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Liadaki K, Zafiriou E, Giannoulis T, Alexouda S, Chaidaki K, Gidarokosta P, Roussaki-Schulze AV, Tsiogkas SG, Daponte A, Mamuris Z, Bogdanos DP, Moschonas NK, Sarafidou T. PDE4 Gene Family Variants Are Associated with Response to Apremilast Treatment in Psoriasis. Genes (Basel) 2024; 15:369. [PMID: 38540428 PMCID: PMC10970167 DOI: 10.3390/genes15030369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/07/2024] [Accepted: 03/14/2024] [Indexed: 06/14/2024] Open
Abstract
Moderate-to-severe psoriasis (Ps) treatment includes systemic drugs and biological agents. Apremilast, a small molecule primarily metabolized by cytochrome CYP3A4, modulates the immune system by specifically inhibiting phosphodiesterase type 4 (PDE4) isoforms and is currently used for the treatment of Ps and psoriatic arthritis (PsA). Clinical trials and real-world data showed variable efficacy in response among Ps patients underlying the need for personalized therapy. This study implements a candidate-gene and a network-based approach to identify genetic markers associated with apremilast response in forty-nine Greek Ps patients. Our data revealed an association of sixty-four SNPs within or near PDE4 and CYP3A4 genes, four SNPs in ncRNAs ANRIL, LINC00941 and miR4706, which influence the abundance or function of PDE4s, and thirty-three SNPs within fourteen genes whose protein products either interact directly with PDE4 proteins or constitute components of the cAMP signaling pathway which is modulated by PDE4s. Notably, fifty-six of the aforementioned SNPs constitute eQTLs for the respective genes in relevant to psoriasis tissues/cells implying that these variants could be causal. Our analysis provides a number of novel genetic variants that, upon validation in larger cohorts, could be utilized as predictive markers regarding the response of Ps patients to apremilast treatment.
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Affiliation(s)
- Kalliopi Liadaki
- Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis, 41500 Larissa, Greece; (K.L.); (Z.M.)
| | - Efterpi Zafiriou
- Department of Dermatology, Faculty of Medicine, School of Health Sciences, University of Thessaly, Viopolis, 41500 Larissa, Greece; (E.Z.); (K.C.); (P.G.); (A.-V.R.-S.)
| | | | - Sofia Alexouda
- Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis, 41500 Larissa, Greece; (K.L.); (Z.M.)
| | - Kleoniki Chaidaki
- Department of Dermatology, Faculty of Medicine, School of Health Sciences, University of Thessaly, Viopolis, 41500 Larissa, Greece; (E.Z.); (K.C.); (P.G.); (A.-V.R.-S.)
| | - Polyxeni Gidarokosta
- Department of Dermatology, Faculty of Medicine, School of Health Sciences, University of Thessaly, Viopolis, 41500 Larissa, Greece; (E.Z.); (K.C.); (P.G.); (A.-V.R.-S.)
| | - Angeliki-Viktoria Roussaki-Schulze
- Department of Dermatology, Faculty of Medicine, School of Health Sciences, University of Thessaly, Viopolis, 41500 Larissa, Greece; (E.Z.); (K.C.); (P.G.); (A.-V.R.-S.)
| | - Sotirios G. Tsiogkas
- Department of Rheumatology and Clinical Immunology, Faculty of Medicine, School of Health Sciences, University of Thessaly, Viopolis, 41500 Larissa, Greece; (S.G.T.); (A.D.); (D.P.B.)
| | - Athina Daponte
- Department of Rheumatology and Clinical Immunology, Faculty of Medicine, School of Health Sciences, University of Thessaly, Viopolis, 41500 Larissa, Greece; (S.G.T.); (A.D.); (D.P.B.)
| | - Zissis Mamuris
- Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis, 41500 Larissa, Greece; (K.L.); (Z.M.)
| | - Dimitrios P. Bogdanos
- Department of Rheumatology and Clinical Immunology, Faculty of Medicine, School of Health Sciences, University of Thessaly, Viopolis, 41500 Larissa, Greece; (S.G.T.); (A.D.); (D.P.B.)
| | - Nicholas K. Moschonas
- School of Medicine, University of Patras, 26500 Patras, Greece
- Foundation for Research and Technology Hellas, Institute of Chemical Engineering Sciences, 26504 Patras, Greece
| | - Theologia Sarafidou
- Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis, 41500 Larissa, Greece; (K.L.); (Z.M.)
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Wang J, Shi C, Cheng M, Lu Y, Zhang X, Li F, Sun Y, Li X, Li X, Zeng Y, Wang C, Cao X. Effects of the Zbtb1 Gene on Chromatin Spatial Structure and Lymphatic Development: Combined Analysis of Hi-C, ATAC-Seq and RNA-Seq. Front Cell Dev Biol 2022; 10:874525. [PMID: 35547816 PMCID: PMC9081333 DOI: 10.3389/fcell.2022.874525] [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: 02/15/2022] [Accepted: 03/30/2022] [Indexed: 11/15/2022] Open
Abstract
Zbtb1 (zinc finger and BTB domain containing 1) is a member of mammalian zbtb gene family. A series of bioinformatics analysis was carried out for the EL4 cell and the Zbtb1-deficient EL4 cell by Hi-C, ATAC-seq and RNA-seq techniques. Finally, Hi-C results showed that the intensity of chromatin interaction in the deletion group decreased with distance, the degree of chromosome interaction decreased significantly, the AB division region changed significantly, and the compactness of TAD structure decreased; The results of ATAC-seq showed that the open area and degree of chromatin in the deletion group decreased; 7778 differentially expressed mRNAs were found by RNA-seq. Our experimental results for the first time expounded the significance of Zbtb1 gene for T cell development, lymphocyte production and apoptosis from the aspects of chromosome spatial structure and chromatin opening degree, and provided relevant theoretical basis and data support for the in-depth study of related Zbtb1 genes in the future.
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Affiliation(s)
- Junhong Wang
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China
- Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Agricultural University, Changchun, China
- Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, China
- Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Chunwei Shi
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China
- Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Agricultural University, Changchun, China
- Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, China
- Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Mingyang Cheng
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China
- Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Agricultural University, Changchun, China
- Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, China
- Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Yiyuan Lu
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China
- Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Agricultural University, Changchun, China
- Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, China
- Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Xiaoyu Zhang
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China
- Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Agricultural University, Changchun, China
- Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, China
- Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Fengdi Li
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China
- Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Agricultural University, Changchun, China
- Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, China
- Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Yu Sun
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China
- Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Agricultural University, Changchun, China
- Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, China
- Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Xiaoxu Li
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China
- Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Agricultural University, Changchun, China
- Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, China
- Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Xinyang Li
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China
- Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Agricultural University, Changchun, China
- Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, China
- Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, China
| | - Yan Zeng
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China
- Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Agricultural University, Changchun, China
- Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, China
- Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, China
- *Correspondence: Yan Zeng, ; Chunfeng Wang, ; Xin Cao,
| | - Chunfeng Wang
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China
- Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Agricultural University, Changchun, China
- Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, China
- Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, China
- *Correspondence: Yan Zeng, ; Chunfeng Wang, ; Xin Cao,
| | - Xin Cao
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, China
- Jilin Provincial Key Laboratory of Animal Microecology and Healthy Breeding, Jilin Agricultural University, Changchun, China
- Jilin Provincial Engineering Research Center of Animal Probiotics, Jilin Agricultural University, Changchun, China
- Key Laboratory of Animal Production and Product Quality Safety of Ministry of Education, Jilin Agricultural University, Changchun, China
- *Correspondence: Yan Zeng, ; Chunfeng Wang, ; Xin Cao,
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Hernández-Quiles M, Baak R, Borgman A, den Haan S, Sobrevals Alcaraz P, van Es R, Kiss-Toth E, Vos H, Kalkhoven E. Comprehensive Profiling of Mammalian Tribbles Interactomes Implicates TRIB3 in Gene Repression. Cancers (Basel) 2021; 13:6318. [PMID: 34944947 PMCID: PMC8699236 DOI: 10.3390/cancers13246318] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/10/2021] [Accepted: 12/13/2021] [Indexed: 12/30/2022] Open
Abstract
The three human Tribbles (TRIB) pseudokinases have been implicated in a plethora of signaling and metabolic processes linked to cancer initiation and progression and can potentially be used as biomarkers of disease and prognosis. While their modes of action reported so far center around protein-protein interactions, the comprehensive profiling of TRIB interactomes has not been reported yet. Here, we have developed a robust mass spectrometry (MS)-based proteomics approach to characterize Tribbles' interactomes and report a comprehensive assessment and comparison of the TRIB1, -2 and -3 interactomes, as well as domain-specific interactions for TRIB3. Interestingly, TRIB3, which is predominantly localized in the nucleus, interacts with multiple transcriptional regulators, including proteins involved in gene repression. Indeed, we found that TRIB3 repressed gene transcription when tethered to DNA in breast cancer cells. Taken together, our comprehensive proteomic assessment reveals previously unknown interacting partners and functions of Tribbles proteins that expand our understanding of this family of proteins. In addition, our findings show that MS-based proteomics provides a powerful tool to unravel novel pseudokinase biology.
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Affiliation(s)
- Miguel Hernández-Quiles
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands; (M.H.-Q.); (R.B.); (A.B.); (S.d.H.)
| | - Rosalie Baak
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands; (M.H.-Q.); (R.B.); (A.B.); (S.d.H.)
| | - Anouska Borgman
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands; (M.H.-Q.); (R.B.); (A.B.); (S.d.H.)
| | - Suzanne den Haan
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands; (M.H.-Q.); (R.B.); (A.B.); (S.d.H.)
| | - Paula Sobrevals Alcaraz
- Oncode Institute and Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands; (P.S.A.); (R.v.E.); (H.V.)
| | - Robert van Es
- Oncode Institute and Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands; (P.S.A.); (R.v.E.); (H.V.)
| | - Endre Kiss-Toth
- Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield S10 2TN, UK;
| | - Harmjan Vos
- Oncode Institute and Molecular Cancer Research, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands; (P.S.A.); (R.v.E.); (H.V.)
| | - Eric Kalkhoven
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands; (M.H.-Q.); (R.B.); (A.B.); (S.d.H.)
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Rakhra G, Rakhra G. Zinc finger proteins: insights into the transcriptional and post transcriptional regulation of immune response. Mol Biol Rep 2021; 48:5735-5743. [PMID: 34304391 PMCID: PMC8310398 DOI: 10.1007/s11033-021-06556-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 07/08/2021] [Indexed: 12/18/2022]
Abstract
BACKGROUND Zinc finger proteins encompass one of the unique and large families of proteins with diversified biological functions in the human body. These proteins are primarily considered to be DNA binding transcription factors; however, owing to the diverse array of zinc-finger domains, they are able to interact with molecules other than DNA like RNA, proteins, lipids and PAR (poly-ADP-ribose). Evidences from recent scientific studies have provided an insight into the potential functions of zinc finger proteins in immune system regulation both at the transcriptional and post transcriptional level. However, the mechanism and importance of zinc finger proteins in the regulation of immune response is not very well defined and understood. This review highlights in detail the importance of zinc finger proteins in the regulation of immune system at transcriptional and post transcriptional level. CONCLUSION Different types of zinc finger proteins are involved in immune system regulation and their mechanism of regulation is discussed herewith.
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Affiliation(s)
- Gurseen Rakhra
- Department of Nutrition & Dietetics, Faculty of Allied Health Sciences, Manav Rachna International Institute of Research & Studies, Faridabad, Haryana, 121004, India
| | - Gurmeen Rakhra
- Department of Biochemistry, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, India.
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Cheng ZY, He TT, Gao XM, Zhao Y, Wang J. ZBTB Transcription Factors: Key Regulators of the Development, Differentiation and Effector Function of T Cells. Front Immunol 2021; 12:713294. [PMID: 34349770 PMCID: PMC8326903 DOI: 10.3389/fimmu.2021.713294] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 07/06/2021] [Indexed: 12/12/2022] Open
Abstract
The development and differentiation of T cells represents a long and highly coordinated, yet flexible at some points, pathway, along which the sequential and dynamic expressions of different transcriptional factors play prominent roles at multiple steps. The large ZBTB family comprises a diverse group of transcriptional factors, and many of them have emerged as critical factors that regulate the lineage commitment, differentiation and effector function of hematopoietic-derived cells as well as a variety of other developmental events. Within the T-cell lineage, several ZBTB proteins, including ZBTB1, ZBTB17, ZBTB7B (THPOK) and BCL6 (ZBTB27), mainly regulate the development and/or differentiation of conventional CD4/CD8 αβ+ T cells, whereas ZBTB16 (PLZF) is essential for the development and function of innate-like unconventional γδ+ T & invariant NKT cells. Given the critical role of T cells in host defenses against infections/tumors and in the pathogenesis of many inflammatory disorders, we herein summarize the roles of fourteen ZBTB family members in the development, differentiation and effector function of both conventional and unconventional T cells as well as the underlying molecular mechanisms.
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Affiliation(s)
- Zhong-Yan Cheng
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Ting-Ting He
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Xiao-Ming Gao
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
| | - Ying Zhao
- Department of Pathophysiology, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
| | - Jun Wang
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, China
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Li J, Su X, Wang Y, Yang W, Pan Y, Su C, Zhang X. Genome-wide identification and expression analysis of the BTB domain-containing protein gene family in tomato. Genes Genomics 2017; 40:1-15. [PMID: 29892895 DOI: 10.1007/s13258-017-0604-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 08/03/2017] [Indexed: 01/01/2023]
Abstract
BTB (broad-complex, tramtrack, and bric-a-brac) family proteins are characterized by the presence of a protein-protein interaction BTB domain. BTB proteins have diverse functions, including transcriptional regulation, protein degradation, chromatin remodeling, and cytoskeletal regulation. However, little is known about this gene family in tomato (Solanum lycopersicum), the most important model plant for crop species. In this study, 38 BTB genes were identified based on tomato whole-genome sequence. Phylogenetic analysis of BTB proteins in tomato revealed that SlBTB proteins could be divided into at least 4 subfamilies. The SlBTB proteins contains 1-3 BTB domains, and several other types of functional domains, including KCTD (Potassium channel tetramerization domain-containing), the MATH (meprin and TRAF homology), ANK (Ankyrin repeats), NPR1 (nonexpressor of pathogenesis-related proteins1), NPH3 (Nonphototropic Hypocotyl 3), TAZ zinc finger, C-terminal Kelch, Skp1 and Arm (Armadillo/beta-catenin-like repeat) domains are also found in some tomato BTB proteins. Moreover, their expression patterns in tissues/stages, in response to different abiotic stress treatments and hormones were also investigated. This study provides the first comprehensive analysis of BTB gene family in the tomato genome. The data will undoubtedly be useful for better understanding the potential functions of BTB genes, and their possible roles in mediating hormone cross-talk and abiotic stress in tomato as well as in some other relative species.
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Affiliation(s)
- Jinhua Li
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education; College of Horticulture and Landscape Architechture, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing, 400715, China
| | - Xiaoxing Su
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education; College of Horticulture and Landscape Architechture, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing, 400715, China
| | - Yinlei Wang
- Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Wei Yang
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education; College of Horticulture and Landscape Architechture, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing, 400715, China
| | - Yu Pan
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education; College of Horticulture and Landscape Architechture, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing, 400715, China
| | - Chenggang Su
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education; College of Horticulture and Landscape Architechture, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing, 400715, China
| | - Xingguo Zhang
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education; College of Horticulture and Landscape Architechture, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing, 400715, China.
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Genome wide microarray based expression profiles associated with BmNPV resistance and susceptibility in Indian silkworm races of Bombyx mori. Genomics 2015; 106:393-403. [PMID: 26376410 DOI: 10.1016/j.ygeno.2015.09.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 08/19/2015] [Accepted: 09/09/2015] [Indexed: 11/23/2022]
Abstract
The molecular mechanism involved in BmNPV resistance was investigated using a genome wide microarray in midgut tissue of Indian silkworm Bombyx mori. In resistant race (Sarupat), 735 genes up-regulated and 589 genes down-regulated at 12 h post BmNPV infection. Similarly, in case of susceptible race (CSR-2), 2183 genes up-regulated and 2115 genes down-regulated. Among these, nine up-regulated and eight down-regulated genes were validated using real-time qPCR analysis. In Sarupat, vacuolar protein sorting associated, Xfin-like protein and carboxypeptidase E-like protein genes significantly up-regulated in infected midgut; prominently down-regulated genes were glutamate receptor ionotropic kainite 2-like, BTB/POZ domain and transferrin. Considerably up-regulated genes in the CSR-2 were peptidoglycan recognition protein S6 precursor and rapamycin while the conspicuous down-regulated genes were facilitated trehalose transporter and zinc transporter ZIP1-like gene. The up-regulation of genes in resistant race after BmNPV infection indicates their possible role in antiviral immune response.
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Gupta VA, Beggs AH. Kelch proteins: emerging roles in skeletal muscle development and diseases. Skelet Muscle 2014; 4:11. [PMID: 24959344 PMCID: PMC4067060 DOI: 10.1186/2044-5040-4-11] [Citation(s) in RCA: 103] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 05/06/2014] [Indexed: 12/11/2022] Open
Abstract
Our understanding of genes that cause skeletal muscle disease has increased tremendously over the past three decades. Advances in approaches to genetics and genomics have aided in the identification of new pathogenic mechanisms in rare genetic disorders and have opened up new avenues for therapeutic interventions by identification of new molecular pathways in muscle disease. Recent studies have identified mutations of several Kelch proteins in skeletal muscle disorders. The Kelch superfamily is one of the largest evolutionary conserved gene families. The 66 known family members all possess a Kelch-repeat containing domain and are implicated in diverse biological functions. In skeletal muscle development, several Kelch family members regulate the processes of proliferation and/or differentiation resulting in normal functioning of mature muscles. Importantly, many Kelch proteins function as substrate-specific adaptors for Cullin E3 ubiquitin ligase (Cul3), a core component of the ubiquitin-proteasome system to regulate the protein turnover. This review discusses the emerging roles of Kelch proteins in skeletal muscle function and disease.
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Affiliation(s)
- Vandana A Gupta
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, 300 Longwood Ave., Boston, MA 02115, USA
| | - Alan H Beggs
- Division of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, 300 Longwood Ave., Boston, MA 02115, USA
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Identification and Expression Profiling of the BTB Domain-Containing Protein Gene Family in the Silkworm, Bombyx mori. Int J Genomics 2014; 2014:865065. [PMID: 24895545 PMCID: PMC4033408 DOI: 10.1155/2014/865065] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Revised: 04/05/2014] [Accepted: 04/07/2014] [Indexed: 11/30/2022] Open
Abstract
The BTB domain is a conserved protein-protein interaction motif. In this study, we identified 56 BTB domain-containing protein genes in the silkworm, in addition to 46 in the honey bee, 55 in the red flour beetle, and 53 in the monarch butterfly. Silkworm BTB protein genes were classified into nine subfamilies according to their domain architecture, and most of them could be mapped on the different chromosomes. Phylogenetic analysis suggests that silkworm BTB protein genes may have undergone a duplication event in three subfamilies: BTB-BACK-Kelch, BTB-BACK-PHR, and BTB-FLYWCH. Comparative analysis demonstrated that the orthologs of each of 13 BTB protein genes present a rigorous orthologous relationship in the silkworm and other surveyed insects, indicating conserved functions of these genes during insect evolution. Furthermore, several silkworm BTB protein genes exhibited sex-specific expression in larval tissues or at different stages during metamorphosis. These findings not only contribute to a better understanding of the evolution of insect BTB protein gene families but also provide a basis for further investigation of the functions of BTB protein genes in the silkworm.
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Aulakh SS, Veilleux RE, Dickerman AW, Tang G, Flinn BS. Characterization and RNA-seq analysis of underperformer, an activation-tagged potato mutant. PLANT MOLECULAR BIOLOGY 2014; 84:635-658. [PMID: 24306493 DOI: 10.1007/s11103-013-0159-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Accepted: 11/21/2013] [Indexed: 06/02/2023]
Abstract
The potato cv. Bintje and a Bintje activation-tagged mutant, underperformer (up) were compared. Mutant up plants grown in vitro were dwarf, with abundant axillary shoot growth, greater tuber yield, altered tuber traits and early senescence compared to wild type. Under in vivo conditions, the dwarf and early senescence phenotypes of the mutant remained, but the up plants exhibited a lower tuber yield and fewer axillary shoots compared to wild type. Southern blot analyses indicated a single T-DNA insertion in the mutant, located on chromosome 10. Initial PCR-based gene expression studies indicated transcriptional activation/repression of several genes in the mutant flanking the insertion. The gene immediately flanking the right border of the T-DNA insertion, which encoded an uncharacterized Broad complex, Tramtrac, Bric-a-brac; also known as Pox virus and Zinc finger (BTB/POZ) domain-containing protein (StBTB/POZ1) containing an Armadillo repeat region, was up-regulated in the mutant. Global gene expression comparisons between Bintje and up using RNA-seq on leaves from 60 day-old plants revealed a dataset of over 1,600 differentially expressed genes. Gene expression analyses suggested a variety of biological processes and pathways were modified in the mutant, including carbohydrate and lipid metabolism, cell division and cell cycle activity, biotic and abiotic stress responses, and proteolysis.
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Kim H, Dejsuphong D, Adelmant G, Ceccaldi R, Yang K, Marto JA, D'Andrea AD. Transcriptional repressor ZBTB1 promotes chromatin remodeling and translesion DNA synthesis. Mol Cell 2014; 54:107-118. [PMID: 24657165 DOI: 10.1016/j.molcel.2014.02.017] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 01/07/2014] [Accepted: 02/07/2014] [Indexed: 12/27/2022]
Abstract
Timely DNA replication across damaged DNA is critical for maintaining genomic integrity. Translesion DNA synthesis (TLS) allows bypass of DNA lesions using error-prone TLS polymerases. The E3 ligase RAD18 is necessary for proliferating cell nuclear antigen (PCNA) monoubiquitination and TLS polymerase recruitment; however, the regulatory steps upstream of RAD18 activation are less understood. Here, we show that the UBZ4 domain-containing transcriptional repressor ZBTB1 is a critical upstream regulator of TLS. The UBZ4 motif is required for PCNA monoubiquitination and survival after UV damage. ZBTB1 associates with KAP-1, a transcriptional repressor whose phosphorylation relaxes chromatin after DNA damage. ZBTB1 depletion impairs formation of phospho-KAP-1 at UV damage sites and reduces RAD18 recruitment. Furthermore, phosphorylation of KAP-1 is necessary for efficient PCNA modification. We propose that ZBTB1 is required for localizing phospho-KAP-1 to chromatin and enhancing RAD18 accessibility. Collectively, our study implicates a ubiquitin-binding protein in orchestrating chromatin remodeling during DNA repair.
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Affiliation(s)
- Hyungjin Kim
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Donniphat Dejsuphong
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Guillaume Adelmant
- Blais Proteomic Center, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Raphael Ceccaldi
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Kailin Yang
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jarrod A Marto
- Blais Proteomic Center, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Alan D D'Andrea
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
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12
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The role of BTB-zinc finger transcription factors during T cell development and in the regulation of T cell-mediated immunity. Curr Top Microbiol Immunol 2014; 381:21-49. [PMID: 24850219 DOI: 10.1007/82_2014_374] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The proper regulation of the development and function of peripheral helper and cytotoxic T cell lineages is essential for T cell-mediated adaptive immunity. Progress made during the last 10-15 years led to the identification of several transcription factors and transcription factor networks that control the development and function of T cell subsets. Among the transcription factors identified are also several members of the so-called BTB/POZ domain containing zinc finger (ZF) transcription factor family (BTB-ZF), and important roles of BTB-ZF factors have been described. In this review, we will provide an up-to-date overview about the role of BTB-ZF factors during T cell development and in peripheral T cells.
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13
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Gene expression profiling in treatment-naive schizophrenia patients identifies abnormalities in biological pathways involving AKT1 that are corrected by antipsychotic medication. Int J Neuropsychopharmacol 2013; 16:1483-503. [PMID: 23442539 DOI: 10.1017/s1461145713000035] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Distinct gene expression profiles can be detected in peripheral blood mononuclear cells (PBMCs) in patients with schizophrenia; however, little is known about the effects of antipsychotic medication. This study compared gene expression profiles in PMBCs from treatment-naive patients with schizophrenia before and after antipsychotic drug treatment. PBMCs were obtained from 10 treatment-naive schizophrenia patients before and 6 wk after initiating antipsychotic drug treatment and compared to PMBCs collected from 11 healthy community volunteers. Genome-wide expression profiling was conducted using Illumina HumanHT-12 expression bead arrays and analysed using significance analysis of microarrays. This analysis identified 624 genes with altered expression (208 up-regulated, 416 down-regulated) prior to antipsychotic treatment (p < 0.05) including schizophrenia-associated genes AKT1, DISC1 and DGCR6. After 6-8 wk treatment of patients with risperidone or risperidone in combination with haloperidol, only 106 genes were altered, suggesting that the treatment corrected the expression of a large proportion of genes back to control levels. However, 67 genes continued to show the same directional change in expression after treatment. Ingenuity® pathway analysis and gene set enrichment analysis implicated dysregulation of biological functions and pathways related to inflammation and immunity in patients with schizophrenia. A number of the top canonical pathways dysregulated in treatment-naive patients signal through AKT1 that was up-regulated. After treatment, AKT1 returned to control levels and less dysregulation of these canonical pathways was observed. This study supports immune dysfunction and pathways involving AKT1 in the aetiopathophysiology of schizophrenia and their response to antipsychotic medication.
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14
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Davis EJ, Lachaud C, Appleton P, Macartney TJ, Näthke I, Rouse J. DVC1 (C1orf124) recruits the p97 protein segregase to sites of DNA damage. Nat Struct Mol Biol 2012; 19:1093-100. [PMID: 23042607 DOI: 10.1038/nsmb.2394] [Citation(s) in RCA: 116] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Accepted: 08/30/2012] [Indexed: 02/07/2023]
Abstract
Ubiquitin-binding domains (UBDs) are crucial for recruiting many proteins to sites of DNA damage. Here we characterize C1orf124 (Spartan; referred to as DVC1), which has an UBZ4-type UBD found predominantly in DNA repair proteins. DVC1 associates with DNA replication factories and localizes to sites of DNA damage in human cells, in a manner that requires the ability of the DVC1 UBZ domain to bind to ubiquitin polymers in vitro and a conserved PCNA-interacting motif. DVC1 interacts with the p97 protein 'segregase'. We show that DVC1 recruits p97 to sites of DNA damage, where we propose that p97 facilitates the extraction of the translesion synthesis (TLS) polymerase (Pol) η during DNA repair to prevent excessive TLS and limit the incidence of mutations induced by DNA damage. We introduce DVC1 as a regulator of cellular responses to DNA damage that prevents mutations when DNA damage occurs.
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Affiliation(s)
- Emily J Davis
- Medical Research Council Protein Phosphorylation Unit, Sir James Black Centre, University of Dundee, Dundee, Scotland, UK
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15
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Punwani D, Simon K, Choi Y, Dutra A, Gonzalez-Espinosa D, Pak E, Naradikian M, Song CH, Zhang J, Bodine DM, Puck JM. Transcription factor zinc finger and BTB domain 1 is essential for lymphocyte development. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2012; 189:1253-64. [PMID: 22753936 PMCID: PMC3401355 DOI: 10.4049/jimmunol.1200623] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Absent T lymphocytes were unexpectedly found in homozygotes of a transgenic mouse from an unrelated project. T cell development did not progress beyond double-negative stage 1 thymocytes, resulting in a hypocellular, vestigial thymus. B cells were present, but NK cell number and B cell isotype switching were reduced. Transplantation of wild-type hematopoietic cells corrected the defect, which was traced to a deletion involving five contiguous genes at the transgene insertion site on chromosome 12C3. Complementation using bacterial artificial chromosome transgenesis implicated zinc finger BTB-POZ domain protein 1 (Zbtb1) in the immunodeficiency, confirming its role in T cell development and suggesting involvement in B and NK cell differentiation. Targeted disruption of Zbtb1 recapitulated the T(-)B(+)NK(-) SCID phenotype of the original transgenic animal. Knockouts for Zbtb1 had expanded populations of bone marrow hematopoietic stem cells and also multipotent and early lymphoid lineages, suggesting a differentiation bottleneck for common lymphoid progenitors. Expression of mRNA encoding Zbtb1, a predicted transcription repressor, was greatest in hematopoietic stem cells, thymocytes, and pre-B cells, highlighting its essential role in lymphoid development.
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MESH Headings
- Animals
- Cell Differentiation/genetics
- Cell Differentiation/immunology
- Hematopoietic Stem Cells/cytology
- Hematopoietic Stem Cells/immunology
- Hematopoietic Stem Cells/metabolism
- Lymphocyte Subsets/cytology
- Lymphocyte Subsets/immunology
- Lymphocyte Subsets/metabolism
- Mice
- Mice, Inbred C57BL
- Mice, Knockout
- Mice, SCID
- Mice, Transgenic
- NIH 3T3 Cells
- Precursor Cells, B-Lymphoid/cytology
- Precursor Cells, B-Lymphoid/immunology
- Precursor Cells, B-Lymphoid/metabolism
- Precursor Cells, T-Lymphoid/cytology
- Precursor Cells, T-Lymphoid/immunology
- Precursor Cells, T-Lymphoid/metabolism
- RNA, Messenger/biosynthesis
- Repressor Proteins/deficiency
- Repressor Proteins/genetics
- Repressor Proteins/physiology
- Zinc Fingers/immunology
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Affiliation(s)
- Divya Punwani
- Dept. of Pediatrics, University of California San Francisco, San Francisco, CA 91413; USA
| | - Karen Simon
- National Human Genome Research Institute, NIH, Bethesda, MD 20892; USA
| | - Youngnim Choi
- Dept. of Oromaxillofacial Infection & Immunity, School of Dentistry, Seoul National University, Seoul, Korea 28 Yungun-dong, Jongno-gu, Seoul 110-74928
| | - Amalia Dutra
- National Human Genome Research Institute, NIH, Bethesda, MD 20892; USA
| | | | - Evgenia Pak
- National Human Genome Research Institute, NIH, Bethesda, MD 20892; USA
| | - Martin Naradikian
- Dept. of Pediatrics, University of California San Francisco, San Francisco, CA 91413; USA
- University of Pennsylvania, Philadelphia, Pennsylvania, PA 19104; USA
| | - Chang-Hwa Song
- Dept. of Pediatrics, University of California San Francisco, San Francisco, CA 91413; USA
- Dept. of Microbiology, College of Medicine, Chungnam National University, South Korea
| | - Jenny Zhang
- Dept. of Pediatrics, University of California San Francisco, San Francisco, CA 91413; USA
| | - David M. Bodine
- National Human Genome Research Institute, NIH, Bethesda, MD 20892; USA
| | - Jennifer M. Puck
- Dept. of Pediatrics, University of California San Francisco, San Francisco, CA 91413; USA
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