPR-Cas9/RNA interference (RNAi) screening assays. Pansensitive and panresistant genes to 21 NCCN-recommended drugs with concordant mRNA and protein expression were identified. DGKE and WDR47 were found with significant associations with responses to both systemic therapies and radiotherapy in lung cancer. Based on our identified miRNA-regulated molecular machinery, an inhibitor of PDK1/Akt BX-912, an anthracycline antibiotic daunorubicin, and a multi-targeted protein kinase inhibitor midostaurin were discovered as potential repositioning drugs for treating lung cancer. These findings have implications for improving lung cancer diagnosis, optimizing treatment selection, and discovering new drug options for better patient outcomes.
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Affiliation(s)
- Qing Ye
- West Virginia University Cancer Institute, West Virginia University, Morgantown, WV 26506, USA
| | - Rebecca Raese
- West Virginia University Cancer Institute, West Virginia University, Morgantown, WV 26506, USA
| | - Dajie Luo
- West Virginia University Cancer Institute, West Virginia University, Morgantown, WV 26506, USA
| | - Shu Cao
- West Virginia University Cancer Institute, West Virginia University, Morgantown, WV 26506, USA
| | - Ying-Wooi Wan
- West Virginia University Cancer Institute, West Virginia University, Morgantown, WV 26506, USA
| | - Yong Qian
- Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV 26505, USA
| | - Nancy Lan Guo
- West Virginia University Cancer Institute, West Virginia University, Morgantown, WV 26506, USA
- Department of Occupational and Environmental Health Sciences, School of Public Health, West Virginia University, Morgantown, WV 26506, USA
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Snyder-Talkington BN, Dong C, Singh S, Raese R, Qian Y, Porter DW, Wolfarth MG, Guo NL. Multi-Walled Carbon Nanotube-Induced Gene Expression Biomarkers for Medical and Occupational Surveillance. Int J Mol Sci 2019; 20:E2635. [PMID: 31146342 PMCID: PMC6600433 DOI: 10.3390/ijms20112635] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 05/21/2019] [Accepted: 05/24/2019] [Indexed: 12/19/2022] Open
Abstract
As the demand for multi-walled carbon nanotube (MWCNT) incorporation into industrial and biomedical applications increases, so does the potential for unintentional pulmonary MWCNT exposure, particularly among workers during manufacturing. Pulmonary exposure to MWCNTs raises the potential for development of lung inflammation, fibrosis, and cancer among those exposed; however, there are currently no effective biomarkers for detecting lung fibrosis or predicting the risk of lung cancer resulting from MWCNT exposure. To uncover potential mRNAs and miRNAs that could be used as markers of exposure, this study compared in vivo mRNA and miRNA expression in lung tissue and blood of mice exposed to MWCNTs with in vitro mRNA and miRNA expression from a co-culture model of human lung epithelial and microvascular cells, a system previously shown to have a higher overall genome-scale correlation with mRNA expression in mouse lungs than either cell type grown separately. Concordant mRNAs and miRNAs identified by this study could be used to drive future studies confirming human biomarkers of MWCNT exposure. These potential biomarkers could be used to assess overall worker health and predict the occurrence of MWCNT-induced diseases.
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Affiliation(s)
| | - Chunlin Dong
- West Virginia University Cancer Institute, West Virginia University, Morgantown, WV 26506, USA.
| | - Salvi Singh
- West Virginia University Cancer Institute, West Virginia University, Morgantown, WV 26506, USA.
| | - Rebecca Raese
- West Virginia University Cancer Institute, West Virginia University, Morgantown, WV 26506, USA.
| | - Yong Qian
- National Institute for Occupational and Environmental Safety and Health, 1095 Willowdale Rd., Morgantown, WV 26505, USA.
| | - Dale W Porter
- National Institute for Occupational and Environmental Safety and Health, 1095 Willowdale Rd., Morgantown, WV 26505, USA.
| | - Michael G Wolfarth
- National Institute for Occupational and Environmental Safety and Health, 1095 Willowdale Rd., Morgantown, WV 26505, USA.
| | - Nancy L Guo
- West Virginia University Cancer Institute, West Virginia University, Morgantown, WV 26506, USA.
- Department of Occupational and Environmental Health Sciences, School of Public Health, West Virginia University, Morgantown, WV 26506, USA.
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Dymacek JM, Snyder-Talkington BN, Raese R, Dong C, Singh S, Porter DW, Ducatman B, Wolfarth MG, Andrew ME, Battelli L, Castranova V, Qian Y, Guo NL. Similar and Differential Canonical Pathways and Biological Processes Associated With Multiwalled Carbon Nanotube and Asbestos-Induced Pulmonary Fibrosis: A 1-Year Postexposure Study. Int J Toxicol 2018; 37:276-284. [PMID: 29916280 DOI: 10.1177/1091581818779038] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Respiratory exposure to multiwalled carbon nanotubes (MWCNT) or asbestos results in fibrosis; however, the mechanisms to reach this end point may be different. A previous study by our group identified pulmonary effects and significantly altered messenger RNA (mRNA) signaling pathways following exposure to 1, 10, 40, and 80 µg MWCNT and 120 µg crocidolite asbestos on mouse lungs over time at 1-month, 6-month, and 1-year postexposure following pulmonary aspiration. As a continuation to the above study, this current study took an in-depth look at the signaling pathways involved in fibrosis development at a single time point, 1 year, and exposure, 40 µg MWCNT, the lowest exposure at which fibrosis was pathologically evident. The 120 µg asbestos exposure was included to compare MWCNT-induced fibrosis with asbestos-induced fibrosis. A previously validated computational model was used to identify mRNAs with expression profiles matching the fibrosis pathology patterns from exposed mouse lungs. mRNAs that matched the pathology patterns were then input into ingenuity pathway analysis to determine potential signaling pathways and physiological disease functions inherent to MWCNT and asbestos exposure. Both MWCNT and asbestos exposure induced changes in mouse lungs regarding gene expression, cell proliferation, and survival, while MWCNT uniquely induced alterations in pathways involved in oxidative phosphorylation, mitochondrial dysfunction, and transcription. Asbestos exposure produced unique alterations in pathways involved in sustained inflammation. Although typically considered similar due to scale and fiber-like appearance, the different compositional properties inherent to either MWCNT or asbestos may play a role in their ability to induce fibrosis after pulmonary exposure.
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Affiliation(s)
- Julian M Dymacek
- 1 West Virginia University Cancer Institute, West Virginia University, Morgantown, WV, USA.,2 Department of Mathematics and Computer Science, Longwood University, Farmville, VA, USA
| | | | - Rebecca Raese
- 1 West Virginia University Cancer Institute, West Virginia University, Morgantown, WV, USA
| | - Chunlin Dong
- 1 West Virginia University Cancer Institute, West Virginia University, Morgantown, WV, USA
| | - Salvi Singh
- 1 West Virginia University Cancer Institute, West Virginia University, Morgantown, WV, USA
| | - Dale W Porter
- 3 National Institute of Occupational and Environmental Safety and Health, Morgantown, WV, USA
| | - Barbara Ducatman
- 1 West Virginia University Cancer Institute, West Virginia University, Morgantown, WV, USA.,4 Department of Pathology, West Virginia University, Morgantown, WV, USA
| | - Michael G Wolfarth
- 3 National Institute of Occupational and Environmental Safety and Health, Morgantown, WV, USA
| | - Michal E Andrew
- 3 National Institute of Occupational and Environmental Safety and Health, Morgantown, WV, USA
| | - Lori Battelli
- 3 National Institute of Occupational and Environmental Safety and Health, Morgantown, WV, USA
| | - Vincent Castranova
- 5 Department of Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, WV, USA
| | - Yong Qian
- 3 National Institute of Occupational and Environmental Safety and Health, Morgantown, WV, USA
| | - Nancy L Guo
- 1 West Virginia University Cancer Institute, West Virginia University, Morgantown, WV, USA.,6 Department of Occupational and Environmental Health Sciences, School of Public Health, West Virginia University, Morgantown, WV, USA
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Snyder-Talkington BN, Dong C, Porter DW, Ducatman B, Wolfarth MG, Andrew M, Battelli L, Raese R, Castranova V, Guo NL, Qian Y. Multiwalled carbon nanotube-induced pulmonary inflammatory and fibrotic responses and genomic changes following aspiration exposure in mice: A 1-year postexposure study. J Toxicol Environ Health A 2016; 79:352-66. [PMID: 27092743 PMCID: PMC4899319 DOI: 10.1080/15287394.2016.1159635] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 02/25/2016] [Indexed: 05/25/2023]
Abstract
Pulmonary exposure to multiwalled carbon nanotubes (MWCNT) induces an inflammatory and rapid fibrotic response, although the long-term signaling mechanisms are unknown. The aim of this study was to examine the effects of 1, 10, 40, or 80 μg MWCNT administered by pharyngeal aspiration on bronchoalveolar lavage (BAL) fluid for polymorphonuclear cell (PMN) infiltration, lactate dehydrogenase (LDH) activity, and lung histopathology for inflammatory and fibrotic responses in mouse lungs 1 mo, 6 mo, and 1 yr postexposure. Further, a 120-μg crocidolite asbestos group was incorporated as a positive control for comparative purposes. Results showed that MWCNT increased BAL fluid LDH activity and PMN infiltration in a dose-dependent manner at all three postexposure times. Asbestos exposure elevated LDH activity at all 3 postexposure times and PMN infiltration at 1 mo and 6 mo postexposure. Pathological changes in the lung, the presence of MWCNT or asbestos, and fibrosis were noted at 40 and 80 μg MWCNT and in asbestos-exposed mice at 1 yr postexposure. To determine potential signaling pathways involved with MWCNT-associated pathological changes in comparison to asbestos, up- and down-regulated gene expression was determined in lung tissue at 1 yr postexposure. Exposure to MWCNT tended to favor those pathways involved in immune responses, specifically T-cell responses, whereas exposure to asbestos tended to favor pathways involved in oxygen species production, electron transport, and cancer. Data indicate that MWCNT are biopersistent in the lung and induce inflammatory and fibrotic pathological alterations similar to those of crocidolite asbestos, but may reach these endpoints by different mechanisms.
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Affiliation(s)
- Brandi N. Snyder-Talkington
- Pathology and Physiology Research Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV 26505, USA
| | - Chunlin Dong
- Mary Babb Randolph Cancer Center, West Virginia University, Morgantown, WV 26506-9300, USA
| | - Dale W. Porter
- Pathology and Physiology Research Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV 26505, USA
| | - Barbara Ducatman
- Department of Pathology, West Virginia University, Morgantown, WV 26506, USA
| | - Michael G. Wolfarth
- Pathology and Physiology Research Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV 26505, USA
| | - Michael Andrew
- Pathology and Physiology Research Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV 26505, USA
| | - Lori Battelli
- Pathology and Physiology Research Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV 26505, USA
| | - Rebecca Raese
- Mary Babb Randolph Cancer Center, West Virginia University, Morgantown, WV 26506-9300, USA
| | - Vincent Castranova
- Department of Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, WV 26506, USA
| | - Nancy L. Guo
- Mary Babb Randolph Cancer Center, West Virginia University, Morgantown, WV 26506-9300, USA
| | - Yong Qian
- Pathology and Physiology Research Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV 26505, USA
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Snyder-Talkington BN, Dong C, Sargent LM, Porter DW, Staska LM, Hubbs AF, Raese R, McKinney W, Chen BT, Battelli L, Lowry DT, Reynolds SH, Castranova V, Qian Y, Guo NL. mRNAs and miRNAs in whole blood associated with lung hyperplasia, fibrosis, and bronchiolo-alveolar adenoma and adenocarcinoma after multi-walled carbon nanotube inhalation exposure in mice. J Appl Toxicol 2016; 36:161-74. [PMID: 25926378 PMCID: PMC4418205 DOI: 10.1002/jat.3157] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 03/02/2015] [Accepted: 03/03/2015] [Indexed: 12/28/2022]
Abstract
Inhalation exposure to multi-walled carbon nanotubes (MWCNT) in mice results in inflammation, fibrosis and the promotion of lung adenocarcinoma; however, the molecular basis behind these pathologies is unknown. This study determined global mRNA and miRNA profiles in whole blood from mice exposed by inhalation to MWCNT that correlated with the presence of lung hyperplasia, fibrosis, and bronchiolo-alveolar adenoma and adenocarcinoma. Six-week-old, male, B6C3F1 mice received a single intraperitoneal injection of either the DNA-damaging agent methylcholanthrene (MCA, 10 µg g(-1) body weight) or vehicle (corn oil). One week after injections, mice were exposed by inhalation to MWCNT (5 mg m(-3), 5 hours per day, 5 days per week) or filtered air (control) for a total of 15 days. At 17 months post-exposure, mice were euthanized and examined for the development of pathological changes in the lung, and whole blood was collected and analyzed using microarray analysis for global mRNA and miRNA expression. Numerous mRNAs and miRNAs in the blood were significantly up- or down-regulated in animals developing pathological changes in the lung after MCA/corn oil administration followed by MWCNT/air inhalation, including fcrl5 and miR-122-5p in the presence of hyperplasia, mthfd2 and miR-206-3p in the presence of fibrosis, fam178a and miR-130a-3p in the presence of bronchiolo-alveolar adenoma, and il7r and miR-210-3p in the presence of bronchiolo-alveolar adenocarcinoma, among others. The changes in miRNA and mRNA expression, and their respective regulatory networks, identified in this study may potentially serve as blood biomarkers for MWCNT-induced lung pathological changes.
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Affiliation(s)
- Brandi N. Snyder-Talkington
- Pathology and Physiology Research Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV 26505, USA
| | - Chunlin Dong
- Mary Babb Randolph Cancer Center, West Virginia University, Morgantown, WV 26506-9300, USA
| | - Linda M. Sargent
- Pathology and Physiology Research Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV 26505, USA
| | - Dale W. Porter
- Pathology and Physiology Research Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV 26505, USA
| | | | - Ann F. Hubbs
- Pathology and Physiology Research Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV 26505, USA
| | - Rebecca Raese
- Mary Babb Randolph Cancer Center, West Virginia University, Morgantown, WV 26506-9300, USA
| | - Walter McKinney
- Pathology and Physiology Research Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV 26505, USA
| | - Bean T. Chen
- Pathology and Physiology Research Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV 26505, USA
| | - Lori Battelli
- Pathology and Physiology Research Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV 26505, USA
| | - David T. Lowry
- Pathology and Physiology Research Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV 26505, USA
| | - Steven H. Reynolds
- Pathology and Physiology Research Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV 26505, USA
| | - Vincent Castranova
- Department of Basic Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, WV 26506, USA
| | - Yong Qian
- Pathology and Physiology Research Branch, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Morgantown, WV 26505, USA
| | - Nancy L. Guo
- Mary Babb Randolph Cancer Center, West Virginia University, Morgantown, WV 26506-9300, USA
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