1
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Lischer C, Eberhardt M, Flamann C, Berges J, Güse E, Wessely A, Weich A, Retzlaff J, Dörrie J, Schaft N, Wiesinger M, März J, Schuler-Thurner B, Knorr H, Gupta S, Singh KP, Schuler G, Heppt MV, Koch EAT, van Kleef ND, Freen-van Heeren JJ, Turksma AW, Wolkenhauer O, Hohberger B, Berking C, Bruns H, Vera J. Gene network-based and ensemble modeling-based selection of tumor-associated antigens with a predicted low risk of tissue damage for targeted immunotherapy. J Immunother Cancer 2024; 12:e008104. [PMID: 38724462 PMCID: PMC11086525 DOI: 10.1136/jitc-2023-008104] [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] [Accepted: 04/23/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND Tumor-associated antigens and their derived peptides constitute an opportunity to design off-the-shelf mainline or adjuvant anti-cancer immunotherapies for a broad array of patients. A performant and rational antigen selection pipeline would lay the foundation for immunotherapy trials with the potential to enhance treatment, tremendously benefiting patients suffering from rare, understudied cancers. METHODS We present an experimentally validated, data-driven computational pipeline that selects and ranks antigens in a multipronged approach. In addition to minimizing the risk of immune-related adverse events by selecting antigens based on their expression profile in tumor biopsies and healthy tissues, we incorporated a network analysis-derived antigen indispensability index based on computational modeling results, and candidate immunogenicity predictions from a machine learning ensemble model relying on peptide physicochemical characteristics. RESULTS In a model study of uveal melanoma, Human Leukocyte Antigen (HLA) docking simulations and experimental quantification of the peptide-major histocompatibility complex binding affinities confirmed that our approach discriminates between high-binding and low-binding affinity peptides with a performance similar to that of established methodologies. Blinded validation experiments with autologous T-cells yielded peptide stimulation-induced interferon-γ secretion and cytotoxic activity despite high interdonor variability. Dissecting the score contribution of the tested antigens revealed that peptides with the potential to induce cytotoxicity but unsuitable due to potential tissue damage or instability of expression were properly discarded by the computational pipeline. CONCLUSIONS In this study, we demonstrate the feasibility of the de novo computational selection of antigens with the capacity to induce an anti-tumor immune response and a predicted low risk of tissue damage. On translation to the clinic, our pipeline supports fast turn-around validation, for example, for adoptive T-cell transfer preparations, in both generalized and personalized antigen-directed immunotherapy settings.
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Affiliation(s)
- Christopher Lischer
- Hautklinik, Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Martin Eberhardt
- Hautklinik, Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Cindy Flamann
- BZKF, Erlangen, Germany
- Department of Hematology and Oncology, Universitätsklinikum Erlangen and FAU Erlangen-Nürnberg, Erlangen, Germany
| | - Johannes Berges
- BZKF, Erlangen, Germany
- Department of Hematology and Oncology, Universitätsklinikum Erlangen and FAU Erlangen-Nürnberg, Erlangen, Germany
| | - Esther Güse
- Hautklinik, Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Anja Wessely
- Hautklinik, Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Adrian Weich
- Hautklinik, Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Jimmy Retzlaff
- Hautklinik, Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Jan Dörrie
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
- Universitätsklinikum Erlangen, Erlangen, Germany
| | - Niels Schaft
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
- Universitätsklinikum Erlangen, Erlangen, Germany
| | - Manuel Wiesinger
- Hautklinik, Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Johannes März
- Hautklinik, Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Beatrice Schuler-Thurner
- Hautklinik, Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Harald Knorr
- Department of Ophthalmology, Universitätsklinikum Erlangen and FAU Erlangen-Nürnberg, Erlangen, Germany
- CCC Erlangen-EMN, Erlangen, Germany
| | - Shailendra Gupta
- Department of Systems Biology and Bioinformatics, Universität Rostock, Rostock, Germany
| | - Krishna Pal Singh
- Department of Systems Biology and Bioinformatics, Universität Rostock, Rostock, Germany
| | - Gerold Schuler
- Hautklinik, Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Markus Vincent Heppt
- Hautklinik, Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Elias Andreas Thomas Koch
- Hautklinik, Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | | | | | | | - Olaf Wolkenhauer
- Department of Systems Biology and Bioinformatics, Universität Rostock, Rostock, Germany
| | - Bettina Hohberger
- Department of Ophthalmology, Universitätsklinikum Erlangen and FAU Erlangen-Nürnberg, Erlangen, Germany
- CCC Erlangen-EMN, Erlangen, Germany
| | - Carola Berking
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
- Department of Dermatology, FAU Erlangen-Nürnberg, Erlangen, Germany
| | - Heiko Bruns
- BZKF, Erlangen, Germany
- Department of Hematology and Oncology, Universitätsklinikum Erlangen and FAU Erlangen-Nürnberg, Erlangen, Germany
| | - Julio Vera
- Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
- Department of Dermatology, FAU Erlangen-Nürnberg, Erlangen, Germany
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2
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Lee IH, Kong SW. ADGR: Admixture-Informed Differential Gene Regulation. Genes (Basel) 2023; 14:147. [PMID: 36672888 PMCID: PMC9859415 DOI: 10.3390/genes14010147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/15/2022] [Accepted: 01/03/2023] [Indexed: 01/06/2023] Open
Abstract
The regulatory elements in proximal and distal regions of genes are involved in the regulation of gene expression. Risk alleles in intronic and intergenic regions may alter gene expression by modifying the binding affinity and stability of diverse DNA-binding proteins implicated in gene expression regulation. By focusing on the local ancestral structure of coding and regulatory regions using the paired whole-genome sequence and tissue-wide transcriptome datasets from the Genotype-Tissue Expression project, we investigated the impact of genetic variants, in aggregate, on tissue-specific gene expression regulation. Local ancestral origins of the coding region, immediate and distant upstream regions, and distal regulatory region were determined using RFMix with the reference panel from the 1000 Genomes Project. For each tissue, inter-individual variation of gene expression levels explained by concordant or discordant local ancestry between coding and regulatory regions was estimated. Compared to European, African descent showed more frequent change in local ancestral structure, with shorter haplotype blocks. The expression level of the Adenosine Deaminase Like (ADAL) gene was significantly associated with admixed ancestral structure in the regulatory region across multiple tissue types. Further validations are required to understand the impact of the local ancestral structure of regulatory regions on gene expression regulation in humans and other species.
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Affiliation(s)
- In-Hee Lee
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, MA 02215, USA
| | - Sek Won Kong
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, MA 02215, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
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3
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Dai Y, Kawaguchi T, Nishio M, Otani J, Tashiro H, Terai Y, Sasaki R, Maehama T, Suzuki A. The TIGD5 gene located in 8q24 and frequently amplified in ovarian cancers is a tumor suppressor. Genes Cells 2022; 27:633-642. [PMID: 36054307 DOI: 10.1111/gtc.12980] [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: 07/26/2022] [Accepted: 08/10/2022] [Indexed: 01/27/2023]
Abstract
Ovarian cancer (OC) is the fifth most common cancer of female cancer death and leading cause of lethal gynecological cancers. High-grade serous ovarian carcinoma (HGSOC) is an aggressive malignancy that is rapidly fatal. Many cases of OC show amplification of the 8q24 chromosomal region, which contains the well-known oncogene MYC. Although MYC amplification is more frequently observed in OCs than in other tumor types, due to the large size of the 8q24 amplicon, the functions of the vast majority of the genes it contains are still unknown. The TIGD5 gene is located at 8q24.3 and encodes a nuclear protein with a DNA-binding motif, but its precise role is obscure. We show here that TIGD5 often co-amplifies with MYC in OCs, and that OC patients with high TIGD5 mRNA expression have a poor prognosis. However, we also found that TIGD5 overexpression in ovarian cancer cell lines unexpectedly suppressed their growth, adhesion, and invasion in vitro, and also reduced tumor growth in xenografted nude mice in vivo. Thus, our work suggests that TIGD5 may in fact operate as a tumor suppressor in OCs rather than as an oncogene.
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Affiliation(s)
- Yuntao Dai
- Division of Molecular and Cellular Biology, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
- Division of Radiation Oncology, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Tetsuya Kawaguchi
- Division of Molecular and Cellular Biology, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
- Department of Obstetrics and Gynecology, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Miki Nishio
- Division of Molecular and Cellular Biology, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Junji Otani
- Division of Molecular and Cellular Biology, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Hironori Tashiro
- Department of Health Sciences, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Yoshito Terai
- Department of Obstetrics and Gynecology, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Ryohei Sasaki
- Division of Radiation Oncology, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Tomohiko Maehama
- Division of Molecular and Cellular Biology, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Akira Suzuki
- Division of Molecular and Cellular Biology, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
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4
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Rawlins LE, Almousa H, Khan S, Collins SC, Milev MP, Leslie J, Saint-Dic D, Khan V, Hincapie AM, Day JO, McGavin L, Rowley C, Harlalka GV, Vancollie VE, Ahmad W, Lelliott CJ, Gul A, Yalcin B, Crosby AH, Sacher M, Baple EL. Biallelic variants in TRAPPC10 cause a microcephalic TRAPPopathy disorder in humans and mice. PLoS Genet 2022; 18:e1010114. [PMID: 35298461 PMCID: PMC8963566 DOI: 10.1371/journal.pgen.1010114] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 03/29/2022] [Accepted: 02/20/2022] [Indexed: 11/25/2022] Open
Abstract
The highly evolutionarily conserved transport protein particle (TRAPP) complexes (TRAPP II and III) perform fundamental roles in subcellular trafficking pathways. Here we identified biallelic variants in TRAPPC10, a component of the TRAPP II complex, in individuals with a severe microcephalic neurodevelopmental disorder. Molecular studies revealed a weakened interaction between mutant TRAPPC10 and its putative adaptor protein TRAPPC2L. Studies of patient lymphoblastoid cells revealed an absence of TRAPPC10 alongside a concomitant absence of TRAPPC9, another key TRAPP II complex component associated with a clinically overlapping neurodevelopmental disorder. The TRAPPC9/10 reduction phenotype was recapitulated in TRAPPC10-/- knockout cells, which also displayed a membrane trafficking defect. Notably, both the reduction in TRAPPC9 levels and the trafficking defect in these cells could be rescued by wild type but not mutant TRAPPC10 gene constructs. Moreover, studies of Trappc10-/- knockout mice revealed neuroanatomical brain defects and microcephaly, paralleling findings seen in the human condition as well as in a Trappc9-/- mouse model. Together these studies confirm autosomal recessive TRAPPC10 variants as a cause of human disease and define TRAPP-mediated pathomolecular outcomes of importance to TRAPPC9 and TRAPPC10 mediated neurodevelopmental disorders in humans and mice. Microcephalic neurodevelopmental disorders are a group of conditions that are often inherited in families, involving small head size and abnormal brain development and function. This often results in delayed development of an affected child, affecting their movement, language and/or non-verbal communication and learning, as well as seizures and neuropsychiatric problems. A group of proteins called the transport protein particles (TRAPPs) are important for the transport of cargos inside cells. Alterations within a number of the TRAPP proteins have previously been associated with human inherited diseases called the ‘TRAPPopathies’, which involve neurodevelopmental and skeletal abnormalities. Here we show that TRAPPC10 gene alterations cause a new TRAPPopathy microcephalic neurodevelopmental disorder, and we provide a detailed clinical description of the condition termed ‘TRAPPC10-related disorder’. Our studies in mice lacking the TRAPPC10 gene identified similar features to those of affected humans, including small brain size and skeletal abnormalities. Our molecular studies showed that an affected individual with an alteration in the TRAPPC10 gene has no functional TRAPPC10 protein in their cells, which in turn causes a reduction in levels of another important TRAPP molecule, TRAPPC9. Cells lacking TRAPPC10 also display abnormalities in cellular transport processes. Together our data confirm alterations in TRAPPC10 as a cause of a microcephalic neurodevelopmental disorder in both humans and mice.
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Affiliation(s)
- Lettie E. Rawlins
- RILD Wellcome Wolfson Medical Research Centre, RD&E (Wonford) NHS Foundation Trust, University of Exeter Medical School, Exeter, United Kingdom
- Peninsula Clinical Genetics Service, Royal Devon & Exeter Hospital (Heavitree), Exeter, United Kingdom
| | - Hashem Almousa
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Shazia Khan
- RILD Wellcome Wolfson Medical Research Centre, RD&E (Wonford) NHS Foundation Trust, University of Exeter Medical School, Exeter, United Kingdom
- Department of Biological Sciences, International Islamic University, Islamabad, Pakistan
| | - Stephan C. Collins
- Institute of Genetics and Molecular and Cellular Biology, Inserm, Illkirch, France
- Inserm, University of Bourgogne Franche-Comté, Dijon, France
| | - Miroslav P. Milev
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Joseph Leslie
- RILD Wellcome Wolfson Medical Research Centre, RD&E (Wonford) NHS Foundation Trust, University of Exeter Medical School, Exeter, United Kingdom
| | - Djenann Saint-Dic
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Valeed Khan
- Department of Molecular Diagnostics, Rehman Medical Institute, Peshawar, Pakistan
| | | | - Jacob O. Day
- RILD Wellcome Wolfson Medical Research Centre, RD&E (Wonford) NHS Foundation Trust, University of Exeter Medical School, Exeter, United Kingdom
- Faculty of Health, University of Plymouth, Plymouth, United Kingdom
| | - Lucy McGavin
- University Hospitals Plymouth NHS Trust, Plymouth, United Kingdom
| | | | - Gaurav V. Harlalka
- RILD Wellcome Wolfson Medical Research Centre, RD&E (Wonford) NHS Foundation Trust, University of Exeter Medical School, Exeter, United Kingdom
- Department of Pharmacology, Rajarshi Shahu College of Pharmacy, Malvihir, Buldana, India
| | | | - Wasim Ahmad
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | | | - Asma Gul
- Department of Biological Sciences, International Islamic University, Islamabad, Pakistan
| | - Binnaz Yalcin
- Institute of Genetics and Molecular and Cellular Biology, Inserm, Illkirch, France
- Inserm, University of Bourgogne Franche-Comté, Dijon, France
| | - Andrew H. Crosby
- RILD Wellcome Wolfson Medical Research Centre, RD&E (Wonford) NHS Foundation Trust, University of Exeter Medical School, Exeter, United Kingdom
| | - Michael Sacher
- Department of Biology, Concordia University, Montreal, Quebec, Canada
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada
| | - Emma L. Baple
- RILD Wellcome Wolfson Medical Research Centre, RD&E (Wonford) NHS Foundation Trust, University of Exeter Medical School, Exeter, United Kingdom
- Peninsula Clinical Genetics Service, Royal Devon & Exeter Hospital (Heavitree), Exeter, United Kingdom
- * E-mail:
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5
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Cai Y, Zhang Y, Chen H, Sun XH, Zhang P, Zhang L, Liao MY, Zhang F, Xia ZY, Man RYK, Feinberg MW, Leung SWS. MicroRNA-17-3p suppresses NF-κB-mediated endothelial inflammation by targeting NIK and IKKβ binding protein. Acta Pharmacol Sin 2021; 42:2046-2057. [PMID: 33623121 PMCID: PMC8633290 DOI: 10.1038/s41401-021-00611-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 01/03/2021] [Indexed: 01/31/2023] Open
Abstract
Nuclear factor kappa B (NF-κB) activation contributes to many vascular inflammatory diseases. The present study tested the hypothesis that microRNA-17-3p (miR-17-3p) suppresses the pro-inflammatory responses via NF-κB signaling in vascular endothelium. Human umbilical vein endothelial cells (HUVECs), transfected with or without miR-17-3p agomir/antagomir, were exposed to lipopolysaccharide (LPS), and the inflammatory responses were determined. The cellular target of miR-17-3p was examined with dual-luciferase reporter assay. Mice were treated with miR-17-3p agomir and the degree of LPS-induced inflammation was determined. In HUVECs, LPS caused upregulation of miR-17-3p. Overexpression of miR-17-3p in HUVECs inhibited NIK and IKKβ binding protein (NIBP) protein expression and suppressed LPS-induced phosphorylation of inhibitor of kappa Bα (IκBα) and NF-κB-p65. The reduced NF-κB activity was paralleled by decreased protein levels of NF-κB-target gene products including pro-inflammatory cytokine [interleukin 6], chemokines [interleukin 8 and monocyte chemoattractant protein-1] and adhesion molecules [vascular cell adhesion molecule-1, intercellular adhesion molecule-1 and E-selectin]. Immunostaining revealed that overexpression of miR-17-3p reduced monocyte adhesion to LPS-stimulated endothelial cells. Inhibition of miR-17-3p with antagomir has the opposite effect on LPS-induced inflammatory responses in HUVECs. The anti-inflammatory effect of miR-17-3p was mimicked by NIBP knockdown. In mice treated with LPS, miR-17-3p expression was significantly increased. Systemic administration of miR-17-3p for 3 days suppressed LPS-induced NF-κB activation and monocyte adhesion to endothelium in lung tissues of the mice. In conclusion, miR-17-3p inhibits LPS-induced NF-κB activation in HUVECs by targeting NIBP. The findings therefore suggest that miR-17-3p is a potential therapeutic target/agent in the management of vascular inflammatory diseases.
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Affiliation(s)
- Yin Cai
- Department of Pharmacology and Pharmacy, The University of Hong Kong, Hong Kong, China
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong, China
- Department of Anaesthesiology, The University of Hong Kong, Hong Kong, China
| | - Yu Zhang
- Department of Pharmacology and Pharmacy, The University of Hong Kong, Hong Kong, China
| | - Hui Chen
- Department of Pharmacology and Pharmacy, The University of Hong Kong, Hong Kong, China
| | - Xing-Hui Sun
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Peng Zhang
- Department of Pharmacology and Pharmacy, The University of Hong Kong, Hong Kong, China
| | - Lu Zhang
- Department of Pharmacology and Pharmacy, The University of Hong Kong, Hong Kong, China
| | - Meng-Yang Liao
- Department of Cardiology, Institute of Cardiovascular Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Fang Zhang
- Department of Pharmacology, Medical College of Qingdao University, Qingdao, 266021, China
| | - Zheng-Yuan Xia
- Department of Anaesthesiology, The University of Hong Kong, Hong Kong, China
| | - Ricky Ying-Keung Man
- Department of Pharmacology and Pharmacy, The University of Hong Kong, Hong Kong, China
| | - Mark W Feinberg
- Department of Medicine, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Susan Wai-Sum Leung
- Department of Pharmacology and Pharmacy, The University of Hong Kong, Hong Kong, China.
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6
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Sherman BT, Hu X, Singh K, Haine L, Rupert AW, Neaton JD, Lundgren JD, Imamichi T, Chang W, Lane HC. Genome-wide association study of high-sensitivity C-reactive protein, D-dimer, and interleukin-6 levels in multiethnic HIV+ cohorts. AIDS 2021; 35:193-204. [PMID: 33095540 PMCID: PMC7789909 DOI: 10.1097/qad.0000000000002738] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 07/28/2020] [Accepted: 10/12/2020] [Indexed: 12/31/2022]
Abstract
OBJECTIVES Elevated levels of interleukin-6 (IL-6), D-dimer, and C-reactive protein (hsCRP) are associated with increased incidence of comorbid disease and mortality among people living with HIV (PLWH). Prior studies suggest a genetic basis for these biomarker elevations in the general population. The study objectives are to identify the genetic basis for these biomarkers among PLWH. METHODS Baseline levels of hsCRP, D-dimer, and IL-6, and single nucleotide polymorphisms (SNPs) were determined for 7768 participants in three HIV treatment trials. Single variant analysis was performed for each biomarker on samples from each of three ethnic groups [African (AFR), Admixed American (AMR), European (EUR)] within each trial including covariates relevant to biomarker levels. For each ethnic group, the results were pooled across trials, then further pooled across ethnicities. RESULTS The transethnic analysis identified three, two, and one known loci associated with hsCRP, D-dimer, and IL-6 levels, respectively, and two novel loci, FGB and GCNT1, associated with D-dimer levels. Lead SNPs exhibited similar effects across ethnicities. Additionally, three novel, ethnic-specific loci were identified: CATSPERG associated with D-dimer in AFR and PROX1-AS1 and TRAPPC9 associated with IL-6 in AFR and AMR, respectively. CONCLUSION Eleven loci associated with three biomarker levels were identified in PLWH from the three studies including six loci known in the general population and five novel loci associated with D-dimer and IL-6 levels. These findings support the hypothesis that host genetics may partially contribute to chronic inflammation in PLWH and help to identify potential targets for intervention of serious non-AIDS complications.
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Affiliation(s)
- Brad T. Sherman
- Laboratory of Human Retrovirology and Immunoinformatics, Frederick National Laboratory for Cancer Research, Frederick
| | - Xiaojun Hu
- Laboratory of Human Retrovirology and Immunoinformatics, Frederick National Laboratory for Cancer Research, Frederick
| | - Kanal Singh
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland
| | - Lillian Haine
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, Minnesota
| | - Adam W. Rupert
- AIDS Monitoring Laboratory, Applied and Developmental Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - James D. Neaton
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, Minnesota
| | - Jens D. Lundgren
- Centre of Excellence for Health, Immunity and Infections, Department of Infectious Diseases, Rigshospitalet, University of Copenhagen, Denmark
| | - Tomozumi Imamichi
- Laboratory of Human Retrovirology and Immunoinformatics, Frederick National Laboratory for Cancer Research, Frederick
| | - Weizhong Chang
- Laboratory of Human Retrovirology and Immunoinformatics, Frederick National Laboratory for Cancer Research, Frederick
| | - H. Clifford Lane
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland
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7
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Cancer-driving mutations and variants of components of the membrane trafficking core machinery. Life Sci 2020; 264:118662. [PMID: 33127517 DOI: 10.1016/j.lfs.2020.118662] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/17/2020] [Accepted: 10/22/2020] [Indexed: 12/12/2022]
Abstract
The core machinery for vesicular membrane trafficking broadly comprises of coat proteins, RABs, tethering complexes and SNAREs. As cellular membrane traffic modulates key processes of mitogenic signaling, cell migration, cell death and autophagy, its dysregulation could potentially results in increased cell proliferation and survival, or enhanced migration and invasion. Changes in the levels of some components of the core machinery of vesicular membrane trafficking, likely due to gene amplifications and/or alterations in epigenetic factors (such as DNA methylation and micro RNA) have been extensively associated with human cancers. Here, we provide an overview of association of membrane trafficking with cancer, with a focus on mutations and variants of coat proteins, RABs, tethering complex components and SNAREs that have been uncovered in human cancer cells/tissues. The major cellular and molecular cancer-driving or suppression mechanisms associated with these components of the core membrane trafficking machinery shall be discussed.
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8
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Bodnar B, DeGruttola A, Zhu Y, Lin Y, Zhang Y, Mo X, Hu W. Emerging role of NIK/IKK2-binding protein (NIBP)/trafficking protein particle complex 9 (TRAPPC9) in nervous system diseases. Transl Res 2020; 224:55-70. [PMID: 32434006 PMCID: PMC7442628 DOI: 10.1016/j.trsl.2020.05.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 05/02/2020] [Accepted: 05/05/2020] [Indexed: 02/05/2023]
Abstract
NFκB signaling and protein trafficking network play important roles in various biological and pathological processes. NIK-and-IKK2-binding protein (NIBP), also known as trafficking protein particle complex 9 (TRAPPC9), is a prototype member of a novel protein family, and has been shown to regulate both NFκB signaling pathway and protein transport/trafficking. NIBP is extensively expressed in the nervous system and plays an important role in regulating neurogenesis and neuronal differentiation. NIBP/TRAPPC9 mutations have been linked to an autosomal recessive intellectual disability syndrome, called NIBP Syndrome, which is characterized by nonsyndromic autosomal recessive intellectual disability along with other symptoms such as obesity, microcephaly, and facial dysmorphia. As more cases of NIBP Syndrome are identified, new light is being shed on the role of NIBP/TRAPPC9 in the central nervous system developments and diseases. NIBP is also involved in the enteric nervous system. This review will highlight the importance of NIBP/TRAPPC9 in central and enteric nervous system diseases, and the established possible mechanisms for developing a potential therapeutic.
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Affiliation(s)
- Brittany Bodnar
- Center for Metabolic Disease Research, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania; MD/PhD and Biomedical Sciences Graduate Program, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania
| | - Arianna DeGruttola
- Center for Metabolic Disease Research, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania; MD/PhD and Biomedical Sciences Graduate Program, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania
| | - Yuanjun Zhu
- Center for Metabolic Disease Research, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania; Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania; Department of Molecular and Cellular Pharmacology, Peking University School of Pharmaceutical Sciences, Beijing, China
| | - Yuan Lin
- Center for Metabolic Disease Research, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania; Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania
| | - Yonggang Zhang
- Center for Stem Cell Research and Application, Institute of Blood Transfusion, Chinese Academy of Medical Sciences & Peking Union Medical College (CAMS & PUMC), Chengdu, China
| | - Xianming Mo
- Laboratory of Stem Cell Biology, State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu, China
| | - Wenhui Hu
- Center for Metabolic Disease Research, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania; MD/PhD and Biomedical Sciences Graduate Program, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania; Department of Pathology and Laboratory Medicine, Temple University Lewis Katz School of Medicine, Philadelphia, Pennsylvania.
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9
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Brouwer WP, Chan HLY, Lampertico P, Hou J, Tangkijvanich P, Reesink HW, Zhang W, Mangia A, Tanwandee T, Montalto G, Simon K, Ormeci N, Chen L, Tabak F, Gunsar F, Flisiak R, Ferenci P, Akdogan M, Akyuz F, Hirankarn N, Jansen L, Wong VWS, Soffredini R, Liang X, Chen S, Groothuismink ZMA, Santoro R, Jaroszewicz J, Ozaras R, Kozbial K, Brahmania M, Xie Q, Chotiyaputta W, Xun Q, Pazgan-Simon M, Oztas E, Verhey E, Montanari NR, Sun J, Hansen BE, Boonstra A, Janssen HLA. Genome-wide Association Study Identifies Genetic Variants Associated With Early and Sustained Response to (Pegylated) Interferon in Chronic Hepatitis B Patients: The GIANT-B Study. Clin Infect Dis 2020; 69:1969-1979. [PMID: 30715261 PMCID: PMC6853659 DOI: 10.1093/cid/ciz084] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 03/11/2019] [Indexed: 02/07/2023] Open
Abstract
Background (Pegylated) Interferon ([Peg]IFN) therapy leads to response in a minority of chronic hepatitis B (CHB) patients. Host genetic determinants of response are therefore in demand. Methods In this genome-wide association study (GWAS), CHB patients, treated with (Peg)IFN for at least 12 weeks ± nucleos(t)ide analogues within randomized trials or as standard of care, were recruited at 21 centers from Europe, Asia, and North America. Response at 24 weeks after (Peg)IFN treatment was defined as combined hepatitis B e antigen (HBeAg) loss with hepatitis B virus (HBV) DNA <2000 IU/mL, or an HBV DNA <2000 IU/mL for HBeAg-negative patients. Results Of 1144 patients, 1058 (92%) patients were included in the GWAS analysis. In total, 282 (31%) patients achieved the response and 4% hepatitis B surface antigen (HBsAg) loss. GWAS analysis stratified by HBeAg status, adjusted for age, sex, and the 4 ancestry components identified PRELID2 rs371991 (B= −0.74, standard error [SE] = 0.16, P = 3.44 ×10–6) for HBeAg-positive patients. Importantly, PRELID2 was cross-validated for long-term response in HBeAg-negative patients. G3BP2 rs3821977 (B = 1.13, SE = 0.24, P = 2.46 × 10–6) was associated with response in HBeAg-negative patients. G3BP2 has a role in the interferon pathway and was further examined in peripheral blood mononuclear cells of healthy controls stimulated with IFNα and TLR8. After stimulation, less production of IP-10 and interleukin (IL)-10 proteins and more production of IL-8 were observed with the G3BP2 G-allele. Conclusions Although no genome-wide significant hits were found, the current GWAS identified genetic variants associated with (Peg)IFN response in CHB. The current findings could pave the way for gene polymorphism-guided clinical counseling, both in the setting of (Peg)IFN and the natural history, and possibly for new immune-modulating therapies. Clinical Trials Registation NCT01401400.
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Affiliation(s)
- Willem P Brouwer
- Gastroenterology and Hepatology, Erasmus Medical Center Rotterdam, The Netherlands
| | - Henry L Y Chan
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Italy
| | - Pietro Lampertico
- Centro di riferimento per la diagnosi e lo studio delle malattie del fegato e delle vie biliari "Angela Maria ed Antonio Migliavacca" Center for Liver Disease, Division of Gastroenterology and Hepatology, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico di natura pubblica Cà Granda Ospedale Maggiore Policlinico, University of Milan, Italy
| | - Jinlin Hou
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Hepatology Unit and Dept of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | | | | | - Wenhong Zhang
- Clinical Center Hepatitis, Institute of Biomedical Science, Huashan hospital "Fu Dan University," Shanghai, China
| | - Alessandra Mangia
- Istituto di Ricovero e Cura a Carattere Scientifico di natura pubblica Casa Sollievo della Sofferenza, Foggia, Italy
| | - Tawesak Tanwandee
- Division of Gastroenterology, Department of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Giuseppe Montalto
- Biomedical Department of Internal Medicine and Specialties, University of Palermo, Italy
| | - Kris Simon
- Wroclaw University of Medicine Department of Infectious Diseases and Hepatology, Poland
| | | | - Liang Chen
- Shanghai Public Health Center "Fu Dan University," China
| | - Fehmi Tabak
- Cerrahpasa Medical Faculty, Department of Infectious Diseases, Istanbul
| | | | - Robert Flisiak
- Department of Infectious Diseases and Hepatology, Medical University of Bialystok, Poland
| | | | | | - Filiz Akyuz
- Istanbul Üniversitesi Istanbul Tip Fakültesi Hastanesi, Istanbul, Turkey
| | | | - Louis Jansen
- Academic Medical Centre, Amsterdam, The Netherlands
| | - Vincent Wai-Sun Wong
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Italy
| | - Roberta Soffredini
- Centro di riferimento per la diagnosi e lo studio delle malattie del fegato e delle vie biliari "Angela Maria ed Antonio Migliavacca" Center for Liver Disease, Division of Gastroenterology and Hepatology, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico di natura pubblica Cà Granda Ospedale Maggiore Policlinico, University of Milan, Italy
| | - Xieer Liang
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Hepatology Unit and Dept of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Shalom Chen
- Clinical Center Hepatitis, Institute of Biomedical Science, Huashan hospital "Fu Dan University," Shanghai, China
| | | | - Rosanna Santoro
- Istituto di Ricovero e Cura a Carattere Scientifico di natura pubblica Casa Sollievo della Sofferenza, Foggia, Italy
| | - Jerzy Jaroszewicz
- Department of Infectious Diseases and Hepatology, Medical University of Bialystok, Poland.,Department of Infectious Diseases and Hepatology, Medical University of Silesia, Katowice, Poland
| | - Resat Ozaras
- Cerrahpasa Medical Faculty, Department of Infectious Diseases, Istanbul
| | | | - Mayur Brahmania
- Liver Clinic, Toronto General Hospital, University Health Network, Toronto, Canada
| | - Qing Xie
- Shanghai Ruijin Hospital, Jiao Tong University School of Medicine, Shanghai, China
| | - Watcharasak Chotiyaputta
- Division of Gastroenterology, Department of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Qi Xun
- Shanghai Public Health Center "Fu Dan University," China
| | - Monika Pazgan-Simon
- Wroclaw University of Medicine Department of Infectious Diseases and Hepatology, Poland
| | | | - Elke Verhey
- Gastroenterology and Hepatology, Erasmus Medical Center Rotterdam, The Netherlands
| | - Noé R Montanari
- Gastroenterology and Hepatology, Erasmus Medical Center Rotterdam, The Netherlands
| | - Jian Sun
- State Key Laboratory of Organ Failure Research, Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Hepatology Unit and Dept of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Bettina E Hansen
- Gastroenterology and Hepatology, Erasmus Medical Center Rotterdam, The Netherlands
| | - Andre Boonstra
- Gastroenterology and Hepatology, Erasmus Medical Center Rotterdam, The Netherlands
| | - Harry L A Janssen
- Gastroenterology and Hepatology, Erasmus Medical Center Rotterdam, The Netherlands.,Liver Clinic, Toronto General Hospital, University Health Network, Toronto, Canada
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10
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Sui C, Song Z, Yu H, Wang H. Prognostic significance of TPX2 and NIBP in esophageal cancer. Oncol Lett 2019; 18:4221-4229. [PMID: 31516617 PMCID: PMC6732995 DOI: 10.3892/ol.2019.10747] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 07/10/2019] [Indexed: 12/17/2022] Open
Abstract
The expression of targeting protein for Xenopus kinesin-like protein 2 (TPX2) and NIK-IKK-β binding protein (NIBP) in patients with esophageal cancer were investigated. A total of 250 samples of cancer tissue and 250 samples of adjacent normal tissue were collected from 250 patients who underwent radical resection of esophageal cancer in Weihai Central Hospital from March 2011 to February 2014. RT-qPCR was used to detect the relative expression of TPX2 and NIBP. The relative expression of TPX2 and NIBP in esophageal cancer tissues was statistically higher than those in adjacent normal tissues (P<0.05). TPX2 and NIBP levels in tumor tissues with lymph node metastasis were significantly higher than those in tissues without lymph node metastasis (P<0.05). There was a significant difference in the relative expression of TPX2 and NIBP in different degrees of infiltration (P<0.05). Tissues with a TPX2 level equal to or higher than the average TPX2 level (1.465) were divided into TPX2 high expression group, while tissues with a TPX2 level below the average were divided into TPX2 low expression group. The 5-year overall survival rate of TPX2 high expression group was significantly lower than that of TPX2 low expression group (P<0.05). Tissues with a NIBP level equal to or higher than the average NIBP level (0.498) were included in the NIBP high expression group, while tissues with a NIBP level below the average were included in the NIBP low expression group. The 5-year overall survival rate of NIBP high expression group was significantly lower than that of NIBP low expression group (P<0.05). TPX2, NIBP, TNM staging, lymph node metastasis, and degree of infiltration were independent prognostic factors affecting overall survival (P<0.05). In conclusion, owing to their high expression in esophageal cancer tissues, TPX2 and NIBP are potentially important biomarkers for the evaluation of TNM stage, metastasis, and prognosis of esophageal cancer.
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Affiliation(s)
- Chao Sui
- Department of Medical Oncology, Weihai Central Hospital, Weihai, Shandong 264400, P.R. China
| | - Zhifang Song
- Department of Oncology, Weihai Central Hospital, Weihai, Shandong 264400, P.R. China
| | - Huimin Yu
- Department of Medical Oncology, Weihai Central Hospital, Weihai, Shandong 264400, P.R. China
| | - Haiwen Wang
- Department of Thoracic Surgery, Weihai Central Hospital, Weihai, Shandong 264400, P.R. China
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11
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Sacher M, Shahrzad N, Kamel H, Milev MP. TRAPPopathies: An emerging set of disorders linked to variations in the genes encoding transport protein particle (TRAPP)-associated proteins. Traffic 2018; 20:5-26. [PMID: 30152084 DOI: 10.1111/tra.12615] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 08/23/2018] [Accepted: 08/26/2018] [Indexed: 02/06/2023]
Abstract
The movement of proteins between cellular compartments requires the orchestrated actions of many factors including Rab family GTPases, Soluble NSF Attachment protein REceptors (SNAREs) and so-called tethering factors. One such tethering factor is called TRAnsport Protein Particle (TRAPP), and in humans, TRAPP proteins are distributed into two related complexes called TRAPP II and III. Although thought to act as a single unit within the complex, in the past few years it has become evident that some TRAPP proteins function independently of the complex. Consistent with this, variations in the genes encoding these proteins result in a spectrum of human diseases with diverse, but partially overlapping, phenotypes. This contrasts with other tethering factors such as COG, where variations in the genes that encode its subunits all result in an identical phenotype. In this review, we present an up-to-date summary of all the known disease-related variations of genes encoding TRAPP-associated proteins and the disorders linked to these variations which we now call TRAPPopathies.
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Affiliation(s)
- Michael Sacher
- Department of Biology, Concordia University, Montreal, Quebec, Canada.,Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada
| | - Nassim Shahrzad
- Department of Medicine, University of California, San Francisco, California
| | - Hiba Kamel
- Department of Biology, Concordia University, Montreal, Quebec, Canada
| | - Miroslav P Milev
- Department of Biology, Concordia University, Montreal, Quebec, Canada
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12
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Mbimba T, Hussein NJ, Najeed A, Safadi FF. TRAPPC9: Novel insights into its trafficking and signaling pathways in health and disease (Review). Int J Mol Med 2018; 42:2991-2997. [PMID: 30272317 DOI: 10.3892/ijmm.2018.3889] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 08/14/2018] [Indexed: 11/06/2022] Open
Abstract
Trafficking protein particle complex 9 (TRAPPC9) is a protein subunit of the transport protein particle II (TRAPPII), which has been reported to be important in the trafficking of cargo from the endoplasmic reticulum (ER) to the Golgi, and in intra‑Golgi and endosome‑to‑Golgi transport in yeast cells. In mammalian cells, TRAPPII has been shown to be important in Golgi vesicle tethering and intra‑Golgi transport. TRAPPC9 is considered to be a novel molecule capable of modulating the activation of nuclear factor‑κB (NF‑κB). Mutations in TRAPPC9 have been linked to a rare consanguineous hereditary form of mental retardation, as part of the NF‑κB pathways. In addition, TRAPPC9 has been reported to be involved in breast and colon cancer and liver diseases. The present review highlights the most recent publications on the structure, expression and function of TRAPPC9, and its association with various human diseases.
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Affiliation(s)
- Thomas Mbimba
- Department of Anatomy and Neurobiology, College of Medicine, Northeast Ohio Medical University, Rootstown, OH 44272, USA
| | - Nazar J Hussein
- Department of Anatomy and Neurobiology, College of Medicine, Northeast Ohio Medical University, Rootstown, OH 44272, USA
| | - Ayesha Najeed
- Department of Anatomy and Neurobiology, College of Medicine, Northeast Ohio Medical University, Rootstown, OH 44272, USA
| | - Fayez F Safadi
- Department of Anatomy and Neurobiology, College of Medicine, Northeast Ohio Medical University, Rootstown, OH 44272, USA
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13
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NF-κB pathways in the development and progression of colorectal cancer. Transl Res 2018; 197:43-56. [PMID: 29550444 DOI: 10.1016/j.trsl.2018.02.002] [Citation(s) in RCA: 143] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 02/13/2018] [Accepted: 02/14/2018] [Indexed: 12/12/2022]
Abstract
Nuclear factor-κB (NF-κB) has been widely implicated in the development and progression of cancer. In colorectal cancer (CRC), NF-κB has a key role in cancer-related processes such as cell proliferation, apoptosis, angiogenesis, and metastasis. The role of NF-κB in CRC is complex, owed to the cross talk with other signaling pathways. Although there is sufficient evidence gained from cell lines and animal models that NF-κB is involved in cancer-related processes, because of a lack of studies in human tissue, the clinical evidence of its importance is limited in patients with CRC. This review summarizes evidence relating to how NF-κB is involved in the development and progression of CRC and comments on future work to be carried out.
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14
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Takamura T, Suguro H, Mikami Y, Iwase T, Komiyama Y, Kuyama K, Komiyama K, Oki H. Comparison of gene expression profiles of gingival carcinoma Ca9-22 cells and colorectal adenocarcinoma HT-29 cells to identify potentially important mediators of SLPI-induced cell migration. J Oral Sci 2018. [PMID: 28637988 DOI: 10.2334/josnusd.16-0534] [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: 11/01/2022]
Abstract
Secretory leukocyte protease inhibitor (SLPI) is a serine protease inhibitor whose expression level is positively correlated with tumor aggressiveness and metastatic potential. However, the mechanism underlying SLPI-induced enhancement of malignant phenotype is not completely understood. The malignancy of cancer cells is highly dependent on cell migration activity. Our previous study revealed that gingival carcinoma Ca9-22 cells, but not colorectal adenocarcinoma HT-29 cells, expressed SLPI. Therefore, we investigated the migration activity of these two cell types to understand the nature of SLPI-mediated tumor aggressiveness and metastatic potential. In vitro wound healing assay indicated that HT-29 cells and SLPI-deleted Ca9-22 cells showed lower migration activity than wild-type Ca9-22 cells, suggesting that SLPI-induced cell migration plays an important role in tumor aggressiveness and metastatic potential. In addition, our gene expression profiling study based on microarray data for the three cell types identified a number of candidates, including LCP1 and GLI, that could be key molecules in the mechanism of SLPI-induced cell migration.
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Affiliation(s)
- Tsuyoshi Takamura
- Department of Oral and Maxillofacial Surgery, Nihon University School of Dentistry
| | - Hisashi Suguro
- Department of Endodontics, Nihon University School of Dentistry
| | - Yoshikazu Mikami
- Division of Microscopic Anatomy, Niigata University Graduate School of Medical and Dental Sciences
| | - Takashi Iwase
- Department of Pathology, Nihon University School of Dentistry
| | - Yusuke Komiyama
- Department of Oral and Maxillofacial Surgery, Dokkyo Medical University School of Medicine
| | - Kayo Kuyama
- Department of Oral Pathology, Nihon University School of Dentistry at Matsudo
| | - Kazuo Komiyama
- Department of Pathology, Nihon University School of Dentistry
| | - Hiderou Oki
- Department of Oral and Maxillofacial Surgery, Nihon University School of Dentistry
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15
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Lin DC, Wang MR, Koeffler HP. Genomic and Epigenomic Aberrations in Esophageal Squamous Cell Carcinoma and Implications for Patients. Gastroenterology 2018; 154:374-389. [PMID: 28757263 PMCID: PMC5951382 DOI: 10.1053/j.gastro.2017.06.066] [Citation(s) in RCA: 172] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Revised: 06/05/2017] [Accepted: 06/07/2017] [Indexed: 12/28/2022]
Abstract
Esophageal squamous cell carcinoma (ESCC) is a common malignancy without effective therapy. The exomes of more than 600 ESCCs have been sequenced in the past 4 years, and numerous key aberrations have been identified. Recently, researchers reported both inter- and intratumor heterogeneity. Although these are interesting observations, their clinical implications are unclear due to the limited number of samples profiled. Epigenomic alterations, such as changes in DNA methylation, histone acetylation, and RNA editing, also have been observed in ESCCs. However, it is not clear what proportion of ESCC cells carry these epigenomic aberrations or how they contribute to tumor development. We review the genomic and epigenomic characteristics of ESCCs, with a focus on emerging themes. We discuss their clinical implications and future research directions.
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Affiliation(s)
- De-Chen Lin
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California.
| | - Ming-Rong Wang
- State Key Laboratory of Molecular Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - H. Phillip Koeffler
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California,Cancer Science Institute of Singapore, National University of Singapore, Singapore,National University Cancer Institute, National University Hospital Singapore, Singapore
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16
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Li L, Yang W, Yue H, He F, Xu S, Wei Q, Chen P, Peng Q, Deng S, Long P. Expression of NIBP and its clinical significance in human early colorectal cancer. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2017; 10:8633-8639. [PMID: 31966720 PMCID: PMC6965483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Accepted: 06/20/2017] [Indexed: 06/10/2023]
Abstract
AIM To investigate the expression of NIBP and its clinical significance in early colorectal cancer. PATIENTS AND METHODS With immunohistochemistry, the expression of NIBP was detected in 23 patients of early colorectal cancer tissues, 102 patients of invasive colorectal cancer tissues, 32 patients of adenoma and 20 patients of normal tissues. The relationship between NIBP expression and clinicopathological characteristic of colorectal cancer were also analyzed. RESULT We found that the positive rates of NIBP was higher in early colorectal cancer tissues (82.6%, 19/23) than those in adenomas and normal tissues (x2=29.07, P<0.05), but not significant than those in invasive colorectal cancer (x2=1.79, P>0.05). Positivity for T1N0M0, T2N0M0, II, III and IV was 82.6% (19/23), 80.0% (4/5), 78.0% (32/41), 63.6% (21/33), 56.5% (13/23), respectively. With the increase in TNM stage, the positive rate of NIBP decreased, the positive rate of T1N0M0 is highest than other TNM stages, but no statistically significant (P>0.05). CONCLUSION These results suggested that NIBP is highly expressed in human early colorectal cancer tissues. NIBP might involve in the tumorigenesis and probably serve as a new marker for human early colorectal cancer.
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Affiliation(s)
- Lifu Li
- Department of Gastroenterology, The Third Affiliated Hospital of Southern Medical UniversityNo. 183 Zhongshan Road West, Guangzhou, Guangdong Province, China
| | - Wenjuan Yang
- Department of The Fifth Hepatology, The Ninth Hospital of NanchangJiangxi Province, China
| | - Hui Yue
- Department of Gastroenterology, The Third Affiliated Hospital of Southern Medical UniversityNo. 183 Zhongshan Road West, Guangzhou, Guangdong Province, China
| | - Fengjian He
- Department of Gastroenterology, The Third Affiliated Hospital of Southern Medical UniversityNo. 183 Zhongshan Road West, Guangzhou, Guangdong Province, China
| | - Shenghao Xu
- Department of Gastroenterology, The Third Affiliated Hospital of Southern Medical UniversityNo. 183 Zhongshan Road West, Guangzhou, Guangdong Province, China
| | - Qingzhu Wei
- Department of Gastroenterology, The Third Affiliated Hospital of Southern Medical UniversityNo. 183 Zhongshan Road West, Guangzhou, Guangdong Province, China
| | - Peisheng Chen
- Department of Gastroenterology, The Third Affiliated Hospital of Southern Medical UniversityNo. 183 Zhongshan Road West, Guangzhou, Guangdong Province, China
| | - Qianqian Peng
- Department of Gastroenterology, The Third Affiliated Hospital of Southern Medical UniversityNo. 183 Zhongshan Road West, Guangzhou, Guangdong Province, China
| | - Sanhua Deng
- Department of Gastroenterology, The Third Affiliated Hospital of Southern Medical UniversityNo. 183 Zhongshan Road West, Guangzhou, Guangdong Province, China
| | - Peiqi Long
- Department of Gastroenterology, The Third Affiliated Hospital of Southern Medical UniversityNo. 183 Zhongshan Road West, Guangzhou, Guangdong Province, China
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17
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Shi Y, Yang F, Wei S, Xu G. Identification of Key Genes Affecting Results of Hyperthermia in Osteosarcoma Based on Integrative ChIP-Seq/TargetScan Analysis. Med Sci Monit 2017; 23:2042-2048. [PMID: 28453502 PMCID: PMC5419091 DOI: 10.12659/msm.901191] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Background The purpose of this study was to research the effects of hyperthermia on osteosarcoma (OS) by integrating the Chromatin Immunoprecipitation with the generation sequencing (ChIP-Seq) and TargetScan analysis of heat shock transcription factor 1 (HSF1). Material/Methods The HSF1 ChIP-seq dataset of GSE60984 was downloaded from the Gene Expressed Omnibus (GEO) database. The HSF1-binding sites were screened by MACS2 in OS cells after 10 and 20 min of hyperthermia, and they were annotated using the ChIPseeker package. The overlapped genes were selected out when HSF1-binding sites were located in the promoter region. The Database for Annotation, Visualization, and Integrated Discovery (DAVID) was used to perform Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of the overlaps. The miRNA-gene pairs of the overlaps were screened out via TargetScan, and the miRNA-gene-regulated network was constructed by Cytoscape software. Results 1880 and 1283 genes of promoter regions were obtained in the osteosarcoma cells after 10 and 20 min of hyperthermia, respectively, and 889 of them were overlapped. The overlapped genes were enriched in 122 GO terms and 3 KEGG pathways. There were 13 657 pairs involved in the miRNA-gene regulated network of the overlaps. Conclusions Some biomarkers were identified for OS treated with hyperthermia. Moreover, some GO terms (regulation of programmed cell death and regulation of cell death) and pathways (p53 signaling pathway, methane metabolism, and viral myocarditis) might be involved.
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Affiliation(s)
- Yuxia Shi
- Department of Bone and Soft-Tissue Tumor, Shanxi Tumor Hospital, Taiyuan, Shanxi, China (mainland)
| | - Fan Yang
- Department of Bone and Soft-Tissue Tumor, Shanxi Tumor Hospital, Taiyuan, Shanxi, China (mainland)
| | - Shuqing Wei
- Department of Geriatric, Shanxi Tumor Hospital, Taiyuan, Shanxi, China (mainland)
| | - Gang Xu
- Department of Bone and Soft-Tissue Tumor, Shanxi Tumor Hospital, Taiyuan, Shanxi, China (mainland)
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18
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Qin M, Zhang J, Xu C, Peng P, Tan L, Liu S, Huang J. Knockdown of NIK and IKKβ-Binding Protein (NIBP) Reduces Colorectal Cancer Metastasis through Down-Regulation of the Canonical NF-κΒ Signaling Pathway and Suppression of MAPK Signaling Mediated through ERK and JNK. PLoS One 2017; 12:e0170595. [PMID: 28125661 PMCID: PMC5268490 DOI: 10.1371/journal.pone.0170595] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 01/06/2017] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Despite the identification of many signaling pathways involved in colorectal cancer (CRC) tumorigenesis, metastatic CRC still remains one of the major causes of cancer related death. NIK and IKKβ-binding protein (NIBP) is one of the key regulators of the NF-κB signaling pathway, which has been implicated in CRC metastasis. The aim of this study was to investigate the possible role of NIBP in CRC metastasis through its regulation of NF-κΒ and extracellular regulated kinase/c-Janus kinase (ERK/JNK) signaling pathways. METHODS In this study NIBP, phosphorylated (p)-p65, p-ERK1/2, and p-JNK1/2 expression was examined in 130 CRC, and 25 adenoma tissue samples were studied by immunohistochemistry. NIBP shRNA knockdown was performed in HCT116 cells, and NF-κB and ERK/JNK pathway activity was measured after TNF-α stimulation in vitro and in vivo. RESULTS We found that NIBP, p-p65, p-ERK1/2, and p-JNK1/2 expression was higher in late stages of CRC compared to early stages or adenomas. Expression of p-p65, p-IκBα, p-IκBβ, p-ERK1/2, and p-JNK1/2 was inhibited in TNF-α stimulated HCT116 cells following NIBP knockdown. Nevertheless, p-ERK1/2 expression in un-transfected and NIBP knockdown HCT116 cells remained the same in the absence of TNF-α stimulation. Furthermore, cell motility and invasion were reduced in HCT116 cells following NIBP knockdown even after TNF-α treatment. Finally, primary tumor weight and liver metastasis were reduced in nude mice with orthotopically transplanted NIBP knockdown of HCT116 cells. CONCLUSION In conclusion, we demonstrated that NIBP knockdown reduces colorectal cancer metastasis through down-regulation of canonical NF-κΒ signaling and suppression of ERK and JNK signaling.
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Affiliation(s)
- Mengbin Qin
- Department of Gastroenterology, The First Affiliated Hospital, Guangxi Medical University, Nanning, China
| | - Jinxiu Zhang
- Department of Gastroenterology, The First Affiliated Hospital, Guangxi Medical University, Nanning, China
| | - Chunyan Xu
- Department of Gastroenterology, The First Affiliated Hospital, Guangxi Medical University, Nanning, China
| | - Peng Peng
- Department of Gastroenterology, The First Affiliated Hospital, Guangxi Medical University, Nanning, China
| | - Lin Tan
- Department of Gastroenterology, The First Affiliated Hospital, Guangxi Medical University, Nanning, China
| | - Shiquan Liu
- Department of Gastroenterology, The First Affiliated Hospital, Guangxi Medical University, Nanning, China
| | - Jiean Huang
- Department of Gastroenterology, The First Affiliated Hospital, Guangxi Medical University, Nanning, China
- * E-mail:
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Kim JJ, Lipatova Z, Segev N. TRAPP Complexes in Secretion and Autophagy. Front Cell Dev Biol 2016; 4:20. [PMID: 27066478 PMCID: PMC4811894 DOI: 10.3389/fcell.2016.00020] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 03/04/2016] [Indexed: 12/13/2022] Open
Abstract
TRAPP is a highly conserved modular multi-subunit protein complex. Originally identified as a “transport protein particle” with a role in endoplasmic reticulum-to-Golgi transport, its multiple subunits and their conservation from yeast to humans were characterized in the late 1990s. TRAPP attracted attention when it was shown to act as a Ypt/Rab GTPase nucleotide exchanger, GEF, in the 2000s. Currently, three TRAPP complexes are known in yeast, I, II, and III, and they regulate two different intracellular trafficking pathways: secretion and autophagy. Core TRAPP contains four small subunits that self assemble to a stable complex, which has a GEF activity on Ypt1. Another small subunit, Trs20/Sedlin, is an adaptor required for the association of core TRAPP with larger subunits to form TRAPP II and TRAPP III. Whereas the molecular structure of the core TRAPP complex is resolved, the architecture of the larger TRAPP complexes, including their existence as dimers and multimers, is less clear. In addition to its Ypt/Rab GEF activity, and thereby an indirect role in vesicle tethering through Ypt/Rabs, a direct role for TRAPP as a vesicle tether has been suggested. This idea is based on TRAPP interactions with vesicle coat components. While much of the basic information about TRAPP complexes comes from yeast, mutations in TRAPP subunits were connected to human disease. In this review we will summarize new information about TRAPP complexes, highlight new insights about their function and discuss current controversies and future perspectives.
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Affiliation(s)
- Jane J Kim
- Department of Biological Sciences, University of Illinois at Chicago Chicago, IL, USA
| | - Zhanna Lipatova
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago Chicago, IL, USA
| | - Nava Segev
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago Chicago, IL, USA
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NIK- and IKKβ-binding protein promotes colon cancer metastasis by activating the classical NF-κB pathway and MMPs. Tumour Biol 2015; 37:5979-90. [DOI: 10.1007/s13277-015-4433-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 11/11/2015] [Indexed: 12/11/2022] Open
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