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Egger T, Morano L, Blanchard MP, Basbous J, Constantinou A. Spatial organization and functions of Chk1 activation by TopBP1 biomolecular condensates. Cell Rep 2024; 43:114064. [PMID: 38578830 DOI: 10.1016/j.celrep.2024.114064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 02/14/2024] [Accepted: 03/21/2024] [Indexed: 04/07/2024] Open
Abstract
Assembly of TopBP1 biomolecular condensates triggers activation of the ataxia telangiectasia-mutated and Rad3-related (ATR)/Chk1 signaling pathway, which coordinates cell responses to impaired DNA replication. Here, we used optogenetics and reverse genetics to investigate the role of sequence-specific motifs in the formation and functions of TopBP1 condensates. We propose that BACH1/FANCJ is involved in the partitioning of BRCA1 within TopBP1 compartments. We show that Chk1 is activated at the interface of TopBP1 condensates and provide evidence that these structures arise at sites of DNA damage and in primary human fibroblasts. Chk1 phosphorylation depends on the integrity of a conserved arginine motif within TopBP1's ATR activation domain (AAD). Its mutation uncouples Chk1 activation from TopBP1 condensation, revealing that optogenetically induced Chk1 phosphorylation triggers cell cycle checkpoints and slows down replication forks in the absence of DNA damage. Together with previous work, these data suggest that the intrinsically disordered AAD encodes distinct molecular steps in the ATR/Chk1 pathway.
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Affiliation(s)
- Tom Egger
- Institut de Génétique Humaine, Université de Montpellier, CNRS, Montpellier, France
| | - Laura Morano
- Institut de Génétique Humaine, Université de Montpellier, CNRS, Montpellier, France
| | - Marie-Pierre Blanchard
- Montpellier Ressources Imageries, BioCampus, Université de Montpellier, CNRS, Montpellier, France
| | - Jihane Basbous
- Institut de Génétique Humaine, Université de Montpellier, CNRS, Montpellier, France.
| | - Angelos Constantinou
- Institut de Génétique Humaine, Université de Montpellier, CNRS, Montpellier, France
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Higdon AL, Won NH, Brar GA. Truncated protein isoforms generate diversity of protein localization and function in yeast. Cell Syst 2024; 15:388-408.e4. [PMID: 38636458 DOI: 10.1016/j.cels.2024.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 01/21/2024] [Accepted: 03/20/2024] [Indexed: 04/20/2024]
Abstract
Genome-wide measurement of ribosome occupancy on mRNAs has enabled empirical identification of translated regions, but high-confidence detection of coding regions that overlap annotated coding regions has remained challenging. Here, we report a sensitive and robust algorithm that revealed the translation of 388 N-terminally truncated proteins in budding yeast-more than 30-fold more than previously known. We extensively experimentally validated them and defined two classes. The first class lacks large portions of the annotated protein and tends to be produced from a truncated transcript. We show that two such cases, Yap5truncation and Pus1truncation, have condition-specific regulation and distinct functions from their respective annotated isoforms. The second class of truncated protein isoforms lacks only a small region of the annotated protein and is less likely to be produced from an alternative transcript isoform. Many display different subcellular localizations than their annotated counterpart, representing a common strategy for dual localization of otherwise functionally identical proteins. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Andrea L Higdon
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Center for Computational Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Nathan H Won
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Gloria A Brar
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Center for Computational Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
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3
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Liang J, Gong X, Hu X, You C, Zhou J, Gao Y, Zong J, Liu Y. Integrated genetic analysis of diabetic complications: Bioinformatics insights into foot ulcers, neuropathy and peripheral artery disease. Int Wound J 2024; 21:e14748. [PMID: 38358067 PMCID: PMC10867868 DOI: 10.1111/iwj.14748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Accepted: 01/23/2024] [Indexed: 02/16/2024] Open
Abstract
Diabetic foot ulcers (DFU), diabetic peripheral neuropathy (DPN) and peripheral arterial disease (PAD) are common complications of diabetes mellitus, while diabetic peripheral neuropathy and peripheral arterial disease contribute to the pathogenesis of diabetic foot ulcers, and the pathogenic mechanisms between these three diseases still need further investigation. The keywords 'diabetic foot ulcer', 'diabetic peripheral neuropathy' and 'atherosclerosis' were used to search for related gene sets in the GEO database. Differentially expressed genes (DEGs) were screened and analysed for GO, KEGG and enrichR functional enrichment. Potential three disease biomarkers were identified by SVM-SVM-RFE and LASSO regression analysis. The results were also validated using external datasets and discriminability was measured by area under the ROC curve (AUC). Finally, biomarkers and co-upregulated genes were analysed through the GSEA and Attie Laboratories diabetes databases. A total of 11 shared genes (KRT16, CD24, SAMD9L, SRGAP2, FGL2, GPR34, DDIT4, NFE2L3, FBLN5, ANXA3 and CPA3), two biomarkers (SAMD9L and FGL2) and one co-upregulated gene (CD24) were screened. GO and KEGG pathway analysis of DEGs, enrichr enrichment analysis of shared differential genes and GSEA analysis of biomarkers showed that these significant genes were mainly focused on vasoregulatory, inflammatory-oxidative stress and immunomodulatory pathways. In this study, we used bioinformatics to investigate the intrinsic relationship and potential mechanisms of three common lower extremity complications of diabetes and identified two pivotal genes using the LASSO model and the SVM-RFE algorithm, which will further help clinicians to understand the relationship between diabetic complications, improve the diagnosis and treatment of diabetic foot problems and help doctors to identify the potential risk factors of diabetic foot.
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Affiliation(s)
- Jiaru Liang
- Department of Rehabilitation MedicineThe First Affiliated Hospital of Dalian Medical UniversityDalianChina
- Institute (College) of Integrative MedicineDalian Medical UniversityDalianChina
| | - Xiaoyang Gong
- Department of Rehabilitation MedicineThe First Affiliated Hospital of Dalian Medical UniversityDalianChina
| | - Xuyang Hu
- Institute (College) of Integrative MedicineDalian Medical UniversityDalianChina
| | - Chong You
- Institute (College) of Integrative MedicineDalian Medical UniversityDalianChina
| | - Jiaqi Zhou
- Department of Rehabilitation MedicineThe First Affiliated Hospital of Dalian Medical UniversityDalianChina
| | - Yuling Gao
- Department of Rehabilitation MedicineThe First Affiliated Hospital of Dalian Medical UniversityDalianChina
| | - Junwei Zong
- Department of Orthopaedic SurgeryThe First Affiliated Hospital of Dalian Medical UniversityDalianChina
| | - Yong Liu
- Department of Rehabilitation MedicineThe First Affiliated Hospital of Dalian Medical UniversityDalianChina
- Institute (College) of Integrative MedicineDalian Medical UniversityDalianChina
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Peng Y, Zhao K, Zheng R, Chen J, Zhu X, Xie K, Huang R, Zhan S, Su Q, Shen M, Niu M, Chen X, Peng D, Ahmad S, Liu ZJ, Zhou Y. A Comprehensive Analysis of Auxin Response Factor Gene Family in Melastoma dodecandrum Genome. Int J Mol Sci 2024; 25:806. [PMID: 38255880 PMCID: PMC10815038 DOI: 10.3390/ijms25020806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/04/2024] [Accepted: 01/05/2024] [Indexed: 01/24/2024] Open
Abstract
Auxin Response Factors (ARFs) mediate auxin signaling and govern diverse biological processes. However, a comprehensive analysis of the ARF gene family and identification of their key regulatory functions have not been conducted in Melastoma dodecandrum, leading to a weak understanding of further use and development for this functional shrub. In this study, we successfully identified a total of 27 members of the ARF gene family in M. dodecandrum and classified them into Class I-III. Class II-III showed more significant gene duplication than Class I, especially for MedARF16s. According to the prediction of cis-regulatory elements, the AP2/ERF, BHLH, and bZIP transcription factor families may serve as regulatory factors controlling the transcriptional pre-initiation expression of MedARF. Analysis of miRNA editing sites reveals that miR160 may play a regulatory role in the post-transcriptional expression of MeARF. Expression profiles revealed that more than half of the MedARFs exhibited high expression levels in the stem compared to other organs. While there are some specific genes expressed only in flowers, it is noteworthy that MedARF16s, MedARF7A, and MedARF9B, which are highly expressed in stems, also demonstrate high expressions in other organs of M. dodecandrum. Further hormone treatment experiments revealed that these MedARFs were sensitive to auxin changes, with MedARF6C and MedARF7A showing significant and rapid changes in expression upon increasing exogenous auxin. In brief, our findings suggest a crucial role in regulating plant growth and development in M. dodecandrum by responding to changes in auxin. These results can provide a theoretical basis for future molecular breeding in Myrtaceae.
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Affiliation(s)
- Yukun Peng
- Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.P.); (R.Z.); (J.C.); (X.Z.); (K.X.); (R.H.); (S.Z.); (Q.S.); (M.N.); (X.C.); (D.P.); (S.A.)
| | - Kai Zhao
- College of Life Sciences, Fujian Normal University, Fuzhou 350117, China; (K.Z.); (M.S.)
| | - Ruiyue Zheng
- Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.P.); (R.Z.); (J.C.); (X.Z.); (K.X.); (R.H.); (S.Z.); (Q.S.); (M.N.); (X.C.); (D.P.); (S.A.)
| | - Jiemin Chen
- Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.P.); (R.Z.); (J.C.); (X.Z.); (K.X.); (R.H.); (S.Z.); (Q.S.); (M.N.); (X.C.); (D.P.); (S.A.)
| | - Xuanyi Zhu
- Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.P.); (R.Z.); (J.C.); (X.Z.); (K.X.); (R.H.); (S.Z.); (Q.S.); (M.N.); (X.C.); (D.P.); (S.A.)
| | - Kai Xie
- Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.P.); (R.Z.); (J.C.); (X.Z.); (K.X.); (R.H.); (S.Z.); (Q.S.); (M.N.); (X.C.); (D.P.); (S.A.)
| | - Ruiliu Huang
- Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.P.); (R.Z.); (J.C.); (X.Z.); (K.X.); (R.H.); (S.Z.); (Q.S.); (M.N.); (X.C.); (D.P.); (S.A.)
| | - Suying Zhan
- Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.P.); (R.Z.); (J.C.); (X.Z.); (K.X.); (R.H.); (S.Z.); (Q.S.); (M.N.); (X.C.); (D.P.); (S.A.)
| | - Qiuli Su
- Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.P.); (R.Z.); (J.C.); (X.Z.); (K.X.); (R.H.); (S.Z.); (Q.S.); (M.N.); (X.C.); (D.P.); (S.A.)
| | - Mingli Shen
- College of Life Sciences, Fujian Normal University, Fuzhou 350117, China; (K.Z.); (M.S.)
| | - Muqi Niu
- Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.P.); (R.Z.); (J.C.); (X.Z.); (K.X.); (R.H.); (S.Z.); (Q.S.); (M.N.); (X.C.); (D.P.); (S.A.)
| | - Xiuming Chen
- Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.P.); (R.Z.); (J.C.); (X.Z.); (K.X.); (R.H.); (S.Z.); (Q.S.); (M.N.); (X.C.); (D.P.); (S.A.)
| | - Donghui Peng
- Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.P.); (R.Z.); (J.C.); (X.Z.); (K.X.); (R.H.); (S.Z.); (Q.S.); (M.N.); (X.C.); (D.P.); (S.A.)
| | - Sagheer Ahmad
- Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.P.); (R.Z.); (J.C.); (X.Z.); (K.X.); (R.H.); (S.Z.); (Q.S.); (M.N.); (X.C.); (D.P.); (S.A.)
| | - Zhong-Jian Liu
- Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.P.); (R.Z.); (J.C.); (X.Z.); (K.X.); (R.H.); (S.Z.); (Q.S.); (M.N.); (X.C.); (D.P.); (S.A.)
| | - Yuzhen Zhou
- Ornamental Plant Germplasm Resources Innovation & Engineering Application Research Center, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Y.P.); (R.Z.); (J.C.); (X.Z.); (K.X.); (R.H.); (S.Z.); (Q.S.); (M.N.); (X.C.); (D.P.); (S.A.)
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5
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Sue N, Thai LM, Saito A, Boyer CK, Fordham AM, Yan C, Davenport A, Tao J, Bensellam M, Cantley J, Shi YC, Stephens SB, Imaizumi K, Biden TJ. Independent activation of CREB3L2 by glucose fills a regulatory gap in mouse β-cells by co-ordinating insulin biosynthesis with secretory granule formation. Mol Metab 2024; 79:101845. [PMID: 38013154 PMCID: PMC10755490 DOI: 10.1016/j.molmet.2023.101845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 11/22/2023] [Accepted: 11/23/2023] [Indexed: 11/29/2023] Open
Abstract
OBJECTIVE Although individual steps have been characterized, there is little understanding of the overall process whereby glucose co-ordinates the biosynthesis of insulin with its export out of the endoplasmic reticulum (ER) and incorporation into insulin secretory granules (ISGs). Here we investigate a role for the transcription factor CREB3L2 in this context. METHODS MIN6 cells and mouse islets were analysed by immunoblotting after treatment with glucose, fatty acids, thapsigargin and various inhibitors. Knockdown of CREB3L2 was achieved using si or sh constructs by transfection, or viral delivery. In vivo metabolic phenotyping was conducted after deletion of CREB3L2 in β-cells of adult mice using Ins1-CreER+. Islets were isolated for RNAseq and assays of glucose-stimulated insulin secretion (GSIS). Trafficking was monitored in islet monolayers using a GFP-tagged proinsulin construct that allows for synchronised release from the ER. RESULTS With a Km ≈3.5 mM, glucose rapidly (T1/2 0.9 h) increased full length (FL) CREB3L2 followed by a slower rise (T1/2 2.5 h) in its transcriptionally-active cleavage product, P60 CREB3L2. Glucose stimulation repressed the ER stress marker, CHOP, and this was partially reverted by knockdown of CREB3L2. Activation of CREB3L2 by glucose was not due to ER stress, however, but a combination of O-GlcNAcylation, which impaired proteasomal degradation of FL-CREB3L2, and mTORC1 stimulation, which enhanced its conversion to P60. cAMP generation also activated CREB3L2, but independently of glucose. Deletion of CREB3L2 inhibited GSIS ex vivo and, following a high-fat diet (HFD), impaired glucose tolerance and insulin secretion in vivo. RNAseq revealed that CREB3L2 regulated genes controlling trafficking to-and-from the Golgi, as well as a broader cohort associated with β-cell compensation during a HFD. Although post-Golgi trafficking appeared intact, knockdown of CREB3L2 impaired the generation of both nascent ISGs and proinsulin condensates in the Golgi, implying a defect in ER export of proinsulin and/or its processing in the Golgi. CONCLUSION The stimulation of CREB3L2 by glucose defines a novel, rapid and direct mechanism for co-ordinating the synthesis, packaging and storage of insulin, thereby minimizing ER overload and optimizing β-cell function under conditions of high secretory demand. Upregulation of CREB3L2 also potentially contributes to the benefits of GLP1 agonism and might in itself constitute a novel means of treating β-cell failure.
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Affiliation(s)
- Nancy Sue
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, NSW 2010, Australia
| | - Le May Thai
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, NSW 2010, Australia
| | - Atsushi Saito
- Department of Biochemistry, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Cierra K Boyer
- Fraternal Order of Eagles Diabetes Research Center, Department of Internal Medicine, University of Iowa, Iowa City, IA 52246, USA
| | - Ashleigh M Fordham
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, NSW 2010, Australia
| | - Chenxu Yan
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, NSW 2010, Australia
| | - Aimee Davenport
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, NSW 2010, Australia
| | - Jiang Tao
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, NSW 2010, Australia
| | - Mohammed Bensellam
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, NSW 2010, Australia
| | - James Cantley
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, NSW 2010, Australia
| | - Yan-Chuan Shi
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, NSW 2010, Australia; St Vincent's Clinical School, Faculty of Medicine, The University of New South Wales, Sydney, Australia
| | - Samuel B Stephens
- Fraternal Order of Eagles Diabetes Research Center, Department of Internal Medicine, University of Iowa, Iowa City, IA 52246, USA
| | - Kazunori Imaizumi
- Department of Biochemistry, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Trevor J Biden
- Garvan Institute of Medical Research, 384 Victoria St, Darlinghurst, NSW 2010, Australia; St Vincent's Clinical School, Faculty of Medicine, The University of New South Wales, Sydney, Australia.
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Sharma AE, Dermawan JK, Sherrod AE, Chopra S, Maki RG, Antonescu CR. When molecular outsmarts morphology: Malignant ossifying fibromyxoid tumors masquerading as osteosarcomas, including a novel CREBZF::PHF1 fusion. Genes Chromosomes Cancer 2024; 63:e23206. [PMID: 37819540 DOI: 10.1002/gcc.23206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/26/2023] [Accepted: 09/23/2023] [Indexed: 10/13/2023] Open
Abstract
We present two cases of malignant ossifying fibromyxoid tumor (OFMT) which eluded diagnosis due to compelling clinicopathologic mimicry, compounded by similarly elusive underlying molecular drivers. The first is of a clavicle mass in a 69 year-old female, which histologically showed an infiltrative nested and trabeculated proliferation of monomorphic cells giving rise to scattered spicules of immature woven bone. Excepting SATB2 positivity, the lesion showed an inconclusive immunoprofile which along with negative PHF1 FISH led to an initial diagnosis of high-grade osteosarcoma. Next generation sequencing (NGS) revealed a particularly rare CREBBP::BCORL1 fusion. The second illustrates the peculiar presentation of a dural-based mass in a 52 year-old female who presented with neurologic dyscrasias. Sections showed a sheeted monotonous proliferation of ovoid to spindle cells, but in contrast to Case #1, the tumor contained an exuberance of reticular osteoid and woven bone deposition mimicking malignant osteogenic differentiation. NGS showed a novel CREBZF::PHF1 fusion. Both tumors recurred locally less than 1 year post-operatively. As such we reiterate that careful morphologic examination is axiomatic to any diagnosis in our discipline, but this paradigm must shift to recognize that molecular diagnostics can provide closure where traditional tools have notable limitations.
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Affiliation(s)
- Aarti E Sharma
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Department of Pathology and Laboratory Medicine, Hospital for Special Surgery, New York, New York, USA
| | - Josephine K Dermawan
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Andy E Sherrod
- Department of Pathology, University of Southern California, Keck School of Medicine, Los Angeles, California, USA
| | - Shefali Chopra
- Department of Pathology, University of Southern California, Keck School of Medicine, Los Angeles, California, USA
| | - Robert G Maki
- Department of Medicine, Sarcoma Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Cristina R Antonescu
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
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7
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Zhao Y, Yu Z, Song Y, Fan L, Lei T, He Y, Hu S. The Regulatory Network of CREB3L1 and Its Roles in Physiological and Pathological Conditions. Int J Med Sci 2024; 21:123-136. [PMID: 38164349 PMCID: PMC10750332 DOI: 10.7150/ijms.90189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 10/26/2023] [Indexed: 01/03/2024] Open
Abstract
CREB3 subfamily belongs to the bZIP transcription factor family and comprises five members. Normally they are located on the endoplasmic reticulum (ER) membranes and proteolytically activated through RIP (regulated intramembrane proteolysis) on Golgi apparatus to liberate the N-terminus to serve as transcription factors. CREB3L1 acting as one of them transcriptionally regulates the expressions of target genes and exhibits distinct functions from the other members of CREB3 family in eukaryotes. Physiologically, CREB3L1 involves in the regulation of bone morphogenesis, neurogenesis, neuroendocrine, secretory cell differentiation, and angiogenesis. Pathologically, CREB3L1 implicates in the modulation of osteogenesis imperfecta, low grade fibro myxoid sarcoma (LGFMS), sclerosing epithelioid fibrosarcoma (SEF), glioma, breast cancer, thyroid cancer, and tissue fibrosis. This review summarizes the upstream and downstream regulatory network of CREB3L1 and thoroughly presents our current understanding of CREB3L1 research progress in both physiological and pathological conditions with special focus on the novel findings of CREB3L1 in cancers.
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Affiliation(s)
- Ying Zhao
- Department of Anesthesiology and Perioperative Medicine, Xi'an People's Hospital (Xi'an Fourth Hospital), Northwest University, Xi'an, Shaanxi Province, China
| | - Zhou Yu
- Department of Plastic Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi Province, China
| | - Yajuan Song
- Department of Plastic Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi Province, China
| | - Liumeizi Fan
- Department of Anesthesiology and Perioperative Medicine, Xi'an People's Hospital (Xi'an Fourth Hospital), Northwest University, Xi'an, Shaanxi Province, China
| | - Ting Lei
- Department of Anesthesiology and Perioperative Medicine, Xi'an People's Hospital (Xi'an Fourth Hospital), Northwest University, Xi'an, Shaanxi Province, China
| | - Yinbin He
- Department of Anesthesiology and Perioperative Medicine, Xi'an People's Hospital (Xi'an Fourth Hospital), Northwest University, Xi'an, Shaanxi Province, China
| | - Sheng Hu
- Department of Anesthesiology and Perioperative Medicine, Xi'an People's Hospital (Xi'an Fourth Hospital), Northwest University, Xi'an, Shaanxi Province, China
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8
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Daian E Silva DSO, Cox LJ, Rocha AS, Lopes-Ribeiro Á, Souza JPC, Franco GM, Prado JLC, Pereira-Santos TA, Martins ML, Coelho-Dos-Reis JGA, Gomes-de-Pinho TM, Da Fonseca FG, Barbosa-Stancioli EF. Preclinical assessment of an anti-HTLV-1 heterologous DNA/MVA vaccine protocol expressing a multiepitope HBZ protein. Virol J 2023; 20:304. [PMID: 38115107 PMCID: PMC10731796 DOI: 10.1186/s12985-023-02264-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 12/07/2023] [Indexed: 12/21/2023] Open
Abstract
BACKGROUND Human T-lymphotropic virus 1 (HTLV-1) is associated with the development of several pathologies and chronic infection in humans. The inefficiency of the available treatments and the challenge in developing a protective vaccine highlight the need to produce effective immunotherapeutic tools. The HTLV-1 basic leucine zipper (bZIP) factor (HBZ) plays an important role in the HTLV-1 persistence, conferring a survival advantage to infected cells by reducing the HTLV-1 proteins expression, allowing infected cells to evade immune surveillance, and enhancing cell proliferation leading to increased proviral load. METHODS We have generated a recombinant Modified Virus Vaccinia Ankara (MVA-HBZ) and a plasmid DNA (pcDNA3.1(+)-HBZ) expressing a multiepitope protein based on peptides of HBZ to study the immunogenic potential of this viral-derived protein in BALB/c mice model. Mice were immunized in a prime-boost heterologous protocol and their splenocytes (T CD4+ and T CD8+) were immunophenotyped by flow cytometry and the humoral response was evaluated by ELISA using HBZ protein produced in prokaryotic vector as antigen. RESULTS T CD4+ and T CD8+ lymphocytes cells stimulated by HBZ-peptides (HBZ42-50 and HBZ157-176) showed polyfunctional double positive responses for TNF-α/IFN-γ, and TNF-α/IL-2. Moreover, T CD8+ cells presented a tendency in the activation of effector memory cells producing granzyme B (CD44+High/CD62L-Low), and the activation of Cytotoxic T Lymphocytes (CTLs) and cytotoxic responses in immunized mice were inferred through the production of granzyme B by effector memory T cells and the expression of CD107a by CD8+ T cells. The overall data is consistent with a directive and effector recall response, which may be able to operate actively in the elimination of HTLV-1-infected cells and, consequently, in the reduction of the proviral load. Sera from immunized mice, differently from those of control animals, showed IgG-anti-HBZ production by ELISA. CONCLUSIONS Our results highlight the potential of the HBZ multiepitope protein expressed from plasmid DNA and a poxviral vector as candidates for therapeutic vaccine.
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Affiliation(s)
- D S O Daian E Silva
- Laboratório de Virologia Básica e Aplicada, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Campus Pampulha, Belo Horizonte, MG, CEP 31270-901, Brazil
- GIPH - Grupo Interdisciplinar de Pesquisas em HTLV, Interdisciplinary HTLV Research Group, Belo Horizonte, Brazil
| | - L J Cox
- Laboratório de Virologia Básica e Aplicada, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Campus Pampulha, Belo Horizonte, MG, CEP 31270-901, Brazil
- GIPH - Grupo Interdisciplinar de Pesquisas em HTLV, Interdisciplinary HTLV Research Group, Belo Horizonte, Brazil
| | - A S Rocha
- Laboratório de Virologia Básica e Aplicada, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Campus Pampulha, Belo Horizonte, MG, CEP 31270-901, Brazil
- GIPH - Grupo Interdisciplinar de Pesquisas em HTLV, Interdisciplinary HTLV Research Group, Belo Horizonte, Brazil
| | - Á Lopes-Ribeiro
- Laboratório de Virologia Básica e Aplicada, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Campus Pampulha, Belo Horizonte, MG, CEP 31270-901, Brazil
| | - J P C Souza
- Centro de Tecnologia de Vacinas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, 31270-901, Brazil
| | - G M Franco
- Laboratório de Virologia Básica e Aplicada, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Campus Pampulha, Belo Horizonte, MG, CEP 31270-901, Brazil
- GIPH - Grupo Interdisciplinar de Pesquisas em HTLV, Interdisciplinary HTLV Research Group, Belo Horizonte, Brazil
| | - J L C Prado
- Laboratório de Virologia Básica e Aplicada, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Campus Pampulha, Belo Horizonte, MG, CEP 31270-901, Brazil
| | - T A Pereira-Santos
- Laboratório de Virologia Básica e Aplicada, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Campus Pampulha, Belo Horizonte, MG, CEP 31270-901, Brazil
- GIPH - Grupo Interdisciplinar de Pesquisas em HTLV, Interdisciplinary HTLV Research Group, Belo Horizonte, Brazil
| | - M L Martins
- GIPH - Grupo Interdisciplinar de Pesquisas em HTLV, Interdisciplinary HTLV Research Group, Belo Horizonte, Brazil
- Gerência de Desenvolvimento Técnico Científico, Fundação Centro de Hematologia e Hemoterapia do Estado de Minas Gerais - Hemominas, Belo Horizonte, Brazil
| | - J G A Coelho-Dos-Reis
- Laboratório de Virologia Básica e Aplicada, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Campus Pampulha, Belo Horizonte, MG, CEP 31270-901, Brazil
- GIPH - Grupo Interdisciplinar de Pesquisas em HTLV, Interdisciplinary HTLV Research Group, Belo Horizonte, Brazil
| | - T M Gomes-de-Pinho
- Centro de Tecnologia de Vacinas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, 31270-901, Brazil
| | - F G Da Fonseca
- Laboratório de Virologia Básica e Aplicada, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Campus Pampulha, Belo Horizonte, MG, CEP 31270-901, Brazil
- Centro de Tecnologia de Vacinas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, 31270-901, Brazil
| | - E F Barbosa-Stancioli
- Laboratório de Virologia Básica e Aplicada, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Campus Pampulha, Belo Horizonte, MG, CEP 31270-901, Brazil.
- GIPH - Grupo Interdisciplinar de Pesquisas em HTLV, Interdisciplinary HTLV Research Group, Belo Horizonte, Brazil.
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Zhou J, Xu M, Chen Z, Huang L, Wu Z, Huang Z, Liu L. circ_SPEF2 Regulates the Balance of Treg Cells by Regulating miR-16-5p/BACH2 in Lymphoma and Participates in the Immune Response. Tissue Eng Regen Med 2023; 20:1145-1159. [PMID: 37801226 PMCID: PMC10645944 DOI: 10.1007/s13770-023-00585-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 08/06/2023] [Accepted: 08/11/2023] [Indexed: 10/07/2023] Open
Abstract
BACKGROUND This study aims to explore the potential mechanism of action of the newly discovered hsa_circ_0128899 (circSPEF2) in diffuse large B-cell lymphoma (DLBCL). METHODS circSPEF2, miR-16-5p and BTB and CNC homologue 2 (BACH2) expression patterns in DLBCL patients and cell lines were studied by RT-qPCR. The biological function of circSPEF2 in vitro and in vivo was investigated by function acquisition experiments. The proliferation activity of lymphoma cells was detected by MTT. Bax, Caspase-3, and Bcl-2 were determined by Western Blot. Apoptosis and the ratio of CD4 to Treg of immune cells in the co-culture system were analyzed by flow cytometry. The mechanism of action of circSPEF2 in DLBCL progression was further investigated by RIP and dual luciferase reporter experiments. RESULTS circSPEF2 was a circRNA with abnormally down-regulated expression in DLBCL. Increasing circSPEF2 expression inhibited the proliferative activity and induced apoptosis of lymphoma cells in vitro and in vivo, as well as increased CD4+T cells and decreased Treg cell proportion of immune cells in the tumor microenvironment. Mechanically, circSPEF2 was bound to miR-16-5p expression, while BACH2 was targeted by miR-16-5p. circSPEF2 overexpression-mediated effects on lymphoma progression were reversible by upregulating miR-16-5p or downregulating BACH2. CONCLUSIONS circSPEF2 can influence DLBCL progression by managing cellular proliferation and apoptosis and the proportion of immune cells Treg and CD4 through the miR-16-5p/BACH2 axis.
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Affiliation(s)
- Jie Zhou
- Department of Hematology, Huazhong University of Science and Technology Tongji Medical College Affiliated Union Hospital, No. 1277 Jiefang Avenue, Jianghan District, Wuhan City, 430022, Hubei Province, China
| | - Min Xu
- Department of Hematology, Huazhong University of Science and Technology Tongji Medical College Affiliated Union Hospital, No. 1277 Jiefang Avenue, Jianghan District, Wuhan City, 430022, Hubei Province, China
| | - ZhaoZhao Chen
- Department of Hematology, Huazhong University of Science and Technology Tongji Medical College Affiliated Union Hospital, No. 1277 Jiefang Avenue, Jianghan District, Wuhan City, 430022, Hubei Province, China
| | - LinLin Huang
- Department of Hematology, Huazhong University of Science and Technology Tongji Medical College Affiliated Union Hospital, No. 1277 Jiefang Avenue, Jianghan District, Wuhan City, 430022, Hubei Province, China
| | - ZhuoLin Wu
- Department of Hematology, Huazhong University of Science and Technology Tongji Medical College Affiliated Union Hospital, No. 1277 Jiefang Avenue, Jianghan District, Wuhan City, 430022, Hubei Province, China
| | - ZhongPei Huang
- Department of Hematology, Huazhong University of Science and Technology Tongji Medical College Affiliated Union Hospital, No. 1277 Jiefang Avenue, Jianghan District, Wuhan City, 430022, Hubei Province, China
| | - Lin Liu
- Department of Hematology, Huazhong University of Science and Technology Tongji Medical College Affiliated Union Hospital, No. 1277 Jiefang Avenue, Jianghan District, Wuhan City, 430022, Hubei Province, China.
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10
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Lin K, Wang Y, Li Y, Wang Y. Identification of biomarkers associated with pediatric asthma using machine learning algorithms: A review. Medicine (Baltimore) 2023; 102:e36070. [PMID: 38013370 PMCID: PMC10681392 DOI: 10.1097/md.0000000000036070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 10/20/2023] [Indexed: 11/29/2023] Open
Abstract
Pediatric asthma is a complex disease with a multifactorial etiology. The identification of biomarkers associated with pediatric asthma can provide insights into the pathogenesis of the disease and aid in the development of novel diagnostic and therapeutic strategies. This study aimed to identify potential biomarkers for pediatric asthma using Weighted Gene Co-expression Network Analysis (WGCNA) and machine learning algorithms. We obtained gene expression data from publicly available databases and performed WGCNA to identify gene co-expression modules associated with pediatric asthma. We then used machine learning algorithms, including random forest, lasso regression algorithm, and support vector machine-recursive feature elimination, to classify asthma cases and controls based on the identified gene modules. We also performed functional enrichment analyses to investigate the biological functions of the identified genes.We detected 24,544 genes exhibiting differential expression between controlled and uncontrolled genes from the GSE135192 dataset. In the combined WCGNA analysis, a total of 104 co-expression genes were screened, both controlled and uncontrolled. After screening, 11 hub genes were identified. They were AK2, PDK4, PER3, GZMH, NUMBL, NRL, SCO2, CREBZF, LARP1B, RXFP1, and VDAC3P1. The areas under their receiver operating characteristic curve were above 0.78. Our study identified potential biomarkers for pediatric asthma using WGCNA and machine learning algorithms. Our findings suggest that 11 hub genes could be used as novel diagnostic markers and treatment targets for pediatric asthma. These findings provide new insights into the pathogenesis of pediatric asthma and may aid in the development of novel diagnostic and therapeutic strategies.
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Affiliation(s)
- Kexin Lin
- Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang Province, China
| | - Yijie Wang
- Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang Province, China
| | - Yongjun Li
- Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang Province, China
| | - Youpeng Wang
- The Second Affiliated Hospital of Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang Province, China
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11
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Gouveia Roque C, Chung KM, McCurdy EP, Jagannathan R, Randolph LK, Herline-Killian K, Baleriola J, Hengst U. CREB3L2-ATF4 heterodimerization defines a transcriptional hub of Alzheimer's disease gene expression linked to neuropathology. Sci Adv 2023; 9:eadd2671. [PMID: 36867706 PMCID: PMC9984184 DOI: 10.1126/sciadv.add2671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
Gene expression is changed by disease, but how these molecular responses arise and contribute to pathophysiology remains less understood. We discover that β-amyloid, a trigger of Alzheimer's disease (AD), promotes the formation of pathological CREB3L2-ATF4 transcription factor heterodimers in neurons. Through a multilevel approach based on AD datasets and a novel chemogenetic method that resolves the genomic binding profile of dimeric transcription factors (ChIPmera), we find that CREB3L2-ATF4 activates a transcription network that interacts with roughly half of the genes differentially expressed in AD, including subsets associated with β-amyloid and tau neuropathologies. CREB3L2-ATF4 activation drives tau hyperphosphorylation and secretion in neurons, in addition to misregulating the retromer, an endosomal complex linked to AD pathogenesis. We further provide evidence for increased heterodimer signaling in AD brain and identify dovitinib as a candidate molecule for normalizing β-amyloid-mediated transcriptional responses. The findings overall reveal differential transcription factor dimerization as a mechanism linking disease stimuli to the development of pathogenic cellular states.
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Affiliation(s)
- Cláudio Gouveia Roque
- The Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Kyung Min Chung
- The Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Ethan P. McCurdy
- Integrated Program in Cellular, Molecular, and Biomedical Studies, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Radhika Jagannathan
- Division of Aging and Dementia, Department of Neurology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Lisa K. Randolph
- Doctoral Program in Neurobiology and Behavior, Columbia University, New York, NY, USA
| | - Krystal Herline-Killian
- The Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Jimena Baleriola
- The Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Achucarro Basque Center for Neuroscience, Leioa, Spain
- IKERBASQUE Basque Foundation for Science, Bilbao, Spain
- Department of Cell Biology and Histology, University of the Basque Country, Leioa, Spain
| | - Ulrich Hengst
- The Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Department of Pathology and Cell Biology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
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12
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Datta S, Cano M, Satyanarayana G, Liu T, Wang L, Wang J, Cheng J, Itoh K, Sharma A, Bhutto I, Kannan R, Qian J, Sinha D, Handa JT. Mitophagy initiates retrograde mitochondrial-nuclear signaling to guide retinal pigment cell heterogeneity. Autophagy 2023; 19:966-983. [PMID: 35921555 PMCID: PMC9980637 DOI: 10.1080/15548627.2022.2109286] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 11/02/2022] Open
Abstract
Age-related macular degeneration (AMD), the leading cause of blindness among the elderly, is without treatment for early disease. Degenerative retinal pigment epithelial (RPE) cell heterogeneity is a well-recognized but understudied pathogenic factor. Due to the daily phagocytosis of photoreceptor outer segments, unique photo-oxidative stress, and high metabolism for maintaining vision, the RPE has robust macroautophagy/autophagy, and mitochondrial and antioxidant networks. However, the autophagy subtype, mitophagy, in the RPE and AMD is understudied. Here, we found decreased PINK1 (PTEN induced kinase 1) in perifoveal RPE of early AMD eyes. PINK1-deficient RPE have impaired mitophagy and mitochondrial function that triggers death-resistant epithelial-mesenchymal transition (EMT). This reprogramming is mediated by novel retrograde mitochondrial-nuclear signaling (RMNS) through superoxide, NFE2L2 (NFE2 like bZIP transcription factor 2), TXNRD1 (thioredoxin reductase 1), and phosphoinositide 3-kinase (PI3K)-AKT (AKT serine/threonine kinase) that induced canonical transcription factors ZEB1 (zinc finger E-box binding homeobox 1) and SNAI1 (Snail family transcriptional repressor 1) and an EMT transcriptome. NFE2L2 deficiency disrupted RMNS that paradoxically normalized morphology but decreased function and viability. Thus, RPE heterogeneity is defined by the interaction of two cytoprotective pathways that is triggered by mitophagy function. By neutralizing the consequences of impaired mitophagy, an antioxidant dendrimer tropic for the RPE and mitochondria, EMT (a recognized AMD alteration) was abrogated to offer potential therapy for early AMD, a stage without treatment.Abbreviations: ACTB: actin beta; AKT: AKT serine/threonine kinase; AMD: age-related macular degeneration; CCCP: cyanide m-chlorophenyl hydrazone; CDH1: cadherin 1; DAVID: Database for Annotation, Visualization and Integrated Discovery; DHE: dihydroethidium; D-NAC: N-acetyl-l-cysteine conjugated to a poly(amido amine) dendrimer; ECAR: extracellular acidification rate; EMT: epithelial-mesenchymal transition; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; GSEA: Gene Set Enrichment Analysis; HSPD1: heat shock protein family D (Hsp60) member 1; IVT: intravitreal; KD: knockdown; LMNA, lamin A/C; MAP1LC3B: microtubule associated protein 1 light chain 3 beta; MMP: mitochondrial membrane potential; NAC: N-acetyl-l-cysteine; NQO1: NAD(P)H quinone dehydrogenase 1; NFE2L2: NFE2 like bZIP transcription factor 2; O2-: superoxide anion; OCR: oxygen consumption rate; PI3K: phosphoinositide 3-kinase; PINK1: PTEN induced kinase 1; RMNS: retrograde mitochondrial-nuclear signaling; ROS: reactive oxygen species; RPE: retinal pigment epithelium; SNAI1: snail family transcriptional repressor 1; TJP1: tight junction protein 1; TPP-D-NAC: triphenyl phosphinium and N-acetyl-l-cysteine conjugated to a poly(amido amine) dendrimer; TIMM23: translocase of inner mitochondrial membrane 23; TOMM20: translocase of outer mitochondrial membrane 20; Trig: trigonelline; TXNRD1: thioredoxin reductase 1; VIM: vimentin; WT: wild-type; ZEB1: zinc finger E-box binding homeobox 1.
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Affiliation(s)
- Sayantan Datta
- Wilmer Eye Institute, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Ophthalmology, Emory University School of Medicine, Atlanta, GAUSA
| | - Marisol Cano
- Wilmer Eye Institute, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Ganesh Satyanarayana
- Department of Ophthalmology, Emory University School of Medicine, Atlanta, GAUSA
| | - Tongyun Liu
- Wilmer Eye Institute, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Lei Wang
- Wilmer Eye Institute, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Jie Wang
- Wilmer Eye Institute, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Jie Cheng
- Wilmer Eye Institute, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Kie Itoh
- Department of Cell Biology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Anjali Sharma
- Wilmer Eye Institute, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Imran Bhutto
- Wilmer Eye Institute, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | | | - Jiang Qian
- Wilmer Eye Institute, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Debasish Sinha
- Department of Ophthalmology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - James T. Handa
- Wilmer Eye Institute, Johns Hopkins School of Medicine, Baltimore, MD, USA
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Wang X, Zha W, Yao B, Yang L, Wang S. Genetic Interaction of Global Regulators AflatfA and AflatfB Mediating Development, Stress Response and Aflatoxins B1 Production in Aspergillus flavus. Toxins (Basel) 2022; 14:toxins14120857. [PMID: 36548754 PMCID: PMC9785671 DOI: 10.3390/toxins14120857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/01/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
Aspergillus flavus produces carcinogenic and mutagenic aflatoxins, which cause economic losses and risk of food safety by contaminating grains, food and feed. In this study, we characterized two bZIP transcription factors, AflatfA and AflatfB, and their genetic interaction. Compared to the wild type (WT), AflatfA deletion and AflatfA and AflatfB double deletion both caused retarded vegetative growth of mycelia. Relative to WT, the AflatfA deletion strain (ΔAflatfA) and AflatfA and AflatfB double deletion strain (ΔAflatfAΔAflatfB) produced more sclerotia, whereas the AflatfB deletion strain (ΔAflatfB) produced less sclerotia. After 4 °C preservation and incubation at 50 °C, conidia viability dramatically decreased in the ΔAflatfA and ΔAflatfAΔAflatfB but ΔAflatfB mutants, whereas conidia viability of the ΔAflatfAΔAflatfB strain was higher after storage at 4 °C than in AflatfA mutant. Conidia of ΔAflatfA, ΔAflatfB and ΔAflatfAΔAflatfB strains significantly increased in sensitivity to H2O2 in comparison with WT. Compared to WT, the mycelium of ΔAflatfA and ΔAflatfB strains were more sensitive to H2O2; conversely, the ΔAflatfAΔAflatfB strain showed less sensitivity to H2O2. ΔAflatfA and ΔAflatfAΔAflatfB strains displayed less sensitivity to the osmotic reagents NaCl, KCl and Sorbitol, in comparison with WT and ΔAflatfB strains. When on YES medium and hosts corn and peanut, ΔAflatfA and ΔAflatfAΔAflatfB strains produced less aflatoxin B1 (AFB1) than ΔAflatfB, and the AFB1 yield of ΔAflatfB was higher than that of WT. When WT and mutants were inoculated on corn and peanut, the ΔAflatfA and ΔAflatfAΔAflatfB but not ΔAflatfB mutants produced less conidia than did WT. Taken together, this study reveals that AflatfA controls more cellular processes, and the function of AflatfA is stronger than that of AflatfB when of the same process is regulated, except the response to H2O2, which might result from the effect of AflatfA on the transcriptional level of AflatfB.
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14
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Cushing KC, Du X, Chen Y, Stetson LC, Kuppa A, Chen VL, Kahlenberg JM, Gudjonsson JE, Vanderwerff B, Higgins PDR, Speliotes EK. Inflammatory Bowel Disease Risk Variants Are Associated with an Increased Risk of Skin Cancer. Inflamm Bowel Dis 2022; 28:1667-1676. [PMID: 35018451 PMCID: PMC9924040 DOI: 10.1093/ibd/izab336] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Indexed: 01/30/2023]
Abstract
BACKGROUND Inflammatory bowel disease is associated with an increased risk of skin cancer. The aims of this study were to determine whether IBD susceptibility variants are also associated with skin cancer susceptibility and if such risk is augmented by use of immune-suppressive therapy. METHODS The discovery cohort included participants in the UK Biobank. The validation cohort included participants in the Michigan Genomics Initiative. The primary outcome of interest was skin cancer, subgrouped into nonmelanoma skin cancers (NMSC) and melanoma skin cancers (MSC). Multivariable logistic regression with matched controls (3 controls:1 case) was performed to identify genomic predictors of skin malignancy in the discovery cohort. Variants with P < .05 were tested for replication in the validation cohort. Validated Single nucleotide polymorphisms were then evaluated for effect modification by immune-suppressive medications. RESULTS The discovery cohort included 10,247 cases of NMSC and 1883 cases of MSC. The validation cohort included 7334 cases of NMSC and 3304 cases of MSC. Twenty-nine variants were associated with risk of NMSC in the discovery cohort, of which 5 replicated in the validation cohort (increased risk, rs7773324-A [DUSP22; IRF4], rs2476601-G [PTPN22], rs1847472-C [BACH2], rs72810983-A [CPEB4]; decreased risk, rs6088765-G [PROCR; MMP24]). Twelve variants were associated with risk of MSC in the discovery cohort, of which 4 were replicated in the validation cohort (increased risk, rs61839660-T [IL2RA]; decreased risk, rs17391694-C [GIPC2; MGC27382], rs6088765-G [PROCR; MMP24], and rs1728785-C [ZFP90]). No effect modification was observed. CONCLUSIONS The results of this study highlight shared genetic susceptibility across IBD and skin cancer, with increased risk of NMSC in those who carry risk variants in IRF4, PTPN22, CPEB4, and BACH2 and increased risk of MSC in those who carry a risk variant in IL2RA.
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Affiliation(s)
- Kelly C Cushing
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, MI, USA
| | - Xiaomeng Du
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, MI, USA
| | - Yanhua Chen
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, MI, USA
| | - L C Stetson
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, MI, USA
| | - Annapurna Kuppa
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, MI, USA
| | - Vincent L Chen
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, MI, USA
| | - J Michelle Kahlenberg
- Department of Internal Medicine, Division of Rheumatology, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Brett Vanderwerff
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Peter D R Higgins
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, MI, USA
| | - Elizabeth K Speliotes
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
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15
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Han Q, Tan W, Zhao Y, Yang F, Yao X, Lin H, Zhang D. Salicylic acid-activated BIN2 phosphorylation of TGA3 promotes Arabidopsis PR gene expression and disease resistance. EMBO J 2022; 41:e110682. [PMID: 35950443 PMCID: PMC9531300 DOI: 10.15252/embj.2022110682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 06/28/2022] [Accepted: 07/21/2022] [Indexed: 11/09/2022] Open
Abstract
The plant defense hormone, salicylic acid (SA), plays essential roles in immunity and systemic acquired resistance. Salicylic acid induced by the pathogen is perceived by the receptor nonexpressor of pathogenesis-related genes 1 (NPR1), which is recruited by TGA transcription factors to induce the expression of pathogenesis-related (PR) genes. However, the mechanism by which post-translational modifications affect TGA's transcriptional activity by salicylic acid signaling/pathogen infection is not well-established. Here, we report that the loss-of-function mutant of brassinosteroid insensitive2 (BIN2) and its homologs, bin2-3 bil1 bil2, causes impaired pathogen resistance and insensitivity to SA-induced PR gene expression, whereas the gain-of-function mutant, bin2-1, exhibited enhanced SA signaling and immunity against the pathogen. Our results demonstrate that salicylic acid activates BIN2 kinase, which in turn phosphorylates TGA3 at Ser33 to enhance TGA3 DNA binding ability and NPR1-TGA3 complex formation, leading to the activation of PR gene expression. These findings implicate BIN2 as a new component of salicylic acid signaling, functioning as a key node in balancing brassinosteroid-mediated plant growth and SA-induced immunity.
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Affiliation(s)
- Qing Han
- Ministry of Education Key Laboratory for Bio‐Resource and Eco‐Environment, College of Life Science, State Key Laboratory of Hydraulics and Mountain River EngineeringSichuan UniversityChengduChina
| | - Wenrong Tan
- Ministry of Education Key Laboratory for Bio‐Resource and Eco‐Environment, College of Life Science, State Key Laboratory of Hydraulics and Mountain River EngineeringSichuan UniversityChengduChina
- School of Life Science and EngineeringSouthwest University of Science and TechnologyMianyangChina
| | - Yuqing Zhao
- Ministry of Education Key Laboratory for Bio‐Resource and Eco‐Environment, College of Life Science, State Key Laboratory of Hydraulics and Mountain River EngineeringSichuan UniversityChengduChina
| | - Feng Yang
- Ministry of Education Key Laboratory for Bio‐Resource and Eco‐Environment, College of Life Science, State Key Laboratory of Hydraulics and Mountain River EngineeringSichuan UniversityChengduChina
| | - Xiuhong Yao
- Ministry of Education Key Laboratory for Bio‐Resource and Eco‐Environment, College of Life Science, State Key Laboratory of Hydraulics and Mountain River EngineeringSichuan UniversityChengduChina
| | - Honghui Lin
- Ministry of Education Key Laboratory for Bio‐Resource and Eco‐Environment, College of Life Science, State Key Laboratory of Hydraulics and Mountain River EngineeringSichuan UniversityChengduChina
| | - Dawei Zhang
- Ministry of Education Key Laboratory for Bio‐Resource and Eco‐Environment, College of Life Science, State Key Laboratory of Hydraulics and Mountain River EngineeringSichuan UniversityChengduChina
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16
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Contreras A, Wiesner DL, Kingstad-Bakke B, Lee W, Svaren JP, Klein BS, Suresh M. BACH2 in TRegs Limits the Number of Adipose Tissue Regulatory T Cells and Restrains Type 2 Immunity to Fungal Allergens. J Immunol Res 2022; 2022:6789055. [PMID: 36033397 PMCID: PMC9410868 DOI: 10.1155/2022/6789055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 07/19/2022] [Indexed: 01/28/2023] Open
Abstract
FoxP3+ regulatory T cells (Tregs) are essential for self-tolerance and moderating tissue-damaging inflammation. Tregs that develop and mature in the thymus are classified as central Tregs or effector Tregs based on whether Tregs predominately inhabit secondary lymphoid organs (central Tregs) or tissues (effector Tregs). By generating mice that are conditionally deficient for Bach2 in peripheral Tregs, we have examined the role of Bach2 in regulating Treg homeostasis and effector functions. Unlike global and T cell-specific Bach2-deficient mice, Treg-specific Bach2 ablation did not result in unprovoked TH2 inflammation in the lungs. However, Bach2 deficiency in Tregs led to augmented expressions of IRF4, BATF, and GATA3 and a significant increase in the accumulation of ST2 (IL-33R)+ve effector Tregs in the spleen and visceral adipose tissue (VAT) but not in the lungs. Enhanced Bach2-deficient Treg numbers in VAT was not linked to hyperresponsiveness to exogenous IL-33 in vivo. Most strikingly, Treg-specific Bach2 deficiency resulted in enhanced fungal protease-induced Type 2 allergic inflammation in the lungs, with no detectable effects on Type 1 responses to systemic or respiratory viral infections. In summary, we ascribe vital roles for Bach2 in peripheral Tregs: as a transcriptional checkpoint to limit precocious differentiation into effector Tregs in lymphoid tissues and as a regulator of the functional program that restrains Type 2 but not Type 1 inflammation in lungs. Results presented in this manuscript implicate dysregulated Tregs in the pathogenesis of airway hypersensitivities, asthma, and other allergic disorders.
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Affiliation(s)
- Amanda Contreras
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, 53706 WI, USA
| | - Darin L. Wiesner
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, 53706 WI, USA
| | - Brock Kingstad-Bakke
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, 53706 WI, USA
| | - Woojong Lee
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, 53706 WI, USA
| | - John P. Svaren
- Department of Comparative Biosciences, University of Wisconsin-Madison, Madison, 53706 WI, USA
| | - Bruce S. Klein
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, 53706 WI, USA
| | - M. Suresh
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, 53706 WI, USA
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17
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Liu C, Liu Q, Mou Z. A direct link between BR and SA signaling: Negative regulation of TGA4 by BIN2. Mol Plant 2022; 15:1254-1256. [PMID: 35689390 DOI: 10.1016/j.molp.2022.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 06/07/2022] [Accepted: 06/08/2022] [Indexed: 06/15/2023]
Affiliation(s)
- Cheng Liu
- Department of Microbiology and Cell Science, University of Florida, P.O. Box 110700, Gainesville, FL 32611, USA
| | - Qingcai Liu
- Department of Microbiology and Cell Science, University of Florida, P.O. Box 110700, Gainesville, FL 32611, USA
| | - Zhonglin Mou
- Department of Microbiology and Cell Science, University of Florida, P.O. Box 110700, Gainesville, FL 32611, USA.
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18
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Mason GA. A bZIP transcription factor accelerates the transition to reproductive tuber growth and aging in Solanum tuberosum. Plant Physiol 2022; 189:1194-1195. [PMID: 35485196 PMCID: PMC9237667 DOI: 10.1093/plphys/kiac182] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 03/18/2022] [Indexed: 06/14/2023]
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19
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Fichna M, Żurawek M, Słomiński B, Sumińska M, Czarnywojtek A, Rozwadowska N, Fichna P, Myśliwiec M, Ruchała M. Polymorphism in BACH2 gene is a marker of polyglandular autoimmunity. Endocrine 2021; 74:72-79. [PMID: 33966174 PMCID: PMC8440266 DOI: 10.1007/s12020-021-02743-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 04/23/2021] [Indexed: 11/06/2022]
Abstract
PURPOSE Genetically predisposed individuals may develop several autoimmune diseases-autoimmune polyendocrine syndromes (APS). APS types 2-4, are complex disorders, which combine various organ-specific autoimmune conditions. Recent reports support the considerable role of the BACH2 gene in immune cell differentiation and shifting the T-cell balance towards regulatory T-cells. BACH2 polymorphisms are associated with autoimmune disorders, including Addison's disease (AD), Graves' disease (GD), and probably type 1 diabetes (T1D). Our study was aimed to investigate the BACH2 variant, rs3757247, in endocrine autoimmunity in the Polish population. METHODS The analysis comprised 346 individuals with APS, 387 with T1D only, and 568 controls. Genotyping was performed using TaqMan chemistry. RESULTS APS type 2 was found in 219 individuals, type 3 in 102, and type 4 in 25 subjects. Overall, AD was diagnosed in 244 subjects, Hashimoto's thyroiditis-in 238, T1D-in 127, GD-in 58, vitiligo and chronic gastritis each in 40 patients, celiac disease-in 28, premature menopause in 18, and alopecia in 4 patients. Minor T allele at rs3757247 was found in 56.4% APS vs. 44.1% control alleles (OR 1.59; 95%CI: 1.30-1.95, p < 0.0001). The distribution of genotypes revealed excess TT homozygotes in the APS cohort (33.2 vs. 20.1% in controls, p < 0.0001). The frequencies of rs3757247 alleles and genotypes in T1D patients did not present significant differences vs. controls (p-values > 0.05). CONCLUSIONS These results provide evidence of the association between BACH2 polymorphism and polyglandular autoimmunity. Since carriers of rs3757247 display increased risk for additional autoimmune conditions, this variant could identify individuals prone to develop APS.
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Affiliation(s)
- Marta Fichna
- Department of Endocrinology, Metabolism and Internal Medicine, Poznan University of Medical Sciences, Poznan, Poland.
| | - Magdalena Żurawek
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Bartosz Słomiński
- Department of Medical Immunology, Faculty of Medicine, Medical University of Gdansk, Gdansk, Poland
| | - Marta Sumińska
- Department of Paediatric Diabetes and Obesity, Poznan University of Medical Sciences, Poznan, Poland
| | - Agata Czarnywojtek
- Department of Pharmacology, Poznan University of Medical Sciences, Poznan, Poland
| | | | - Piotr Fichna
- Department of Paediatric Diabetes and Obesity, Poznan University of Medical Sciences, Poznan, Poland
| | - Małgorzata Myśliwiec
- Department of Paediatrics, Diabetology and Endocrinology, Faculty of Medicine, Medical University of Gdansk, Gdansk, Poland
| | - Marek Ruchała
- Department of Endocrinology, Metabolism and Internal Medicine, Poznan University of Medical Sciences, Poznan, Poland
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Hu Y, Gu J, Wang Y, Lin J, Yu H, Yang F, Wu S, Yin J, Lv H, Ji X, Wang S. Promotion Effect of EGCG on the Raised Expression of IL-23 through the Signaling of STAT3-BATF2-c-JUN/ATF2. J Agric Food Chem 2021; 69:7898-7909. [PMID: 34227806 DOI: 10.1021/acs.jafc.1c02433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Tea polyphenol of epigallocatechin-3-gallate (EGCG) has been verified to possess multiple biological activities. Interleukin-23 (IL-23) is a heterodimeric cytokine consisting of two subunits of IL-23p19 and IL-12p40, with the functionality in regulating the production of cytokines under physiological or pathological conditions. By serendipity, the raised expression of IL-23 was observed after treating cells with EGCG, whereas the detailed mechanism remains poorly understood. This study was proposed to investigate the signaling related to EGCG-induced IL-23. The raised expression of IL-23 was confirmed primarily by intraperitoneally injecting with different concentrations of EGCG (0, 20, 50, 80 mg/kg) into BALB/c mice, and the raised expression was confirmed by quantitative real-time polymerase chain reaction (qRT-PCR) and western blot. Results from enzyme-linked immunosorbent assay (ELISA) revealed the increase of IL-23 in serum from 116.09 to 153.90 pg/mL after treating with EGCG. The same results were also observed in RAW264.7 and peritoneal macrophages after treating with EGCG (0, 1, 5, 10, 25 μM) with the increased tendency of IL-23 in cultural medium (7.98 to 25.38 pg/mL for RAW264.7; 3.64 to 260.93 pg/mL for peritoneal macrophages). After preliminary exploration of the signaling related to the increased IL-23, the classical signaling pathways and key transcription factors, such as nuclear factor kappa-B (NF-κB), mitogen-activated protein kinase (MAPK) signaling pathways, and interferon regulatory factor 5 (IRF5), were demonstrated with no relevant contribution. A further study revealed the involvement of the key transcription factor of BATF2, which could antagonistically modulate the transcription and translation of IL-23. The signaling of STAT3-BATF2-c-JUN/ATF2-IL-23 has been further verified in RAW264.7 macrophages using the STAT3 inhibitor of AG490 and the activator of Colivelin TFA. The results indicated that EGCG inhibits the phosphorylation of STAT3 to facilitate the decreased level of BATF2, which contributed to the increased level of IL-23 by the enhancing heterodimerization of c-JUN and ATF2.
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Affiliation(s)
- Yaozhong Hu
- Tianjin Key Laboratory of Food Science and Health, School of Medicine, Nankai University, Tianjin 300071, China
| | - Jiaxin Gu
- Tianjin Key Laboratory of Food Science and Health, School of Medicine, Nankai University, Tianjin 300071, China
| | - Yi Wang
- Tianjin Key Laboratory of Food Science and Health, School of Medicine, Nankai University, Tianjin 300071, China
| | - Jing Lin
- Tianjin Key Laboratory of Food Science and Health, School of Medicine, Nankai University, Tianjin 300071, China
| | - Huaning Yu
- Guangdong Midea Kitchen Appliances Manufacturing Co., Ltd, Guangdong 528000, China
| | - Feier Yang
- Tianjin Key Laboratory of Food Science and Health, School of Medicine, Nankai University, Tianjin 300071, China
| | - Sihao Wu
- Tianjin Key Laboratory of Food Science and Health, School of Medicine, Nankai University, Tianjin 300071, China
| | - Jia Yin
- Tianjin Key Laboratory of Food Science and Health, School of Medicine, Nankai University, Tianjin 300071, China
| | - Huan Lv
- Tianjin Key Laboratory of Food Science and Health, School of Medicine, Nankai University, Tianjin 300071, China
| | - Xuemeng Ji
- Tianjin Key Laboratory of Food Science and Health, School of Medicine, Nankai University, Tianjin 300071, China
| | - Shuo Wang
- Tianjin Key Laboratory of Food Science and Health, School of Medicine, Nankai University, Tianjin 300071, China
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Brites C, Grassi MF, Quaresma JAS, Ishak R, Vallinoto ACR. Pathogenesis of HTLV-1 infection and progression biomarkers: An overview. Braz J Infect Dis 2021; 25:101594. [PMID: 34256025 PMCID: PMC9392164 DOI: 10.1016/j.bjid.2021.101594] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/12/2021] [Accepted: 06/03/2021] [Indexed: 12/12/2022] Open
Abstract
Infection by human T-cell lymphotropic virus type 1 (HTLV-1) occurs in lymphocytes, which travel throughout the body, thus affecting several target organs and causing varied clinical outcomes, particularly in populations that are underserved and do not have access to healthcare. However, the mechanism of pathogenesis is not yet fully understood. The TAX and HTLV-1 basic leucine zipper factor (HBZ) proteins maintain viral persistence and affect pathogenesis through cell proliferation and immune and inflammatory responses that accompany each clinical manifestation. TAX expression leads to inhibition of transcription error control, OX40 overexpression, and cell proliferation in adult T-cell leukemia (ATL). OX40 levels are elevated in the central nervous system (CNS), and the expression of TAX in the CNS causes neuronal damage and loss of immune reactivity among patients with HTLV-1-associated myelopathy (HAM). HBZ reduces viral replication and suppresses the immune response. Its cell compartmentalization has been associated with the pathogenesis of HAM (cytoplasmic localization) and ATL (nuclear localization). TAX and HBZ seem to act antagonistically in immune responses, affecting the pathogenesis of HTLV-1 infection. The progression from HTLV-1 infection to disease is a consequence of HTLV-1 replication in CD4+ T and CD8+ T lymphocytes and the imbalance between proinflammatory and anti-inflammatory cytokines. The compartmentalization of HBZ suggests that this protein may be an additional tool for assessing immune and inflammatory responses, in addition to those already recognized as potential biomarkers associated with progression from infection to disease (including human leukocyte antigen (HLA), killer immunoglobulin-like receptors (KIR), interleukin (IL)-6, IL-10, IL-28, Fas, Fas ligand, interferon (IFN)-γ, tumor necrosis factor (TNF)-α, and mannose-binding lectin).
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Affiliation(s)
- Carlos Brites
- Federal University of Bahia (UFBA), Professor Edgard Santos University Hospital Complex, Laboratory of Infectious Diseases Research, Salvador, BA, Brazil
| | | | | | - Ricardo Ishak
- Federal University of Pará (UFPA), Institute of Biological Sciences, Laboratory of Virology, Belém, PA, Brazil
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22
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Chen S, Ma T, Song S, Li X, Fu P, Wu W, Liu J, Gao Y, Ye W, Dry IB, Lu J. Arabidopsis downy mildew effector HaRxLL470 suppresses plant immunity by attenuating the DNA-binding activity of bZIP transcription factor HY5. New Phytol 2021; 230:1562-1577. [PMID: 33586184 DOI: 10.1111/nph.17280] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 02/01/2021] [Indexed: 05/27/2023]
Abstract
The oomycete pathogen Hyaloperonospora arabidopsidis delivers diverse effector proteins into host plant cells to suppress the plant's innate immunity. In this study, we investigate the mechanism of action of a conserved RxLR effector, HaRxLL470, in suppressing plant immunity. Genomic, molecular and biochemical analyses were performed to investigate the function of HaRxLL470 and the mechanism of the interaction between HaRxLL470 and the target host protein during H. arabidopsidis infection. We report that HaRxLL470 enhances plant susceptibility to H. arabidopsidis isolate Noco2 by interacting with the host photomorphogenesis regulator protein HY5. Our results demonstrate that HY5 is not only an important component in the regulation of light signalling, but also positively regulates host plant immunity against H. arabidopsidis by transcriptional activation of defense-related genes. We show that the interaction between HaRxLL470 and HY5 compromises the function of HY5 as a transcription factor by attenuating its DNA-binding activity. The present study demonstrates that HY5 positively regulates host plant defense against H. arabidopsidis whereas HaRxLL470, a conserved RxLR effector across oomycete pathogens, enhances pathogenicity by interacting with HY5 and suppressing transcriptional activation of defense-related genes.
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Affiliation(s)
- Shuyun Chen
- Center for Viticulture and Enology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Tao Ma
- Center for Viticulture and Enology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Shiren Song
- Center for Viticulture and Enology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xinlong Li
- Center for Viticulture and Enology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Peining Fu
- Center for Viticulture and Enology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wei Wu
- Center for Viticulture and Enology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jiaqi Liu
- Center for Viticulture and Enology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yu Gao
- Center for Viticulture and Enology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wenxiu Ye
- Center for Viticulture and Enology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Ian B Dry
- CSIRO Agriculture & Food, Urrbrae, SA, 5064, Australia
| | - Jiang Lu
- Center for Viticulture and Enology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
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Labarta-Bajo L, Zúñiga EI. BAtCHing stem-like T cells during exhaustion. Nat Immunol 2021; 22:274-276. [PMID: 33627884 PMCID: PMC9258450 DOI: 10.1038/s41590-021-00891-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Long-term pathogen and tumor control as well as checkpoint immunotherapies rely on ‘stem-like’ CD8+ T cells. New results uncover BACH2 as a key regulator of this subpopulation and solve an important piece of the puzzle.
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Affiliation(s)
- Lara Labarta-Bajo
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
- Molecular Neurobiology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Elina I Zúñiga
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA.
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24
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Kang G, Yan D, Chen X, Yang L, Zeng R. HbWRKY82, a novel IIc WRKY transcription factor from Hevea brasiliensis associated with abiotic stress tolerance and leaf senescence in Arabidopsis. Physiol Plant 2021; 171:151-160. [PMID: 33034379 DOI: 10.1111/ppl.13238] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 09/18/2020] [Accepted: 09/30/2020] [Indexed: 06/11/2023]
Abstract
WRKY group transcription factors of model plants and major crops are confirmed to play essential roles in stress responses, senescence, secondary metabolism processes and hormone signal transduction. Previous studies have identified 81 HbWRKY genes from Hevea brasiliensis (the Pará rubber tree), but the functions of HbWRKYs in response to abiotic stresses and leaf senescence are unclear. In this study, one novel group IIc WRKY transcription factor named HbWRKY82 was identified and characterized as a stress-associated WRKY in rubber tree. Transient expression and transcriptional activation analyses indicated that HbWRKY82 encoded a nuclear protein and functioned as a transcription activator. The transcription levels of HbWRKY82 were induced by exogenous Ethrel (ET) (ethylene releaser) and abscisic acid (ABA) stimulations, down-regulated in tapping panel dryness rubber trees, and also exhibits significant decrease during the progression of leaf senescence. Overexpression of HbWRKY82 in Arabidopsis improved the tolerance to dehydration and salinity, and decreased the sensitivity to exogenous ABA. Moreover, real-time quantitative PCR analysis demonstrated that HbWRKY82 regulated the transcriptional expression of several stress-responsive genes (DREB1A, ERD10, HKT1, P5CS, RD22, RD29B, SKOR), leaf senescence marker genes (EIN3, WRKY53, NAP), ROS-related genes (RbohD, CSD1, CSD2, FSD3) and hormone signaling genes (EIN3, ABF3, ABF4). Collectively, our findings suggested that HbWRKY82 might function as an important transcriptional regulator in ET- and ABA-mediated leaf senescence and abiotic stress responses, and also be involved in tapping panel dryness, latex flow and regeneration processes of rubber trees via participating in the ET and reactive oxygen species signaling pathways.
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Affiliation(s)
- Guijuan Kang
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture and Rural Affairs, P. R. China ' State Key Laboratory Incubation Base for Cultivation & Physiology of Tropical Crops, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Dong Yan
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture and Rural Affairs, P. R. China ' State Key Laboratory Incubation Base for Cultivation & Physiology of Tropical Crops, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Xiaoli Chen
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture and Rural Affairs, P. R. China ' State Key Laboratory Incubation Base for Cultivation & Physiology of Tropical Crops, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Lifu Yang
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture and Rural Affairs, P. R. China ' State Key Laboratory Incubation Base for Cultivation & Physiology of Tropical Crops, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Rizhong Zeng
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture and Rural Affairs, P. R. China ' State Key Laboratory Incubation Base for Cultivation & Physiology of Tropical Crops, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
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25
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Vasquez-Rifo A, Ricci EP, Ambros V. Pseudomonas aeruginosa cleaves the decoding center of Caenorhabditis elegans ribosomes. PLoS Biol 2020; 18:e3000969. [PMID: 33259473 PMCID: PMC7707567 DOI: 10.1371/journal.pbio.3000969] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 10/22/2020] [Indexed: 11/27/2022] Open
Abstract
Pathogens such as Pseudomonas aeruginosa advantageously modify animal host physiology, for example, by inhibiting host protein synthesis. Translational inhibition of insects and mammalian hosts by P. aeruginosa utilizes the well-known exotoxin A effector. However, for the infection of Caenorhabditis elegans by P. aeruginosa, the precise pathways and mechanism(s) of translational inhibition are not well understood. We found that upon exposure to P. aeruginosa PA14, C. elegans undergoes a rapid loss of intact ribosomes accompanied by the accumulation of ribosomes cleaved at helix 69 (H69) of the 26S ribosomal RNA (rRNA), a key part of ribosome decoding center. H69 cleavage is elicited by certain virulent P. aeruginosa isolates in a quorum sensing (QS)–dependent manner and independently of exotoxin A–mediated translational repression. H69 cleavage is antagonized by the 3 major host defense pathways defined by the pmk-1, fshr-1, and zip-2 genes. The level of H69 cleavage increases with the bacterial exposure time, and it is predominantly localized in the worm’s intestinal tissue. Genetic and genomic analysis suggests that H69 cleavage leads to the activation of the worm’s zip-2-mediated defense response pathway, consistent with translational inhibition. Taken together, our observations suggest that P. aeruginosa deploys a virulence mechanism to induce ribosome degradation and H69 cleavage of host ribosomes. In this manner, P. aeruginosa would impair host translation and block antibacterial responses. During infection of the nematode Caenorhabditis elegans by the bacterium Pseudomonas aeruginosa, a bacterial virulence mechanism leads to the cleavage of host ribosomal RNAs at the decoding center, thereby shutting down translation.
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Affiliation(s)
- Alejandro Vasquez-Rifo
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- * E-mail: (AV-R); (VA)
| | - Emiliano P. Ricci
- Laboratoire de Biologie et Modélisation de la Cellule, Université de Lyon, École normale supérieure de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5239, INSERM U1210 Lyon, France
| | - Victor Ambros
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- * E-mail: (AV-R); (VA)
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Cardoso JV, Perini JA, Machado DE, Pinto R, Medeiros R. Systematic review of genome-wide association studies on susceptibility to endometriosis. Eur J Obstet Gynecol Reprod Biol 2020; 255:74-82. [PMID: 33113402 DOI: 10.1016/j.ejogrb.2020.10.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 10/01/2020] [Accepted: 10/08/2020] [Indexed: 12/11/2022]
Abstract
Endometriosis is a complex and heterogeneous disease in which extrinsic and intrinsic factors, such as genetics, provide to the disease development. Genome-wide association (GWA) studies may be essential to recognize genetic variants associated with the endometriosis risk. However, in the current literature there are some conflicting results between these studies. The aim of the present study was to undertake a systematic review about endometriosis GWA studies, to describe the disease-associated genes and single nucleotide polymorphisms (SNPs) to try to understand the endometriosis etiopathogenesis, besides to discuss possible bias of conflicting results among these studies. This study is a systematic review of GWA studies in endometriosis published until December 31th, 2019 by PubMed database, considering the following descriptors: endometriosis and ("polymorphism" or "SNP" or "genetic polymorphism" or "variants" or "locus") and ("GWA" or "Genome-wide" or "Genome wide" or "Genetic association study"). The included studies were analyzed with methodological rigor (STROBE and PRISMA) to enable better quality of case-control and meta-analysis studies, respectively. Of the 88 articles found, only 15 were eligible. All articles had appropriate quality evaluated by STROBE and PRISMA checklists (77% and 81%, respectively). Overall, 35,022 endometriosis cases and 181,760 controls were analyzed. The number of participants in each study was quite different (171 to 17,045 for the cases and 308 to 150,021 for the controls), with a predominance of European ethnicity. Most endometriosis cases (86%) were diagnosed by surgery, while selection of the control group was different among studies. About 47% performed only one stage (discovery stage) and 53% performed both the discovery and replication analyses. Eleven genes/SNPs were associated with endometriosis risk in more than one article (chromosome 1, 2, 6, 7, 9 and 12; WNT4, GREB1, FN1, IL1A, ETAA1, RND3, ID4, NFE2L3, CDKN2B-AS1 and VEZT). SNPs were localized in intergenic and intronic regions, their risk allele frequencies varied among the studies and their results were conflicting. In summary, WNT4 rs7521902, GREB1 rs13394619, FN1 rs1250248, IL1A rs6542095 and VEZT rs10859871 variants are highlighted due to high frequency and pathways and function that each gene influences in the development of endometriosis. However, the replication and validation of these variants in different populations are necessary for a better understanding of the endometriosis etiopathogenesis, in order to optimize the diagnosis and improve the efficiency of clinical treatment of the disease.
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Affiliation(s)
- Jéssica Vilarinho Cardoso
- Research Laboratory of Pharmaceutical Sciences, State University Centre of the West Zone, Rio de Janeiro, Brazil; Program of Post-graduation in Public Health and Environment, National School of Public Health, Oswald Cruz Foundation, Rio de Janeiro, RJ, Brazil
| | - Jamila Alessandra Perini
- Research Laboratory of Pharmaceutical Sciences, State University Centre of the West Zone, Rio de Janeiro, Brazil; Program of Post-graduation in Public Health and Environment, National School of Public Health, Oswald Cruz Foundation, Rio de Janeiro, RJ, Brazil.
| | - Daniel Escorsim Machado
- Research Laboratory of Pharmaceutical Sciences, State University Centre of the West Zone, Rio de Janeiro, Brazil
| | - Ricardo Pinto
- Molecular Oncology Group-CI, Portuguese Institute of Oncology, Porto, Portugal
| | - Rui Medeiros
- Molecular Oncology Group-CI, Portuguese Institute of Oncology, Porto, Portugal
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Wang D, Jiang Y, Sun-Waterhouse DX, Zhai H, Guan H, Rong X, Li F, Yu JC, Li DP. MicroRNA-based regulatory mechanisms underlying the synergistic antioxidant action of quercetin and catechin in H 2O 2-stimulated HepG2 cells: Roles of BACH1 in Nrf2-dependent pathways. Free Radic Biol Med 2020; 153:122-131. [PMID: 32344103 DOI: 10.1016/j.freeradbiomed.2020.04.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 04/20/2020] [Accepted: 04/21/2020] [Indexed: 12/21/2022]
Abstract
The microRNA-based mechanisms underlying the antioxidant action(s) of co-existing flavonoids in response to oxidative stress are of high interest. This study aimed to extend the existing knowledge and provide insights into the potential regulatory network in response to oxidative stress and the co-presence of quercetin and catechin antioxidants, via a preclinical approach using H2O2-stimulated HepG2 cells. It was confirmed that BACH1 serves as an essential and direct negative regulator of the Keap1-Nrf2 signaling pathway and the antioxidant synergism between quercetin and catechin. BACH1 promoted reactive oxygen species (ROS) accumulation while inhibiting cell growth, which could be reversed by the synergistic action of let-7a-5p and miR-25-3p in the co-presence of quercetin and catechin. Both let-7a-5p and miR-25-3p could directly regulate the expression and function of BACH1 (e.g. upregulation of the two miRNAs could rescue largely overexpression of BACH1). Although these molecular interactions likely represented only some aspects of the overall regulatory network, this research confirms the feasibility of the combined uses of dietary flavonoids with chemopreventive properties in synergy during multiple-target interactions and multiple-pathway regulation.
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Affiliation(s)
- Dan Wang
- College of Food Science and Engineering, Shandong Agricultural University, Key Laboratory of Food Processing Technology and Quality Control of Shandong Higher Education Institutes, Taian, PR China; Shandong Institute of Pomology, Taian, PR China
| | - Yang Jiang
- College of Food Science and Engineering, Shandong Agricultural University, Key Laboratory of Food Processing Technology and Quality Control of Shandong Higher Education Institutes, Taian, PR China
| | - Dong-Xiao Sun-Waterhouse
- College of Food Science and Engineering, Shandong Agricultural University, Key Laboratory of Food Processing Technology and Quality Control of Shandong Higher Education Institutes, Taian, PR China; School of Chemical Sciences, The University of Auckland, New Zealand
| | - Hao Zhai
- Shandong Institute of Pomology, Taian, PR China
| | - Hui Guan
- College of Food Science and Engineering, Shandong Agricultural University, Key Laboratory of Food Processing Technology and Quality Control of Shandong Higher Education Institutes, Taian, PR China
| | - Xue Rong
- College of Food Science and Engineering, Shandong Agricultural University, Key Laboratory of Food Processing Technology and Quality Control of Shandong Higher Education Institutes, Taian, PR China
| | - Feng Li
- College of Food Science and Engineering, Shandong Agricultural University, Key Laboratory of Food Processing Technology and Quality Control of Shandong Higher Education Institutes, Taian, PR China
| | - Jia-Cheng Yu
- College of Food Science and Engineering, Shandong Agricultural University, Key Laboratory of Food Processing Technology and Quality Control of Shandong Higher Education Institutes, Taian, PR China
| | - Da-Peng Li
- College of Food Science and Engineering, Shandong Agricultural University, Key Laboratory of Food Processing Technology and Quality Control of Shandong Higher Education Institutes, Taian, PR China.
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Rusch HL, Robinson J, Yun S, Osier ND, Martin C, Brewin CR, Gill JM. Gene expression differences in PTSD are uniquely related to the intrusion symptom cluster: A transcriptome-wide analysis in military service members. Brain Behav Immun 2019; 80:904-908. [PMID: 31039430 PMCID: PMC6752960 DOI: 10.1016/j.bbi.2019.04.039] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Revised: 04/18/2019] [Accepted: 04/26/2019] [Indexed: 11/19/2022] Open
Abstract
Posttraumatic stress disorder (PTSD) is associated with wide-spread immune dysregulation; however, little is known about the gene expression differences attributed to each PTSD symptom cluster. This is an important consideration when identifying diagnostic and treatment response markers in highly comorbid populations with mental and physical health conditions that share symptoms. To this aim, we utilized a transcriptome-wide analysis of differential gene expression in peripheral blood by comparing military service members: (1) with vs. without PTSD, (2) with high vs. low PTSD cluster symptom severity, and (3) with improved vs. not improved PTSD symptoms following 4-8 weeks of evidenced-based sleep treatment. Data were analyzed at a ±2.0-fold change magnitude with subsequent gene ontology-based pathway analysis. In participants with PTSD (n = 39), 89 differentially expressed genes were identified, and 94% were upregulated. In participants with high intrusion symptoms (n = 22), 1040 differentially expressed genes were identified, and 98% were upregulated. No differentially expressed genes were identified for the remaining two PTSD symptom clusters. Ten genes (C5orf24, RBAK, CREBZF, CD69, PMAIP1, AGL, ZNF644, ANKRD13C, ESCO1, and ZCCHC10) were upregulated in participants with PTSD and high intrusion symptoms at baseline and downregulated in participants with improved PTSD symptoms following treatment. Pathway analysis identified upregulated immune response systems and metabolic networks with a NF-kB hub, which were downregulated with symptom reduction. Molecular biomarkers implicated in intrusion symptoms and PTSD symptom improvement may inform the development of therapeutic targets for precise treatment of PTSD.
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Affiliation(s)
- Heather L Rusch
- National Institute of Nursing Research, National Institutes of Health, Bethesda, MD 20892, United States.
| | - Jeffrey Robinson
- National Institute of Nursing Research, National Institutes of Health, Bethesda, MD 20892, United States
| | - Sijung Yun
- Yotta Biomed, LLC, Bethesda, MD 20817, United States
| | - Nicole D Osier
- National Institute of Nursing Research, National Institutes of Health, Bethesda, MD 20892, United States
| | - Christiana Martin
- National Institute of Nursing Research, National Institutes of Health, Bethesda, MD 20892, United States
| | - Chris R Brewin
- University College London, London WC1E 6BT, United Kingdom
| | - Jessica M Gill
- National Institute of Nursing Research, National Institutes of Health, Bethesda, MD 20892, United States
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Abstract
It is well known that E3 ubiquitin ligase COP1 is a negative regulator of plant photomorphogenesis. However, COP1 acts as a positive regulator under UV-B light. A recent study (Ren et al. Proc. Natl. Acad. Sci. U. S. A. 2019;116:4722-4731) proposes a two-step protein degradation model to explain how COP1 switches its role in response to UV-B light.
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Affiliation(s)
- Huanhuan Jin
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Ziqiang Zhu
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China.
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Yu Y. New Interacting Partners of BLADE-ON-PETIOLE in Regulation of Plant Development. Plant Physiol 2019; 180:697-698. [PMID: 31160524 PMCID: PMC6548281 DOI: 10.1104/pp.19.00459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Affiliation(s)
- Yunqing Yu
- Assistant Features Editor
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
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Mach J. Corn ChIPs and RNA-seq: Researchers Dip into Advanced Tools and Resources to Examine bZIP Transcription Factor Function in the Maize Endosperm. Plant Cell 2018; 30:2641-2642. [PMID: 30464034 PMCID: PMC6305974 DOI: 10.1105/tpc.18.00882] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
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Abstract
Acute graft-versus-host disease (GVHD) in the gut is common following hematopoetic cell transplantation (HCT) and is associated with high mortality. However, it remains unclear whether Th1 or Th17 CD4+ T cells can initiate acute gut GVHD. In this issue of the JCI, Ullrich and colleagues identified a subset of CD4+ T cells that express high levels of IL-7Rα and granulocyte-macrophage CSF (IL-7RαhiGM-CSF+) cells that are involved in the induction of acute gut GVHD in murine models. The IL-7RαhiGM-CSF+ effector memory cells were BATF dependent, RORγt independent, produced large amounts of GM-CSF and IFN-γ, and released little IL-17. CD4+IL-7RαhiGM-CSF+ cells were not classical Th17 cells but had more of a Th1-like phenotype, despite their dependence on BATF. This work suggests that targeting the IL-7R/BATF/GM-CSF axis has therapeutic potential for treating acute gut GVHD.
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Yang W, Zhang W, Wang X. Post-translational control of ABA signalling: the roles of protein phosphorylation and ubiquitination. Plant Biotechnol J 2017; 15:4-14. [PMID: 27767245 PMCID: PMC5253474 DOI: 10.1111/pbi.12652] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 10/15/2016] [Accepted: 10/18/2016] [Indexed: 05/05/2023]
Abstract
The plant phytohormone abscisic acid (ABA) plays significant roles in integrating environmental signals with embryogenesis, germination, seedling establishment, the floral transition and the adaptation of plants to stressful environments by modulating stomatal movement and stress-responsive gene expression. ABA signalling consists of ABA perception, signal transduction and ABA-induced responses. ABA receptors such as members of the PYR/PYL family, group A type 2C protein phosphatases (as negative regulators), SnRK2 protein kinases (as positive regulators), bZIP transcription factors and ion channels are key components of ABA signalling. Post-translational modifications, including dephosphorylation, phosphorylation and ubiquitination, play important roles in regulating ABA signalling. In this review, we focus on the roles of post-translational modifications in ABA signalling. The studies presented provide a detailed picture of the ABA signalling network.
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Affiliation(s)
- Wenqi Yang
- Rice Research InstituteShenyang Agricultural UniversityShenyangChina
| | - Wei Zhang
- Rice Research InstituteShenyang Agricultural UniversityShenyangChina
| | - Xiaoxue Wang
- Rice Research InstituteShenyang Agricultural UniversityShenyangChina
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Liu A, Gao F, Kanno Y, Jordan MC, Kamiya Y, Seo M, Ayele BT. Regulation of wheat seed dormancy by after-ripening is mediated by specific transcriptional switches that induce changes in seed hormone metabolism and signaling. PLoS One 2013; 8:e56570. [PMID: 23437172 PMCID: PMC3577873 DOI: 10.1371/journal.pone.0056570] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Accepted: 01/14/2013] [Indexed: 01/14/2023] Open
Abstract
Treatments that promote dormancy release are often correlated with changes in seed hormone content and/or sensitivity. To understand the molecular mechanisms underlying the role of after-ripening (seed dry storage) in triggering hormone related changes and dormancy decay in wheat (Triticum aestivum), temporal expression patterns of genes related to abscisic acid (ABA), gibberellin (GA), jasmonate and indole acetic acid (IAA) metabolism and signaling, and levels of the respective hormones were examined in dormant and after-ripened seeds in both dry and imbibed states. After-ripening mediated developmental switch from dormancy to germination appears to be associated with declines in seed sensitivity to ABA and IAA, which are mediated by transcriptional repressions of PROTEIN PHOSPHATASE 2C, SNF1-RELATED PROTEIN KINASE2, ABA INSENSITIVE5 and LIPID PHOSPHATE PHOSPHTASE2, and AUXIN RESPONSE FACTOR and RELATED TO UBIQUITIN1 genes. Transcriptomic analysis of wheat seed responsiveness to ABA suggests that ABA inhibits the germination of wheat seeds partly by repressing the transcription of genes related to chromatin assembly and cell wall modification, and activating that of GA catabolic genes. After-ripening induced seed dormancy decay in wheat is also associated with the modulation of seed IAA and jasmonate contents. Transcriptional control of members of the ALLENE OXIDE SYNTHASE, 3-KETOACYL COENZYME A THIOLASE, LIPOXYGENASE and 12-OXOPHYTODIENOATE REDUCTASE gene families appears to regulate seed jasmonate levels. Changes in the expression of GA biosynthesis genes, GA 20-OXIDASE and GA 3-OXIDASE, in response to after-ripening implicate this hormone in enhancing dormancy release and germination. These findings have important implications in the dissection of molecular mechanisms underlying regulation of seed dormancy in cereals.
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Affiliation(s)
- Aihua Liu
- Department of Plant Science, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Feng Gao
- Department of Plant Science, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Yuri Kanno
- RIKEN Plant Science Center, Tsurumi, Yokohama, Japan
| | - Mark C. Jordan
- Cereal Research Centre, Agriculture and Agri-Food Canada, Winnipeg, Manitoba, Canada
| | - Yuji Kamiya
- RIKEN Plant Science Center, Tsurumi, Yokohama, Japan
| | - Mitsunori Seo
- RIKEN Plant Science Center, Tsurumi, Yokohama, Japan
| | - Belay T. Ayele
- Department of Plant Science, University of Manitoba, Winnipeg, Manitoba, Canada
- * E-mail:
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Matsuoka M. Guest editorial: a new era of ATL and HTLV-1 research. Int J Hematol 2011; 94:429. [PMID: 21969188 DOI: 10.1007/s12185-011-0940-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Revised: 09/17/2011] [Accepted: 09/20/2011] [Indexed: 11/28/2022]
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Babiychuk E, Vandepoele K, Wissing J, Garcia-Diaz M, De Rycke R, Akbari H, Joubès J, Beeckman T, Jänsch L, Frentzen M, Van Montagu MCE, Kushnir S. Plastid gene expression and plant development require a plastidic protein of the mitochondrial transcription termination factor family. Proc Natl Acad Sci U S A 2011; 108:6674-9. [PMID: 21464319 PMCID: PMC3081001 DOI: 10.1073/pnas.1103442108] [Citation(s) in RCA: 119] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Plastids are DNA-containing organelles unique to plant cells. In Arabidopsis, one-third of the genes required for embryo development encode plastid-localized proteins. To help understand the role of plastids in embryogenesis and postembryonic development, we characterized proteins of the mitochondrial transcription termination factor (mTERF) family, which in animal models, comprises DNA-binding regulators of mitochondrial transcription. Of 35 Arabidopsis mTERF proteins, 11 are plastid-localized. Genetic complementation shows that at least one plastidic mTERF, BELAYA SMERT' (BSM), is required for embryogenesis. The main postembryonic phenotypes of genetic mosaics with the bsm mutation are severe abnormalities in leaf development. Mutant bsm cells are albino, are compromised in growth, and suffer defects in global plastidic gene expression. The bsm phenotype could be phenocopied by inhibition of plastid translation with spectinomycin. Plastid translation is essential for cell viability in dicotyledonous species such as tobacco but not in monocotyledonous maize. Here, genetic interactions between BSM and the gene encoding plastid homomeric acetyl-CoA carboxylase ACC2 suggest that there is a functional redundancy in malonyl-CoA biosynthesis that permits bsm cell survival in Arabidopsis. Overall, our results indicate that biosynthesis of malonyl-CoA and plastid-derived systemic growth-promoting compounds are the processes that link plant development and plastid gene expression.
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Affiliation(s)
- Elena Babiychuk
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Genetics, Ghent University, 9052 Ghent, Belgium
| | - Klaas Vandepoele
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Genetics, Ghent University, 9052 Ghent, Belgium
| | - Josef Wissing
- Abteilung Zellbiologie, Helmholtz-Zentrum für Infektionsforschung GmbH, 38124 Braunschweig, Germany
| | - Miguel Garcia-Diaz
- Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794-8651
| | - Riet De Rycke
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Genetics, Ghent University, 9052 Ghent, Belgium
| | - Hana Akbari
- Institut für Biologie I, Spezielle Botanik, Rheinisch-Westfälische Technische Hochschule Aachen, 52056 Aachen, Germany; and
| | - Jérôme Joubès
- Université Victor Ségalen Bordeaux 2, Laboratoire de Biogenèse Membranaire, Centre National de la Recherche Scientifique, 33076 Bordeaux Cedex, France
| | - Tom Beeckman
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Genetics, Ghent University, 9052 Ghent, Belgium
| | - Lothar Jänsch
- Abteilung Zellbiologie, Helmholtz-Zentrum für Infektionsforschung GmbH, 38124 Braunschweig, Germany
| | - Margrit Frentzen
- Institut für Biologie I, Spezielle Botanik, Rheinisch-Westfälische Technische Hochschule Aachen, 52056 Aachen, Germany; and
| | | | - Sergei Kushnir
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Plant Biotechnology and Genetics, Ghent University, 9052 Ghent, Belgium
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Dai BD, Cao YY, Huang S, Xu YG, Gao PH, Wang Y, Jiang YY. Baicalein induces programmed cell death in Candida albicans. J Microbiol Biotechnol 2009; 19:803-809. [PMID: 19734718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Recent evidence has revealed the occurrence of an apoptotic phenotype in Candida albicans that is inducible with environmental stresses such as acetic acid, hydrogen peroxide, and amphotericin B. In the present study, we found that the Chinese herbal medicine Baicalein (BE), which was one of the skullcapflavones, can induce apoptosis in C. albicans. The apoptotic effects of BE were detected by flow cytometry using Annexin V-FITC and DAPI, and it was confirmed by transmission electron microscopy analysis. After exposure to 4 microg/ml BE for 12 h, about 10% of C. albicans cells were apoptotic. Both the increasing intracellular levels of reactive oxygen species (ROS) and upregulation of some redox-related genes (CAP1, SOD2, TRR1) were observed. Furthermore, we compared the survivals of CAP1 deleted, wild-type, and overexpressed strains and found that Cap1p attenuated BE-initiated cell death, which was coherent with a higher mRNA level of the CAP1 gene. In addition, the mitochondrial membrane potential of C. albicans cells changed significantly ( p<0.001) upon BE treatment compared with control. Taken together, our results indicate that BE treatment induces apoptosis in C.albicans cells, and the apoptosis was associated with the breakdown of mitochondrial membrane potential.
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Affiliation(s)
- Bao-Di Dai
- School of Pharmarcy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, P.R. China
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Kumaki Y, Ukai-Tadenuma M, Uno KID, Nishio J, Masumoto KH, Nagano M, Komori T, Shigeyoshi Y, Hogenesch JB, Ueda HR. Analysis and synthesis of high-amplitude Cis-elements in the mammalian circadian clock. Proc Natl Acad Sci U S A 2008; 105:14946-51. [PMID: 18815372 PMCID: PMC2553039 DOI: 10.1073/pnas.0802636105] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2008] [Indexed: 01/06/2023] Open
Abstract
Mammalian circadian clocks consist of regulatory loops mediated by Clock/Bmal1-binding elements, DBP/E4BP4 binding elements, and RevErbA/ROR binding elements. As a step toward system-level understanding of the dynamic transcriptional regulation of the oscillator, we constructed and used a mammalian promoter/enhancer database (http://promoter.cdb.riken.jp/) with computational models of the Clock/Bmal1-binding elements, DBP/E4BP4 binding elements, and RevErbA/ROR binding elements to predict new targets of the clock and subsequently validated these targets at the level of the cell and organism. We further demonstrated the predictive nature of these models by generating and testing synthetic regulatory elements that do not occur in nature and showed that these elements produced high-amplitude circadian gene regulation. Biochemical experiments to characterize these synthetic elements revealed the importance of the affinity balance between transactivators and transrepressors in generating high-amplitude circadian transcriptional output. These results highlight the power of comparative genomics approaches for system-level identification and knowledge-based design of dynamic regulatory circuits.
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Affiliation(s)
- Yuichi Kumaki
- *Laboratory for Systems Biology and
- INTEC Systems Institute, Inc., 1-3-3 Shinsuna, Koto-ku, Tokyo 136-0075, Japan
| | | | - Ken-ichiro D. Uno
- Functional Genomics Unit, Center for Developmental Biology, RIKEN, 2-2-3 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Junko Nishio
- Functional Genomics Unit, Center for Developmental Biology, RIKEN, 2-2-3 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Koh-hei Masumoto
- *Laboratory for Systems Biology and
- Department of Anatomy and Neurobiology, Kinki University School of Medicine, 377-2 Ohno-Higashi, Osaka-Sayama, Osaka 589-8511, Japan; and
| | - Mamoru Nagano
- Department of Anatomy and Neurobiology, Kinki University School of Medicine, 377-2 Ohno-Higashi, Osaka-Sayama, Osaka 589-8511, Japan; and
| | - Takashi Komori
- INTEC Systems Institute, Inc., 1-3-3 Shinsuna, Koto-ku, Tokyo 136-0075, Japan
| | - Yasufumi Shigeyoshi
- Department of Anatomy and Neurobiology, Kinki University School of Medicine, 377-2 Ohno-Higashi, Osaka-Sayama, Osaka 589-8511, Japan; and
| | - John B. Hogenesch
- Institute for Translational Medicine and Therapeutics and the Department of Pharmacology, University of Pennsylvania School of Medicine, 810 Biomedical Research Building II/III, 421 Curie Boulevard, Philadelphia, PA 19104-6160
| | - Hiroki R. Ueda
- *Laboratory for Systems Biology and
- Functional Genomics Unit, Center for Developmental Biology, RIKEN, 2-2-3 Minatojima-Minamimachi, Chuo-ku, Kobe 650-0047, Japan
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40
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Kitao H, Fujinaka Y, Kubo N, Nakanoko T, Yoshinaga K, Tokunaga E, Saeki H, Endo K, Morita M, Kakeji Y, Maehara Y. [Fanconi anemia and genomic instability]. Fukuoka Igaku Zasshi 2008; 99:115-122. [PMID: 18833937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Affiliation(s)
- Hiroyuki Kitao
- Department of Molecular Oncology, Graduate School of Medical Sciences, Kyushu University
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Abstract
The yeast DNA-binding protein GCN4 forms a homo-dimer through a self-complementary coiled-coil interface. In this article, we describe how such coiled-coils might be bistable and, through Molecular Dynamics computations on the GCN4 coiled coil, we show that the coiled coil can indeed switch between the two states by a pathway in which there is a progressive "flipping" of consecutive steps along the interface. We discuss the general implications of potentially bistable coiled-coil interfaces for allosteric signal-transmission mechanisms along homo-dimeric coiled coils and for the packing of helices in globular proteins.
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Affiliation(s)
- Charles A Laughton
- School of Pharmacy, University of Nottingham, Nottingham NG7 2RD, United Kingdom
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42
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Seong KM, Baek JH, Ahn BY, Yu MH, Kim J. Rpn10p is a receptor for ubiquitinated Gcn4p in proteasomal proteolysis. Mol Cells 2007; 24:194-9. [PMID: 17978571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023] Open
Abstract
GCN4 is a typical eukaryotic transcriptional activator that is implicated in the expression of many genes involved in amino acids and purine biosyntheses under stress conditions. It is degraded by 26S proteasomes following ubiquitination. However, the immediate receptor for ubiquitinated Gcn4p has not yet been identified. We investigated whether ubiquitinated Gcn4p binds directly to Rpn10p as the ubiquitinated substrate receptor of the 26S proteasome. We found that the level of Gcn4p increased in cells deleted for Rpn10p but not in cells deleted for RAD23 and DSK2, the other ubiquitinated substrate receptors and, unlike Rpn10p, neither of these proteins recognized ubiquitinated Gcn4p. These results suggest that Rpn10p is the receptor that binds the polyubiquitin chain during ubiquitin-dependent proteolysis of Gcn4p.
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Affiliation(s)
- Ki Moon Seong
- School of Life Sciences and Biotechnology, Korea University, Seoul 136-701, Korea
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43
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Abstract
The TBP (TATA-box-binding protein), Tbp1p, plays a vital role in all three classes of transcription by RNA polymerases I-III. A TBP1(E186D) mutation had been described that affected interaction of Tbp1p with TFIIB (transcription factor IIB) and that caused slow-growth, temperature-sensitivity, 3-aminotriazole-sensitivity as well as a gal(-) phenotype. We used the TBP1(E186D) mutant for suppressor screens, and we isolated TFIIB/SUA7(E202G) as an allele-specific suppressor of all phenotypes caused by the TBP1(E186D) mutation. Our results show that the SUA7(E202G) mutation restored binding of TFIIB to Tbp1(E186D)p. In addition, we observed that Tbp1(E186D)p was expressed at a lower level than wild-type Tbp1p, and that SUA7(E202G) restored the protein level of Tbp1(E186D)p. This suggested that the TBP1(E186D) mutation might have generated its phenotypes by making Tbp1p the limiting factor for activated transcription. DNA microarray analysis indicated that the TBP1(E186D) temperature-sensitivity and slow-growth phenotypes might have been caused by insufficient amounts of Tbp1p for efficient transcription of the rRNA genes by RNA polymerase I.
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Affiliation(s)
- Boon Shang Chew
- Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Singapore 117597, Singapore
| | - Norbert Lehming
- Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Singapore 117597, Singapore
- To whom correspondence should be addressed (email )
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De Filippi L, Fournier M, Cameroni E, Linder P, De Virgilio C, Foti M, Deloche O. Membrane stress is coupled to a rapid translational control of gene expression in chlorpromazine-treated cells. Curr Genet 2007; 52:171-85. [PMID: 17710403 DOI: 10.1007/s00294-007-0151-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2007] [Revised: 07/30/2007] [Accepted: 07/31/2007] [Indexed: 11/25/2022]
Abstract
Chlorpromazine (CPZ) is a small permeable cationic amphiphilic molecule that inserts into membrane bilayers and binds to anionic lipids such as poly-phosphoinositides (PIs). Since PIs play important roles in many cellular processes, including signaling and membrane trafficking pathways, it has been proposed that CPZ affects cellular growth functions by preventing the recruitment of proteins with specific PI-binding domains. In this study, we have investigated the biological effects of CPZ in the yeast Saccharomyces cerevisiae. We screened a collection of approximately 4,800 gene knockout mutants, and found that mutants defective in membrane trafficking between the late-Golgi and endosomal compartments are highly sensitive to CPZ. Microscopy and transport analyses revealed that CPZ affects membrane structure of organelles, blocks membrane transport and activates the unfolded protein response (UPR). In addition, CPZ-treatment induces phosphorylation of the translation initiation factor (eIF2alpha), which reduces the general rate of protein synthesis and stimulates the production of Gcn4p, a major transcription factor that is activated in response to environmental stresses. Altogether, our results reveal that membrane stress within the cells rapidly activates an important gene expression program, which is followed by a general inhibition of protein synthesis. Remarkably, the increase of phosphorylated eIF2alpha and protein synthesis inhibition were also detected in CPZ-treated NIH-3T3 fibroblasts, suggesting the existence of a conserved mechanism of translational regulation that operates during a membrane stress.
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Affiliation(s)
- Loic De Filippi
- Département de Microbiologie et Médecine Moléculaire, Centre Médical Universitaire, Université de Genève, 1 rue Michel-Servet, 1211 Geneva 4, Switzerland
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45
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Balakrishnan G, Hu Y, Case MA, Spiro TG. Microsecond melting of a folding intermediate in a coiled-coil peptide, monitored by T-jump/UV Raman spectroscopy. J Phys Chem B 2007; 110:19877-83. [PMID: 17020373 DOI: 10.1021/jp061987f] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A truncated version of the GCN4 coiled-coil peptide has been studied by ultraviolet resonance Raman (UVRR) spectroscopy with 197 nm excitation, where amide modes are optimally enhanced. Although the CD melting curve could be satisfactorily described with a two-state transition having Tm = 30 degrees C, singular value decomposition of the UVRR data yielded three principal components, whose temperature dependence implicates an intermediate form between the folded and unfolded forms, with formation and melting temperatures of 10 and 40 degrees C. Two alpha-helical amide III bands, at 1340 and 1300 cm(-1), melted out selectively at 10 and 40 degrees C, respectively, and are assigned to hydrated and unhydrated helical regions. The hydrated regions are proposed to be melted in the intermediate form, while the unhydrated regions are intact. Time-resolved UVRR spectra following laser-induced temperature jumps revealed two relaxations, with time constants of 0.2 and 15 mus. These are suggested to reflect the melting times of hydrated and unhydrated helices. The unhydrated helical region may be associated with a 14-residue "trigger" sequence that has been identified in the C-terminal half of GCN4. Dehydration of helices may be a key step in the folding of coiled-coils.
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46
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Yang HT, Hsu CP, Hwang MJ. An analytical rate expression for the kinetics of gene transcription mediated by dimeric transcription factors. J Biochem 2007; 142:135-44. [PMID: 17652330 DOI: 10.1093/jb/mvm151] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
To model gene transcription kinetics, empirical fitting with the Hill function or S-system is often used. In this study, we derived an analytical expression for gene transcription rates in a manner similar to that developed for enzyme kinetics to describe the kinetics of gene transcription mediated by dimeric transcription factors (TFs) such as Gcn4p, a Saccharomyces cerevisiae master gene regulator. We showed that the analytical rate expression and its parameters estimated from several sets of experimental data could accurately reproduce the experimentally measured promoter-binding activity of Gcn4p. Furthermore, the analytical rate expression allowed us to derive analytically, rather than fit empirically, the parameters of the Hill function and S-system for use in modelling transcription kinetics. We found that a plot of gene transcription rate against Gcn4p concentration gave a sigmoidal dose-response curve with a positive co-operativity Hill coefficient (approximately 1.25), in accordance with previous experimental findings on the promoter binding of dimeric TFs. The characteristics of the dose-response curve around the estimated cellular Gcn4p concentration suggest that transcription regulation is efficiently controlled under physiological conditions. This work is a useful initial step towards analytically modelling and simulating complicated gene transcription networks.
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Affiliation(s)
- Hsih-Te Yang
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan
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Martín-Marcos P, Hinnebusch AG, Tamame M. Ribosomal protein L33 is required for ribosome biogenesis, subunit joining, and repression of GCN4 translation. Mol Cell Biol 2007; 27:5968-85. [PMID: 17548477 PMCID: PMC1952170 DOI: 10.1128/mcb.00019-07] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We identified a mutation in the 60S ribosomal protein L33A (rpl33a-G76R) that elicits derepression of GCN4 translation (Gcd- phenotype) by allowing scanning preinitiation complexes to bypass inhibitory upstream open reading frame 4 (uORF4) independently of prior uORF1 translation and reinitiation. At 37 degrees C, rpl33a-G76R confers defects in 60S biogenesis comparable to those produced by the deletion of RPL33A (DeltaA). At 28 degrees C, however, the 60S biogenesis defect is less severe in rpl33a-G76R than in DeltaA cells, yet rpl33a-G76R confers greater derepression of GCN4 and a larger reduction in general translation. Hence, it appears that rpl33a-G76R has a stronger effect on ribosomal-subunit joining than does a comparable reduction of wild-type 60S levels conferred by DeltaA. We suggest that rpl33a-G76R alters the 60S subunit in a way that impedes ribosomal-subunit joining and thereby allows 48S rRNA complexes to abort initiation at uORF4, resume scanning, and initiate downstream at GCN4. Because overexpressing tRNAiMet suppresses the Gcd- phenotype of rpl33a-G76R cells, dissociation of tRNAiMet from the 40S subunit may be responsible for abortive initiation at uORF4 in this mutant. We further demonstrate that rpl33a-G76R impairs the efficient processing of 35S and 27S pre-rRNAs and reduces the accumulation of all four mature rRNAs, indicating an important role for L33 in the biogenesis of both ribosomal subunits.
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Affiliation(s)
- Pilar Martín-Marcos
- Instituto de Microbiología Bioquímica, CSIC/Universidad de Salamanca, Edificio Departamental de Biología, Campus Miguel de Unamuno, 37007 Salamanca, Spain
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Tian C, Kasuga T, Sachs MS, Glass NL. Transcriptional profiling of cross pathway control in Neurospora crassa and comparative analysis of the Gcn4 and CPC1 regulons. Eukaryot Cell 2007; 6:1018-29. [PMID: 17449655 PMCID: PMC1951524 DOI: 10.1128/ec.00078-07] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2007] [Accepted: 04/16/2007] [Indexed: 11/20/2022]
Abstract
Identifying and characterizing transcriptional regulatory networks is important for guiding experimental tests on gene function. The characterization of regulatory networks allows comparisons among both closely and distantly related species, providing insight into network evolution, which is predicted to correlate with the adaptation of different species to particular environmental niches. One of the most intensely studied regulatory factors in the yeast Saccharomyces cerevisiae is the bZIP transcription factor Gcn4p. Gcn4p is essential for a global transcriptional response when S. cerevisiae experiences amino acid starvation. In the filamentous ascomycete Neurospora crassa, the ortholog of GCN4 is called the cross pathway control-1 (cpc-1) gene; it is required for the ability of N. crassa to induce a number of amino acid biosynthetic genes in response to amino acid starvation. Here, we deciphered the CPC1 regulon by profiling transcription in wild-type and cpc-1 mutant strains with full-genome N. crassa 70-mer oligonucleotide microarrays. We observed that at least 443 genes were direct or indirect CPC1 targets; these included 67 amino acid biosynthetic genes, 16 tRNA synthetase genes, and 13 vitamin-related genes. Comparison among the N. crassa CPC1 transcriptional profiling data set and the Gcn4/CaGcn4 data sets from S. cerevisiae and Candida albicans revealed a conserved regulon of 32 genes, 10 of which are predicted to be directly regulated by Gcn4p/CPC1. The 32-gene conserved regulon comprises mostly amino acid biosynthetic genes. The comparison of regulatory networks in species with clear orthology among genes sheds light on how gene interaction networks evolve.
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Affiliation(s)
- Chaoguang Tian
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California 94720-3102, Oregon Health and Science University, Beaverton, Oregon 97006-8921
| | - Takao Kasuga
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California 94720-3102, Oregon Health and Science University, Beaverton, Oregon 97006-8921
| | - Matthew S. Sachs
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California 94720-3102, Oregon Health and Science University, Beaverton, Oregon 97006-8921
| | - N. Louise Glass
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California 94720-3102, Oregon Health and Science University, Beaverton, Oregon 97006-8921
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Mohammad-Qureshi SS, Haddad R, Hemingway EJ, Richardson JP, Pavitt GD. Critical contacts between the eukaryotic initiation factor 2B (eIF2B) catalytic domain and both eIF2beta and -2gamma mediate guanine nucleotide exchange. Mol Cell Biol 2007; 27:5225-34. [PMID: 17526738 PMCID: PMC1951959 DOI: 10.1128/mcb.00495-07] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Diverse guanine nucleotide exchange factors (GEFs) regulate the activity of GTP binding proteins. One of the most complicated pairs is eukaryotic initiation factor 2B (eIF2B) and eIF2, which function during protein synthesis initiation in eukaryotes. We have mutated conserved surface residues within the eIF2B GEF domain, located at the eIF2Bepsilon C terminus. Extensive genetic and biochemical characterization established how these residues contribute to GEF activity. We find that the universally conserved residue E569 is critical for activity and that even a conservative E569D substitution is lethal in vivo. Several mutations within residues close to E569 have no discernible effect on growth or GCN4 expression, but an alanine substitution at the adjacent L568 is cold sensitive and deregulates GCN4 activity at 15 degrees C. The mutation of W699, found on a separate surface approximately 40 A from E569, is also lethal. Binding studies show that W699 is critical for interaction with eIF2beta, while L568 and E569 are not. In contrast, all three residues are critical for interaction with eIF2gamma. These data show that multiple contacts between eIF2gamma and eIF2Bepsilon mediate nucleotide exchange.
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50
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Abstract
An efficient oxidative stress response (OSR) is important for the facultative pathogenic yeast Candida albicans to survive within the human host. We used a large scale 2-D protein gel electrophoresis approach to analyze the stress response mechanisms of C. albicans after treatment with hydrogen peroxide and the thiol oxidizing agent, diamide. Quantitation of in vivo protein synthesis after pulse labeling of the proteins with radioactive L-[35S]-methionine resulted in characteristic proteome signatures for hydrogen peroxide and diamide with significant overlap of 21 up-regulated proteins for both stressors. Among the induced proteins were enzymes with known antioxidant functions like catalase or thioredoxin reductase and a set of oxidoreductases. 2-D gel analysis of mutants in the CAP1 gene revealed that the synthesis of 12 proteins is controlled by the oxidative stress regulator Cap1p. Stressing its importance for the C. albicans OSR, all 12 proteins were also induced after oxidative challenge by hydrogen peroxide or diamide.
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Affiliation(s)
- Harald Kusch
- Institut für Molekulare Infektionsbiologie, Julius-Maximilians-Universität, Würzburg, Germany.
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