1
|
Wang J, Chai B, Yang Y, Chen C, Ren Y, Li Y, Wang ZQ, Li T. JADE1 is dispensable for the brain development in mice. Biochem Biophys Res Commun 2024; 695:149421. [PMID: 38171233 DOI: 10.1016/j.bbrc.2023.149421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Accepted: 12/20/2023] [Indexed: 01/05/2024]
Abstract
In mammalian brain development, WNT signaling balances proliferation and differentiation of neural progenitor cells, and is essential for the maintenance of regular brain development. JADE1 is a candidate transcription co-factor essential for DNA replication, cell division, and cell cycle regulation. In 293T cells, JADE1 is stabilized by von Hippel-Lindau protein pVHL, promotes the β-catenin ubiquitination and thus blunts canonical WNT signaling. Furthermore, JADE1 inhibits β-catenin-induced ectopic axis formation in Xenopus embryos. However, JADE1's role in mammalian brain development remains unknown. Here, we generated a new Jade1 knockout mouse line using CRISPR-Cas9 technology. We found that JADE1 null resulted in decreased survival rate, reduced body weight and brain weight in mice. However, histological analysis revealed a normal brain development. Furthermore, Jade1 null neural progenitor cells proliferated normally in vivo and in vitro. RNA-seq analysis further showed that JADE1 loss did not affect the cerebral cortex gene expression. Our findings indicate that JADE1 is dispensable for developing the cerebral cortex in mice.
Collapse
Affiliation(s)
- Jingpeng Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Baihui Chai
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Yanlang Yang
- Department of Nephrology, Affiliated Yijishan Hospital, Wannan Medical College, Wuhu, China
| | - Chengyan Chen
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Yaoxin Ren
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Yan Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Zhao-Qi Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China; Faculty of Biological Sciences, Friedrich-Schiller-University of Jena, Jena, Germany
| | - Tangliang Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China; School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, China.
| |
Collapse
|
2
|
Sulzbach Denardin M, Bumiller-Bini Hoch V, Salviano-Silva A, Lobo-Alves SC, Adelman Cipolla G, Malheiros D, Augusto DG, Wittig M, Franke A, Pföhler C, Worm M, van Beek N, Goebeler M, Sárdy M, Ibrahim S, Busch H, Schmidt E, Hundt JE, Petzl-Erler ML, Beate Winter Boldt A. Genetic Association and Differential RNA Expression of Histone (De)Acetylation-Related Genes in Pemphigus Foliaceus-A Possible Epigenetic Effect in the Autoimmune Response. Life (Basel) 2023; 14:60. [PMID: 38255677 PMCID: PMC10821360 DOI: 10.3390/life14010060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 12/23/2023] [Accepted: 12/25/2023] [Indexed: 01/24/2024] Open
Abstract
Pemphigus foliaceus (PF) is an autoimmune skin blistering disease characterized by antidesmoglein-1 IgG production, with an endemic form (EPF) in Brazil. Genetic and epigenetic factors have been associated with EPF, but its etiology is still not fully understood. To evaluate the genetic association of histone (de)acetylation-related genes with EPF susceptibility, we evaluated 785 polymorphisms from 144 genes, for 227 EPF patients and 194 controls. Carriers of HDAC4_rs4852054*A were more susceptible (OR = 1.79, p = 0.0038), whereas those with GSE1_rs13339618*A (OR = 0.57, p = 0.0011) and homozygotes for PHF21A_rs4756055*A (OR = 0.39, p = 0.0006) were less susceptible to EPF. These variants were not associated with sporadic PF (SPF) in German samples of 75 SPF patients and 150 controls, possibly reflecting differences in SPF and EPF pathophysiology. We further evaluated the expression of histone (de)acetylation-related genes in CD4+ T lymphocytes, using RNAseq. In these cells, we found a higher expression of KAT2B, PHF20, and ZEB2 and lower expression of KAT14 and JAD1 in patients with active EPF without treatment compared to controls from endemic regions. The encoded proteins cause epigenetic modifications related to immune cell differentiation and cell death, possibly affecting the immune response in patients with PF.
Collapse
Affiliation(s)
- Maiara Sulzbach Denardin
- Laboratory of Human Molecular Genetics, Department of Genetics, Federal University of Paraná (UFPR), Curitiba 81531-980, Brazil; (M.S.D.); (V.B.-B.H.); (S.C.L.-A.); (G.A.C.); (D.M.); (D.G.A.); (M.L.P.-E.)
| | - Valéria Bumiller-Bini Hoch
- Laboratory of Human Molecular Genetics, Department of Genetics, Federal University of Paraná (UFPR), Curitiba 81531-980, Brazil; (M.S.D.); (V.B.-B.H.); (S.C.L.-A.); (G.A.C.); (D.M.); (D.G.A.); (M.L.P.-E.)
- Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná (UFPR), Curitiba 81531-980, Brazil
| | - Amanda Salviano-Silva
- Laboratory of Human Molecular Genetics, Department of Genetics, Federal University of Paraná (UFPR), Curitiba 81531-980, Brazil; (M.S.D.); (V.B.-B.H.); (S.C.L.-A.); (G.A.C.); (D.M.); (D.G.A.); (M.L.P.-E.)
- Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná (UFPR), Curitiba 81531-980, Brazil
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Sara Cristina Lobo-Alves
- Laboratory of Human Molecular Genetics, Department of Genetics, Federal University of Paraná (UFPR), Curitiba 81531-980, Brazil; (M.S.D.); (V.B.-B.H.); (S.C.L.-A.); (G.A.C.); (D.M.); (D.G.A.); (M.L.P.-E.)
- Research Institut Pelé Pequeno Príncipe, Curitiba 80250-060, Brazil
| | - Gabriel Adelman Cipolla
- Laboratory of Human Molecular Genetics, Department of Genetics, Federal University of Paraná (UFPR), Curitiba 81531-980, Brazil; (M.S.D.); (V.B.-B.H.); (S.C.L.-A.); (G.A.C.); (D.M.); (D.G.A.); (M.L.P.-E.)
| | - Danielle Malheiros
- Laboratory of Human Molecular Genetics, Department of Genetics, Federal University of Paraná (UFPR), Curitiba 81531-980, Brazil; (M.S.D.); (V.B.-B.H.); (S.C.L.-A.); (G.A.C.); (D.M.); (D.G.A.); (M.L.P.-E.)
- Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná (UFPR), Curitiba 81531-980, Brazil
| | - Danillo G. Augusto
- Laboratory of Human Molecular Genetics, Department of Genetics, Federal University of Paraná (UFPR), Curitiba 81531-980, Brazil; (M.S.D.); (V.B.-B.H.); (S.C.L.-A.); (G.A.C.); (D.M.); (D.G.A.); (M.L.P.-E.)
- Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Michael Wittig
- Institute of Clinical Molecular Biology (IKMB), Christian-Albrechts-University of Kiel, 24105 Kiel, Germany; (M.W.); (A.F.)
| | - Andre Franke
- Institute of Clinical Molecular Biology (IKMB), Christian-Albrechts-University of Kiel, 24105 Kiel, Germany; (M.W.); (A.F.)
| | - Claudia Pföhler
- Department of Dermatology, Saarland University Medical Center, 66421 Homburg, Germany;
| | - Margitta Worm
- Division of Allergy and Immunology, Department of Dermatology, Venerology and Allergy, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany;
| | - Nina van Beek
- Department of Dermatology, University of Lübeck, 23562 Lübeck, Germany; (N.v.B.); (E.S.)
| | - Matthias Goebeler
- Department of Dermatology, Venereology and Allergology, University Hospital Würzburg, 97080 Würzburg, Germany;
| | - Miklós Sárdy
- Department of Dermatology and Allergy, University Hospital, LMU Munich, 80539 Munich, Germany;
- Department of Dermatology, Venereology and Dermatooncology, Semmelweis University, 1085 Budapest, Hungary
| | - Saleh Ibrahim
- College of Medicine and Health Sciences, Khalifa University, Abu Dhabi 127788, United Arab Emirates;
- Lübeck Institute of Experimental Dermatology (LIED), University of Lübeck, 23562 Lübeck, Germany; (H.B.); (J.E.H.)
| | - Hauke Busch
- Lübeck Institute of Experimental Dermatology (LIED), University of Lübeck, 23562 Lübeck, Germany; (H.B.); (J.E.H.)
| | - Enno Schmidt
- Department of Dermatology, University of Lübeck, 23562 Lübeck, Germany; (N.v.B.); (E.S.)
- Lübeck Institute of Experimental Dermatology (LIED), University of Lübeck, 23562 Lübeck, Germany; (H.B.); (J.E.H.)
| | - Jennifer Elisabeth Hundt
- Lübeck Institute of Experimental Dermatology (LIED), University of Lübeck, 23562 Lübeck, Germany; (H.B.); (J.E.H.)
| | - Maria Luiza Petzl-Erler
- Laboratory of Human Molecular Genetics, Department of Genetics, Federal University of Paraná (UFPR), Curitiba 81531-980, Brazil; (M.S.D.); (V.B.-B.H.); (S.C.L.-A.); (G.A.C.); (D.M.); (D.G.A.); (M.L.P.-E.)
- Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná (UFPR), Curitiba 81531-980, Brazil
| | - Angelica Beate Winter Boldt
- Laboratory of Human Molecular Genetics, Department of Genetics, Federal University of Paraná (UFPR), Curitiba 81531-980, Brazil; (M.S.D.); (V.B.-B.H.); (S.C.L.-A.); (G.A.C.); (D.M.); (D.G.A.); (M.L.P.-E.)
- Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná (UFPR), Curitiba 81531-980, Brazil
| |
Collapse
|
3
|
Murphy C, Gornés Pons G, Keogh A, Ryan L, McCarra L, Jose CM, Kesar S, Nicholson S, Fitzmaurice GJ, Ryan R, Young V, Cuffe S, Finn SP, Gray SG. An Analysis of JADE2 in Non-Small Cell Lung Cancer (NSCLC). Biomedicines 2023; 11:2576. [PMID: 37761019 PMCID: PMC10526426 DOI: 10.3390/biomedicines11092576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 06/26/2023] [Accepted: 06/29/2023] [Indexed: 09/29/2023] Open
Abstract
The JADE family comprises three members encoded by individual genes and roles for these proteins have been identified in chromatin remodeling, cell cycle progression, cell regeneration and the DNA damage response. JADE family members, and in particular JADE2 have not been studied in any great detail in cancer. Using a series of standard biological and bioinformatics approaches we investigated JADE2 expression in surgically resected non-small cell lung cancer (NSCLC) for both mRNA and protein to examine for correlations between JADE2 expression and overall survival. Additional correlations were identified using bioinformatic analyses on multiple online datasets. Our analysis demonstrates that JADE2 expression is significantly altered in NSCLC. High expression of JADE2 is associated with a better 5-year overall survival. Links between JADE2 mRNA expression and a number of mutated genes were identified, and associations between JADE2 expression and tumor mutational burden and immune cell infiltration were explored. Potential new drugs that can target JADE2 were identified. The results of this biomarker-driven study suggest that JADE2 may have potential clinical utility in the diagnosis, prognosis and stratification of patients into various therapeutically targetable options.
Collapse
Affiliation(s)
- Ciara Murphy
- Department of Histopathology, Labmed Directorate, St. James’s Hospital, D08 NHY1 Dublin, Ireland (S.P.F.)
- Thoracic Oncology Research Group, Central Pathology Laboratory, Trinity St. James’s Cancer Institute (TSJCI), St. James’s Hospital, D08 RX0X Dublin, Ireland (A.K.)
| | - Glòria Gornés Pons
- Thoracic Oncology Research Group, Central Pathology Laboratory, Trinity St. James’s Cancer Institute (TSJCI), St. James’s Hospital, D08 RX0X Dublin, Ireland (A.K.)
- Faculty of Biology, University of Barcelona, 08025 Barcelona, Spain
| | - Anna Keogh
- Thoracic Oncology Research Group, Central Pathology Laboratory, Trinity St. James’s Cancer Institute (TSJCI), St. James’s Hospital, D08 RX0X Dublin, Ireland (A.K.)
- Department of Histopathology and Morbid Anatomy, Trinity College Dublin, D02 PN40 Dublin, Ireland
| | - Lisa Ryan
- Department of Histopathology, Labmed Directorate, St. James’s Hospital, D08 NHY1 Dublin, Ireland (S.P.F.)
| | - Lorraine McCarra
- Department of Histopathology, Labmed Directorate, St. James’s Hospital, D08 NHY1 Dublin, Ireland (S.P.F.)
| | - Chris Maria Jose
- School of Medicine, Trinity College Dublin, D02 PN40 Dublin, Ireland
| | - Shagun Kesar
- School of Medicine, Trinity College Dublin, D02 PN40 Dublin, Ireland
| | - Siobhan Nicholson
- Department of Histopathology, Labmed Directorate, St. James’s Hospital, D08 NHY1 Dublin, Ireland (S.P.F.)
| | - Gerard J. Fitzmaurice
- Surgery, Anaesthesia and Critical Care Directorate, St. James’s Hospital, D08 NHY1 Dublin, Ireland (V.Y.)
| | - Ronan Ryan
- Surgery, Anaesthesia and Critical Care Directorate, St. James’s Hospital, D08 NHY1 Dublin, Ireland (V.Y.)
| | - Vincent Young
- Surgery, Anaesthesia and Critical Care Directorate, St. James’s Hospital, D08 NHY1 Dublin, Ireland (V.Y.)
| | - Sinead Cuffe
- HOPE Directorate, St. James’s Hospital, D08 NHY1 Dublin, Ireland
| | - Stephen P. Finn
- Department of Histopathology, Labmed Directorate, St. James’s Hospital, D08 NHY1 Dublin, Ireland (S.P.F.)
- Thoracic Oncology Research Group, Central Pathology Laboratory, Trinity St. James’s Cancer Institute (TSJCI), St. James’s Hospital, D08 RX0X Dublin, Ireland (A.K.)
- Department of Histopathology and Morbid Anatomy, Trinity College Dublin, D02 PN40 Dublin, Ireland
| | - Steven G. Gray
- Thoracic Oncology Research Group, Central Pathology Laboratory, Trinity St. James’s Cancer Institute (TSJCI), St. James’s Hospital, D08 RX0X Dublin, Ireland (A.K.)
- Department of Clinical Medicine, Trinity College Dublin, D02 PN40 Dublin, Ireland
- School of Biological Sciences, Technological University Dublin, D07 XT95 Dublin, Ireland
| |
Collapse
|
4
|
Wong R, Zhang Y, Zhao H, Ma D. Circular RNAs in organ injury: recent development. J Transl Med 2022; 20:533. [PMID: 36401311 PMCID: PMC9673305 DOI: 10.1186/s12967-022-03725-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 10/24/2022] [Indexed: 11/19/2022] Open
Abstract
Circular ribonucleic acids (circRNAs) are a class of long non-coding RNA that were once regarded as non-functional transcription byproducts. However, recent studies suggested that circRNAs may exhibit important regulatory roles in many critical biological pathways and disease pathologies. These studies have identified significantly differential expression profiles of circRNAs upon changes in physiological and pathological conditions of eukaryotic cells. Importantly, a substantial number of studies have suggested that circRNAs may play critical roles in organ injuries. This review aims to provide a summary of recent studies on circRNAs in organ injuries with respect to (1) changes in circRNAs expression patterns, (2) main mechanism axi(e)s, (3) therapeutic implications and (4) future study prospective. With the increasing attention to this research area and the advancement in high-throughput nucleic acid sequencing techniques, our knowledge of circRNAs may bring fruitful outcomes from basic and clinical research.
Collapse
|
5
|
Sales de Queiroz A, Sales Santa Cruz G, Jean-Marie A, Mazauric D, Roux J, Cazals F. Gene prioritization based on random walks with restarts and absorbing states, to define gene sets regulating drug pharmacodynamics from single-cell analyses. PLoS One 2022; 17:e0268956. [PMID: 36342924 PMCID: PMC9639845 DOI: 10.1371/journal.pone.0268956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 05/12/2022] [Indexed: 11/09/2022] Open
Abstract
Prioritizing genes for their role in drug sensitivity, is an important step in understanding drugs mechanisms of action and discovering new molecular targets for co-treatment. To formalize this problem, we consider two sets of genes X and P respectively composing the gene signature of cell sensitivity at the drug IC50 and the genes involved in its mechanism of action, as well as a protein interaction network (PPIN) containing the products of X and P as nodes. We introduce Genetrank, a method to prioritize the genes in X for their likelihood to regulate the genes in P. Genetrank uses asymmetric random walks with restarts, absorbing states, and a suitable renormalization scheme. Using novel so-called saturation indices, we show that the conjunction of absorbing states and renormalization yields an exploration of the PPIN which is much more progressive than that afforded by random walks with restarts only. Using MINT as underlying network, we apply Genetrank to a predictive gene signature of cancer cells sensitivity to tumor-necrosis-factor-related apoptosis-inducing ligand (TRAIL), performed in single-cells. Our ranking provides biological insights on drug sensitivity and a gene set considerably enriched in genes regulating TRAIL pharmacodynamics when compared to the most significant differentially expressed genes obtained from a statistical analysis framework alone. We also introduce gene expression radars, a visualization tool embedded in MA plots to assess all pairwise interactions at a glance on graphical representations of transcriptomics data. Genetrank is made available in the Structural Bioinformatics Library (https://sbl.inria.fr/doc/Genetrank-user-manual.html). It should prove useful for mining gene sets in conjunction with a signaling pathway, whenever other approaches yield relatively large sets of genes.
Collapse
Affiliation(s)
| | | | | | | | - Jérémie Roux
- CNRS UMR 7284, Inserm U 1081, Institut de Recherche sur le Cancer et le Vieillissement de Nice, Centre Antoine Lacassagne, Universite Côte d’Azur, Nice, France
- * E-mail: (FC); (JR)
| | - Frédéric Cazals
- Inria, Université Côte d’Azur, Nice, France
- * E-mail: (FC); (JR)
| |
Collapse
|
6
|
Farrell K, Kim S, Han N, Iida MA, Gonzalez EM, Otero-Garcia M, Walker JM, Richardson TE, Renton AE, Andrews SJ, Fulton-Howard B, Humphrey J, Vialle RA, Bowles KR, de Paiva Lopes K, Whitney K, Dangoor DK, Walsh H, Marcora E, Hefti MM, Casella A, Sissoko CT, Kapoor M, Novikova G, Udine E, Wong G, Tang W, Bhangale T, Hunkapiller J, Ayalon G, Graham RR, Cherry JD, Cortes EP, Borukov VY, McKee AC, Stein TD, Vonsattel JP, Teich AF, Gearing M, Glass J, Troncoso JC, Frosch MP, Hyman BT, Dickson DW, Murray ME, Attems J, Flanagan ME, Mao Q, Mesulam MM, Weintraub S, Woltjer RL, Pham T, Kofler J, Schneider JA, Yu L, Purohit DP, Haroutunian V, Hof PR, Gandy S, Sano M, Beach TG, Poon W, Kawas CH, Corrada MM, Rissman RA, Metcalf J, Shuldberg S, Salehi B, Nelson PT, Trojanowski JQ, Lee EB, Wolk DA, McMillan CT, Keene CD, Latimer CS, Montine TJ, Kovacs GG, Lutz MI, Fischer P, Perrin RJ, Cairns NJ, Franklin EE, Cohen HT, Raj T, Cobos I, Frost B, Goate A, White Iii CL, Crary JF. Genome-wide association study and functional validation implicates JADE1 in tauopathy. Acta Neuropathol 2022; 143:33-53. [PMID: 34719765 PMCID: PMC8786260 DOI: 10.1007/s00401-021-02379-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/13/2021] [Accepted: 10/24/2021] [Indexed: 01/07/2023]
Abstract
Primary age-related tauopathy (PART) is a neurodegenerative pathology with features distinct from but also overlapping with Alzheimer disease (AD). While both exhibit Alzheimer-type temporal lobe neurofibrillary degeneration alongside amnestic cognitive impairment, PART develops independently of amyloid-β (Aβ) plaques. The pathogenesis of PART is not known, but evidence suggests an association with genes that promote tau pathology and others that protect from Aβ toxicity. Here, we performed a genetic association study in an autopsy cohort of individuals with PART (n = 647) using Braak neurofibrillary tangle stage as a quantitative trait. We found some significant associations with candidate loci associated with AD (SLC24A4, MS4A6A, HS3ST1) and progressive supranuclear palsy (MAPT and EIF2AK3). Genome-wide association analysis revealed a novel significant association with a single nucleotide polymorphism on chromosome 4 (rs56405341) in a locus containing three genes, including JADE1 which was significantly upregulated in tangle-bearing neurons by single-soma RNA-seq. Immunohistochemical studies using antisera targeting JADE1 protein revealed localization within tau aggregates in autopsy brains with four microtubule-binding domain repeats (4R) isoforms and mixed 3R/4R, but not with 3R exclusively. Co-immunoprecipitation in post-mortem human PART brain tissue revealed a specific binding of JADE1 protein to four repeat tau lacking N-terminal inserts (0N4R). Finally, knockdown of the Drosophila JADE1 homolog rhinoceros (rno) enhanced tau-induced toxicity and apoptosis in vivo in a humanized 0N4R mutant tau knock-in model, as quantified by rough eye phenotype and terminal deoxynucleotidyl transferase dUTP nick end-labeling (TUNEL) in the fly brain. Together, these findings indicate that PART has a genetic architecture that partially overlaps with AD and other tauopathies and suggests a novel role for JADE1 as a modifier of neurofibrillary degeneration.
Collapse
Affiliation(s)
- Kurt Farrell
- Department of Pathology, Neuropathology Brain Bank and Research CoRE, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place Box 1194, New York, NY, 10029, USA
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Artificial Intelligence and Human Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - SoongHo Kim
- Department of Pathology, Neuropathology Brain Bank and Research CoRE, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place Box 1194, New York, NY, 10029, USA
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Artificial Intelligence and Human Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Natalia Han
- Department of Pathology, Neuropathology Brain Bank and Research CoRE, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place Box 1194, New York, NY, 10029, USA
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Artificial Intelligence and Human Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Megan A Iida
- Department of Pathology, Neuropathology Brain Bank and Research CoRE, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place Box 1194, New York, NY, 10029, USA
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Artificial Intelligence and Human Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Elias M Gonzalez
- Department of Cell Systems and Anatomy, Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, the Sam and Ann Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
| | - Marcos Otero-Garcia
- Department of Pathology and Laboratory Medicine, Division of Neuropathology, University of California, Los Angeles, CA, USA
| | - Jamie M Walker
- Department of Pathology and Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, UT Health San Antonio, San Antonio, TX, USA
| | - Timothy E Richardson
- Department of Pathology and Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, UT Health San Antonio, San Antonio, TX, USA
| | - Alan E Renton
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Shea J Andrews
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Brian Fulton-Howard
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jack Humphrey
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ricardo A Vialle
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kathryn R Bowles
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Katia de Paiva Lopes
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kristen Whitney
- Department of Pathology, Neuropathology Brain Bank and Research CoRE, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place Box 1194, New York, NY, 10029, USA
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Artificial Intelligence and Human Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Diana K Dangoor
- Department of Pathology, Neuropathology Brain Bank and Research CoRE, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place Box 1194, New York, NY, 10029, USA
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Artificial Intelligence and Human Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hadley Walsh
- Department of Pathology, Neuropathology Brain Bank and Research CoRE, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place Box 1194, New York, NY, 10029, USA
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Artificial Intelligence and Human Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Edoardo Marcora
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marco M Hefti
- Department of Pathology, University of Iowa, Iowa City, IA, USA
| | - Alicia Casella
- Department of Pathology, Neuropathology Brain Bank and Research CoRE, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place Box 1194, New York, NY, 10029, USA
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Artificial Intelligence and Human Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Cheick T Sissoko
- Department of Pathology, Neuropathology Brain Bank and Research CoRE, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place Box 1194, New York, NY, 10029, USA
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Artificial Intelligence and Human Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Manav Kapoor
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gloriia Novikova
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Evan Udine
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Garrett Wong
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Weijing Tang
- Department of Pathology, Stanford University, Palo Alto, USA
| | - Tushar Bhangale
- Department of Human Genetics, Genentech, South San Francisco, CA, USA
| | - Julie Hunkapiller
- Department of Human Genetics, Genentech, South San Francisco, CA, USA
| | - Gai Ayalon
- Neumora Therapeutics, South San Francisco, CA, USA
| | | | - Jonathan D Cherry
- Department of Pathology (Neuropathology), VA Medical Center, Boston University School of Medicine, Boston, MA, USA
| | - Etty P Cortes
- Department of Pathology, Neuropathology Brain Bank and Research CoRE, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place Box 1194, New York, NY, 10029, USA
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Valeriy Y Borukov
- Department of Pathology, Neuropathology Brain Bank and Research CoRE, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place Box 1194, New York, NY, 10029, USA
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ann C McKee
- Department of Pathology (Neuropathology), VA Medical Center, Boston University School of Medicine, Boston, MA, USA
| | - Thor D Stein
- Department of Pathology (Neuropathology), VA Medical Center, Boston University School of Medicine, Boston, MA, USA
| | - Jean-Paul Vonsattel
- Department of Pathology and Cell Biology, Department of Neurology, and the Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, USA
| | - Andy F Teich
- Department of Pathology and Cell Biology, Department of Neurology, and the Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, USA
| | - Marla Gearing
- Department of Pathology and Laboratory Medicine (Neuropathology) and Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Jonathan Glass
- Department of Pathology and Laboratory Medicine (Neuropathology) and Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Juan C Troncoso
- Department of Pathology, Division of Neuropathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Matthew P Frosch
- Department of Neurology and Pathology, Harvard Medical School and Massachusetts General Hospital, Charlestown, MA, USA
| | - Bradley T Hyman
- Department of Neurology and Pathology, Harvard Medical School and Massachusetts General Hospital, Charlestown, MA, USA
| | | | | | - Johannes Attems
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Margaret E Flanagan
- Department of Pathology (Neuropathology), Northwestern Cognitive Neurology and Alzheimer Disease Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Qinwen Mao
- Department of Pathology (Neuropathology), Northwestern Cognitive Neurology and Alzheimer Disease Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - M-Marsel Mesulam
- Department of Pathology (Neuropathology), Northwestern Cognitive Neurology and Alzheimer Disease Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Sandra Weintraub
- Department of Pathology (Neuropathology), Northwestern Cognitive Neurology and Alzheimer Disease Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Randy L Woltjer
- Department of Pathology, Oregon Health Sciences University, Portland, OR, USA
| | - Thao Pham
- Department of Pathology, Oregon Health Sciences University, Portland, OR, USA
| | - Julia Kofler
- Department of Pathology (Neuropathology), University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Julie A Schneider
- Departments of Pathology (Neuropathology) and Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
| | - Lei Yu
- Departments of Pathology (Neuropathology) and Neurological Sciences, Rush University Medical Center, Chicago, IL, USA
| | - Dushyant P Purohit
- Department of Pathology, Neuropathology Brain Bank and Research CoRE, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place Box 1194, New York, NY, 10029, USA
- Department of Psychiatry, Alzheimer's Disease Research Center, James J. Peters VA Medical Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Vahram Haroutunian
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Alzheimer's Disease Research Center, James J. Peters VA Medical Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Patrick R Hof
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sam Gandy
- Department of Psychiatry, Alzheimer's Disease Research Center, James J. Peters VA Medical Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neurology, Center for Cognitive Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mary Sano
- Department of Psychiatry, Alzheimer's Disease Research Center, James J. Peters VA Medical Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Thomas G Beach
- Department of Neuropathology, Banner Sun Health Research Institute, Sun City, AZ, USA
| | - Wayne Poon
- Department of Neurology, Department of Epidemiology, Institute for Memory Impairments and Neurological Disorders, UC Irvine, Irvine, CA, USA
| | - Claudia H Kawas
- Department of Neurology, Department of Neurobiology and Behavior, Institute for Memory Impairments and Neurological Disorders, UC Irvine, Irvine, CA, USA
| | - María M Corrada
- Department of Neurology, Department of Epidemiology, Institute for Memory Impairments and Neurological Disorders, UC Irvine, Irvine, CA, USA
| | - Robert A Rissman
- Department of Neurosciences University of California and the Veterans Affairs San Diego Healthcare System, La Jolla, San Diego, California, USA
| | - Jeff Metcalf
- Department of Neurosciences University of California and the Veterans Affairs San Diego Healthcare System, La Jolla, San Diego, California, USA
| | - Sara Shuldberg
- Department of Neurosciences University of California and the Veterans Affairs San Diego Healthcare System, La Jolla, San Diego, California, USA
| | - Bahar Salehi
- Department of Neurosciences University of California and the Veterans Affairs San Diego Healthcare System, La Jolla, San Diego, California, USA
| | - Peter T Nelson
- Department of Pathology (Neuropathology) and Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - John Q Trojanowski
- Center for Neurodegenerative Disease Research, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Edward B Lee
- Center for Neurodegenerative Disease Research, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - David A Wolk
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Corey T McMillan
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - C Dirk Keene
- Department of Laboratory Medicine and Pathology, University of f Medicine, Seattle, WA, USA
| | - Caitlin S Latimer
- Department of Laboratory Medicine and Pathology, University of f Medicine, Seattle, WA, USA
| | - Thomas J Montine
- Department of Laboratory Medicine and Pathology, University of f Medicine, Seattle, WA, USA
- Department of Pathology, Stanford University, Palo Alto, USA
| | - Gabor G Kovacs
- Laboratory Medicine Program, Krembil Brain Institute, University Health Network, Toronto, ON, Canada
- Tanz Centre for Research in Neurodegenerative Disease and Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Institute of Neurology, Medical University of Vienna, Vienna, Austria
| | - Mirjam I Lutz
- Institute of Neurology, Medical University of Vienna, Vienna, Austria
| | - Peter Fischer
- Department of Psychiatry, Danube Hospital, Vienna, Austria
| | - Richard J Perrin
- Department of Pathology and Immunology, Department of Neurology, Knight Alzheimer Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Nigel J Cairns
- College of Medicine and Health, University of Exeter, Exeter, UK
| | - Erin E Franklin
- Department of Pathology and Immunology, Department of Neurology, Knight Alzheimer Disease Research Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Herbert T Cohen
- Departments of Medicine, Pathology, and Pharmacology, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA
| | - Towfique Raj
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Inma Cobos
- Department of Pathology, Stanford University, Palo Alto, USA
| | - Bess Frost
- Department of Cell Systems and Anatomy, Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, the Sam and Ann Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, TX, 78229, USA
| | - Alison Goate
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Charles L White Iii
- Department of Pathology (Neuropathology), University of Texas Southwestern Medical School, Dallas, TX, USA
| | - John F Crary
- Department of Pathology, Neuropathology Brain Bank and Research CoRE, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place Box 1194, New York, NY, 10029, USA.
- Nash Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Artificial Intelligence and Human Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| |
Collapse
|
7
|
Zhou R, Feng Y, Ye J, Han Z, Liang Y, Chen Q, Xu X, Huang Y, Jia Z, Zhong W. Prediction of Biochemical Recurrence-Free Survival of Prostate Cancer Patients Leveraging Multiple Gene Expression Profiles in Tumor Microenvironment. Front Oncol 2021; 11:632571. [PMID: 34631510 PMCID: PMC8495167 DOI: 10.3389/fonc.2021.632571] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 08/19/2021] [Indexed: 12/11/2022] Open
Abstract
Tumor-adjacent normal (TAN) tissues, which constitute tumor microenvironment and are different from healthy tissues, provide critical information at molecular levels that can be used to differentiate aggressive tumors from indolent tumors. In this study, we analyzed 52 TAN samples from the Cancer Genome Atlas (TCGA) prostate cancer patients and developed a 10-gene prognostic model that can accurately predict biochemical recurrence-free survival based on the profiles of these genes in TAN tissues. The predictive ability was validated using TAN samples from an independent cohort. These 10 prognostic genes in tumor microenvironment are different from the prognostic genes detected in tumor tissues, indicating distinct progression-related mechanisms in two tissue types. Bioinformatics analysis showed that the prognostic genes in tumor microenvironment were significantly enriched by p53 signaling pathway, which may represent the crosstalk tunnels between tumor and its microenvironment and pathways involving cell-to-cell contact and paracrine/endocrine signaling. The insight acquired by this study has advanced our knowledge of the potential role of tumor microenvironment in prostate cancer progression.
Collapse
Affiliation(s)
- Rui Zhou
- School of Medicine, South China University of Technology, Guangzhou, China
| | - Yuanfa Feng
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People’s Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Jianheng Ye
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People’s Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Zhaodong Han
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People’s Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Yuxiang Liang
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People’s Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| | - Qingbiao Chen
- Affiliated Foshan Hospital of Southern Medical University, Southern Medical University, Foshan, China
| | - Xiaoming Xu
- Department of Urology, Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, China
| | - Yuhan Huang
- Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, United States
| | - Zhenyu Jia
- Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, United States
| | - Weide Zhong
- School of Medicine, South China University of Technology, Guangzhou, China
- Department of Urology, Guangdong Key Laboratory of Clinical Molecular Medicine and Diagnostics, Guangzhou First People’s Hospital, School of Medicine, South China University of Technology, Guangzhou, China
| |
Collapse
|
8
|
Tian X, Hu Y, Liu Y, Yang Z, Xie H, Zhou L, Zheng S. Circular RNA Microarray Analyses in Hepatic Ischemia-Reperfusion Injury With Ischemic Preconditioning Prevention. Front Med (Lausanne) 2021; 8:626948. [PMID: 33763433 PMCID: PMC7982475 DOI: 10.3389/fmed.2021.626948] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 01/25/2021] [Indexed: 12/12/2022] Open
Abstract
Ischemic preconditioning (IPC) represents an effective intervention to relieve hepatic ischemia-reperfusion injury (IRI). Systematic detection of circRNA expression revealing the protection effect of IPC still remains to be elucidated. Here, we applied a microarray to detect circRNA and mRNA expression in ischemic liver with and without IPC (n = 3 in each group). Compared with the sham group, there were 39 circRNAs and 432 mRNAs increased and 38 circRNAs and 254 mRNAs decreased (fold change ≥1.5, P < 0.05) in the group of hepatic IRI. As the result of IPC intervention, 43 circRNAs and 64 mRNAs were increased, and 7 circRNAs and 31 mRNAs were decreased in the IPC group when compared with IRI. We then identified circRNA_017753 as the most possible target that may closely relate to IPC protective signaling and predicted Jade1 as the target related to circRNA_017753. Three possible circRNA-miRNA-mRNA axes were constructed that may play a vital role in protective mechanisms in IPC. The study for the first time systematically detects the dysregulated circRNAs and mRNAs in response to hepatic IRI and IPC intervention. Our profile and bioinformatic analysis provide numerous novel clues to understanding the pathophysiologic mechanism of IPC protection against hepatic IRI.
Collapse
Affiliation(s)
- Xinyao Tian
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Combined Multi-organ Transplantation, National Health Commission of PRC, Hangzhou, China
| | - Yan Hu
- Department of Pharmacy, Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Yuanxing Liu
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhe Yang
- Department of Hepatobiliary and Pancreatic Surgery, Department of Liver Transplantation, Shulan (Hangzhou) Hospital, Hangzhou, China
| | - Haiyang Xie
- Key Laboratory of Combined Multi-organ Transplantation, National Health Commission of PRC, Hangzhou, China
| | - Lin Zhou
- Key Laboratory of Combined Multi-organ Transplantation, National Health Commission of PRC, Hangzhou, China
| | - Shusen Zheng
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Key Laboratory of Combined Multi-organ Transplantation, National Health Commission of PRC, Hangzhou, China.,Department of Hepatobiliary and Pancreatic Surgery, Department of Liver Transplantation, Shulan (Hangzhou) Hospital, Hangzhou, China
| |
Collapse
|
9
|
Structural basis for renal cancer by the dynamics of pVHL-dependent JADE1 stabilization and β-catenin regulation. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2018; 145:65-77. [PMID: 30528740 DOI: 10.1016/j.pbiomolbio.2018.12.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 11/19/2018] [Accepted: 12/06/2018] [Indexed: 11/21/2022]
Abstract
Renal cancer is the major cause of mortality due to abnormal functioning of von Hippel-Lindau (pVHL) and Jade Family PHD Finger 1 (JADE1) complex. E3 ubiquitin ligase JADE1 is stabilized by pVHL interaction through its plant homeodomains (PHDs). JADE1 acts as a renal tumor suppressor that promotes the ubiquitination and degradation of β-catenin by inhibiting canonical WNT signalling. Current study focuses on the structural characterization of reported missense mutations in pVHL through in silico approaches. The predicted 3-dimensional structures of pVHLWT, pVHLY98H, pVHLY112H, pVHLL118P and pVHLR167W were subjected to binding analysis against JADE1 through molecular docking and simulation assays. In all cases, JADE1 binding was observed at the β-domain, except pVHLL118P that exhibited binding with JADE1 through its α-domain. Our results signify that JADE1 stabilization is induced by pVHL α-domain, while β-domain is required for JADE1 binding. pVHL binding was mediated through β1 and β2-strands against the concave surface of the JADE1-PHD domain. The pVHL-JADE1 complex was evaluated to scrutinize the β-catenin-binding interface, which suggested the contribution of both α and β-domains of pVHL in β-catenin binding. The eleven-residue (Tyr30-Thr40) β-catenin segment exhibited association in a bipartite manner with pVHL-JADE1 complex. The presented model depicts a pVHL-JADE1 interface for the cooperative regulation of β-catenin binding. We propose that reduced JADE1 stabilization in case of pVHLL118P and pVHLR167W may correlate with the increased activity of β-catenin that may lead to renal cancer through β-catenin de-repression. Overall, β-catenin targeting mechanism coupled with the structural knowledge of JADE1-pVHL complex will provide better understanding of renal cancer pathogenesis.
Collapse
|
10
|
Abstract
The von Hippel–Lindau (VHL) gene is a two-hit tumor suppressor gene and is linked to the development of the most common form of kidney cancer, clear cell renal carcinoma; blood vessel tumors of the retina, cerebellum, and spinal cord called hemangioblastomas; and tumors of the sympathoadrenal nervous system called paragangliomas. The VHL gene product, pVHL, is the substrate recognition subunit of a cullin-dependent ubiquitin ligase that targets the α subunits of hypoxia-inducible factor (HIF) for destruction when oxygen is plentiful. Mounting evidence implicates HIF2 in the pathogenesis of pVHL-defective tumors and has provided a conceptual foundation for the development of drugs to treat them that inhibit HIF2-responsive gene products such as VEGF and, more recently, HIF2 itself. pVHL has additional, noncanonical functions that are cancer relevant, including roles related to the primary cilium, chromosome stability, extracellular matrix formation, and survival signaling.
Collapse
Affiliation(s)
- William G. Kaelin
- Howard Hughes Medical Institute, Dana-Farber Cancer Institute, and Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA
| |
Collapse
|
11
|
Histone modifications: A review about the presence of this epigenetic phenomenon in carcinogenesis. Pathol Res Pract 2017; 213:1329-1339. [DOI: 10.1016/j.prp.2017.06.013] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 05/23/2017] [Accepted: 06/24/2017] [Indexed: 12/26/2022]
|
12
|
Hashemi S, Fernandez Martinez JL, Saligan L, Sonis S. Exploring Genetic Attributions Underlying Radiotherapy-Induced Fatigue in Prostate Cancer Patients. J Pain Symptom Manage 2017; 54:326-339. [PMID: 28797855 DOI: 10.1016/j.jpainsymman.2017.04.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 03/23/2017] [Accepted: 04/13/2017] [Indexed: 12/16/2022]
Abstract
CONTEXT Despite numerous proposed mechanisms, no definitive pathophysiology underlying radiotherapy-induced fatigue (RIF) has been established. However, the dysregulation of a set of 35 genes was recently validated to predict development of fatigue in prostate cancer patients receiving radiotherapy. OBJECTIVES To hypothesize novel pathways, and provide genetic targets for currently proposed pathways implicated in RIF development through analysis of the previously validated gene set. METHODS The gene set was analyzed for all phenotypic attributions implicated in the phenotype of fatigue. Initially, a "directed" approach was used by querying specific fatigue-related sub-phenotypes against all known phenotypic attributions of the gene set. Then, an "undirected" approach, reviewing the entirety of the literature referencing the 35 genes, was used to increase analysis sensitivity. RESULTS The dysregulated genes attribute to neural, immunological, mitochondrial, muscular, and metabolic pathways. In addition, certain genes suggest phenotypes not previously emphasized in the context of RIF, such as ionizing radiation sensitivity, DNA damage, and altered DNA repair frequency. Several genes also associated with prostate cancer depression, possibly emphasizing variable radiosensitivity by RIF-prone patients, which may have palliative care implications. Despite the relevant findings, many of the 35 RIF-predictive genes are poorly characterized, warranting their investigation. CONCLUSION The implications of herein presented RIF pathways are purely theoretical until specific end-point driven experiments are conducted in more congruent contexts. Nevertheless, the presented attributions are informative, directing future investigation to definitively elucidate RIF's pathoetiology. This study demonstrates an arguably comprehensive method of approaching known differential expression underlying a complex phenotype, to correlate feasible pathophysiology.
Collapse
Affiliation(s)
- Sepehr Hashemi
- Harvard School of Dental Medicine, Boston, Massachusetts, USA
| | | | - Leorey Saligan
- National Institutes of Health, National Institute of Nursing Research, Bethesda, Maryland, USA
| | - Stephen Sonis
- Harvard School of Dental Medicine, Boston, Massachusetts, USA; Biomodels LLC, Watertown, Massachusetts, USA; Brigham and Women's Hospital, Boston, Massachusetts, USA.
| |
Collapse
|
13
|
Vallée Marcotte B, Guénard F, Cormier H, Lemieux S, Couture P, Rudkowska I, Vohl MC. Plasma Triglyceride Levels May Be Modulated by Gene Expression of IQCJ, NXPH1, PHF17 and MYB in Humans. Int J Mol Sci 2017; 18:ijms18020257. [PMID: 28134766 PMCID: PMC5343793 DOI: 10.3390/ijms18020257] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 01/12/2017] [Accepted: 01/17/2017] [Indexed: 02/07/2023] Open
Abstract
A genome-wide association study (GWAS) by our group identified loci associated with the plasma triglyceride (TG) response to ω-3 fatty acid (FA) supplementation in IQCJ, NXPH1, PHF17 and MYB. Our aim is to investigate potential mechanisms underlying the associations between single nucleotide polymorphisms (SNPs) in the four genes and TG levels following ω-3 FA supplementation. 208 subjects received 3 g/day of ω-3 FA (1.9–2.2 g of EPA and 1.1 g of docosahexaenoic acid (DHA)) for six weeks. Plasma TG were measured before and after the intervention. 67 SNPs were selected to increase the density of markers near GWAS hits. Genome-wide expression and methylation analyses were conducted on respectively 30 and 35 participants’ blood sample together with in silico analyses. Two SNPs of IQCJ showed different affinities to splice sites depending on alleles. Expression levels were influenced by genotype for one SNP in NXPH1 and one in MYB. Associations between 12 tagged SNPs of IQCJ, 26 of NXPH1, seven of PHF17 and four of MYB and gene-specific CpG site methylation levels were found. The response of plasma TG to ω-3 FA supplementation may be modulated by the effect of DNA methylation on expression levels of genes revealed by GWAS.
Collapse
Affiliation(s)
- Bastien Vallée Marcotte
- Institute of Nutrition and Functional Foods (INAF), Laval University, 2440 Hochelaga Blvd, Quebec, QC G1V 0A6, Canada.
| | - Frédéric Guénard
- Institute of Nutrition and Functional Foods (INAF), Laval University, 2440 Hochelaga Blvd, Quebec, QC G1V 0A6, Canada.
| | - Hubert Cormier
- Institute of Nutrition and Functional Foods (INAF), Laval University, 2440 Hochelaga Blvd, Quebec, QC G1V 0A6, Canada.
| | - Simone Lemieux
- Institute of Nutrition and Functional Foods (INAF), Laval University, 2440 Hochelaga Blvd, Quebec, QC G1V 0A6, Canada.
| | - Patrick Couture
- Institute of Nutrition and Functional Foods (INAF), Laval University, 2440 Hochelaga Blvd, Quebec, QC G1V 0A6, Canada.
- CHU de Québec Research Center-Endocrinology and Nephrology, 2705 Laurier Blvd, Quebec, QC G1V 4G2, Canada.
| | - Iwona Rudkowska
- CHU de Québec Research Center-Endocrinology and Nephrology, 2705 Laurier Blvd, Quebec, QC G1V 4G2, Canada.
| | - Marie-Claude Vohl
- Institute of Nutrition and Functional Foods (INAF), Laval University, 2440 Hochelaga Blvd, Quebec, QC G1V 0A6, Canada.
- CHU de Québec Research Center-Endocrinology and Nephrology, 2705 Laurier Blvd, Quebec, QC G1V 4G2, Canada.
| |
Collapse
|
14
|
Mishra S, Peterson K, Yin L, Berger A, Fan J, Wistow G. Accumulation of cholesterol and increased demand for zinc in serum-deprived RPE cells. Mol Vis 2016; 22:1387-1404. [PMID: 28003730 PMCID: PMC5166821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 12/08/2016] [Indexed: 11/03/2022] Open
Abstract
PURPOSE Having observed that confluent ARPE-19 cells (derived from human RPE) survive well in high-glucose serum-free medium (SFM) without further feeding for several days, we investigated the expression profile of RPE cells under the same conditions. METHODS Expression profiles were examined with microarray and quantitative PCR (qPCR) analyses, followed by western blot analysis of key regulated proteins. The effects of low-density lipoprotein (LDL) and zinc supplementation were examined with qPCR. Immunofluorescence was used to localize the LDL receptor and to examine LDL uptake. Cellular cholesterol levels were measured with filipin binding. Expression patterns in primary fetal RPE cells were compared using qPCR. RESULTS Microarray analyses of gene expression in ARPE-19, confirmed with qPCR, showed upregulation of lipid and cholesterol biosynthesis pathways in SFM. At the protein level, the cholesterol synthesis control factor SRBEF2 was activated, and other key lipid synthesis proteins increased. Supplementation of SFM with LDL reversed the upregulation of lipid and cholesterol synthesis genes, but not of cholesterol transport genes. The LDL receptor relocated to the plasma membrane, and LDL uptake was activated by day 5-7 in SFM, suggesting increased demand for cholesterol. Confluent ARPE-19 cells in SFM accumulated intracellular cholesterol, compared with cells supplemented with serum, over 7 days. Over the same time course in SFM, the expression of metallothioneins decreased while the major zinc transporter was upregulated, consistent with a parallel increase in demand for zinc. Supplementation with zinc reversed expression changes for metallothionein genes, but not for other zinc-related genes. Similar patterns of regulation were also seen in primary fetal human RPE cells in SFM. CONCLUSIONS ARPE-19 cells respond to serum deprivation and starvation with upregulation of the lipid and cholesterol pathways, accumulation of intracellular cholesterol, and increased demand for zinc. Similar trends are seen in primary fetal RPE cells. Cholesterol accumulation basal to RPE is a prominent feature of age-related macular degeneration (AMD), while dietary zinc is protective. It is conceivable that accumulating defects in Bruch's membrane and dysfunction of the choriocapillaris could impede transport between RPE and vasculature in AMD. Thus, this pattern of response to serum deprivation in RPE-derived cells may have relevance for some aspects of the progression of AMD.
Collapse
Affiliation(s)
- Sanghamitra Mishra
- Section on Molecular Structure and Functional Genomics, National Eye Institute, National Institutes of Health, Bethesda, MD
| | - Katherine Peterson
- Section on Molecular Structure and Functional Genomics, National Eye Institute, National Institutes of Health, Bethesda, MD
| | - Lili Yin
- Section on Molecular Structure and Functional Genomics, National Eye Institute, National Institutes of Health, Bethesda, MD
| | - Alan Berger
- Lowe Family Genomics Core, Johns Hopkins University - School of Medicine, Baltimore, MD
| | - Jianguo Fan
- Section on Molecular Structure and Functional Genomics, National Eye Institute, National Institutes of Health, Bethesda, MD
| | - Graeme Wistow
- Section on Molecular Structure and Functional Genomics, National Eye Institute, National Institutes of Health, Bethesda, MD
| |
Collapse
|
15
|
Havasi A, Lu W, Cohen HT, Beck L, Wang Z, Igwebuike C, Borkan SC. Blocking peptides and molecular mimicry as treatment for kidney disease. Am J Physiol Renal Physiol 2016; 312:F1016-F1025. [PMID: 27654896 DOI: 10.1152/ajprenal.00601.2015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Revised: 08/25/2016] [Accepted: 09/16/2016] [Indexed: 12/29/2022] Open
Abstract
Protein mimotopes, or blocking peptides, are small therapeutic peptides that prevent protein-protein interactions by selectively mimicking a native binding domain. Inexpensive technology facilitates straightforward design and production of blocking peptides in sufficient quantities to allow preventive and therapeutic trials in both in vitro and in vivo experimental disease models. The kidney is an ideal peptide target, since small molecules undergo rapid filtration and efficient bulk absorption by tubular epithelial cells. Because the half-life of peptides is markedly prolonged in the kidneys compared with the bloodstream, blocking peptides are an attractive tool for treating diverse renal diseases, including ischemia, proteinuric states, such as membranous nephropathy and focal and segmental glomerulosclerosis, and renal cell carcinoma. Therapeutic peptides represent one of the fastest-growing reagent classes for novel drug development in human disease, partly because of their ease of administration, high binding affinity, and minimal off-target effects. This review introduces the concepts of blocking peptide design, production, and administration and highlights the potential use of therapeutic peptides to prevent or treat specific renal diseases.
Collapse
Affiliation(s)
- Andrea Havasi
- Renal Section, Boston University Medical Center, Boston, Massachusetts
| | - Weining Lu
- Renal Section, Boston University Medical Center, Boston, Massachusetts
| | - Herbert T Cohen
- Renal Section, Boston University Medical Center, Boston, Massachusetts
| | - Laurence Beck
- Renal Section, Boston University Medical Center, Boston, Massachusetts
| | - Zhiyong Wang
- Renal Section, Boston University Medical Center, Boston, Massachusetts
| | | | - Steven C Borkan
- Renal Section, Boston University Medical Center, Boston, Massachusetts
| |
Collapse
|
16
|
Xiao-Fen W, Ting C, Jie L, Deng-Yang M, Qing-Feng Z, Xin L. Correlation analysis of VHL and Jade-1 gene expression in human renal cell carcinoma. Open Med (Wars) 2016; 11:226-230. [PMID: 28352799 PMCID: PMC5329830 DOI: 10.1515/med-2016-0043] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 05/19/2016] [Indexed: 01/07/2023] Open
Abstract
Objective The aim of this study was to investigate the correlation of von Hippel-Lindau tumor suppressor (VHL) mRNA expression and jade family PHD finger 1 (Jade-1) gene expression in patients with renal cell carcinoma (RCC). Another aim of this study was to analyze the relationship of these two genes with clinicalpathological features of the RCC patients. Methods A total of 75 RCC patients who received surgically therapy in our hospital were included. All patients had complete pathological data. The expression of VHL/Jade-1 was determined by real-time polymerase chain reaction (RT-PCR). Results VHL and Jade-1 were both obviously downregulated in RCC tissues than that of the matched normal tissues, and both negatively correlated with tumor size as well as tumor grade. And we found a fine association of VHL gene expression with Jade-1. Conclusion VHL/Jade-1 exhibited significantly decreased expression in RCC tissues and was closely related to the clinical prognosis of patients. The finding of VHL expression positively correlated with Jade-1 expression shed light and provided crucial evidence on the connection of VHL protein with Wnt/b-catenin pathway.
Collapse
Affiliation(s)
- Wu Xiao-Fen
- Department of Urology Surgery, The Central Hospital of Lishui City, Lishui, 323000, People's Republic of China
| | - Chen Ting
- Department of Urology Surgery, The Central Hospital of Lishui City, Lishui, 323000, People's Republic of China
| | - Li Jie
- Department of Urology Surgery, The Central Hospital of Lishui City, Lishui, 323000, People's Republic of China
| | - Ma Deng-Yang
- Department of Urology Surgery, The Central Hospital of Lishui City, Lishui, 323000, People's Republic of China
| | - Zhu Qing-Feng
- Department of Urology Surgery, The Central Hospital of Lishui City, Lishui, 323000, People's Republic of China
| | - Lian Xin
- Department of Urology Surgery, The Central Hospital of Lishui City, Lishui, 323000, People's Republic of China
| |
Collapse
|
17
|
Vallée Marcotte B, Cormier H, Guénard F, Rudkowska I, Lemieux S, Couture P, Vohl MC. Novel Genetic Loci Associated with the Plasma Triglyceride Response to an Omega-3 Fatty Acid Supplementation. JOURNAL OF NUTRIGENETICS AND NUTRIGENOMICS 2016; 9:1-11. [PMID: 27160456 DOI: 10.1159/000446024] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 04/07/2016] [Indexed: 11/19/2022]
Abstract
BACKGROUND A recent genome-wide association study (GWAS) by our group identified 13 loci associated with the plasma triglyceride (TG) response to omega-3 (n-3) fatty acid (FA) supplementation. This study aimed to test whether single-nucleotide polymorphisms (SNPs) within the IQCJ, NXPH1, PHF17 and MYB genes are associated with the plasma TG response to an n-3 FA supplementation. METHODS A total of 208 subjects followed a 6-week n-3 FA supplementation of 5 g/day of fish oil (1.9-2.2 g of eicosapentaenoic acid and 1.1 g of docosahexaenoic acid). Measurements of plasma lipids were made before and after the supplementation. Sixty-seven tagged SNPs were selected to increase the density of markers near GWAS hits. RESULTS In a repeated model, independent effects of the genotype and the gene-supplementation interaction were associated with plasma TG. Genotype effects were observed with two SNPs of NXPH1, and gene-diet interactions were observed with ten SNPs of IQCJ, four SNPs of NXPH1 and three SNPs of MYB. Positive and negative responders showed different genotype frequencies with nine SNPs of IQCJ, two SNPs of NXPH1 and two SNPs of MYB. CONCLUSION Fine mapping in GWAS-associated loci allowed the identification of SNPs partly explaining the large interindividual variability observed in plasma TG levels in response to an n-3 FA supplementation.
Collapse
|
18
|
Panchenko MV. Structure, function and regulation of jade family PHD finger 1 (JADE1). Gene 2016; 589:1-11. [PMID: 27155521 DOI: 10.1016/j.gene.2016.05.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 04/28/2016] [Accepted: 05/01/2016] [Indexed: 12/24/2022]
Abstract
The family of JADE proteins includes three paralogues encoded by individual genes and designated PHF17 (JADE1), PHF16 (JADE2), and PHF15 (JADE3). All three JADE proteins bear in tandem two Plant Homeo-domains (PHD) which are zinc finger domains. This review focuses on one member of the JADE family, JADE1. Studies addressing the biochemical, cellular and biological role of JADE1 are discussed. Recent discoveries of JADE1 function in the regulation of the epithelial cell cycle with potential relevance to disease are presented. Unresolved questions and future directions are formulated.
Collapse
Affiliation(s)
- Maria V Panchenko
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine, United States.
| |
Collapse
|
19
|
Borgal L, Rinschen MM, Dafinger C, Liebrecht VI, Abken H, Benzing T, Schermer B. Jade-1S phosphorylation induced by CK1α contributes to cell cycle progression. Cell Cycle 2016; 15:1034-45. [PMID: 26919559 PMCID: PMC4889251 DOI: 10.1080/15384101.2016.1152429] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 02/04/2016] [Indexed: 12/13/2022] Open
Abstract
The PHD zinc finger protein Jade-1S is a component of the HBO1 histone acetyltransferase complex and binds chromatin in a cell cycle-dependent manner. Jade-1S also acts as an E3 ubiquitin ligase for the canonical Wnt effector protein β-catenin and is influenced by CK1α-mediated phosphorylation. To further elucidate the functional impact of this phosphorylation, we used a stable, low-level expression system to express either wild-type or mutant Jade-1S lacking the N-terminal CK1α phosphorylation motif. Interactome analyses revealed that the Jade-1S mutant unable to be phosphorylated by CK1α has an increased binding affinity to proteins involved in chromatin remodelling, histone deacetylation, transcriptional repression, and ribosome biogenesis. Interestingly, cells expressing the mutant displayed an elongated cell shape and a delay in cell cycle progression. Finally, phosphoproteomic analyses allowed identification of a Jade-1S site phosphorylated in the presence of CK1α but closely resembling a PLK1 phosphorylation motif. Our data suggest that Jade-1S phosphorylation at an N-terminal CK1α motif creates a PLK1 phospho-binding domain. We propose CK1α phosphorylation of Jade 1S to serve as a molecular switch, turning off chromatin remodelling functions of Jade-1S and allowing timely cell cycle progression. As Jade-1S protein expression in the kidney is altered upon renal injury, this could contribute to understanding mechanisms underlying epithelial injury repair.
Collapse
Affiliation(s)
- Lori Borgal
- Department II of Internal Medicine; University of Cologne; Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC); University of Cologne; Cologne, Germany
| | - Markus M. Rinschen
- Department II of Internal Medicine; University of Cologne; Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC); University of Cologne; Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne; Cologne, Germany
| | - Claudia Dafinger
- Department II of Internal Medicine; University of Cologne; Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC); University of Cologne; Cologne, Germany
| | - Valérie I. Liebrecht
- Center for Molecular Medicine Cologne (CMMC); University of Cologne; Cologne, Germany
- Department I of Internal Medicine; University of Cologne; Cologne, Germany
| | - Hinrich Abken
- Center for Molecular Medicine Cologne (CMMC); University of Cologne; Cologne, Germany
- Department I of Internal Medicine; University of Cologne; Cologne, Germany
| | - Thomas Benzing
- Department II of Internal Medicine; University of Cologne; Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC); University of Cologne; Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne; Cologne, Germany
- Systems Biology of Ageing Cologne; University of Cologne; Cologne, Germany
| | - Bernhard Schermer
- Department II of Internal Medicine; University of Cologne; Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC); University of Cologne; Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne; Cologne, Germany
- Systems Biology of Ageing Cologne; University of Cologne; Cologne, Germany
| |
Collapse
|
20
|
MYST2 acetyltransferase expression and Histone H4 Lysine acetylation are suppressed in AML. Exp Hematol 2015; 43:794-802.e4. [DOI: 10.1016/j.exphem.2015.05.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Revised: 05/26/2015] [Accepted: 05/29/2015] [Indexed: 02/04/2023]
|
21
|
Siriwardana NS, Meyer RD, Panchenko MV. The novel function of JADE1S in cytokinesis of epithelial cells. Cell Cycle 2015; 14:2821-34. [PMID: 26151225 DOI: 10.1080/15384101.2015.1068476] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
JADE1 belongs to a small family of PHD zinc finger proteins that interacts with histone acetyl transferase (HAT) HBO1 and is associated with chromatin. We recently reported JADE1 chromatin shuttling and phosphorylation during G2/M to G1 transition, which was sensitive to Aurora A inhibition. In the current study we examined mechanisms of the cell cycle regulation by the small isoform of JADE1 protein, JADE1S, and report data showing that JADE1S has a novel function in the regulation of cytokinesis. Using FACS assays, we show that, JADE1S depletion facilitated rates of G1-cells accumulation in synchronously dividing HeLa cell cultures. Depletion of JADE1S protein in asynchronously dividing cells decreased the proportion of cytokinetic cells, and increased the proportion of multi-nuclear cells, indicative of premature and failed cytokinesis. In contrast, moderate overexpression of JADE1S increased the number of cytokinetic cells in time- and dose- dependent manner, indicating cytokinetic delay. Pharmacological inhibition of Aurora B kinase resulted in the release of JADE1S-mediated cytokinetic delay and allowed progression of abscission in cells over-expressing JADE1S. Finally, we show that JADE1S protein localized to centrosomes in interphase and mitotic cells, while during cytokinesis JADE1S localized to the midbody. Neither JADE1L nor partner of JADE1, HAT HBO1 was localized to the centrosomes or midbodies. Our study identifies the novel role for JADE1S in regulation of cytokinesis and suggests function in Aurora B kinase-mediated cytokinesis checkpoint.
Collapse
|
22
|
Stetson LC, Pearl T, Chen Y, Barnholtz-Sloan JS. Computational identification of multi-omic correlates of anticancer therapeutic response. BMC Genomics 2014; 15 Suppl 7:S2. [PMID: 25573145 PMCID: PMC4243102 DOI: 10.1186/1471-2164-15-s7-s2] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Background A challenge in precision medicine is the transformation of genomic data into knowledge that can be used to stratify patients into treatment groups based on predicted clinical response. Although clinical trials remain the only way to truly measure drug toxicities and effectiveness, as a scientific community we lack the resources to clinically assess all drugs presently under development. Therefore, an effective preclinical model system that enables prediction of anticancer drug response could significantly speed the broader adoption of personalized medicine. Results Three large-scale pharmacogenomic studies have screened anticancer compounds in greater than 1000 distinct human cancer cell lines. We combined these datasets to generate and validate multi-omic predictors of drug response. We compared drug response signatures built using a penalized linear regression model and two non-linear machine learning techniques, random forest and support vector machine. The precision and robustness of each drug response signature was assessed using cross-validation across three independent datasets. Fifteen drugs were common among the datasets. We validated prediction signatures for eleven out of fifteen tested drugs (17-AAG, AZD0530, AZD6244, Erlotinib, Lapatinib, Nultin-3, Paclitaxel, PD0325901, PD0332991, PF02341066, and PLX4720). Conclusions Multi-omic predictors of drug response can be generated and validated for many drugs. Specifically, the random forest algorithm generated more precise and robust prediction signatures when compared to support vector machines and the more commonly used elastic net regression. The resulting drug response signatures can be used to stratify patients into treatment groups based on their individual tumor biology, with two major benefits: speeding the process of bringing preclinical drugs to market, and the repurposing and repositioning of existing anticancer therapies.
Collapse
|
23
|
Han X, Gui B, Xiong C, Zhao L, Liang J, Sun L, Yang X, Yu W, Si W, Yan R, Yi X, Zhang D, Li W, Li L, Yang J, Wang Y, Sun YE, Zhang D, Meng A, Shang Y. Destabilizing LSD1 by Jade-2 promotes neurogenesis: an antibraking system in neural development. Mol Cell 2014; 55:482-94. [PMID: 25018020 DOI: 10.1016/j.molcel.2014.06.006] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Revised: 03/24/2014] [Accepted: 05/15/2014] [Indexed: 12/12/2022]
Abstract
Histone H3K4 demethylase LSD1 plays an important role in stem cell biology, especially in the maintenance of the silencing of differentiation genes. However, how the function of LSD1 is regulated and the differentiation genes are derepressed are not understood. Here, we report that elimination of LSD1 promotes embryonic stem cell (ESC) differentiation toward neural lineage. We showed that the destabilization of LSD1 occurs posttranscriptionally via the ubiquitin-proteasome pathway by an E3 ubiquitin ligase, Jade-2. We demonstrated that Jade-2 is a major LSD1 negative regulator during neurogenesis in vitro and in vivo in both mouse developing cerebral cortices and zebra fish embryos. Apparently, Jade-2-mediated degradation of LSD1 acts as an antibraking system and serves as a quick adaptive mechanism for re-establishing epigenetic landscape without more laborious transcriptional regulations. As a potential anticancer strategy, Jade-2-mediated LSD1 degradation could potentially be used in neuroblastoma cells to induce differentiation toward postmitotic neurons.
Collapse
Affiliation(s)
- Xiao Han
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education, Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing 100191, China
| | - Bin Gui
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education, Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing 100191, China
| | - Cong Xiong
- State Key Laboratory of Biomembrane and Membrane Engineering, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Linnan Zhao
- Key Laboratory of Mental Health, Ministry of Health, Peking University Health Science Center, Beijing 100191, China
| | - Jing Liang
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education, Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing 100191, China
| | - Luyang Sun
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education, Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing 100191, China
| | - Xiaohan Yang
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education, Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing 100191, China
| | - Wenhua Yu
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education, Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing 100191, China
| | - Wenzhe Si
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education, Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing 100191, China
| | - Ruorong Yan
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education, Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing 100191, China
| | - Xia Yi
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education, Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing 100191, China
| | - Di Zhang
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education, Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing 100191, China
| | - Wanjin Li
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education, Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing 100191, China
| | - Lifang Li
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education, Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing 100191, China
| | - Jianguo Yang
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education, Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing 100191, China
| | - Yan Wang
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China
| | - Yi Eve Sun
- Translational Center for Stem Cell Research, Tongji Hospital, Stem Cell Research Center, Tongji University School of Medicine, Shanghai 200065, China; Departments of Psychiatry and Behavioral Sciences and Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Dai Zhang
- Key Laboratory of Mental Health, Ministry of Health, Peking University Health Science Center, Beijing 100191, China
| | - Anming Meng
- State Key Laboratory of Biomembrane and Membrane Engineering, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yongfeng Shang
- Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education, Department of Biochemistry and Molecular Biology, Peking University Health Science Center, Beijing 100191, China; 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin 300070, China.
| |
Collapse
|
24
|
DesRochers TM, Palma E, Kaplan DL. Tissue-engineered kidney disease models. Adv Drug Deliv Rev 2014; 69-70:67-80. [PMID: 24361391 DOI: 10.1016/j.addr.2013.12.002] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 12/08/2013] [Accepted: 12/09/2013] [Indexed: 02/08/2023]
Abstract
Renal disease represents a major health problem that often results in end-stage renal failure necessitating dialysis and eventually transplantation. Historically these diseases have been studied with patient observation and screening, animal models, and two-dimensional cell culture. In this review, we focus on recent advances in tissue engineered kidney disease models that have the capacity to compensate for the limitations of traditional modalities. The cells and materials utilized to develop these models are discussed and tissue engineered models of polycystic kidney disease, drug-induced nephrotoxicity, and the glomerulus are examined in detail. The application of these models has the potential to direct future disease treatments and preclinical drug development.
Collapse
|
25
|
Melis JPM, Derks KWJ, Pronk TE, Wackers P, Schaap MM, Zwart E, van Ijcken WFJ, Jonker MJ, Breit TM, Pothof J, van Steeg H, Luijten M. In vivo murine hepatic microRNA and mRNA expression signatures predicting the (non-)genotoxic carcinogenic potential of chemicals. Arch Toxicol 2014; 88:1023-34. [PMID: 24390151 DOI: 10.1007/s00204-013-1189-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 12/18/2013] [Indexed: 01/06/2023]
Abstract
There is a high need to improve the assessment of, especially non-genotoxic, carcinogenic features of chemicals. We therefore explored a toxicogenomics-based approach using genome-wide microRNA and mRNA expression profiles upon short-term exposure in mice. For this, wild-type mice were exposed for seven days to three different classes of chemicals, i.e., four genotoxic carcinogens (GTXC), seven non-genotoxic carcinogens (NGTXC), and five toxic non-carcinogens. Hepatic expression patterns of mRNA and microRNA transcripts were determined after exposure and used to assess the discriminative power of the in vivo transcriptome for GTXC and NGTXC. A final classifier set, discriminative for GTXC and NGTXC, was generated from the transcriptomic data using a tiered approach. This appeared to be a valid approach, since the predictive power of the final classifier set in three different classifier algorithms was very high for the original training set of chemicals. Subsequent validation in an additional set of chemicals revealed that the predictive power for GTXC remained high, in contrast to NGTXC, which appeared to be more troublesome. Our study demonstrated that the in vivo microRNA-ome has less discriminative power to correctly identify (non-)genotoxic carcinogen classes. The results generally indicate that single mRNA transcripts do have the potential to be applied in risk assessment, but that additional (genomic) strategies are necessary to correctly predict the non-genotoxic carcinogenic potential of a chemical.
Collapse
Affiliation(s)
- Joost P M Melis
- Center for Health Protection, National Institute for Public Health and the Environment (RIVM), P.O. Box 1, 3720 BA, Bilthoven, The Netherlands
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
26
|
Iizuka M, Susa T, Takahashi Y, Tamamori-Adachi M, Kajitani T, Okinaga H, Fukusato T, Okazaki T. Histone acetyltransferase Hbo1 destabilizes estrogen receptor α by ubiquitination and modulates proliferation of breast cancers. Cancer Sci 2013; 104:1647-55. [PMID: 24125069 DOI: 10.1111/cas.12303] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 10/07/2013] [Accepted: 10/08/2013] [Indexed: 12/25/2022] Open
Abstract
The estrogen receptor (ER) is a key molecule for growth of breast cancers. It has been a successful target for treatment of breast cancers. Elucidation of the ER expression mechanism is of importance for designing therapeutics for ER-positive breast cancers. However, the detailed mechanism of ER stability is still unclear. Here, we report that histone acetyltransferase Hbo1 promotes destabilization of estrogen receptor α (ERα) in breast cancers through lysine 48-linked ubiquitination. The acetyltransferase activity of Hbo1 is linked to its activity for ERα ubiquitination. Depletion of Hbo1 and anti-estrogen treatment displayed a potent growth suppression of breast cancer cell line. Hbo1 modulated transcription by ERα. Mutually exclusive expression of Hbo1 and ERα was observed in roughly half of the human breast tumors examined in the present study. Modulation of ER stability by Hbo1 in breast cancers may provide a novel therapeutic possibility.
Collapse
Affiliation(s)
- Masayoshi Iizuka
- Department of Biochemistry, Teikyo University School of Medicine, Tokyo, Japan
| | | | | | | | | | | | | | | |
Collapse
|
27
|
Labno-Kirszniok K, Nieszporek T, Wiecek A, Helbig G, Lubinski J. Acute myeloid leukemia in a 38-year-old hemodialyzed patient with von Hippel-Lindau disease. Hered Cancer Clin Pract 2013; 11:11. [PMID: 23968328 PMCID: PMC3846582 DOI: 10.1186/1897-4287-11-11] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2013] [Accepted: 07/30/2013] [Indexed: 01/03/2023] Open
Abstract
Von Hippel-Lindau disease (VHL disease) is a hereditary cancer predisposition syndrome caused by mutations of the von Hippel-Lindau tumor suppressor gene. The gene product, pVHL, regulates the level of proteins that play a central role in protecting cells against hypoxia. Clinical hallmarks of von Hippel-Lindau disease are the development of central nervous system hemangioblastomas, renal cell carcinoma, pheochromocytoma, neuroendocrine tumors and endolymphatic sac tumors. In this article the case of a 38-year old hemodialyzed patient who became ill with acute myeloid leukemia (AML) three years after being diagnosed with von Hippel-Lindau disease is presented. After cytostatic treatment the patient went into complete hematologic remission but there was still residual disease at the genetic level. After consolidation therapy patient developed bone marrow aplasia and severe pneumonia. Despite intensive treatment the patient died from acute respiratory failure. In this paper we present for the first time a case of von Hippel-Lindau disease associated with acute myeloid leukemia. No evidence of relationship between VHL disease and blood cancers has been demonstrated so far. Despite the fact that there is an increased risk of cancer development in hemodialyzed patients, cancer is a relatively rare cause of death in the dialysed population, and the most common malignancies are genitourinary cancers. It seems likely that development of acute myeloid leukemia in patient with VHL disease can be related to epigenetic alterations of the VHL gene, but further studies are needed.
Collapse
Affiliation(s)
- Katarzyna Labno-Kirszniok
- Department of Nephrology, Endocrinology and Metabolic Diseases, Medical University of Silesia, Francuska Street 20/24, Katowice 40-027, Poland.
| | | | | | | | | |
Collapse
|
28
|
Zeng L, Bai M, Mittal AK, El-Jouni W, Zhou J, Cohen DM, Zhou MI, Cohen HT. Candidate tumor suppressor and pVHL partner Jade-1 binds and inhibits AKT in renal cell carcinoma. Cancer Res 2013; 73:5371-80. [PMID: 23824745 DOI: 10.1158/0008-5472.can-12-4707] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The von Hippel-Lindau (VHL) tumor suppressor pVHL is lost in the majority of clear-cell renal cell carcinomas (RCC). Activation of the PI3K/AKT/mTOR pathway is also common in RCC, with PTEN loss occurring in approximately 30% of the cases, but other mechanisms responsible for activating AKT at a wider level in this setting are undefined. Plant homeodomain protein Jade-1 (PHF17) is a candidate renal tumor suppressor stabilized by pVHL. Here, using kinase arrays, we identified phospho-AKT1 as an important target of Jade-1. Overexpressing or silencing Jade-1 in RCC cells increased or decreased levels of endogenous phospho-AKT/AKT1. Furthermore, reintroducing pVHL into RCC cells increased endogenous Jade-1 and suppressed endogenous levels of phospho-AKT, which colocalized with and bound to Jade-1. The N-terminus of Jade-1 bound both the catalytic domain and the C-terminal regulatory tail of AKT, suggesting a mechanism through which Jade-1 inhibited AKT kinase activity. Intriguingly, RCC precursor cells where Jade-1 was silenced exhibited an increased capacity for AKT-dependent anchorage-independent growth, in support of a tumor suppressor function for Jade-1 in RCC. In support of this concept, an in silico expression analysis suggested that reduced Jade-1 expression is a poor prognostic factor in clear-cell RCC that is associated with activation of an AKT1 target gene signature. Taken together, our results identify 2 mechanisms for Jade-1 fine control of AKT/AKT1 in RCC, through loss of pVHL, which decreases Jade-1 protein, or through attenuation in Jade-1 expression. These findings help explain the pathologic cooperativity in clear-cell RCC between PTEN inactivation and pVHL loss, which leads to decreased Jade-1 levels that superactivate AKT. In addition, they prompt further investigation of Jade-1 as a candidate biomarker and tumor suppressor in clear-cell RCC.
Collapse
Affiliation(s)
- Liling Zeng
- Renal and Hematology/Oncology Sections, Departments of Medicine and Pathology, Boston Medical Center and Boston University School of Medicine, Boston, USA
| | | | | | | | | | | | | | | |
Collapse
|
29
|
Petrini I, Rajan A, Pham T, Voeller D, Davis S, Gao J, Wang Y, Giaccone G. Whole genome and transcriptome sequencing of a B3 thymoma. PLoS One 2013; 8:e60572. [PMID: 23577124 PMCID: PMC3618227 DOI: 10.1371/journal.pone.0060572] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Accepted: 02/28/2013] [Indexed: 11/19/2022] Open
Abstract
Molecular pathology of thymomas is poorly understood. Genomic aberrations are frequently identified in tumors but no extensive sequencing has been reported in thymomas. Here we present the first comprehensive view of a B3 thymoma at whole genome and transcriptome levels. A 55-year-old Caucasian female underwent complete resection of a stage IVA B3 thymoma. RNA and DNA were extracted from a snap frozen tumor sample with a fraction of cancer cells over 80%. We performed array comparative genomic hybridization using Agilent platform, transcriptome sequencing using HiSeq 2000 (Illumina) and whole genome sequencing using Complete Genomics Inc platform. Whole genome sequencing determined, in tumor and normal, the sequence of both alleles in more than 95% of the reference genome (NCBI Build 37). Copy number (CN) aberrations were comparable with those previously described for B3 thymomas, with CN gain of chromosome 1q, 5, 7 and X and CN loss of 3p, 6, 11q42.2-qter and q13. One translocation t(11;X) was identified by whole genome sequencing and confirmed by PCR and Sanger sequencing. Ten single nucleotide variations (SNVs) and 2 insertion/deletions (INDELs) were identified; these mutations resulted in non-synonymous amino acid changes or affected splicing sites. The lack of common cancer-associated mutations in this patient suggests that thymomas may evolve through mechanisms distinctive from other tumor types, and supports the rationale for additional high-throughput sequencing screens to better understand the somatic genetic architecture of thymoma.
Collapse
Affiliation(s)
- Iacopo Petrini
- Medical Oncology Branch, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Arun Rajan
- Medical Oncology Branch, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Trung Pham
- Medical Oncology Branch, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Donna Voeller
- Medical Oncology Branch, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Sean Davis
- Genetics Branch, National Cancer Institute, Bethesda, Maryland, United States of America
| | - James Gao
- Medical Oncology Branch, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Yisong Wang
- Medical Oncology Branch, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Giuseppe Giaccone
- Medical Oncology Branch, National Cancer Institute, Bethesda, Maryland, United States of America
| |
Collapse
|
30
|
Havasi A, Haegele JA, Gall JM, Blackmon S, Ichimura T, Bonegio RG, Panchenko MV. Histone acetyl transferase (HAT) HBO1 and JADE1 in epithelial cell regeneration. THE AMERICAN JOURNAL OF PATHOLOGY 2012; 182:152-62. [PMID: 23159946 DOI: 10.1016/j.ajpath.2012.09.017] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Revised: 09/09/2012] [Accepted: 09/20/2012] [Indexed: 12/31/2022]
Abstract
HBO1 acetylates lysine residues of histones and is involved in DNA replication and gene transcription. Two isoforms of JADE1, JADE1S and JADE1L, bind HBO1 and promote acetylation of histones in chromatin context. We characterized the role of JADE1-HBO1 complexes in vitro and in vivo during epithelial cell replication. Down-regulation of JADE1 by siRNA diminished the rate of DNA synthesis in cultured cells, decreased endogenous HBO1 protein expression, and prevented chromatin recruitment of replication factor Mcm7, demonstrating that JADE1 is required for cell proliferation. We used a murine model of acute kidney injury to examine expression of HBO1-JADE1S/L in injured and regenerating epithelial tissue. In control kidneys, JADE1S, JADE1L, and HBO1 were expressed in nuclei of proximal and distal tubular epithelial cells. Ischemia and reperfusion injury resulted in an initial decrease in JADE1S, JADE1L, and HBO1 protein levels, which returned to baseline during renal recovery. HBO1 and JADE1S recovered as cell proliferation reached its maximum, whereas JADE1L recovered after bulk proliferation had ceased. The temporal expression of JADE1S correlated with the acetylation of histone H4 on lysines 5 and 12, but not with acetylation of histone H3 on lysine 14, demonstrating that the JADE1S-HBO1 complex specifically marks H4 during epithelial cell proliferation. These data implicate JADE1-HBO1 complex in acute kidney injury and suggest distinct roles for JADE1 isoforms during epithelial cell recovery.
Collapse
Affiliation(s)
- Andrea Havasi
- Department of Pathology, Boston University School of Medicine, Boston, Massachusetts 02118, USA
| | | | | | | | | | | | | |
Collapse
|
31
|
Foy RL, Chitalia VC, Panchenko MV, Zeng L, Lopez D, Lee JW, Rana SV, Boletta A, Qian F, Tsiokas L, Piontek KB, Germino GG, Zhou MI, Cohen HT. Polycystin-1 regulates the stability and ubiquitination of transcription factor Jade-1. Hum Mol Genet 2012; 21:5456-71. [PMID: 23001567 DOI: 10.1093/hmg/dds391] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Autosomal-dominant polycystic kidney disease (ADPKD) and von Hippel-Lindau (VHL) disease lead to large kidney cysts that share pathogenetic features. The polycystin-1 (PC1) and pVHL proteins may therefore participate in the same key signaling pathways. Jade-1 is a pro-apoptotic and growth suppressive ubiquitin ligase for beta-catenin and transcriptional coactivator associated with histone acetyltransferase activity that is stabilized by pVHL in a manner that correlates with risk of VHL renal disease. Thus, a relationship between Jade-1 and PC1 was sought. Full-length PC1 bound, stabilized and colocalized with Jade-1 and inhibited Jade-1 ubiquitination. In contrast, the cytoplasmic tail or the naturally occurring C-terminal fragment of PC1 (PC1-CTF) promoted Jade-1 ubiquitination and degradation, suggesting a dominant-negative mechanism. ADPKD-associated PC1 mutants failed to regulate Jade-1, indicating a potential disease link. Jade-1 ubiquitination was mediated by Siah-1, an E3 ligase that binds PC1. By controlling Jade-1 abundance, PC1 and the PC1-CTF differentially regulate Jade-1-mediated transcriptional activity. A key target of PC1, the cyclin-dependent kinase inhibitor p21, is also up-regulated by Jade-1. Through Jade-1, PC1 and PC1 cleaved forms may exert fine control of beta-catenin and canonical Wnt signaling, a critical pathway in cystic renal disease. Thus, Jade-1 is a transcription factor and ubiquitin ligase whose activity is regulated by PC1 in a manner that is physiologic and may correlate with disease. Jade-1 may be an important therapeutic target in renal cystogenesis.
Collapse
Affiliation(s)
- Rebecca L Foy
- Renal Section, Boston University Medical Center, Boston, MA 02118, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
32
|
Lian X, Duan X, Wu X, Li C, Chen S, Wang S, Cai Y, Weng Z. Expression and clinical significance of von Hippel-Lindau downstream genes: Jade-1 and β-catenin related to renal cell carcinoma. Urology 2012; 80:485.e7-13. [PMID: 22516360 DOI: 10.1016/j.urology.2012.02.024] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Revised: 02/10/2012] [Accepted: 02/14/2012] [Indexed: 10/28/2022]
Abstract
OBJECTIVE To investigate the expression of Jade-1 and β-catenin and their effect in the development of renal cell carcinoma (RCC). METHODS The expression of Jade-1 and β-catenin in 11 normal kidney tissue specimens (normal group) and 60 RCC specimens (RCC group) was determined using real-time polymerase chain reaction and immunohistochemistry. Also, their effect on early relapses of RCC was analyzed after 5 years of follow-up. RESULTS The expression of Jade-1 protein in the RCC group was significantly lower than that in the normal group (0.1655 vs 0.7438, P < .05), and the expression of β-catenin protein was significantly greater than that in the normal group (0.2756 vs 0.0855, P < .05). The expression of Jade-1 mRNA in the RCC group was 0.202 times that in the normal group, which were lower (P < .05). The expression of β-catenin mRNA was 1.014 times that in the normal group (P > .05). The expression of Jade-1 protein and β-catenin protein in poorly differentiated RCC specimens was significantly lower and higher than the expression in the well-differentiated RCC specimen (P < .05), respectively. Patients with negative Jade-1 expression and positive β-catenin expression were found to have shorter survival on univariate analysis (P < .05). CONCLUSION RCC with a low expression of Jade-1 and high expression of β-catenin is associated with a poor outcome and decreased survival.
Collapse
Affiliation(s)
- Xin Lian
- Department of Urology, Lishui Central Hospital, Wenzhou Medical College, Zhejiang, People's Republic of China
| | | | | | | | | | | | | | | |
Collapse
|
33
|
Conserved molecular interactions within the HBO1 acetyltransferase complexes regulate cell proliferation. Mol Cell Biol 2011; 32:689-703. [PMID: 22144582 DOI: 10.1128/mcb.06455-11] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Acetyltransferase complexes of the MYST family with distinct substrate specificities and functions maintain a conserved association with different ING tumor suppressor proteins. ING complexes containing the HBO1 acetylase are a major source of histone H3 and H4 acetylation in vivo and play critical roles in gene regulation and DNA replication. Here, our molecular dissection of HBO1/ING complexes unravels the protein domains required for their assembly and function. Multiple PHD finger domains present in different subunits bind the histone H3 N-terminal tail with a distinct specificity toward lysine 4 methylation status. We show that natively regulated association of the ING4/5 PHD domain with HBO1-JADE determines the growth inhibitory function of the complex, linked to its tumor suppressor activity. Functional genomic analyses indicate that the p53 pathway is a main target of the complex, at least in part through direct transcription regulation at the initiation site of p21/CDKN1A. These results demonstrate the importance of ING association with MYST acetyltransferases in controlling cell proliferation, a regulated link that accounts for the reported tumor suppressor activities of these complexes.
Collapse
|
34
|
Ghanta KS, Li DQ, Eswaran J, Kumar R. Gene profiling of MTA1 identifies novel gene targets and functions. PLoS One 2011; 6:e17135. [PMID: 21364872 PMCID: PMC3045407 DOI: 10.1371/journal.pone.0017135] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2010] [Accepted: 01/21/2011] [Indexed: 12/20/2022] Open
Abstract
Background Metastasis-associated protein 1 (MTA1), a master dual co-regulatory protein is found to be an integral part of NuRD (Nucleosome Remodeling and Histone Deacetylation) complex, which has indispensable transcriptional regulatory functions via histone deacetylation and chromatin remodeling. Emerging literature establishes MTA1 to be a valid DNA-damage responsive protein with a significant role in maintaining the optimum DNA-repair activity in mammalian cells exposed to genotoxic stress. This DNA-damage responsive function of MTA1 was reported to be a P53-dependent and independent function. Here, we investigate the influence of P53 on gene regulation function of Mta1 to identify novel gene targets and functions of Mta1. Methods Gene expression analysis was performed on five different mouse embryonic fibroblasts (MEFs) samples (i) the Mta1 wild type, (ii) Mta1 knock out (iii) Mta1 knock out in which Mta1 was reintroduced (iv) P53 knock out (v) P53 knock out in which Mta1 was over expressed using Affymetrix Mouse Exon 1.0 ST arrays. Further Hierarchical Clustering, Gene Ontology analysis with GO terms satisfying corrected p-value<0.1, and the Ingenuity Pathway Analysis were performed. Finally, RT-qPCR was carried out on selective candidate genes. Significance/Conclusion This study represents a complete genome wide screen for possible target genes of a coregulator, Mta1. The comparative gene profiling of Mta1 wild type, Mta1 knockout and Mta1 re-expression in the Mta1 knockout conditions define “bona fide” Mta1 target genes. Further extensive analyses of the data highlights the influence of P53 on Mta1 gene regulation. In the presence of P53 majority of the genes regulated by Mta1 are related to inflammatory and anti-microbial responses whereas in the absence of P53 the predominant target genes are involved in cancer signaling. Thus, the presented data emphasizes the known functions of Mta1 and serves as a rich resource which could help us identify novel Mta1 functions.
Collapse
Affiliation(s)
- Krishna Sumanth Ghanta
- McCormick Genomic and Proteomic Center, The George Washington University Medical Center, Washington, D.C., United States of America
| | - Da-Qiang Li
- Department of Biochemistry and Molecular Biology, The George Washington University Medical Center, Washington, D.C., United States of America
| | - Jeyanthy Eswaran
- McCormick Genomic and Proteomic Center, The George Washington University Medical Center, Washington, D.C., United States of America
- Department of Biochemistry and Molecular Biology, The George Washington University Medical Center, Washington, D.C., United States of America
- * E-mail:
| | - Rakesh Kumar
- McCormick Genomic and Proteomic Center, The George Washington University Medical Center, Washington, D.C., United States of America
- Department of Biochemistry and Molecular Biology, The George Washington University Medical Center, Washington, D.C., United States of America
| |
Collapse
|
35
|
Nydam ML, Harrison RG. INTROGRESSION DESPITE SUBSTANTIAL DIVERGENCE IN A BROADCAST SPAWNING MARINE INVERTEBRATE. Evolution 2010; 65:429-42. [DOI: 10.1111/j.1558-5646.2010.01153.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
36
|
Cole AM, Ridgway RA, Derkits SE, Parry L, Barker N, Clevers H, Clarke AR, Sansom OJ. p21 loss blocks senescence following Apc loss and provokes tumourigenesis in the renal but not the intestinal epithelium. EMBO Mol Med 2010; 2:472-86. [PMID: 20976827 PMCID: PMC3394507 DOI: 10.1002/emmm.201000101] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2010] [Revised: 09/28/2010] [Accepted: 09/29/2010] [Indexed: 12/21/2022] Open
Abstract
Senescence has been implicated as an important mechanism of tumour suppression in a number of human malignancies, including colorectal cancer (CRC). However, we still have a relatively poor understanding of how the underlying mutations that occur in cancer cause senescence and its relevance in vivo. The Apc gene is mutated in approximately 80% of CRC as the initiating event, but rarely elsewhere. In this study we have examined the capacity of Apc loss to induce senescence in the intestinal epithelium compared to the renal epithelium. Within the renal epithelium, loss of Apc function led to an induction of senescence, however, bypassing senescence through combined Apc and p21 or Ink4A gene deletion rapidly initiated renal carcinoma. Within the intestinal epithelium, loss of Apc did not induce senescence. Moreover, combined Apc and p21 or Ink4A loss had no impact upon tumourigenesis. Taken together, these results show that Apc loss in vivo invokes a senescence program in a context-dependent fashion, and implies senescence may play a key barrier to tumourigenesis in the kidney. However, in CRC, escape from senescence is likely to only be a barrier in cancers initiated by other mutations.
Collapse
Affiliation(s)
| | | | | | - Lee Parry
- School of Biosciences, University of CardiffCardiff, UK
| | - Nick Barker
- Hubrecht Institute for Developmental Biology and Stem Cell Research, University Medical Centre UtrechtUtrecht, Netherlands
| | - Hans Clevers
- Hubrecht Institute for Developmental Biology and Stem Cell Research, University Medical Centre UtrechtUtrecht, Netherlands
| | - Alan R Clarke
- School of Biosciences, University of CardiffCardiff, UK
| | | |
Collapse
|
37
|
Piekielko-Witkowska A, Wiszomirska H, Wojcicka A, Poplawski P, Boguslawska J, Tanski Z, Nauman A. Disturbed expression of splicing factors in renal cancer affects alternative splicing of apoptosis regulators, oncogenes, and tumor suppressors. PLoS One 2010; 5:e13690. [PMID: 21082031 PMCID: PMC2972751 DOI: 10.1371/journal.pone.0013690] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Accepted: 10/07/2010] [Indexed: 12/02/2022] Open
Abstract
Background Clear cell renal cell carcinoma (ccRCC) is the most common type of renal cancer. One of the processes disturbed in this cancer type is alternative splicing, although phenomena underlying these disturbances remain unknown. Alternative splicing consists of selective removal of introns and joining of residual exons of the primary transcript, to produce mRNA molecules of different sequence. Splicing aberrations may lead to tumoral transformation due to synthesis of impaired splice variants with oncogenic potential. In this paper we hypothesized that disturbed alternative splicing in ccRCC may result from improper expression of splicing factors, mediators of splicing reactions. Methodology/Principal Findings Using real-time PCR and Western-blot analysis we analyzed expression of seven splicing factors belonging to SR proteins family (SF2/ASF, SC35, SRp20, SRp75, SRp40, SRp55 and 9G8), and one non-SR factor, hnRNP A1 (heterogeneous nuclear ribonucleoprotein A1) in 38 pairs of tumor-control ccRCC samples. Moreover, we analyzed splicing patterns of five genes involved in carcinogenesis and partially regulated by analyzed splicing factors: RON, CEACAM1, Rac1, Caspase-9, and GLI1. Conclusions/Significance We found that the mRNA expression of splicing factors was disturbed in tumors when compared to paired controls, similarly as levels of SF2/ASF and hnRNP A1 proteins. The correlation coefficients between expression levels of specific splicing factors were increased in tumor samples. Moreover, alternative splicing of five analyzed genes was also disturbed in ccRCC samples and splicing pattern of two of them, Caspase-9 and CEACAM1 correlated with expression of SF2/ASF in tumors. We conclude that disturbed expression of splicing factors in ccRCC may possibly lead to impaired alternative splicing of genes regulating tumor growth and this way contribute to the process of carcinogenesis.
Collapse
Affiliation(s)
| | - Hanna Wiszomirska
- Department of Biochemistry and Molecular Biology, The Medical Centre of Postgraduate Education, Warsaw, Poland
| | - Anna Wojcicka
- Department of Biochemistry and Molecular Biology, The Medical Centre of Postgraduate Education, Warsaw, Poland
| | - Piotr Poplawski
- Department of Biochemistry and Molecular Biology, The Medical Centre of Postgraduate Education, Warsaw, Poland
| | - Joanna Boguslawska
- Department of Biochemistry and Molecular Biology, The Medical Centre of Postgraduate Education, Warsaw, Poland
| | | | - Alicja Nauman
- Department of Biochemistry and Molecular Biology, The Medical Centre of Postgraduate Education, Warsaw, Poland
- * E-mail:
| |
Collapse
|
38
|
Musselman CA, Kutateladze TG. PHD fingers: epigenetic effectors and potential drug targets. Mol Interv 2010; 9:314-23. [PMID: 20048137 DOI: 10.1124/mi.9.6.7] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The plant homeodomain (PHD) finger is found in many chromatin-remodeling proteins. This small approximately 65-residue domain functions as an "effector" that binds specific epigenetic marks on histone tails, recruiting transcription factors and nucleosome-associated complexes to chromatin. Mutations in the PHD finger or deletion of this domain are linked to a number of human diseases, including cancer, mental retardation, and immunodeficiency. PHD finger-containing proteins may become valuable diagnostic markers and targets to prevent and treat these disorders. In this review, we highlight the progress recently made in understanding the functional significance of chromatin targeting by mammalian PHD fingers, detail the molecular mechanisms and structural features of "histone code" recognition, and discuss the therapeutic potential of PHD fingers.
Collapse
|
39
|
Saksouk N, Avvakumov N, Champagne KS, Hung T, Doyon Y, Cayrou C, Paquet E, Ullah M, Landry AJ, Côté V, Yang XJ, Gozani O, Kutateladze TG, Côté J. HBO1 HAT complexes target chromatin throughout gene coding regions via multiple PHD finger interactions with histone H3 tail. Mol Cell 2009; 33:257-65. [PMID: 19187766 DOI: 10.1016/j.molcel.2009.01.007] [Citation(s) in RCA: 136] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2008] [Revised: 11/18/2008] [Accepted: 01/13/2009] [Indexed: 02/07/2023]
Abstract
The HBO1 HAT protein is the major source of histone H4 acetylation in vivo and has been shown to play critical roles in gene regulation and DNA replication. A distinctive characteristic of HBO1 HAT complexes is the presence of three PHD finger domains in two different subunits: tumor suppressor proteins ING4/5 and JADE1/2/3. Biochemical and functional analyses indicate that these domains interact with histone H3 N-terminal tail region, but with a different specificity toward its methylation status. Their combinatorial action is essential in regulating chromatin binding and substrate specificity of HBO1 complexes, as well as cell growth. Importantly, localization analyses on the human genome indicate that HBO1 complexes are enriched throughout the coding regions of genes, supporting a role in transcription elongation. These results underline the importance and versatility of PHD finger domains in regulating chromatin association and histone modification crosstalk within a single protein complex.
Collapse
Affiliation(s)
- Nehmé Saksouk
- Laval University Cancer Research Center, Hôtel-Dieu de Québec (CHUQ), Quebec City, QC, Canada
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
40
|
Sirintrapun SJ, Parwani AV. Molecular Pathology of the Genitourinary Tract: Molecular Pathology of Kidney and Testes. Surg Pathol Clin 2009; 2:199-223. [PMID: 26838102 DOI: 10.1016/j.path.2008.08.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
With the advent of newer molecular technologies, our knowledge of cellular mechanisms with tumors of the kidney and testis has grown exponentially. Molecular technologies have led to better understanding of interplay between the von Hippel-Lindau gene and angiogenic cytokines in renal cancer and isochromosome 12p in testicular neoplasms. The result has been development of antiangiogenic-targeted therapy within recent years that has become the mainstay treatment for metastatic renal cell cancer. In the near future, classification and diagnosis of renal and testicular tumors through morphologic analysis will be supplemented by molecular information correlating to prognosis and targeted therapy. This article outlines tumor molecular pathology of the kidney and testis encompassing current genomic, epigenomic, and proteonomic findings.
Collapse
Affiliation(s)
- S Joseph Sirintrapun
- Pathology Informatics, University of Pittsburgh Medical Center, Pittsburgh, PA 15232, USA
| | - Anil V Parwani
- Department of Pathology, University of Pittsburgh Medical Center Shadyside Hospital, Room WG 07, 5230 Centre Avenue, Pittsburgh, PA 15232, USA.
| |
Collapse
|
41
|
Berndt JD, Moon RT, Major MB. Beta-catenin gets jaded and von Hippel-Lindau is to blame. Trends Biochem Sci 2009; 34:101-4. [PMID: 19217300 DOI: 10.1016/j.tibs.2008.12.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2008] [Revised: 12/08/2008] [Accepted: 12/10/2008] [Indexed: 11/19/2022]
Abstract
Numerous studies have pointed to interactions between the tumor suppressor von Hippel-Lindau (VHL) and the oncogenic Wnt-beta-catenin signaling cascade; however, the mechanism of this crosstalk has remained elusive. Among other roles, VHL can promote the stabilization of Jade-1. Now, recent findings provide compelling evidence that Jade-1 ubiquitylates beta-catenin, leading to its degradation. Thus, the loss of VHL, as seen in clear cell renal cell carcinoma, could lead to tumor formation through beta-catenin de-repression.
Collapse
Affiliation(s)
- Jason D Berndt
- Howard Hughes Medical Institute, Department of Pharmacology and Institute for Stem Cell and Regenerative Medicine, University of Washington School of Medicine, Box 357370, Seattle, WA 98109, USA.
| | | | | |
Collapse
|
42
|
Seidl C, Port M, Apostolidis C, Bruchertseifer F, Schwaiger M, Senekowitsch-Schmidtke R, Abend M. Differential gene expression triggered by highly cytotoxic alpha-emitter-immunoconjugates in gastric cancer cells. Invest New Drugs 2009; 28:49-60. [PMID: 19139817 DOI: 10.1007/s10637-008-9214-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2008] [Accepted: 12/19/2008] [Indexed: 12/20/2022]
Abstract
Immunoconjugates composed of the alpha-emitter (213)Bi and the monoclonal antibody d9MAb specifically target HSC45-M2 gastric cancer cells expressing mutant d9-E-cadherin. These conjugates efficiently killed tumor cells in a nude mouse peritoneal carcinomatosis model. To elucidate the molecular responses of HSC45-M2 cells to alpha-emitter irradiation, whole genome gene expression profiling was performed. For that purpose HSC45-M2 cells were incubated with lethal doses of (213)Bi-d9MAb. RNA was isolated at 6, 24 and 48 h after irradiation, transcribed into cDNA and hybridized to whole genome microarrays. Results of microarray analysis were validated using RTQ-PCR showing correspondence of approximately 90%. Following incubation with (213)Bi-d9MAb, 682-1125 genes showed upregulation and 666-1278 genes showed downregulation at one time point, each. Eight genes appeared upregulated and 12 genes downregulated throughout. Molecular functions and biological processes of differentially expressed genes were categorized according to the PANTHER database. Following (213)Bi-d9MAb irradiation also a time-dependent shift in terms of overrepresentation of biological processes was observed. Among the genes showing continuous upregulation, COL4A2, NEDD9 and C3 have not been associated with the cellular response to high LET radiation so far. The same holds true for WWP2, RFX3, HIST4H4 and JADE1 that showed continuous downregulation. According to PANTHER, three of the consistently upregulated (ITM2C, FLJ11000, MSMB) and downregulated (HCG9, GAS2L3, FLJ21439) genes, respectively, have not been associated with any biological process or molecular function so far. Thus, these findings revealed interesting new targets for selective elimination of tumor cells and new insights regarding response of tumor cells to alpha-emitter exposure.
Collapse
Affiliation(s)
- Christof Seidl
- Department of Nuclear Medicine, Technische Universität München, Ismaninger Strasse 22, 81675, Munich, Germany.
| | | | | | | | | | | | | |
Collapse
|
43
|
Sepulveda DE, Andrews BA, Asenjo JA, Papoutsakis ET. Comparative transcriptional analysis of embryoid body versus two-dimensional differentiation of murine embryonic stem cells. Tissue Eng Part A 2009; 14:1603-14. [PMID: 18433312 DOI: 10.1089/ten.tea.2007.0331] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Understanding the process of ex vivo embryonic stem (ES) cell differentiation is important for generating higher yields of desirable cell types or lineages and for understanding fundamental aspects of ES differentiation. We used DNA microarray analysis to investigate the differentiation of mouse ES cells cultured under three differentiation conditions. Embryoid body (EB) formation was compared to differentiation on surfaces coated with either gelatin (GEL) or matrigel (MAT). Based on the transcriptional patterns of a list of literature-based "stemness" genes, ES cell differentiation on the two coated surfaces appeared similar but not identical to EB differentiation. A notable difference was the GEL and MAT upregulation but EB downregulation of nine such stemness genes, which are related to cell adhesion and epithelial differentiation. Further, GEL and MAT differentiation showed higher expression of bone formation-related genes (Spp1, Csf1, Gsn, Bmp8b, Crlf1). Gene ontology analysis shows an increase in the expression of genes related to migration and cell structure in all three conditions. Overall, GEL and MAT conditions resulted in a more similar to each other transcriptional profile than to the EB condition, and such differences are apparently related to higher nutrient and metabolite gradients and limitations in the EB versus the GEL or MAT cultures.
Collapse
Affiliation(s)
- Dario E Sepulveda
- Department of Chemical Engineering and Biotechnology, Centre for Biochemical Engineering and Biotechnology, Institute for Cell Dynamics and Biotechnology (ICDB), University of Chile, Santiago, Chile
| | | | | | | |
Collapse
|
44
|
Role of the VHL (von Hippel-Lindau) gene in renal cancer: a multifunctional tumour suppressor. Biochem Soc Trans 2008; 36:472-8. [PMID: 18481984 DOI: 10.1042/bst0360472] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The VHL (von Hippel-Lindau) tumour-suppressor gene is inactivated in VHL disease and in sporadic cases of CCRCC [clear-cell RCC (renal cell carcinoma)]. pVHL (VHL protein) functions as part of an E3 ubiquitin ligase complex that targets proteins for proteasomal degradation. The best-characterized substrate is HIF-alpha (hypoxia-inducible factor-alpha). Loss of pVHL and subsequent up-regulation of HIF target genes has been attributed to the highly vascular nature of these neoplasms. However, pVHL does not just function as the executioner of HIF-alpha. Additional functions of pVHL that may be important in preventing CCRCC tumorigenesis have been identified, including primary cilium maintenance, assembly of the extracellular matrix and roles in the stabilization of p53 and Jade-1 (gene for apoptosis and differentiation in epithelia). Current evidence indicates that pVHL probably requires additional co-operating signalling pathways for CCRCC initiation and tumorigenesis.
Collapse
|
45
|
|
46
|
Jade-1 inhibits Wnt signalling by ubiquitylating beta-catenin and mediates Wnt pathway inhibition by pVHL. Nat Cell Biol 2008; 10:1208-16. [PMID: 18806787 PMCID: PMC2830866 DOI: 10.1038/ncb1781] [Citation(s) in RCA: 135] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2008] [Accepted: 09/04/2008] [Indexed: 12/15/2022]
Abstract
The von Hippel-Lindau protein pVHL suppresses renal tumorigenesis in part by promoting the degradation of hypoxia-inducible HIF-alpha transcription factors; additional mechanisms have been proposed. pVHL also stabilizes the plant homeodomain protein Jade-1, which is a candidate renal tumour suppressor that may correlate with renal cancer risk. Here we show that Jade-1 binds the oncoprotein beta-catenin in Wnt-responsive fashion. Moreover, Jade-1 destabilizes wild-type beta-catenin but not a cancer-causing form of beta-catenin. Whereas the well-established beta-catenin E3 ubiquitin ligase component beta-TrCP ubiquitylates only phosphorylated beta-catenin, Jade-1 ubiquitylates both phosphorylated and non-phosphorylated beta-catenin and therefore regulates canonical Wnt signalling in both Wnt-off and Wnt-on phases. Thus, the different characteristics of beta-TrCP and Jade-1 may ensure optimal Wnt pathway regulation. Furthermore, pVHL downregulates beta-catenin in a Jade-1-dependent manner and inhibits Wnt signalling, supporting a role for Jade-1 and Wnt signalling in renal tumorigenesis. The pVHL tumour suppressor and the Wnt tumorigenesis pathway are therefore directly linked through Jade-1.
Collapse
|
47
|
Foy RL, Song IY, Chitalia VC, Cohen HT, Saksouk N, Cayrou C, Vaziri C, Côté J, Panchenko MV. Role of Jade-1 in the histone acetyltransferase (HAT) HBO1 complex. J Biol Chem 2008; 283:28817-26. [PMID: 18684714 DOI: 10.1074/jbc.m801407200] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Regulation of global chromatin acetylation is important for chromatin remodeling. A small family of Jade proteins includes Jade-1L, Jade-2, and Jade-3, each bearing two mid-molecule tandem plant homology domain (PHD) zinc fingers. We previously demonstrated that the short isoform of Jade-1L protein, Jade-1, is associated with endogenous histone acetyltransferase (HAT) activity. It has been found that Jade-1L/2/3 proteins co-purify with a novel HAT complex, consisting of HBO1, ING4/5, and Eaf6. We investigated a role for Jade-1/1L in the HBO1 complex. When overexpressed individually, neither Jade-1/1L nor HBO1 affected histone acetylation. However, co-expression of Jade-1/1L and HBO1 increased acetylation of the bulk of endogenous histone H4 in epithelial cells in a synergistic manner, suggesting that Jade1/1L positively regulates HBO1 HAT activity. Conversely, small interfering RNA-mediated depletion of endogenous Jade resulted in reduced levels of H4 acetylation. Moreover, HBO1-mediated H4 acetylation activity was enhanced severalfold by the presence of Jade-1/1L in vitro. The removal of PHD fingers affected neither binding nor mutual Jade-1-HBO1 stabilization but completely abrogated the synergistic Jade-1/1L- and HBO1-mediated histone H4 acetylation in live cells and in vitro with reconstituted oligonucleosome substrates. Therefore, PHDs are necessary for Jade-1/1L-induced acetylation of nucleosomal histones by HBO1. In contrast to Jade-1/1L, the PHD zinc finger protein ING4/5 failed to synergize with HBO1 to promote histone acetylation. The physical interaction of ING4/5 with HBO1 occurred in the presence of Jade-1L or Jade-3 but not with the Jade-1 short isoform. In summary, this study demonstrates that Jade-1/1L are crucial co-factors for HBO1-mediated histone H4 acetylation.
Collapse
Affiliation(s)
- Rebecca L Foy
- Department of Medicine, Section of Nephrology, Boston University School of Medicine and Medical Center, Evans Biomedical Research Center, Boston, Massachusetts 02118, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
48
|
Hueber PA, Iglesias D, Chu LL, Eccles M, Goodyer P. In vivo validation of PAX2 as a target for renal cancer therapy. Cancer Lett 2008; 265:148-55. [PMID: 18439754 DOI: 10.1016/j.canlet.2008.02.016] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2008] [Revised: 01/31/2008] [Accepted: 02/06/2008] [Indexed: 10/22/2022]
Abstract
PAX genes are frequently overexpressed in human cancer tissue and appear to contribute to the tumor phenotype, suggesting that they may be potential targets for cancer therapy. In particular, aberrant PAX2 expression has been reported in a high proportion of primary tumors, including the majority of renal cell carcinomas (RCC). We recently demonstrated that PAX2 suppresses cisplatin-induced apoptosis in cultured RCC cells. We hypothesized that silencing of PAX2 expression might partially overcome the notorious resistance of renal cell carcinomas to chemotherapy in vivo. In this report, we show that a PAX2 shRNA successfully knocks down PAX2 mRNA and protein levels in an RCC cell line (ACHN). ACHN cells stably transfected with shRNAs targeted against the PAX2 homeodomain are 3-6-fold more susceptible to cisplatin-induced caspase-3 activation than control ACHN cells line. Furthermore, growth of subcutaneous ACHN/shPAX2 xenografts in nude mice is significantly more responsive to cisplatin therapy than control ACHN cell tumors. Our observations validate PAX2 as a potential therapeutic gene target in renal cancer and suggest that adjunctive PAX2 knockdown may enhance the efficacy of other chemotherapeutic agents.
Collapse
Affiliation(s)
- Pierre-Alain Hueber
- Department of Experimental Medicine, McGill University, Montreal Children's Hospital Research Institute, 2300 Tupper Street, 4060 Ste-Catherine West Montreal, Que., Canada H3Z2Z3
| | | | | | | | | |
Collapse
|
49
|
Sepúlveda DE, Andrews BA, Asenjo JA, Papoutsakis ET. Comparative Transcriptional Analysis of Embryoid Body Versus Two-Dimensional Differentiation of Murine Embryonic Stem Cells. Tissue Eng Part A 2008. [DOI: 10.1089/tea.2007.0331] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
|
50
|
Abstract
Hbo1 is a histone acetyltransferase (HAT) that is required for global histone H4 acetylation, steroid-dependent transcription, and chromatin loading of MCM2-7 during DNA replication licensing. It is the catalytic subunit of protein complexes that include ING and JADE proteins, growth regulatory factors and candidate tumor suppressors. These complexes are thought to act via tumor suppressor p53, but the molecular mechanisms and links between stress signaling and chromatin, are currently unknown. Here, we show that p53 physically interacts with Hbo1 and negatively regulates its HAT activity in vitro and in cells. Two physiological stresses that stabilize p53, hyperosmotic shock and DNA replication fork arrest, also inhibit Hbo1 HAT activity in a p53-dependent manner. Hyperosmotic stress during G(1) phase specifically inhibits the loading of the MCM2-7 complex, providing an example of the chromatin output of this pathway. These results reveal a direct regulatory connection between p53-responsive stress signaling and Hbo1-dependent chromatin pathways.
Collapse
|