1
|
Hou J, Liu W, Yan M, Ren Y, Qian C, Fu Y, Wang H, Li Z. Unveiling heterogeneity and prognostic markers in ductal breast cancer through single-cell RNA-seq. Cancer Cell Int 2024; 24:266. [PMID: 39068476 PMCID: PMC11282761 DOI: 10.1186/s12935-024-03325-1] [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: 11/01/2023] [Accepted: 04/10/2024] [Indexed: 07/30/2024] Open
Abstract
BACKGROUND Breast cancer (BC) is a heterogeneous disease, with the ductal subtype exhibiting significant cellular diversity that influences prognosis and response to treatment. Single-cell RNA sequencing data from the GEO database were utilized in this study to investigate the underlying mechanisms of cellular heterogeneity and to identify potential prognostic markers and therapeutic targets. METHODS Bioinformatics analysis was conducted using R packages to analyze the single-cell sequencing data. The presence of highly variable genes and differences in malignant potency within the same BC samples were examined. Differential gene expression and biological function between Type 1 and Type 2 ductal epithelial cells were identified. Lasso regression and Cox proportional hazards regression analyses were employed to identify genes associated with patient prognosis. Experimental validation was performed in vitro and in vivo to confirm the functional relevance of the identified genes. RESULTS The analysis revealed notable heterogeneity among BC cells, with the presence of highly variable genes and differences in malignant behavior within the same samples. Significant disparities in gene expression and biological function were identified between Type 1 and Type 2 ductal epithelial cells. Through regression analyses, CYP24A1 and TFPI2 were identified as pivotal genes associated with patient prognosis. Kaplan-Meier curves demonstrated their prognostic significance, and experimental validation confirmed their inhibitory effects on malignant behaviors of ductal BC cells. CONCLUSION This study highlights the cellular heterogeneity in ductal subtype breast cancer and delineates the differential gene expressions and biological functions between Type 1 and Type 2 ductal epithelial cells. The genes CYP24A1 and TFPI2 emerged as promising prognostic markers and therapeutic targets, exhibiting inhibitory effects on BC cell malignancy in vitro and in vivo. These findings offer the potential for improved BC management and the development of targeted treatment strategies.
Collapse
Affiliation(s)
- Jianxun Hou
- The Second Department of Breast Surgery, Harbin Medical University Cancer Hospital, No. 150, Haping Road, Nangang District, Harbin, Heilongjiang Province, 150081, P. R. China
| | - Wei Liu
- The Fourth Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, 150081, P. R. China
| | - Meihong Yan
- The Second Department of Breast Surgery, Harbin Medical University Cancer Hospital, No. 150, Haping Road, Nangang District, Harbin, Heilongjiang Province, 150081, P. R. China
| | - Yanlv Ren
- The Second Department of Breast Surgery, Harbin Medical University Cancer Hospital, No. 150, Haping Road, Nangang District, Harbin, Heilongjiang Province, 150081, P. R. China
| | - Cheng Qian
- The Second Department of Breast Surgery, Harbin Medical University Cancer Hospital, No. 150, Haping Road, Nangang District, Harbin, Heilongjiang Province, 150081, P. R. China
| | - Yingqiang Fu
- The Second Department of Breast Surgery, Harbin Medical University Cancer Hospital, No. 150, Haping Road, Nangang District, Harbin, Heilongjiang Province, 150081, P. R. China
| | - Hongbin Wang
- The Second Department of Breast Surgery, Harbin Medical University Cancer Hospital, No. 150, Haping Road, Nangang District, Harbin, Heilongjiang Province, 150081, P. R. China.
| | - Zhigao Li
- The Second Department of Breast Surgery, Harbin Medical University Cancer Hospital, No. 150, Haping Road, Nangang District, Harbin, Heilongjiang Province, 150081, P. R. China.
| |
Collapse
|
2
|
Périco LL, Vegso AJ, Baggio CH, MacNaughton WK. Protease-activated receptor 2 drives migration in a colon cancer cell line but not in noncancerous human epithelial cells. Am J Physiol Gastrointest Liver Physiol 2024; 326:G525-G542. [PMID: 38440826 DOI: 10.1152/ajpgi.00284.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 02/02/2024] [Accepted: 02/06/2024] [Indexed: 03/06/2024]
Abstract
The inflamed mucosa contains a complex assortment of proteases that may participate in wound healing or the development of inflammation-associated colon cancer. We sought to determine the role of protease-activated receptor 2 (PAR2) in epithelial wound healing in both untransformed and transformed colonic epithelial cells. Monolayers of primary epithelial cells derived from organoids cultivated from patient colonic biopsies and of the T84 colon cancer cell line were grown to confluence, wounded in the presence of a selective PAR2-activating peptide, and healing was visualized by live cell microscopy. Inhibitors of various signaling molecules were used to assess the relevant pathways responsible for wound healing. Activation of PAR2 induced an enhanced wound-healing response in T84 cells but not primary cells. The PAR2-enhanced wound-healing response was associated with the development of lamellipodia in cells at the wound edge, consistent with sheet migration. The response to PAR2 activation in T84 cells was completely dependent on Src kinase activity and partially dependent on Rac1 activity. The Src-associated signaling molecules, focal adhesion kinase, and epidermal growth factor receptor, which typically mediate wound-healing responses, were not involved in the PAR2 response. Experiments repeated in the presence of the inflammatory cytokines TNF and IFNγ revealed a synergistically enhanced PAR2 wound-healing response in T84s but not primary cells. The epithelial response to proteases may be different between primary and cancer cells and is accentuated in the presence of inflammatory cytokines. Our findings have implications for understanding epithelial restitution in the context of inflammatory bowel disease (IBD) and inflammation-associated colon cancer.NEW & NOTEWORTHY Protease-activated receptor 2 enhances wound healing in the T84 colon cancer cell line, but not in primary cells derived from patient biopsies, an effect that is synergistically enhanced in the presence of the inflammatory cytokines TNF and IFNγ.
Collapse
Affiliation(s)
- Larissa Lucena Périco
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Calvin, Phoebe and Joan Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Andrew J Vegso
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Calvin, Phoebe and Joan Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Cristiane H Baggio
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Calvin, Phoebe and Joan Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Wallace K MacNaughton
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Calvin, Phoebe and Joan Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| |
Collapse
|
3
|
Kempf CL, Sammani S, Bermudez T, Song JH, Hernon VR, Hufford MK, Burt J, Camp SM, Dudek SM, Garcia JG. Critical Role for the Lung Endothelial Non‐Muscle Myosin Light Chain Kinase Isoform in the Severity of Inflammatory Murine Lung Injury. Pulm Circ 2022; 12:e12061. [PMID: 35514774 PMCID: PMC9063969 DOI: 10.1002/pul2.12061] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 03/06/2022] [Accepted: 03/07/2022] [Indexed: 11/06/2022] Open
Affiliation(s)
- Carrie L. Kempf
- Department of Medicine University of Arizona Health Sciences Tucson AZ USA
| | - Saad Sammani
- Department of Medicine University of Arizona Health Sciences Tucson AZ USA
| | - Tadeo Bermudez
- Department of Medicine University of Arizona Health Sciences Tucson AZ USA
| | - Jin H. Song
- Department of Medicine University of Arizona Health Sciences Tucson AZ USA
| | | | - Matthew K. Hufford
- Department of Medicine University of Arizona Health Sciences Tucson AZ USA
| | - Jessica Burt
- Department of Medicine University of Arizona Health Sciences Tucson AZ USA
| | - Sara M. Camp
- Department of Medicine University of Arizona Health Sciences Tucson AZ USA
| | - Steven M. Dudek
- Department of Medicine University of Illinois at Chicago Chicago IL USA
| | - Joe G.N. Garcia
- Department of Medicine University of Arizona Health Sciences Tucson AZ USA
| |
Collapse
|
4
|
Wang S, Meng F, Liu Y, Xia S, Wang R. Exogenous inositol ameliorates the effects of acute ammonia toxicity on intestinal oxidative status, immune response, apoptosis, and tight junction barriers of great blue-spotted mudskippers (Boleophthalmus pectinirostris). Comp Biochem Physiol C Toxicol Pharmacol 2021; 240:108911. [PMID: 33075492 DOI: 10.1016/j.cbpc.2020.108911] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/22/2020] [Accepted: 09/27/2020] [Indexed: 01/12/2023]
Abstract
Ammonia toxicity can disrupt the intestinal health of aquatic animals. It is important to find substances that alleviate these adverse effects. The present study explored the possible protective role of myo-inositol (MI) in ammonia-induced toxicity in the fish intestine. Great blue-spotted mudskippers (Boleophthalmus pectinirostris) accumulated in artificial seawater (15‰ salinity, n = 600) were randomly selected and intraperitoneally injected with NaCl (0.68%) or MI (2.5 mg/g fish in 0.68% NaCl) then exposed to artificial seawater alone (NaCl and MI group) or seawater containing 57.025 mmol/L ammonium chloride (NH3 and NH3 + MI group). After a 24-h experiment, it showed that ammonia exposure down-regulated the mRNA expression levels of intestinal barrier function proteins (Zo-1, Ocln, Cldn-5, Cldn-12, and Cldn-15) and anti-inflammatory cytokines (Tgf-β and Il-10) while the acute ammonia stress up-regulated the apoptosis genes (p53, Bax, Caspase-3, and Caspase-9) and pro-inflammatory cytokines (Tnf-α and Il-1β). Furthermore, ammonia challenge also induced oxidative stress, as the malondialdehyde and the protein carbonyl contents were increased. In addition, ammonia stress down-regulated the antioxidant enzymes (Cu/Zn-Sod, Cat, Gpx, and Gst) activities as well as their gene transcription levels. The administration of the exogenous myo-inositol greatly ameliorated the ammonia-induced changes in redox capacity, immune response, apoptosis, inflammation, and tight junction barrier function to levels similar to those of the NaCl group. Furthermore, fish injected with MI alone showed no significant changes compared with the NaCl group. Taken together, pretreatment with myo-inositol had no obvious side-effects and effectively protected the mudskippers' intestine from the toxicity caused by acute ammonia stress.
Collapse
Affiliation(s)
- Shidong Wang
- School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Fanxing Meng
- School of Marine Sciences, Ningbo University, Ningbo 315211, China.
| | - Yang Liu
- School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Silei Xia
- School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Rixin Wang
- School of Marine Sciences, Ningbo University, Ningbo 315211, China.
| |
Collapse
|
5
|
Yin L, Zhao Y, Zhou XQ, Yang C, Feng L, Liu Y, Jiang WD, Wu P, Zhou J, Zhao J, Jiang J. Effect of dietary isoleucine on skin mucus barrier and epithelial physical barrier functions of hybrid bagrid catfish Pelteobagrus vachelli × Leiocassis longirostris. FISH PHYSIOLOGY AND BIOCHEMISTRY 2020; 46:1759-1774. [PMID: 32654084 DOI: 10.1007/s10695-020-00826-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 05/21/2020] [Indexed: 06/11/2023]
Abstract
The study investigated the effects of dietary isoleucine (Ile) on skin mucus barrier and epithelial physical barrier functions of hybrid bagrid catfish Pelteobagrus vachelli × Leiocassis longirostris. A total of 630 fish (33.11 ± 0.09 g) were fed semi-purified isonitrogenous diets containing 5.0 (control), 7.5, 10.0, 12.5, 15.0, 17.5, and 20.0 g Ile kg -1 diet for 8 weeks. The results indicated that dietary Ile increased (P < 0.05) in skin (1) mucus protein content and antimicrobial activity against three gram-negative bacteria (Aeromonas hydrophila, Escherichia coli, and Yersinia ruckeri) and two gram-positive bacteria (Streptococcus agalactiae and Staphylococcus aureus), (2) mucus lysofew information is available about the influencezyme (LZM), acid phosphatase (ACP), and alkaline phosphatase (AKP) activities, and complement 3 and 4 (C3 and C4) and immunoglobulin M (IgM) contents, (3) intelectin 1 (intl1), intelectin 2 (intl2), c-type-lysozyme (c-LZM), g-type-lysozyme (g-LZM), and β-defensin mRNA levels. Dietary Ile decreased (P < 0.05) reactive oxygen species (ROS), malondialdehyde (MDA), and protein carbonyl (PC) contents, and up-regulated (P < 0.05) CuZnSOD, GST, GPX1a, muc5ac, muc5b, zonula occludens-1 (ZO-1), zonula occludens-2 (ZO-2), occludin, and claudin 3 mRNA levels in skin. These results indicated that Ile improved skin mucus barrier function via increasing mucus protein, C3 and C4, and IgM contents and antibacterial factors activities, and promoted epithelial physical barrier function via decreasing skin antioxidant damage and improving tight junction structure in hybrid bagrid catfish.
Collapse
Affiliation(s)
- Long Yin
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ye Zhao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiao-Qiu Zhou
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, 611130, China
- Fish Nutrition and Safety Production University Key Laboratory of Sichuan Province, Sichuan Agricultural University, Ya'an, 625014, China
| | - Chao Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Lin Feng
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, 611130, China
- Fish Nutrition and Safety Production University Key Laboratory of Sichuan Province, Sichuan Agricultural University, Ya'an, 625014, China
| | - Yang Liu
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, 611130, China
- Fish Nutrition and Safety Production University Key Laboratory of Sichuan Province, Sichuan Agricultural University, Ya'an, 625014, China
| | - Wei-Dan Jiang
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, 611130, China
- Fish Nutrition and Safety Production University Key Laboratory of Sichuan Province, Sichuan Agricultural University, Ya'an, 625014, China
| | - Pei Wu
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, 611130, China
- Fish Nutrition and Safety Production University Key Laboratory of Sichuan Province, Sichuan Agricultural University, Ya'an, 625014, China
| | - Jian Zhou
- Fisheries Institute of Sichuan Academy of Agricultural Science, Chengdu, 611731, China
| | - Juan Zhao
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, 611130, China.
- Fish Nutrition and Safety Production University Key Laboratory of Sichuan Province, Sichuan Agricultural University, Ya'an, 625014, China.
| | - Jun Jiang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
- Animal Nutrition Institute, Sichuan Agricultural University, Chengdu, 611130, China.
- Fish Nutrition and Safety Production University Key Laboratory of Sichuan Province, Sichuan Agricultural University, Ya'an, 625014, China.
| |
Collapse
|
6
|
Myosin light chain kinase is a potential target for hypopharyngeal cancer treatment. Biomed Pharmacother 2020; 131:110665. [PMID: 32920510 PMCID: PMC8122670 DOI: 10.1016/j.biopha.2020.110665] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 08/08/2020] [Accepted: 08/20/2020] [Indexed: 02/07/2023] Open
Abstract
Hypopharyngeal cancer is squamous cell carcinoma (SCC) with the worst prognosis among the head and neck cancers. Overall, the 5-year survival rate remains poor although diagnostic imaging, radiation, chemotherapy, and surgical techniques have been improved. The mortality of patients with hypopharyngeal cancer is partly due to an increased likelihood of developing a second primary malignancy and metastasis. In this study, we found that MLCK expression, compared to healthy tissue, was up-regulated in hypopharyngeal tumor tissue. Of particular interest, a low 5-year survival rate was positively correlated with MLCK expression. We hypothesized that MLCK might be a target for hypopharyngeal cancer prognosis and treatment. In order to explore the function of MLCK in the development of cancer, we knockdown MLCK in hypopharyngeal cancer FaDu cells. The results showed that MLCK knockdown reduced the migration and invasion of FaDu cells. 4-amino-2-trifluoromethyl-phenyl retinate (ATPR) is the derivative of all-trans retinoic acid (ATRA), which was able to reduce both MLCK expression and activity in FaDu cells. ATPR induced FaDu cells apoptosis in a dose-dependent manner and also inhibited cell growth both in vivo and in vitro. Further experiments showed that overexpression of MLCK reduced ATPR induced-migration inhibition while increase of ATPR induced apoptosis, which suggested that MLCK was involved in ATPR's anti-cancer function. In conclusion, MLCK is a novel prognostic marker and therapeutic target for hypopharyngeal cancer. By targeting MLCK, ATPR exhibits its potential application in the treatment of this type of cancer.
Collapse
|
7
|
Ko EA, Lee H, Sanders KM, Koh SD, Zhou T. Expression of Alpha-type Platelet-derived Growth Factor Receptor-influenced Genes Predicts Clinical Outcome in Glioma. Transl Oncol 2019; 13:233-240. [PMID: 31869747 PMCID: PMC6933209 DOI: 10.1016/j.tranon.2019.10.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 10/04/2019] [Accepted: 10/07/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Alpha-type platelet-derived growth factor receptor (PDGFRα) is a cell surface tyrosine kinase receptor for members of the platelet-derived growth factor family. PDGFRα plays an important role in the regulation of several biological processes and contributes to the pathophysiology of a broad range of human cancers, including glioma. Here, we hypothesize that the genes directly or indirectly influenced by PDGFRα might be useful for prognosis in glioma. METHODS By comparing the genome-wide gene expression pattern between PDGFRα+ and PDGFRα- cells from human oligodendrocyte progenitor, we defined the genes potentially influenced by PDGFRα. RESULTS The PDGFRα-influenced genes are strongly associated with cancer-related pathways. We subsequently developed a prognostic gene signature derived from the PDGFRα-influenced genes. This gene signature is able to predict clinical outcome of glioma. This signature is also independent of traditional prognostic factors of glioma. Resampling tests indicate that the prognostic power of this gene signature outperforms random gene sets selected from human genome. More importantly, this signature is superior to the random gene signatures selected from glioma related genes. CONCLUSIONS Despite the absence of clear elucidation of molecular mechanisms, this study suggests the vital role of PDGFRα in carcinogenesis. Furthermore, the PDGFRα-based gene signature provides a promising prognostic tool for glioma and validates PDGFRα as a novel and effective therapeutic target in human cancers.
Collapse
Affiliation(s)
- Eun-A Ko
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA
| | - Haeyeong Lee
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA
| | - Kenton M Sanders
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA
| | - Sang Don Koh
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA.
| | - Tong Zhou
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA.
| |
Collapse
|
8
|
Lynn H, Sun X, Casanova N, Gonzales-Garay M, Bime C, Garcia JGN. Genomic and Genetic Approaches to Deciphering Acute Respiratory Distress Syndrome Risk and Mortality. Antioxid Redox Signal 2019; 31:1027-1052. [PMID: 31016989 PMCID: PMC6939590 DOI: 10.1089/ars.2018.7701] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Significance: Acute respiratory distress syndrome (ARDS) is a severe, highly heterogeneous critical illness with staggering mortality that is influenced by environmental factors, such as mechanical ventilation, and genetic factors. Significant unmet needs in ARDS are addressing the paucity of validated predictive biomarkers for ARDS risk and susceptibility that hamper the conduct of successful clinical trials in ARDS and the complete absence of novel disease-modifying therapeutic strategies. Recent Advances: The current ARDS definition relies on clinical characteristics that fail to capture the diversity of disease pathology, severity, and mortality risk. We undertook a comprehensive survey of the available ARDS literature to identify genes and genetic variants (candidate gene and limited genome-wide association study approaches) implicated in susceptibility to developing ARDS in hopes of uncovering novel biomarkers for ARDS risk and mortality and potentially novel therapeutic targets in ARDS. We further attempted to address the well-known health disparities that exist in susceptibility to and mortality from ARDS. Critical Issues: Bioinformatic analyses identified 201 ARDS candidate genes with pathway analysis indicating a strong predominance in key evolutionarily conserved inflammatory pathways, including reactive oxygen species, innate immunity-related inflammation, and endothelial vascular signaling pathways. Future Directions: Future studies employing a system biology approach that combines clinical characteristics, genomics, transcriptomics, and proteomics may allow for a better definition of biologically relevant pathways and genotype-phenotype connections and result in improved strategies for the sub-phenotyping of diverse ARDS patients via molecular signatures. These efforts should facilitate the potential for successful clinical trials in ARDS and yield a better fundamental understanding of ARDS pathobiology.
Collapse
Affiliation(s)
- Heather Lynn
- Department of Physiological Sciences and University of Arizona, Tucson, Arizona.,Department of Health Sciences, University of Arizona, Tucson, Arizona
| | - Xiaoguang Sun
- Department of Health Sciences, University of Arizona, Tucson, Arizona
| | - Nancy Casanova
- Department of Health Sciences, University of Arizona, Tucson, Arizona
| | | | - Christian Bime
- Department of Health Sciences, University of Arizona, Tucson, Arizona
| | - Joe G N Garcia
- Department of Health Sciences, University of Arizona, Tucson, Arizona
| |
Collapse
|
9
|
Gladilin E, Ohse S, Boerries M, Busch H, Xu C, Schneider M, Meister M, Eils R. TGFβ-induced cytoskeletal remodeling mediates elevation of cell stiffness and invasiveness in NSCLC. Sci Rep 2019; 9:7667. [PMID: 31113982 PMCID: PMC6529472 DOI: 10.1038/s41598-019-43409-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 01/25/2019] [Indexed: 02/07/2023] Open
Abstract
Importance of growth factor (GF) signaling in cancer progression is widely acknowledged. Transforming growth factor beta (TGFβ) is known to play a key role in epithelial-to-mesenchymal transition (EMT) and metastatic cell transformation that are characterized by alterations in cell mechanical architecture and behavior towards a more robust and motile single cell phenotype. However, mechanisms mediating cancer type specific enhancement of cell mechanical phenotype in response to TGFβ remain poorly understood. Here, we combine high-throughput mechanical cell phenotyping, microarray analysis and gene-silencing to dissect cytoskeletal mediators of TGFβ-induced changes in mechanical properties of on-small-cell lung carcinoma (NSCLC) cells. Our experimental results show that elevation of rigidity and invasiveness of TGFβ-stimulated NSCLC cells correlates with upregulation of several cytoskeletal and motor proteins including vimentin, a canonical marker of EMT, and less-known unconventional myosins. Selective probing of gene-silenced cells lead to identification of unconventional myosin MYH15 as a novel mediator of elevated cell rigidity and invasiveness in TGFβ-stimulated NSCLC cells. Our experimental results provide insights into TGFβ-induced cytoskeletal remodeling of NSCLC cells and suggest that mediators of elevated cell stiffness and migratory activity such as unconventional cytoskeletal and motor proteins may represent promising pharmaceutical targets for restraining invasive spread of lung cancer.
Collapse
Affiliation(s)
- E Gladilin
- German Cancer Research Center, Div. Bioinformatics and Omics Data Analytics, Mathematikon - Berliner Str. 41, 69120, Heidelberg, Germany. .,University Heidelberg, BioQuant, Im Neuenheimer Feld 267, 69120, Heidelberg, Germany. .,Leibniz Institute of Plant Genetics and Crop Plant Research, OT Gatersleben Corrensstrasse 3, 06466, Seeland, Germany.
| | - S Ohse
- University of Freiburg, Institute of Molecular Medicine and Cell Research (IMMZ), Stefan-Meier-Str. 17, 79104, Freiburg, Germany
| | - M Boerries
- University of Freiburg, Institute of Molecular Medicine and Cell Research (IMMZ), Stefan-Meier-Str. 17, 79104, Freiburg, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department for Biometry, Epidemiology and Medical Bioinformatics and Comprehensive Cancer Center Freiburg (CCCF), University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, Breisacherstrasse 153, 79110, Freiburg, Germany
| | - H Busch
- University of Freiburg, Institute of Molecular Medicine and Cell Research (IMMZ), Stefan-Meier-Str. 17, 79104, Freiburg, Germany.,University of Lübeck, Institute of Experimental Dermatology, Ratzeburger Allee 160, 23538, Lübeck, Germany
| | - C Xu
- Thoraxklinik at Heidelberg University Hospital, Amalienstr. 5, 69126, Heidelberg, Germany
| | - M Schneider
- Thoraxklinik at Heidelberg University Hospital, Amalienstr. 5, 69126, Heidelberg, Germany.,Translational Lung Research Center Heidelberg (TLRC-H), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
| | - M Meister
- Thoraxklinik at Heidelberg University Hospital, Amalienstr. 5, 69126, Heidelberg, Germany
| | - R Eils
- Center for Digital Health, Berlin Institute of Health, and Charité Universitätsmedizin Berlin, Kapelle-Ufer 2, 10117, Berlin, Germany.,Health Data Science Unit, Heidelberg University Hospital, Im Neuenheimer Feld 267, 69120, Heidelberg, Germany
| |
Collapse
|
10
|
Single nucleotide polymorphisms in the MYLKP1 pseudogene are associated with increased colon cancer risk in African Americans. PLoS One 2018; 13:e0200916. [PMID: 30161129 PMCID: PMC6116948 DOI: 10.1371/journal.pone.0200916] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 07/04/2018] [Indexed: 12/18/2022] Open
Abstract
INTRODUCTION Pseudogenes are paralogues of functional genes historically viewed as defunct due to either the lack of regulatory elements or the presence of frameshift mutations. Recent evidence, however, suggests that pseudogenes may regulate gene expression, although the functional role of pseudogenes remains largely unknown. We previously reported that MYLKP1, the pseudogene of MYLK that encodes myosin light chain kinase (MLCK), is highly expressed in lung and colon cancer cell lines and tissues but not in normal lung or colon. The MYLKP1 promoter is minimally active in normal bronchial epithelial cells but highly active in lung adenocarcinoma cells. In this study, we further validate MYLKP1 as an oncogene via elucidation of the functional role of MYLKP1 genetic variants in colon cancer risk. METHODS Proliferation and migration assays were performed in MYLKP1-transfected colon and lung cancer cell lines (H441, A549) and commercially-available normal lung and colon cells. Fourteen MYLKP1 SNPs (MAFs >0.01) residing within the 4 kb MYLKP1 promoter region, the core 1.4 kb of MYLKP1 gene, and a 4 kb enhancer region were selected and genotyped in a colorectal cancer cohort. MYLKP1 SNP influences on activity of MYLKP1 promoter (2kb) was assessed by dual luciferase reporter assay. RESULTS Cancer cell lines, H441 and A549, exhibited increased MYLKP1 expression, increased MYLKP1 luciferase promoter activity, increased proliferation and migration. Genotyping studies identified two MYLKP1 SNPs (rs12490683; rs12497343) that significantly increase risk of colon cancer in African Americans compared to African American controls. Rs12490683 and rs12497343 further increase MYLKP1 promoter activity compared to the wild type MYLKP1 promoter. CONCLUSION MYLKP1 is a cancer-promoting pseudogene whose genetic variants differentially enhance cancer risk in African American populations.
Collapse
|
11
|
Ko EA, Sanders KM, Zhou T. A transcriptomic insight into the impacts of mast cells in lung, breast, and colon cancers. Oncoimmunology 2017; 6:e1360457. [PMID: 29147625 DOI: 10.1080/2162402x.2017.1360457] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 07/20/2017] [Accepted: 07/21/2017] [Indexed: 01/09/2023] Open
Abstract
To date, the exact impact of mast cells in tumor microenvironment is still controversial because of inconsistency in observations regarding the relationship between mast cell infiltrates and cancer development and prognosis. The discrepancies in previous studies have motivated us to examine the roles of mast cells in cancer pathology from different perspectives. Here, we investigated the impact of mast cells on transcriptomic profiles in the tissue microenvironment. Mice carrying the W-sh mutation in c-kit (KitW-sh ) are deficient in mast cell production and were used to assess the influence of mast cells on gene expression. By examining the transcriptomic profile among wild-type mice, KitW-sh mice, and KitW-sh mice with mast cell engraftment, we identified a list of "mast cell-dependent genes," which are enriched for cancer-related pathways. Utilizing whole-genome gene expression data from both mouse models and human cancer patients, we demonstrated that the expression profile of the mast cell-dependent genes differs between tumor and normal tissues from lung, breast, and colon, respectively. Mast cell infiltration is potentially increased in tumors compared with normal tissues, suggesting that mast cells might participate in tumor development. Accordingly, a prognostic molecular signature was developed based on the mast cell-dependent genes, which predicted recurrence-free survival for human patients with lung, breast, and colon cancers, respectively. Our study provides a novel transcriptomic insight into the impact of mast cells in the tumor microenvironment, though further experimental investigation is needed to validate the exact role of individual mast cell-dependent genes in different cancers.
Collapse
Affiliation(s)
- Eun-A Ko
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, Nevada, USA
| | - Kenton M Sanders
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, Nevada, USA
| | - Tong Zhou
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, Nevada, USA
| |
Collapse
|
12
|
Zhou T, Casanova N, Pouladi N, Wang T, Lussier Y, Knox KS, Garcia JGN. Identification of Jak-STAT signaling involvement in sarcoidosis severity via a novel microRNA-regulated peripheral blood mononuclear cell gene signature. Sci Rep 2017; 7:4237. [PMID: 28652588 PMCID: PMC5484682 DOI: 10.1038/s41598-017-04109-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 05/10/2017] [Indexed: 11/28/2022] Open
Abstract
Sarcoidosis is a granulomatous lung disorder of unknown cause. The majority of individuals with sarcoidosis spontaneously achieve full remission (uncomplicated sarcoidosis), however, ~20% of sarcoidosis-affected individuals experience progressive lung disease or cardiac and nervous system involvement (complicated sarcoidosis). We investigated peripheral blood mononuclear cell (PBMC) microRNA and protein-coding gene expression data from healthy controls and patients with uncomplicated or complicated sarcoidosis. We identified 46 microRNAs and 1,559 genes that were differentially expressed across a continuum of sarcoidosis severity (healthy control → uncomplicated sarcoidosis → complicated sarcoidosis). A total of 19 microRNA-mRNA regulatory pairs were identified within these deregulated microRNAs and mRNAs, which consisted of 17 unique protein-coding genes yielding a 17-gene signature. Pathway analysis of the 17-gene signature revealed Jak-STAT signaling pathway as the most significantly represented pathway. A severity score was assigned to each patient based on the expression of the 17-gene signature and a significant increasing trend in the severity score was observed from healthy control, to uncomplicated sarcoidosis, and finally to complicated sarcoidosis. In addition, this microRNA-regulated gene signature differentiates sarcoidosis patients from healthy controls in independent validation cohorts. Our study suggests that PBMC gene expression is useful in diagnosis of sarcoidosis.
Collapse
Affiliation(s)
- Tong Zhou
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, 89557, USA
| | - Nancy Casanova
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, University of Arizona Health Sciences, Tucson, AZ, 78721, USA
| | - Nima Pouladi
- Center for Bioinformatics and Biostatistics, University of Arizona Health Sciences, Tucson, AZ, 78721, USA
| | - Ting Wang
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, University of Arizona Health Sciences, Tucson, AZ, 78721, USA
| | - Yves Lussier
- Center for Bioinformatics and Biostatistics, University of Arizona Health Sciences, Tucson, AZ, 78721, USA
| | - Kenneth S Knox
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, University of Arizona Health Sciences, Tucson, AZ, 78721, USA
| | - Joe G N Garcia
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, University of Arizona Health Sciences, Tucson, AZ, 78721, USA.
| |
Collapse
|
13
|
Xiong Y, Wang C, Shi L, Wang L, Zhou Z, Chen D, Wang J, Guo H. Myosin Light Chain Kinase: A Potential Target for Treatment of Inflammatory Diseases. Front Pharmacol 2017; 8:292. [PMID: 28588494 PMCID: PMC5440522 DOI: 10.3389/fphar.2017.00292] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Accepted: 05/08/2017] [Indexed: 01/30/2023] Open
Abstract
Myosin light chain kinase (MLCK) induces contraction of the perijunctional apical actomyosin ring in response to phosphorylation of the myosin light chain. Abnormal expression of MLCK has been observed in respiratory diseases, pancreatitis, cardiovascular diseases, cancer, and inflammatory bowel disease. The signaling pathways involved in MLCK activation and triggering of endothelial barrier dysfunction are discussed in this review. The pharmacological effects of regulating MLCK expression by inhibitors such as ML-9, ML-7, microbial products, naturally occurring products, and microRNAs are also discussed. The influence of MLCK in inflammatory diseases starts with endothelial barrier dysfunction. The effectiveness of anti-MLCK treatment may depend on alleviation of that primary pathological mechanism. This review summarizes evidence for the potential benefits of anti-MLCK agents in the treatment of inflammatory disease and the importance of avoiding treatment-related side effects, as MLCK is widely expressed in many different tissues.
Collapse
Affiliation(s)
- Yongjian Xiong
- Central Laboratory, The First Affiliated Hospital, Dalian Medical UniversityDalian, China
| | - Chenou Wang
- Laboratory Animal Center, Dalian Medical UniversityDalian, China
| | - Liqiang Shi
- Laboratory Animal Center, Dalian Medical UniversityDalian, China
| | - Liang Wang
- Laboratory Animal Center, Dalian Medical UniversityDalian, China
| | - Zijuan Zhou
- Laboratory Animal Center, Dalian Medical UniversityDalian, China
| | - Dapeng Chen
- Laboratory Animal Center, Dalian Medical UniversityDalian, China
| | - Jingyu Wang
- Laboratory Animal Center, Dalian Medical UniversityDalian, China
| | - Huishu Guo
- Central Laboratory, The First Affiliated Hospital, Dalian Medical UniversityDalian, China
| |
Collapse
|
14
|
Mok SRS, Mohan S, Grewal N, Elfant AB, Judge TA. A genetic database can be utilized to identify potential biomarkers for biphenotypic hepatocellular carcinoma-cholangiocarcinoma. J Gastrointest Oncol 2016; 7:570-9. [PMID: 27563447 DOI: 10.21037/jgo.2016.04.01] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Biphenotypic hepatocellular carcinoma-cholangiocarcinoma (HCC-CC) is an uncommon primary liver neoplasm. Due to limitations in radiologic imaging for the diagnosis of this condition, biopsy is a common method for diagnosis, which is invasive and holds potential complications. To identify alternative means for obtaining the diagnosis and assessing the prognosis of this condition, we evaluated biomarkers for biphenotypic HCC-CC using a genetic database. METHODS To evaluate the genetic associations with each variable we utilized GeneCards(®), The Human Gene Compendium (http://www.genecards.org). The results of our search were entered into the Pathway Interaction Database from the National Cancer Institute (PID-NCI) (http://pid.nci.nih.gov), to generate a biomolecule interaction map. RESULTS The results of our query yielded 690 genes for HCC, 98 genes for CC and 50 genes for HCC-CC. Genes depicted in this analysis demonstrate the role of hormonal regulation, embryonic development, cell surface adhesion, cytokeratin stability, mucin production, metalloproteinase regulation, Ras signaling, metabolism and apoptosis. Examples of previously described markers included hepatocyte growth factor (HGF), mesenchymal epithelial transition (MET) and Kirsten rat sarcoma viral oncogene homolog (KRAS). Novel markers included phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha (PIK3CA), GPC3, choline kinase alpha (CHKA), prostaglandin-endoperoxide synthase 2 (PTGS2), telomerase reverse transcriptase (TERT), myeloid cell leukemia 1 (MCL1) and N-acetyltransferase 2 (NAT2). CONCLUSIONS GeneCards is a useful research tool in the genetic analysis of low frequency malignancies. Utilizing this tool we identified several biomarkers are methods for diagnosing HCC-CC. Finally, utilizing these methods, HCC-CC was found to be predominantly a subtype of CC.
Collapse
Affiliation(s)
- Shaffer R S Mok
- Division of Gastroenterology and Liver Diseases, Department of Medicine, Cooper Medical School of Rowan University, MD Anderson Cancer Center at Cooper, Mount Laurel, NJ, USA
| | - Sachin Mohan
- Division of Gastroenterology and Liver Diseases, Department of Medicine, Cooper Medical School of Rowan University, MD Anderson Cancer Center at Cooper, Mount Laurel, NJ, USA
| | - Navjot Grewal
- Division of Gastroenterology and Liver Diseases, Department of Medicine, Cooper Medical School of Rowan University, MD Anderson Cancer Center at Cooper, Mount Laurel, NJ, USA
| | - Adam B Elfant
- Division of Gastroenterology and Liver Diseases, Department of Medicine, Cooper Medical School of Rowan University, MD Anderson Cancer Center at Cooper, Mount Laurel, NJ, USA
| | - Thomas A Judge
- Division of Gastroenterology and Liver Diseases, Department of Medicine, Cooper Medical School of Rowan University, MD Anderson Cancer Center at Cooper, Mount Laurel, NJ, USA
| |
Collapse
|
15
|
Bime C, Zhou T, Wang T, Slepian MJ, Garcia JGN, Hecker L. Reactive oxygen species-associated molecular signature predicts survival in patients with sepsis. Pulm Circ 2016; 6:196-201. [PMID: 27252846 DOI: 10.1086/685547] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Sepsis-related multiple organ dysfunction syndrome is a leading cause of death in intensive care units. There is overwhelming evidence that oxidative stress plays a significant role in the pathogenesis of sepsis-associated multiple organ failure; however, reactive oxygen species (ROS)-associated biomarkers and/or diagnostics that define mortality or predict survival in sepsis are lacking. Lung or peripheral blood gene expression analysis has gained increasing recognition as a potential prognostic and/or diagnostic tool. The objective of this study was to identify ROS-associated biomarkers predictive of survival in patients with sepsis. In-silico analyses of expression profiles allowed the identification of a 21-gene ROS-associated molecular signature that predicts survival in sepsis patients. Importantly, this signature performed well in a validation cohort consisting of sepsis patients aggregated from distinct patient populations recruited from different sites. Our signature outperforms randomly generated signatures of the same signature gene size. Our findings further validate the critical role of ROSs in the pathogenesis of sepsis and provide a novel gene signature that predicts survival in sepsis patients. These results also highlight the utility of peripheral blood molecular signatures as biomarkers for predicting mortality risk in patients with sepsis, which could facilitate the development of personalized therapies.
Collapse
Affiliation(s)
- Christian Bime
- Department of Medicine, University of Arizona, Tucson, Arizona, USA
| | - Tong Zhou
- Department of Medicine, University of Arizona, Tucson, Arizona, USA
| | - Ting Wang
- Department of Medicine, University of Arizona, Tucson, Arizona, USA
| | - Marvin J Slepian
- Department of Medicine, University of Arizona, Tucson, Arizona, USA; Department of Biomedical Engineering, University of Arizona, Tucson, Arizona, USA
| | - Joe G N Garcia
- Department of Medicine, University of Arizona, Tucson, Arizona, USA
| | - Louise Hecker
- Department of Medicine, University of Arizona, Tucson, Arizona, USA; Southern Arizona Veterans Administration Health Care System, Tucson, Arizona, USA
| |
Collapse
|
16
|
Qian Z, Lv J, Kelly GT, Wang H, Zhang X, Gu W, Yin X, Wang T, Zhou T. Expression of nuclear factor, erythroid 2-like 2-mediated genes differentiates tuberculosis. Tuberculosis (Edinb) 2016; 99:56-62. [PMID: 27450006 DOI: 10.1016/j.tube.2016.04.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 04/18/2016] [Accepted: 04/19/2016] [Indexed: 12/17/2022]
Abstract
During infection and host defense, nuclear factor, erythroid 2-like 2 (Nrf2) dependent signaling is an efficient antioxidant defensive mechanism used by host cells to control the destructive effects of reactive oxygen species. This allows for effective defense responses against microbes while minimizing oxidative injury to the host cell itself. As a central regulator of antioxidant genes, Nrf2 has gained great attention in its pivotal role in infection, especially in tuberculosis (TB), the top infectious disease killer worldwide. To elucidate the genes potentially regulated by Nrf2 in TB, we conducted a meta-analysis on published gene expression datasets. Firstly, we compared the global gene expression profiles between control and Nrf2-deficient human cells. The differentially expressed genes were deemed as "Nrf2-mediated genes". Next, the whole blood gene expression pattern of TB patients was compared with that of healthy controls, pneumonia patients, and lung cancer patients. We found that the genes deregulated in TB significantly overlap with the Nrf2-mediated genes. Based on the intersection of Nrf2-mediated and TB-regulated genes, we identified an Nrf2-mediated 17-gene signature, which reflects a cluster of gene ontology terms highly related to TB physiology. We demonstrated that the 17-gene signature can be used to distinguish TB patients from healthy controls and patients with latent TB infection, pneumonia, or lung cancer. Also, the Nrf2-mediated gene signature can be used as an indicator of the anti-TB therapeutic response. More importantly, we confirmed that the predictive power of the Nrf2-mediated 17-gene signature is significantly better than the random gene sets selected from the human transcriptome. Also, the 17-gene signature performs even better than the random gene signatures selected from TB-associated genes. Our study confirms the central role of Nrf2 in TB pathogenesis and provides a novel and useful diagnostic method to differentiate TB patients from other human subjects.
Collapse
Affiliation(s)
- Zhongqing Qian
- Key Laboratory of Anhui Province for Infection and Immunology, Bengbu Medical College, 2600 Donghai Avenue, Bengbu, Anhui, 233003, China.
| | - Jingzhu Lv
- Department of Biochemistry and Molecular Biology, Bengbu Medical College, 2600 Donghai Avenue, Bengbu, Anhui, 233003, China.
| | - Gabriel T Kelly
- Department of Medicine, The University of Arizona, 1656 East Mabel Street, Tucson, AZ, 85724, USA.
| | - Hongtao Wang
- Key Laboratory of Anhui Province for Infection and Immunology, Bengbu Medical College, 2600 Donghai Avenue, Bengbu, Anhui, 233003, China.
| | - Xiaojie Zhang
- Key Laboratory of Anhui Province for Infection and Immunology, Bengbu Medical College, 2600 Donghai Avenue, Bengbu, Anhui, 233003, China.
| | - Wanjun Gu
- Research Center for Learning Sciences, Southeast University, 2 Sipailou, Nanjing, Jiangsu, 210096, China.
| | - Xiaofeng Yin
- Department of Orthopedics and Trauma, Peking University People's Hospital, Beijing, 100044, China.
| | - Ting Wang
- Department of Medicine, The University of Arizona, 1656 East Mabel Street, Tucson, AZ, 85724, USA.
| | - Tong Zhou
- Department of Physiology and Cell Biology, The University of Nevada School of Medicine, Reno, NV, 89557, USA.
| |
Collapse
|
17
|
Qian Z, Zhou T, Gurguis CI, Xu X, Wen Q, Lv J, Fang F, Hecker L, Cress AE, Natarajan V, Jacobson JR, Zhang DD, Garcia JGN, Wang T. Nuclear factor, erythroid 2-like 2-associated molecular signature predicts lung cancer survival. Sci Rep 2015; 5:16889. [PMID: 26596768 PMCID: PMC4657037 DOI: 10.1038/srep16889] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 10/01/2015] [Indexed: 01/24/2023] Open
Abstract
Nuclear factor, erythroid 2-like 2 (NFE2L2), a transcription factor also known as NF-E2-related factor 2 (Nrf2), is a key cytoprotective gene that regulates critical antioxidant and stress-responsive genes. Nrf2 has been demonstrated to be a promising therapeutic target and useful biomarker in malignant disease. We hypothesized that NFE2L2-mediated gene expression would reflect cancer severity and progression. We conducted a meta-analysis of microarray data for 240 NFE2L2-mediated genes that were enriched in tumor tissues. We then developed a risk scoring system based on NFE2L2 gene expression profiling and designated 50 tumor-associated genes as the NFE2L2-associated molecular signature (NAMS). We tested the relationship between this gene expression signature and both recurrence-free survival and overall survival in lung cancer patients. We find that NAMS predicts clinical outcome in the training cohort and in 12 out of 20 validation cohorts. Cox proportional hazard regressions indicate that NAMS is a robust prognostic gene signature, independent of other clinical and pathological factors including patient age, gender, smoking, gene alteration, MYC level, and cancer stage. NAMS is an excellent predictor of recurrence-free survival and overall survival in human lung cancer. This gene signature represents a promising prognostic biomarker in human lung cancer.
Collapse
Affiliation(s)
- Zhongqing Qian
- Key Laboratory of Anhui Province for Infection and Immunology, Bengbu Medical College, Bengbu 233003, China.,Arizona Respiratory Center and Department of Medicine, The University of Arizona, Tucson, Arizona, USA
| | - Tong Zhou
- Arizona Respiratory Center and Department of Medicine, The University of Arizona, Tucson, Arizona, USA
| | - Christopher I Gurguis
- Arizona Respiratory Center and Department of Medicine, The University of Arizona, Tucson, Arizona, USA
| | - Xiaoyan Xu
- Arizona Respiratory Center and Department of Medicine, The University of Arizona, Tucson, Arizona, USA
| | - Qing Wen
- Department of Pharmacy, Jinan Central Hospital, Jinan, Shandong, China.,Department of Pharmacology and Toxicology, The University of Arizona, Tucson, Arizona, USA
| | - Jingzhu Lv
- Department of Biochemistry and Molecular Biology, Bengbu Medical College, Bengbu 233003, China
| | - Fang Fang
- Key Laboratory of Anhui Province for Infection and Immunology, Bengbu Medical College, Bengbu 233003, China
| | - Louise Hecker
- Arizona Respiratory Center and Department of Medicine, The University of Arizona, Tucson, Arizona, USA.,Southern Arizona VA Health Care System, Tucson, AZ 85723, USA
| | - Anne E Cress
- Arizona Cancer Center and Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ, USA
| | - Viswanathan Natarajan
- Department of Pharmacology, The University of Illinois at Chicago, Chicago, IL, USA.,Department of Medicine, The University of Illinois at Chicago, Chicago, IL, USA
| | - Jeffrey R Jacobson
- Department of Medicine, The University of Illinois at Chicago, Chicago, IL, USA
| | - Donna D Zhang
- Department of Pharmacology and Toxicology, The University of Arizona, Tucson, Arizona, USA
| | - Joe G N Garcia
- Arizona Respiratory Center and Department of Medicine, The University of Arizona, Tucson, Arizona, USA
| | - Ting Wang
- Arizona Respiratory Center and Department of Medicine, The University of Arizona, Tucson, Arizona, USA
| |
Collapse
|
18
|
Wang R, Gurguis CI, Gu W, Ko EA, Lim I, Bang H, Zhou T, Ko JH. Ion channel gene expression predicts survival in glioma patients. Sci Rep 2015; 5:11593. [PMID: 26235283 PMCID: PMC4522676 DOI: 10.1038/srep11593] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 05/28/2015] [Indexed: 12/12/2022] Open
Abstract
Ion channels are important regulators in cell proliferation, migration, and apoptosis. The malfunction and/or aberrant expression of ion channels may disrupt these important biological processes and influence cancer progression. In this study, we investigate the expression pattern of ion channel genes in glioma. We designate 18 ion channel genes that are differentially expressed in high-grade glioma as a prognostic molecular signature. This ion channel gene expression based signature predicts glioma outcome in three independent validation cohorts. Interestingly, 16 of these 18 genes were down-regulated in high-grade glioma. This signature is independent of traditional clinical, molecular, and histological factors. Resampling tests indicate that the prognostic power of the signature outperforms random gene sets selected from human genome in all the validation cohorts. More importantly, this signature performs better than the random gene signatures selected from glioma-associated genes in two out of three validation datasets. This study implicates ion channels in brain cancer, thus expanding on knowledge of their roles in other cancers. Individualized profiling of ion channel gene expression serves as a superior and independent prognostic tool for glioma patients.
Collapse
Affiliation(s)
- Rong Wang
- Department of Oncology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, China
| | | | - Wanjun Gu
- Research Center for Learning Sciences, Southeast University, Nanjing, Jiangsu 210096, China
| | - Eun A Ko
- Department of Pharmacology, University of Nevada School of Medicine, Reno, NV 89557, USA
| | - Inja Lim
- Department of Physiology, College of Medicine, Chung-Ang University, Seoul 156-756, South Korea
| | - Hyoweon Bang
- Department of Physiology, College of Medicine, Chung-Ang University, Seoul 156-756, South Korea
| | - Tong Zhou
- Department of Medicine, University of Arizona, Tucson, AZ 85721, USA
| | - Jae-Hong Ko
- Department of Physiology, College of Medicine, Chung-Ang University, Seoul 156-756, South Korea
| |
Collapse
|
19
|
Expression of tumor necrosis factor-alpha-mediated genes predicts recurrence-free survival in lung cancer. PLoS One 2014; 9:e115945. [PMID: 25548907 PMCID: PMC4280165 DOI: 10.1371/journal.pone.0115945] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 11/26/2014] [Indexed: 12/25/2022] Open
Abstract
In this study, we conducted a meta-analysis on high-throughput gene expression data to identify TNF-α-mediated genes implicated in lung cancer. We first investigated the gene expression profiles of two independent TNF-α/TNFR KO murine models. The EGF receptor signaling pathway was the top pathway associated with genes mediated by TNF-α. After matching the TNF-α-mediated mouse genes to their human orthologs, we compared the expression patterns of the TNF-α-mediated genes in normal and tumor lung tissues obtained from humans. Based on the TNF-α-mediated genes that were dysregulated in lung tumors, we developed a prognostic gene signature that effectively predicted recurrence-free survival in lung cancer in two validation cohorts. Resampling tests suggested that the prognostic power of the gene signature was not by chance, and multivariate analysis suggested that this gene signature was independent of the traditional clinical factors and enhanced the identification of lung cancer patients at greater risk for recurrence.
Collapse
|