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Liu Z, Georgakopoulos-Soares I, Ahituv N, Wong KC. Risk scoring based on DNA methylation-driven related DEGs for colorectal cancer prognosis with systematic insights. Life Sci 2023; 316:121413. [PMID: 36682524 DOI: 10.1016/j.lfs.2023.121413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 01/13/2023] [Accepted: 01/16/2023] [Indexed: 01/22/2023]
Abstract
Colorectal cancer is a common malignant tumor of the digestive tract. Despite advances in diagnostic techniques and medications. Its prognosis remains challenging. DNA methylation-driven related circulating tumor cells have attracted enormous interest in diagnosing owing to their non-invasive nature and early recognition properties. However, the mechanism through which risk biomarkers act remains elusive. Here, we designed a risk model based on differentially expressed genes, DNA methylation, robust, and survival-related factors in the framework of Cox regression. The model has satisfactory performance and is independently verified by an external and isolated dataset in terms of C-index value, ROC, and tROC. The model was applied to Colorectal cancer patients who were subsequently divided into high- and low-risk groups. Functional annotations, genomic alterations, tumor immune environment, and drug sensitivity were analyzed. We observed that up-regulated genes are associated with epithelial cell differentiation and MAPK signaling pathways. The down-regulated genes are related to IL-7 signaling and apoptosis-induced DNA fragmentation. Interestingly, the immune system was inhibited in high-risk groups. High-frequency mutation genes tend to co-occur. High-risk score patients are related to copy number amplification events. To address the challenges, we suggested eleven and twenty-one drugs that are sensitive to low- and high-risk patients. Finally, an artificial neural network was provided to evaluate the immunotherapeutic efficiency. Taken together, the findings demonstrated that our risk score model is robust and reliable for evaluating the prognosis with novel diagnostic and treatment targets. It also yields benefits for the treatment and provides unique insights into developing therapeutic strategies.
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Affiliation(s)
- Zhe Liu
- Department of Computer Science, City University of Hong Kong, Hong Kong, China
| | - Ilias Georgakopoulos-Soares
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA; Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA; Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA; Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
| | - Ka-Chun Wong
- Department of Computer Science, City University of Hong Kong, Hong Kong, China.
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2
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Zhao X, Qi Y, Wu T, Cheng G. Phosphoproteomic Analysis of the Jejunum Tissue Response to Colostrum and Milk Feeding in Dairy Calves during the Passive Immunity Period. Animals (Basel) 2022; 13:ani13010145. [PMID: 36611753 PMCID: PMC9817995 DOI: 10.3390/ani13010145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 12/21/2022] [Accepted: 12/28/2022] [Indexed: 12/31/2022] Open
Abstract
Improvements in the feeding of calves are of increasing importance for the development of the dairy industry. While colostrum is essential for the health of newborn calves, knowledge of protein phosphorylation alterations in neonatal calves that are fed colostrum or mature milk is lacking. Here, mid-jejunum tissue samples were collected from calves that received colostrum or milk. Subsequently, the jejunum phosphoproteome was analyzed using a phosphopeptide enrichment method, i.e., titanium immobilized metal ion affinity chromatography, coupled with liquid chromatography-tandem mass spectrometry. A total of 2093 phosphopeptides carrying unique 1851 phosphorylation sites corresponding to 1180 phosphoproteins were identified. Of the 1180 phosphoproteins, 314 phosphorylation sites on 241 proteins were differentially expressed between the groups. Gene ontology analysis indicated that the phosphoproteins were strongly associated with developmental and macromolecule metabolic processes, signal transduction, and responses to stimuli and insulin. Pathway analysis showed that the spliceosome, Hippo, insulin, and neurotrophin signaling pathways were enriched. These results reveal the expression pattern and changes in the function of phosphoproteins in bovine jejunum tissues under different feeding conditions and provide further insights into the crucial role of colostrum feeding during the early stages of life.
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Affiliation(s)
- Xiaowei Zhao
- Correspondence: ; Tel.: +86-551-65146065; Fax: +86-551-62160275
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3
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Zhao XW, Zhu HL, Qi YX, Wu T, Huang DW, Cheng GL, Yang YX, Bu DP, Hu H, Meng LF. Regulatory role of phosphoproteins in the development of bovine small intestine during early life. J Dairy Sci 2022; 105:9240-9252. [PMID: 36175223 DOI: 10.3168/jds.2022-21983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 06/20/2022] [Indexed: 11/19/2022]
Abstract
The small intestine is the primary site of nutrient digestion and absorption, which plays a key role in the survival of neonatal calves. A comprehensive assessment of the phosphoproteomic changes in the small intestine of neonatal calves is unavailable; therefore, we used phosphopeptide enrichment coupled with liquid chromatography-tandem mass spectrometry to investigate the changes in the phosphoproteome profile in the bovine small intestine during the first 36 h of life. Twelve neonatal male calves were assigned to one of the following groups: (1) calves not fed colostrum and slaughtered approximately 2 h postpartum (n = 3), (2) calves fed colostrum at 1 to 2 h and slaughtered 8 h postpartum (n = 3), (3) calves fed 2 colostrum meals (at 1-2 and 10-12 h) and slaughtered 24 h postpartum (n = 3), (4) calves fed 3 colostrum meals (at 1-2, 10-12, and 22-24 h) and slaughtered 36 h postpartum (n = 3). Mid-duodenal, jejunal, and ileal samples of the calves were collected after slaughter. We identified 1,678 phosphoproteins with approximately 3,080 phosphosites, which were mainly Ser (89.9%), Thr (9.8%), and Tyr (0.3%) residues; they belonged to the prodirected (52.9%), basic (20.4%), acidic (16.6%), and Tyr-directed (1.7%) motif categories. The regional differentially expressed phosphoproteins included zonula occludens 2, sorting nexin 12, and protein kinase C, which are mainly associated with developmental processes, intracellular transport, vesicle-mediated transport, and immune system process. They are enriched in the endocytosis, tight junction, insulin signaling, and focal adhesion pathways. The temporal differentially expressed phosphoproteins included occludin, epsin 1, and bridging integrator 1, which were mainly associated with macromolecule metabolic process, cell adhesion, and growth. They were enriched in the spliceosomes, adherens junctions, and tight junctions. The observed changes in the phosphoproteins in the tissues of small intestine suggest the protein phosphorylation plays an important role in nutrient transport and immune response of calves during early life, which needs to be confirmed in a larger study.
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Affiliation(s)
- X W Zhao
- Anhui Key Laboratory of Animal and Poultry Product Safety Engineering, Institute of Animal Science and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - H L Zhu
- Anhui Key Laboratory of Animal and Poultry Product Safety Engineering, Institute of Animal Science and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Y X Qi
- Anhui Key Laboratory of Animal and Poultry Product Safety Engineering, Institute of Animal Science and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - T Wu
- Anhui Key Laboratory of Animal and Poultry Product Safety Engineering, Institute of Animal Science and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - D W Huang
- Anhui Key Laboratory of Animal and Poultry Product Safety Engineering, Institute of Animal Science and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - G L Cheng
- Anhui Key Laboratory of Animal and Poultry Product Safety Engineering, Institute of Animal Science and Veterinary Medicine, Anhui Academy of Agricultural Sciences, Hefei 230031, China
| | - Y X Yang
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China.
| | - D P Bu
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - H Hu
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, China
| | - L F Meng
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, China
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Systematic Analysis of Genetic and Pathway Determinants of Eribulin Sensitivity across 100 Human Cancer Cell Lines from the Cancer Cell Line Encyclopedia (CCLE). Cancers (Basel) 2022; 14:cancers14184532. [PMID: 36139690 PMCID: PMC9496846 DOI: 10.3390/cancers14184532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/09/2022] [Accepted: 09/13/2022] [Indexed: 11/17/2022] Open
Abstract
Eribulin, a natural product-based microtubule targeting agent with cytotoxic and noncytotoxic mechanisms, is FDA approved for certain patients with advanced breast cancer and liposarcoma. To investigate the feasibility of developing drug-specific predictive biomarkers, we quantified antiproliferative activities of eribulin versus paclitaxel and vinorelbine against 100 human cancer cell lines from the Cancer Cell Line Encyclopedia, and correlated results with publicly available databases to identify genes and pathways associated with eribulin response, either uniquely or shared with paclitaxel or vinorelbine. Mean expression ratios of 11,985 genes between the most and least sensitive cell line quartiles were sorted by p-values and drug overlaps, yielding 52, 29 and 80 genes uniquely associated with eribulin, paclitaxel and vinorelbine, respectively. Further restriction to minimum 2-fold ratios followed by reintroducing data from the middle two quartiles identified 9 and 13 drug-specific unique fingerprint genes for eribulin and vinorelbine, respectively; surprisingly, no gene met all criteria for paclitaxel. Interactome and Reactome pathway analyses showed that unique fingerprint genes of both drugs were primarily associated with cellular signaling, not microtubule-related pathways, although considerable differences existed in individual pathways identified. Finally, four-gene (C5ORF38, DAAM1, IRX2, CD70) and five-gene (EPHA2, NGEF, SEPTIN10, TRIP10, VSIG10) multivariate regression models for eribulin and vinorelbine showed high statistical correlation with drug-specific responses across the 100 cell lines and accurately calculated predicted mean IC50s for the most and least sensitive cell line quartiles as surrogates for responders and nonresponders, respectively. Collectively, these results provide a foundation for developing drug-specific predictive biomarkers for eribulin and vinorelbine.
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Environmental Exposures and Lung Aging: Molecular Mechanisms and Implications for Improving Respiratory Health. Curr Environ Health Rep 2021; 8:281-293. [PMID: 34735706 PMCID: PMC8567983 DOI: 10.1007/s40572-021-00328-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
PURPOSE OF REVIEW Inhaled environmental exposures cause over 12 million deaths per year worldwide. Despite localized efforts to reduce environmental exposures, tobacco smoking and air pollution remain the urgent public health challenges that are contributing to the growing prevalence of respiratory diseases. The purpose of this review is to describe the mechanisms through which inhaled environmental exposures accelerate lung aging and cause overt lung disease. RECENT FINDINGS Environmental exposures related to fossil fuel and tobacco combustion and occupational exposures related to silica and coal mining generate oxidative stress and inflammation in the lungs. Sustained oxidative stress causes DNA damage, epigenetic instability, mitochondrial dysfunction, and cell cycle arrest in key progenitor cells in the lung. As a result, critical repair mechanisms are impaired, leading to premature destruction of the lung parenchyma. Inhaled environmental exposures accelerate lung aging by injuring the lungs and damaging the cells responsible for wound healing. Interventions that minimize exposure to noxious antigens are critical to improve lung health, and novel research is required to expand our knowledge of therapies that may slow or prevent premature lung aging.
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Low expression of CIP4 in predicting worse overall survival: A potential biomarker for laryngeal cancer. PLoS One 2021; 16:e0253545. [PMID: 34570775 PMCID: PMC8475988 DOI: 10.1371/journal.pone.0253545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 06/07/2021] [Indexed: 12/24/2022] Open
Abstract
Previous reports indicate that Cdc42-interacting protein-4 (CIP4) has previously been reported to plays an important role in the progression of various cancers. However, its correlation with laryngeal cancer (LC) remains unreported. Data from TCGA and GEO databases were used to evaluate the role of CIP4 in LC. Based on GEO and TCGA datasets, we analyzed the differences in CIP4 expression between normal and tumor samples. The Wilcoxon signed-rank test was used to analyze the relationship between clinical features and CIP4. Cox regression and the Kaplan-Meier analyses were used to identify the clinical characteristics associated with the overall survival. Also, the GEPIA database was used to confirm the relationship between CIP4 and overall survival. Lastly, Gene Set Enrichment Analysis (GSEA) was performed based on the TCGA dataset. CIP4 expression in LC was significantly associated with gender and tumor stage (p-values<0.05). Similar to GEPIA validation, Kaplan-Meier survival analysis demonstrated that LC with CIP4-low exhibited a worse prognosis than that with CIP4-high. Univariate analysis revealed that CIP4-high significantly correlated with better overall survival (HR: 0.522, 95% CI: 0.293–0.830, P = 0.026). Besides, multivariate analysis revealed that CIP4 remained independently associated with the overall survival (HR: 0.61, 95% CI: 0.326–0.912, P = 0.012). GSEA showed that the p53, WNT signaling, TGF-β signaling pathways, etc. were enriched in a phenotype high CIP4 expression. In summary, the CIP4 gene is a potential prognostic molecular marker for patients diagnosed with laryngeal cancer. Moreover, the p53, WNT signaling, and TGF-β signaling pathways are potentially associated with CIP4 in LC.
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7
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Seefelder M, Kochanek S. A meta-analysis of transcriptomic profiles of Huntington's disease patients. PLoS One 2021; 16:e0253037. [PMID: 34111223 PMCID: PMC8191979 DOI: 10.1371/journal.pone.0253037] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 05/27/2021] [Indexed: 12/22/2022] Open
Abstract
Description of robust transcriptomic alterations in Huntington’s disease is essential to identify targets for biochemical studies and drug development. We analysed publicly available transcriptome data from the brain and blood of 220 HD patients and 241 healthy controls and identified 737 and 661 genes with robustly altered mRNA levels in the brain and blood of HD patients, respectively. In the brain, a subnetwork of 320 genes strongly correlated with HD and was enriched in transport-related genes. Bioinformatical analysis of this subnetwork highlighted CDC42, PAK1, YWHAH, NFY, DLX1, HMGN3, and PRMT3. Moreover, we found that CREB1 can regulate 78.0% of genes whose mRNA levels correlated with HD in the blood of patients. Alterations in protein transport, metabolism, transcriptional regulation, and CDC42-mediated functions are likely central features of HD. Further our data substantiate the role of transcriptional regulators that have not been reported in the context of HD (e.g. DLX1, HMGN3 and PRMT3) and strongly suggest dysregulation of NFY and its target genes across tissues. A large proportion of the identified genes such as CDC42 were also altered in Parkinson’s (PD) and Alzheimer’s disease (AD). The observed dysregulation of CDC42 and YWHAH in samples from HD, AD and PD patients indicates that those genes and their upstream regulators may be interesting therapeutic targets.
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Affiliation(s)
- Manuel Seefelder
- Department of Gene Therapy, Ulm University, Ulm, Germany
- * E-mail:
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8
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Venkat S, Tisdale AA, Schwarz JR, Alahmari AA, Maurer HC, Olive KP, Eng KH, Feigin ME. Alternative polyadenylation drives oncogenic gene expression in pancreatic ductal adenocarcinoma. Genome Res 2020; 30:347-360. [PMID: 32029502 PMCID: PMC7111527 DOI: 10.1101/gr.257550.119] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 02/04/2020] [Indexed: 01/08/2023]
Abstract
Alternative polyadenylation (APA) is a gene regulatory process that dictates mRNA 3'-UTR length, resulting in changes in mRNA stability and localization. APA is frequently disrupted in cancer and promotes tumorigenesis through altered expression of oncogenes and tumor suppressors. Pan-cancer analyses have revealed common APA events across the tumor landscape; however, little is known about tumor type-specific alterations that may uncover novel events and vulnerabilities. Here, we integrate RNA-sequencing data from the Genotype-Tissue Expression (GTEx) project and The Cancer Genome Atlas (TCGA) to comprehensively analyze APA events in 148 pancreatic ductal adenocarcinomas (PDACs). We report widespread, recurrent, and functionally relevant 3'-UTR alterations associated with gene expression changes of known and newly identified PDAC growth-promoting genes and experimentally validate the effects of these APA events on protein expression. We find enrichment for APA events in genes associated with known PDAC pathways, loss of tumor-suppressive miRNA binding sites, and increased heterogeneity in 3'-UTR forms of metabolic genes. Survival analyses reveal a subset of 3'-UTR alterations that independently characterize a poor prognostic cohort among PDAC patients. Finally, we identify and validate the casein kinase CSNK1A1 (also known as CK1alpha or CK1a) as an APA-regulated therapeutic target in PDAC. Knockdown or pharmacological inhibition of CSNK1A1 attenuates PDAC cell proliferation and clonogenic growth. Our single-cancer analysis reveals APA as an underappreciated driver of protumorigenic gene expression in PDAC via the loss of miRNA regulation.
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Affiliation(s)
- Swati Venkat
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14263, USA
| | - Arwen A Tisdale
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14263, USA
| | - Johann R Schwarz
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14263, USA
| | - Abdulrahman A Alahmari
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14263, USA
| | - H Carlo Maurer
- Klinikum rechts der Isar, II. Medizinische Klinik, Technische Universität München, 81675 Munich, Germany
| | - Kenneth P Olive
- Herbert Irving Comprehensive Cancer Center, Department of Medicine, Division of Digestive and Liver Diseases, Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York 10032, USA
| | - Kevin H Eng
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14263, USA
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14263, USA
| | - Michael E Feigin
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, New York 14263, USA
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Wu X, Huang Q, Javed R, Zhong J, Gao H, Liang H. Effect of tobacco smoking on the epigenetic age of human respiratory organs. Clin Epigenetics 2019; 11:183. [PMID: 31801625 PMCID: PMC6894291 DOI: 10.1186/s13148-019-0777-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 11/12/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Smoking leads to the aging of organs. However, no studies have been conducted to quantify the effect of smoking on the aging of respiratory organs and the aging-reversing ability of smoking cessation. RESULTS We collected genome-wide methylation datasets of buccal cells, airway cells, esophagus tissue, and lung tissue from non-smokers, smokers, and ex-smokers. We used the "epigenetic clock" method to quantify the epigenetic age acceleration in the four organs. The statistical analyses showed the following: (1) Smoking increased the epigenetic age of airway cells by an average of 4.9 years and lung tissue by 4.3 years. (2) After smoking ceased, the epigenetic age acceleration in airway cells (but not in lung tissue) slowed to a level that non-smokers had. (3) The epigenetic age acceleration in airway cells and lung tissue showed no gender difference. CONCLUSIONS Smoking can accelerate the epigenetic age of human respiratory organs, but the effect varies among organs and can be reversed by smoking cessation. Our study provides a powerful incentive to reduce tobacco consumption autonomously.
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Affiliation(s)
- Xiaohui Wu
- Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, No. 9 Jinsui Road, Guangzhou, 510623, Guangdong, China.,Department of Medical Genetics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China.,Guangdong Technology and Engineering Research Center for Molecular Diagnostics of Human Genetic Diseases, Guangzhou, Guangdong, China.,Guangdong Province Key Laboratory of Psychiatric Disorders, Guangzhou, Guangdong, China
| | - Qingsheng Huang
- Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, No. 9 Jinsui Road, Guangzhou, 510623, Guangdong, China
| | - Ruheena Javed
- Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, No. 9 Jinsui Road, Guangzhou, 510623, Guangdong, China
| | - Jiayong Zhong
- Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, No. 9 Jinsui Road, Guangzhou, 510623, Guangdong, China
| | - Huan Gao
- Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, No. 9 Jinsui Road, Guangzhou, 510623, Guangdong, China
| | - Huiying Liang
- Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, No. 9 Jinsui Road, Guangzhou, 510623, Guangdong, China.
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Pineda B, Diaz-Lagares A, Pérez-Fidalgo JA, Burgués O, González-Barrallo I, Crujeiras AB, Sandoval J, Esteller M, Lluch A, Eroles P. A two-gene epigenetic signature for the prediction of response to neoadjuvant chemotherapy in triple-negative breast cancer patients. Clin Epigenetics 2019; 11:33. [PMID: 30786922 PMCID: PMC6381754 DOI: 10.1186/s13148-019-0626-0] [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: 11/23/2018] [Accepted: 01/31/2019] [Indexed: 01/14/2023] Open
Abstract
Background Pathological complete response (pCR) after neoadjuvant chemotherapy (NAC) in triple-negative breast cancer (TNBC) varies between 30 and 40% approximately. To provide further insight into the prediction of pCR, we evaluated the role of an epigenetic methylation-based signature. Methods Epigenetic assessment of DNA extracted from biopsy archived samples previous to NAC from TNBC patients was performed. Patients included were categorized according to previous response to NAC in responder (pCR or residual cancer burden, RCB = 0) or non-responder (non-pCR or RCB > 0) patients. A methyloma study was performed in a discovery cohort by the Infinium HumanMethylation450 BeadChip (450K array) from Illumina. The epigenetic silencing of those methylated genes in the discovery cohort were validated by bisulfite pyrosequencing (PyroMark Q96 System version 2.0.6, Qiagen) and qRT-PCR in an independent cohort of TN patients and in TN cell lines. Results Twenty-four and 30 patients were included in the discovery and validation cohorts, respectively. In the discovery cohort, nine genes were differentially methylated: six presented higher methylation in non-responder patients (LOC641519, LEF1, HOXA5, EVC2, TLX3, CDKL2) and three greater methylation in responder patients (FERD3L, CHL1, and TRIP10). After validation, a two-gene (FER3L and TRIP10) epigenetic score predicted RCB = 0 with an area under the ROC curve (AUC) = 0.905 (95% CI = 0.805–1.000). Patients with a positive epigenetic two-gene score showed 78.6% RCB = 0 versus only 10.7% RCB = 0 if signature were negative. Conclusions These results suggest that pCR in TNBC could be accurately predicted with an epigenetic signature of FERD3L and TRIP10 genes. Further prospective validation of these findings is warranted. Electronic supplementary material The online version of this article (10.1186/s13148-019-0626-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Begoña Pineda
- Biomedical Research Institute (INCLIVA), Valencia, Spain.,Department of Physiology, Faculty of Medicine, University of Valencia, Valencia, Spain.,Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain
| | - Angel Diaz-Lagares
- Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain.,Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain.,Present Address: Cancer Epigenomics, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), CIBERONC, Santiago de Compostela, Spain
| | - José Alejandro Pérez-Fidalgo
- Biomedical Research Institute (INCLIVA), Valencia, Spain.,Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain.,Oncology Department, Hospital Clínico Universitario de Valencia, Valencia, Spain
| | - Octavio Burgués
- Biomedical Research Institute (INCLIVA), Valencia, Spain.,Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain.,Pathology Department, Hospital Clínico Universitario de Valencia, Valencia, Spain
| | | | - Ana B Crujeiras
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain.,Present Address: Laboratory of Epigenomics in Endocrinology and Nutrition, Instituto de Investigacion Sanitaria (IDIS), Complejo Hospitalario Universitario de Santiago (CHUS), Santiago de Compostela University (USC) and CIBER Fisiopatologia de la Obesidad y Nutricion (CIBERobn), Madrid, Spain
| | - Juan Sandoval
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain.,Biomarkers and Precision Medicne Unit (UByMP), Instituto de Investigación Sanitaria La Fe (IISLaFeValencia), Valencia, Spain
| | - Manel Esteller
- Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain.,Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Spain.,Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Badalona, Barcelona, Catalonia, Spain
| | - Ana Lluch
- Biomedical Research Institute (INCLIVA), Valencia, Spain.,Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain.,Oncology Department, Hospital Clínico Universitario de Valencia, Valencia, Spain
| | - Pilar Eroles
- Biomedical Research Institute (INCLIVA), Valencia, Spain. .,Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain. .,COST action, CA15204, Brussels, Belgium.
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11
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Vidaki A, Ballard D, Aliferi A, Miller TH, Barron LP, Syndercombe Court D. DNA methylation-based forensic age prediction using artificial neural networks and next generation sequencing. Forensic Sci Int Genet 2017; 28:225-236. [PMID: 28254385 PMCID: PMC5392537 DOI: 10.1016/j.fsigen.2017.02.009] [Citation(s) in RCA: 130] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 02/07/2017] [Accepted: 02/16/2017] [Indexed: 12/19/2022]
Abstract
The ability to estimate the age of the donor from recovered biological material at a crime scene can be of substantial value in forensic investigations. Aging can be complex and is associated with various molecular modifications in cells that accumulate over a person's lifetime including epigenetic patterns. The aim of this study was to use age-specific DNA methylation patterns to generate an accurate model for the prediction of chronological age using data from whole blood. In total, 45 age-associated CpG sites were selected based on their reported age coefficients in a previous extensive study and investigated using publicly available methylation data obtained from 1156 whole blood samples (aged 2-90 years) analysed with Illumina's genome-wide methylation platforms (27K/450K). Applying stepwise regression for variable selection, 23 of these CpG sites were identified that could significantly contribute to age prediction modelling and multiple regression analysis carried out with these markers provided an accurate prediction of age (R2=0.92, mean absolute error (MAE)=4.6 years). However, applying machine learning, and more specifically a generalised regression neural network model, the age prediction significantly improved (R2=0.96) with a MAE=3.3 years for the training set and 4.4 years for a blind test set of 231 cases. The machine learning approach used 16 CpG sites, located in 16 different genomic regions, with the top 3 predictors of age belonged to the genes NHLRC1, SCGN and CSNK1D. The proposed model was further tested using independent cohorts of 53 monozygotic twins (MAE=7.1 years) and a cohort of 1011 disease state individuals (MAE=7.2 years). Furthermore, we highlighted the age markers' potential applicability in samples other than blood by predicting age with similar accuracy in 265 saliva samples (R2=0.96) with a MAE=3.2 years (training set) and 4.0 years (blind test). In an attempt to create a sensitive and accurate age prediction test, a next generation sequencing (NGS)-based method able to quantify the methylation status of the selected 16 CpG sites was developed using the Illumina MiSeq® platform. The method was validated using DNA standards of known methylation levels and the age prediction accuracy has been initially assessed in a set of 46 whole blood samples. Although the resulted prediction accuracy using the NGS data was lower compared to the original model (MAE=7.5years), it is expected that future optimization of our strategy to account for technical variation as well as increasing the sample size will improve both the prediction accuracy and reproducibility.
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Affiliation(s)
- Athina Vidaki
- Department of Pharmacy and Forensic Science, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London, UK.
| | - David Ballard
- Department of Pharmacy and Forensic Science, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London, UK.
| | - Anastasia Aliferi
- Department of Pharmacy and Forensic Science, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London, UK
| | - Thomas H Miller
- Department of Pharmacy and Forensic Science, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London, UK
| | - Leon P Barron
- Department of Pharmacy and Forensic Science, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London, UK
| | - Denise Syndercombe Court
- Department of Pharmacy and Forensic Science, King's College London, Franklin-Wilkins Building, 150 Stamford Street, London, UK
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12
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Cumming BM, Rahman MA, Lamprecht DA, Rohde KH, Saini V, Adamson JH, Russell DG, Steyn AJC. Mycobacterium tuberculosis arrests host cycle at the G1/S transition to establish long term infection. PLoS Pathog 2017; 13:e1006389. [PMID: 28542477 PMCID: PMC5456404 DOI: 10.1371/journal.ppat.1006389] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 06/02/2017] [Accepted: 04/28/2017] [Indexed: 02/08/2023] Open
Abstract
Signals modulating the production of Mycobacterium tuberculosis (Mtb) virulence factors essential for establishing long-term persistent infection are unknown. The WhiB3 redox regulator is known to regulate the production of Mtb virulence factors, however the mechanisms of this modulation are unknown. To advance our understanding of the mechanisms involved in WhiB3 regulation, we performed Mtb in vitro, intraphagosomal and infected host expression analyses. Our Mtb expression analyses in conjunction with extracellular flux analyses demonstrated that WhiB3 maintains bioenergetic homeostasis in response to available carbon sources found in vivo to establish Mtb infection. Our infected host expression analysis indicated that WhiB3 is involved in regulation of the host cell cycle. Detailed cell-cycle analysis revealed that Mtb infection inhibited the macrophage G1/S transition, and polyketides under WhiB3 control arrested the macrophages in the G0-G1 phase. Notably, infection with the Mtb whiB3 mutant or polyketide mutants had little effect on the macrophage cell cycle and emulated the uninfected cells. This suggests that polyketides regulated by Mtb WhiB3 are responsible for the cell cycle arrest observed in macrophages infected with the wild type Mtb. Thus, our findings demonstrate that Mtb WhiB3 maintains bioenergetic homeostasis to produce polyketide and lipid cyclomodulins that target the host cell cycle. This is a new mechanism whereby Mtb modulates the immune system by altering the host cell cycle to promote long-term persistence. This new knowledge could serve as the foundation for new host-directed therapeutic discovery efforts that target the host cell cycle.
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Affiliation(s)
| | | | - Dirk A. Lamprecht
- Africa Health Research Institute, Durban, KwaZulu Natal, South Africa
| | - Kyle H. Rohde
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida, United States of America
| | - Vikram Saini
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - John H. Adamson
- Africa Health Research Institute, Durban, KwaZulu Natal, South Africa
| | - David G. Russell
- Cornell University College of Veterinary Medicine, C5 171 Veterinary Medical Center, Ithaca, New York, United States of America
| | - Adrie J. C. Steyn
- Africa Health Research Institute, Durban, KwaZulu Natal, South Africa
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Centers for AIDS Research and Free Radical Biology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- School of Laboratory Medicine and Medical Sciences, Nelson R. Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
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13
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Erasmus JC, Bruche S, Pizarro L, Maimari N, Pogglioli T, Tomlinson C, Lees J, Zalivina I, Wheeler A, Alberts A, Russo A, Braga VMM. Defining functional interactions during biogenesis of epithelial junctions. Nat Commun 2016; 7:13542. [PMID: 27922008 PMCID: PMC5150262 DOI: 10.1038/ncomms13542] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 10/13/2016] [Indexed: 12/26/2022] Open
Abstract
In spite of extensive recent progress, a comprehensive understanding of how actin cytoskeleton remodelling supports stable junctions remains to be established. Here we design a platform that integrates actin functions with optimized phenotypic clustering and identify new cytoskeletal proteins, their functional hierarchy and pathways that modulate E-cadherin adhesion. Depletion of EEF1A, an actin bundling protein, increases E-cadherin levels at junctions without a corresponding reinforcement of cell–cell contacts. This unexpected result reflects a more dynamic and mobile junctional actin in EEF1A-depleted cells. A partner for EEF1A in cadherin contact maintenance is the formin DIAPH2, which interacts with EEF1A. In contrast, depletion of either the endocytic regulator TRIP10 or the Rho GTPase activator VAV2 reduces E-cadherin levels at junctions. TRIP10 binds to and requires VAV2 function for its junctional localization. Overall, we present new conceptual insights on junction stabilization, which integrate known and novel pathways with impact for epithelial morphogenesis, homeostasis and diseases. Formation and reinforcement of E-cadherin-mediated adhesion depends on intracellular trafficking and interactions with the actin cytoskeleton, but how these are coordinated is not known. Here the authors conduct a focused phenotypic screen to identify new pathways regulating cell–cell junction homeostasis.
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Affiliation(s)
- J C Erasmus
- National Heart and Lung Institute, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK
| | - S Bruche
- National Heart and Lung Institute, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK
| | - L Pizarro
- National Heart and Lung Institute, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK.,Computing Department, Imperial College London, London SW7 2AZ, UK
| | - N Maimari
- National Heart and Lung Institute, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK.,Bioengineering Department, Faculty of Engineering, Imperial College London, London SW7 2AZ, UK
| | - T Pogglioli
- National Heart and Lung Institute, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK
| | - C Tomlinson
- Department of Surgery &Cancer, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK
| | - J Lees
- Department Structural and Molecular Biology, University College London, London WC1E 6BT, UK
| | - I Zalivina
- National Heart and Lung Institute, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK
| | - A Wheeler
- National Heart and Lung Institute, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK
| | - A Alberts
- Van Andel Institute, Grand Rapids, Michigan 49503, USA
| | - A Russo
- Computing Department, Imperial College London, London SW7 2AZ, UK
| | - V M M Braga
- National Heart and Lung Institute, Faculty of Medicine, Imperial College London, London SW7 2AZ, UK
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14
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Ouadid-Ahidouch H, Rodat-Despoix L, Matifat F, Morin G, Ahidouch A. DNA methylation of channel-related genes in cancers. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:2621-8. [PMID: 25703813 DOI: 10.1016/j.bbamem.2015.02.015] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Revised: 02/04/2015] [Accepted: 02/12/2015] [Indexed: 12/31/2022]
Abstract
DNA methylation at CpG sites is an epigenetic mechanism that regulates cellular gene expression. In cancer cells, aberrant methylation is correlated with the abnormalities in expression of genes that are known to be involved in the particular characteristics of cancer cells such as proliferation, apoptosis, migration or invasion. During the past 30 years, accumulating data have definitely convinced the scientific community that ion channels are involved in cancerogenesis and cancer properties. As they are situated at the cell surface, they might be prime targets in the development of new therapeutic strategies besides their potential use as prognostic factors. Despite the progress in our understanding of the remodeling of ion channels in cancer cells, the molecular mechanisms underlying their over- or down-expression remained enigmatic. In this review, we aimed to summarize the available data on gene promoter methylation of ion channels and to investigate their clinical significance as novel biomarkers in cancer. This article is part of a Special Issue entitled: Membrane channels and transporters in cancers.
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Affiliation(s)
- Halima Ouadid-Ahidouch
- UFR Sciences, EA 4667, Laboratory of Cell and Molecular Physiology, University of Picardie Jules Verne, SFR CAP-SANTE (FED 4231), Amiens, France.
| | - Lise Rodat-Despoix
- UFR Sciences, EA 4667, Laboratory of Cell and Molecular Physiology, University of Picardie Jules Verne, SFR CAP-SANTE (FED 4231), Amiens, France
| | - Fabrice Matifat
- UFR Sciences, EA 4667, Laboratory of Cell and Molecular Physiology, University of Picardie Jules Verne, SFR CAP-SANTE (FED 4231), Amiens, France
| | - Gilles Morin
- EA 4666 and Department of Molecular and Clinical Genetics, Amiens University Hospital, University of Picardie Jules Verne, Amiens, France
| | - Ahmed Ahidouch
- UFR Sciences, EA 4667, Laboratory of Cell and Molecular Physiology, University of Picardie Jules Verne, SFR CAP-SANTE (FED 4231), Amiens, France; Department of Biology, Faculty of Sciences, Ibn Zohr University, Agadir Morocco
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15
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CIP4 promotes lung adenocarcinoma metastasis and is associated with poor prognosis. Oncogene 2014; 34:3527-35. [PMID: 25174397 PMCID: PMC4978543 DOI: 10.1038/onc.2014.280] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 07/21/2014] [Accepted: 07/23/2014] [Indexed: 12/28/2022]
Abstract
Aberrant Epidermal growth factor receptor (EGFR) signaling in non-small cell lung cancer (NSCLC) is linked to tumor progression, metastasis, and poor survival rates. Here, we report the role of Cdc42-interacting protein 4 (CIP4) in the regulation of NSCLC cell invasiveness and tumor metastasis. CIP4 was highly expressed in a panel of NSCLC cell lines and normal lung epithelial cell lines. Stable knock-down (KD) of CIP4 in lung adenocarcinoma H1299 cells, expressing wild-type EGFR, led to increased EGFR levels on the cell surface, and defects in sustained activation of Erk kinase in H1299 cells treated with EGF. CIP4 localized to leading edge projections in NSCLC cells, and CIP4 KD cells displayed defects in EGF-induced cell motility and invasion through extracellular matrix. This correlated with reduced expression and activity of matrix metalloproteinase-2 (MMP-2) in CIP4 KD cells compared to control. In xenograft assays, CIP4 silencing had no effect on tumor growth, but resulted in significant defects in spontaneous metastases to the lungs from these subcutaneous tumors. This correlated with reduced expression of the Erk target gene Zeb1, and the Zeb1 target gene MMP-2 in CIP4 KD tumors compared to control. CIP4 also enhanced rates of metastasis to the liver and lungs in an intrasplenic experimental metastasis model. In human NSCLC tumor sections, CIP4 expression was elevated ≥ 2-fold in 43% of adenocarcinomas and 32% of squamous carcinomas compared to adjacent normal lung tissues. Analysis of microarray data for NSCLC patients also revealed that high CIP4 transcript levels correlated with reduced overall survival. Together, these results identify CIP4 as a positive regulator of NSCLC metastasis, and a potential poor prognostic biomarker in lung adenocarcinoma.
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16
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Bauer KM, Watts TN, Buechler S, Hummon AB. Proteomic and functional investigation of the colon cancer relapse-associated genes NOX4 and ITGA3. J Proteome Res 2014; 13:4910-8. [PMID: 25096929 PMCID: PMC4227555 DOI: 10.1021/pr500557n] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Colon cancer is a major cause of cancer-related deaths worldwide. Adjuvant chemotherapy significantly reduces mortality in stage III colon cancer; however, it is only marginally effective in stage II patients. There is also increasing evidence that right-side colon cancer is different from left-side colon cancer. We have observed that the genes altered in expression between the poor and good prognosis tumors vary significantly depending on whether the malignancy originates on the right or left side of the colon. We have identified NADPH oxidase 4 (NOX4) to be highly predictive of relapse in stage II left-side colon cancer, whereas integrin alpha 3 beta 1 (ITGA3) is predictive of relapse in stage II right-side colon cancer. To investigate the underlying molecular mechanisms, we are analyzing the effect of ITGA3 and NOX4 silencing via RNA interference and pharmacological inhibition on global protein expression patterns via iTRAQ labeling and mass spectrometry in colon cancer cells. On the basis of bioinformatic analysis, the functions of these genes were assessed through phenotypic assays, revealing roles in cell migration and reactive oxygen species generation. These biomarkers for relapse risk are of clinical interest and lead to insight into how a tumor progresses to metastasis.
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Affiliation(s)
- Kerry M Bauer
- Harper Cancer Research Institute, ‡Department of Chemistry & Biochemistry, and §Department of Applied and Computational Mathematics and Statistics, University of Notre Dame , Notre Dame, Indiana 46556, United States
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17
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Chen YL, Kuo MH, Lin PY, Chuang WL, Hsu CC, Chu PY, Lee CH, Huang THM, Leu YW, Hsiao SH. ENSA expression correlates with attenuated tumor propagation in liver cancer. Biochem Biophys Res Commun 2013; 442:56-61. [DOI: 10.1016/j.bbrc.2013.10.165] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Accepted: 10/31/2013] [Indexed: 01/15/2023]
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18
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Leu YW, Huang THM, Hsiao SH. Epigenetic reprogramming of mesenchymal stem cells. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 754:195-211. [PMID: 22956503 DOI: 10.1007/978-1-4419-9967-2_10] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Mesenchymal stem cells (MSCs) are multipotent stem cells of mesodermal origin that can be isolated from various sources and induced into different cell types. Although MSCs possess immune privilege and are more easily obtained than embryonic stem cells, their propensity to tumorigenesis has not been fully explored. Epigenomic changes in DNA methylation and chromatin structure have been hypothesized to be critical in the determination of lineage-specific differentiation and tumorigenesis of MSCs, but this has not been formally proven. We applied a targeted DNA methylation method to methylate a Polycomb group protein-governed gene, Trip10, in MSCs, which accelerated the cell fate determination of MSCs. In addition, targeted methylation of HIC1 and RassF1A, both tumor suppressor genes, transformed MSCs into tumor stem cell-like cells. This new method will allow better control of the differentiation of MSCs and their use in downstream applications.
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Affiliation(s)
- Yu-Wei Leu
- Department of Life Science, National Chung Cheng University, Chia-Yi 621, Taiwan.
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19
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Chen Y, Aardema J, Misra A, Corey SJ. BAR proteins in cancer and blood disorders. INTERNATIONAL JOURNAL OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2012; 3:198-208. [PMID: 22773959 PMCID: PMC3388730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Accepted: 04/18/2012] [Indexed: 06/01/2023]
Abstract
Remodeling of the membrane and cytoskeleton is involved in a wide range of normal and pathologic cellular function. These are complex, highly-coordinated biochemical and biophysical processes involving dozens of proteins. Serving as a scaffold for a variety of proteins and possessing a domain that interacts with plasma membranes, the BAR family of proteins contribute to a range of cellular functions characterized by membrane and cytoskeletal remodeling. There are several subgroups of BAR proteins: BAR, N-BAR, I-BAR, and F-BAR. They differ in their ability to induce angles of membrane curvature and in their recruitment of effector proteins. Evidence is accumulating that BAR proteins contribute to cancer cell invasion, T cell trafficking, phagocytosis, and platelet production. In this review, we discuss the physiological function of BAR proteins and discuss how they contribute to blood and cancer disorders.
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Affiliation(s)
- Yolande Chen
- Departments of Pediatrics and Cell & Molecular Biology, Children’s Memorial Hospital, Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of MedicineChicago, IL
| | - Jorie Aardema
- Departments of Pediatrics and Cell & Molecular Biology, Children’s Memorial Hospital, Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of MedicineChicago, IL
| | - Ashish Misra
- Division of Cardiology, Department of Medicine, Yale University School of MedicineNew Haven, CT, USA
| | - Seth J Corey
- Departments of Pediatrics and Cell & Molecular Biology, Children’s Memorial Hospital, Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of MedicineChicago, IL
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20
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Sigismund S, Confalonieri S, Ciliberto A, Polo S, Scita G, Di Fiore PP. Endocytosis and signaling: cell logistics shape the eukaryotic cell plan. Physiol Rev 2012; 92:273-366. [PMID: 22298658 DOI: 10.1152/physrev.00005.2011] [Citation(s) in RCA: 236] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Our understanding of endocytosis has evolved remarkably in little more than a decade. This is the result not only of advances in our knowledge of its molecular and biological workings, but also of a true paradigm shift in our understanding of what really constitutes endocytosis and of its role in homeostasis. Although endocytosis was initially discovered and studied as a relatively simple process to transport molecules across the plasma membrane, it was subsequently found to be inextricably linked with almost all aspects of cellular signaling. This led to the notion that endocytosis is actually the master organizer of cellular signaling, providing the cell with understandable messages that have been resolved in space and time. In essence, endocytosis provides the communications and supply routes (the logistics) of the cell. Although this may seem revolutionary, it is still likely to be only a small part of the entire story. A wealth of new evidence is uncovering the surprisingly pervasive nature of endocytosis in essentially all aspects of cellular regulation. In addition, many newly discovered functions of endocytic proteins are not immediately interpretable within the classical view of endocytosis. A possible framework, to rationalize all this new knowledge, requires us to "upgrade" our vision of endocytosis. By combining the analysis of biochemical, biological, and evolutionary evidence, we propose herein that endocytosis constitutes one of the major enabling conditions that in the history of life permitted the development of a higher level of organization, leading to the actuation of the eukaryotic cell plan.
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Affiliation(s)
- Sara Sigismund
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy
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21
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Frullanti E, Colombo F, Falvella FS, Galvan A, Noci S, De Cecco L, Incarbone M, Alloisio M, Santambrogio L, Nosotti M, Tosi D, Pastorino U, Dragani TA. Association of lung adenocarcinoma clinical stage with gene expression pattern in noninvolved lung tissue. Int J Cancer 2012; 131:E643-8. [PMID: 22223368 DOI: 10.1002/ijc.27426] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Accepted: 12/08/2011] [Indexed: 11/06/2022]
Abstract
Associations between clinical outcome of cancer patients and the gene expression signature in primary tumors at time of diagnosis have been reported. To test whether gene expression patterns in noninvolved lung tissue might correlate with clinical stage in lung adenocarcinoma (ADCA) patients, we compared the transcriptome of noninvolved lung samples from 60 ADCA smoker patients of clinical stage I versus 60 patients with stage>I. Quantitative PCR of 10 genes with the most significant differential expression confirmed the statistical association with clinical stage in eight genes, six of which were downregulated in high-stage patients. Five of these six genes were also downregulated in lung ADCA tissue as compared to noninvolved tissue. Studies in vitro indicated that four of the genes (SLC14A1, SMAD6, TMEM100 and TXNIP) inhibited colony formation of lung cancer cell lines transfected to overexpress the genes, suggesting their potential tumor-suppressor activity. Our findings suggest that individual variations in the transcriptional profile of noninvolved lung tissue may reflect the lung ADCA patient's predisposition to tumor aggressiveness.
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Affiliation(s)
- Elisa Frullanti
- Department of Predictive and Preventive Medicine, Fondazione IRCCS, Istituto Nazionale Tumori, Milan, Italy
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22
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Xiang TX, Yuan Y, Li LL, Wang ZH, Dan LY, Chen Y, Ren GS, Tao Q. Aberrant promoter CpG methylation and its translational applications in breast cancer. CHINESE JOURNAL OF CANCER 2011; 32:12-20. [PMID: 22059908 PMCID: PMC3845590 DOI: 10.5732/cjc.011.10344] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Breast cancer is a complex disease driven by multiple factors including both genetic and epigenetic alterations. Recent studies revealed that abnormal gene expression induced by epigenetic changes, including aberrant promoter methylation and histone modification, plays a critical role in human breast Carcinogenesis. Silencing of tumor suppressor genes (TSGs) by promoter CpG methylation facilitates cells growth and survival advantages and further results in tumor initiation and progression, thus directly contributing to breast tumorigenesis. Usually, aberrant promoter methylation of TSGs, which can be reversed by pharmacological reagents, occurs at the early stage of tumorigenesis and therefore may serve as a potential tumor marker for early diagnosis and therapeutic targeting of breast cancer. In this review, we summarize the epigenetic changes of multiple TSGs involved in breast pathogenesis and their potential clinical applications as tumor markers for early detection and treatment of breast cancer.
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Affiliation(s)
- Ting-Xiu Xiang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
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