1
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Ferreira AMC, Altemani JMC, Macedo LT, Lourenço GJ, Lima CSP. Genetic variability in cisplatin metabolic pathways and outcome of locally advanced head and neck squamous cell carcinoma patients. Sci Rep 2023; 13:16762. [PMID: 37798436 PMCID: PMC10556039 DOI: 10.1038/s41598-023-44040-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 10/03/2023] [Indexed: 10/07/2023] Open
Abstract
Advanced head and neck squamous cell carcinoma (HNSCC) patients have been treated with cisplatin (CDDP) chemoradiation, and the variability of treatment effects has been attributed to single nucleotide variants (SNVs) in genes of metabolic pathways. This study investigated the roles of GSTM1, GSTT1, GSTP1 c.313A>G, XPC c.2815A>C, XPD c.934G>A and c.2251A>C, XPF c.2505T>C, ERCC1 c.354C>T, MLH1 c.93G>A, MSH2 c.211+9C>G, MSH3 c.3133G>A, EXO1 c.1765G>A, TP53 c.215G>C, CASP3 c.-1191A>G and c.-182-247G>T, FAS c.-1378G>A and c.-671A>G and FASL c.-844C>T SNVs in outcome of 109 patients treated with CDDP chemoradiation. Genotypes were identified in genomic DNA by PCR-based methods. Conventional criteria and tests analyzed response and survival. Patients with XPC c.2815AC or CC had 3.43 times more chances of presenting partial response or stable disease. Patients with FAS c.-671GG, GSTM1 present plus XPC c.2815AA, or plus XPD c.934GG, or plus XPD c.2251AA, or plus TP53 c.215GC or CC, and XPD c.2251AA plus XPF c.2505TT had up to 2.70 and 2.37 times more chances of presenting tumor progression and evolving to death, respectively. Our data indicate, for the first time, preliminary evidence that combined SNVs of CDDP metabolism act as independent prognostic factors and can be used to select patients for distinct treatments.
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Affiliation(s)
- Ana Maria Castro Ferreira
- Laboratory of Cancer Genetics, Faculty of Medical Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - João Maurício Carrasco Altemani
- Department of Anesthesiology, Oncology and Radiology, Faculty of Medical Sciences, University of Campinas, Rua Alexander Fleming, 181, Cidade Universitária "Zeferino Vaz", Barão Geraldo, Campinas, São Paulo, CEP: 13083-970, Brazil
| | - Ligia Traldi Macedo
- Laboratory of Cancer Genetics, Faculty of Medical Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - Gustavo Jacob Lourenço
- Laboratory of Cancer Genetics, Faculty of Medical Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - Carmen Silvia Passos Lima
- Laboratory of Cancer Genetics, Faculty of Medical Sciences, University of Campinas, Campinas, São Paulo, Brazil.
- Department of Anesthesiology, Oncology and Radiology, Faculty of Medical Sciences, University of Campinas, Rua Alexander Fleming, 181, Cidade Universitária "Zeferino Vaz", Barão Geraldo, Campinas, São Paulo, CEP: 13083-970, Brazil.
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2
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Asgari R, Bidmeshkipour A, Mansouri K, Bakhtiari M, Mozafari H, Abdolmaleki A. Fas cell surface death receptor/Fas ligand genetic variants in gastric cancer patients: A case-control study. Indian J Med Res 2022; 156:77-82. [PMID: 36124496 PMCID: PMC9903394 DOI: 10.4103/ijmr.ijmr_2058_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Background & objectives Various studies have suggested a correlation between Fas cell surface death receptor/Fas ligand (FAS/FASL) variants and multiple types of cancers. The present study aimed to investigate the association between FAS-670A/G and FASL-844C/T and the synergistic effects of both variants on the risk of gastric cancer (GC) in the Kurdish population of west of Iran. Methods This study was conducted by polymerase chain reaction-restriction fragment length polymorphism technique using MvaI and BsrDI restriction enzymes in 98 GC patients and 103 healthy control individuals. Results According to the obtained results, a significant association (P=0.008) of FASL polymorphism among GC patients and the control group was detected. Furthermore, no significant differences were found in the FAS polymorphism frequencies between GC patients and the control group. Codominant and dominant models in FASL polymorphism showed significant protective effects against GC [odds ratio (OR)=0.307, 95% confidence interval (CI) (0.134-0.705), P=0.005; OR=0.205, 95% CI (0.058-0.718), P=0.013 and OR=0.295, 95% CI (0.129-0.673), P=0.004 for models of codominant CC vs. CT, codominant CC vs. TT and dominant, respectively]. Furthermore, the presence of both FAS-670G and FASL-844T alleles represented a significant protective effect against GC occurrence [OR=0.420, 95% CI (0.181-0.975), P=0.043]. Interpretation & conclusions So far, we believe this is the first study, the results of which suggest that FASL gene variation and its synergistic effects with FAS gene could be associated with the risk of GC in the Kurdish population in the west of Iran.
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Affiliation(s)
| | - Ali Bidmeshkipour
- Department of Biology, Faculty of Sciences, Razi University, Kermanshah, Iran,For correspondence: Dr Ali Bidmeshkipour, Department of Biology, Faculty of Sciences, Razi University, Kermanshah, Iran e-mail:
| | | | - Mitra Bakhtiari
- Fertility and Infertility Research Center, Health Technology Institute, Kermanshah, Iran
| | | | - Amir Abdolmaleki
- Department of Anatomical Sciences & Cell Biology, Kermanshah University of Medical Sciences, Kermanshah, Iran
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3
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Borilova Linhartova P, Gachova D, Lipovy B. Responsiveness to i.v. immunoglobulin therapy in patients with toxic epidermal necrolysis: A novel pharmaco-immunogenetic concept. J Dermatol 2020; 47:1236-1248. [PMID: 32935409 DOI: 10.1111/1346-8138.15583] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/30/2020] [Accepted: 08/03/2020] [Indexed: 12/15/2022]
Abstract
Toxic epidermal necrolysis (TEN) represents a rare drug-induced autoimmune reaction with delayed-type hypersensitivity that initiates the process of developing massive keratinocyte apoptosis, dominantly in the dermoepidermal junction. Although the etiopathophysiology has not yet been fully elucidated, the binding of Fas ligand (FasL, CD95L) to the Fas receptor (CD95) was shown to play a key role in the induction of apoptosis in this syndrome. The knowledge of the role of immunoglobulin G (IgG) in inhibition of Fas-mediated apoptosis contributed to the introduction of i.v. Ig (IVIg) in the therapy of TEN patients. Despite great enthusiasm for this therapy at the end of the 1990s, subsequent studies in various populations and meta-analyses could not unequivocally confirm the efficacy of the IVIg-based treatment concept. Today, therefore, we are faced with the dilemmas of how to adjust therapy of TEN patients most effectively, which patients could benefit from IVIg therapy and what dose of the preparation should be administrated. The ground-breaking question is: do the host genetic profiles influence the responsiveness and side-effects of IVIg therapy in TEN patients? Based on recent pharmacological, immunological and genetic findings, we suggest that the variability of IVIg therapy outcomes in TEN patients may be related to functional variants in Fas, FasL and Fc-γ receptor genes. This novel concept could lead to improved quality of care for patients with TEN, facilitating personalized therapy to reduce mortality.
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Affiliation(s)
- Petra Borilova Linhartova
- Institute of Medical Genetics, Faculty of Medicine, Masaryk University, Brno, Czech Republic.,Department of Pathophysiology, Faculty of Medicine, Masaryk University, Brno, Czech Republic.,Clinic of Stomatology, Faculty of Medicine, Masaryk University, Brno, Czech Republic.,Department of Molecular Pharmacy, Faculty of Pharmacy, Masaryk University, Brno, Czech Republic.,Clinic of Maxillofacial Surgery, Institution shared with University Hospital Brno, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Daniela Gachova
- Department of Pathophysiology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Bretislav Lipovy
- Department of Burns and Plastic Surgery, Institution shared with University Hospital Brno, Faculty of Medicine, Masaryk University, Brno, Czech Republic
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4
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Costa EFD, Lima TRP, Lopes-Aguiar L, Nogueira GAS, Visacri MB, Quintanilha JCF, Pincinato EC, Calonga L, Mariano FV, Altemani AMDAM, Altemani JMC, Moriel P, Chone CT, Ramos CD, Lima CSP. FAS and FASL variations in outcomes of tobacco- and alcohol-related head and neck squamous cell carcinoma patients. Tumour Biol 2020; 42:1010428320938494. [PMID: 32628088 DOI: 10.1177/1010428320938494] [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: 12/24/2022] Open
Abstract
Radiotherapy and cisplatin lead to cell killing in head and neck squamous cell carcinoma patients, but adverse events and response to treatment are not the same in patients with similar clinicopathological aspects. The aim of this prospective study was to evaluate the roles of TP53 c.215G > C, FAS c.-671A > G, FAS c.-1378G > A, FASL c.-844 C > T, CASP3 c.-1191A > G, and CASP3 c.-182-247G > T single nucleotide variants in toxicity, response rate, and survival of cisplatin chemoradiation-treated head and neck squamous cell carcinoma patients. Genomic DNA was analyzed by polymerase chain reaction for genotyping. Differences between groups of patients were analyzed by chi-square test or Fisher's exact test, multiple logistic regression analysis, and Cox hazards model. One hundred nine patients with head and neck squamous cell carcinoma were enrolled in study. All patients were smokers and/or alcoholics. Patients with FAS c.-671GG genotype, FAS c.-671AG or GG genotype, and FASL c.-844CC genotype had 5.52 (95% confidence interval (CI): 1.42-21.43), 4.03 (95% CI: 1.51-10.79), and 5.77 (95% CI: 1.23-27.04) more chances of presenting chemoradiation-related anemia of grades 2-4, lymphopenia of grade 3 or 4, and ototoxicity of all grades, respectively, than those with the remaining genotypes. FAS c.-671GG genotype was also seen as an independent predictor of shorter event-free survival (hazard ratio (HR): 2.05; P = 0.007) and overall survival (HR: 1.83; P = 0.02) in our head and neck squamous cell carcinoma patients. These findings present, for the first time, preliminary evidence that inherited abnormalities in apoptosis pathway, related to FAS c.-671A > G and FASL c.-844 C > T single nucleotide variants, can alter toxicity and survival of tobacco- and alcohol-related head and neck squamous cell carcinoma patients homogeneously treated with cisplatin chemoradiation.
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Affiliation(s)
| | - Tathiane Regine Penna Lima
- Department of Internal Medicine, Faculty of Medical Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - Leisa Lopes-Aguiar
- Department of Internal Medicine, Faculty of Medical Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | | | - Marília Berlofa Visacri
- Department of Clinical Pathology, Faculty of Medical Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | | | - Eder Carvalho Pincinato
- Department of Internal Medicine, Faculty of Medical Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - Luciane Calonga
- Department of Ophthalmology and Otorhinolaryngology, Faculty of Medical Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - Fernanda Viviane Mariano
- Department of Pathology, Faculty of Medical Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | | | | | - Patrícia Moriel
- Department of Clinical Pathology, Faculty of Medical Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - Carlos Takahiro Chone
- Department of Ophthalmology and Otorhinolaryngology, Faculty of Medical Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - Celso Dario Ramos
- Department of Radiology, Faculty of Medical Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - Carmen Silvia Passos Lima
- Department of Internal Medicine, Faculty of Medical Sciences, University of Campinas, Campinas, São Paulo, Brazil
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5
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Shi W, Fornes O, Wasserman WW. Gene expression models based on transcription factor binding events confer insight into functional cis-regulatory variants. Bioinformatics 2020; 35:2610-2617. [PMID: 30541050 PMCID: PMC6662294 DOI: 10.1093/bioinformatics/bty992] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 10/17/2018] [Accepted: 12/10/2018] [Indexed: 01/03/2023] Open
Abstract
Motivation Deciphering the functional roles of cis-regulatory variants is a critical challenge in genome analysis and interpretation. It has been hypothesized that altered transcription factor (TF) binding events are a central mechanism by which cis-regulatory variants impact gene expression levels. However, we lack a computational framework to understand and quantify such mechanistic contributions. Results We present TF2Exp, a gene-based framework to predict the impact of altered TF-binding events on gene expression levels. Using data from lymphoblastoid cell lines, TF2Exp models were applied successfully to predict the expression levels of 3196 genes. Alterations within DNase I hypersensitive, CTCF-bound and tissue-specific TF-bound regions were the greatest contributing features to the models. TF2Exp models performed as well as models based on common variants, both in cross-validation and external validation. Combining TF alteration and common variant features can further improve model performance. Unlike variant-based models, TF2Exp models have the unique advantage to evaluate the functional impact of variants in linkage disequilibrium and uncommon variants. We find that adding TF-binding events altered only by uncommon variants could increase the number of predictable genes (R2 > 0.05). Taken together, TF2Exp represents a key step towards interpreting the functional roles of cis-regulatory variants in the human genome. Availability and implementation The code and model training results are publicly available at https://github.com/wqshi/TF2Exp. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Wenqiang Shi
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada.,Bioinformatics Graduate Program, University of British Columbia, Vancouver, BC, Canada.,Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Oriol Fornes
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Wyeth W Wasserman
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
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6
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Catar RA, Chen L, Cuff SM, Kift-Morgan A, Eberl M, Kettritz R, Kamhieh-Milz J, Moll G, Li Q, Zhao H, Kawka E, Zickler D, Parekh G, Davis P, Fraser DJ, Dragun D, Eckardt KU, Jörres A, Witowski J. Control of neutrophil influx during peritonitis by transcriptional cross-regulation of chemokine CXCL1 by IL-17 and IFN-γ. J Pathol 2020; 251:175-186. [PMID: 32232854 DOI: 10.1002/path.5438] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 02/08/2020] [Accepted: 03/23/2020] [Indexed: 02/06/2023]
Abstract
Neutrophil infiltration is a hallmark of peritoneal inflammation, but mechanisms regulating neutrophil recruitment in patients with peritoneal dialysis (PD)-related peritonitis are not fully defined. We examined 104 samples of PD effluent collected during acute peritonitis for correspondence between a broad range of soluble parameters and neutrophil counts. We observed an association between peritoneal IL-17 and neutrophil levels. This relationship was evident in effluent samples with low but not high IFN-γ levels, suggesting a differential effect of IFN-γ concentration on neutrophil infiltration. Surprisingly, there was no association of neutrophil numbers with the level of CXCL1, a key IL-17-induced neutrophil chemoattractant. We investigated therefore the production of CXCL1 by human peritoneal mesothelial cells (HPMCs) under in vitro conditions mimicking clinical peritonitis. Stimulation of HPMCs with IL-17 increased CXCL1 production through induction of transcription factor SP1 and activation of the SP1-binding region of the CXCL1 promoter. These effects were amplified by TNFα. In contrast, IFN-γ dose-dependently suppressed IL-17-induced SP1 activation and CXCL1 production through a transcriptional mechanism involving STAT1. The SP1-mediated induction of CXCL1 was also observed in HPMCs exposed to PD effluent collected during peritonitis and containing IL-17 and TNFα, but not IFN-γ. Supplementation of the effluent with IFN-γ led to a dose-dependent activation of STAT1 and a resultant inhibition of SP1-induced CXCL1 expression. Transmesothelial migration of neutrophils in vitro increased upon stimulation of HPMCs with IL-17 and was reduced by IFN-γ. In addition, HPMCs were capable of binding CXCL1 at their apical cell surface. These observations indicate that changes in relative peritoneal concentrations of IL-17 and IFN-γ can differently engage SP1-STAT1, impacting on mesothelial cell transcription of CXCL1, whose release and binding to HPMC surface may determine optimal neutrophil recruitment and retention during peritonitis. © 2020 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Rusan A Catar
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Lei Chen
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin, Berlin, Germany
| | - Simone M Cuff
- Division of Infection & Immunity, School of Medicine, Cardiff University, Cardiff, UK
| | - Ann Kift-Morgan
- Division of Infection & Immunity, School of Medicine, Cardiff University, Cardiff, UK
| | - Matthias Eberl
- Division of Infection & Immunity, School of Medicine, Cardiff University, Cardiff, UK
- Systems Immunity Research Institute, Cardiff University, Cardiff, UK
| | - Ralph Kettritz
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin, Berlin, Germany
- Experimental and Clinical Research Center, Max-Delbrück-Center für Molekulare Medizin in der Helmholtz-Gemeinschaft, Berlin, Germany
| | - Julian Kamhieh-Milz
- Department of Transfusion Medicine, Charité-Universitätsmedizin, Berlin, Germany
| | - Guido Moll
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin, Berlin, Germany
- BIH Center for Regenerative Therapies (BCRT), Charité Universitätsmedizin, Berlin, Germany
- Berlin-Brandenburg School for Regenerative Therapies, Charité Universitätsmedizin, Berlin, Germany
- Julius Wolff Institute, Charité Universitätsmedizin, Berlin, Germany
| | - Qing Li
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin, Berlin, Germany
| | - Hongfan Zhao
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin, Berlin, Germany
| | - Edyta Kawka
- Department of Pathophysiology, Poznan University of Medical Sciences, Poznan, Poland
| | - Daniel Zickler
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin, Berlin, Germany
| | - Gita Parekh
- Mologic Ltd, Bedford Technology Park, Thurleigh, Bedford, UK
| | - Paul Davis
- Mologic Ltd, Bedford Technology Park, Thurleigh, Bedford, UK
| | - Donald J Fraser
- Division of Infection & Immunity, School of Medicine, Cardiff University, Cardiff, UK
- Systems Immunity Research Institute, Cardiff University, Cardiff, UK
- Wales Kidney Research Unit, Cardiff University, Cardiff, UK
| | - Duska Dragun
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Kai-Uwe Eckardt
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin, Berlin, Germany
| | - Achim Jörres
- Department of Medicine I, Nephrology, Transplantation and Medical Intensive Care, University Witten/Herdecke, Medical Center Cologne-Merheim, Cologne, Germany
| | - Janusz Witowski
- Department of Nephrology and Medical Intensive Care, Charité-Universitätsmedizin, Berlin, Germany
- Department of Pathophysiology, Poznan University of Medical Sciences, Poznan, Poland
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7
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Li G, Xie Q, Yang Z, Wang L, Zhang X, Zuo B, Zhang S, Yang A, Jia L. Sp1-mediated epigenetic dysregulation dictates HDAC inhibitor susceptibility of HER2-overexpressing breast cancer. Int J Cancer 2019; 145:3285-3298. [PMID: 31111958 DOI: 10.1002/ijc.32425] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 04/23/2019] [Accepted: 05/13/2019] [Indexed: 12/17/2023]
Abstract
Human epidermal growth factor receptor 2 (HER2/erbB2) is a key driver and therapeutic target for breast cancer. The treatment of HER2-positive breast cancer remains a clinical challenge largely due to the limited understanding of HER2-driving oncogenic signaling and the frequent resistance to simply HER2-targeted therapy. Here, we show that the histone deacetylase inhibitor, trichostatin A (TSA), suppresses HER2-overexpressing breast cancer via upregulation of miR-146a and the resultant repression of its oncogenic targets, interleukin-1 receptor-associated kinase 1 and the chemokine receptor CXCR4. Mechanistically, histone H3K56 acetylation and deacetylation on the MIR146A promoter are catalyzed respectively by the acetyltransferase p300 and histone deacetylase 1 (HDAC1), both of which are recruited to the genomic loci by the transcription factor specificity protein 1 (Sp1). HER2 signaling phosphorylates Sp1 and induces its predominant association with HDAC1, but not p300, leading to histone hypoacetylation and silencing of MIR146A. In addition, the death receptor Fas is similarly downregulated by the aforementioned epigenetic paradigm, indicating its wide involvement in impairing tumor suppressor gene expression. Consequently, TSA synergizes with lapatinib, a tyrosine kinase inhibitor of HER2, to suppress breast cancer in vitro and in rodent models. These findings demonstrate a novel mechanism of HER2-driven carcinogenesis and suggest the applicability of combined HER2 and HDAC targeting in breast cancer therapy.
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MESH Headings
- Animals
- Breast Neoplasms/drug therapy
- Breast Neoplasms/genetics
- Cell Line, Tumor
- Down-Regulation/drug effects
- Down-Regulation/genetics
- Epigenesis, Genetic/genetics
- Female
- Gene Expression Regulation, Neoplastic/drug effects
- Gene Expression Regulation, Neoplastic/genetics
- Histone Deacetylase 1/genetics
- Histone Deacetylase Inhibitors/pharmacology
- Histone Deacetylases/genetics
- Humans
- MCF-7 Cells
- Mice
- Mice, Inbred BALB C
- Mice, Nude
- Promoter Regions, Genetic/drug effects
- Promoter Regions, Genetic/genetics
- Receptor, ErbB-2/genetics
- Sp1 Transcription Factor/genetics
- Transcription, Genetic/drug effects
- Transcription, Genetic/genetics
- Transcriptional Activation/drug effects
- Transcriptional Activation/genetics
- Up-Regulation/drug effects
- Up-Regulation/genetics
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Affiliation(s)
- Guoyin Li
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, China
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, China
| | - Qiaosheng Xie
- Department of Immunology, Fourth Military Medical University, Xi'an, China
- Department of Radiation Oncology, China-Japan Friendship Hospital, Beijing, China
| | - Zhiwei Yang
- Department of Applied Physics, School of Science, Xi'an Jiaotong University, Xi'an, China
| | - Lei Wang
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, China
| | - Xiang Zhang
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, China
| | - Baile Zuo
- Department of Immunology, Fourth Military Medical University, Xi'an, China
| | - Shengli Zhang
- Department of Applied Physics, School of Science, Xi'an Jiaotong University, Xi'an, China
| | - Angang Yang
- Department of Immunology, Fourth Military Medical University, Xi'an, China
| | - Lintao Jia
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, China
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8
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Song X, Tang T, Li C, Liu X, Zhou L. CBX8 and CD96 Are Important Prognostic Biomarkers of Colorectal Cancer. Med Sci Monit 2018; 24:7820-7827. [PMID: 30383736 PMCID: PMC6225733 DOI: 10.12659/msm.908656] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is one of the most common malignancies worldwide, with high morbidity and mortality rates. The purpose of this study was to identify potential biomarkers in the progression of CRC. MATERIAL AND METHODS Gene and isoform expression datasets of CRC was downloaded from The Cancer Genome Atlas (TCGA). EBSeq of R was used for the normalization of gene and isoform expression, as well as the identification of differential expression genes (DEGs) and isoforms (DEIs) of CRC samples compared with normal samples. The enriched functions of DEGs and DEIs were obtained based on the Database for Annotation, Visualization and Integrated Discovery (DAVID). An independent dataset, GSE38832, was downloaded from the Gene Expression Omnibus (GEO) database for survival analysis of genes with sustained decreased/increased expression values at both gene and isoform levels with the development of CRC. RESULTS A total of 2301 genes and 4241 isoforms were found to be significantly differentially expressed in stage I-IV CRC samples. They are closely associated with muscle or cell system activity. Sixteen genes were screened out with sustained decreased/increased expression values at both gene and isoform levels with the development of CRC. Aberrant CBX8 and CD96 expressions were found to be significantly associated with CRC survival. CONCLUSIONS Through combined analysis of gene and isoform expression profiles, we identified several potential biomarkers that may play an important role in the development of CRC and could be helpful in its early diagnosis and treatment.
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Affiliation(s)
- Xin Song
- Department of General Surgery, China-Japan Friendship Hospital, Beijing, China (mainland)
| | - Tao Tang
- Department of General Surgery, China-Japan Friendship Hospital, Beijing, China (mainland)
| | - Chaofeng Li
- Department of General Surgery, China-Japan Friendship Hospital, Beijing, China (mainland)
| | - Xin Liu
- Department of General Surgery, China-Japan Friendship Hospital, Beijing, China (mainland)
| | - Lei Zhou
- Department of General Surgery, China-Japan Friendship Hospital, Beijing, China (mainland)
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9
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Single Nucleotide Polymorphism in SMAD7 and CHI3L1 and Colorectal Cancer Risk. Mediators Inflamm 2018; 2018:9853192. [PMID: 30498395 PMCID: PMC6222239 DOI: 10.1155/2018/9853192] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 08/01/2018] [Accepted: 08/16/2018] [Indexed: 02/08/2023] Open
Abstract
Colorectal cancer (CRC) is one of the leading cancers throughout the world. It represents the third most common cancer and the fourth in mortality. Most of CRC are sporadic, arise with no known high-penetrant genetic variation and with no previous family history. The etiology of sporadic CRC is considered to be multifactorial and arises from the interaction of genetic variants of low-penetrant genes and environmental risk factors. The most common well-studied genetic variation is single nucleotide polymorphisms (SNPs). SNP arises as a point mutation. If the frequency of the sequence variation reaches 1% or more in the population, it is referred to as polymorphism, but if it is lower than 1%, the allele is typically considered as a mutation. Lots of SNPs have been associated with CRC development and progression, for example, genes of TGF-β1 and CHI3L1 pathways. TGF-β1 is a pleiotropic cytokine with a dual role in cancer development and progression. TGF-β1 mediates its actions through canonical and noncanonical pathways. The most important negative regulatory protein for TGF-β1 activity is termed SMAD7. The production of TGF-β can be controlled by another protein called YKL-40. YKL-40 is a glycoprotein with an important role in cancer initiation and metastasis. YKL-40 is encoded by the CHI3L1 gene. The aim of the present review is to give a brief introduction of CRC, SNP, and examples of some SNPs that have been documented to be associated with CRC. We also discuss two important signaling pathways TGF-β1 and CHI3L1 that influence the incidence and progression of CRC.
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10
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Rehman S, Saba N, Naz M, Ahmed P, Munir S, Sajjad S, Tabassum S, Naseem L. Single-Nucleotide Polymorphisms of FAS and FASL Genes and Risk of Idiopathic Aplastic Anemia. Immunol Invest 2018; 47:484-491. [PMID: 29611722 DOI: 10.1080/08820139.2018.1458106] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
FAS/FASL signaling system plays a vital role in the regulation of apoptosis, envisaged as a death process required for immune surveillance to prevent autoimmunity and tumorigenesis along with several other biological activities. Several single-nucleotide polymorphisms (SNPs) of FAS/FASL system can result in aberrant apoptosis, which can cause different cancers and autoimmune diseases. Aplastic anemia (AA) is an autoimmune dysfunction characterized by peripheral blood pancytopenia associated with hypoplasia of bone marrow. The aim of this study was to screen Pakistani AA patients and controls for two Fas SNPs rs2234767 and rs1800682 and two FASLG SNPs rs763110 and rs5030772. Genotyping of 392 DNA samples was done by Tetra-ARMS polymerase chain reaction. Genotypic frequencies of Fas rs1800682 and FASLG rs5030772 showed significance difference in their distribution in both controls and patients, while Fas rs2234767 and FASLG rs763110 SNPs had no such difference. Carriers of rs1800682 AG+GG had a very odd ratio of 4.63, with 95% confidence interval (CI) of 3.01-7.11, while individuals with FASLG rs5030772 AG+GG were more common in controls than patients with OR 0.53 and 95% CI of 0.34-0.83. Cumulative effects of these SNPs were analyzed, and they showed almost similar trends; however, Fas rs2234767 and FASLG rs763110 genotypes in combination with Fas rs1800682 and FASLG rs5030772 demonstrated significant association. This study provided information that endorsed the involvement of FAS/FASL system SNPs in the pathogenesis of AA; further studies should be designed to understand the exact role of SNPs that can help in early diagnosis and treatment.
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Affiliation(s)
- Sadia Rehman
- a Institute of Biomedical and Genetic Engineering Islamabad , Pakistan
| | - Nusrat Saba
- a Institute of Biomedical and Genetic Engineering Islamabad , Pakistan
| | - Madiha Naz
- b Islamic International University Islamabad , Pakistan
| | - Parvez Ahmed
- c Armed forces Bone Marrow Transplantation Centre Rawalpindi , Pakistan
| | - Saeeda Munir
- a Institute of Biomedical and Genetic Engineering Islamabad , Pakistan
| | - Sumaira Sajjad
- a Institute of Biomedical and Genetic Engineering Islamabad , Pakistan
| | | | - Lubna Naseem
- d Pakistan Institute of Medical Sciences Islamabad , Pakistan
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11
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Jin Y, Zhou T, Li N, Liu S, Xu X, Pan Y, Tan S, Shi H, Yang Y, Yuan Z, Wang W, Luo J, Gao D, Dunham R, Liu Z. JAK and STAT members in channel catfish: Identification, phylogenetic analysis and expression profiling after Edwardsiella ictaluri infection. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2018; 81:334-341. [PMID: 29274790 DOI: 10.1016/j.dci.2017.12.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 12/20/2017] [Accepted: 12/20/2017] [Indexed: 06/07/2023]
Abstract
The Janus kinase/signal transducers and activators of transcription (JAK/STAT) signaling pathway is one of the main pleiotropic cascades used to transmit information from extracellular receptors to the nucleus, which results in DNA transcription and expression of genes involved in immunity, proliferation, differentiation, migration, apoptosis, and cell survival. Members of JAK family and STAT family have been extensively studied in different mammalian species because of their important roles in innate and adaptive immune responses. However, they have not been systematically studied among teleost fish species. In this study, five JAK family members and eight STAT family members were identified and characterized from channel catfish. Phylogenetic analysis was conducted to properly annotate these genes. Syntenic analysis was also conducted to establish orthology, and confirm the results from phylogenetic analysis. Compared to mammals, more members of the JAK and STAT family were identified in channel catfish genome. Expression of JAK and STAT family members was detected in healthy catfish tissues, but was induced in gill, liver, and intestine after bacterial challenge. Notably, the significant upregulation of STAT1b gene in catfish liver, gill and intestine after Edwardsiella ictaluri infection supported the notion that high STAT1 expression are involved in defense against pathogens. Collectively, the increased expression of JAK and STAT members in tested tissues suggested their crucial function in defending the host against pathogen invasion.
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Affiliation(s)
- Yulin Jin
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA.
| | - Tao Zhou
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA.
| | - Ning Li
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA.
| | - Shikai Liu
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA.
| | - Xiaoyan Xu
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA.
| | - Ying Pan
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA.
| | - Suxu Tan
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA.
| | - Huitong Shi
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA.
| | - Yujia Yang
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA.
| | - Zihao Yuan
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA.
| | - Wenwen Wang
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA.
| | - Jian Luo
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA.
| | - Dongya Gao
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA.
| | - Rex Dunham
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA.
| | - Zhanjiang Liu
- Department of Biology, College of Art and Sciences, Syracuse University, Syracuse, NY 13244, USA.
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12
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Abstract
Transcription is regulated by transcription factor (TF) binding at promoters and distal regulatory elements and histone modifications that control the accessibility of these elements. Chromatin immunoprecipitation followed by sequencing (ChIP-seq) has become the standard assay for identifying genome-wide protein-DNA interactions in vitro and in vivo. As large-scale ChIP-seq data sets have been collected for different TFs and histone modifications, their potential to predict gene expression can be used to test hypotheses about the mechanisms of gene regulation. In addition, complementary functional genomics assays provide a global view of chromatin accessibility and long-range cis-regulatory interactions that are being combined with TF binding and histone remodeling to study the regulation of gene expression. Thus, ChIP-seq analysis is now widely integrated with other functional genomics assays to better understand gene regulatory mechanisms. In this review, we discuss advances and challenges in integrating ChIP-seq data to identify context-specific chromatin states associated with gene activity. We describe the overall computational design of integrating ChIP-seq data with other functional genomics assays. We also discuss the challenges of extending these methods to low-input ChIP-seq assays and related single-cell assays.
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Affiliation(s)
| | - Ali Mortazavi
- Corresponding author: Ali Mortazavi, Department of Developmental and Cell Biology, 2300 Biological Sciences 3, University of California, Irvine, CA 92697, USA. Tel: (949)824-6762; E-mail:
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13
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Vallinoto ACR, Santana BB, Queiroz MAF, da Silva ANMR, Cayres-Vallinoto IMV, da Costa CA, de Sousa MS, Ishak R. Family Aggregation of HTLV-1 Infection Associated with FAS -670A/G Polymorphism: A Case Report. Front Microbiol 2018; 8:2685. [PMID: 29379480 PMCID: PMC5775226 DOI: 10.3389/fmicb.2017.02685] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 12/26/2017] [Indexed: 12/16/2022] Open
Abstract
Human T-lymphotropic virus 1 (HTLV-1) infection has been associated with ATL and inflammatory diseases but remains a neglected health problem. HTLV-1 associated diseases were originally described as sporadic entities, but family aggregations have been reported. Viral, genetic, immunological and behavioral factors were used to explain family clusters, but until now a clear explanation remains uncertain. In the present study we report, for the first time, a family cluster of diseased persons presenting the infection across three generations associated with FAS -670A/G polymorphism.
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Affiliation(s)
- Antonio C R Vallinoto
- Laboratório de Virologia, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
| | - Bárbara B Santana
- Laboratório de Virologia, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
| | - Maria A F Queiroz
- Laboratório de Virologia, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
| | - Andrea N M R da Silva
- Laboratório de Virologia, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
| | | | - Carlos A da Costa
- Núcleo de Medicina Tropical, Universidade Federal do Pará, Belém, Brazil
| | - Maisa S de Sousa
- Núcleo de Medicina Tropical, Universidade Federal do Pará, Belém, Brazil
| | - Ricardo Ishak
- Laboratório de Virologia, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
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14
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Meng Q, Wang S, Tang W, Wu S, Gao N, Zhang C, Cao X, Li X, Zhang Z, Aschner M, Jin H, Huang Y, Chen R. XRCC1 mediated the development of cervival cancer through a novel Sp1/Krox-20 swich. Oncotarget 2017; 8:86217-86226. [PMID: 29156789 PMCID: PMC5689679 DOI: 10.18632/oncotarget.21040] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 08/09/2017] [Indexed: 01/18/2023] Open
Abstract
Cervical cancer is the second leading cause of mortality among women. Impairment of the base excision repair (BER) pathway is one of the major causes of the initiation and progression of cervical cancer. However, whether the polymorphisms of the BER pathway components (i.e., HOGG1, XRCC1, ADPRT, and APE1) can affect the risk of cervical cancer remains unknown. Herein, we applied a hospital-based case-control study covering two independent cohorts and a subsequent functional assay to determine the roles of the single nucleotide polymorphisms (SNPs) of the BER pathway genes in cervical cancer. Results indicated that the XRCC1 rs3213245 (-77TC) TT genotype was associated with an increased risk of cervical cancer. The immunohistochemistry assay showed that XRCC1 protein expression levels were upregulated in cervical cancer patients with the XRCC1 rs3213245 CC genotype compared with the CT or TT genotypes. Further, results from ChIP assay showed that Sp1 could bind to the −77 site and that the rs3213245 C genotype promoted the binding of Sp1 to the XRCC1 promoter. Moreover, ChIP/Re-ChIP assays revealed that transcription factor Krox-20 was recruited to the XRCC1 rs3213245 mutation region and regulated the transcription of the XRCC1 gene by interacting with Sp1, ultimately mediated cervical cancer development. In summary, the findings indicated that the functional XRCC1 SNP rs3213245 was associated with the risk of cervical cancer based on the Sp1/Krox-20 switch.
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Affiliation(s)
- Qingtao Meng
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China
| | - Shizhi Wang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China
| | - Weiyan Tang
- Medical Oncology, Jiangsu Cancer Hospital, Nanjing, China
| | - Shenshen Wu
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China
| | - Na Gao
- Institute of Bioinformatics, Heinrich Heine University, Düsseldorf, Germany
| | - Chengcheng Zhang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China
| | - Xiaoli Cao
- Clinical Lab, Nantong Tumor Hospital, Nantong, China
| | - Xiaobo Li
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China
| | - Zhengdong Zhang
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Cancer Center, Nanjing Medical University, Nanjing, China
| | - Michael Aschner
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Hua Jin
- Core Laboratory, Nantong Tumor Hospital, Nantong, China
| | - Yue Huang
- Department of Pathology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Rui Chen
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, China.,State Key Laboratory of Respiratory Disease, Institute for Chemical Carcinogenesis, Guangzhou Medical University, Guangzhou, China
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15
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Zhang X, Li X, Tan F, Yu N, Pei H. STAT1 Inhibits MiR-181a Expression to Suppress Colorectal Cancer Cell Proliferation Through PTEN/Akt. J Cell Biochem 2017; 118:3435-3443. [PMID: 28322462 DOI: 10.1002/jcb.26000] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 03/17/2017] [Indexed: 11/08/2022]
Abstract
Signal transducers and activators of transcription 1 (STAT1) exhibits tumor-suppressor properties by inhibiting oncogenic pathways and promoting tumor immunosurveillance. MicroRNAs, a group of non-coding endogenous ones, may regulate gene expression and plays specific roles in tumorigenesis. Recently, miR-181a has been reported to be associated with poor prognosis of colorectal cancer (CRC). Using human colorectal cancer cell lines, we demonstrated that STAT1 suppresses both LoVo and SW480 cell growth by down-regulating miR-181a. STAT1 regulates the expression of miR-181a through binding to the elements in the miR-181a's promoter region. Further, we revealed that miR-181a accelerates CRC cell proliferation through phosphatase and tensin homolog on chromosome ten (PTEN). In addition, PTEN protein was upregulated in response to STAT1 overexpression or miR-181a inhibition, downregulated in response to STAT1 knockdown or miR-181a overexpression. Without changes on the AKT protein level, p-AKT was downregulated by STAT1 overexpression or miR-181a inhibition while upregulated by STAT1 knockdown or miR-181a overexpression, indicating PTEN/Akt pathway activated in STAT1/miR-181a regulation of CRC cell proliferation. Taken together, our findings shed new light on the STAT1/miR-181a/PTEN pathway in colorectal cancer and add new insight regarding the carcinogenesis of colorectal cancer. J. Cell. Biochem. 118: 3435-3443, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Xingwen Zhang
- Department of Gastrointestinal Surgery, Xiangya Hospital, Central South University, Changsha, 410008, P.R. China.,Department of Emergency, Hunan Provincial People's Hospital, P.R. China
| | - Xiang Li
- Department of Emergency, Hunan Provincial People's Hospital, P.R. China
| | - Fengbo Tan
- Department of Gastrointestinal Surgery, Xiangya Hospital, Central South University, Changsha, 410008, P.R. China
| | - Nanhui Yu
- Department of Gastrointestinal Surgery, Xiangya Hospital, Central South University, Changsha, 410008, P.R. China
| | - Haiping Pei
- Department of Gastrointestinal Surgery, Xiangya Hospital, Central South University, Changsha, 410008, P.R. China
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16
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Hamada T, Keum N, Nishihara R, Ogino S. Molecular pathological epidemiology: new developing frontiers of big data science to study etiologies and pathogenesis. J Gastroenterol 2017; 52:265-275. [PMID: 27738762 PMCID: PMC5325774 DOI: 10.1007/s00535-016-1272-3] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 09/22/2016] [Indexed: 02/07/2023]
Abstract
Molecular pathological epidemiology (MPE) is an integrative field that utilizes molecular pathology to incorporate interpersonal heterogeneity of a disease process into epidemiology. In each individual, the development and progression of a disease are determined by a unique combination of exogenous and endogenous factors, resulting in different molecular and pathological subtypes of the disease. Based on "the unique disease principle," the primary aim of MPE is to uncover an interactive relationship between a specific environmental exposure and disease subtypes in determining disease incidence and mortality. This MPE approach can provide etiologic and pathogenic insights, potentially contributing to precision medicine for personalized prevention and treatment. Although breast, prostate, lung, and colorectal cancers have been among the most commonly studied diseases, the MPE approach can be used to study any disease. In addition to molecular features, host immune status and microbiome profile likely affect a disease process, and thus serve as informative biomarkers. As such, further integration of several disciplines into MPE has been achieved (e.g., pharmaco-MPE, immuno-MPE, and microbial MPE), to provide novel insights into underlying etiologic mechanisms. With the advent of high-throughput sequencing technologies, available genomic and epigenomic data have expanded dramatically. The MPE approach can also provide a specific risk estimate for each disease subgroup, thereby enhancing the impact of genome-wide association studies on public health. In this article, we present recent progress of MPE, and discuss the importance of accounting for the disease heterogeneity in the era of big-data health science and precision medicine.
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Affiliation(s)
- Tsuyoshi Hamada
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, 450 Brookline Ave., Room SM1036, Boston, MA, 02215, USA
| | - NaNa Keum
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Reiko Nishihara
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, 450 Brookline Ave., Room SM1036, Boston, MA, 02215, USA.
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
| | - Shuji Ogino
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, 450 Brookline Ave., Room SM1036, Boston, MA, 02215, USA.
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Division of MPE Molecular Pathological Epidemiology, Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, 450 Brookline Ave., Room SM1036, Boston, MA, 02215, USA.
- Department of Oncologic Pathology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA.
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17
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Deplancke B, Alpern D, Gardeux V. The Genetics of Transcription Factor DNA Binding Variation. Cell 2016; 166:538-554. [PMID: 27471964 DOI: 10.1016/j.cell.2016.07.012] [Citation(s) in RCA: 244] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Indexed: 12/23/2022]
Abstract
Most complex trait-associated variants are located in non-coding regulatory regions of the genome, where they have been shown to disrupt transcription factor (TF)-DNA binding motifs. Variable TF-DNA interactions are therefore increasingly considered as key drivers of phenotypic variation. However, recent genome-wide studies revealed that the majority of variable TF-DNA binding events are not driven by sequence alterations in the motif of the studied TF. This observation implies that the molecular mechanisms underlying TF-DNA binding variation and, by extrapolation, inter-individual phenotypic variation are more complex than originally anticipated. Here, we summarize the findings that led to this important paradigm shift and review proposed mechanisms for local, proximal, or distal genetic variation-driven variable TF-DNA binding. In addition, we discuss the biomedical implications of these findings for our ability to dissect the molecular role(s) of non-coding genetic variants in complex traits, including disease susceptibility.
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Affiliation(s)
- Bart Deplancke
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
| | - Daniel Alpern
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Vincent Gardeux
- Laboratory of Systems Biology and Genetics, Institute of Bioengineering, Ecole Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
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18
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Wu S, Wang S, Fu Y, Tang W, Jin H, Meng Q, Zhang C, Cui M, Cao X, Li X, Zhang Z, Chen R. A novel mechanism of rs763110 polymorphism contributing to cervical cancer risk by affecting the binding affinity of C/EBPβ and OCT1 complex to chromatin. Int J Cancer 2016; 140:756-763. [DOI: 10.1002/ijc.30490] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 10/18/2016] [Indexed: 01/28/2023]
Affiliation(s)
- Shenshen Wu
- State Key Laboratory of Bioelectronics; Southeast University; Nanjing China
- Key Laboratory of Environmental Medicine Engineering; Ministry of Education, School of Public Health, Southeast University; Nanjing China
| | - Shizhi Wang
- Key Laboratory of Environmental Medicine Engineering; Ministry of Education, School of Public Health, Southeast University; Nanjing China
| | - You Fu
- School of Continuing Education; Nanjing Medical University; Nanjing China
| | - Weiyan Tang
- Medical Oncology; Jiangsu Cancer Hospital; Nanjing China
| | - Hua Jin
- Core Laboratory; Nantong Tumor Hospital; Nantong China
| | - Qingtao Meng
- Key Laboratory of Environmental Medicine Engineering; Ministry of Education, School of Public Health, Southeast University; Nanjing China
| | - Chengcheng Zhang
- Key Laboratory of Environmental Medicine Engineering; Ministry of Education, School of Public Health, Southeast University; Nanjing China
| | - Mengjing Cui
- Key Laboratory of Environmental Medicine Engineering; Ministry of Education, School of Public Health, Southeast University; Nanjing China
| | - Xiaoli Cao
- Clinical Lab; Nantong Tumor Hospital; Nantong China
| | - Xiaobo Li
- Key Laboratory of Environmental Medicine Engineering; Ministry of Education, School of Public Health, Southeast University; Nanjing China
| | - Zhengdong Zhang
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment; Cancer Center, Nanjing Medical University; Nanjing China
| | - Rui Chen
- State Key Laboratory of Bioelectronics; Southeast University; Nanjing China
- Key Laboratory of Environmental Medicine Engineering; Ministry of Education, School of Public Health, Southeast University; Nanjing China
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19
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Imperfect Symmetry of Sp1 and Core Promoter Sequences Regulates Early and Late Virus Gene Expression of the Bidirectional BK Polyomavirus Noncoding Control Region. J Virol 2016; 90:10083-10101. [PMID: 27581987 DOI: 10.1128/jvi.01008-16] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 08/22/2016] [Indexed: 01/01/2023] Open
Abstract
Rearrangements or point mutations in the noncoding control region (NCCR) of BK polyomavirus (BKPyV) have been associated with higher viral loads and more pronounced organ pathology in immunocompromised patients. The respective alterations affect a multitude of transcription factor binding sites (TFBS) but consistently cause increased expression of the early viral gene region (EVGR) at the expense of late viral gene region (LVGR) expression. By mutating TFBS, we identified three phenotypic groups leading to strong, intermediate, or impaired EVGR expression and corresponding BKPyV replication. Unexpectedly, Sp1 TFBS mutants either activated or inhibited EVGR expression when located proximal to the LVGR (sp1-4) or the EVGR (sp1-2), respectively. We now demonstrate that the bidirectional balance of EVGR and LVGR expression is dependent on affinity, strand orientation, and the number of Sp1 sites. Swapping the LVGR-proximal high-affinity SP1-4 with the EVGR-proximal low-affinity SP1-2 in site strand flipping or inserting an additional SP1-2 site caused a rearranged NCCR phenotype of increased EVGR expression and faster BKPyV replication. The 5' rapid amplification of cDNA ends revealed an imperfect symmetry between the EVGR- and LVGR-proximal parts of the NCCR, consisting of TATA and TATA-like elements, initiator elements, and downstream promoter elements. Mutation or deletion of the archetypal LVGR promoter, which is found in activated NCCR variants, abrogated LVGR expression, which could be restored by providing large T antigen (LTag) in trans Thus, whereas Sp1 sites control the initial EVGR-LVGR expression balance, LTag expression can override inactivation of the LVGR promoter and acts as a key driver of LVGR expression independently of the Sp1 sites and core promoter elements. IMPORTANCE Polyomaviridae currently comprise more than 70 members, including 13 human polyomaviruses (PyVs), all of which share a bidirectional genome organization mediated by the NCCR, which determines species and host cell specificity, persistence, replication, and virulence. Here, we demonstrate that the BKPyV NCCR is fine-tuned by an imperfect symmetry of core promoter elements centered around TATA and TATA-like sequences close to the EVGR and LVGR, respectively, which are governed by the directionality and affinity of two Sp1 sites. The data indicated that the BKPyV NCCR is poised toward EVGR expression, which can be readily unlatched by a simple switch affecting Sp1 binding. The resulting LTag, which is the major EVGR protein, drives viral genome replication, renders subsequent LVGR expression independently of archetypal promoter elements, and can overcome enhancer/promoter mutations and deletions. The data are pivotal for understanding how human PyV NCCRs mediate secondary host cell specificity, reactivation, and virulence in their natural hosts.
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20
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Ceramide mediates FasL-induced caspase 8 activation in colon carcinoma cells to enhance FasL-induced cytotoxicity by tumor-specific cytotoxic T lymphocytes. Sci Rep 2016; 6:30816. [PMID: 27487939 PMCID: PMC4973238 DOI: 10.1038/srep30816] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 07/11/2016] [Indexed: 12/13/2022] Open
Abstract
FasL-mediated cytotoxicity is one of the mechanisms that CTLs use to kill tumor cells. However, human colon carcinoma often deregulates the Fas signaling pathway to evade host cancer immune surveillance. We aimed at testing the hypothesis that novel ceramide analogs effectively modulate Fas function to sensitize colon carcinoma cells to FasL-induced apoptosis. We used rational design and synthesized twenty ceramide analogs as Fas function modulators. Five ceramide analogs, IG4, IG7, IG14, IG17, and IG19, exhibit low toxicity and potent activity in sensitization of human colon carcinoma cells to FasL-induced apoptosis. Functional deficiency of Fas limits both FasL and ceramide analogs in the induction of apoptosis. Ceramide enhances FasL-induced activation of the MAPK, NF-κB, and caspase 8 despite induction of potent tumor cell death. Finally, a sublethal dose of several ceramide analogs significantly increased CTL-mediated and FasL-induced apoptosis of colon carcinoma cells. We have therefore developed five novel ceramide analogs that act at a sublethal dose to enhance the efficacy of tumor-specific CTLs, and these ceramide analogs hold great promise for further development as adjunct agents in CTL-based colon cancer immunotherapy.
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21
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Wang M, Wang Z, Wang XJ, Jin TB, Dai ZM, Kang HF, Guan HT, Ma XB, Liu XH, Dai ZJ. Distinct role of the Fas rs1800682 and FasL rs763110 polymorphisms in determining the risk of breast cancer among Han Chinese females. DRUG DESIGN DEVELOPMENT AND THERAPY 2016; 10:2359-67. [PMID: 27524883 PMCID: PMC4966568 DOI: 10.2147/dddt.s111084] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Background In recent years, studies have demonstrated that polymorphisms in the promoters of Fas and FasL are significantly associated with breast cancer risk. However, the results of these studies were inconsistent. This case–control study was performed to explore the associations between Fas rs1800682 and FasL rs763110 polymorphisms and breast cancer. Materials and methods A hospital-based case–control study of 560 Han Chinese females with breast cancer (583 controls) was conducted. The MassARRAY system was used to search for a possible association between the disease risk and the two single nucleotide polymorphisms, Fas rs1800682 and FasL rs763110. Statistical analyses were performed using SNPStats software to conduct Pearson’s chi-square tests in five different genetic models. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated after adjustment to age and body mass index. PHASE v2.1 software was used to reconstruct all common haplotypes. Results A statistically significant association was found between Fas rs1800682 and increased breast cancer risk (AG vs AA: OR =1.37, 95% CI =1.06–1.78; AA+AG vs GG: OR =1.32, 95% CI =1.04–1.66), and also it was found that the FasL rs763110 polymorphism may decrease the risk. Stratified analyses demonstrated that the rs763110 polymorphism was associated with lower breast cancer risk among postmenopausal females (heterozygote model: OR =0.69, 95% CI =0.49–0.97; dominant model: OR =0.70, 95% CI =0.51–0.96). The T allele of rs763110 was also associated with a decreased risk of lymph node metastasis (allele model: OR =0.75, 95% CI =0.57–0.97) and an increased risk of the breast cancer being human epidermal growth factor receptor 2 positive (allele model: OR =1.37, 95% CI =1.03–1.18). Moreover, haplotype analysis showed that Ars1800682Trs763110 was associated to a statistically significant degree with lower risk of breast cancer (OR =0.70, 95% CI =0.53–0.91). Conclusion These data suggest that the presence of Fas rs1800683 is an important risk factor for breast cancer, whereas FasL rs763110 may exert a protective effect against the onset of breast cancer.
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Affiliation(s)
- Meng Wang
- Department of Oncology, Second Affiliated Hospital of Xi'an Jiaotong University
| | - Zheng Wang
- Department of Medical Oncology, Xi'an Central Hospital
| | - Xi-Jing Wang
- Department of Oncology, Second Affiliated Hospital of Xi'an Jiaotong University
| | - Tian-Bo Jin
- National Engineering Research Center for Miniaturized Detection Systems, School of Life Sciences, Northwest University
| | - Zhi-Ming Dai
- Department of Anesthesia, Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, People's Republic of China
| | - Hua-Feng Kang
- Department of Oncology, Second Affiliated Hospital of Xi'an Jiaotong University
| | - Hai-Tao Guan
- Department of Oncology, Second Affiliated Hospital of Xi'an Jiaotong University
| | - Xiao-Bin Ma
- Department of Oncology, Second Affiliated Hospital of Xi'an Jiaotong University
| | - Xing-Han Liu
- Department of Oncology, Second Affiliated Hospital of Xi'an Jiaotong University
| | - Zhi-Jun Dai
- Department of Oncology, Second Affiliated Hospital of Xi'an Jiaotong University
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