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Vahedi SM, Salek Ardestani S, Banabazi MH, Clark KF. Strong selection signatures for Aleutian disease tolerance acting on novel candidate genes linked to immune and cellular responses in American mink (Neogale vison). Sci Rep 2024; 14:1035. [PMID: 38200094 PMCID: PMC10781757 DOI: 10.1038/s41598-023-51039-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
Aleutian disease (AD) is a multi-systemic infectious disease in American mink (Neogale vison) caused by Aleutian mink disease virus (AMDV). This study aimed to identify candidate regions and genes underlying selection for response against AMDV using whole-genome sequence (WGS) data. Three case-control selection signatures studies were conducted between animals (N = 85) producing high versus low antibody levels against AMDV, grouped by counter immunoelectrophoresis (CIEP) test and two enzyme-linked immunosorbent assays (ELISA). Within each study, selection signals were detected using fixation index (FST) and nucleotide diversity (θπ ratios), and validated by cross-population extended haplotype homozygosity (XP-EHH) test. Within- and between-studies overlapping results were then evaluated. Within-studies overlapping results indicated novel candidate genes related to immune and cellular responses (e.g., TAP2, RAB32), respiratory system function (e.g., SPEF2, R3HCC1L), and reproduction system function (e.g., HSF2, CFAP206) in other species. Between-studies overlapping results identified three large segments under strong selection pressure, including two on chromosome 1 (chr1:88,770-98,281 kb and chr1:114,133-120,473) and one on chromosome 6 (chr6:37,953-44,279 kb). Within regions with strong signals, we found novel candidate genes involved in immune and cellular responses (e.g., homologous MHC class II genes, ITPR3, VPS52) in other species. Our study brings new insights into candidate regions and genes controlling AD response.
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Affiliation(s)
- Seyed Milad Vahedi
- Department of Animal Science and Aquaculture, Dalhousie University, Bible Hill, NS, B2N5E3, Canada
| | | | - Mohammad Hossein Banabazi
- Department of Animal Breeding and Genetics (HGEN), Centre for Veterinary Medicine and Animal Science (VHC), Swedish University of Agricultural Sciences (SLU), 75007, Uppsala, Sweden.
- Department of Biotechnology, Animal Science Research Institute of IRAN (ASRI),, Agricultural Research, Education & Extension Organization (AREEO), Karaj, 3146618361, Iran.
| | - K Fraser Clark
- Department of Animal Science and Aquaculture, Dalhousie University, Bible Hill, NS, B2N5E3, Canada.
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2
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Abstract
Intramuscular fat (IMF) content is an important economic factor in beef production. However, knowledge on the key factors controlling bovine IMF is limited. In this study, using weighted gene co-expression network analysis (WGCNA), nine modules were identified and the number of transcripts in these modules ranged from 36 to 3191. Two modules were found to be significantly associated with fat deposition and three genes (TCAP, MYH7, and TNNC1) were further identified by Protein-protein interaction (PPI), which may be the hub genes regulating bovine IMF deposition. In addition, considering the genetic variation, the PCK1 gene was found by functional enrichment analysis of overlapping genes, which was previously reported to be involved in IMF deposition. We noted that the core promoter region of buffalo PCK1 binds to transcription factors involved in lipid metabolism while cattle PCK1 binds transcription factors involved in muscle development. The results suggest that PCK1 participated in IMF deposition of buffalo and cattle in different ways. In summary, gene expression networks and new candidate genes associated with IMF deposition identified in this study. This would lay the foundation for further research into the molecular regulatory mechanisms underlying bovine IMF deposition.
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Affiliation(s)
- Xue Feng
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, School of Agriculture, Ningxia University, Yinchuan, China
| | - Cuili Pan
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, School of Agriculture, Ningxia University, Yinchuan, China
| | - Shuang Liu
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, School of Agriculture, Ningxia University, Yinchuan, China
| | - Honghong Hu
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, School of Agriculture, Ningxia University, Yinchuan, China
| | - Yun Ma
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, School of Agriculture, Ningxia University, Yinchuan, China
- College of Life Sciences, Xinyang Normal University, Xinyang, China
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3
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Kim HM, Kang B, Park S, Park H, Kim C, Lee H, Yoo M, Kweon MN, Im SH, Kim T, Roh TY. Forkhead box protein D2 suppresses colorectal cancer by reprogramming enhancer interactions. Nucleic Acids Res 2023; 51:6143-6155. [PMID: 37158258 PMCID: PMC10325893 DOI: 10.1093/nar/gkad361] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 04/19/2023] [Accepted: 04/26/2023] [Indexed: 05/10/2023] Open
Abstract
Somatic stem cells contribute to normal tissue homeostasis, and their epigenomic features play an important role in regulating tissue identities or developing disease states. Enhancers are one of the key players controlling chromatin context-specific gene expression in a spatial and temporal manner while maintaining tissue homeostasis, and their dysregulation leads to tumorigenesis. Here, epigenomic and transcriptomic analyses reveal that forkhead box protein D2 (FOXD2) is a hub for the gene regulatory network exclusive to large intestinal stem cells, and its overexpression plays a significant role in colon cancer regression. FOXD2 is positioned at the closed chromatin and facilitates mixed-lineage leukemia protein-4 (MLL4/KMT2D) binding to deposit H3K4 monomethylation. De novo FOXD2-mediated chromatin interactions rewire the regulation of p53-responsive genes and induction of apoptosis. Taken together, our findings illustrate the novel mechanistic details of FOXD2 in suppressing colorectal cancer growth and suggest its function as a chromatin-tuning factor and a potential therapeutic target for colorectal cancer.
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Affiliation(s)
- Hyo-Min Kim
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Byunghee Kang
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Sohyun Park
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Hyorim Park
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Chan Johng Kim
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Hyeonji Lee
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Mijoung Yoo
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Mi-Na Kweon
- Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea
| | - Sin-Hyeog Im
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
- Institute of Convergence Science, Yonsei University, Seoul 03722, Republic of Korea
- ImmunoBiome, Inc., Pohang 37666, Republic of Korea
| | - Tae Il Kim
- Department of Internal Medicine, Institute of Gastroenterology, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Tae-Young Roh
- Department of Life Sciences, Ewha Womans University, Seoul 03760, Republic of Korea
- Sysgenlab Inc., Pohang 37673, Republic of Korea
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4
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Ge D, Feijó A, Wen Z, Abramov AV, Lu L, Cheng J, Pan S, Ye S, Xia L, Jiang X, Vogler AP, Yang Q. Demographic History and Genomic Response to Environmental Changes in a Rapid Radiation of Wild Rats. Mol Biol Evol 2021; 38:1905-1923. [PMID: 33386846 PMCID: PMC8097305 DOI: 10.1093/molbev/msaa334] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
For organisms to survive and prosper in a harsh environment, particularly under rapid climate change, poses tremendous challenges. Recent studies have highlighted the continued loss of megafauna in terrestrial ecosystems and the subsequent surge of small mammals, such as rodents, bats, lagomorphs, and insectivores. However, the ecological partitioning of these animals will likely lead to large variation in their responses to environmental change. In the present study, we investigated the evolutionary history and genetic adaptations of white-bellied rats (Niviventer Marshall, 1976), which are widespread in the natural terrestrial ecosystems in Asia but also known as important zoonotic pathogen vectors and transmitters. The southeastern Qinghai-Tibet Plateau was inferred as the origin center of this genus, with parallel diversification in temperate and tropical niches. Demographic history analyses from mitochondrial and nuclear sequences of Niviventer demonstrated population size increases and range expansion for species in Southeast Asia, and habitat generalists elsewhere. Unexpectedly, population increases were seen in N. eha, which inhabits the highest elevation among Niviventer species. Genome scans of nuclear exons revealed that among the congeneric species, N. eha has the largest number of positively selected genes. Protein functions of these genes are mainly related to olfaction, taste, and tumor suppression. Extensive genetic modification presents a major strategy in response to global changes in these alpine species.
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Affiliation(s)
- Deyan Ge
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, China
| | - Anderson Feijó
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, China
| | - Zhixin Wen
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, China
| | - Alexei V Abramov
- Zoological Institute, Russian Academy of Sciences, Saint Petersburg, Russia.,Joint Russian-Vietnamese Tropical Research and Technological Centre, Hanoi, Vietnam
| | - Liang Lu
- State Key Laboratory for Infectious Diseases Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jilong Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, China
| | - Shengkai Pan
- CAS Key Lab of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Sicheng Ye
- Center for Computational Genomics, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Lin Xia
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, China
| | - Xuelong Jiang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Alfried P Vogler
- Department of Life Sciences, Natural History Museum, London, United Kingdom.,Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, United Kingdom
| | - Qisen Yang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Chaoyang District, Beijing, China
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Huang L, Garrett Injac S, Cui K, Braun F, Lin Q, Du Y, Zhang H, Kogiso M, Lindsay H, Zhao S, Baxter P, Adekunle A, Man TK, Zhao H, Li XN, Lau CC, Wong STC. Systems biology-based drug repositioning identifies digoxin as a potential therapy for groups 3 and 4 medulloblastoma. Sci Transl Med 2019; 10:10/464/eaat0150. [PMID: 30355798 DOI: 10.1126/scitranslmed.aat0150] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 06/26/2018] [Accepted: 10/01/2018] [Indexed: 01/01/2023]
Abstract
Medulloblastoma (MB) is the most common malignant brain tumor of childhood. Although outcomes have improved in recent decades, new treatments are still needed to improve survival and reduce treatment-related complications. The MB subtypes groups 3 and 4 represent a particular challenge due to their intragroup heterogeneity, which limits the options for "rational" targeted therapies. Here, we report a systems biology approach to drug repositioning that integrates a nonparametric, bootstrapping-based simulated annealing algorithm and a 3D drug functional network to characterize dysregulated driver signaling networks, thereby identifying potential drug candidates. From more than 1300 drug candidates studied, we identified five members of the cardiac glycoside family as potentially inhibiting the growth of groups 3 and 4 MB and subsequently confirmed this in vitro. Systemic in vivo treatment of orthotopic patient-derived xenograft (PDX) models of groups 3 and 4 MB with digoxin, a member of the cardiac glycoside family approved for the treatment of heart failure, prolonged animal survival at plasma concentrations known to be tolerated in humans. These results demonstrate the power of a systematic drug repositioning method in identifying a potential treatment for MB. Our strategy could potentially be used to accelerate the repositioning of treatments for other human cancers that lack clearly defined rational targets.
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Affiliation(s)
- Lei Huang
- Department of Systems Medicine and Bioengineering, Houston Methodist Research Institute and Cancer Center, Weill Cornell Medicine, Houston, TX 77030, USA
| | - Sarah Garrett Injac
- Preclinical Neuro-Oncology Research Program, Baylor College of Medicine, Houston, TX 77030, USA.,Texas Children's Cancer and Hematology Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kemi Cui
- Department of Systems Medicine and Bioengineering, Houston Methodist Research Institute and Cancer Center, Weill Cornell Medicine, Houston, TX 77030, USA
| | - Frank Braun
- Preclinical Neuro-Oncology Research Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Qi Lin
- Preclinical Neuro-Oncology Research Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yuchen Du
- Preclinical Neuro-Oncology Research Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Huiyuan Zhang
- Preclinical Neuro-Oncology Research Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mari Kogiso
- Preclinical Neuro-Oncology Research Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Holly Lindsay
- Preclinical Neuro-Oncology Research Program, Baylor College of Medicine, Houston, TX 77030, USA.,Texas Children's Cancer and Hematology Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sibo Zhao
- Preclinical Neuro-Oncology Research Program, Baylor College of Medicine, Houston, TX 77030, USA.,Texas Children's Cancer and Hematology Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Patricia Baxter
- Preclinical Neuro-Oncology Research Program, Baylor College of Medicine, Houston, TX 77030, USA.,Texas Children's Cancer and Hematology Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Adesina Adekunle
- Department of Pathology, Texas Children's Hospital, Houston, TX 77030, USA
| | - Tsz-Kwong Man
- Texas Children's Cancer and Hematology Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hong Zhao
- Department of Systems Medicine and Bioengineering, Houston Methodist Research Institute and Cancer Center, Weill Cornell Medicine, Houston, TX 77030, USA
| | - Xiao-Nan Li
- Preclinical Neuro-Oncology Research Program, Baylor College of Medicine, Houston, TX 77030, USA. .,Texas Children's Cancer and Hematology Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ching C Lau
- Texas Children's Cancer and Hematology Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Stephen T C Wong
- Department of Systems Medicine and Bioengineering, Houston Methodist Research Institute and Cancer Center, Weill Cornell Medicine, Houston, TX 77030, USA.
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6
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Chung YT, Pasquinelli V, Jurado JO, Wang X, Yi N, Barnes PF, Garcia VE, Samten B. Elevated Cyclic AMP Inhibits Mycobacterium tuberculosis-Stimulated T-cell IFN-γ Secretion Through Type I Protein Kinase A. J Infect Dis 2019; 217:1821-1831. [PMID: 29438524 DOI: 10.1093/infdis/jiy079] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 02/06/2018] [Indexed: 12/31/2022] Open
Abstract
Cyclic adenosine monophosphate (cAMP) is critical in immune regulation, and its role in tuberculosis infection remains unclear. We determined the levels of cAMP in peripheral blood mononuclear cells (PBMC) from tuberculosis patients and the mechanisms for cAMP suppression of IFN-γ production. PBMC from tuberculosis patients contained significantly elevated cAMP than latent tuberculosis infected subjects (LTBI), with an inverse correlation with IFN-γ production. Consistent with this, the expression of cAMP response element binding protein (CREB), activating transcription factor (ATF)-2 and c-Jun were reduced in tuberculosis patients compared with LTBI. PKA type I specific cAMP analogs inhibited Mtb-stimulated IFN-g production by PBMC through suppression of Mtb-induced IFN-γ promoter binding activities of CREB, ATF-2, and c-Jun and also miR155, the target miRNA of these transcription factors. Neutralizing both IL-10 and TGF-β1 or supplementation of IL-12 restored cAMP-suppressed IFN-g production. We conclude that increased cAMP inhibits IFN-g production through PKA type I pathway in tuberculosis infection.
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Affiliation(s)
- Yoon-Tae Chung
- Department of Pulmonary Immunology, University of Texas Health Science Center, Tyler
| | - Virginia Pasquinelli
- Centro de Investigaciones y Transferencia del Noroeste de la Provincia de Buenos Aires, Universidad Nacional del Noroeste de la Provincia de Buenos Aires- Consejo Nacional de Investigaciones Científicas y Técnicas, Junín, Argentina
| | - Javier O Jurado
- Departamento de Química Biológica, and Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Argentina
| | - Xisheng Wang
- Department of Pulmonary Immunology, University of Texas Health Science Center, Tyler
| | - Na Yi
- Department of Pulmonary Immunology, University of Texas Health Science Center, Tyler
| | - Peter F Barnes
- Department of Pulmonary Immunology, University of Texas Health Science Center, Tyler
| | - Veronica E Garcia
- Departamento de Química Biológica, and Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Argentina
| | - Buka Samten
- Department of Pulmonary Immunology, University of Texas Health Science Center, Tyler
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7
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Baranski TJ, Kraja AT, Fink JL, Feitosa M, Lenzini PA, Borecki IB, Liu CT, Cupples LA, North KE, Province MA. A high throughput, functional screen of human Body Mass Index GWAS loci using tissue-specific RNAi Drosophila melanogaster crosses. PLoS Genet 2018; 14:e1007222. [PMID: 29608557 PMCID: PMC5897035 DOI: 10.1371/journal.pgen.1007222] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 04/12/2018] [Accepted: 01/25/2018] [Indexed: 12/30/2022] Open
Abstract
Human GWAS of obesity have been successful in identifying loci associated with adiposity, but for the most part, these are non-coding SNPs whose function, or even whose gene of action, is unknown. To help identify the genes on which these human BMI loci may be operating, we conducted a high throughput screen in Drosophila melanogaster. Starting with 78 BMI loci from two recently published GWAS meta-analyses, we identified fly orthologs of all nearby genes (± 250KB). We crossed RNAi knockdown lines of each gene with flies containing tissue-specific drivers to knock down (KD) the expression of the genes only in the brain and the fat body. We then raised the flies on a control diet and compared the amount of fat/triglyceride in the tissue-specific KD group compared to the driver-only control flies. 16 of the 78 BMI GWAS loci could not be screened with this approach, as no gene in the 500-kb region had a fly ortholog. Of the remaining 62 GWAS loci testable in the fly, we found a significant fat phenotype in the KD flies for at least one gene for 26 loci (42%) even after correcting for multiple comparisons. By contrast, the rate of significant fat phenotypes in RNAi KD found in a recent genome-wide Drosophila screen (Pospisilik et al. (2010) is ~5%. More interestingly, for 10 of the 26 positive regions, we found that the nearest gene was not the one that showed a significant phenotype in the fly. Specifically, our screen suggests that for the 10 human BMI SNPs rs11057405, rs205262, rs9925964, rs9914578, rs2287019, rs11688816, rs13107325, rs7164727, rs17724992, and rs299412, the functional genes may NOT be the nearest ones (CLIP1, C6orf106, KAT8, SMG6, QPCTL, EHBP1, SLC39A8, ADPGK /ADPGK-AS1, PGPEP1, KCTD15, respectively), but instead, the specific nearby cis genes are the functional target (namely: ZCCHC8, VPS33A, RSRC2; SPDEF, NUDT3; PAGR1; SETD1, VKORC1; SGSM2, SRR; VASP, SIX5; OTX1; BANK1; ARIH1; ELL; CHST8, respectively). The study also suggests further functional experiments to elucidate mechanism of action for genes evolutionarily conserved for fat storage. Human Genome Wide Association Studies have successfully found thousands of novel genetic variants associated with many diseases. While these undoubtedly point to new biology, the field has been slowed in exploiting these new findings to reach a better understanding of exactly how they confer increased risk. Many, if not most, appear to be regulatory not coding variants, so their immediate consequence is not obvious. A real rate limiting step is even identifying which gene these variants might be regulating, and in what tissues they are operating to increase disease risk. In the absence of any other information, a first order assumption is that they may be more likely to be regulating a nearby gene, and such variants are often initially annotated by the “nearest” gene until their function is more definitively validated. Exploiting the idea that many genes may have conserved function across species, we conducted a high-throughput screen of fruit-fly orthologs of human genes nearby 78 well validated GWAS variants for human obesity, in order to more precisely identify the gene(s) of action. We systematically knocked down the function of each of these nearby genes in the brain and fat-body of the flies, raised them on a standard diet, and compared their percent body fat with control flies, in order to validate which genes showed a fat response. 43% of the time when fly orthologs existed in the region, we were able to identify the causal gene. Interestingly, nearly half the time (46%), it was not the nearest gene but another nearby one that regulated fat.
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Affiliation(s)
- Thomas J. Baranski
- Department of Internal Medicine, Division of Endocrinology, Metabolism and Lipid Research, Washington University School of Medicine, St. Louis, Missouri, United States of America
- * E-mail: (TJB); (MAP)
| | - Aldi T. Kraja
- Department of Genetics and Center for Genome Sciences and Systems Biology, Division of Statistical Genomics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Jill L. Fink
- Department of Internal Medicine, Division of Endocrinology, Metabolism and Lipid Research, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Mary Feitosa
- Department of Genetics and Center for Genome Sciences and Systems Biology, Division of Statistical Genomics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Petra A. Lenzini
- Department of Genetics and Center for Genome Sciences and Systems Biology, Division of Statistical Genomics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Ingrid B. Borecki
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Ching-Ti Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, United States of America
| | - L. Adrienne Cupples
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, United States of America
| | - Kari E. North
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Michael A. Province
- Department of Genetics and Center for Genome Sciences and Systems Biology, Division of Statistical Genomics, Washington University School of Medicine, St. Louis, Missouri, United States of America
- * E-mail: (TJB); (MAP)
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Conesa-Zamora P, García-Solano J, Turpin MDC, Sebastián-León P, Torres-Moreno D, Estrada E, Tuomisto A, Wilce J, Mäkinen MJ, Pérez-Guillermo M, Conesa A. Methylome profiling reveals functions and genes which are differentially methylated in serrated compared to conventional colorectal carcinoma. Clin Epigenetics 2015; 7:101. [PMID: 26388956 PMCID: PMC4574063 DOI: 10.1186/s13148-015-0128-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 08/31/2015] [Indexed: 12/31/2022] Open
Abstract
Background Serrated adenocarcinoma (SAC) is a recently recognized colorectal cancer (CRC) subtype accounting for 7.5–8.7 % of CRCs. It has been shown that SAC has a worse prognosis and different histological and molecular features compared to conventional carcinoma (CC) but, to date, there is no study analysing its methylome profile. Results The methylation status of 450,000 CpG sites using the Infinium Human Methylation 450 BeadChip array was investigated in 103 colorectal specimens, including 39 SACs and 34 matched CCs, from Spanish and Finnish patients. Microarray data showed a higher representation of morphogenesis-, neurogenesis-, cytoskeleton- and vesicle transport-related functions and also significant differential methylation of 15 genes, including the iodothyronine deiodinase DIO3 and the forkhead family transcription factor FOXD2 genes which were validated at the CpG, mRNA and protein level using pyrosequencing, methylation-specific PCR, quantitative polymerase chain reaction (qPCR) and immunohistochemistry. A quantification study of the methylation status of CpG sequences in FOXD2 demonstrated a novel region controlling gene expression. Moreover, differences in these markers were also evident when comparing SAC with CRC showing molecular and histological features of high-level microsatellite instability. Conclusions This methylome study demonstrates distinct epigenetic regulation patterns in SAC which are consistent to previous expression profile studies and that DIO3 and FOXD2 might be molecular targets for a specific histology-oriented treatment of CRC. Electronic supplementary material The online version of this article (doi:10.1186/s13148-015-0128-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pablo Conesa-Zamora
- Department of Pathology, Santa Lucía General University Hospital (HGUSL), C/Mezquita s/n, 30202 Cartagena, Spain ; Facultad de Ciencias de la Salud, Catholic University of Murcia (UCAM), Murcia, Spain
| | - José García-Solano
- Department of Pathology, Santa Lucía General University Hospital (HGUSL), C/Mezquita s/n, 30202 Cartagena, Spain ; Facultad de Ciencias de la Salud, Catholic University of Murcia (UCAM), Murcia, Spain
| | | | - Patricia Sebastián-León
- Department of Bioinformatics and Genomics, Centro de Investigación Príncipe Felipe (CIPF), Yúfera, 3, 46012 Valencia, Spain
| | - Daniel Torres-Moreno
- Department of Pathology, Santa Lucía General University Hospital (HGUSL), C/Mezquita s/n, 30202 Cartagena, Spain
| | - Eduardo Estrada
- Department of Social Psychology and Methodology, Autónoma University, Madrid, Spain
| | - Anne Tuomisto
- Department of Pathology, University of Oulu, Oulu, Finland
| | - Jamie Wilce
- Department of Pathology, Santa Lucía General University Hospital (HGUSL), C/Mezquita s/n, 30202 Cartagena, Spain
| | | | - Miguel Pérez-Guillermo
- Department of Pathology, Santa Lucía General University Hospital (HGUSL), C/Mezquita s/n, 30202 Cartagena, Spain
| | - Ana Conesa
- Department of Bioinformatics and Genomics, Centro de Investigación Príncipe Felipe (CIPF), Yúfera, 3, 46012 Valencia, Spain ; Microbiology and Cell Science, Institute of Food and Agricultural Science, University of Florida, Gainesville, USA
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9
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Peng SL. Interactions of Fox proteins with inflammatory transcription-factor pathways. Expert Rev Clin Immunol 2014; 2:869-76. [DOI: 10.1586/1744666x.2.6.869] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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10
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Stakkestad Ø, Larsen ACV, Kvissel AK, Eikvar S, Ørstavik S, Skålhegg BS. Protein kinase A type I activates a CRE-element more efficiently than protein kinase A type II regardless of C subunit isoform. BMC BIOCHEMISTRY 2011; 12:7. [PMID: 21303506 PMCID: PMC3060122 DOI: 10.1186/1471-2091-12-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2010] [Accepted: 02/08/2011] [Indexed: 12/16/2022]
Abstract
Background Protein kinase A type I (PKAI) and PKAII are expressed in most of the eukaryotic cells examined. PKA is a major receptor for cAMP and specificity is achieved partly through tissue-dependent expression and subcellular localization of subunits with different biochemical properties. In addition posttranslational modifications help fine tune PKA activity, distribution and interaction in the cell. In spite of this the functional significance of two forms of PKA in one cell has not been fully determined. Here we have tested the ability of PKAI and PKAII formed by expression of the regulatory (R) subunits RIα or RIIα in conjunction with Cα1 or Cβ2 to activate a co-transfected luciferace reporter gene, controlled by the cyclic AMP responsive element-binding protein (CREB) in vivo. Results We show that PKAI when expressed at equal levels as PKAII was significantly (p < 0.01) more efficient in inducing Cre-luciferace activity at saturating concentrations of cAMP. This result was obtained regardless of catalytic subunit identity. Conclusion We suggest that differential effects of PKAI and PKAII in inducing Cre-luciferace activity depend on R and not C subunit identity.
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Affiliation(s)
- Øystein Stakkestad
- Department of Nutrition, Institute for Basic Medical Sciences, University of Oslo, Sognsvannsveien 9, P,O, Box 1046 Blindern, N- 0316 OSLO, Norway
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Wijchers PJEC, Burbach JPH, Smidt MP. In control of biology: of mice, men and Foxes. Biochem J 2006; 397:233-46. [PMID: 16792526 PMCID: PMC1513289 DOI: 10.1042/bj20060387] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2006] [Revised: 05/04/2006] [Accepted: 05/05/2006] [Indexed: 12/11/2022]
Abstract
Forkhead proteins comprise a highly conserved family of transcription factors, named after the original forkhead gene in Drosophila. To date, over 100 forkhead genes have been identified in a large variety of species, all sharing the evolutionary conserved 'forkhead' DNA-binding domain, and the cloning and characterization of forkhead genes have continued in recent years. Forkhead transcription factors regulate the expression of countless genes downstream of important signalling pathways in most, if not all, tissues and cell types. Recent work has provided novel insights into the mechanisms that contribute to their functional diversity, including functional protein domains and interactions of forkheads with other transcription factors. Studies using loss- and gain-of-function models have elucidated the role of forkhead factors in developmental biology and cellular functions such as metabolism, cell division and cell survival. The importance of forkhead transcription factors is underlined by the developmental defects observed in mutant model organisms, and multiple human disorders and cancers which can be attributed to mutations within members of the forkhead gene family. This review provides a comprehensive overview of current knowledge on forkhead transcription factors, from structural organization and regulatory mechanisms to cellular and developmental functions in mice and humans. Finally, we will discuss how novel insights gained from involvement of 'Foxes' in the mechanisms underlying human pathology may create new opportunities for treatment strategies.
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Key Words
- cell cycle
- development
- forkhead
- fox
- immunoregulation
- transcription factor
- cbp, creb (camp-response-element-binding protein)-binding protein
- ccnb, cyclin b
- cdk, cyclin-dependent kinase
- cki, cdk inhibitor
- dyrk1a, dual-specificity tyrosine-phosphorylated and -regulated kinase 1a
- er, oestrogen receptor
- fha, forkhead-associated domain
- fm, foxh1 motif
- fox, forkhead box
- gadd45a, growth arrest and dna-damage-inducible protein 45α
- hdac, histone deacetylase
- iκb, inhibitory κb
- ikkβ, iκb kinase β
- mh domain, mothers against decapentaplegic homology domain
- nf-κb, nuclear factor κb
- nls, nuclear localization signal
- pkb, protein kinase b
- plk-1, polo-like kinase 1
- scf, skp2/cullin/f-box
- sgk, serum- and glucocorticoid-induced protein kinase
- smad, similar to mothers against decapentaplegic
- sid, smad-interaction domain
- sim, smad-interaction motif
- tgfβ, transforming growth factor β
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Affiliation(s)
- Patrick J E C Wijchers
- Rudolf Magnus Institute of Neuroscience, Department of Pharmacology and Anatomy, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands.
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