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Salisbury SJ, Daniels RR, Monaghan SJ, Bron JE, Villamayor PR, Gervais O, Fast MD, Sveen L, Houston RD, Robinson N, Robledo D. Keratinocytes drive the epithelial hyperplasia key to sea lice resistance in coho salmon. BMC Biol 2024; 22:160. [PMID: 39075472 PMCID: PMC11287951 DOI: 10.1186/s12915-024-01952-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 06/28/2024] [Indexed: 07/31/2024] Open
Abstract
BACKGROUND Salmonid species have followed markedly divergent evolutionary trajectories in their interactions with sea lice. While sea lice parasitism poses significant economic, environmental, and animal welfare challenges for Atlantic salmon (Salmo salar) aquaculture, coho salmon (Oncorhynchus kisutch) exhibit near-complete resistance to sea lice, achieved through a potent epithelial hyperplasia response leading to rapid louse detachment. The molecular mechanisms underlying these divergent responses to sea lice are unknown. RESULTS We characterized the cellular and molecular responses of Atlantic salmon and coho salmon to sea lice using single-nuclei RNA sequencing. Juvenile fish were exposed to copepodid sea lice (Lepeophtheirus salmonis), and lice-attached pelvic fin and skin samples were collected 12 h, 24 h, 36 h, 48 h, and 60 h after exposure, along with control samples. Comparative analysis of control and treatment samples revealed an immune and wound-healing response that was common to both species, but attenuated in Atlantic salmon, potentially reflecting greater sea louse immunomodulation. Our results revealed unique but complementary roles of three layers of keratinocytes in the epithelial hyperplasia response leading to rapid sea lice rejection in coho salmon. Our results suggest that basal keratinocytes direct the expansion and mobility of intermediate and, especially, superficial keratinocytes, which eventually encapsulate the parasite. CONCLUSIONS Our results highlight the key role of keratinocytes in coho salmon's sea lice resistance and the diverged biological response of the two salmonid host species when interacting with this parasite. This study has identified key pathways and candidate genes that could be manipulated using various biotechnological solutions to improve Atlantic salmon sea lice resistance.
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Affiliation(s)
- S J Salisbury
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK.
| | - R Ruiz Daniels
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - S J Monaghan
- Institute of Aquaculture, University of Stirling, Stirling, UK
| | - J E Bron
- Institute of Aquaculture, University of Stirling, Stirling, UK
| | - P R Villamayor
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
- Department of Genetics, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - O Gervais
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - M D Fast
- Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, Canada
| | | | - R D Houston
- Benchmark Genetics, 1 Pioneer BuildingMilton Bridge, Edinburgh TechnopolePenicuik, UK
| | - N Robinson
- Nofima AS, Tromsø, Norway.
- Sustainable Aquaculture Laboratory - Temperate and Tropical (SALTT), Deakin University, Melbourne, VIC, 3225, Australia.
| | - D Robledo
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK.
- Department of Genetics, University of Santiago de Compostela, Santiago de Compostela, Spain.
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Rajalingam A, Ganjiwale A. Identification of common genetic factors and immune-related pathways associating more than two autoimmune disorders: implications on risk, diagnosis, and treatment. Genomics Inform 2024; 22:10. [PMID: 38956704 PMCID: PMC11221123 DOI: 10.1186/s44342-024-00004-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 12/22/2023] [Indexed: 07/04/2024] Open
Abstract
Autoimmune disorders (ADs) are chronic conditions resulting from failure or breakdown of immunological tolerance, resulting in the host immune system attacking its cells or tissues. Recent studies report shared effects, mechanisms, and evolutionary origins among ADs; however, the possible factors connecting them are unknown. This study attempts to identify gene signatures commonly shared between different autoimmune disorders and elucidate their molecular pathways linking the pathogenesis of these ADs using an integrated gene expression approach. We employed differential gene expression analysis across 19 datasets of whole blood/peripheral blood cell samples with five different autoimmune disorders (rheumatoid arthritis, multiple sclerosis, systemic lupus erythematosus, Crohn's disease, and type 1 diabetes) to get nine key genes-EGR1, RUNX3, SMAD7, NAMPT, S100A9, S100A8, CYBB, GATA2, and MCEMP1 that were primarily involved in cell and leukocyte activation, leukocyte mediated immunity, IL-17, AGE-RAGE signaling in diabetic complications, prion disease, and NOD-like receptor signaling confirming its role in immune-related pathways. Combined with biological interpretations such as gene ontology (GO), pathway enrichment, and protein-protein interaction (PPI) network, our current study sheds light on the in-depth research on early detection, diagnosis, and prognosis of different ADs.
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Affiliation(s)
- Aruna Rajalingam
- Department of Life Science, Bangalore University, Bangalore, Karnataka, 560056, India
| | - Anjali Ganjiwale
- Department of Life Science, Bangalore University, Bangalore, Karnataka, 560056, India.
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SimiC enables the inference of complex gene regulatory dynamics across cell phenotypes. Commun Biol 2022; 5:351. [PMID: 35414121 PMCID: PMC9005655 DOI: 10.1038/s42003-022-03319-7] [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: 07/07/2021] [Accepted: 03/24/2022] [Indexed: 11/08/2022] Open
Abstract
Single-cell RNA-Sequencing has the potential to provide deep biological insights by revealing complex regulatory interactions across diverse cell phenotypes at single-cell resolution. However, current single-cell gene regulatory network inference methods produce a single regulatory network per input dataset, limiting their capability to uncover complex regulatory relationships across related cell phenotypes. We present SimiC, a single-cell gene regulatory inference framework that overcomes this limitation by jointly inferring distinct, but related, gene regulatory dynamics per phenotype. We show that SimiC uncovers key regulatory dynamics missed by previously proposed methods across a range of systems, both model and non-model alike. In particular, SimiC was able to uncover CAR T cell dynamics after tumor recognition and key regulatory patterns on a regenerating liver, and was able to implicate glial cells in the generation of distinct behavioral states in honeybees. SimiC hence establishes a new approach to quantitating regulatory architectures between distinct cellular phenotypes, with far-reaching implications for systems biology.
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Szczepińska T, Mollah AF, Plewczynski D. Genomic Marks Associated with Chromatin Compartments in the CTCF, RNAPII Loop and Genomic Windows. Int J Mol Sci 2021; 22:ijms222111591. [PMID: 34769020 PMCID: PMC8584073 DOI: 10.3390/ijms222111591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/21/2021] [Accepted: 10/22/2021] [Indexed: 11/28/2022] Open
Abstract
The nature of genome organization into two basic structural compartments is as yet undiscovered. However, it has been indicated to be a mechanism of gene expression regulation. Using the classification approach, we ranked genomic marks that hint at compartmentalization. We considered a broad range of marks, including GC content, histone modifications, DNA binding proteins, open chromatin, transcription and genome regulatory segmentation in GM12878 cells. Genomic marks were defined over CTCF or RNAPII loops, which are basic elements of genome 3D structure, and over 100 kb genomic windows. Experiments were carried out to empirically assess the whole set of features, as well as the individual features in classification of loops/windows, into compartment A or B. Using Monte Carlo Feature Selection and Analysis of Variance, we constructed a ranking of feature importance for classification. The best simple indicator of compartmentalization is DNase-seq open chromatin measurement for CTCF loops, H3K4me1 for RNAPII loops and H3K79me2 for genomic windows. Among DNA binding proteins, this is RUNX3 transcription factor for loops and RNAPII for genomic windows. Chromatin state prediction methods that indicate active elements like promoters, enhancers or heterochromatin enhance the prediction of loop segregation into compartments. However, H3K9me3, H4K20me1, H3K27me3 histone modifications and GC content poorly indicate compartments.
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Affiliation(s)
- Teresa Szczepińska
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland; (T.S.); (A.F.M.)
- CEZAMAT, Warsaw University of Technology, Poleczki 19, 02-822 Warsaw, Poland
| | - Ayatullah Faruk Mollah
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland; (T.S.); (A.F.M.)
- Department of Computer Science and Engineering, Aliah University, Kolkata 700160, India
| | - Dariusz Plewczynski
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland; (T.S.); (A.F.M.)
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Koszykowa 75, 00-662 Warsaw, Poland
- Correspondence: ; Tel.: +48-22-554-3654; Fax: +48-22-554-0801
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Mussbacher M, Salzmann M, Haigl B, Basílio J, Hochreiter B, Gleitsmann V, Moser B, Hoesel B, Suur BE, Puhm F, Ungerböck C, Kuttke M, Forteza MJ, Binder CJ, Ketelhuth DF, Assinger A, Schmid JA. Ikk2-mediated inflammatory activation of arterial endothelial cells promotes the development and progression of atherosclerosis. Atherosclerosis 2020; 307:21-31. [DOI: 10.1016/j.atherosclerosis.2020.06.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 05/14/2020] [Accepted: 06/05/2020] [Indexed: 10/23/2022]
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Corradin O, Cohen AJ, Luppino JM, Bayles IM, Schumacher FR, Scacheri PC. Modeling disease risk through analysis of physical interactions between genetic variants within chromatin regulatory circuitry. Nat Genet 2016; 48:1313-1320. [PMID: 27643537 PMCID: PMC5083135 DOI: 10.1038/ng.3674] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 08/22/2016] [Indexed: 12/21/2022]
Abstract
SNPs associated with disease susceptibility often reside in enhancer clusters, or super-enhancers. Constituents of these enhancer clusters cooperate to regulate target genes and often extend beyond the linkage disequilibrium (LD) blocks containing risk SNPs identified in genome-wide association studies (GWAS). We identified 'outside variants', defined as SNPs in weak LD with GWAS risk SNPs that physically interact with risk SNPs as part of a target gene's regulatory circuitry. These outside variants further explain variation in target gene expression beyond that explained by GWAS-associated SNPs. Additionally, the clinical risk associated with GWAS SNPs is considerably modified by the genotype of outside variants. Collectively, these findings suggest a potential model in which outside variants and GWAS SNPs that physically interact in 3D chromatin collude to influence target transcript levels as well as clinical risk. This model offers an additional hypothesis for the source of missing heritability for complex traits.
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Affiliation(s)
- Olivia Corradin
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA
| | - Andrea J Cohen
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Jennifer M Luppino
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Ian M Bayles
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Fredrick R Schumacher
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio, USA
| | - Peter C Scacheri
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio, USA
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio, USA
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Maccani JZ, Maccani MA. Altered placental DNA methylation patterns associated with maternal smoking: current perspectives. ADVANCES IN GENOMICS AND GENETICS 2015; 2015:205-214. [PMID: 26203295 PMCID: PMC4507353 DOI: 10.2147/agg.s61518] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The developmental origins of health and disease hypothesis states that adverse early life exposures can have lasting, detrimental effects on lifelong health. Exposure to maternal cigarette smoking during pregnancy is associated with morbidity and mortality in offspring, including increased risks for miscarriage, stillbirth, low birth weight, preterm birth, asthma, obesity, altered neurobehavior, and other conditions. Maternal cigarette smoking during pregnancy interferes with placental growth and functioning, and it has been proposed that this may occur through the disruption of normal and necessary placental epigenetic patterns. Epigenome-wide association studies have identified a number of differentially methylated placental genes that are associated with maternal smoking during pregnancy, including RUNX3, PURA, GTF2H2, GCA, GPR135, and HKR1. The placental methylation status of RUNX3 and NR3C1 has also been linked to adverse infant outcomes, including preterm birth and low birth weight, respectively. Candidate gene analyses have also found maternal smoking-associated placental methylation differences in the NR3C1, CYP1A1, HTR2A, and HSD11B2 genes, as well as in the repetitive elements LINE-1 and AluYb8. The differential methylation patterns of several genes have been confirmed to also exhibit altered gene expression patterns, including CYP1A1, CYP19A1, NR3C1, and HTR2A. Placental methylation patterns associated with maternal smoking during pregnancy may be largely gene-specific and tissue-specific and, to a lesser degree, involve global changes. It is important for future research to investigate the mechanistic roles that these differentially methylated genes may play in mediating the association between maternal smoking during pregnancy and disease in later life, as well as to elucidate the potential influence of emerging tobacco product use during pregnancy, including the use of electronic cigarettes, on placental epigenetics.
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Affiliation(s)
- Jennifer Zj Maccani
- Penn State Tobacco Center of Regulatory Science, College of Medicine, Department of Public Health Sciences, Hershey, PA, USA
| | - Matthew A Maccani
- Penn State Tobacco Center of Regulatory Science, College of Medicine, Department of Public Health Sciences, Hershey, PA, USA
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8
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Hor YT, Voon DCC, Koo JKW, Wang H, Lau WM, Ashktorab H, Chan SL, Ito Y. A role for RUNX3 in inflammation-induced expression of IL23A in gastric epithelial cells. Cell Rep 2014; 8:50-8. [PMID: 25008775 PMCID: PMC4307917 DOI: 10.1016/j.celrep.2014.06.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Revised: 01/27/2014] [Accepted: 06/04/2014] [Indexed: 12/31/2022] Open
Abstract
RUNX3 functions as a tumor suppressor in the gastric epithelium, where its inactivation is frequently observed during carcinogenesis. We identified IL23A as a RUNX3 target gene in gastric epithelial cells. This was confirmed in a series of in vitro analyses in gastric epithelial cell lines. In elucidating the underlying regulatory network, we uncovered a prominent role for the TNF-α/NF-κB pathway in activating IL23A transcription. Moreover, the activating effect of TNF-α was markedly augmented by the infection of Helicobacter pylori, the primary cause of human gastritis. Of note, H. pylori utilized the CagA/SHP2 pathway to activate IL23A, as well as the induction of the NOD1 pathway by iE-DAP. Importantly, RUNX3 synergized strongly with these physiologically relevant stimuli to induce IL23A. Lastly, we present evidence for the secretion of IL23A by gastric epithelial cells in a form that is distinct from canonical IL-23 (IL23A/IL12B).
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Affiliation(s)
- Yit Teng Hor
- Cancer Stem Cells and Biology Programme, Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore; NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 117456, Singapore
| | - Dominic Chih-Cheng Voon
- Cancer Stem Cells and Biology Programme, Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Jason Kin Wai Koo
- Cancer Stem Cells and Biology Programme, Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Huajing Wang
- Cancer Stem Cells and Biology Programme, Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Wen Min Lau
- Cancer Stem Cells and Biology Programme, Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Hassan Ashktorab
- Cancer Center and Gastroenterology Division, Department of Medicine, Howard University Hospital, 2041 Georgia Avenue N.W., Washington, DC 20060, USA
| | - Shing Leng Chan
- Cancer Stem Cells and Biology Programme, Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Yoshiaki Ito
- Cancer Stem Cells and Biology Programme, Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore.
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Maccani JZJ, Koestler DC, Houseman EA, Marsit CJ, Kelsey KT. Placental DNA methylation alterations associated with maternal tobacco smoking at the RUNX3 gene are also associated with gestational age. Epigenomics 2013; 5:619-30. [PMID: 24283877 PMCID: PMC3982305 DOI: 10.2217/epi.13.63] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
AIMS The developmental origins of health and disease hypothesis states that later-life disease may be influenced by the quality of the in utero environment. Environmental toxicants can have detrimental effects on fetal development, potentially through effects on placental development and function. Maternal smoking during pregnancy is associated with low birth weight, preterm birth and other complications, and exposure to cigarette smoke in utero has been linked to gross pathologic and molecular changes to the placenta, including differential DNA methylation in placental tissue. The aim of this study was to investigate the relationship between maternal smoking during pregnancy, methylation changes in the placenta and gestational age. MATERIALS & METHODS We used Illumina(®)'s (CA, USA) Human Methylation27 BeadChip technology platform to investigate the methylation status of 21,551 autosomal, non-SNP-associated CpG loci in DNA extracted from 206 human placentas and examined loci whose variation in methylation was associated with maternal smoking during pregnancy. RESULTS We found that methylation patterns of a number of loci within the RUNX3 gene were significantly associated with smoking during pregnancy, and one of these loci was associated with decreased gestational age (p = 0.04). CONCLUSION Our findings, demonstrating maternal smoking-induced changes in DNA methylation at specific loci, suggest a mechanism by which in utero tobacco smoke exposure could exert its detrimental effects upon the health of the fetus.
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Affiliation(s)
- Jennifer ZJ Maccani
- Department of Pathology & Laboratory Medicine, Brown University, Providence, RI, USA
| | - Devin C Koestler
- Section of Biostatistics & Epidemiology, Department of Community & Family Medicine, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | | | - Carmen J Marsit
- Section of Biostatistics & Epidemiology, Department of Community & Family Medicine, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
- Department of Pharmacology & Toxicology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Karl T Kelsey
- Department of Pathology & Laboratory Medicine, Brown University, Providence, RI, USA
- Department of Epidemiology, Brown University, Providence, RI, USA
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Zhai FX, Liu XF, Fan RF, Long ZJ, Fang ZG, Lu Y, Zheng YJ, Lin DJ. RUNX3 is involved in caspase-3-dependent apoptosis induced by a combination of 5-aza-CdR and TSA in leukaemia cell lines. J Cancer Res Clin Oncol 2011; 138:439-49. [PMID: 22179198 DOI: 10.1007/s00432-011-1113-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2011] [Accepted: 12/05/2011] [Indexed: 11/29/2022]
Abstract
PURPOSE Epigenetic therapy has had a significant impact on the management of haematologic malignancies. The aim of this study was to assess whether 5-aza-CdR and TSA inhibit the growth of leukaemia cells and induce caspase-3-dependent apoptosis by upregulating RUNX3 expression. METHODS K562 and Reh cells were treated with 5-aza-CdR, TSA or both compounds. RT-PCR and Western blot analyses were used to examine the expression of RUNX3 at the mRNA and protein levels, respectively. Immunofluorescence microscopy was used to detect the cellular location of RUNX3. Additionally, after K562 cells were transfected with RUNX3, apoptosis and proliferation were studied using Annexin V staining and MTT assays. RESULTS The expression of RUNX3 in leukaemia cell lines was markedly less than that in the controls. Demethylating drug 5-aza-CdR could induce RUNX3 expression, but the combination of TSA and 5-aza-CdR had a greater effect than did treatment with a single compound. The combination of 5-aza-CdR and TSA induced the translocation of RUNX3 from the cytoplasm into the nucleus. TSA enhanced apoptosis induced by 5-aza-CdR, and Annexin V and Hoechst 33258 staining showed that the combination induced apoptosis but not necrosis. Furthermore, apoptosis was dependent on the caspase-3 pathway. RUNX3 overexpression in K562 cells led to growth inhibition and apoptosis and potentiated the effects of 5-aza-CdR induction. CONCLUSION RUNX3 plays an important role in leukaemia cellular functions, and the induction of RUNX3-mediated effects may contribute to the therapeutic value of combination TSA and 5-aza-CdR treatment.
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Affiliation(s)
- Feng-Xian Zhai
- Department of Hematology, The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou 510630, China
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Lim B, Ju H, Kim M, Kang C. Increased genetic susceptibility to intestinal-type gastric cancer is associated with increased activity of the RUNX3 distal promoter. Cancer 2011; 117:5161-71. [PMID: 21523770 DOI: 10.1002/cncr.26161] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2011] [Revised: 02/24/2011] [Accepted: 03/10/2011] [Indexed: 01/17/2023]
Abstract
BACKGROUND The runt-related transcription factor RUNX3 plays essential roles in various types of tumors, including gastric cancer. Epigenetic changes in the methylation of the RUNX3 proximal promoter, but not common genetic changes in RUNX3, have been associated with both changes in the gene expression and development of the cancer. METHODS A case-control association study was conducted by genotyping 865 unrelated Korean subjects. Subsequent functional studies were performed to reveal functional implication of genetic association. RESULTS Several single-nucleotide polymorphisms (SNPs) in RUNX3 were significantly associated with susceptibility to intestinal-type gastric cancer (.0028 ≤ P ≤ .022) but not diffuse-type gastric cancer (.70 ≤ P ≤ .96). The risk-associated, minor variant of an intestinal-type gastric cancer-associated SNP in the RUNX3 distal promoter (rs7528484) significantly increased promoter activity in a CREB1-dependent manner. The distal promoter-derived, 33 kDa isoform of RUNX3 increased the activity of transcription factor nuclear factor kappa B (NF-κB), which had been activated by Helicobacter pylori infection, a risk factor for intestinal-type gastric cancer, and the expression of the interleukin-1β gene (IL1B), an NF-κB target genetically and functionally associated with gastric cancer. In contrast, the proximal promoter-derived, 44 kDa isoform of RUNX3 decreased both NF-κB activity and IL1B expression. CONCLUSIONS In addition to epigenetic changes in the RUNX3 proximal promoter, genetic changes in the distal promoter may be associated with susceptibility to intestinal-type gastric cancer by increasing promoter activity. Functionally, 2 RUNX3 isoforms may contribute differentially to intestinal-type gastric cancer susceptibility, at least in part through regulating NF-κB activity and IL1B expression.
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Affiliation(s)
- Byungho Lim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, Korea
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12
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Levkovitz L, Yosef N, Gershengorn MC, Ruppin E, Sharan R, Oron Y. A novel HMM-based method for detecting enriched transcription factor binding sites reveals RUNX3 as a potential target in pancreatic cancer biology. PLoS One 2010; 5:e14423. [PMID: 21203558 PMCID: PMC3008686 DOI: 10.1371/journal.pone.0014423] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2010] [Accepted: 09/10/2010] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Pancreatic adenocarcinoma (PAC) is one of the most intractable malignancies. In order to search for potential new therapeutic targets, we relied on computational methods aimed at identifying transcription factor binding sites (TFBSs) over-represented in the promoter regions of genes differentially expressed in PAC. Though many computational methods have been implemented to accomplish this, none has gained overall acceptance or produced proven novel targets in PAC. To this end we have developed DEMON, a novel method for motif detection. METHODOLOGY DEMON relies on a hidden Markov model to score the appearance of sequence motifs, taking into account all potential sites in a promoter of potentially varying binding affinities. We demonstrate DEMON's accuracy on simulated and real data sets. Applying DEMON to PAC-related data sets identifies the RUNX family as highly enriched in PAC-related genes. Using a novel experimental paradigm to distinguish between normal and PAC cells, we find that RUNX3 mRNA (but not RUNX1 or RUNX2 mRNAs) exhibits time-dependent increases in normal but not in PAC cells. These increases are accompanied by changes in mRNA levels of putative RUNX gene targets. CONCLUSIONS The integrated application of DEMON and a novel differentiation system led to the identification of a single family member, RUNX3, which together with four of its putative targets showed a robust response to a differentiation stimulus in healthy cells, whereas this regulatory mechanism was absent in PAC cells, emphasizing RUNX3 as a promising target for further studies.
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Affiliation(s)
- Liron Levkovitz
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- School of Computer Science, Tel Aviv University, Tel Aviv, Israel
| | - Nir Yosef
- School of Computer Science, Tel Aviv University, Tel Aviv, Israel
| | - Marvin C. Gershengorn
- Clinical Endocrinology Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Eytan Ruppin
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- School of Computer Science, Tel Aviv University, Tel Aviv, Israel
| | - Roded Sharan
- School of Computer Science, Tel Aviv University, Tel Aviv, Israel
- * E-mail: (RS); (YO)
| | - Yoram Oron
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- * E-mail: (RS); (YO)
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Bone KR, Gruper Y, Goldenberg D, Levanon D, Groner Y. Translation regulation of Runx3. Blood Cells Mol Dis 2010; 45:112-6. [PMID: 20554226 DOI: 10.1016/j.bcmd.2010.04.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2010] [Accepted: 04/06/2010] [Indexed: 11/25/2022]
Abstract
Runx3 protein products that are translated from the distal (P1)- and proximal (P2)-promoter transcripts appear on Western blots as a 47-46kDa doublet corresponding to full-length proteins bearing the P1- and P2-N-termini respectively. An additional 44kDa protein band, the origin and nature of which was unclear, is also detected. Transfection of full-length Runx3 cDNA bearing the P2 N-terminus (P2-cDNA) into HEK293 cells resulted in expression of both 46 and 44kDa proteins. Sequence analysis of the P2-cDNA revealed an in-frame ATG 90bp downstream (+90ATG) of the proximal +1ATG. Insertion of an N-terminal HA-tag into P2-cDNA immediately downstream of the +1ATG produced HA-tagged 46kDa and untagged 44kDa proteins, consistent with the possibility that the latter was translated through initiation at the internal +90ATG site. Deleting or blocking the activity of the +1ATG, the natural cap-dependent translation initiation site in P2-cDNA, abrogated production of the 46kDa Runx3 protein while facilitating production of the 44kDa product. These findings supported the notion that Runx3 44kDa protein resulted from internal translation initiation at the +90ATG. Northern blot and RT-PCR analyses performed on RNA from P2-cDNA transfected cells showed a single transcript and product respectively, of the expected size, ruling out the possibility that the 44kDa protein was translated from transcripts originating at a cryptic promoter or produced by alternative splicing. Taken together, the data indicate that the 44kDa protein results from translation initiation at the internal ATG and that Runx3, like its family members Runx1 and Runx2, contains a mechanism for internal mRNA translation initiation.
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Affiliation(s)
- Karen Rae Bone
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, Israel
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Zagami CJ, Zusso M, Stifani S. Runx transcription factors: lineage-specific regulators of neuronal precursor cell proliferation and post-mitotic neuron subtype development. J Cell Biochem 2009; 107:1063-72. [PMID: 19507194 DOI: 10.1002/jcb.22221] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Runt-related (RUNX) genes encode evolutionarily conserved transcription factors that play essential roles during development and adult tissue homeostasis. RUNX proteins regulate the transition from proliferation to differentiation in a variety of cell lineages. Moreover, they control the diversification of distinct cellular phenotypes in numerous tissues. Alterations of RUNX functions are associated with several cancers and other human pathologies, underscoring the vital roles of these transcription factors in adult organs. Insights into the functions and regulations of mammalian RUNX proteins have been provided mostly by studies of RUNX involvement in mechanisms of hematopoietic and skeletal development and disease. A growing number of recent investigations are revealing new functions for RUNX family members during the development of the mammalian nervous system. This review will discuss recent progress in the study of RUNX protein involvement in mammalian neural development, with emphasis on the differentiation of olfactory, sensory, and motor neuron lineages.
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The human CD6 gene is transcriptionally regulated by RUNX and Ets transcription factors in T cells. Mol Immunol 2009; 46:2226-35. [DOI: 10.1016/j.molimm.2009.04.018] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2009] [Accepted: 04/16/2009] [Indexed: 11/23/2022]
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Levanon D, Groner Y. Runx3-deficient mouse strains circa 2008: Resemblance and dissimilarity. Blood Cells Mol Dis 2009; 43:1-5. [DOI: 10.1016/j.bcmd.2009.01.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2009] [Accepted: 01/05/2009] [Indexed: 11/30/2022]
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17
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Hsu PI, Hsieh HL, Lee J, Lin LF, Chen HC, Lu PJ, Hsiao M. Loss of RUNX3 expression correlates with differentiation, nodal metastasis, and poor prognosis of gastric cancer. Ann Surg Oncol 2009; 16:1686-94. [PMID: 19290488 DOI: 10.1245/s10434-009-0428-2] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2008] [Revised: 01/03/2009] [Accepted: 02/13/2009] [Indexed: 12/28/2022]
Abstract
BACKGROUND RUNX3 is a major growth regulator of gastric epithelial cells that is involved in gastric tumorigenesis in both humans and mice. In this study, we investigated the involvement of RUNX3 in tumor progression, and in the prognosis of human gastric cancer. METHODS We analyzed the extent of RUNX3 protein expression by immunohistochemistry in 95 primary gastric adenocarcinomas, and correlated expression levels with clinicopathological parameters. We examined the effects of pFlag/RUNX3 on cell growth, apoptosis, and caspase-3 expression in AGS and SNU1 gastric cancer cell lines by colony-forming assay, terminal deoxynucleotidyl transferase (TdT)-mediate deoxyuridine triphosphatase (dUTP) nick-end labeling (TUNEL) assay, and Western blot analysis, respectively. The pFlag/RUNX3 effects on AGS invasion and migration potentials were also evaluated. RESULTS RUNX3 expression was lost in 37 (39%) cases of gastric cancer. The expression of RUNX3 in diffuse- and mixed-type cancers was less frequent than expression in intestinal-type cancer (P < 0.001 and P = 0.001, respectively). In addition, the loss of RUNX3 expression was associated with lymph node metastasis (P = 0.02), and correlated with poor gastric cancer survival (P = 0.018). The growth of gastric cancer cells was suppressed after pFlag/RUNX3 transfection. The re-expression of RUNX3 resulted in the upregulation of caspase-3 and promoted apoptosis. Furthermore, Re-expression of RUNX3 induced significant inhibitions of AGS cell invasion and migration in vitro. CONCLUSIONS This work shows that loss of RUNX3 expression is highly associated with lymph node metastasis and poor prognosis of gastric cancer. The re-expression of RUNX3 may induce apoptosis and inhibit the growth as well as invasion/migration of cancer cells. These results indicate that the targeting of the RUNX3 pathway could represent a potential modality for treating gastric cancer.
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Affiliation(s)
- Ping-I Hsu
- Department of Internal Medicine, Kaohsiung Veterans General Hospital and National Yang-Ming University, Taiwan.
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Hollingsworth JW, Maruoka S, Boon K, Garantziotis S, Li Z, Tomfohr J, Bailey N, Potts EN, Whitehead G, Brass DM, Schwartz DA. In utero supplementation with methyl donors enhances allergic airway disease in mice. J Clin Invest 2008; 118:3462-9. [PMID: 18802477 PMCID: PMC2542847 DOI: 10.1172/jci34378] [Citation(s) in RCA: 191] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2007] [Accepted: 07/30/2008] [Indexed: 11/17/2022] Open
Abstract
Asthma is a complex heritable disease that is increasing in prevalence and severity, particularly in developed countries such as the United States, where 11% of the population is affected. The contribution of environmental and genetic factors to this growing epidemic is currently not well understood. We developed the hypothesis, based on previous literature, that changes in DNA methylation resulting in aberrant gene transcription may enhance the risk of developing allergic airway disease. Our findings indicate that in mice, a maternal diet supplemented with methyl donors enhanced the severity of allergic airway disease that was inherited transgenerationally. Using a genomic approach, we discovered 82 gene-associated loci that were differentially methylated after in utero supplementation with a methyl-rich diet. These methylation changes were associated with decreased transcriptional activity and increased disease severity. Runt-related transcription factor 3 (Runx3), a gene known to negatively regulate allergic airway disease, was found to be excessively methylated, and Runx3 mRNA and protein levels were suppressed in progeny exposed in utero to a high-methylation diet. Moreover, treatment with a demethylating agent increased Runx3 gene transcription, further supporting our claim that a methyl-rich diet can affect methylation status and consequent transcriptional regulation. Our findings indicate that dietary factors can modify the heritable risk of allergic airway disease through epigenetic mechanisms during a vulnerable period of fetal development in mice.
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Affiliation(s)
- John W Hollingsworth
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, Duke University Medical Center, Durham, North Carolina 27710, USA.
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Transcriptional repression of the RUNX3/AML2 gene by the t(8;21) and inv(16) fusion proteins in acute myeloid leukemia. Blood 2008; 112:3391-402. [PMID: 18663147 DOI: 10.1182/blood-2008-02-137083] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
RUNX3/AML2 is a Runt domain transcription factor like RUNX1/AML1 and RUNX2/AML3. Regulated by 2 promoters P1 and P2, RUNX3 is frequently inactivated by P2 methylation in solid tumors. Growing evidence has suggested a role of this transcription factor in hematopoiesis. However, genetic alterations have not been reported in blood cancers. In this study on 73 acute myeloid leukemia (AML) patients (44 children and 29 adults), we first showed that high RUNX3 expression among childhood AML was associated with a shortened event-free survival, and RUNX3 was significantly underexpressed in the prognostically favorable subgroup of AML with the t(8;21) and inv(16) translocations. We further demonstrated that this RUNX3 repression was mediated not by P2 methylation, but RUNX1-ETO and CBFbeta-MYH11, the fusion products of t(8;21) and inv(16), via a novel transcriptional mechanism that acts directly or indirectly in collaboration with RUNX1, on 2 conserved RUNX binding sites in the P1 promoter. In in vitro studies, ectopically expressed RUNX1-ETO and CBFbeta-MYH11 also inhibited endogenous RUNX3 expression. Taken together, RUNX3 was the first transcriptional target found to be commonly repressed by the t(8;21) and inv(16) fusion proteins and might have an important role in core-binding factor AML.
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20
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Ito Y. RUNX genes in development and cancer: regulation of viral gene expression and the discovery of RUNX family genes. Adv Cancer Res 2008; 99:33-76. [PMID: 18037406 DOI: 10.1016/s0065-230x(07)99002-8] [Citation(s) in RCA: 168] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Mouse embryonal carcinoma (EC) cells, also called teratocarcinoma stem cells, are nonpermissive for polyomavirus growth, whereas differentiated derivatives of the cells are permissive. Mutant viruses capable of growing in EC cells can be isolated. They have genomic alterations within the viral enhancer, which is required for viral gene expression and DNA replication. This viral regulatory region was considered as a potential probe for mouse cell differentiation. The 24-bp-long A element within the enhancer was identified as a minimum element, which also shows a lower activity in EC cells compared with the differentiated cells. Transcription factors PEA1/AP1, PEA2/PEBP2, and PEA3/ETS were identified as A element-binding proteins. All of them are absent in EC cells and induced to be expressed when the cells are differentiated. Although PEBP2 has a weaker transactivation activity compared with other two, it is essential for the enhancer function of the A element. Purification and cDNA cloning revealed that PEBP2 has two subunits, DNA-binding alpha (PEBP2alpha) and non-DNA-binding beta (PEBP2beta). PEBP2alpha was found to be highly homologous to a Drosophila segmentation gene, runt, and a human gene AML1 that was identified as a part of the fusion gene, AML1/ETO (MTG8) generated by t(8;21) chromosome translocation associated with acute myelogenous leukemia (AML). Core-binding factor (CBF), which interacts with a murine retrovirus enhancer, was found to be identical to PEBP2. runt, PEBP2alpha and AML1 are now termed RUNX family, which are involved in cell specification during development. There are three mammalian RUNX genes, RUNX1, RUNX2, and RUNX3. RUNX1 is essential for generation of hematopoietic stem cells and is involved in human leukemia. RUNX2 is essential for skeletal development and has an oncogenic potential. RUNX3 is expressed in wider ranges of tissues and has multiple roles. Among others, RUNX3 is a major tumor suppressor of gastric and many other solid tumors.
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Affiliation(s)
- Yoshiaki Ito
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
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Gregg JP, Lit L, Baron CA, Hertz-Picciotto I, Walker W, Davis RA, Croen LA, Ozonoff S, Hansen R, Pessah IN, Sharp FR. Gene expression changes in children with autism. Genomics 2007; 91:22-9. [PMID: 18006270 DOI: 10.1016/j.ygeno.2007.09.003] [Citation(s) in RCA: 130] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2007] [Revised: 09/11/2007] [Accepted: 09/15/2007] [Indexed: 01/30/2023]
Abstract
The objective of this study was to identify gene expression differences in blood differences in children with autism (AU) and autism spectrum disorder (ASD) compared to general population controls. Transcriptional profiles were compared with age- and gender-matched, typically developing children from the general population (GP). The AU group was subdivided based on a history of developmental regression (A-R) or a history of early onset (A-E without regression). Total RNA from blood was processed on human Affymetrix microarrays. Thirty-five children with AU (17 with early onset autism and 18 with autism with regression) and 14 ASD children (who did not meet criteria for AU) were compared to 12 GP children. Unpaired t tests (corrected for multiple comparisons with a false discovery rate of 0.05) detected a number of genes that were regulated more than 1.5-fold for AU versus GP (n=55 genes), for A-E versus GP (n=140 genes), for A-R versus GP (n=20 genes), and for A-R versus A-E (n=494 genes). No genes were significantly regulated for ASD versus GP. There were 11 genes shared between the comparisons of all autism subgroups to GP (AU, A-E, and A-R versus GP) and these genes were all expressed in natural killer cells and many belonged to the KEGG natural killer cytotoxicity pathway (p=0.02). A subset of these genes (n=7) was tested with qRT-PCR and all genes were found to be differentially expressed (p<0.05). We conclude that the gene expression data support emerging evidence for abnormalities in peripheral blood leukocytes in autism that could represent a genetic and/or environmental predisposition to the disorder.
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Affiliation(s)
- Jeffrey P Gregg
- Department of Pathology, University of California at Davis Medical Center, Sacramento, CA 95817, USA. University of California at Davis, Davis, CA 95616, USA.
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Abstract
In the last decade, the identification of enzymes that regulate acetylation of histones and nonhistone proteins has revealed the key role of dynamic acetylation and deacetylation in various cellular processes. Mammalian histone deacetylases (HDACs), which catalyse the removal of acetyl groups from lysine residues, are grouped into three classes, on the basis of similarity to yeast counterparts. An abundance of experimental evidence has established class IIa HDACs as crucial transcriptional regulators of various developmental and differentiation processes. In the past 5 years, a tremendous effort has been dedicated to characterizing the regulation of these enzymes. In this review, we summarize the latest discoveries in the field and discuss the molecular and structural determinants of class IIa HDACs regulation. Finally, we emphasize that comprehension of the mechanisms underlying class IIa HDAC functions is essential for potential therapeutic applications.
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Affiliation(s)
- M Martin
- Cellular and Molecular Biology Unit, FUSAGx, Gembloux, Belgium
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