1
|
Holst S, Weber AK, Meier F, Otte J, Petzsch P, Reifenberger J, Wachtmeister T, Westphal D, Ziemer M, Wruck W, Adjaye J, Betz RC, Rütten A, Surowy HM, Redler S. Gene expression profiling in porocarcinoma indicates heterogeneous tumor development and substantiates poromas as precursor lesions. J Dtsch Dermatol Ges 2024; 22:1115-1124. [PMID: 38899945 DOI: 10.1111/ddg.15445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 04/02/2024] [Indexed: 06/21/2024]
Abstract
BACKGROUND AND OBJECTIVES Malignant sweat gland tumors are rare, with the most common being eccrine porocarcinoma (EP). Approximately 18% of benign eccrine poroma (EPO) transit to EP. Previous research has provided first insights into the mutational landscape of EP. However, only few studies have performed gene expression analyses. This leaves a gap in the understanding of EP biology and potential drivers of malignant transformation from EPO to EP. METHODS Transcriptome profiling of 23 samples of primary EP and normal skin (NS). Findings from the EP samples were then tested in 17 samples of EPO. RESULTS Transcriptome profiling revealed diversity in gene expression and indicated biologically heterogeneous sub-entities as well as widespread gene downregulation in EP. Downregulated genes included CD74, NDGR1, SRRM2, CDC42, ANXA2, KFL9 and NOP53. Expression levels of CD74, NDGR1, SRRM2, ANXA2, and NOP53 showed a stepwise-reduction in expression from NS via EPO to EP, thus supporting the hypothesis that EPO represents a transitional state in EP development. CONCLUSIONS We demonstrated that EP is molecularly complex and that evolutionary trajectories correspond to tumor initiation and progression. Our results provide further evidence implicating the p53 axis and the EGFR pathway. Larger samples are warranted to confirm our findings.
Collapse
Affiliation(s)
- Svenja Holst
- Institute of Human Genetics, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Anna K Weber
- Institute of Human Genetics, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Friedegund Meier
- Department of Dermatology, University Hospital Carl Gustav Carus, TU Dresden, Germany
- Skin Cancer Center at the University Cancer Centre Dresden and National Center for Tumor Diseases, Dresden, Germany
| | - Jörg Otte
- Institute for Stem Cell Research and Regenerative Medicine, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institute, Stockholm, Sweden
| | - Patrick Petzsch
- Biological and Medical Research Centre (BMFZ), Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Julia Reifenberger
- Department of Dermatology, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Thorsten Wachtmeister
- Biological and Medical Research Centre (BMFZ), Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Dana Westphal
- Department of Dermatology, University Hospital Carl Gustav Carus, TU Dresden, Germany
- Skin Cancer Center at the University Cancer Centre Dresden and National Center for Tumor Diseases, Dresden, Germany
| | - Mirjana Ziemer
- Department of Dermatology, University Medical Center Leipzig, Leipzig, Germany
| | - Wasco Wruck
- Institute for Stem Cell Research and Regenerative Medicine, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - James Adjaye
- Institute for Stem Cell Research and Regenerative Medicine, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Regina C Betz
- Institute of Human Genetics, University of Bonn, Medical Faculty and University Hospital Bonn, Bonn, Germany
| | - Arno Rütten
- Dermatopathology, Bodensee, Siemensstrasse 6/1, 88048, Friedrichshafen, Germany
| | - Harald M Surowy
- Institute of Human Genetics, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Silke Redler
- Institute of Human Genetics, Medical Faculty and University Hospital Düsseldorf, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| |
Collapse
|
2
|
Holst S, Weber AK, Meier F, Otte J, Petzsch P, Reifenberger J, Wachtmeister T, Westphal D, Ziemer M, Wruck W, Adjaye J, Betz RC, Rütten A, Surowy HM, Redler S. Genexpressionsprofile beim Porokarzinom deuten auf heterogene Tumorentwicklung hin und untermauern Porome als Vorläuferläsionen. J Dtsch Dermatol Ges 2024; 22:1115-1125. [PMID: 39105214 DOI: 10.1111/ddg.15445_g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 04/02/2024] [Indexed: 08/07/2024]
Abstract
ZusammenfassungHintergrund und ZieleMaligne Schweißdrüsentumoren sind selten, wobei das ekkrine Porokarzinom (EP) das häufigste ist. Etwa 18 % der benignen ekkrinen Porome (EPO) entwickeln sich zum EP. Wissenschaftliche Studien haben erste Einblicke in die Mutationslandschaft von EPs geliefert. Allerdings wurden in nur wenigen Studien Genexpressionsanalysen durchgeführt. Dies hinterlässt eine Lücke im Verständnis der EP‐Biologie und potenzieller Treiber der malignen Transformation von EPO zu EP.MethodenEs wurde eine Transkriptomanalyse von 23 Proben primärer EP und normaler Haut (NH) durchgeführt. Die Ergebnisse aus den EP‐Proben wurden dann an 17 EP‐Proben getestet.ErgebnisseDas Transkriptom‐Profiling zeigte eine Vielfalt in der Genexpression und deutete auf biologisch heterogene Subeinheiten sowie eine weit verbreitete Herunterregulierung von Genen im EP hin. Herunterregulierte Gene umfassten CD74, NDGR1, SRRM2, CDC42, ANXA2, KFL9 und NOP53. Die Expressionsniveaus von CD74, NDGR1, SRRM2, ANXA2 und NOP53 zeigten eine stufenweise Abnahme der Expression von NH über EPO zu EP, was die Hypothese unterstützt, dass das EPO einen Zwischenschritt in der EP‐Entwicklung darstellt.SchlussfolgerungenDie Studie zeigt, dass das EP molekular komplex ist und der evolutionäre Verlauf der Tumorinitiierung und ‐progression entspricht. Die Ergebnisse legen eine Beteiligung der p53‐Achse und des EGFR‐Signalwegs nahe. Eine größere Probenanzahl ist erforderlich, um diese Ergebnisse zu bestätigen.
Collapse
Affiliation(s)
- Svenja Holst
- Institut für Humangenetik, Medizinische Fakultät und Universitätsklinikum Düsseldorf, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Deutschland
| | - Anna K Weber
- Institut für Humangenetik, Medizinische Fakultät und Universitätsklinikum Düsseldorf, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Deutschland
| | - Friedegund Meier
- Klinik für Dermatologie, Universitätsklinikum Carl Gustav Carus, TU Dresden, Deutschland
- Hautkrebszentrum am Universitätskrebszentrum Dresden und Nationales Zentrum für Tumorerkrankungen, Dresden, Deutschland
| | - Jörg Otte
- Institut für Stammzellforschung und Regenerative Medizin, Medizinische Fakultät und Universitätsklinikum Düsseldorf, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Deutschland
- Einheit für Kinderkrebsforschung, Abteilung für Frauen- und Kinderheilkunde, Karolinska-Institut, Stockholm, Schweden
| | - Patrick Petzsch
- Biologisch-Medizinisches Forschungszentrum (BMFZ), Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Deutschland
| | - Julia Reifenberger
- Klinik für Dermatologie, Medizinische Fakultät und Universitätsklinikum Düsseldorf, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Deutschland
| | - Thorsten Wachtmeister
- Biologisch-Medizinisches Forschungszentrum (BMFZ), Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Deutschland
| | - Dana Westphal
- Klinik für Dermatologie, Universitätsklinikum Carl Gustav Carus, TU Dresden, Deutschland
- Hautkrebszentrum am Universitätskrebszentrum Dresden und Nationales Zentrum für Tumorerkrankungen, Dresden, Deutschland
| | - Mirjana Ziemer
- Klinik für Dermatologie, Universitätsklinikum Leipzig, Leipzig, Deutschland
| | - Wasco Wruck
- Institut für Stammzellforschung und Regenerative Medizin, Medizinische Fakultät und Universitätsklinikum Düsseldorf, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Deutschland
| | - James Adjaye
- Institut für Stammzellforschung und Regenerative Medizin, Medizinische Fakultät und Universitätsklinikum Düsseldorf, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Deutschland
| | - Regina C Betz
- Institut für Humangenetik, Universität Bonn, Medizinische Fakultät und Universitätsklinikum Bonn, Bonn, Deutschland
| | - Arno Rütten
- Dermatopathologie, Bodensee, Siemensstrasse 6/1, 88048 Friedrichshafen, Deutschland
| | - Harald M Surowy
- Institut für Humangenetik, Medizinische Fakultät und Universitätsklinikum Düsseldorf, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Deutschland
| | - Silke Redler
- Institut für Humangenetik, Medizinische Fakultät und Universitätsklinikum Düsseldorf, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Deutschland
| |
Collapse
|
3
|
Chin FW, Hussin H, Chau DM, Ong TA, Yunus R, Abdul Razack AH, Yusoff K, Chan SC, Veerakumarasivam A. Differential Protein Expression Patterns of HOXA13 and HOXB13 Are Associated with Bladder Cancer Progression. Diagnostics (Basel) 2023; 13:2636. [PMID: 37627895 PMCID: PMC10453033 DOI: 10.3390/diagnostics13162636] [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: 05/30/2023] [Revised: 07/02/2023] [Accepted: 07/08/2023] [Indexed: 08/27/2023] Open
Abstract
Bladder cancer is a common urological cancer and has the highest recurrence rate of any cancer. The aim of our study was to profile and characterize the protein expression of homeobox A13 (HOXA13) and homeobox B13 (HOXB13) genes in Malaysian bladder cancer patients. The protein expression of HOXA13 and HOXB13 in formalin-fixed paraffin-embedded (FFPE) bladder cancer tissues was determined by immunohistochemistry (IHC) analysis. The association between HOXA13/HOXB13 protein expression and demographic/clinicopathological characteristics of the bladder cancer patients was determined by chi-square analysis. Approximately 63.6% of the bladder cancer tissues harbored high HOXA13 expression. High HOXA13 expression was significantly associated with non-muscle invasive bladder cancer, lower tumor grade, higher number of lymph node metastases, and recurrence risk. In contrast, low HOXB13 expression (including those with negative expression) was observed in 71.6% of the bladder cancer tissues analyzed. Low HOXB13 expression was significantly associated with muscle-invasive bladder cancer, higher tumor stage, tumor grade, and metastatic risk. Both HOXA13 and HOXB13 protein expression were found to be associated with bladder tumorigenesis. The putative oncogenic and tumor suppressive roles of HOXA13 and HOXB13, respectively, suggest their potential utility as biomarkers in bladder cancer.
Collapse
Affiliation(s)
- Fee-Wai Chin
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia
| | - Huzlinda Hussin
- Department of Pathology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia
| | - De-Ming Chau
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia
| | - Teng-Aik Ong
- Department of Surgery, Faculty of Medicine, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Rosna Yunus
- Department of Pathology, Hospital Kuala Lumpur, Kuala Lumpur 50586, Malaysia
| | | | - Khatijah Yusoff
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia
- Malaysia Genome and Vaccine Institute, National Institutes of Biotechnology Malaysia, Kajang 43000, Selangor, Malaysia
| | - Soon-Choy Chan
- Malaysia Genome and Vaccine Institute, National Institutes of Biotechnology Malaysia, Kajang 43000, Selangor, Malaysia
- School of Liberal Arts, Science and Technology, Perdana University, Kuala Lumpur 50490, Malaysia
| | - Abhi Veerakumarasivam
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia
- Malaysia Genome and Vaccine Institute, National Institutes of Biotechnology Malaysia, Kajang 43000, Selangor, Malaysia
- School of Medical and Life Sciences, Sunway University, Bandar Sunway 47500, Selangor, Malaysia
| |
Collapse
|
4
|
Huang DY, Lu ST, Chen YS, Cheng CY, Lin WW. Epigenetic upregulation of spleen tyrosine kinase in cancer cells through p53-dependent downregulation of DNA methyltransferase. Exp Cell Res 2023; 425:113540. [PMID: 36889573 DOI: 10.1016/j.yexcr.2023.113540] [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: 12/29/2022] [Revised: 02/25/2023] [Accepted: 03/04/2023] [Indexed: 03/08/2023]
Abstract
Syk is a tumor suppressor gene in some solid tumors. Currently, it remains unknown how Syk gene hypermethylation is controlled by DNA methyltransferase (DNMT) and p53. In colorectal cancer HCT116 cells, we found that protein and mRNA levels of Syk were much higher in WT than in p53-/- cells. Both p53 inhibitor PFT-α and p53 silencing can reduce the protein and mRNA expression of Syk in WT cells, while DNMT inhibitor 5-Aza-2'-dC can increase Syk expression in p53-/- cells. Interestingly, the DNMT expression in p53-/- HCT116 cells was higher than that in WT cells. PFT-α can not only enhance Syk gene methylation but also increase DNMT1 protein and mRNA levels in WT HCT116 cells. In metastatic lung cancer cell lines A549 and PC9, which express WT p53 and gain function of p53, respectively, PFT-α can also downregulate Syk mRNA and protein expression. However, the Syk methylation level was increased by PFT-α in A549 but not in PC9 cells. Likewise, 5-Aza-2'-dC transcriptionally increased Syk gene expression in A549 cells, but not in PC9 cells. In summary methylation of Syk promoter requires DNMT1, and p53 can upregulate Syk expression via downregulation of DNMT1 at the transcriptional level.
Collapse
Affiliation(s)
- Duen-Yi Huang
- Department of Pharmacology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Shang-Te Lu
- Graduate Institute of Medical Sciences, Taipei Medical University, Taipei, Taiwan
| | - Yuan-Shen Chen
- Department of Neurosurgery, National Taiwan University Hospital Yunlin Branch, Douliu, 64041, Taiwan
| | - Ching-Yuan Cheng
- Department of Pharmacology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Wan-Wan Lin
- Department of Pharmacology, College of Medicine, National Taiwan University, Taipei, Taiwan; Graduate Institute of Medical Sciences, Taipei Medical University, Taipei, Taiwan.
| |
Collapse
|
5
|
Liang T, Wu X, Wang L, Ni Z, Fan Y, Wu P, Wang H, Niu Y, Huang H. Clinical significance and diagnostic value of QPCT, SCEL and TNFRSF12A in papillary thyroid cancer. Pathol Res Pract 2023; 245:154431. [PMID: 37060824 DOI: 10.1016/j.prp.2023.154431] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 02/23/2023] [Accepted: 03/27/2023] [Indexed: 04/05/2023]
Abstract
PURPOSE To identify specific novel genes that could be used as diagnostic and prognostic factors in papillary thyroid carcinoma (PTC). METHODS Screening of differential genes by RNA sequencing (RNA-Seq) in normal thyroid, Hashimoto's thyroiditis, PTC combined with Hashimoto's thyroiditis and PTC tissues. The genes QPCT, SCEL and TNFRSF12A were selected by qRT-PCR and immunohistochemical pre-experiments. The GEPIA2 database, qRT-PCR, and immunohistochemical studies were used to confirm the target genes QPCT, SCEL, and TNFRSF12A. ROC curves were used to assess the diagnostic usefulness of these 3 genes for PTC in more detail. RESULTS Functional enrichment analysis showed that QPCT, SCEL and TNFRSF12A were enriched in the pathways for peptidyl-pyroglutamic acid biosynthesis, keratinocyte differentiation, WNT signaling, apoptosis. GEPIA2 database analysis revealed that QPCT, SCEL and TNFRSF12A were high in thyroid cancer, and TC patients with lower TNFRSF12A levels had short survival. QPCT, SCEL and TNFRSF12A were elevated in PTC and thyroid adenoma. The mRNA diagnostic values were as follows: for QPCT, AUROC = 0.891, 95% CI, 0.835-0.947; for SCEL, AUROC = 0.921, 95% CI, 0.869-0.974; for TNFRSF12A, AUROC = 0.884, 95% CI, 0.809-0.958. Immunohistochemical results showed that QPCT, SCEL, and TNFRSF12A differed to varying degrees between subgroups of thyroid tissue. SCEL was associated with BRAF V600E mutation status and stratification of recurrence risk, while TNFRSF12A was associated with Cyclin D1. The protein diagnostic values were as follows: for QPCT, AUROC = 0.752, 95% CI, 0.685-0.819; for SCEL, AUROC = 0.715, 95% CI, 0.645-0.784; for TNFRSF12A, AUROC = 0.660, 95% CI, 0.587-0.734. CONCLUSION QPCT, SCEL and TNFRSF12A are expected to be diagnostic markers for PTC.
Collapse
|
6
|
Tsai KC, Zhang YX, Kao HY, Fung KM, Tseng TS. Pharmacophore-driven identification of human glutaminyl cyclase inhibitors from foods, plants and herbs unveils the bioactive property and potential of Azaleatin in the treatment of Alzheimer's disease. Food Funct 2022; 13:12632-12647. [PMID: 36416361 DOI: 10.1039/d2fo02507h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Alzheimer's disease (AD) is the leading cause of disabilities in old age and a rapidly growing condition in the elderly population. AD brings significant burden and has a devastating impact on public health, society and the global economy. Thus, developing new therapeutics to combat AD is imperative. Human glutaminyl cyclase (hQC), which catalyzes the formation of neurotoxic pyroglutamate (pE)-modified β-amyloid (Aβ) peptides, is linked to the amyloidogenic process that leads to the initiation of AD. Hence, hQC is an essential target for developing anti-AD therapeutics. Here, we systematically screened and identified hQC inhibitors from natural products by pharmacophore-driven inhibitor screening coupled with biochemical and biophysical examinations. We employed receptor-ligand pharmacophore generation to build pharmacophore models and Phar-MERGE and Phar-SEN for inhibitor screening through ligand-pharmacophore mapping. About 11 and 24 hits identified from the Natural Product and Traditional Chinese Medicine databases, respectively, showed diverse hQC inhibitory abilities. Importantly, the inhibitors TCM1 (Azaleatin; IC50 = 1.1 μM) and TCM2 (Quercetin; IC50 = 4.3 μM) found in foods and plants exhibited strong inhibitory potency against hQC. Furthermore, the binding affinity and molecular interactions were analyzed by surface plasmon resonance (SPR) and molecular modeling/simulations to explore the possible modes of action of Azaleatin and Quercetin. Our study successfully screened and characterized the foundational biochemical and biophysical properties of Azaleatin and Quercetin toward targeting hQC, unveiling their bioactive potential in the treatment of AD.
Collapse
Affiliation(s)
- Keng-Chang Tsai
- National Research Institute of Chinese Medicine, Ministry of Health and Welfare, Taipei, Taiwan. .,Ph.D. Program in Medical Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Yi-Xuan Zhang
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan.
| | - Hsiang-Yun Kao
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan.
| | - Kit-Man Fung
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan. .,Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan
| | - Tien-Sheng Tseng
- Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan.
| |
Collapse
|
7
|
Gao DZ, Yang YS, Wang Z, Zhao XF. Expression profile and prognostic significance of HOXB13 in rectal cancer. Int J Biol Markers 2022; 37:140-148. [PMID: 35296171 DOI: 10.1177/17246008221076151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND This study aimed to investigate the expression pattern and prognostic significance of HOXB13 in rectal cancer. METHODS HOXB13 expression in rectal cancer and normal adjacent tissues was detected by reverse transcriptase-polymerase chain reaction and immunohistochemistry, and its clinicopathological characteristics and prognosis were statistically tested. Furthermore, we evaluated the association between tumor immune infiltrating cells and HOXB13 using the tumor immune estimation resource (TIMER) database. The potential biological mechanism associated with HOXB13 overexpression was investigated by gene set enrichment analysis (GSEA). RESULTS The expression of HOXB13 messenger RNA and protein in human rectal cancer tissues were significantly higher than those in the normal adjacent tissues (P < 0.05). HOXB13 expression was significantly correlated with depth of invasion, lymphatic invasion, lymph node metastasis, distant metastasis, and pathological tumor node metastasis stage (P < 0.05). Kaplan-Meier survival curves confirmed that HOXB13 overexpression was correlated negatively with overall survival and disease-free survival in rectal cancer (P < 0.05). Also, multivariate Cox regression analysis demonstrated that HOXB13 expression, age, and lymphatic invasion were independent prognostic factors in rectal cancer (P < 0.05). Plus, the results from the TIMER database indicated that HOXB13 expression has a significant association with several immune cell infiltrates. Finally, the GSEA results indicated that HOXB13 participated in the various immune-associated processes, including natural killer cell-mediated cytotoxicity and the T-cell receptor signaling pathway. CONCLUSION Our study showed an essential role of HOXB13 in rectal cancer immunity and prognosis. Significantly, the overexpression of HOXB13 leads to the worse prognosis for patients with rectal cancer, which will contribute to understanding molecular mechanisms associated with tumor pathogenesis and prognosis in this disease.
Collapse
Affiliation(s)
- Da-Zhi Gao
- Department of General Surgery, 194043Dalian University Affiliated Xinhua Hospital, Dalian 116021, China
| | - Yu-Shen Yang
- Department of General Surgery, 194043Dalian University Affiliated Xinhua Hospital, Dalian 116021, China
| | - Zhun Wang
- Department of General Surgery, 194043Dalian University Affiliated Xinhua Hospital, Dalian 116021, China
| | - Xue-Feng Zhao
- Department of General Surgery, 194043Dalian University Affiliated Xinhua Hospital, Dalian 116021, China
| |
Collapse
|
8
|
Martinez R, Huang W, Buck H, Rea S, Defnet AE, Kane MA, Shapiro P. Proteomic Changes in the Monolayer and Spheroid Melanoma Cell Models of Acquired Resistance to BRAF and MEK1/2 Inhibitors. ACS OMEGA 2022; 7:3293-3311. [PMID: 35128241 PMCID: PMC8811929 DOI: 10.1021/acsomega.1c05361] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 12/31/2021] [Indexed: 06/14/2023]
Abstract
Extracellular signal-regulated kinase-1/2 (ERK1/2) pathway inhibitors are important therapies for treating many cancers. However, acquired resistance to most protein kinase inhibitors limits their ability to provide durable responses. Approximately 50% of malignant melanomas contain activating mutations in BRAF, which promotes cancer cell survival through the direct phosphorylation of the mitogen-activated protein kinase MAPK/ERK 1/2 (MEK1/2) and the activation of ERK1/2. Although the combination treatment with BRAF and MEK1/2 inhibitors is a recommended approach to treat melanoma, the development of drug resistance remains a barrier to achieving long-term patient benefits. Few studies have compared the global proteomic changes in BRAF/MEK1/2 inhibitor-resistant melanoma cells under different growth conditions. The current study uses high-resolution label-free mass spectrometry to compare relative protein changes in BRAF/MEK1/2 inhibitor-resistant A375 melanoma cells grown as monolayers or spheroids. While approximately 66% of proteins identified were common in the monolayer and spheroid cultures, only 6.2 or 3.6% of proteins that significantly increased or decreased, respectively, were common between the drug-resistant monolayer and spheroid cells. Drug-resistant monolayers showed upregulation of ERK-independent signaling pathways, whereas drug-resistant spheroids showed primarily elevated catabolic metabolism to support oxidative phosphorylation. These studies highlight the similarities and differences between monolayer and spheroid cell models in identifying actionable targets to overcome drug resistance.
Collapse
Affiliation(s)
- Ramon Martinez
- Department
of Pharmaceutical Sciences, University of
Maryland School of Pharmacy, 20 Penn Street, Baltimore, Maryland 21201, United
States
| | - Weiliang Huang
- Department
of Pharmaceutical Sciences, University of
Maryland School of Pharmacy, 20 Penn Street, Baltimore, Maryland 21201, United
States
| | - Heather Buck
- Nathan
Schnaper Internship Program in Translational Cancer Research, Marlene
and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, 22S. Greene Street, Baltimore, Maryland 21201, United States
| | - Samantha Rea
- Nathan
Schnaper Internship Program in Translational Cancer Research, Marlene
and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, 22S. Greene Street, Baltimore, Maryland 21201, United States
| | - Amy E. Defnet
- Department
of Pharmaceutical Sciences, University of
Maryland School of Pharmacy, 20 Penn Street, Baltimore, Maryland 21201, United
States
| | - Maureen A. Kane
- Department
of Pharmaceutical Sciences, University of
Maryland School of Pharmacy, 20 Penn Street, Baltimore, Maryland 21201, United
States
| | - Paul Shapiro
- Department
of Pharmaceutical Sciences, University of
Maryland School of Pharmacy, 20 Penn Street, Baltimore, Maryland 21201, United
States
| |
Collapse
|
9
|
Li X, Chen S, Zhu Y, Fei J, Song L, Sun G, Niu W, Guo L, Wang J. Comprehensive bioinformatics analyses identified Homeobox B9 as a potential prognostic biomarker and therapeutic target for gastric cancer. J Gastrointest Oncol 2021; 12:2132-2149. [PMID: 34790380 DOI: 10.21037/jgo-21-598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 10/16/2021] [Indexed: 12/24/2022] Open
Abstract
Background The Homeobox B (HOXB) family promotes tumor progression, but the mechanism of its action in gastric cancer (GC) is unclear. We sought to identify the HOXB family members that are critical to the prognosis of GC patients. Methods The Oncomine, Gene Expression Profiling Interactive Analysis (GEPIA), cBioPortal, UALCAN, Kaplan-Meier plotter, and the GeneMANIA databases were used to analyze the messenger RNA (mRNA) expression levels, prognostic value, and gene-gene interaction network of the HOXB9 family members in GC. The expression of HOXB9 in GC and its relationship with various clinicopathological parameters and the prognosis of patients were verified by immunohistochemistry. Results The expression of HOXB3, HOXB5, HOXB6, HOXB7, HOXB9, and HOXB13 mRNA was significantly upregulated in GC. There was a significant correlation between the upregulation of HOXB3, HOXB5, and HOXB9 mRNA and a low overall survival (OS) rate. The high expression of HOXB7, HOXB9, and HOXB13 mRNA was closely correlated to tumor grade and stage. HOXB9 was the HOXB family member most closely related to the occurrence and development of GC. A further analysis showed that HOXB9 might be involved in deoxyribonucleic acid repair and division regulation. A validation study showed that the advanced cancer group had a higher level of HOXB9 expression than the early cancer group. The high expression of HOXB9 in gastric tissue plays an important role in the survival and prognosis of GC patients. Conclusions HOXB family members have different degrees of abnormal expression in GC. High HOXB9 expression in GC tissues was significantly correlated with a worse prognosis. Thus, HOXB9 is a potential novel biomarker and therapeutic target for GC.
Collapse
Affiliation(s)
- Xiaofei Li
- Department of Gastroenterology, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, China
| | - Shujia Chen
- Department of Gastroenterology, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, China
| | - Yinghui Zhu
- Department of Gastroenterology, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, China
| | - Jiayue Fei
- Department of Gastroenterology, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, China
| | - Liaoyuan Song
- Department of Gastroenterology, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, China
| | - Guoyan Sun
- Department of Gastroenterology, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, China
| | - Wei Niu
- Department of Gastroenterology, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, China
| | - Lianyi Guo
- Department of Gastroenterology, The First Affiliated Hospital of Jinzhou Medical University, Jinzhou, China
| | - Jiwei Wang
- Department of Gastrointestinal Surgery, Xuzhou Central Hospital, Xuzhou, China
| |
Collapse
|
10
|
Li B, Kong X, Post H, Raaijmakers L, Peeper DS, Altelaar M. Proteomics and Phosphoproteomics Profiling of Drug-Addicted BRAFi-Resistant Melanoma Cells. J Proteome Res 2021; 20:4381-4392. [PMID: 34343000 PMCID: PMC8419860 DOI: 10.1021/acs.jproteome.1c00331] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Indexed: 11/29/2022]
Abstract
Acquired resistance to MAPK inhibitors limits the clinical efficacy in melanoma treatment. We and others have recently shown that BRAF inhibitor (BRAFi)-resistant melanoma cells can develop a dependency on the therapeutic drugs to which they have acquired resistance, creating a vulnerability for these cells that can potentially be exploited in cancer treatment. In drug-addicted melanoma cells, it was shown that this induction of cell death was preceded by a specific ERK2-dependent phenotype switch; however, the underlying molecular mechanisms are largely lacking. To increase the molecular understanding of this drug dependency, we applied a mass spectrometry-based proteomic approach on BRAFi-resistant BRAFMUT 451Lu cells, in which ERK1, ERK2, and JUNB were silenced separately using CRISPR-Cas9. Inactivation of ERK2 and, to a lesser extent, JUNB prevents drug addiction in these melanoma cells, while, conversely, knockout of ERK1 fails to reverse this phenotype, showing a response similar to that of control cells. Our analysis reveals that ERK2 and JUNB share comparable proteome responses dominated by reactivation of cell division. Importantly, we find that EMT activation in drug-addicted melanoma cells upon drug withdrawal is affected by silencing ERK2 but not ERK1. Moreover, transcription factor (regulator) enrichment shows that PIR acts as an effector of ERK2 and phosphoproteome analysis reveals that silencing of ERK2 but not ERK1 leads to amplification of GSK3 kinase activity. Our results depict possible mechanisms of drug addiction in melanoma, which may provide a guide for therapeutic strategies in drug-resistant melanoma.
Collapse
Affiliation(s)
- Bohui Li
- Biomolecular
Mass Spectrometry and Proteomics Group, Utrecht Institute for Pharmaceutical
Science, Utrecht University, Utrecht 3584 CH, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Xiangjun Kong
- Division
of Molecular Oncology and Immunology, The
Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Harm Post
- Biomolecular
Mass Spectrometry and Proteomics Group, Utrecht Institute for Pharmaceutical
Science, Utrecht University, Utrecht 3584 CH, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Linsey Raaijmakers
- Biomolecular
Mass Spectrometry and Proteomics Group, Utrecht Institute for Pharmaceutical
Science, Utrecht University, Utrecht 3584 CH, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| | - Daniel S. Peeper
- Division
of Molecular Oncology and Immunology, The
Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
| | - Maarten Altelaar
- Biomolecular
Mass Spectrometry and Proteomics Group, Utrecht Institute for Pharmaceutical
Science, Utrecht University, Utrecht 3584 CH, The Netherlands
- Netherlands
Proteomics Center, Padualaan
8, 3584 CH Utrecht, The Netherlands
| |
Collapse
|
11
|
Epigenetic Regulation in Melanoma: Facts and Hopes. Cells 2021; 10:cells10082048. [PMID: 34440824 PMCID: PMC8392422 DOI: 10.3390/cells10082048] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 07/31/2021] [Accepted: 08/02/2021] [Indexed: 12/25/2022] Open
Abstract
Cutaneous melanoma is a lethal disease, even when diagnosed in advanced stages. Although recent progress in biology and treatment has dramatically improved survival rates, new therapeutic approaches are still needed. Deregulation of epigenetics, which mainly controls DNA methylation status and chromatin remodeling, is implied not only in cancer initiation and progression, but also in resistance to antitumor drugs. Epigenetics in melanoma has been studied recently in both melanoma preclinical models and patient samples, highlighting its potential role in different phases of melanomagenesis, as well as in resistance to approved drugs such as immune checkpoint inhibitors and MAPK inhibitors. This review summarizes what is currently known about epigenetics in melanoma and dwells on the recognized and potential new targets for testing epigenetic drugs, alone or together with other agents, in advanced melanoma patients.
Collapse
|
12
|
Xu C, Wang YN, Wu H. Glutaminyl Cyclase, Diseases, and Development of Glutaminyl Cyclase Inhibitors. J Med Chem 2021; 64:6549-6565. [PMID: 34000808 DOI: 10.1021/acs.jmedchem.1c00325] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Pyroglutamate (pE) modification, catalyzed mainly by glutaminyl cyclase (QC), is prevalent throughout nature and is particularly important in mammals including humans for the maturation of hormones, peptides, and proteins. In humans, the upregulation of QC is involved in multiple diseases and conditions including Alzheimer's disease, Huntington's disease, melanomas, thyroid carcinomas, accelerated atherosclerosis, septic arthritics, etc. This upregulation catalyzes the generation of modified mediators such as pE-amyloid beta (Aß) and pE-chemokine ligand 2 (CCL2) peptides. Not surprisingly, QC has emerged as a reasonable target for the development of therapeutics to combat these diseases and conditions. In this manuscript the deleterious effects of upregulated QC resulting in disease manifestation are reviewed, along with progress on the development of QC inhibitors.
Collapse
Affiliation(s)
- Chenshu Xu
- School of Pharmaceutical Sciences, Health Science Center, Shenzhen University, Shenzhen 518060, China
| | - Yi-Nan Wang
- School of Pharmaceutical Sciences, Health Science Center, Shenzhen University, Shenzhen 518060, China
| | - Haiqiang Wu
- School of Pharmaceutical Sciences, Health Science Center, Shenzhen University, Shenzhen 518060, China
| |
Collapse
|
13
|
Li Y, Shi J, Yang J, Ge S, Zhang J, Jia R, Fan X. Uveal melanoma: progress in molecular biology and therapeutics. Ther Adv Med Oncol 2020; 12:1758835920965852. [PMID: 33149769 PMCID: PMC7586035 DOI: 10.1177/1758835920965852] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 09/16/2020] [Indexed: 12/15/2022] Open
Abstract
Uveal melanoma (UM) is the most common intraocular malignancy in adults. So far, no systemic therapy or standard treatment exists to reduce the risk of metastasis and improve overall survival of patients. With the increased knowledge regarding the molecular pathways that underlie the oncogenesis of UM, it is expected that novel therapeutic approaches will be available to conquer this disease. This review provides a summary of the current knowledge of, and progress made in understanding, the pathogenesis, genetic mutations, epigenetics, and immunology of UM. With the advent of the omics era, multi-dimensional big data are publicly available, providing an innovation platform to develop effective targeted and personalized therapeutics for UM patients. Indeed, recently, a great number of therapies have been reported specifically for UM caused by oncogenic mutations, as well as other etiologies. In this review, special attention is directed to advancements in targeted therapies. In particular, we discuss the possibilities of targeting: GNAQ/GNA11, PLCβ, and CYSLTR2 mutants; regulators of G-protein signaling; the secondary messenger adenosine diphosphate (ADP)-ribosylation factor 6 (ARF6); downstream pathways, such as those involving mitogen-activated protein kinase/MEK/extracellular signal-related kinase, protein kinase C (PKC), phosphoinositide 3-kinase/Akt/mammalian target of rapamycin (mTOR), Trio/Rho/Rac/Yes-associated protein, and inactivated BAP1; and immune-checkpoint proteins cytotoxic T-lymphocyte antigen 4 and programmed cell-death protein 1/programmed cell-death ligand 1. Furthermore, we conducted a survey of completed and ongoing clinical trials applying targeted and immune therapies for UM. Although drug combination therapy based on the signaling pathways involved in UM has made great progress, targeted therapy is still an unmet medical need.
Collapse
Affiliation(s)
- Yongyun Li
- Department of Ophthalmology, Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
| | - Jiahao Shi
- Department of Ophthalmology, Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
| | - Jie Yang
- Department of Ophthalmology, Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
| | - Shengfang Ge
- Department of Ophthalmology, Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, China
| | - Jianming Zhang
- National Research Center for Translational Medicine, Shanghai State Key Laboratory of Medical Genomics, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Renbing Jia
- Department of Ophthalmology, Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhizaoju Road, Huangpu District, Shanghai 200001, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200001, China
| | - Xianqun Fan
- Department of Ophthalmology, Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhizaoju Road, Huangpu District, Shanghai 200001, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, 833 Zhizaoju Road, Huangpu District, Shanghai 200001, China
| |
Collapse
|
14
|
Yamamoto Y, Matsusaka K, Fukuyo M, Rahmutulla B, Matsue H, Kaneda A. Higher methylation subtype of malignant melanoma and its correlation with thicker progression and worse prognosis. Cancer Med 2020; 9:7194-7204. [PMID: 32406600 PMCID: PMC7541157 DOI: 10.1002/cam4.3127] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 04/08/2020] [Accepted: 04/23/2020] [Indexed: 01/12/2023] Open
Abstract
Malignant melanoma (MM) is the most life‐threatening disease among all skin malignancies, and recent genome‐wide studies reported BRAF, RAS, and NF1 as the most frequently mutated driver genes. While epigenetic aberrations are known to contribute to the oncogenic activity seen in various cancers, their role in MM has not been fully investigated. To investigate the role of epigenetic aberrations in MM, we performed genome‐wide DNA methylation analysis of 51 clinical MM samples using Infinium 450k beadarray. Hierarchical clustering analysis stratified MM into two DNA methylation epigenotypes: high‐ and low‐methylation subgroups. Tumor thickness was significantly greater in case of high‐methylation tumors than low‐methylation tumors (8.3 ± 5.3 mm vs 4.5 ± 2.9 mm, P = .003). Moreover, prognosis was significantly worse in high‐methylation cases (P = .03). Twenty‐seven genes were found to undergo significant and frequent hypermethylation in high‐methylation subgroup, where TFPI2 was identified as the most frequently hypermethylated gene. MM cases with lower expression levels of TFPI2 showed significantly worse prognosis (P = .001). Knockdown of TFPI2 in two MM cell lines, CHL‐1 and G361, resulted in significant increases of cell proliferation and invasion. These indicate that MM can be stratified into at least two different epigenetic subgroups, that the MM subgroup with higher DNA methylation shows a more progressive phenotype, and that methylation of TFPI2 may contribute to the tumor progression of MM.
Collapse
Affiliation(s)
- Yosuke Yamamoto
- Department of Dermatology, Graduate School of Medicine, Chiba University, Chiba, Japan.,Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Keisuke Matsusaka
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Masaki Fukuyo
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan.,Department of Genome Research and Development, Kazusa DNA Research Institute, Chiba, Japan
| | - Bahityar Rahmutulla
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Hiroyuki Matsue
- Department of Dermatology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Atsushi Kaneda
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| |
Collapse
|
15
|
Pogribna M, Koonce NA, Mathew A, Word B, Patri AK, Lyn-Cook B, Hammons G. Effect of titanium dioxide nanoparticles on DNA methylation in multiple human cell lines. Nanotoxicology 2020; 14:534-553. [PMID: 32031460 DOI: 10.1080/17435390.2020.1723730] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 01/07/2020] [Accepted: 01/24/2020] [Indexed: 12/27/2022]
Abstract
Nanoscale titanium dioxide (TiO2) is manufactured in wide scale, with a range of applications in consumer products. Significant toxicity of TiO2 nanoparticles has, however, been recognized, suggesting considerable risk to human health. To evaluate fully their toxicity, assessment of the epigenetic action of these nanoparticles is critical. However, only few studies are available examining capability of nanoparticles to alter epigenetic integrity. In the present study, the effect of TiO2 nanoparticles exposure on DNA methylation, a major epigenetic mechanism, was investigated in in vitro cellular model systems. A panel of cells relevant to portals of human exposure (Caco-2 (colorectal), HepG2 (liver), NL20 (lung), and A-431 (skin)) was exposed to TiO2 nanoparticles to assess effects on global methylation, gene-specific methylation, and expression levels of DNA methyltransferases, MBD2, and UHRF1. Global methylation was determined by enzyme-linked immunosorbent assay-based immunochemical analysis. Degree of promoter methylation across a defined panel of genes was evaluated using EpiTect Methyl II Signature PCR System Array technology. Expression of DNMT1, DNMT3a, DNMT3b, MBD2, and URHF1 was quantified by qRT-PCR. Decrease in global DNA methylation in cell lines Caco-2, HepG2, and A-431 exposed to TiO2 nanoparticles was shown. Across four cell lines, eight genes (CDKN1A, DNAJC15, GADD45A, GDF15, INSIG1, SCARA3, TP53, and BNIP3) were identified in which promotors were methylated after exposure. Altered expression of these genes is associated with disease etiology. The results also revealed aberrant expression of epigenetic regulatory genes involved in DNA methylation (DNMT1, DNMT3a, DNMT3b, MBD2, and UHRF1) in TiO2 exposed cells, which was cell type dependent. Findings from this study clearly demonstrate the impact of TiO2 nanoparticles exposure on DNA methylation in multiple cell types, supporting potential involvement of this epigenetic mechanism in the toxicity of TiO2 nanoparticles. Hence for complete assessment of potential risk from nanoparticle exposure, epigenetic studies are critical.
Collapse
Affiliation(s)
- Marta Pogribna
- Division of Biochemical Toxicity, FDA/National Center for Toxicological Research, Jefferson, AR, USA
| | - Nathan A Koonce
- Nanotechology Core, FDA/National Center for Toxicological Research, Jefferson, AR, USA
| | - Ammu Mathew
- Nanotechology Core, FDA/National Center for Toxicological Research, Jefferson, AR, USA
| | - Beverly Word
- Division of Biochemical Toxicity, FDA/National Center for Toxicological Research, Jefferson, AR, USA
| | - Anil K Patri
- Nanotechology Core, FDA/National Center for Toxicological Research, Jefferson, AR, USA
| | - Beverly Lyn-Cook
- Division of Biochemical Toxicity, FDA/National Center for Toxicological Research, Jefferson, AR, USA
| | - George Hammons
- Division of Biochemical Toxicity, FDA/National Center for Toxicological Research, Jefferson, AR, USA
| |
Collapse
|
16
|
Zuo L, Tan T, Wei C, Wang H, Tan L, Hao Y, Qian J, Chen Y, Wu C. HOXB13 expression is correlated with hepatic inflammatory activity of patients with hepatic fibrosis. J Mol Histol 2020; 51:183-189. [PMID: 32200464 DOI: 10.1007/s10735-020-09868-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Accepted: 03/18/2020] [Indexed: 01/10/2023]
Abstract
Liver fibrosis is a common pathological process of chronic hepatic injury, preceded by the chronic inflammation. The homeobox B13 (HOXB13) gene, a member of HOX family, plays diverse biological roles in embryonic development, carcinogenesis, and many inflammatory diseases. However, the expression of HOXB13 in chronic liver diseases including hepatic fibrosis remains to be defined. In present study, 55 patients with hepatic fibrosis, 15 patients of hepatocellular carcinoma, and 17 healthy controls were enrolled in this study. Pathological specimens were collected through liver biopsy or surgical resection. The degree of hepatic inflammation (G0-G4) and fibrosis (S0-S4) of hepatic fibrosis was scored based on the modified histology activity index. Intrahepatic HOXB13 expression was analyzed using immunohistochemistry analysis. Compared with healthy subjects, both patients with hepatic fibrosis and patients with hepatocellular carcinoma exhibited significant accumulations of HOXB13+ cells in the liver (p < 0.05). Additionally, the number of HOXB13+ cell was significantly elevated along with the increment of hepatic inflammatory activities, but not fibrosis stages, among these liver fibrosis samples (p < 0.01). Furthermore, the quantity of HOXB13+ cells were also positively correlated with hepatic enzymes, alanine transaminase (r = 0.299, p = 0.041) and aspartate aminotransferase (r = 0.317, p = 0.013) in our cohort of hepatic fibrosis. In conclusion, our study identified a strong hepatic expression of HOXB13 among patients with hepatic fibrosis, which strongly associated with the degree of hepatic inflammatory activity for patients with hepatic fibrosis, suggesting an important role of HOXB13 during the pathogenesis of liver fibrogenesis.
Collapse
Affiliation(s)
- Lingyun Zuo
- Department of Infectious Diseases, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, Jiangsu, China
- Department of Gastroenterology, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Tingting Tan
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Cheng Wei
- Department of Gastroenterology, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Huali Wang
- Department of Gastroenterology, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Luxuan Tan
- Department of Gastroenterology, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Yingying Hao
- Department of Intensive Care Units, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, Jiangsu, China
| | - Jingjing Qian
- Department of Gastroenterology, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Yuxin Chen
- Department of Laboratory Medicine, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, Jiangsu, China.
| | - Chao Wu
- Department of Infectious Diseases, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, Jiangsu, China.
| |
Collapse
|
17
|
The mitochondrial negative regulator MCJ modulates the interplay between microbiota and the host during ulcerative colitis. Sci Rep 2020; 10:572. [PMID: 31953445 PMCID: PMC6969106 DOI: 10.1038/s41598-019-57348-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 12/17/2019] [Indexed: 01/14/2023] Open
Abstract
Recent evidences indicate that mitochondrial genes and function are decreased in active ulcerative colitis (UC) patients, in particular, the activity of Complex I of the electron transport chain is heavily compromised. MCJ is a mitochondrial inner membrane protein identified as a natural inhibitor of respiratory chain Complex I. The induction of experimental colitis in MCJ-deficient mice leads to the upregulation of Timp3 expression resulting in the inhibition of TACE activity that likely inhibits Tnf and Tnfr1 shedding from the cell membrane in the colon. MCJ-deficient mice also show higher expression of Myd88 and Tlr9, proinflammatory genes and disease severity. Interestingly, the absence of MCJ resulted in distinct microbiota metabolism and composition, including a member of the gut community in UC patients, Ruminococcus gnavus. These changes provoked an effect on IgA levels. Gene expression analyses in UC patients showed decreased levels of MCJ and higher expression of TIMP3, suggesting a relevant role of mitochondrial genes and function among active UC. The MCJ deficiency disturbs the regulatory relationship between the host mitochondria and microbiota affecting disease severity. Our results indicate that mitochondria function may be an important factor in the pathogenesis. All together support the importance of MCJ regulation during UC.
Collapse
|
18
|
Kassouf T, Larive RM, Morel A, Urbach S, Bettache N, Marcial Medina MC, Mèrezègue F, Freiss G, Peter M, Boissière-Michot F, Solassol J, Montcourrier P, Coopman P. The Syk Kinase Promotes Mammary Epithelial Integrity and Inhibits Breast Cancer Invasion by Stabilizing the E-Cadherin/Catenin Complex. Cancers (Basel) 2019; 11:cancers11121974. [PMID: 31817924 PMCID: PMC6966528 DOI: 10.3390/cancers11121974] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 11/28/2019] [Accepted: 12/04/2019] [Indexed: 12/20/2022] Open
Abstract
While first discovered in immunoreceptor signaling, the Syk protein kinase behaves as a tumor and metastasis suppressor in epithelial cells. Its reduced expression in breast and other carcinomas is correlated with decreased survival and increased metastasis risk, but its action mechanism remains largely unknown. Using phosphoproteomics we found that Syk phosphorylated E-cadherin and α-, β-, and p120-catenins on multiple tyrosine residues that concentrate at intercellular junctions. Increased Syk expression and activation enhanced E-cadherin/catenin phosphorylation, promoting their association and complex stability. In human breast cancer cells, Syk stimulated intercellular aggregation, E-cadherin recruitment and retention at adherens junctions, and promoted epithelial integrity, whereas it inhibited cell migration and invasion. Opposite effects were obtained with Syk knockdown or non-phosphorylatable mutant E-cadherin expression. Mechanistically, Syk stimulated the interaction of the E-cadherin/catenin complex with zonula occludens proteins and the actin cytoskeleton. Conditional Syk knockout in the lactating mouse mammary gland perturbed alveologenesis and disrupted E-cadherin localization at adherens junctions, corroborating the observations in cells. Hence, Syk is involved in the maintenance of the epithelial integrity of the mammary gland via the phosphorylation and stabilization of the E-cadherin/catenin adherens junction complex, thereby inhibiting cell migration and malignant tumor invasion.
Collapse
Affiliation(s)
- Toufic Kassouf
- IRCM, Inserm, CNRS, Universit@#xE9; de Montpellier, ICM, 208 Rue des Apothicaires, 34298 Montpellier, France; (T.K.); (R.M.L.); (G.F.); (M.P.); (J.S.)
- CRBM, CNRS, Université de Montpellier, 1919 Route de Mende, 34293 Montpellier, France;
| | - Romain Maxime Larive
- IRCM, Inserm, CNRS, Universit@#xE9; de Montpellier, ICM, 208 Rue des Apothicaires, 34298 Montpellier, France; (T.K.); (R.M.L.); (G.F.); (M.P.); (J.S.)
- IBMM, Université de Montpellier, CNRS, ENSCM, 15 avenue Charles Flahault - BP 14491, 34093 Montpellier, France;
| | - Anne Morel
- CRBM, CNRS, Université de Montpellier, 1919 Route de Mende, 34293 Montpellier, France;
| | - Serge Urbach
- Functional Proteomics Platform, IGF, Université de Montpellier, CNRS, INSERM, 141 rue de la Cardonille, 34094 Montpellier, France;
| | - Nadir Bettache
- IBMM, Université de Montpellier, CNRS, ENSCM, 15 avenue Charles Flahault - BP 14491, 34093 Montpellier, France;
| | | | - Fabrice Mèrezègue
- BioMV Department, Université de Montpellier CC25000, Place Eugène Bataillon, 34095 Montpellier, France;
| | - Gilles Freiss
- IRCM, Inserm, CNRS, Universit@#xE9; de Montpellier, ICM, 208 Rue des Apothicaires, 34298 Montpellier, France; (T.K.); (R.M.L.); (G.F.); (M.P.); (J.S.)
| | - Marion Peter
- IRCM, Inserm, CNRS, Universit@#xE9; de Montpellier, ICM, 208 Rue des Apothicaires, 34298 Montpellier, France; (T.K.); (R.M.L.); (G.F.); (M.P.); (J.S.)
| | | | - Jérôme Solassol
- IRCM, Inserm, CNRS, Universit@#xE9; de Montpellier, ICM, 208 Rue des Apothicaires, 34298 Montpellier, France; (T.K.); (R.M.L.); (G.F.); (M.P.); (J.S.)
| | - Philippe Montcourrier
- IRCM, Inserm, CNRS, Universit@#xE9; de Montpellier, ICM, 208 Rue des Apothicaires, 34298 Montpellier, France; (T.K.); (R.M.L.); (G.F.); (M.P.); (J.S.)
| | - Peter Coopman
- IRCM, Inserm, CNRS, Universit@#xE9; de Montpellier, ICM, 208 Rue des Apothicaires, 34298 Montpellier, France; (T.K.); (R.M.L.); (G.F.); (M.P.); (J.S.)
- Correspondence: ; Tel.: +33-467-61-3191
| |
Collapse
|
19
|
Xie B, Bai B, Xu Y, Liu Y, Lv Y, Gao X, Wu F, Fang Z, Lou Y, Pan H, Han W. Tumor-suppressive function and mechanism of HOXB13 in right-sided colon cancer. Signal Transduct Target Ther 2019; 4:51. [PMID: 31815008 PMCID: PMC6882800 DOI: 10.1038/s41392-019-0086-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 10/07/2019] [Accepted: 10/10/2019] [Indexed: 01/05/2023] Open
Abstract
Right-sided colon cancer (RCC) and left-sided colon cancer (LCC) differ in their clinical and molecular features. An investigation of differentially expressed genes (DEGs) between RCC and LCC could contribute to targeted therapy for colon cancer, especially RCC, which has a poor prognosis. Here, we identified HOXB13, which was significantly less expressed in RCC than in LCC and associated with prognosis in RCC, by using 5 datasets from the Gene Expression Omnibus (GEO). Tissue sample analysis showed that HOXB13 was differentially expressed between normal and only RCC tumor tissues. HOXB13 inhibited colon cancer cell proliferation and induced apoptosis both in vitro and in vivo. Furthermore, we found that HOXB13 might be regulated by DNMT3B and suppress C-myc expression to exert antitumor effects via β-catenin/TCF4 signals in RCC. In conclusion, the current study is the first to demonstrate that HOXB13 has a tumor-suppressive effect in RCC. High expression levels of HOXB13 are associated with prolonged overall survival in patients with RCC. The DNMT3B-HOXB13-C-myc signaling axis might be a molecular target for the treatment of RCC.
Collapse
Affiliation(s)
- Binbin Xie
- Department of Medical Oncology; Sir Run Run Shaw Hospital; School of Medicine, Zhejiang University, Hangzhou, 310016 PR China
| | - Bingjun Bai
- Department of Colorectal Surgery; Sir Run Run Shaw Hospital; School of Medicine, Zhejiang University, Hangzhou, 310016 PR China
| | - Yuzi Xu
- Department of Stomatology; Stomatology Hospital; School of Medicine, Zhejiang University, Hangzhou, 310000 PR China
| | - Yunlong Liu
- Department of Medical Oncology; Sir Run Run Shaw Hospital; School of Medicine, Zhejiang University, Hangzhou, 310016 PR China
| | - Yiming Lv
- Department of Colorectal Surgery; Sir Run Run Shaw Hospital; School of Medicine, Zhejiang University, Hangzhou, 310016 PR China
| | - Xing Gao
- Department of Medical Oncology; The Second Affiliated Hospital of Suzhou University; School of Medicine, Suzhou University, Suzhou, 215000 PR China
| | - Fei Wu
- School of Medicine, Anhui University of Science and Technology, Huainan, 232001 PR China
| | - Zhipeng Fang
- Department of Medical Oncology; Sir Run Run Shaw Hospital; School of Medicine, Zhejiang University, Hangzhou, 310016 PR China
| | - Ying Lou
- Department of Medical Oncology; Sir Run Run Shaw Hospital; School of Medicine, Zhejiang University, Hangzhou, 310016 PR China
| | - Hongming Pan
- Department of Medical Oncology; Sir Run Run Shaw Hospital; School of Medicine, Zhejiang University, Hangzhou, 310016 PR China
| | - Weidong Han
- Department of Medical Oncology; Sir Run Run Shaw Hospital; School of Medicine, Zhejiang University, Hangzhou, 310016 PR China
| |
Collapse
|
20
|
RNA Sequencing revealed differentially expressed genes functionally associated with immunity and tumor suppression during latent phase infection of a vv + MDV in chickens. Sci Rep 2019; 9:14182. [PMID: 31578366 PMCID: PMC6775254 DOI: 10.1038/s41598-019-50561-x] [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: 07/14/2018] [Accepted: 09/11/2019] [Indexed: 11/08/2022] Open
Abstract
Very virulent plus Marek's disease (MD) virus (vv + MDV) induces tumors in relatively resistant lines of chickens and early mortality in highly susceptible lines of chickens. The vv + MDV also triggers a series of cellular responses in both types of chickens. We challenged birds sampled from a highly inbred chicken line (line 63) that is relatively resistant to MD and from another inbred line (line 72) that is highly susceptible to MD with a vv + MDV. RNA-sequencing analysis was performed with samples extracted from spleen tissues taken at 10-day and 21-day post infection (dpi). A total of 64 and 106 differentially expressed genes was identified in response to the vv + MDV challenge at latent phase in the resistant and susceptible lines of chickens, respectively. Direct comparisons between samples of the two lines identified 90 and 126 differentially expressed genes for control and MDV challenged groups, respectively. The differentially expressed gene profiles illustrated that intensive defense responses were significantly induced by vv + MDV at 10 dpi and 21 dpi but with slight changes in the resistant line. In contrast, vv + MDV induced a measurable suppression of gene expression associated with host defense at 10 dpi but followed by an apparent activation of the defense response at 21 dpi in the susceptible line of chickens. The observed difference in gene expression between the two genetic lines of chickens in response to MDV challenge during the latent phase provided a piece of indirect evidence that time points for MDV reactivation differ between the genetic lines of chickens with different levels of genetic resistance to MD. Early MDV reactivation might be necessary and potent to host defense system readiness for damage control of tumorigenesis and disease progression, which consequently results in measurable differences in phenotypic characteristics including early mortality (8 to 20 dpi) and tumor incidence between the resistant and susceptible lines of chickens. Combining differential gene expression patterns with reported GO function terms and quantitative trait loci, a total of 27 top genes was selected as highly promising candidate genes for genetic resistance to MD. These genes are functionally involved with virus process (F13A1 and HSP90AB1), immunity (ABCB1LB, RGS5, C10ORF58, OSF-2, MMP7, CXCL12, GAL1, GAL2, GAL7, HVCN1, PDE4D, IL4I1, PARP9, EOMES, MPEG1, PDK4, CCLI10, K60 and FST), and tumor suppression (ADAMTS2, LXN, ARRDC3, WNT7A, CLDN1 and HPGD). It is anticipated that these findings will facilitate advancement in the fundamental understanding on mechanisms of genetic resistance to MD. In addition, such advancement may also provide insights on tumor virus-induced tumorigenesis in general and help the research community recognize MD study may serve as a good model for oncology study involving tumor viruses.
Collapse
|
21
|
Wang X, Wang L, Yu X, Li Y, Liu Z, Zou Y, Zheng Y, He Z, Wu H. Glutaminyl cyclase inhibitor exhibits anti-inflammatory effects in both AD and LPS-induced inflammatory model mice. Int Immunopharmacol 2019; 75:105770. [DOI: 10.1016/j.intimp.2019.105770] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 07/13/2019] [Accepted: 07/18/2019] [Indexed: 01/08/2023]
|
22
|
Chiang TC, Koss B, Su LJ, Washam CL, Byrum SD, Storey A, Tackett AJ. Effect of Sulforaphane and 5-Aza-2'-Deoxycytidine on Melanoma Cell Growth. MEDICINES 2019; 6:medicines6030071. [PMID: 31252639 PMCID: PMC6789461 DOI: 10.3390/medicines6030071] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 06/21/2019] [Accepted: 06/24/2019] [Indexed: 12/12/2022]
Abstract
Background: UV exposure-induced oxidative stress is implicated as a driving mechanism for melanoma. Increased oxidative stress results in DNA damage and epigenetic dysregulation. Accordingly, we explored whether a low dose of the antioxidant sulforaphane (SFN) in combination with the epigenetic drug 5-aza-2’-deoxycytidine (DAC) could slow melanoma cell growth. SFN is a natural bioactivated product of the cruciferous family, while DAC is a DNA methyltransferase inhibitor. Methods: Melanoma cell growth characteristics, gene transcription profiles, and histone epigenetic modifications were measured after single and combination treatments with SFN and DAC. Results: We detected melanoma cell growth inhibition and specific changes in gene expression profiles upon combinational treatments with SFN and DAC, while no significant alterations in histone epigenetic modifications were observed. Dysregulated gene transcription of a key immunoregulator cytokine—C-C motif ligand 5 (CCL-5)—was validated. Conclusions: These results indicate a potential combinatorial effect of a dietary antioxidant and an FDA-approved epigenetic drug in controlling melanoma cell growth.
Collapse
Affiliation(s)
- Tung-Chin Chiang
- Department of Environmental and Occupational Health, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
| | - Brian Koss
- Department of Biochemistry & Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - L Joseph Su
- Winthrop P. Rockefeller Cancer Institute, Cancer Prevention and Population Sciences Program & Department of Epidemiology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Charity L Washam
- Department of Biochemistry & Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
- Arkansas Children's Research Institute, Little Rock, AR 72202, USA
| | - Stephanie D Byrum
- Department of Biochemistry & Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
- Arkansas Children's Research Institute, Little Rock, AR 72202, USA
| | - Aaron Storey
- Department of Biochemistry & Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Alan J Tackett
- Department of Biochemistry & Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
- Arkansas Children's Research Institute, Little Rock, AR 72202, USA.
| |
Collapse
|
23
|
Wang X, Sun Y, Xu T, Qian K, Huang B, Zhang K, Song Z, Qian T, Shi J, Li L. HOXB13 promotes proliferation, migration, and invasion of glioblastoma through transcriptional upregulation of lncRNA HOXC-AS3. J Cell Biochem 2019; 120:15527-15537. [PMID: 31062400 DOI: 10.1002/jcb.28819] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Revised: 04/02/2019] [Accepted: 04/08/2019] [Indexed: 11/08/2022]
Abstract
HOXB13 exerts a close relation in several human cancers. This study explored the role of HOXB13 in glioblastoma (GBM), a brain tissue with the highest aggressive rate and mortality in adults. Through microarray and immunohistochemistry analyses, HOXB13 was highly expressed in GBM tissues. Furthermore, we showed that high-level expression of HOXB13 in GBM was associated with worse survival, suggesting that HOXB13 could be a prognostic marker for patients with GBM. GBM cells U87 and U251 overexpressing HOXB13 showed enhanced proliferation, migration, and invasion relative to the control cells, while knockdown of HOXB13 led to decreased cell proliferation, migration, and invasion abilities. In addition, dual-luciferase report assay, chromatin immunoprecipitation assay, and quantitative real-time polymerase chain reaction data showed that HOXB13 directly bound to HOXC-AS3 promoter. HOXC-AS3 was involved in HOXB13-induced proliferation, migration, and invasion of GBM cells. In summary, this study revealed the prognostic potential of HOXB13 in GBM. We believed that HOXB13/HOXC-AS3 signaling axis can be served as therapeutic targets for this highly aggressive cancer.
Collapse
Affiliation(s)
- Xi Wang
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yi Sun
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Tuoye Xu
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Kai Qian
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Baosheng Huang
- Department of Neurosurgery, Sir Run Run Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Kaixin Zhang
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China.,Department of Neurosurgery, Huangshan City People's Hospital, Huangshan, Anhui, China
| | - Zewu Song
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Tengda Qian
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jing Shi
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Lixin Li
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| |
Collapse
|
24
|
Single-nucleotide polymorphisms and mRNA expression of CYP1B1 influence treatment response in triple negative breast cancer patients undergoing chemotherapy. J Genet 2018. [DOI: 10.1007/s12041-018-1013-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
25
|
Zhou D, Ota K, Nardin C, Feldman M, Widman A, Wind O, Simon A, Reilly M, Levin LR, Buck J, Wakamatsu K, Ito S, Zippin JH. Mammalian pigmentation is regulated by a distinct cAMP-dependent mechanism that controls melanosome pH. Sci Signal 2018; 11:11/555/eaau7987. [PMID: 30401788 DOI: 10.1126/scisignal.aau7987] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The production of melanin increases skin pigmentation and reduces the risk of skin cancer. Melanin production depends on the pH of melanosomes, which are more acidic in lighter-skinned than in darker-skinned people. We showed that inhibition of soluble adenylyl cyclase (sAC) controlled pigmentation by increasing the pH of melanosomes both in cells and in vivo. Distinct from the canonical melanocortin 1 receptor (MC1R)-dependent cAMP pathway that controls pigmentation by altering gene expression, we found that inhibition of sAC increased pigmentation by increasing the activity of tyrosinase, the rate-limiting enzyme in melanin synthesis, which is more active at basic pH. We demonstrated that the effect of sAC activity on pH and melanin production in human melanocytes depended on the skin color of the donor. Last, we identified sAC inhibitors as a new class of drugs that increase melanosome pH and pigmentation in vivo, suggesting that pharmacologic inhibition of this pathway may affect skin cancer risk or pigmentation conditions.
Collapse
Affiliation(s)
- Dalee Zhou
- Department of Dermatology, Weill Cornell Medical College, New York, NY 10021, USA
| | - Koji Ota
- Department of Dermatology, Weill Cornell Medical College, New York, NY 10021, USA
| | - Charlee Nardin
- Department of Dermatology, Weill Cornell Medical College, New York, NY 10021, USA.,Service de Dermatologie, Centre Hospitalier Universitaire, Besançon 25030, France
| | - Michelle Feldman
- Department of Dermatology, Weill Cornell Medical College, New York, NY 10021, USA
| | - Adam Widman
- Department of Dermatology, Weill Cornell Medical College, New York, NY 10021, USA
| | - Olivia Wind
- Department of Dermatology, Weill Cornell Medical College, New York, NY 10021, USA
| | - Amanda Simon
- Department of Dermatology, Weill Cornell Medical College, New York, NY 10021, USA
| | - Michael Reilly
- Department of Dermatology, Weill Cornell Medical College, New York, NY 10021, USA
| | - Lonny R Levin
- Department of Pharmacology, Weill Cornell Medical College, New York, NY 10065, USA
| | - Jochen Buck
- Department of Pharmacology, Weill Cornell Medical College, New York, NY 10065, USA
| | - Kazumasa Wakamatsu
- Department of Chemistry, Fujita Health University School of Health Sciences, Toyoake 470-1192, Japan
| | - Shosuke Ito
- Department of Chemistry, Fujita Health University School of Health Sciences, Toyoake 470-1192, Japan
| | - Jonathan H Zippin
- Department of Dermatology, Weill Cornell Medical College, New York, NY 10021, USA.
| |
Collapse
|
26
|
Mitsiogianni M, Amery T, Franco R, Zoumpourlis V, Pappa A, Panayiotidis MI. From chemo-prevention to epigenetic regulation: The role of isothiocyanates in skin cancer prevention. Pharmacol Ther 2018; 190:187-201. [DOI: 10.1016/j.pharmthera.2018.06.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
|
27
|
Sui BQ, Zhang CD, Liu JC, Wang L, Dai DQ. HOXB13 expression and promoter methylation as a candidate biomarker in gastric cancer. Oncol Lett 2018; 15:8833-8840. [PMID: 29928325 DOI: 10.3892/ol.2018.8371] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Accepted: 07/03/2017] [Indexed: 12/16/2022] Open
Abstract
Homeobox b13 (HOXB13) is considered to be a tumor suppressor gene in multiple types of human cancer. The present study aimed to identify the difference in expression of HOXB13 mRNA between gastric cancer (GC) tissues and corresponding non-malignant gastric tissues. The clinical significance of HOXB13 mRNA expression was also assessed in GC and a potential association between HOXB13 mRNA expression and DNA promoter methylation was observed. The expression of HOXB13 mRNA was assessed by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and HOXB13 methylation status was assessed by methylation-specific PCR (MSP) in 5 GC cell lines and 85 paired GC and normal gastric tissues. Kaplan-Meier survival curves were used to assess the survival of patients with GC. HOXB13 mRNA expression was significantly lower in primary GC tissues than in corresponding nonmalignant gastric tissues, and decreased HOXB13 expression was associated with poorer differentiation, lymph node metastasis, invasion depth and Tumor-Node-Metastasis (TNM) stage. Kaplan-Meier survival analysis demonstrated that HOXB13 mRNA expression was a significant prognostic indicator of GC patient survival. Furthermore, MSP revealed that the proportion of GC samples with hypermethylated HOXB13 (60.0%, 51/85) was increased compared with the corresponding nonmalignant gastric tissues (11.8%, 10/85). Decreased HOXB13 mRNA expression was due to DNA hypermethylation as following treatment with the DNA methyltransferase inhibitor 5-Aza-dC, HOXB13 expression in the GC MKN-45 cell line was upregulated. The results of the present study indicate that decreased expression of HOXB13 mRNA was associated with tumor differentiation, depth of invasion, lymph node metastases and TNM stage in GC, and it was a significant poor prognostic factor for patients with GC. Aberrant DNA promoter methylation was a crucial reason for the downregulation of HOXB13 mRNA expression.
Collapse
Affiliation(s)
- Bai-Qiang Sui
- Department of Gastrointestinal Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning 110032, P.R. China
| | - Chun-Dong Zhang
- Department of Gastrointestinal Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning 110032, P.R. China
| | - Ji-Chao Liu
- Department of Gastrointestinal Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning 110032, P.R. China
| | - Lei Wang
- Department of Gastrointestinal Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning 110032, P.R. China
| | - Dong-Qiu Dai
- Department of Gastrointestinal Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning 110032, P.R. China
| |
Collapse
|
28
|
Sharma A, Stei MM, Fröhlich H, Holz FG, Loeffler KU, Herwig-Carl MC. Genetic and epigenetic insights into uveal melanoma. Clin Genet 2018; 93:952-961. [PMID: 28902406 DOI: 10.1111/cge.13136] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 08/31/2017] [Accepted: 09/04/2017] [Indexed: 12/18/2022]
Abstract
Uveal melanoma (UM) is the most frequent primary intraocular tumor in Caucasian adults and is potentially fatal if metastases develop. While several prognostic genetic changes have been identified in UM, epigenetic influences are now getting closer attention. Recent technological advances have allowed to exam the human genome to a greater extent and have improved our understanding of several diseases including malignant tumors. In this context, there has been tremendous progress in the field of UM pathogenesis. Herein, we review the literature with emphasis on genetic alterations, epigenetic modifications and signaling pathways as well as possible biomarkers in UM. In addition, different research models for UM are discussed. New insights and major challenges are outlined in order to evaluate the current status for this potentially devastating disease.
Collapse
Affiliation(s)
- A Sharma
- Department of Ophthalmology, University of Bonn, Bonn, Germany.,Department of Neurology, University of Bonn, Bonn, Germany
| | - M M Stei
- Department of Ophthalmology, University of Bonn, Bonn, Germany
| | - H Fröhlich
- Algorithmic Bioinformatics, BIT, University of Bonn, Bonn, Germany.,UCB Biosciences GmbH, Monheim, Germany
| | - F G Holz
- Department of Ophthalmology, University of Bonn, Bonn, Germany
| | - K U Loeffler
- Department of Ophthalmology, University of Bonn, Bonn, Germany
| | - M C Herwig-Carl
- Department of Ophthalmology, University of Bonn, Bonn, Germany
| |
Collapse
|
29
|
N-terminal pyroglutamate formation in CX3CL1 is essential for its full biologic activity. Biosci Rep 2017; 37:BSR20170712. [PMID: 28739588 PMCID: PMC5634468 DOI: 10.1042/bsr20170712] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 07/04/2017] [Accepted: 07/21/2017] [Indexed: 12/11/2022] Open
Abstract
CX3CL1 (fractalkine) is a unique member of the CX3C chemokine family and mediates
both adhesion and cell migration in inflammatory processes. Frequently, the
activity of chemokines depends on a modified N-terminus as described for the
N-terminus of CCL2 modified to a pGlu- (pyroglutamate) residue by QC (glutaminyl
cyclase) activity. Here, we assess the role of the pGlu-modified residue of the
CX3CL1 chemokine domain in human endothelial and smooth muscle cells. For the
first time, we demonstrated using MS that QC (QPCT, gene name
of QC) or its isoenzyme isoQC (iso-glutaminyl cyclase) (QPCTL,
gene name of isoQC) catalyse the formation of N-terminal-modified pGlu-CX3CL1.
Expression of QPCT is co-regulated with its substrates
CCL2 and CX3CL1 in HUVECs (human umbilical
vein endothelial cells) and HCASMCs (human coronary artery smooth muscle cells)
upon stimulation with TNF-α and IL-1β whereas
QPCTL expression is not affected. By contrast, inhibition
of the NF-κB pathway using an IKK2 inhibitor decreased the expression of
the co-regulated targets QPCT, CCL2, and
CX3CL1. Furthermore, RNAi-mediated inhibition of
QPCT expression resulted in a reduction in
CCL2 and CX3CL1 mRNA. In HCASMCs,
N-terminal-modified pGlu1-CX3CL1 induced a significant stronger effect on
phosphorylation of ERK (extracellular signal regulated kinase) 1/2, Akt (protein
kinase B), and p38 (p38 mitogen-activated protein kinase) kinases than the
immature Gln1-CX3CL1 in a time- and concentration-dependent manner. Furthermore,
pGlu1-CX3CL1 affected the expression of CCL2, CX3CL1, and the
adhesion molecule ICAM1/CD54 (intercellular adhesion
molecule-1) inducing in higher expression level compared with its Gln1-variant
in both HCASMCs and HUVECs. These results strongly suggest that QC-catalysed
N-terminal pGlu formation of CX3CL1 is important for the stability or the
interaction with its receptor and opens new insights into the function of QC in
inflammation.
Collapse
|
30
|
Melanocytic nevi and melanoma: unraveling a complex relationship. Oncogene 2017; 36:5771-5792. [PMID: 28604751 DOI: 10.1038/onc.2017.189] [Citation(s) in RCA: 120] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 05/09/2017] [Accepted: 05/10/2017] [Indexed: 12/11/2022]
Abstract
Approximately 33% of melanomas are derived directly from benign, melanocytic nevi. Despite this, the vast majority of melanocytic nevi, which typically form as a result of BRAFV600E-activating mutations, will never progress to melanoma. Herein, we synthesize basic scientific insights and data from mouse models with common observations from clinical practice to comprehensively review melanocytic nevus biology. In particular, we focus on the mechanisms by which growth arrest is established after BRAFV600E mutation. Means by which growth arrest can be overcome and how melanocytic nevi relate to melanoma are also considered. Finally, we present a new conceptual paradigm for understanding the growth arrest of melanocytic nevi in vivo termed stable clonal expansion. This review builds upon the canonical hypothesis of oncogene-induced senescence in growth arrest and tumor suppression in melanocytic nevi and melanoma.
Collapse
|
31
|
Abstract
Melanoma is a malignant tumor of melanocytes and is considered to be the most aggressive cancer among all skin diseases. The pathogenesis of melanoma has not been well documented, which may restrict the research and development of biomarkers and therapies. To date, several genetic and epigenetic factors have been identified as contributing to the development and progression of melanoma. Besides the findings on genetic susceptibilities, the recent progress in epigenetic studies has revealed that loss of the DNA hydroxymethylation mark, 5-hydroxymethylcytosine (5-hmC), along with high levels of DNA methylation at promoter regions of several tumor suppressor genes in melanoma, may serve as biomarkers for melanoma. Moreover, 5-Aza-2′-deoxycytidine, an epigenetic modifier causing DNA demethylation, and ten-eleven translocation family dioxygenase (TET), which catalyzes the generation of 5-hmC, demonstrate therapeutic potential in melanoma treatment. In this review, we will summarize the latest progress in research on DNA methylation/hydroxymethylation in melanoma, and we will discuss and provide insight for epigenetic biomarkers and therapies for melanoma. Particularly, we will discuss the role of DNA hydroxymethylation in melanoma infiltrating immune cells, which may also serve as a potential target for melanoma treatment.
Collapse
|
32
|
Micevic G, Theodosakis N, Bosenberg M. Aberrant DNA methylation in melanoma: biomarker and therapeutic opportunities. Clin Epigenetics 2017; 9:34. [PMID: 28396701 PMCID: PMC5381063 DOI: 10.1186/s13148-017-0332-8] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 03/24/2017] [Indexed: 12/18/2022] Open
Abstract
Aberrant DNA methylation is an epigenetic hallmark of melanoma, known to play important roles in melanoma formation and progression. Recent advances in genome-wide methylation methods have provided the means to identify differentially methylated genes, methylation signatures, and potential biomarkers. However, despite considerable effort and advances in cataloging methylation changes in melanoma, many questions remain unanswered. The aim of this review is to summarize recent developments, emerging trends, and important unresolved questions in the field of aberrant DNA methylation in melanoma. In addition to reviewing recent developments, we carefully synthesize the findings in an effort to provide a framework for understanding the current state and direction of the field. To facilitate clarity, we divided the review into DNA methylation changes in melanoma, biomarker opportunities, and therapeutic developments. We hope this review contributes to accelerating the utilization of the diagnostic, prognostic, and therapeutic potential of DNA methylation for the benefit of melanoma patients.
Collapse
Affiliation(s)
- Goran Micevic
- Department of Dermatology, Yale University School of Medicine, New Haven, CT 06520 USA.,Department of Pathology, Yale University School of Medicine, New Haven, CT 06520 USA
| | - Nicholas Theodosakis
- Department of Dermatology, Yale University School of Medicine, New Haven, CT 06520 USA.,Department of Pathology, Yale University School of Medicine, New Haven, CT 06520 USA
| | - Marcus Bosenberg
- Department of Dermatology, Yale University School of Medicine, New Haven, CT 06520 USA.,Department of Pathology, Yale University School of Medicine, New Haven, CT 06520 USA
| |
Collapse
|
33
|
Ji H, Wang Y, Liu G, Chang L, Chen Z, Zhou D, Xu X, Cui W, Hong Q, Jiang L, Li J, Zhou X, Li Y, Guo Z, Zha Q, Niu Y, Weng Q, Duan S, Wang Q. Elevated OPRD1 promoter methylation in Alzheimer's disease patients. PLoS One 2017; 12:e0172335. [PMID: 28253273 PMCID: PMC5333823 DOI: 10.1371/journal.pone.0172335] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 02/03/2017] [Indexed: 01/21/2023] Open
Abstract
Aberrant DNA methylation has been observed in the patients with Alzheimer’s disease (AD), a common neurodegenerative disorder in the elderly. OPRD1 encodes the delta opioid receptor, a member of the opioid family of G-protein-coupled receptors. In the current study, we compare the DNA methylation levels of OPRD1 promoter CpG sites (CpG1, CpG2, and CpG3) between 51 AD cases and 63 controls using the bisulfite pyrosequencing technology. Our results show that significantly higher CpG3 methylation is found in AD cases than controls. Significant associations are found between several biochemical parameters (including HDL-C and ALP) and CpG3 methylation. Subsequent luciferase reporter gene assay shows that DNA fragment containing the three OPRD1 promoter CpGs is able to regulate gene expression. In summary, our results suggest that OPRD1 promoter hypermethylation is associated with the risk of AD.
Collapse
Affiliation(s)
- Huihui Ji
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Yunliang Wang
- Department of Neurology, the 148 Central Hospital of PLA, Zibo, Shandong, China
| | - Guili Liu
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Lan Chang
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | | | | | - Xuting Xu
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Wei Cui
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Qingxiao Hong
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Liting Jiang
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Jinfeng Li
- Department of Neurology, the 148 Central Hospital of PLA, Zibo, Shandong, China
| | - Xiaohui Zhou
- Department of Internal Medicine for Cadres, the First Affiliated Hospital of Xinjiang Medical University, Urumchi, China
| | - Ying Li
- Ningbo No. 1 Hospital, Ningbo, Zhejiang, China
| | - Zhiping Guo
- School of Medicine, Lishui University, Lishui, Zhejiang, China
| | - Qin Zha
- The Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, China
- * E-mail: (QW); (SD); (QZ)
| | - Yanfang Niu
- The Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, China
| | - Qiuyan Weng
- The Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, China
| | - Shiwei Duan
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
- * E-mail: (QW); (SD); (QZ)
| | - Qinwen Wang
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang, China
- * E-mail: (QW); (SD); (QZ)
| |
Collapse
|
34
|
Seberg HE, Van Otterloo E, Loftus SK, Liu H, Bonde G, Sompallae R, Gildea DE, Santana JF, Manak JR, Pavan WJ, Williams T, Cornell RA. TFAP2 paralogs regulate melanocyte differentiation in parallel with MITF. PLoS Genet 2017; 13:e1006636. [PMID: 28249010 PMCID: PMC5352137 DOI: 10.1371/journal.pgen.1006636] [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: 10/07/2016] [Revised: 03/15/2017] [Accepted: 02/14/2017] [Indexed: 12/20/2022] Open
Abstract
Mutations in the gene encoding transcription factor TFAP2A result in pigmentation anomalies in model organisms and premature hair graying in humans. However, the pleiotropic functions of TFAP2A and its redundantly-acting paralogs have made the precise contribution of TFAP2-type activity to melanocyte differentiation unclear. Defining this contribution may help to explain why TFAP2A expression is reduced in advanced-stage melanoma compared to benign nevi. To identify genes with TFAP2A-dependent expression in melanocytes, we profile zebrafish tissue and mouse melanocytes deficient in Tfap2a, and find that expression of a small subset of genes underlying pigmentation phenotypes is TFAP2A-dependent, including Dct, Mc1r, Mlph, and Pmel. We then conduct TFAP2A ChIP-seq in mouse and human melanocytes and find that a much larger subset of pigmentation genes is associated with active regulatory elements bound by TFAP2A. These elements are also frequently bound by MITF, which is considered the "master regulator" of melanocyte development. For example, the promoter of TRPM1 is bound by both TFAP2A and MITF, and we show that the activity of a minimal TRPM1 promoter is lost upon deletion of the TFAP2A binding sites. However, the expression of Trpm1 is not TFAP2A-dependent, implying that additional TFAP2 paralogs function redundantly to drive melanocyte differentiation, which is consistent with previous results from zebrafish. Paralogs Tfap2a and Tfap2b are both expressed in mouse melanocytes, and we show that mouse embryos with Wnt1-Cre-mediated deletion of Tfap2a and Tfap2b in the neural crest almost completely lack melanocytes but retain neural crest-derived sensory ganglia. These results suggest that TFAP2 paralogs, like MITF, are also necessary for induction of the melanocyte lineage. Finally, we observe a genetic interaction between tfap2a and mitfa in zebrafish, but find that artificially elevating expression of tfap2a does not increase levels of melanin in mitfa hypomorphic or loss-of-function mutants. Collectively, these results show that TFAP2 paralogs, operating alongside lineage-specific transcription factors such as MITF, directly regulate effectors of terminal differentiation in melanocytes. In addition, they suggest that TFAP2A activity, like MITF activity, has the potential to modulate the phenotype of melanoma cells.
Collapse
MESH Headings
- Animals
- Base Sequence
- Binding Sites/genetics
- Cell Differentiation/genetics
- Cell Line
- Cell Line, Tumor
- Cells, Cultured
- Embryo, Mammalian/embryology
- Embryo, Mammalian/metabolism
- Embryo, Nonmammalian/embryology
- Embryo, Nonmammalian/metabolism
- Gene Expression Profiling/methods
- Gene Expression Regulation, Developmental
- Humans
- Melanocytes/metabolism
- Mice, Knockout
- Microphthalmia-Associated Transcription Factor/genetics
- Microphthalmia-Associated Transcription Factor/metabolism
- Microscopy, Confocal
- Mutation
- Pigmentation/genetics
- RNA Interference
- Reverse Transcriptase Polymerase Chain Reaction
- Sequence Homology, Nucleic Acid
- Transcription Factor AP-2/genetics
- Transcription Factor AP-2/metabolism
- Zebrafish
- Zebrafish Proteins/genetics
- Zebrafish Proteins/metabolism
Collapse
Affiliation(s)
- Hannah E. Seberg
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, Iowa, United States of America
| | - Eric Van Otterloo
- SDM-Craniofacial Biology, University of Colorado – Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Stacie K. Loftus
- Genetic Disease Research Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland, United States of America
| | - Huan Liu
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, Iowa, United States of America
| | - Greg Bonde
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, Iowa, United States of America
| | - Ramakrishna Sompallae
- Bioinformatics Division, Iowa Institute of Human Genetics, University of Iowa, Iowa City, Iowa, United States of America
| | - Derek E. Gildea
- Bioinformatics and Scientific Programming Core, Computational and Statistical Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland, United States of America
| | - Juan F. Santana
- Department of Biology, University of Iowa, Iowa City, Iowa, United States of America
| | - J. Robert Manak
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, Iowa, United States of America
- Department of Biology, University of Iowa, Iowa City, Iowa, United States of America
| | - William J. Pavan
- Genetic Disease Research Branch, National Human Genome Research Institute, NIH, Bethesda, Maryland, United States of America
| | - Trevor Williams
- SDM-Craniofacial Biology, University of Colorado – Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Robert A. Cornell
- Interdisciplinary Graduate Program in Genetics, University of Iowa, Iowa City, Iowa, United States of America
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, Iowa, United States of America
| |
Collapse
|
35
|
Basu B, Chakraborty J, Chandra A, Katarkar A, Baldevbhai JRK, Dhar Chowdhury D, Ray JG, Chaudhuri K, Chatterjee R. Genome-wide DNA methylation profile identified a unique set of differentially methylated immune genes in oral squamous cell carcinoma patients in India. Clin Epigenetics 2017; 9:13. [PMID: 28174608 PMCID: PMC5292006 DOI: 10.1186/s13148-017-0314-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 01/19/2017] [Indexed: 01/06/2023] Open
Abstract
Background Oral squamous cell carcinoma (OSCC) is one of the common malignancies in Southeast Asia. Epigenetic changes, mainly the altered DNA methylation, have been implicated in many cancers. Considering the varied environmental and genotoxic exposures among the Indian population, we conducted a genome-wide DNA methylation study on paired tumor and adjacent normal tissues of ten well-differentiated OSCC patients and validated in an additional 53 well-differentiated OSCC and adjacent normal samples. Results Genome-wide DNA methylation analysis identified several novel differentially methylated regions associated with OSCC. Hypermethylation is primarily enriched in the CpG-rich regions, while hypomethylation is mainly in the open sea. Distinct epigenetic drifts for hypo- and hypermethylation across CpG islands suggested independent mechanisms of hypo- and hypermethylation in OSCC development. Aberrant DNA methylation in the promoter regions are concomitant with gene expression. Hypomethylation of immune genes reflect the lymphocyte infiltration into the tumor microenvironment. Comparison of methylome data with 312 TCGA HNSCC samples identified a unique set of hypomethylated promoters among the OSCC patients in India. Pathway analysis of unique hypomethylated promoters indicated that the OSCC patients in India induce an anti-tumor T cell response, with mobilization of T lymphocytes in the neoplastic environment. Survival analysis of these epigenetically regulated immune genes suggested their prominent role in OSCC progression. Conclusions Our study identified a unique set of hypomethylated regions, enriched in the promoters of immune response genes, and indicated the presence of a strong immune component in the tumor microenvironment. These methylation changes may serve as potential molecular markers to define risk and to monitor the prognosis of OSCC patients in India. Electronic supplementary material The online version of this article (doi:10.1186/s13148-017-0314-x) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Baidehi Basu
- Human Genetics Unit, Indian Statistical Institute, 203 B. T. Road, Kolkata, 700108 India
| | - Joyeeta Chakraborty
- Human Genetics Unit, Indian Statistical Institute, 203 B. T. Road, Kolkata, 700108 India
| | - Aditi Chandra
- Human Genetics Unit, Indian Statistical Institute, 203 B. T. Road, Kolkata, 700108 India
| | - Atul Katarkar
- Human Genetics Unit, Indian Statistical Institute, 203 B. T. Road, Kolkata, 700108 India.,Molecular Genetics Division, CSIR-Indian Institute of Chemical biology, 4 Raja S C Mullick Road, Kolkata, 700 032 India
| | | | | | - Jay Gopal Ray
- Dr. R Ahmed Dental College & Hospital, 114, A J C Bose Road, Kolkata, India
| | - Keya Chaudhuri
- Molecular Genetics Division, CSIR-Indian Institute of Chemical biology, 4 Raja S C Mullick Road, Kolkata, 700 032 India
| | - Raghunath Chatterjee
- Human Genetics Unit, Indian Statistical Institute, 203 B. T. Road, Kolkata, 700108 India
| |
Collapse
|
36
|
Chatterjee A, Stockwell PA, Rodger EJ, Parry MF, Eccles MR. scan_tcga tools for integrated epigenomic and transcriptomic analysis of tumor subgroups. Epigenomics 2016; 8:1315-1330. [DOI: 10.2217/epi-2016-0063] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Aim: The Cancer Genome Atlas contains multiple levels of genomic data (mutation, gene expression, DNA methylation, copy number variation) for 33 cancer types for almost 11,000 patients. However, a dearth of appropriate software tools makes it difficult for bench scientists to use these data effectively. Materials & methods: Here, we present a suite of flexible, fast and command line-based scripts that will allow retrieval and analysis of DNA methylation (tool: scan_tcga_methylation.awk), mRNA (tool: scan_tcga_mRNA.awk) and miRNA expression (tool: scan_tcga_miRNAs.awk) from cancer genome atlas network level 3 data. Results: We demonstrate the utility of these tools by analyzing DNA methylation and mRNA expression signatures of 60 frequently deregulated cancer genes and also of 30 miRNAs in primary (n = 102) and metastatic melanoma patients (n = 367). Conclusion: Our analysis illustrates the validity of the scan_tcga tools and reveals the epigenomic signatures and importance of identifying smaller patient subgroups with distinct molecular profiles.
Collapse
Affiliation(s)
- Aniruddha Chatterjee
- Department of Pathology, Dunedin School of Medicine, University of Otago, 270 Great King Street, Dunedin 9054, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, level 2, 3A Symonds Street, Auckland, New Zealand
| | - Peter A Stockwell
- Department of Biochemistry, University of Otago, 710 Cumberland Street, Dunedin 9054, New Zealand
| | - Euan J Rodger
- Department of Pathology, Dunedin School of Medicine, University of Otago, 270 Great King Street, Dunedin 9054, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, level 2, 3A Symonds Street, Auckland, New Zealand
| | - Matthew F Parry
- Department of Mathematics & Statistics, University of Otago, 710 Cumberland Street, Dunedin 9054, New Zealand
| | - Michael R Eccles
- Department of Pathology, Dunedin School of Medicine, University of Otago, 270 Great King Street, Dunedin 9054, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, level 2, 3A Symonds Street, Auckland, New Zealand
| |
Collapse
|
37
|
Fernández-Cabezudo MJ, Faour I, Jones K, Champagne DP, Jaloudi MA, Mohamed YA, Bashir G, Almarzooqi S, Albawardi A, Hashim MJ, Roberts TS, El-Salhat H, El-Taji H, Kassis A, O'Sullivan DE, Christensen BC, DeGregori J, Al-Ramadi BK, Rincon M. Deficiency of mitochondrial modulator MCJ promotes chemoresistance in breast cancer. JCI Insight 2016; 1. [PMID: 27275014 DOI: 10.1172/jci.insight.86873] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Despite major advances in early detection and prognosis, chemotherapy resistance is a major hurdle in the battle against breast cancer. Identifying predictive markers and understanding the mechanisms are key steps to overcoming chemoresistance. Methylation-controlled J protein (MCJ, also known as DNAJC15) is a negative regulator of mitochondrial respiration and has been associated with chemotherapeutic drug sensitivity in cancer cell lines. Here we show, in a retrospective study of a large cohort of breast cancer patients, that low MCJ expression in breast tumors predicts high risk of relapse in patients treated with chemotherapy; however, MCJ expression does not correlate with response to endocrine therapy. In a prospective study in breast cancer patients undergoing neoadjuvant therapy, low MCJ expression also correlates with poor clinical response to chemotherapy and decreased disease-free survival. Using MCJ-deficient mice, we demonstrate that lack of MCJ is sufficient to induce mammary tumor chemoresistance in vivo. Thus, loss of expression of this endogenous mitochondrial modulator in breast cancer promotes the development of chemoresistance.
Collapse
Affiliation(s)
- Maria J Fernández-Cabezudo
- Department of Biochemistry, College of Medicine & Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Issam Faour
- Department of Surgery, Tawam Hospital-Johns Hopkins Medicine, Al-Ain, United Arab Emirates
| | - Kenneth Jones
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Devin P Champagne
- Department of Medicine/Immunobiology Division, University of Vermont, Burlington, Vermont, USA
| | - Mohammed A Jaloudi
- Department of Medical Oncology, Tawam Hospital-Johns Hopkins Medicine, Al-Ain, United Arab Emirates
| | - Yassir A Mohamed
- Department of Medical Microbiology & Immunology, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Ghada Bashir
- Department of Medical Microbiology & Immunology, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Saeeda Almarzooqi
- Department of Pathology, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Alia Albawardi
- Department of Pathology, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - M Jawad Hashim
- Family Medicine, College of Medicine & Health Sciences, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Thomas S Roberts
- Department of Medicine/Immunobiology Division, University of Vermont, Burlington, Vermont, USA
| | - Haytham El-Salhat
- Department of Surgery, Tawam Hospital-Johns Hopkins Medicine, Al-Ain, United Arab Emirates
| | - Hakam El-Taji
- Department of Surgery, Tawam Hospital-Johns Hopkins Medicine, Al-Ain, United Arab Emirates
| | - Adnan Kassis
- Department of Clinical Imaging, Tawam Hospital-Johns Hopkins Medicine, Al-Ain, United Arab Emirates
| | - Dylan E O'Sullivan
- Departments of Epidemiology, Pharmacology and Toxicology, and Community and Family Medicine, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, USA
| | - Brock C Christensen
- Departments of Epidemiology, Pharmacology and Toxicology, and Community and Family Medicine, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, USA
| | - James DeGregori
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Basel K Al-Ramadi
- Department of Medical Microbiology & Immunology, United Arab Emirates University, Al-Ain, United Arab Emirates
| | - Mercedes Rincon
- Department of Medicine/Immunobiology Division, University of Vermont, Burlington, Vermont, USA
| |
Collapse
|
38
|
Yuan H, Kajiyama H, Ito S, Chen D, Shibata K, Hamaguchi M, Kikkawa F, Senga T. HOXB13 and ALX4 induce SLUG expression for the promotion of EMT and cell invasion in ovarian cancer cells. Oncotarget 2016; 6:13359-70. [PMID: 25944620 PMCID: PMC4537020 DOI: 10.18632/oncotarget.3673] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 03/25/2015] [Indexed: 12/12/2022] Open
Abstract
Homeoproteins, a family of transcription factors that have conserved homeobox domains, play critical roles in embryonic development in a wide range of species. Accumulating studies have revealed that homeoproteins are aberrantly expressed in multiple tumors and function as either tumor promoters or suppressors. In this study, we show that two homeoproteins, HOXB13 and ALX4, are associated with epithelial to mesenchymal transition (EMT) and invasion of ovarian cancer cells. HOXB13 and ALX4 formed a complex in cells, and exogenous expression of either protein promoted EMT and invasion. Conversely, depletion of either protein suppressed invasion and induced reversion of EMT. SLUG is a C2H2-type zinc-finger transcription factor that promotes EMT in various cell lines. Knockdown of HOXB13 or ALX4 suppressed SLUG expression, and exogenous expression of either protein promoted SLUG expression. Finally, we showed that SLUG expression was essential for the HOXB13- or ALX4-mediated EMT and invasion. Our results show that HOXB13/SLUG and ALX4/SLUG axes are novel pathways that promote EMT and invasion of ovarian cancer cells.
Collapse
Affiliation(s)
- Hong Yuan
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan
| | - Hiroaki Kajiyama
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan
| | - Satoko Ito
- Division of Cancer Biology, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan
| | - Dan Chen
- Division of Cancer Biology, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan
| | - Kiyosumi Shibata
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan
| | - Michinari Hamaguchi
- Division of Cancer Biology, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan
| | - Fumitaka Kikkawa
- Department of Obstetrics and Gynecology, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan
| | - Takeshi Senga
- Division of Cancer Biology, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan
| |
Collapse
|
39
|
Micevic G, Muthusamy V, Damsky W, Theodosakis N, Liu X, Meeth K, Wingrove E, Santhanakrishnan M, Bosenberg M. DNMT3b Modulates Melanoma Growth by Controlling Levels of mTORC2 Component RICTOR. Cell Rep 2016; 14:2180-2192. [PMID: 26923591 PMCID: PMC4785087 DOI: 10.1016/j.celrep.2016.02.010] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 11/29/2015] [Accepted: 01/27/2016] [Indexed: 01/22/2023] Open
Abstract
DNA methyltransferase DNMT3B is frequently overexpressed in tumor cells and plays important roles during the formation and progression of several cancer types. However, the specific signaling pathways controlled by DNMT3B in cancers, including melanoma, are poorly understood. Here, we report that DNMT3B plays a pro-tumorigenic role in human melanoma and that DNMT3B loss dramatically suppresses melanoma formation in the Braf/Pten mouse melanoma model. Loss of DNMT3B results in hypomethylation of the miR-196b promoter and increased miR-196b expression, which directly targets the mTORC2 component Rictor. Loss of RICTOR in turn prevents mTORC2 activation, which is critical for melanoma formation and growth. These findings establish Dnmt3b as a regulator of melanoma formation through its effect on mTORC2 signaling. Based on these results, DNMT3B is a potential therapeutic target in melanoma.
Collapse
Affiliation(s)
- Goran Micevic
- Department of Dermatology, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Viswanathan Muthusamy
- Department of Dermatology, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Chemistry, Yale University, New Haven, CT 06510, USA
| | - William Damsky
- Department of Dermatology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Nicholas Theodosakis
- Department of Dermatology, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Xiaoni Liu
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Katrina Meeth
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Emily Wingrove
- Department of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Manjula Santhanakrishnan
- Department of Dermatology, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Marcus Bosenberg
- Department of Dermatology, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Pathology, Yale University School of Medicine, New Haven, CT 06520, USA.
| |
Collapse
|
40
|
Common BRAF(V600E)-directed pathway mediates widespread epigenetic silencing in colorectal cancer and melanoma. Proc Natl Acad Sci U S A 2016; 113:1250-5. [PMID: 26787892 DOI: 10.1073/pnas.1525619113] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
During cancer development, it is well established that many genes, including tumor suppressor genes, are hypermethylated and transcriptionally repressed, a phenomenon referred to as epigenetic silencing. In general, the factors involved in, and the mechanistic basis of, epigenetic silencing during cancer development are not well understood. We have recently described an epigenetic silencing pathway, directed by the oncogenic B-Raf proto-oncogene (BRAF) variant BRAF(V600E), that mediates widespread epigenetic silencing in colorectal cancer (CRC). Notably, the BRAF(V600E) mutation is also present in 50-70% of melanomas. Here, we show that the same pathway we identified in CRC also directs epigenetic silencing of a similar set of genes in BRAF-positive melanoma. In both CRC and melanoma, BRAF(V600E) promotes epigenetic silencing through up-regulation of v-maf avian musculoaponeurotic fibrosarcoma oncogene homolog G (MAFG), a transcriptional repressor with sequence-specific DNA-binding activity. The elevated concentration of MAFG drives DNA binding on the promoter. Promoter-bound MAFG recruits a set of corepressors that includes its heterodimeric partner BTB and CNC homology 1, basic leucine zipper transcription factor 1 (BACH1), the chromatin remodeling factor chromodomain helicase DNA-binding protein 8 (CHD8), and the DNA methyltransferase DNMT3B, resulting in hypermethylation and transcriptional silencing. Our results reveal a common BRAF(V600E)-directed transcriptional regulatory pathway that mediates epigenetic silencing in unrelated solid tumors and provide strong support for an instructive model of oncoprotein-directed epigenetic silencing.
Collapse
|
41
|
Abstract
Melanoma, one of the most virulent forms of human malignancy, is the primary cause of mortality from cancers arising from the skin. The prognosis of metastatic melanoma remains dismal despite targeted therapeutic regimens that exploit our growing understanding of cancer immunology and genetic mutations that drive oncogenic cell signaling pathways in cancer. Epigenetic mechanisms, including DNA methylation/demethylation, histone modifications and noncoding RNAs recently have been shown to play critical roles in melanoma pathogenesis. Current evidence indicates that imbalance of DNA methylation and demethylation, dysregulation of histone modification and chromatin remodeling, and altered translational control by noncoding RNAs contribute to melanoma tumorigenesis. Here, we summarize the most recent insights relating to epigenetic markers, focusing on diagnostic potential as well as novel therapeutic approaches for more effective treatment of advanced melanoma.
Collapse
Affiliation(s)
- Weimin Guo
- Program in Dermatopathology, Department of Pathology, Brigham & Women's Hospital, Harvard Medical School, 221 Longwood Ave. EBRC 401, Boston, MA 02115, USA
| | - Ting Xu
- Program in Dermatopathology, Department of Pathology, Brigham & Women's Hospital, Harvard Medical School, 221 Longwood Ave. EBRC 401, Boston, MA 02115, USA
| | - Jonathan J Lee
- Program in Dermatopathology, Department of Pathology, Brigham & Women's Hospital, Harvard Medical School, 221 Longwood Ave. EBRC 401, Boston, MA 02115, USA
| | - George F Murphy
- Program in Dermatopathology, Department of Pathology, Brigham & Women's Hospital, Harvard Medical School, 221 Longwood Ave. EBRC 401, Boston, MA 02115, USA
| | - Christine G Lian
- Program in Dermatopathology, Department of Pathology, Brigham & Women's Hospital, Harvard Medical School, 221 Longwood Ave. EBRC 401, Boston, MA 02115, USA
| |
Collapse
|
42
|
Emamjomeh A, Goliaei B, Torkamani A, Ebrahimpour R, Mohammadi N, Parsian A. Protein-protein interaction prediction by combined analysis of genomic and conservation information. Genes Genet Syst 2015; 89:259-72. [PMID: 25948120 DOI: 10.1266/ggs.89.259] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Protein-protein interactions (PPIs) are highly important because of their main role in cellular processes and biochemical pathways; therefore, PPI can be very useful in the prediction of protein functions. Experimental techniques of PPI detection have certain drawbacks; hence computational methods can be used to complement wet lab techniques. Such methods can be applied to PPI prediction as well as validation of experimental results. Computational algorithms can lead to many false PPI predictions, which in turn result in non-adequate performance. We have developed a novel method based on combined analysis, entitled PPIccc. Three different descriptors for PPIccc included gene co-expression values, codon usage similarity and conservation of surface residues between protein products of a gene pair, which combined to predict PPI. Validation of results based on Human Protein Reference Database (HPRD) indicated improvement of performance in our proposed method. The results also revealed that conservation of surface residues between proteins in combination with codon usage similarity of their related genes increase the performance of PPI prediction. This means that codon usage similarity and surface residues between proteins (only sequence-based features) can predict PPIs as good as PPIccc.
Collapse
|
43
|
Martinez-Cardús A, Vizoso M, Moran S, Manzano JL. Epigenetic mechanisms involved in melanoma pathogenesis and chemoresistance. ANNALS OF TRANSLATIONAL MEDICINE 2015; 3:209. [PMID: 26488005 DOI: 10.3978/j.issn.2305-5839.2015.06.20] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The discovery of highly recurrent mutations in melanoma, such as BRAF(V600E), completely changed the clinical management including therapy of melanoma patients. In the era of Personalized Medicine targeted melanoma therapies showed high response rates, currently evidenced by BRAF inhibitors or immune-stimulating therapies. In addition to genetic biomarkers, epigenetic knowledge in melanoma has undergone a major step forward in recent years. In particular, epigenetics is unveiling new perspectives to fight this disease, providing an encouraging number of DNA methylation based biomarkers that will likely improve patient stratification for prognosis and treatment. In this regard, putative targetable biomarkers or those with predictive value for the outcome of currently applied therapies are promising tools for future precision oncology strategies. In addition, the progress made in genetic and epigenetic profiling technologies and their reconfiguration to real-time clinical screening approaches makes personalized medicine in melanoma an achievable objective in upcoming years.
Collapse
Affiliation(s)
- Anna Martinez-Cardús
- 1 Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet, Barcelona, Catalonia, Spain ; 2 Medical Oncology Service, Catalan Institute of Oncology, Germans Trias i Pujol University Hospital, Badalona, Catalonia, Spain
| | - Miguel Vizoso
- 1 Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet, Barcelona, Catalonia, Spain ; 2 Medical Oncology Service, Catalan Institute of Oncology, Germans Trias i Pujol University Hospital, Badalona, Catalonia, Spain
| | - Sebastian Moran
- 1 Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet, Barcelona, Catalonia, Spain ; 2 Medical Oncology Service, Catalan Institute of Oncology, Germans Trias i Pujol University Hospital, Badalona, Catalonia, Spain
| | - Jose Luis Manzano
- 1 Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, L'Hospitalet, Barcelona, Catalonia, Spain ; 2 Medical Oncology Service, Catalan Institute of Oncology, Germans Trias i Pujol University Hospital, Badalona, Catalonia, Spain
| |
Collapse
|
44
|
Sarkar D, Leung EY, Baguley BC, Finlay GJ, Askarian-Amiri ME. Epigenetic regulation in human melanoma: past and future. Epigenetics 2015; 10:103-21. [PMID: 25587943 PMCID: PMC4622872 DOI: 10.1080/15592294.2014.1003746] [Citation(s) in RCA: 206] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The development and progression of melanoma have been attributed to independent or combined genetic and epigenetic events. There has been remarkable progress in understanding melanoma pathogenesis in terms of genetic alterations. However, recent studies have revealed a complex involvement of epigenetic mechanisms in the regulation of gene expression, including methylation, chromatin modification and remodeling, and the diverse activities of non-coding RNAs. The roles of gene methylation and miRNAs have been relatively well studied in melanoma, but other studies have shown that changes in chromatin status and in the differential expression of long non-coding RNAs can lead to altered regulation of key genes. Taken together, they affect the functioning of signaling pathways that influence each other, intersect, and form networks in which local perturbations disturb the activity of the whole system. Here, we focus on how epigenetic events intertwine with these pathways and contribute to the molecular pathogenesis of melanoma.
Collapse
Key Words
- 5hmC, 5-hydroxymethylcytosine
- 5mC, 5-methylcytosine
- ACE, angiotensin converting enzyme
- ANCR, anti-differentiation non-coding RNA
- ANRIL, antisense noncoding RNA in INK4 locus
- ASK1, apoptosis signal-regulating kinase 1
- ATRA, all-trans retinoic acid
- BANCR, BRAF-activated non-coding RNA
- BCL-2, B-cell lymphoma 2
- BRAF, B-Raf proto-oncogene, serine/threonine kinase
- BRG1, ATP-dependent helicase SMARCA4
- CAF-1, chromatin assembly factor-1
- CBX7, chromobox homolog 7
- CCND1, cyclin D1
- CD28, cluster of differentiation 28
- CDK, cyclin-dependent kinase
- CDKN2A/B, cyclin-dependent kinase inhibitor 2A/B
- CHD8, chromodomain-helicase DNA-binding protein 8
- CREB, cAMP response element-binding protein
- CUDR, cancer upregulated drug resistant
- Cdc6, cell division cycle 6
- DNA methylation/demethylation
- DNMT, DNA methyltransferase
- EMT, epithelial-mesenchymal transition
- ERK, extracellular signal-regulated kinase
- EZH2, enhancer of zeste homolog 2
- GPCRs, G-protein coupled receptors
- GSK3a, glycogen synthase kinase 3 α
- GWAS, genome-wide association study
- HDAC, histone deacetylase
- HOTAIR, HOX antisense intergenic RNA
- IAP, inhibitor of apoptosis
- IDH2, isocitrate dehydrogenase
- IFN, interferon, interleukin 23
- JNK, Jun N-terminal kinase
- Jak/STAT, Janus kinase/signal transducer and activator of transcription
- MAFG, v-maf avian musculoaponeurotic fibrosarcoma oncogene homolog G
- MALAT1, metastasis-associated lung adenocarcinoma transcript 1
- MAPK, mitogen-activated protein kinase
- MC1R, melanocortin-1 receptor
- MGMT, O6-methylguanine-DNA methyltransferase
- MIF, macrophage migration inhibitory factor
- MITF, microphthalmia-associated transcription factor
- MRE, miRNA recognition element
- MeCP2, methyl CpG binding protein 2
- NF-κB, nuclear factor kappa-light-chain-enhancer of activated B cells
- NOD, nucleotide-binding and oligomerization domain
- PBX, pre-B-cell leukemia homeobox
- PEDF, pigment epithelium derived factor
- PI3K, phosphatidylinositol-4, 5-bisphosphate 3-kinase
- PIB5PA, phosphatidylinositol-4, 5-biphosphate 5-phosphatase A
- PKA, protein kinase A
- PRC, polycomb repressor complex
- PSF, PTB associated splicing factor
- PTB, polypyrimidine tract-binding
- PTEN, phosphatase and tensin homolog
- RARB, retinoic acid receptor-β2
- RASSF1A, Ras association domain family 1A
- SETDB1, SET Domain, bifurcated 1
- SPRY4, Sprouty 4
- STAU1, Staufen1
- SWI/SNF, SWItch/Sucrose Non-Fermentable
- TCR, T-cell receptor
- TET, ten eleven translocase
- TGF β, transforming growth factor β
- TINCR, tissue differentiation-inducing non-protein coding RNA
- TOR, target of rapamycin
- TP53, tumor protein 53
- TRAF6, TNF receptor-associated factor 6
- UCA1, urothelial carcinoma-associated 1
- ceRNA, competitive endogenous RNAs
- chromatin modification
- chromatin remodeling
- epigenetics
- gene regulation
- lncRNA, long ncRNA
- melanoma
- miRNA, micro RNA
- ncRNA, non-coding RNA
- ncRNAs
- p14ARF, p14 alternative reading frame
- p16INK4a, p16 inhibitor of CDK4
- pRB, retinoblastoma protein
- snoRNA, small nucleolar RNA
- α-MSHm, α-melanocyte stimulating hormone
Collapse
Affiliation(s)
- Debina Sarkar
- a Auckland Cancer Society Research Center ; University of Auckland ; Auckland , New Zealand
| | | | | | | | | |
Collapse
|
45
|
Law MH, Bishop DT, Lee JE, Brossard M, Martin NG, Moses EK, Song F, Barrett JH, Kumar R, Easton DF, Pharoah PDP, Swerdlow AJ, Kypreou KP, Taylor JC, Harland M, Randerson-Moor J, Akslen LA, Andresen PA, Avril MF, Azizi E, Scarrà GB, Brown KM, Dȩbniak T, Duffy DL, Elder DE, Fang S, Friedman E, Galan P, Ghiorzo P, Gillanders EM, Goldstein AM, Gruis NA, Hansson J, Helsing P, Hočevar M, Höiom V, Ingvar C, Kanetsky PA, Chen WV, Landi MT, Lang J, Lathrop GM, Lubiński J, Mackie RM, Mann GJ, Molven A, Montgomery GW, Novaković S, Olsson H, Puig S, Puig-Butille JA, Qureshi AA, Radford-Smith GL, van der Stoep N, van Doorn R, Whiteman DC, Craig JE, Schadendorf D, Simms LA, Burdon KP, Nyholt DR, Pooley KA, Orr N, Stratigos AJ, Cust AE, Ward SV, Hayward NK, Han J, Schulze HJ, Dunning AM, Bishop JAN, Demenais F, Amos CI, MacGregor S, Iles MM. Genome-wide meta-analysis identifies five new susceptibility loci for cutaneous malignant melanoma. Nat Genet 2015; 47:987-995. [PMID: 26237428 PMCID: PMC4557485 DOI: 10.1038/ng.3373] [Citation(s) in RCA: 187] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 07/09/2015] [Indexed: 12/17/2022]
Abstract
Thirteen common susceptibility loci have been reproducibly associated with cutaneous malignant melanoma (CMM). We report the results of an international 2-stage meta-analysis of CMM genome-wide association studies (GWAS). This meta-analysis combines 11 GWAS (5 previously unpublished) and a further three stage 2 data sets, totaling 15,990 CMM cases and 26,409 controls. Five loci not previously associated with CMM risk reached genome-wide significance (P < 5 × 10(-8)), as did 2 previously reported but unreplicated loci and all 13 established loci. Newly associated SNPs fall within putative melanocyte regulatory elements, and bioinformatic and expression quantitative trait locus (eQTL) data highlight candidate genes in the associated regions, including one involved in telomere biology.
Collapse
|
46
|
Bennett JA, Singh KP, Unnisa Z, Welle SL, Gasiewicz TA. Deficiency in Aryl Hydrocarbon Receptor (AHR) Expression throughout Aging Alters Gene Expression Profiles in Murine Long-Term Hematopoietic Stem Cells. PLoS One 2015. [PMID: 26208102 PMCID: PMC4514744 DOI: 10.1371/journal.pone.0133791] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Dysregulation of hematopoietic stem cell (HSC) signaling can contribute to the development of diseases of the blood system. Lack of aryl hydrocarbon receptor (AhR) has been associated with alterations in gene expression related to HSC function and the subsequent development of a myeloproliferative disorder in aging female mice. We sorted the most primitive population of HSCs with the highest stem cell potential (Long-term, or LT-HSCs) from 18-month-old AhR-null-allele (AhR-KO) and WT mice and analyzed gene expression using microarray to determine alterations in gene expression and cell signaling networks in HSCs that could potentially contribute to the aging phenotype of AhR-KO mice. Comparisons with previous array data from 8-week old mice indicated that aging alone is sufficient to alter gene expression. In addition, a significant number of gene expression differences were observed in aged LT-HSCs that are dependent on both aging and lack of AhR. Pathway analysis of these genes revealed networks related to hematopoietic stem cell activity or function. qPCR was used to confirm the differential expression of a subset of these genes, focusing on genes that may represent novel AhR targets due to the presence of a putative AhR binding site in their upstream regulatory region. We verified differential expression of PDGF-D, Smo, Wdfy1, Zbtb37 and Zfp382. Pathway analysis of this subset of genes revealed overlap between cellular functions of the novel AhR targets and AhR itself. Lentiviral-mediated knockdown of AhR in lineage-negative hematopoietic cells was sufficient to induce changes in all five of the candidate AhR targets identified. Taken together, these data suggest a role for AhR in HSC functional regulation, and identify novel HSC AhR target genes that may contribute to the phenotypes observed in AhR-KO mice.
Collapse
Affiliation(s)
- John A. Bennett
- Department of Environmental Medicine, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Kameshwar P. Singh
- Department of Environmental Medicine, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Zeenath Unnisa
- Department of Environmental Medicine, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Stephen L. Welle
- Department of Medicine, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Thomas A. Gasiewicz
- Department of Environmental Medicine, University of Rochester Medical Center, Rochester, New York, United States of America
- * E-mail:
| |
Collapse
|
47
|
Maia S, Cardoso M, Pinto P, Pinheiro M, Santos C, Peixoto A, Bento MJ, Oliveira J, Henrique R, Jerónimo C, Teixeira MR. Identification of Two Novel HOXB13 Germline Mutations in Portuguese Prostate Cancer Patients. PLoS One 2015; 10:e0132728. [PMID: 26176944 PMCID: PMC4503425 DOI: 10.1371/journal.pone.0132728] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 06/17/2015] [Indexed: 01/01/2023] Open
Abstract
The HOXB13 germline variant G84E (rs138213197) was recently described in men of European descent, with the highest prevalence in Northern Europe. The G84E mutation has not been found in patients of African or Asian ancestry, which may carry other HOXB13 variants, indicating allelic heterogeneity depending on the population. In order to gain insight into the full scope of coding HOXB13 mutations in Portuguese prostate cancer patients, we decided to sequence the entire coding region of the HOXB13 gene in 462 early-onset or familial/hereditary cases. Additionally, we searched for somatic HOXB13 mutations in 178 prostate carcinomas to evaluate their prevalence in prostate carcinogenesis. Three different patients were found to carry in their germline DNA two novel missense variants, which were not identified in 132 control subjects. Both variants are predicted to be deleterious by different in silico tools. No somatic mutations were found. These findings further support the hypothesis that different rare HOXB13 mutations may be found in different ethnic groups. Detection of mutations predisposing to prostate cancer may require re-sequencing rather than genotyping, as appropriate to the population under investigation.
Collapse
Affiliation(s)
- Sofia Maia
- Department of Genetics and Cancer Genetics Group–CI-IPOP, Portuguese Oncology Institute–Porto, Porto, Portugal
| | - Marta Cardoso
- Department of Genetics and Cancer Genetics Group–CI-IPOP, Portuguese Oncology Institute–Porto, Porto, Portugal
| | - Pedro Pinto
- Department of Genetics and Cancer Genetics Group–CI-IPOP, Portuguese Oncology Institute–Porto, Porto, Portugal
| | - Manuela Pinheiro
- Department of Genetics and Cancer Genetics Group–CI-IPOP, Portuguese Oncology Institute–Porto, Porto, Portugal
| | - Catarina Santos
- Department of Genetics and Cancer Genetics Group–CI-IPOP, Portuguese Oncology Institute–Porto, Porto, Portugal
| | - Ana Peixoto
- Department of Genetics and Cancer Genetics Group–CI-IPOP, Portuguese Oncology Institute–Porto, Porto, Portugal
| | - Maria José Bento
- Department of Epidemiology, Portuguese Oncology Institute–Porto, Porto, Portugal
- North Region Cancer Registry, Portuguese Oncology Institute–Porto, Porto, Portugal
- Biomedical Sciences Institute (ICBAS), University of Porto–Porto, Portugal
| | - Jorge Oliveira
- Department of Urology, Portuguese Oncology Institute–Porto, Porto, Portugal
| | - Rui Henrique
- Biomedical Sciences Institute (ICBAS), University of Porto–Porto, Portugal
- Cancer Biology and Epigenetics Group–CI-IPOP, Portuguese Oncology Institute–Porto, Porto, Portugal
- Department of Pathology, Portuguese Oncology Institute–Porto, Porto, Portugal
| | - Carmen Jerónimo
- Biomedical Sciences Institute (ICBAS), University of Porto–Porto, Portugal
- Cancer Biology and Epigenetics Group–CI-IPOP, Portuguese Oncology Institute–Porto, Porto, Portugal
| | - Manuel R. Teixeira
- Department of Genetics and Cancer Genetics Group–CI-IPOP, Portuguese Oncology Institute–Porto, Porto, Portugal
- Biomedical Sciences Institute (ICBAS), University of Porto–Porto, Portugal
- * E-mail:
| |
Collapse
|
48
|
Methylation-dependent SOX9 expression mediates invasion in human melanoma cells and is a negative prognostic factor in advanced melanoma. Genome Biol 2015; 16:42. [PMID: 25885555 PMCID: PMC4378455 DOI: 10.1186/s13059-015-0594-4] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 01/23/2015] [Indexed: 12/18/2022] Open
Abstract
Background Melanoma is the most fatal skin cancer displaying a high degree of molecular heterogeneity. Phenotype switching is a mechanism that contributes to melanoma heterogeneity by altering transcription profiles for the transition between states of proliferation/differentiation and invasion/stemness. As phenotype switching is reversible, epigenetic mechanisms, like DNA methylation, could contribute to the changes in gene expression. Results Integrative analysis of methylation and gene expression datasets of five proliferative and five invasion melanoma cell cultures reveal two distinct clusters. SOX9 is methylated and lowly expressed in the highly proliferative group. SOX9 overexpression results in decreased proliferation but increased invasion in vitro. In a B16 mouse model, sox9 overexpression increases the number of lung metastases. Transcriptional analysis of SOX9-overexpressing melanoma cells reveals enrichment in epithelial to mesenchymal transition (EMT) pathways. Survival analysis of The Cancer Genome Atlas melanoma dataset shows that metastatic patients with high expression levels of SOX9 have significantly worse survival rates. Additional survival analysis on the targets of SOX9 reveals that most SOX9 downregulated genes have survival benefit for metastatic patients. Conclusions Our genome-wide DNA methylation and gene expression study of 10 early passage melanoma cell cultures reveals two phenotypically distinct groups. One of the genes regulated by DNA methylation between the two groups is SOX9. SOX9 induces melanoma cell invasion and metastasis and decreases patient survival. A number of genes downregulated by SOX9 have a negative impact on patient survival. In conclusion, SOX9 is an important gene involved in melanoma invasion and negatively impacts melanoma patient survival. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0594-4) contains supplementary material, which is available to authorized users.
Collapse
|
49
|
Krisenko MO, Geahlen RL. Calling in SYK: SYK's dual role as a tumor promoter and tumor suppressor in cancer. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1853:254-63. [PMID: 25447675 DOI: 10.1016/j.bbamcr.2014.10.022] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 10/21/2014] [Accepted: 10/27/2014] [Indexed: 12/18/2022]
Abstract
SYK (spleen tyrosine kinase) is well-characterized in the immune system as an essential enzyme required for signaling through multiple classes of immune recognition receptors. As a modulator of tumorigenesis, SYK has a bit of a schizophrenic reputation, acting in some cells as a tumor promoter and in others as a tumor suppressor. In many hematopoietic malignancies, SYK provides an important survival function and its inhibition or silencing frequently leads to apoptosis. In cancers of non-immune cells, SYK provides a pro-survival signal, but can also suppress tumorigenesis by restricting epithelial-mesenchymal transition, enhancing cell-cell interactions and inhibiting migration.
Collapse
Affiliation(s)
- Mariya O Krisenko
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue Center for Cancer Research, Purdue University, West Lafayette, IN 47907, United States
| | - Robert L Geahlen
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue Center for Cancer Research, Purdue University, West Lafayette, IN 47907, United States.
| |
Collapse
|
50
|
Wang WH, Childress MO, Geahlen RL. Syk interacts with and phosphorylates nucleolin to stabilize Bcl-x(L) mRNA and promote cell survival. Mol Cell Biol 2014; 34:3788-99. [PMID: 25092868 PMCID: PMC4187708 DOI: 10.1128/mcb.00937-14] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 07/28/2014] [Indexed: 01/07/2023] Open
Abstract
The Syk protein tyrosine kinase, a well-characterized regulator of immune cell function, plays an increasingly recognized role in tumorigenesis as a promoter of cell survival in both hematological and nonhematological malignancies. We show here that the expression of Syk in MCF7 or MDA-MB-231 breast cancer cells or in DG75 B-lymphoma cells protects cells from apoptosis induced by oxidative or genotoxic stress by stabilizing the mRNA for Bcl-x(L), an antiapoptotic protein. Syk binds robustly to nucleolin and phosphorylates it on tyrosine, enhancing its ability to bind the Bcl-x(L) mRNA. Consequently, reducing the level of nucleolin by RNA interference attenuates the ability of Syk to protect cells from stress-induced cell death.
Collapse
Affiliation(s)
- Wen-Horng Wang
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana, USA
| | - Michael O Childress
- Department of Veterinary Clinical Sciences, Purdue University, West Lafayette, Indiana, USA Purdue Center for Cancer Research, Purdue University, West Lafayette, Indiana, USA
| | - Robert L Geahlen
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana, USA Purdue Center for Cancer Research, Purdue University, West Lafayette, Indiana, USA
| |
Collapse
|