1
|
Delanne J, Lecat M, Blackburn P, Klee E, Stumpel C, Stegmann S, Stevens S, Nava C, Heron D, Keren B, Mahida S, Naidu S, Babovic-Vuksanovic D, Herkert J, Torring P, Kibæk M, De Bie I, Pfundt R, Hendriks Y, Ousager L, Bend R, Warren H, Skinner S, Lyons M, Poe C, Chevarin M, Jouan T, Garde A, Thomas Q, Kuentz P, Tisserant E, Duffourd Y, Philippe C, Faivre L, Thauvin-Robinet C. Further clinical and molecular characterization of an XLID syndrome associated with BRWD3 variants, a gene implicate in leukemia-related JAK-STAT pathway. Eur J Med Genet 2022; 66:104670. [DOI: 10.1016/j.ejmg.2022.104670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 10/13/2022] [Accepted: 11/11/2022] [Indexed: 11/21/2022]
|
2
|
Genomic characterization of lymphomas in patients with inborn errors of immunity. Blood Adv 2022; 6:5403-5414. [PMID: 35687490 PMCID: PMC9631701 DOI: 10.1182/bloodadvances.2021006654] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 05/26/2022] [Indexed: 11/20/2022] Open
Abstract
Inborn errors of immunity-associated lymphomas are characterized by distinct clinical features and genetic signatures. Both germline and somatic alterations contribute to lymphomagenesis in patients with inborn errors of immunity.
Patients with inborn errors of immunity (IEI) have a higher risk of developing cancer, especially lymphoma. However, the molecular basis for IEI-related lymphoma is complex and remains elusive. Here, we perform an in-depth analysis of lymphoma genomes derived from 23 IEI patients. We identified and validated disease-causing or -associated germline mutations in 14 of 23 patients involving ATM, BACH2, BLM, CD70, G6PD, NBN, PIK3CD, PTEN, and TNFRSF13B. Furthermore, we profiled somatic mutations in the lymphoma genome and identified 8 genes that were mutated at a significantly higher level in IEI-associated diffuse large B-cell lymphomas (DLBCLs) than in non-IEI DLBCLs, such as BRCA2, NCOR1, KLF2, FAS, CCND3, and BRWD3. The latter, BRWD3, is furthermore preferentially mutated in tumors of a subgroup of activated phosphoinositide 3-kinase δ syndrome patients. We also identified 5 genomic mutational signatures, including 2 DNA repair deficiency-related signatures, in IEI-associated lymphomas and a strikingly high number of inter- and intrachromosomal structural variants in the tumor genome of a Bloom syndrome patient. In summary, our comprehensive genomic characterization of lymphomas derived from patients with rare genetic disorders expands our understanding of lymphomagenesis and provides new insights for targeted therapy.
Collapse
|
3
|
Fixing the GAP: the role of RhoGAPs in cancer. Eur J Cell Biol 2022; 101:151209. [DOI: 10.1016/j.ejcb.2022.151209] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 01/29/2022] [Accepted: 02/08/2022] [Indexed: 12/12/2022] Open
|
4
|
Esmaeili-Fard SM, Gholizadeh M, Hafezian SH, Abdollahi-Arpanahi R. Genes and Pathways Affecting Sheep Productivity Traits: Genetic Parameters, Genome-Wide Association Mapping, and Pathway Enrichment Analysis. Front Genet 2021; 12:710613. [PMID: 34394196 PMCID: PMC8355708 DOI: 10.3389/fgene.2021.710613] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 07/02/2021] [Indexed: 11/13/2022] Open
Abstract
Ewe productivity is a composite and maternal trait that is considered the most important economic trait in sheep meat production. The objective of this study was the application of alternative genome-wide association study (GWAS) approaches followed by gene set enrichment analysis (GSEA) on the ewes’ genome to identify genes affecting pregnancy outcomes and lamb growth after parturition in Iranian Baluchi sheep. Three maternal composite traits at birth and weaning were considered. The traits were progeny birth weight, litter mean weight at birth, total litter weight at birth, progeny weaning weight, litter mean weight at weaning, and total litter weight at weaning. GWASs were performed on original phenotypes as well as on estimated breeding values. The significant SNPs associated with composite traits at birth were located within or near genes RDX, FDX1, ARHGAP20, ZC3H12C, THBS1, and EPG5. Identified genes and pathways have functions related to pregnancy, such as autophagy in the placenta, progesterone production by the placenta, placental formation, calcium ion transport, and maternal immune response. For composite traits at weaning, genes (NR2C1, VEZT, HSD17B4, RSU1, CUBN, VIM, PRLR, and FTH1) and pathways affecting feed intake and food conservation, development of mammary glands cytoskeleton structure, and production of milk components like fatty acids, proteins, and vitamin B-12, were identified. The results show that calcium ion transport during pregnancy and feeding lambs by milk after parturition can have the greatest impact on weight gain as compared to other effects of maternal origin.
Collapse
Affiliation(s)
- Seyed Mehdi Esmaeili-Fard
- Department of Animal Science and Fisheries, Sari Agricultural Sciences and Natural Resources University (SANRU), Sari, Iran
| | - Mohsen Gholizadeh
- Department of Animal Science and Fisheries, Sari Agricultural Sciences and Natural Resources University (SANRU), Sari, Iran
| | - Seyed Hasan Hafezian
- Department of Animal Science and Fisheries, Sari Agricultural Sciences and Natural Resources University (SANRU), Sari, Iran
| | | |
Collapse
|
5
|
Liu G, Li J, Zhang CY, Huang DY, Xu JW. ARHGAP20 Expression Inhibited HCC Progression by Regulating the PI3K-AKT Signaling Pathway. J Hepatocell Carcinoma 2021; 8:271-284. [PMID: 33907697 PMCID: PMC8071084 DOI: 10.2147/jhc.s298554] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 03/25/2021] [Indexed: 02/05/2023] Open
Abstract
INTRODUCTION One of the most common cancers is hepatocellular carcinoma (HCC), which is an aggressive cancer that is associated with high mortality. The expression and role of ARHGAP20 in HCC remain unclear. MATERIALS AND METHODS The expression and clinical role of ARHGAP20 were investigated using online databases and HCC samples from Meizhou People's Hospital. Wound healing assays, transwell migration/invasion assays, and lung metastasis models were performed using nude mice. Gene set enrichment analyses were used to further explore the potential mechanisms. RESULTS Inspired by expression analyses of three different public databases (ie, TIMER, Oncomine, and HCCDB database), we confirmed that ARHGAP20 was downregulated in clinical HCC tumors compared with normal controls. ARHGAP20 expression inhibited HCC migration and invasion in vitro and in vivo. Based on GSEA results, we tested markers of the PI3K-AKT signaling pathway. Interestingly, while ARHGAP20 upregulation suppressed HCC migration/invasion and phosphorylation of AKT/PI3K molecules, exposure to the PI3K-AKT pathway agonist rhIGF-1 partially rescued these phenomena. ARHGAP20 also showed a close correlation with certain components in the HCC immune microenvironment. Furthermore, we revealed that downregulated ARHGAP20 was significantly correlated with larger tumor size and vascular invasion, and could be used as an adverse independent prognostic factor for HCC OS but not RFS. CONCLUSION ARHGAP20 was identified for the first time as a tumor suppressor gene that could inhibit HCC progression by regulating the PI3K-AKT signaling pathway and the immune microenvironment in HCC.
Collapse
Affiliation(s)
- Gao Liu
- Department of Hepatobiliary Surgery, Meizhou People’s Hospital, Meizhou, 514000, People’s Republic of China
- Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou, People’s Republic of China
| | - Jia Li
- Department of Hepatobiliary Surgery, Meizhou People’s Hospital, Meizhou, 514000, People’s Republic of China
- Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou, People’s Republic of China
| | - Cai-Yun Zhang
- Department of Hepatobiliary Surgery, Meizhou People’s Hospital, Meizhou, 514000, People’s Republic of China
- Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou, People’s Republic of China
| | - Dong-Yang Huang
- Center for Molecular Biology, Shantou University Medical College, Shantou, Guangdong, 515041, People’s Republic of China
- Correspondence: Dong-Yang Huang Center for Molecular Biology, Shantou University Medical College, Shantou, Guangdong, 515041, People’s Republic of China Email
| | - Ji-Wei Xu
- Department of Hepatobiliary Surgery, Meizhou People’s Hospital, Meizhou, 514000, People’s Republic of China
- Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou, People’s Republic of China
- Ji-Wei Xu Department of Hepatobiliary Surgery, Meizhou People’s Hospital, No. 38 Huangtang Road, Meizhou, 514000, People’s Republic of ChinaTel +86-13823832715 Email
| |
Collapse
|
6
|
Mundi N, Ghasemi F, Zeng PY, Prokopec SD, Patel K, Kim HAJ, Di Gravio E, MacNeil D, Khan MI, Han MW, Shaikh M, Mendez A, Yoo J, Fung K, Gameiro SF, Palma DA, Mymryk JS, Barrett JW, Boutros PC, Nichols AC. Sex disparities in head & neck cancer driver genes: An analysis of the TCGA dataset. Oral Oncol 2020; 104:104614. [DOI: 10.1016/j.oraloncology.2020.104614] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 12/26/2019] [Accepted: 02/22/2020] [Indexed: 12/20/2022]
|
7
|
Small Molecules Targeting the Specific Domains of Histone-Mark Readers in Cancer Therapy. Molecules 2020; 25:molecules25030578. [PMID: 32013155 PMCID: PMC7037402 DOI: 10.3390/molecules25030578] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 01/20/2020] [Accepted: 01/22/2020] [Indexed: 12/11/2022] Open
Abstract
Epigenetic modifications (or epigenetic tags) on DNA and histones not only alter the chromatin structure, but also provide a recognition platform for subsequent protein recruitment and enable them to acquire executive instructions to carry out specific intracellular biological processes. In cells, different epigenetic-tags on DNA and histones are often recognized by the specific domains in proteins (readers), such as bromodomain (BRD), chromodomain (CHD), plant homeodomain (PHD), Tudor domain, Pro-Trp-Trp-Pro (PWWP) domain and malignant brain tumor (MBT) domain. Recent accumulating data reveal that abnormal intracellular histone modifications (histone marks) caused by tumors can be modulated by small molecule-mediated changes in the activity of the above domains, suggesting that small molecules targeting histone-mark reader domains may be the trend of new anticancer drug development. Here, we summarize the protein domains involved in histone-mark recognition, and introduce recent research findings about small molecules targeting histone-mark readers in cancer therapy.
Collapse
|
8
|
Hong CF, Chen YC, Chen WC, Tu KC, Tsai MH, Chan YK, Yu SS. Construction of diagnosis system and gene regulatory networks based on microarray analysis. J Biomed Inform 2018; 81:61-73. [PMID: 29550394 DOI: 10.1016/j.jbi.2018.03.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Revised: 01/30/2018] [Accepted: 03/12/2018] [Indexed: 01/02/2023]
Abstract
A microarray analysis generally contains expression data of thousands of genes, but most of them are irrelevant to the disease of interest, making analyzing the genes concerning specific diseases complicated. Therefore, filtering out a few essential genes as well as their regulatory networks is critical, and a disease can be easily diagnosed just depending on the expression profiles of a few critical genes. In this study, a target gene screening (TGS) system, which is a microarray-based information system that integrates F-statistics, pattern recognition matching, a two-layer K-means classifier, a Parameter Detection Genetic Algorithm (PDGA), a genetic-based gene selector (GBG selector) and the association rule, was developed to screen out a small subset of genes that can discriminate malignant stages of cancers. During the first stage, F-statistic, pattern recognition matching, and a two-layer K-means classifier were applied in the system to filter out the 20 critical genes most relevant to ovarian cancer from 9600 genes, and the PDGA was used to decide the fittest values of the parameters for these critical genes. Among the 20 critical genes, 15 are associated with cancer progression. In the second stage, we further employed a GBG selector and the association rule to screen out seven target gene sets, each with only four to six genes, and each of which can precisely identify the malignancy stage of ovarian cancer based on their expression profiles. We further deduced the gene regulatory networks of the 20 critical genes by applying the Pearson correlation coefficient to evaluate the correlationship between the expression of each gene at the same stages and at different stages. Correlationships between gene pairs were calculated, and then, three regulatory networks were deduced. Their correlationships were further confirmed by the Ingenuity pathway analysis. The prognostic significances of the genes identified via regulatory networks were examined using online tools, and most represented biomarker candidates. In summary, our proposed system provides a new strategy to identify critical genes or biomarkers, as well as their regulatory networks, from microarray data.
Collapse
Affiliation(s)
- Chun-Fu Hong
- Department of Long-Term Care, National Quemoy University, Kinmen County 892, Taiwan, ROC
| | - Ying-Chen Chen
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung City 402, Taiwan, ROC
| | - Wei-Chun Chen
- Department of Management Information System, National Chung Hsing University, Taichung City 402, Taiwan, ROC
| | - Keng-Chang Tu
- Deparment of Computer Science and Engineering, National Chung Hsing University, Taichung City 402, Taiwan, ROC
| | - Meng-Hsiun Tsai
- Department of Management Information System, National Chung Hsing University, Taichung City 402, Taiwan, ROC.
| | - Yung-Kuan Chan
- Department of Management Information System, National Chung Hsing University, Taichung City 402, Taiwan, ROC.
| | - Shyr Shen Yu
- Deparment of Computer Science and Engineering, National Chung Hsing University, Taichung City 402, Taiwan, ROC
| |
Collapse
|
9
|
Manojlovic Z, Christofferson A, Liang WS, Aldrich J, Washington M, Wong S, Rohrer D, Jewell S, Kittles RA, Derome M, Auclair D, Craig DW, Keats J, Carpten JD. Comprehensive molecular profiling of 718 Multiple Myelomas reveals significant differences in mutation frequencies between African and European descent cases. PLoS Genet 2017; 13:e1007087. [PMID: 29166413 PMCID: PMC5699827 DOI: 10.1371/journal.pgen.1007087] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 10/23/2017] [Indexed: 12/30/2022] Open
Abstract
Multiple Myeloma (MM) is a plasma cell malignancy with significantly greater incidence and mortality rates among African Americans (AA) compared to Caucasians (CA). The overall goal of this study is to elucidate differences in molecular alterations in MM as a function of self-reported race and genetic ancestry. Our study utilized somatic whole exome, RNA-sequencing, and correlated clinical data from 718 MM patients from the Multiple Myeloma Research Foundation CoMMpass study Interim Analysis 9. Somatic mutational analyses based upon self-reported race corrected for ancestry revealed significant differences in mutation frequency between groups. Of interest, BCL7A, BRWD3, and AUTS2 demonstrate significantly higher mutation frequencies among AA cases. These genes are all involved in translocations in B-cell malignancies. Moreover, we detected a significant difference in mutation frequency of TP53 and IRF4 with frequencies higher among CA cases. Our study provides rationale for interrogating diverse tumor cohorts to best understand tumor genomics across populations.
Collapse
Affiliation(s)
- Zarko Manojlovic
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States of America
- Translational Genomics Research Institute, Phoenix, AZ, United States of America
| | | | - Winnie S. Liang
- Translational Genomics Research Institute, Phoenix, AZ, United States of America
| | - Jessica Aldrich
- Translational Genomics Research Institute, Phoenix, AZ, United States of America
| | - Megan Washington
- Translational Genomics Research Institute, Phoenix, AZ, United States of America
| | - Shukmei Wong
- Translational Genomics Research Institute, Phoenix, AZ, United States of America
| | - Daniel Rohrer
- Van Andel Research Institute, Grand Rapids, MI, United States of America
| | - Scott Jewell
- Van Andel Research Institute, Grand Rapids, MI, United States of America
| | - Rick A. Kittles
- Department of Surgery, Division of Population Genetics, University of Arizona, Tuscon, AZ, United States of America
| | - Mary Derome
- Multiple Myeloma Research Foundation, Norwalk, CT, United States of America
| | - Daniel Auclair
- Multiple Myeloma Research Foundation, Norwalk, CT, United States of America
| | - David Wesley Craig
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States of America
| | - Jonathan Keats
- Translational Genomics Research Institute, Phoenix, AZ, United States of America
| | - John D. Carpten
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States of America
- Translational Genomics Research Institute, Phoenix, AZ, United States of America
| |
Collapse
|
10
|
Affiliation(s)
- Guangtao Zhang
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai , 1425 Madison Avenue, New York, New York 10029, United States
| | - Steven G Smith
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai , 1425 Madison Avenue, New York, New York 10029, United States
| | - Ming-Ming Zhou
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai , 1425 Madison Avenue, New York, New York 10029, United States
| |
Collapse
|
11
|
Grotto S, Drouin-Garraud V, Ounap K, Puusepp-Benazzouz H, Schuurs-Hoeijmakers J, Le Meur N, Chambon P, Fehrenbach S, van Bokhoven H, Frébourg T, de Brouwer APM, Saugier-Veber P. Clinical assessment of five patients with BRWD3 mutation at Xq21.1 gives further evidence for mild to moderate intellectual disability and macrocephaly. Eur J Med Genet 2014; 57:200-6. [PMID: 24462886 DOI: 10.1016/j.ejmg.2013.12.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 12/31/2013] [Indexed: 01/22/2023]
Abstract
Truncating mutations of the BRWD3 gene have been reported in two distinct families with in total four patients so far. By using array-CGH, we detected a 74 Kb de novo deletion encompassing exons 11 through 41 of BRWD3 at Xq21.1 in a 20 year old boy presenting with syndromic intellectual disability. In addition, by using exome sequencing, we ascertained a family with a BRWD3 nonsense mutation, p.Tyr1131*, in four males with intellectual disability. We compared the clinical presentation of these five patients to that of the four patients already described in the literature for further delineation of the clinical spectrum in BRWD3-related intellectual disability. The main symptoms are mild to moderate intellectual disability (n = 9/9) with speech delay (n = 8/8), behavioral disturbances (n = 7/8), macrocephaly (n = 7/9), dysmorphic facial features (n = 9/9) including prominent forehead, pointed chin, deep-set eyes, abnormal ears, and broad hands and feet (n = 6/6), and skeletal symptoms (n = 7/7) like pes planus, scoliosis, kyphosis and cubitus valgus.
Collapse
Affiliation(s)
- Sarah Grotto
- Department of Genetics, Rouen University Hospital, Rouen, France
| | | | - Katrin Ounap
- Department of Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia; Department of Pediatrics, University of Tartu, Tartu, Estonia
| | - Helen Puusepp-Benazzouz
- Department of Pediatrics, University of Tartu, Tartu, Estonia; Department of Pediatrics, The Children's Hospital at Westmead, Sydney Children Hospital Network, Sydney, Australia
| | - Janneke Schuurs-Hoeijmakers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands; Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Nathalie Le Meur
- Department of Cytogenetics, EFS Normandie, Bois-Guillaume, France
| | - Pascal Chambon
- Department of Cytogenetics and Reproductive Biology, Rouen University Hospital, Rouen, France
| | | | - Hans van Bokhoven
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands; Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Thierry Frébourg
- Department of Genetics, Rouen University Hospital, Rouen, France; Inserm U1079, Rouen, France; Normandie University, IRIB, Rouen, France
| | - Arjan P M de Brouwer
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands; Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Pascale Saugier-Veber
- Department of Genetics, Rouen University Hospital, Rouen, France; Inserm U1079, Rouen, France; Normandie University, IRIB, Rouen, France.
| |
Collapse
|
12
|
Selective Inhibition of Acetyl-Lysine Effector Domains of the Bromodomain Family in Oncology. NUCLEAR SIGNALING PATHWAYS AND TARGETING TRANSCRIPTION IN CANCER 2014. [DOI: 10.1007/978-1-4614-8039-6_11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
|
13
|
Barbieri I, Cannizzaro E, Dawson MA. Bromodomains as therapeutic targets in cancer. Brief Funct Genomics 2013; 12:219-30. [DOI: 10.1093/bfgp/elt007] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
|
14
|
|
15
|
Chung CW. Small molecule bromodomain inhibitors: extending the druggable genome. PROGRESS IN MEDICINAL CHEMISTRY 2012; 51:1-55. [PMID: 22520470 DOI: 10.1016/b978-0-12-396493-9.00001-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Chun-Wa Chung
- Computational and Structural Sciences, GlaxoSmithKline R&D, Stevenage, SG1 2NY, UK
| |
Collapse
|
16
|
Abstract
Acetylation of lysine residues is a post-translational modification with broad relevance
to cellular signalling and disease biology. Enzymes that ‘write’
(histone acetyltransferases, HATs) and ‘erase’ (histone deacetylases,
HDACs) acetylation sites are an area of extensive research in current drug development,
but very few potent inhibitors that modulate the ‘reading process’
mediated by acetyl lysines have been described. The principal readers of
ɛ-N-acetyl lysine (Kac) marks are
bromodomains (BRDs), which are a diverse family of evolutionary conserved
protein-interaction modules. The conserved BRD fold contains a deep, largely hydrophobic
acetyl lysine binding site, which represents an attractive pocket for the development of
small, pharmaceutically active molecules. Proteins that contain BRDs have been implicated
in the development of a large variety of diseases. Recently, two highly potent and
selective inhibitors that target BRDs of the BET (bromodomains and extra-terminal) family
provided compelling data supporting targeting of these BRDs in inflammation and in an
aggressive type of squamous cell carcinoma. It is likely that BRDs will emerge alongside
HATs and HDACs as interesting targets for drug development for the large number of
diseases that are caused by aberrant acetylation of lysine residues.
Collapse
|
17
|
Herold T, Jurinovic V, Mulaw M, Seiler T, Dufour A, Schneider S, Kakadia PM, Feuring-Buske M, Braess J, Spiekermann K, Mansmann U, Hiddemann W, Buske C, Bohlander SK. Expression analysis of genes located in the minimally deleted regions of 13q14 and 11q22-23 in chronic lymphocytic leukemia-unexpected expression pattern of the RHO GTPase activator ARHGAP20. Genes Chromosomes Cancer 2011; 50:546-58. [DOI: 10.1002/gcc.20879] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2010] [Revised: 03/21/2011] [Accepted: 03/21/2011] [Indexed: 12/31/2022] Open
|
18
|
Poretti G, Kwee I, Bernasconi B, Rancoita PMV, Rinaldi A, Capella C, Zucca E, Neri A, Tibiletti MG, Bertoni F. Chromosome 11q23.1 is an unstable region in B-cell tumor cell lines. Leuk Res 2011; 35:808-13. [PMID: 21420167 DOI: 10.1016/j.leukres.2010.10.032] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2010] [Revised: 10/18/2010] [Accepted: 10/31/2010] [Indexed: 01/08/2023]
Abstract
Chromosome 11q23 region is a frequent target of chromosome aberrations in B-cell lymphoid tumors. Here, we present the cytogenetic and molecular characterization of an amplification affecting 11q23.1 in four cell lines derived from B-cell lymphoid tumors. A minimal common region of amplification of 330 kb was identified in three cell lines using Affymetrix Human Mapping 250K arrays. When analyzed with three BAC clones, the amplifications appeared different at cytogenetic level in each cell line. Possibly affected transcripts were evaluated using tiling arrays, and validated by real time PCR. Since no effect of the amplification at the local transcription level was observed, it is possible that 11q23 amplification might mainly represent the effect of unstable chromosomal region.
Collapse
Affiliation(s)
- Giulia Poretti
- Laboratory of Experimental Oncology and Lymphoma Unit, Oncology Institute of Southern Switzerland (IOSI), Bellinzona, Switzerland
| | | | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Abstract
O-linked N-Acetylglucosamine (O-GlcNAc) post-translational modifications originate from the activity of the hexosamine pathway, and are known to affect intracellular signaling processes. As aberrant responses to microenvironmental signals are a feature of chronic lymphocytic leukemia (CLL), O-GlcNAcylated protein levels were measured in primary CLL cells. In contrast to normal circulating and tonsillar B cells, CLL cells expressed high levels of O-GlcNAcylated proteins, including p53, c-myc and Akt. O-GlcNAcylation in CLL cells increased following activation with cytokines and through toll-like receptors (TLRs), or after loading with hexosamine pathway substrates. However, high baseline O-GlcNAc levels were associated with impaired signaling responses to TLR agonists, chemotherapeutic agents, B cell receptor crosslinking and mitogens. Indolent and aggressive clinical behavior of CLL cells were found to correlate with higher and lower O-GlcNAc levels, respectively. These findings suggest that intracellular O-GlcNAcylation is associated with the pathogenesis of CLL, which could potentially have therapeutic implications.
Collapse
|
20
|
Schwaenen C, Viardot A, Berger H, Barth TFE, Bentink S, Döhner H, Enz M, Feller AC, Hansmann ML, Hummel M, Kestler HA, Klapper W, Kreuz M, Lenze D, Loeffler M, Möller P, Müller-Hermelink HK, Ott G, Rosolowski M, Rosenwald A, Ruf S, Siebert R, Spang R, Stein H, Truemper L, Lichter P, Bentz M, Wessendorf S. Microarray-based genomic profiling reveals novel genomic aberrations in follicular lymphoma which associate with patient survival and gene expression status. Genes Chromosomes Cancer 2009; 48:39-54. [DOI: 10.1002/gcc.20617] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
|
21
|
Cotter FE, Auer RL. Genetic alteration associated with chronic lymphocytic leukemia. Cytogenet Genome Res 2007; 118:310-9. [PMID: 18000385 DOI: 10.1159/000108315] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2007] [Accepted: 03/14/2007] [Indexed: 12/19/2022] Open
Abstract
The genetics of B-cell chronic lymphocytic leukemia (B-CLL) differ considerably from most other forms of hematologic malignancy which are usually characterized by chromosome translocations. B-CLL typically contains chromosomal deletions and chromosomes 13q14 and 11q22-->q23 are the most common. These two regions appear to share a common ancestral origin (Auer et al., 2007b). Overall, chromosomal abnormalities can be found in the majority of patients with B-CLL when using sensitive techniques (Dohneret al., 2000) and possibly reflects an underlying predisposition, with a small but significant number of familial cases. Although single and consistent abnormalities are most common, multiple rearrangements can occur, often with disease progression (Feganetal., 1995; Dohner et al., 2000). Regions of recurrent deletion suggest the presence of tumor suppressor genes if following Knudson's theoretical 2-hit model. However, despite extensive sequencing analysis over the last decade and lack of pathogenic mutations identified, there has been a move away from this suggested hypothesis and alternative mechanisms of gene inactivation involving epigenetic silencing or haploinsufficiency may be considered as more likely in this disease. This review focuses on the common genetic abnormalities in B-CLL and relates them to some of the more recent hypotheses on inactivation of genes within these regions of deletion.
Collapse
Affiliation(s)
- F E Cotter
- Centre for Haematology, Institute of Cell and Molecular Sciences, Barts and the London Queen Mary School of Medicine, London, UK.
| | | |
Collapse
|
22
|
Field M, Tarpey PS, Smith R, Edkins S, O'Meara S, Stevens C, Tofts C, Teague J, Butler A, Dicks E, Barthorpe S, Buck G, Cole J, Gray K, Halliday K, Hills K, Jenkinson A, Jones D, Menzies A, Mironenko T, Perry J, Raine K, Richardson D, Shepherd R, Small A, Varian J, West S, Widaa S, Mallya U, Wooster R, Moon J, Luo Y, Hughes H, Shaw M, Friend KL, Corbett M, Turner G, Partington M, Mulley J, Bobrow M, Schwartz C, Stevenson R, Gecz J, Stratton MR, Futreal PA, Raymond FL. Mutations in the BRWD3 gene cause X-linked mental retardation associated with macrocephaly. Am J Hum Genet 2007; 81:367-74. [PMID: 17668385 PMCID: PMC1950797 DOI: 10.1086/520677] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2007] [Accepted: 04/17/2007] [Indexed: 11/04/2022] Open
Abstract
In the course of systematic screening of the X-chromosome coding sequences in 250 families with nonsyndromic X-linked mental retardation (XLMR), two families were identified with truncating mutations in BRWD3, a gene encoding a bromodomain and WD-repeat domain-containing protein. In both families, the mutation segregates with the phenotype in affected males. Affected males have macrocephaly with a prominent forehead, large cupped ears, and mild-to-moderate intellectual disability. No truncating variants were found in 520 control X chromosomes. BRWD3 is therefore a new gene implicated in the etiology of XLMR associated with macrocephaly and may cause disease by altering intracellular signaling pathways affecting cellular proliferation.
Collapse
|
23
|
Auer RL, Riaz S, Cotter FE. The 13q and 11q B-cell chronic lymphocytic leukaemia-associated regions derive from a common ancestral region in the zebrafish. Br J Haematol 2007; 137:443-53. [PMID: 17488487 DOI: 10.1111/j.1365-2141.2007.06600.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Loss of the long arm of chromosomes 11 and 13 is the most consistent cytogenetic abnormalities for patients with B-cell chronic lymphocytic leukaemia (B-CLL). They suggest the presence of as yet unidentified tumour suppressor genes within well-defined minimal-deleted regions (MinDRs). We have identified 38 orthologues of the human genes in MinDRs in zebrafish cDNA and syntenic regions for the human deletions in the zebrafish genome. One region on chromosome 9 in the zebrafish genome is of potential interest. Within chromosome 9, five genes and two microRNAs were identified with shared synteny to the MinDRs in B-CLL (two genes to human chromosome 11, three to human chromosome 13 and two chromosome 13 microRNAs). The critical region on zebrafish chromosome 9 maps to the MinDR for both human chromosomes, suggesting a common ancestry for B-CLL tumour suppressor genes. Target-selected mutagenesis to identify zebrafish mutants with knock-outs of genes in this region will allow analysis of their in vivo potential for lymphoproliferation and may define causative genes for B-CLL within human chromosomes 11q and 13q. Our study provides an explanation for involvement of both 11q and 13q in B-CLL and the potential to develop animal models for this common lymphoproliferative disorder.
Collapse
Affiliation(s)
- Rebecca L Auer
- Centre for Haematology, Institute of Cell and Molecular Science, Barts & The London, Queen Mary's School of Medicine, 4 Newark Street, London, UK
| | | | | |
Collapse
|
24
|
Kalla C, Scheuermann MO, Kube I, Schlotter M, Mertens D, Döhner H, Stilgenbauer S, Lichter P. Analysis of 11q22-q23 deletion target genes in B-cell chronic lymphocytic leukaemia: evidence for a pathogenic role of NPAT, CUL5, and PPP2R1B. Eur J Cancer 2007; 43:1328-35. [PMID: 17449237 DOI: 10.1016/j.ejca.2007.02.005] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2006] [Revised: 01/31/2007] [Accepted: 02/21/2007] [Indexed: 11/27/2022]
Abstract
Deletion of 11q22-q23 is associated with an aggressive course of B-cell chronic lymphocytic leukaemia (B-CLL). Since only in a subset of these cases biallelic inactivation of ATM was observed, we sought to identify other disease-associated genes within 11q22-q23 by analysing NPAT (cell-cycle regulation), CUL5 (ubiquitin-dependent apoptosis regulation) and PPP2R1B (component of the cell-cycle and apoptosis regulating PP2A) for point mutations and their expression in B-CLL by single-strand conformation polymorphism/sequence analysis of the transcripts and real-time polymerase chain reaction. Though none of the genes were affected by deleterious mutations, we observed a significant down-regulation of NPAT in B-CLL versus CD19+ B cells and of CUL5 in 11q deletion versus non-deletion B-CLL samples and measured reduced PPP2R1B transcript levels in a subset of B-CLL cases. Alternative splicing of PPP2R1B transcripts (skipping of exons 2/3, 3, 9) was associated with a reduced activity of protein phosphatase 2A. Together, these results implicate deregulation of the cell-cycle and apoptosis regulators NPAT, CUL5 and PPP2R1B and a role for these genes in the pathogenesis of B-CLL.
Collapse
Affiliation(s)
- Claudia Kalla
- Division of Molecular Genetics, Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany.
| | | | | | | | | | | | | | | |
Collapse
|
25
|
Arbouzova NI, Zeidler MP. JAK/STAT signalling in Drosophila: insights into conserved regulatory and cellular functions. Development 2006; 133:2605-16. [PMID: 16794031 DOI: 10.1242/dev.02411] [Citation(s) in RCA: 306] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
High levels of interspecies conservation characterise all signal transduction cascades and demonstrate the significance of these pathways over evolutionary time. Here, we review advances in the field of JAK/STAT signalling, focusing on recent developments in Drosophila. In particular, recent results from genetic and genome-wide RNAi screens, as well as studies into the developmental roles played by this pathway, highlight striking levels of physical and functional conservation in processes such as cellular proliferation, immune responses and stem cell maintenance. These insights underscore the value of model organisms for improving our understanding of this human disease-relevant pathway.
Collapse
Affiliation(s)
- Natalia I Arbouzova
- Department of Molecular Developmental Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | | |
Collapse
|
26
|
Gowda A, Byrd JC. Use of prognostic factors in risk stratification at diagnosis and time of treatment of patients with chronic lymphocytic leukemia. Curr Opin Hematol 2006; 13:266-72. [PMID: 16755224 DOI: 10.1097/01.moh.0000231425.46148.b0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW To review risk stratification strategies used in chronic lymphocytic leukemia at diagnosis to predict aggressiveness of disease and, at time of treatment, to predict duration of response. RECENT FINDINGS Several new prognostic factors can better assist clinicians in predicting the aggressiveness of chronic lymphocytic leukemia at diagnosis and the likelihood of maintaining a prolonged remission with treatment. This article reviews older prognostic factors such as beta2-microglobulin and thymidine kinase activity that have been partially validated by recently completed large studies. New prognostic factors such as interphase cytogenetics, immunoglobulin heavy-chain gene mutational analysis, and relevant secondary surrogate markers of immunoglobulin heavy-chain gene, including methylation of the zeta-associated protein gene, lipoprotein lipase overexpression, telomere length, and telomerase activity are reviewed. Some prognostic factors (interphase cytogenetics) but not others (immunoglobulin heavy-chain gene mutational status, zeta-associated protein expression) predict the duration of response to fludarabine-based combination strategies. SUMMARY Recent advances in risk stratification provide clinicians with tools to better predict outcome of chronic lymphocytic leukemia at the time of treatment and response to treatment at the time of developing symptomatic disease.
Collapse
MESH Headings
- Biomarkers, Tumor/analysis
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/diagnosis
- Leukemia, Lymphocytic, Chronic, B-Cell/metabolism
- Leukemia, Lymphocytic, Chronic, B-Cell/therapy
- Prognosis
- Risk Factors
- Treatment Outcome
Collapse
Affiliation(s)
- Aruna Gowda
- Division of Hematology and Oncology, The Ohio State University, Columbus, Ohio 43210, USA
| | | |
Collapse
|
27
|
D'Costa A, Reifegerste R, Sierra S, Moses K. The Drosophila ramshackle gene encodes a chromatin-associated protein required for cell morphology in the developing eye. Mech Dev 2006; 123:591-604. [PMID: 16904300 DOI: 10.1016/j.mod.2006.06.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2005] [Revised: 06/26/2006] [Accepted: 06/28/2006] [Indexed: 12/21/2022]
Abstract
We have identified ramshackle (ram) as a dominant suppressor of hedgehog loss-of-function in the developing Drosophila eye. We have characterized the gene and it encodes a double bromodomain protein with eight WD40 repeats. The Ram protein is localized predominantly to polytene chromosome interbands and is required for the transcription of some genes. ram is an essential gene and null mutants die during larval life. In the developing retina, ram mutant cells have morphological defects including disrupted apical junctions, disorganized actin cytoskeletons and mislocalized nuclei, which are followed by delays in cell-cycle transitions and the expression of differentiation markers. ram is a conserved gene: its vertebrate homolog (WDR9), which lies in Down's Syndrome Critical region 2 (DCR2) is also known to be associated with Brahma-Related-Gene 1 (BRG1).
Collapse
Affiliation(s)
- Allison D'Costa
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30322-3030, USA
| | | | | | | |
Collapse
|
28
|
Müller P, Kuttenkeuler D, Gesellchen V, Zeidler MP, Boutros M. Identification of JAK/STAT signalling components by genome-wide RNA interference. Nature 2005; 436:871-5. [PMID: 16094372 DOI: 10.1038/nature03869] [Citation(s) in RCA: 227] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2005] [Accepted: 05/26/2005] [Indexed: 11/09/2022]
Abstract
Signalling pathways mediating the transduction of information between cells are essential for development, cellular differentiation and homeostasis. Their dysregulation is also frequently associated with human malignancies. The Janus tyrosine kinase/signal transducer and activator of transcription (JAK/STAT) pathway represents one such signalling cascade whose evolutionarily conserved roles include cell proliferation and haematopoiesis. Here we describe a systematic genome-wide survey for genes required for JAK/STAT pathway activity. Analysis of 20,026 RNA interference (RNAi)-induced phenotypes in cultured Drosophila melanogaster haemocyte-like cells identified interacting genes encoding 4 known and 86 previously uncharacterized proteins. Subsequently, cell-based epistasis experiments were used to classify these proteins on the basis of their interaction with known components of the signalling cascade. In addition to multiple human disease gene homologues, we have found the tyrosine phosphatase Ptp61F and the Drosophila homologue of BRWD3, a bromo-domain-containing protein disrupted in leukaemia. Moreover, in vivo analysis demonstrates that disrupted dBRWD3 and overexpressed Ptp61F function as suppressors of leukaemia-like blood cell tumours. This screen represents a comprehensive identification of novel loci required for JAK/STAT signalling and provides molecular insights into an important pathway relevant for human cancer. Human homologues of identified pathway modifiers may constitute targets for therapeutic interventions.
Collapse
Affiliation(s)
- Patrick Müller
- Department of Molecular Developmental Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | | | | | | | | |
Collapse
|
29
|
Kalla C, Mertens D, Lichter P. Response. Genes Chromosomes Cancer 2005. [DOI: 10.1002/gcc.20194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
|
30
|
Yamada T, Sakisaka T, Hisata S, Baba T, Takai Y. RA-RhoGAP, Rap-activated Rho GTPase-activating protein implicated in neurite outgrowth through Rho. J Biol Chem 2005; 280:33026-34. [PMID: 16014623 DOI: 10.1074/jbc.m504587200] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Rap1 and Rho small G proteins have been implicated in the neurite outgrowth, but the functional relationship between Rap1 and Rho in the neurite outgrowth remains to be established. Here we identified a potent Rho GTPase-activating protein (GAP), RA-RhoGAP, as a direct downstream target of Rap1 in the neurite outgrowth. RA-RhoGAP has the RA and GAP domains and showed GAP activity specific for Rho, which was enhanced by the binding of the GTP-bound active form of Rap1 to the RA domain. Overexpression of RA-RhoGAP induced inactivation of Rho for promoting the neurite outgrowth in a Rap1-dependent manner. Knockdown of RA-RhoGAP reduced the Rap1-induced neurite outgrowth. These results indicate that RA-RhoGAP transduces a signal from Rap1 to Rho and regulates the neurite outgrowth.
Collapse
Affiliation(s)
- Tomohiro Yamada
- Department of Molecular Biology and Biochemistry, Osaka University Graduate School of Medicine/Faculty of Medicine, Suita 565-0871, Japan
| | | | | | | | | |
Collapse
|
31
|
Katoh M, Katoh M. ARHGAP20 gene at 11q22.3-q23.1 oncogenomic recombination hot spot. Genes Chromosomes Cancer 2005; 44:109-10; author reply 111-2. [PMID: 15880590 DOI: 10.1002/gcc.20197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
|