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Battista S, Fedele M, Secco L, Ingo AMD, Sgarra R, Manfioletti G. Binding to the Other Side: The AT-Hook DNA-Binding Domain Allows Nuclear Factors to Exploit the DNA Minor Groove. Int J Mol Sci 2024; 25:8863. [PMID: 39201549 PMCID: PMC11354804 DOI: 10.3390/ijms25168863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2024] [Revised: 08/08/2024] [Accepted: 08/10/2024] [Indexed: 09/02/2024] Open
Abstract
The "AT-hook" is a peculiar DNA-binding domain that interacts with DNA in the minor groove in correspondence to AT-rich sequences. This domain has been first described in the HMGA protein family of architectural factors and later in various transcription factors and chromatin proteins, often in association with major groove DNA-binding domains. In this review, using a literature search, we identified about one hundred AT-hook-containing proteins, mainly chromatin proteins and transcription factors. After considering the prototypes of AT-hook-containing proteins, the HMGA family, we review those that have been studied in more detail and that have been involved in various pathologies with a particular focus on cancer. This review shows that the AT-hook is a domain that gives proteins not only the ability to interact with DNA but also with RNA and proteins. This domain can have enzymatic activity and can influence the activity of the major groove DNA-binding domain and chromatin docking modules when present, and its activity can be modulated by post-translational modifications. Future research on the function of AT-hook-containing proteins will allow us to better decipher their function and contribution to the different pathologies and to eventually uncover their mutual influences.
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Affiliation(s)
- Sabrina Battista
- Institute of Experimental Endocrinology and Oncology “G. Salvatore” (IEOS), National Research Council (CNR), 80131 Naples, Italy; (S.B.); (M.F.)
| | - Monica Fedele
- Institute of Experimental Endocrinology and Oncology “G. Salvatore” (IEOS), National Research Council (CNR), 80131 Naples, Italy; (S.B.); (M.F.)
| | - Luca Secco
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (L.S.); (A.M.D.I.)
| | | | - Riccardo Sgarra
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (L.S.); (A.M.D.I.)
| | - Guidalberto Manfioletti
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (L.S.); (A.M.D.I.)
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2
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Zhou Y, Richmond A, Yan C. Harnessing the potential of CD40 agonism in cancer therapy. Cytokine Growth Factor Rev 2024; 75:40-56. [PMID: 38102001 PMCID: PMC10922420 DOI: 10.1016/j.cytogfr.2023.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 11/22/2023] [Indexed: 12/17/2023]
Abstract
CD40 is a member of the tumor necrosis factor (TNF) receptor superfamily of receptors expressed on a variety of cell types. The CD40-CD40L interaction gives rise to many immune events, including the licensing of dendritic cells to activate CD8+ effector T cells, as well as the facilitation of B cell activation, proliferation, and differentiation. In malignant cells, the expression of CD40 varies among cancer types, mediating cellular proliferation, apoptosis, survival and the secretion of cytokines and chemokines. Agonistic human anti-CD40 antibodies are emerging as an option for cancer treatment, and early-phase clinical trials explored its monotherapy or combination with radiotherapy, chemotherapy, immune checkpoint blockade, and other immunomodulatory approaches. In this review, we present the current understanding of the mechanism of action for CD40, along with results from the clinical development of agonistic human CD40 antibodies in cancer treatment (selicrelumab, CDX-1140, APX005M, mitazalimab, 2141-V11, SEA-CD40, LVGN7409, and bispecific antibodies). This review also examines the safety profile of CD40 agonists in both preclinical and clinical settings, highlighting optimized dosage levels, potential adverse effects, and strategies to mitigate them.
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Affiliation(s)
- Yang Zhou
- Tennessee Valley Healthcare System, Department of Veteran Affairs, Nashville, TN, USA; Vanderbilt University School of Medicine, Department of Pharmacology, Nashville, TN, USA
| | - Ann Richmond
- Tennessee Valley Healthcare System, Department of Veteran Affairs, Nashville, TN, USA; Vanderbilt University School of Medicine, Department of Pharmacology, Nashville, TN, USA
| | - Chi Yan
- Tennessee Valley Healthcare System, Department of Veteran Affairs, Nashville, TN, USA; Vanderbilt University School of Medicine, Department of Pharmacology, Nashville, TN, USA.
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3
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Zhang D, Zhang H, Lu J, Hu X. Multiomics Data Reveal the Important Role of ANXA2R in T Cell-mediated Rejection After Renal Transplantation. Transplantation 2024; 108:430-444. [PMID: 37677931 PMCID: PMC10798590 DOI: 10.1097/tp.0000000000004754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/14/2023] [Accepted: 06/29/2023] [Indexed: 09/09/2023]
Abstract
BACKGROUND T cell-mediated rejection (TCMR) is a severe issue after renal transplantation, but research on its T cell-receptor (TCR) repertoire is lacking. This study intended to elucidate the TCR repertoire landscape in TCMR and hence identify novel potential targets. METHODS A total of 12 multiomics data sets were collected. The TRUST4 algorithm was used to construct and analyze the TCR repertoire in renal allografts with TCMR and stable renal function. Then, novel TCR-related key genes were identified through various criteria and literature research. In bulk transcriptome, cell line, single-cell transcriptome data sets, multiple immune cell infiltration algorithms, and gene set enrichment analysis were used to analyze potential mechanisms of the identified key gene. Twenty-three pathological sections were collected for immunofluorescence staining in the clinical cohort. Finally, the diagnostic and prognostic values of ANXA2R were evaluated in multiple renal transplant data sets. RESULTS Allografts with TCMR showed significantly increased clonotype and specific clonal expansion. ANXA2R was found to be a novel key gene for TCMR and showed strong positive connections with the TCR complex and lymphocyte cells, especially CD8 + T cells. Immunofluorescence staining confirmed the existence of ANXA2R + CD8 + T cells, with their percentage significantly elevated in TCMR compared with stable renal function. Finally, both mRNA and protein levels of ANXA2R showed promising diagnostic and prognostic value for renal transplant recipients. CONCLUSIONS ANXA2R , identified as a novel TCR-related gene, had critical roles in clinicopathology, diagnosis, and prognosis in renal transplantation, which offered promising potential therapeutic targets.
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Affiliation(s)
- Di Zhang
- Department of Urology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
- Institute of Urology, Capital Medical University, Beijing, China
| | - He Zhang
- Department of Urology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
- Institute of Urology, Capital Medical University, Beijing, China
| | - Jun Lu
- Department of Pathology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Xiaopeng Hu
- Department of Urology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
- Institute of Urology, Capital Medical University, Beijing, China
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4
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Price TR, Emfinger CH, Schueler KL, King S, Nicholson R, Beck T, Yandell BS, Summers SA, Holland WL, Krauss RM, Keller MP, Attie AD. Identification of genetic drivers of plasma lipoprotein size in the Diversity Outbred mouse population. J Lipid Res 2023; 64:100471. [PMID: 37944753 PMCID: PMC10750189 DOI: 10.1016/j.jlr.2023.100471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 10/28/2023] [Accepted: 10/31/2023] [Indexed: 11/12/2023] Open
Abstract
Despite great progress in understanding lipoprotein physiology, there is still much to be learned about the genetic drivers of lipoprotein abundance, composition, and function. We used ion mobility spectrometry to survey 16 plasma lipoprotein subfractions in 500 Diversity Outbred mice maintained on a Western-style diet. We identified 21 quantitative trait loci (QTL) affecting lipoprotein abundance. To refine the QTL and link them to disease risk in humans, we asked if the human homologs of genes located at each QTL were associated with lipid traits in human genome-wide association studies. Integration of mouse QTL with human genome-wide association studies yielded candidate gene drivers for 18 of the 21 QTL. This approach enabled us to nominate the gene encoding the neutral ceramidase, Asah2, as a novel candidate driver at a QTL on chromosome 19 for large HDL particles (HDL-2b). To experimentally validate Asah2, we surveyed lipoproteins in Asah2-/- mice. Compared to wild-type mice, female Asah2-/- mice showed an increase in several lipoproteins, including HDL. Our results provide insights into the genetic regulation of circulating lipoproteins, as well as mechanisms by which lipoprotein subfractions may affect cardiovascular disease risk in humans.
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Affiliation(s)
- Tara R Price
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Kathryn L Schueler
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Sarah King
- School of Medicine, University of California-San Francisco, San Francisco, CA, USA
| | - Rebekah Nicholson
- Department of Nutrition and Integrative Physiology, University of Utah, Salt Lake City, UT, USA
| | - Tim Beck
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Brian S Yandell
- Department of Statistics, University of Wisconsin-Madison, Madison, WI, USA
| | - Scott A Summers
- Department of Nutrition and Integrative Physiology, University of Utah, Salt Lake City, UT, USA
| | - William L Holland
- Department of Nutrition and Integrative Physiology, University of Utah, Salt Lake City, UT, USA
| | - Ronald M Krauss
- School of Medicine, University of California-San Francisco, San Francisco, CA, USA
| | - Mark P Keller
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Alan D Attie
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA.
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5
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Ho PJ, Khng AJ, Tan BKT, Lim GH, Tan SM, Tan VKM, Tan RSYC, Lim EH, Iau PTC, Chew YJ, Lim YY, Hartman M, Tan EY, Li J. Alterations to DNA methylation patterns induced by chemotherapy treatment are associated with negative impacts on the olfactory pathway. Breast Cancer Res 2023; 25:136. [PMID: 37932858 PMCID: PMC10626732 DOI: 10.1186/s13058-023-01730-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 10/15/2023] [Indexed: 11/08/2023] Open
Abstract
BACKGROUND Exposure to cytotoxic chemotherapy treatment may alter DNA methylation (DNAm) in breast cancer patients. METHODS We performed DNAm analysis in 125 breast cancer patients with blood drawn before and after chemotherapy, using the Illumina MethylationEPIC array. DNAm changes of 588,798 individual CpGs (including 41,207 promoter regions) were evaluated using linear regression models adjusted for monocyte proportion. Gene set enrichment analyses (GSEA) were conducted to identify key Gene Ontology (GO) biological processes or Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways associated with chemotherapy. Results were validated in a separate cohort of breast cancer patients who were treated (n = 1273) and not treated (n = 872) by chemotherapy (1808 blood, 337 saliva). RESULTS A total of 141 differentially methylated CpGs and 11 promoters were significantly associated with chemotherapy after multiple testing corrections in both the paired sample and single time point analyses. GSEA of promoter regions (pre-ranked by test statistics) identified six suppressed biological processes (p < 4.67e-8) related to sensory perception and detection of chemical stimuli, including smell perception (GO:0007606, GO:0007608, GO:0009593, GO:0050906, GO:0050907, and GO:0050911). The same six biological processes were significantly suppressed in the validation dataset (p < 9.02e-14). The KEGG pathway olfactory transduction (hsa04740) was also found to be significantly suppressed (ppaired-samples = 1.72e-9, psingle-timepoint-blood = 2.03e-15 and psingle-timepoint-saliva = 7.52e-56). CONCLUSION The enrichment of imprinted genes within biological processes and pathways suggests a biological mechanism by which chemotherapy could affect the perception of smell.
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Affiliation(s)
- Peh Joo Ho
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Republic of Singapore
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Republic of Singapore
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Republic of Singapore
| | - Alexis Jiaying Khng
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Republic of Singapore
| | - Benita Kiat-Tee Tan
- Department of Breast Surgery, Singapore General Hospital, Singapore, Republic of Singapore
- Division of Surgery and Surgical Oncology, National Cancer Centre Singapore, Singapore, Republic of Singapore
- Department of General Surgery, Sengkang General Hospital, Singapore, Republic of Singapore
| | - Geok Hoon Lim
- KK Breast Department, KK Women's and Children's Hospital, Singapore, 229899, Republic of Singapore
| | - Su-Ming Tan
- Division of Breast Surgery, Changi General Hospital, Singapore, Republic of Singapore
| | - Veronique Kiak Mien Tan
- Department of Breast Surgery, Singapore General Hospital, Singapore, Republic of Singapore
- Division of Surgery and Surgical Oncology, National Cancer Centre Singapore, Singapore, Republic of Singapore
| | - Ryan Shea Ying Cong Tan
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Republic of Singapore
- Oncology Academic Programme, Duke-NUS Medical School, Singapore, Republic of Singapore
| | - Elaine Hsuen Lim
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Republic of Singapore
| | - Philip Tsau-Choong Iau
- Department of Surgery, University Surgical Cluster, National University Health System, Singapore, 119228, Singapore
- Department of General Surgery, Ng Teng Fong General Hospital, 1 Jurong East St 21, Singapore, 609606, Republic of Singapore
| | - Ying Jia Chew
- Department of Surgery, University Surgical Cluster, National University Health System, Singapore, 119228, Singapore
- Department of General Surgery, Ng Teng Fong General Hospital, 1 Jurong East St 21, Singapore, 609606, Republic of Singapore
| | - Yi Ying Lim
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Republic of Singapore
| | - Mikael Hartman
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Republic of Singapore
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Republic of Singapore
- Department of Surgery, University Surgical Cluster, National University Health System, Singapore, 119228, Singapore
| | - Ern Yu Tan
- Department of General Surgery, Tan Tock Seng Hospital, Singapore, 308433, Republic of Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Republic of Singapore
| | - Jingmei Li
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore, 138672, Republic of Singapore.
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Republic of Singapore.
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6
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Wagner AH, Klersy A, Sultan CS, Hecker M. Potential role of soluble CD40 receptor in chronic inflammatory diseases. Biochem Pharmacol 2023; 217:115858. [PMID: 37863325 DOI: 10.1016/j.bcp.2023.115858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/11/2023] [Accepted: 10/12/2023] [Indexed: 10/22/2023]
Abstract
The CD40 receptor and its ligand CD154 are widely expressed in various immune-competent cells. Interaction of CD154 with CD40 is essential for B-cell growth, differentiation, and immunoglobulin class switching. Many other immune-competent cells involved in innate and adaptive immunity communicate through this co-stimulatory ligand-receptor dyad. CD40-CD154 interaction is involved in the pathogenesis of numerous inflammatory and autoimmune diseases. While CD40 and CD154 are membrane-bound proteins, their soluble counterparts are generated by proteolytic cleavage or alternative splicing. This review summarises current knowledge about the impact of single nucleotide polymorphisms in the human CD40 gene and compensatory changes in the plasma level of the soluble CD40 receptor (sCD40) isoform in related pro-inflammatory diseases. It discusses regulation patterns of the disintegrin metalloprotease ADAM17 function leading to ectodomain shedding of transmembrane proteins, such as pro-inflammatory adhesion molecules or CD40. The role of sCD40 as a potential biomarker for chronic inflammatory diseases will also be discussed.
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Affiliation(s)
- A H Wagner
- Department of Cardiovascular Physiology, Heidelberg University, Heidelberg, Germany.
| | - A Klersy
- Department of Cardiovascular Physiology, Heidelberg University, Heidelberg, Germany
| | - C S Sultan
- Department of Medical Chemistry, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - M Hecker
- Department of Cardiovascular Physiology, Heidelberg University, Heidelberg, Germany
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Foreman TW, Nelson CE, Sallin MA, Kauffman KD, Sakai S, Otaizo-Carrasquero F, Myers TG, Barber DL. CD30 co-stimulation drives differentiation of protective T cells during Mycobacterium tuberculosis infection. J Exp Med 2023; 220:e20222090. [PMID: 37097292 PMCID: PMC10130742 DOI: 10.1084/jem.20222090] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 02/24/2023] [Accepted: 04/04/2023] [Indexed: 04/26/2023] Open
Abstract
Control of Mycobacterium tuberculosis (Mtb) infection requires generation of T cells that migrate to granulomas, complex immune structures surrounding sites of bacterial replication. Here we compared the gene expression profiles of T cells in pulmonary granulomas, bronchoalveolar lavage, and blood of Mtb-infected rhesus macaques to identify granuloma-enriched T cell genes. TNFRSF8/CD30 was among the top genes upregulated in both CD4 and CD8 T cells from granulomas. In mice, CD30 expression on CD4 T cells is required for survival of Mtb infection, and there is no major role for CD30 in protection by other cell types. Transcriptomic comparison of WT and CD30-/- CD4 T cells from the lungs of Mtb-infected mixed bone marrow chimeric mice showed that CD30 directly promotes CD4 T cell differentiation and the expression of multiple effector molecules. These results demonstrate that the CD30 co-stimulatory axis is highly upregulated on granuloma T cells and is critical for protective T cell responses against Mtb infection.
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Affiliation(s)
- Taylor W. Foreman
- T Lymphocyte Biology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Christine E. Nelson
- T Lymphocyte Biology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Michelle A. Sallin
- T Lymphocyte Biology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Keith D. Kauffman
- T Lymphocyte Biology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Shunsuke Sakai
- T Lymphocyte Biology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Francisco Otaizo-Carrasquero
- Genomic Technologies Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Timothy G. Myers
- Genomic Technologies Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Daniel L. Barber
- T Lymphocyte Biology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
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8
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Ramírez-González A, Ávila-López P, Bahena-Román M, Contreras-Ochoa CO, Lagunas-Martínez A, Langley E, Manzo-Merino J, Madrid-Marina V, Torres-Poveda K. Critical Role of the Transcription Factor AKNA in T-Cell Activation: An Integrative Bioinformatics Approach. Int J Mol Sci 2023; 24:ijms24044212. [PMID: 36835622 PMCID: PMC9965657 DOI: 10.3390/ijms24044212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/13/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
The human akna gene encodes an AT-hook transcription factor, the expression of which is involved in various cellular processes. The goal of this study was to identify potential AKNA binding sites in genes that participate in T-cell activation and validate selected genes. Here we analyzed ChIP-seq and microarray assays to determine AKNA-binding motifs and the cellular process altered by AKNA in T-cell lymphocytes. In addition, we performed a validation analysis by RT-qPCR to assess AKNA's role in promoting IL-2 and CD80 expression. We found five AT-rich motifs that are potential candidates as AKNA response elements. We identified these AT-rich motifs in promoter regions of more than a thousand genes in activated T-cells, and demonstrated that AKNA induces the expression of genes involved in helper T-cell activation, such as IL-2. The genomic enrichment and prediction of AT-rich motif analyses demonstrated that AKNA is a transcription factor that can potentially modulate gene expression by recognizing AT-rich motifs in a plethora of genes that are involved in different molecular pathways and processes. Among the cellular processes activated by AT-rich genes, we found inflammatory pathways potentially regulated by AKNA, suggesting AKNA is acting as a master regulator during T-cell activation.
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Affiliation(s)
- Abrahan Ramírez-González
- Center for Research on Infectious Diseases, Instituto Nacional de Salud Pública, Cuernavaca 62100, Mexico
| | - Pedro Ávila-López
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Margarita Bahena-Román
- Center for Research on Infectious Diseases, Instituto Nacional de Salud Pública, Cuernavaca 62100, Mexico
| | - Carla O. Contreras-Ochoa
- Center for Research on Infectious Diseases, Instituto Nacional de Salud Pública, Cuernavaca 62100, Mexico
| | - Alfredo Lagunas-Martínez
- Center for Research on Infectious Diseases, Instituto Nacional de Salud Pública, Cuernavaca 62100, Mexico
| | - Elizabeth Langley
- Department of Basic Research, Instituto Nacional de Cancerología, Mexico City 14080, Mexico
| | - Joaquín Manzo-Merino
- Department of Basic Research, Instituto Nacional de Cancerología, Mexico City 14080, Mexico
- Consejo Nacional de Ciencia y Tecnología (CONACyT), Instituto Nacional de Cancerología, Mexico City 03940, Mexico
| | - Vicente Madrid-Marina
- Center for Research on Infectious Diseases, Instituto Nacional de Salud Pública, Cuernavaca 62100, Mexico
| | - Kirvis Torres-Poveda
- Center for Research on Infectious Diseases, Instituto Nacional de Salud Pública, Cuernavaca 62100, Mexico
- Consejo Nacional de Ciencia y Tecnología (CONACyT), Instituto Nacional de Salud Pública, Cuernavaca 03940, Mexico
- Correspondence: ; Tel.:+52-777-3293000 (ext. 2204)
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9
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Tanjak P, Chaiboonchoe A, Suwatthanarak T, Acharayothin O, Thanormjit K, Chanthercrob J, Suwatthanarak T, Wannasuphaphol B, Chumchuen K, Suktitipat B, Sampattavanich S, Korphaisarn K, Pongpaibul A, Poungvarin N, Grove H, Riansuwan W, Trakarnsanga A, Methasate A, Pithukpakorn M, Chinswangwatanakul V. The KRAS-Mutant Consensus Molecular Subtype 3 Reveals an Immunosuppressive Tumor Microenvironment in Colorectal Cancer. Cancers (Basel) 2023; 15:cancers15041098. [PMID: 36831441 PMCID: PMC9953921 DOI: 10.3390/cancers15041098] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 02/03/2023] [Accepted: 02/06/2023] [Indexed: 02/11/2023] Open
Abstract
Colorectal cancers (CRC) with KRAS mutations (KRASmut) are frequently included in consensus molecular subtype 3 (CMS3) with profound metabolic deregulation. We explored the transcriptomic impact of KRASmut, focusing on the tumor microenvironment (TME) and pathways beyond metabolic deregulation. The status of KRASmut in patients with CRC was investigated and overall survival (OS) was compared with wild-type KRAS (KRASwt). Next, we identified CMS, and further investigated differentially expressed genes (DEG) of KRASmut and distinctive pathways. Lastly, we used spatially resolved gene expression profiling to define the effect of KRASmut in the TME regions of CMS3-classified CRC tissues. CRC patients with KRASmut were mainly enriched in CMS3. Their specific enrichments of immune gene signatures in immunosuppressive TME were associated with worse OS. Activation of TGFβ signaling by KRASmut was related to reduced pro-inflammatory and cytokine gene signatures, leading to suppression of immune infiltration. Digital spatial profiling in TME regions of KRASmut CMS3-classified tissues suggested up-regulated genes, CD40, CTLA4, ARG1, STAT3, IDO, and CD274, that could be characteristic of immune suppression in TME. This study may help to depict the complex transcriptomic profile of KRASmut in immunosuppressive TME. Future studies and clinical trials in CRC patients with KRASmut should consider these transcriptional landscapes.
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Affiliation(s)
- Pariyada Tanjak
- Department of Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, Wanglang Road, Bangkok 10700, Thailand
- Siriraj Cancer Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Amphun Chaiboonchoe
- Siriraj Center of Research Excellent for Systems Pharmacology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
- Siriraj Genomics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Tharathorn Suwatthanarak
- Department of Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, Wanglang Road, Bangkok 10700, Thailand
| | - Onchira Acharayothin
- Department of Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, Wanglang Road, Bangkok 10700, Thailand
| | - Kullanist Thanormjit
- Department of Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, Wanglang Road, Bangkok 10700, Thailand
- Siriraj Cancer Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Jantappapa Chanthercrob
- Siriraj Center of Research Excellent for Systems Pharmacology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
- Siriraj Genomics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Thanawat Suwatthanarak
- Department of Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, Wanglang Road, Bangkok 10700, Thailand
- Siriraj Cancer Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Bundit Wannasuphaphol
- Department of Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, Wanglang Road, Bangkok 10700, Thailand
| | - Kemmapon Chumchuen
- Siriraj Genomics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Bhoom Suktitipat
- Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
- Integrative Computational Bioscience Center, Mahidol University, Nakhon Pathom 73170, Thailand
- Division of Medical Bioinformatics, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Somponnat Sampattavanich
- Siriraj Center of Research Excellent for Systems Pharmacology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
- Siriraj Genomics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Krittiya Korphaisarn
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Ananya Pongpaibul
- Department of Pathology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Naravat Poungvarin
- Department of Clinical Pathology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Harald Grove
- Division of Medical Bioinformatics, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Woramin Riansuwan
- Department of Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, Wanglang Road, Bangkok 10700, Thailand
| | - Atthaphorn Trakarnsanga
- Department of Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, Wanglang Road, Bangkok 10700, Thailand
| | - Asada Methasate
- Department of Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, Wanglang Road, Bangkok 10700, Thailand
| | - Manop Pithukpakorn
- Siriraj Genomics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
- Division of Medical Genetics, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Vitoon Chinswangwatanakul
- Department of Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, Wanglang Road, Bangkok 10700, Thailand
- Siriraj Cancer Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
- Correspondence:
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10
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Hrabar J, Petrić M, Cavallero S, Salvemini M, D’Amelio S, Mladineo I. Rat and fish peripheral blood leukocytes respond distinctively to Anisakis pegreffii (Nematoda, Anisakidae) crude extract. Front Cell Infect Microbiol 2022; 12:1042679. [PMID: 36590595 PMCID: PMC9797851 DOI: 10.3389/fcimb.2022.1042679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 11/18/2022] [Indexed: 12/23/2022] Open
Abstract
Infective third-stage larvae (L3) of the marine nematode Anisakis pegreffii cause inflammation and clinical symptoms in humans, their accidental host, that subside and self-resolve in a couple of weeks after L3 die. To characterise the differences in an early immune response of a marine vs. terrestrial host, we stimulated peripheral blood leukocytes (PBLs) of fish (paratenic host) and rat (accidental, human-model host) with A. pegreffii crude extract and analysed PBL transcriptomes 1 and 12 h post-stimulation. Fish and rat PBLs differentially expressed 712 and 493 transcripts, respectively, between 1 and 12 h post-stimulation (false discovery rate, FDR <0.001, logFC >2). While there was a difference in the highest upregulated transcripts between two time-points, the same Gene Ontologies, biological processes (intracellular signal transduction, DNA-dependent transcription, and DNA-regulated regulation of transcription), and molecular functions (ATP and metal ion binding) were enriched in the two hosts, showing an incrementing dynamic between 1 and 12 h. This suggests that the two distinct hosts employ qualitatively different transcript cascades only to achieve the same effect, at least during an early innate immunity response. Activation of later immunity elements and/or a combination of other host's intrinsic conditions may contribute to the death of L3 in the terrestrial host.
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Affiliation(s)
- Jerko Hrabar
- Laboratory of Aquaculture, Institute of Oceanography and Fisheries, Split, Croatia
| | - Mirela Petrić
- University Department of Marine Studies, University of Split, Split, Croatia
| | - Serena Cavallero
- Department of Public Health and Infectious Diseases, University of Rome, Sapienza, Rome, Italy
| | - Marco Salvemini
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Stefano D’Amelio
- Department of Public Health and Infectious Diseases, University of Rome, Sapienza, Rome, Italy
| | - Ivona Mladineo
- Laboratory of Functional Helminthology, Institute of Parasitology, Biology Centre of Czech Academy of Sciences, Ceske Budejovice, Czechia,*Correspondence: Ivona Mladineo,
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11
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Ramírez-González A, Manzo-Merino J, Contreras-Ochoa CO, Bahena-Román M, Aguilar-Villaseñor JM, Lagunas-Martínez A, Rosenstein Y, Madrid Marina V, Torres-Poveda K. Functional Role of AKNA: A Scoping Review. Biomolecules 2021; 11:1709. [PMID: 34827707 PMCID: PMC8615511 DOI: 10.3390/biom11111709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 11/12/2021] [Accepted: 11/13/2021] [Indexed: 11/16/2022] Open
Abstract
Human akna encodes an AT-hook transcription factor whose expression participates in various cellular processes. We conducted a scoping review on the literature regarding the functional role of AKNA according to the evidence found in human and in vivo and in vitro models, stringently following the "PRISMA-ScR" statement recommendations. METHODS We undertook an independent PubMed literature search using the following search terms, AKNA OR AKNA ADJ gene OR AKNA protein, human OR AKNA ADJ functions. Observational and experimental articles were considered. The selected studies were categorized using a pre-determined data extraction form. A narrative summary of the evidence was produced. RESULTS AKNA modulates the expression of CD40 and CD40L genes in immune system cells. It is a negative regulator of inflammatory processes as evidenced by knockout mouse models and observational studies for several autoimmune and inflammatory diseases. Furthermore, AKNA contributes to the de-regulation of the immune system in cancer, and it has been proposed as a susceptibility genetic factor and biomarker in CC, GC, and HNSCC. Finally, AKNA regulates neurogenesis by destabilizing the microtubules dynamics. CONCLUSION Our results provide evidence for the role of AKNA in various cellular processes, including immune response, inflammation, development, cancer, autoimmunity, and neurogenesis.
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Affiliation(s)
- Abrahán Ramírez-González
- Center for Research on Infectious Diseases, Instituto Nacional de Salud Pública, Cuernavaca 62100, Mexico; (A.R.-G.); (C.O.C.-O.); (M.B.-R.); (A.L.-M.); (V.M.M.)
| | - Joaquín Manzo-Merino
- Department of Basic Research, Instituto Nacional de Cancerología, Mexico City 14080, Mexico;
- Consejo Nacional de Ciencia y Tecnología (CONACyT)-Instituto Nacional de Cancerología, Mexico City 03940, Mexico
| | - Carla Olbia Contreras-Ochoa
- Center for Research on Infectious Diseases, Instituto Nacional de Salud Pública, Cuernavaca 62100, Mexico; (A.R.-G.); (C.O.C.-O.); (M.B.-R.); (A.L.-M.); (V.M.M.)
| | - Margarita Bahena-Román
- Center for Research on Infectious Diseases, Instituto Nacional de Salud Pública, Cuernavaca 62100, Mexico; (A.R.-G.); (C.O.C.-O.); (M.B.-R.); (A.L.-M.); (V.M.M.)
| | - José Manasés Aguilar-Villaseñor
- Centro Nacional para la Salud de la Infancia y la Adolescencia (CeNSIA)-Secretaría de Salud Federal, Mexico City 01480, Mexico;
| | - Alfredo Lagunas-Martínez
- Center for Research on Infectious Diseases, Instituto Nacional de Salud Pública, Cuernavaca 62100, Mexico; (A.R.-G.); (C.O.C.-O.); (M.B.-R.); (A.L.-M.); (V.M.M.)
| | - Yvonne Rosenstein
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Mexico City 62210, Mexico;
| | - Vicente Madrid Marina
- Center for Research on Infectious Diseases, Instituto Nacional de Salud Pública, Cuernavaca 62100, Mexico; (A.R.-G.); (C.O.C.-O.); (M.B.-R.); (A.L.-M.); (V.M.M.)
| | - Kirvis Torres-Poveda
- Center for Research on Infectious Diseases, Instituto Nacional de Salud Pública, Cuernavaca 62100, Mexico; (A.R.-G.); (C.O.C.-O.); (M.B.-R.); (A.L.-M.); (V.M.M.)
- CONACyT-Instituto Nacional de Salud Pública, Cuernavaca 03940, Mexico
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12
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A Homozygous AKNA Frameshift Variant Is Associated with Microcephaly in a Pakistani Family. Genes (Basel) 2021; 12:genes12101494. [PMID: 34680889 PMCID: PMC8535656 DOI: 10.3390/genes12101494] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 09/13/2021] [Accepted: 09/21/2021] [Indexed: 12/11/2022] Open
Abstract
Primary microcephaly (MCPH) is a prenatal condition of small brain size with a varying degree of intellectual disability. It is a heterogeneous genetic disorder with 28 associated genes reported so far. Most of these genes encode centrosomal proteins. Recently, AKNA was recognized as a novel centrosomal protein that regulates neurogenesis via microtubule organization, making AKNA a likely candidate gene for MCPH. Using linkage analysis and whole-exome sequencing, we found a frameshift variant in exon 12 of AKNA (NM_030767.4: c.2737delG) that cosegregates with microcephaly, mild intellectual disability and speech impairment in a consanguineous family from Pakistan. This variant is predicted to result in a protein with a truncated C-terminus (p.(Glu913Argfs*42)), which has been shown to be indispensable to AKNA’s localization to the centrosome and a normal brain development. Moreover, the amino acid sequence is altered from the beginning of the second of the two PEST domains, which are rich in proline (P), glutamic acid (E), serine (S), and threonine (T) and common to rapidly degraded proteins. An impaired function of the PEST domains may affect the intracellular half-life of the protein. Our genetic findings compellingly substantiate the predicted candidacy, based on its newly ascribed functional features, of the multifaceted protein AKNA for association with MCPH.
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13
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Meltzer S, Torgunrud A, Abrahamsson H, Solbakken AM, Flatmark K, Dueland S, Bakke KM, Bousquet PA, Negård A, Johansen C, Lyckander LG, Larsen FO, Schou JV, Redalen KR, Ree AH. The circulating soluble form of the CD40 costimulatory immune checkpoint receptor and liver metastasis risk in rectal cancer. Br J Cancer 2021; 125:240-246. [PMID: 33837301 PMCID: PMC8292313 DOI: 10.1038/s41416-021-01377-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 03/10/2021] [Accepted: 03/17/2021] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND In colorectal cancer, the inflamed tumour microenvironment with its angiogenic activities is immune- tolerant and incites progression to liver metastasis. We hypothesised that angiogenic and inflammatory factors in serum samples from patients with non-metastatic rectal cancer could inform on liver metastasis risk. METHODS We measured 84 angiogenic and inflammatory markers in serum sampled at the time of diagnosis within the population-based cohort of 122 stage I-III patients. In a stepwise manner, the statistically strongest proteins associated with time to development of liver metastasis were analysed in the corresponding serum samples from 273 stage II-III rectal cancer patients in three independent cohorts. RESULTS We identified the soluble form of the costimulatory immune checkpoint receptor cluster of differentiation molecule 40 (sCD40) as a marker of liver metastasis risk across all patient cohorts-the higher the sCD40 level, the shorter time to liver metastasis. In patients receiving neoadjuvant treatment, the sCD40 value remained an independent variable associated with progression to liver metastasis along with the local treatment response. Of note, serum sCD40 was not associated with progression to lung metastasis. CONCLUSIONS Circulating sCD40 is a marker of liver metastasis risk in rectal cancer and may be developed for use in clinical practice.
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Affiliation(s)
- Sebastian Meltzer
- grid.411279.80000 0000 9637 455XDepartment of Oncology, Akershus University Hospital, Lørenskog, Norway ,grid.411279.80000 0000 9637 455XDepartment of Clinical Molecular Biology, Akershus University Hospital, Lørenskog, Norway
| | - Annette Torgunrud
- grid.55325.340000 0004 0389 8485Department of Tumour Biology, Oslo University Hospital, Oslo, Norway
| | - Hanna Abrahamsson
- grid.411279.80000 0000 9637 455XDepartment of Oncology, Akershus University Hospital, Lørenskog, Norway ,grid.5510.10000 0004 1936 8921Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Arne Mide Solbakken
- grid.55325.340000 0004 0389 8485Department of Gastroenterological Surgery, Oslo University Hospital, Oslo, Norway
| | - Kjersti Flatmark
- grid.55325.340000 0004 0389 8485Department of Tumour Biology, Oslo University Hospital, Oslo, Norway ,grid.5510.10000 0004 1936 8921Institute of Clinical Medicine, University of Oslo, Oslo, Norway ,grid.55325.340000 0004 0389 8485Department of Gastroenterological Surgery, Oslo University Hospital, Oslo, Norway
| | - Svein Dueland
- grid.55325.340000 0004 0389 8485Department of Oncology, Oslo University Hospital, Oslo, Norway
| | - Kine Mari Bakke
- grid.411279.80000 0000 9637 455XDepartment of Oncology, Akershus University Hospital, Lørenskog, Norway ,grid.5510.10000 0004 1936 8921Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Paula Anna Bousquet
- grid.411279.80000 0000 9637 455XDepartment of Oncology, Akershus University Hospital, Lørenskog, Norway
| | - Anne Negård
- grid.5510.10000 0004 1936 8921Institute of Clinical Medicine, University of Oslo, Oslo, Norway ,grid.411279.80000 0000 9637 455XDepartment of Radiology, Akershus University Hospital, Lørenskog, Norway
| | - Christin Johansen
- grid.411279.80000 0000 9637 455XDepartment of Oncology, Akershus University Hospital, Lørenskog, Norway
| | - Lars Gustav Lyckander
- grid.411279.80000 0000 9637 455XDepartment of Pathology, Akershus University Hospital, Lørenskog, Norway
| | - Finn Ole Larsen
- grid.411646.00000 0004 0646 7402Department of Oncology, Herlev and Gentofte Hospital, Herlev, Denmark
| | - Jakob Vasehus Schou
- grid.411646.00000 0004 0646 7402Department of Oncology, Herlev and Gentofte Hospital, Herlev, Denmark
| | - Kathrine Røe Redalen
- grid.5947.f0000 0001 1516 2393Department of Physics, Norwegian University of Science and Technology, Trondheim, Norway
| | - Anne Hansen Ree
- grid.411279.80000 0000 9637 455XDepartment of Oncology, Akershus University Hospital, Lørenskog, Norway ,grid.5510.10000 0004 1936 8921Institute of Clinical Medicine, University of Oslo, Oslo, Norway
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14
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Zhang Z, Pan Q, Ge H, Xing L, Hong Y, Chen P. Deep learning-based clustering robustly identified two classes of sepsis with both prognostic and predictive values. EBioMedicine 2020; 62:103081. [PMID: 33181462 PMCID: PMC7658497 DOI: 10.1016/j.ebiom.2020.103081] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 09/19/2020] [Accepted: 10/07/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Sepsis is a heterogenous syndrome and individualized management strategy is the key to successful treatment. Genome wide expression profiling has been utilized for identifying subclasses of sepsis, but the clinical utility of these subclasses was limited because of the classification instability, and the lack of a robust class prediction model with extensive external validation. The study aimed to develop a parsimonious class model for the prediction of class membership and validate the model for its prognostic and predictive capability in external datasets. METHODS The Gene Expression Omnibus (GEO) and ArrayExpress databases were searched from inception to April 2020. Datasets containing whole blood gene expression profiling in adult sepsis patients were included. Autoencoder was used to extract representative features for k-means clustering. Genetic algorithms (GA) were employed to derive a parsimonious 5-gene class prediction model. The class model was then applied to external datasets (n = 780) to evaluate its prognostic and predictive performance. FINDINGS A total of 12 datasets involving 1613 patients were included. Two classes were identified in the discovery cohort (n = 685). Class 1 was characterized by immunosuppression with higher mortality than class 2 (21.8% [70/321] vs. 12.1% [44/364]; p < 0.01 for Chi-square test). A 5-gene class model (C14orf159, AKNA, PILRA, STOM and USP4) was developed with GA. In external validation cohorts, the 5-gene class model (AUC: 0.707; 95% CI: 0.664 - 0.750) performed better in predicting mortality than sepsis response signature (SRS) endotypes (AUC: 0.610; 95% CI: 0.521 - 0.700), and performed equivalently to the APACHE II score (AUC: 0.681; 95% CI: 0.595 - 0.767). In the dataset E-MTAB-7581, the use of hydrocortisone was associated with increased risk of mortality (OR: 3.15 [1.13, 8.82]; p = 0.029) in class 2. The effect was not statistically significant in class 1 (OR: 1.88 [0.70, 5.09]; p = 0.211). INTERPRETATION Our study identified two classes of sepsis that showed different mortality rates and responses to hydrocortisone therapy. Class 1 was characterized by immunosuppression with higher mortality rate than class 2. We further developed a 5-gene class model to predict class membership. FUNDING The study was funded by the National Natural Science Foundation of China (Grant No. 81,901,929).
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Affiliation(s)
- Zhongheng Zhang
- Department of Emergency Medicine, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310016, China.
| | - Qing Pan
- College of Information Engineering, Zhejiang University of Technology, 310023, Hangzhou, China.
| | - Huiqing Ge
- Department of Respiratory Care, Sir Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Lifeng Xing
- Department of Emergency Medicine, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310016, China.
| | - Yucai Hong
- Department of Emergency Medicine, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310016, China
| | - Pengpeng Chen
- Department of Emergency Medicine, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310016, China.
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15
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Margaryan A, Lawson DJ, Sikora M, Racimo F, Rasmussen S, Moltke I, Cassidy LM, Jørsboe E, Ingason A, Pedersen MW, Korneliussen T, Wilhelmson H, Buś MM, de Barros Damgaard P, Martiniano R, Renaud G, Bhérer C, Moreno-Mayar JV, Fotakis AK, Allen M, Allmäe R, Molak M, Cappellini E, Scorrano G, McColl H, Buzhilova A, Fox A, Albrechtsen A, Schütz B, Skar B, Arcini C, Falys C, Jonson CH, Błaszczyk D, Pezhemsky D, Turner-Walker G, Gestsdóttir H, Lundstrøm I, Gustin I, Mainland I, Potekhina I, Muntoni IM, Cheng J, Stenderup J, Ma J, Gibson J, Peets J, Gustafsson J, Iversen KH, Simpson L, Strand L, Loe L, Sikora M, Florek M, Vretemark M, Redknap M, Bajka M, Pushkina T, Søvsø M, Grigoreva N, Christensen T, Kastholm O, Uldum O, Favia P, Holck P, Sten S, Arge SV, Ellingvåg S, Moiseyev V, Bogdanowicz W, Magnusson Y, Orlando L, Pentz P, Jessen MD, Pedersen A, Collard M, Bradley DG, Jørkov ML, Arneborg J, Lynnerup N, Price N, Gilbert MTP, Allentoft ME, Bill J, Sindbæk SM, Hedeager L, Kristiansen K, Nielsen R, Werge T, Willerslev E. Population genomics of the Viking world. Nature 2020. [PMID: 32939067 DOI: 10.1038/s41586-020–2688-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The maritime expansion of Scandinavian populations during the Viking Age (about AD 750-1050) was a far-flung transformation in world history1,2. Here we sequenced the genomes of 442 humans from archaeological sites across Europe and Greenland (to a median depth of about 1×) to understand the global influence of this expansion. We find the Viking period involved gene flow into Scandinavia from the south and east. We observe genetic structure within Scandinavia, with diversity hotspots in the south and restricted gene flow within Scandinavia. We find evidence for a major influx of Danish ancestry into England; a Swedish influx into the Baltic; and Norwegian influx into Ireland, Iceland and Greenland. Additionally, we see substantial ancestry from elsewhere in Europe entering Scandinavia during the Viking Age. Our ancient DNA analysis also revealed that a Viking expedition included close family members. By comparing with modern populations, we find that pigmentation-associated loci have undergone strong population differentiation during the past millennium, and trace positively selected loci-including the lactase-persistence allele of LCT and alleles of ANKA that are associated with the immune response-in detail. We conclude that the Viking diaspora was characterized by substantial transregional engagement: distinct populations influenced the genomic makeup of different regions of Europe, and Scandinavia experienced increased contact with the rest of the continent.
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Affiliation(s)
- Ashot Margaryan
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Institute of Molecular Biology, National Academy of Sciences, Yerevan, Armenia.,Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Daniel J Lawson
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK.,School of Statistical Sciences, University of Bristol, Bristol, UK
| | - Martin Sikora
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Fernando Racimo
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Simon Rasmussen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ida Moltke
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Lara M Cassidy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Emil Jørsboe
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Andrés Ingason
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark.,Institute of Biological Psychiatry, Mental Health Services Copenhagen, Copenhagen, Denmark
| | - Mikkel W Pedersen
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Thorfinn Korneliussen
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,HSE University, Russian Federation National Research University Higher School of Economics, Moscow, Russia
| | - Helene Wilhelmson
- Department of Archaeology and Ancient History, Lund University, Lund, Sweden.,Sydsvensk Arkeologi AB, Kristianstad, Sweden
| | - Magdalena M Buś
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Peter de Barros Damgaard
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Rui Martiniano
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Gabriel Renaud
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Department of Health Technology, Section for Bioinformatics, Technical University of Denmark (DTU), Copenhagen, Denmark
| | - Claude Bhérer
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada
| | - J Víctor Moreno-Mayar
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,National Institute of Genomic Medicine (INMEGEN), Mexico City, Mexico
| | - Anna K Fotakis
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Marie Allen
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Raili Allmäe
- Archaeological Research Collection, Tallinn University, Tallinn, Estonia
| | - Martyna Molak
- Museum and Institute of Zoology, Polish Academy of Sciences, Warsaw, Poland
| | - Enrico Cappellini
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Gabriele Scorrano
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Hugh McColl
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Alexandra Buzhilova
- Anuchin Research Institute and Museum of Anthropology, Moscow State University, Moscow, Russia
| | - Allison Fox
- Manx National Heritage, Douglas, Isle of Man
| | - Anders Albrechtsen
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Birgitte Skar
- NTNU University Museum, Department of Archaeology and Cultural History, Trondheim, Norway
| | - Caroline Arcini
- The Archaeologists, National Historical Museums, Stockholm, Sweden
| | - Ceri Falys
- Thames Valley Archaeological Services (TVAS), Reading, UK
| | | | | | - Denis Pezhemsky
- Anuchin Research Institute and Museum of Anthropology, Moscow State University, Moscow, Russia
| | - Gordon Turner-Walker
- Department of Cultural Heritage Conservation, National Yunlin University of Science and Technology, Douliou, Taiwan
| | | | - Inge Lundstrøm
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Ingrid Gustin
- Department of Archaeology and Ancient History, Lund University, Lund, Sweden
| | - Ingrid Mainland
- UHI Archaeology Institute, University of the Highlands and Islands, Kirkwall, UK
| | - Inna Potekhina
- Department of Bioarchaeology, Institute of Archaeology of National Academy of Sciences of Ukraine, Kiev, Ukraine
| | - Italo M Muntoni
- Soprintendenza Archeologia, Belle Arti e Paesaggio per le Province di Barletta, Andria, Trani e Foggia, Foggia, Italy
| | - Jade Cheng
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Jesper Stenderup
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Jilong Ma
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Julie Gibson
- UHI Archaeology Institute, University of the Highlands and Islands, Kirkwall, UK
| | - Jüri Peets
- Archaeological Research Collection, Tallinn University, Tallinn, Estonia
| | | | - Katrine H Iversen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Health Technology, Section for Bioinformatics, Technical University of Denmark (DTU), Copenhagen, Denmark
| | | | - Lisa Strand
- NTNU University Museum, Department of Archaeology and Cultural History, Trondheim, Norway
| | - Louise Loe
- Heritage Burial Services, Oxford Archaeology, Oxford, UK
| | | | - Marek Florek
- Institute of Archaeology, Maria Curie-Sklodowska University in Lublin, Lublin, Poland
| | | | - Mark Redknap
- Department of History and Archaeology, Amgueddfa Cymru-National Museum Wales, Cardiff, UK
| | - Monika Bajka
- Trzy Epoki Archaeological Service, Klimontów, Poland
| | | | | | - Natalia Grigoreva
- Department of Slavic-Finnish Archaeology, Institute for the History of Material Culture, Russian Academy of Sciences, Saint Petersburg, Russia
| | | | - Ole Kastholm
- Department of Research and Heritage, Roskilde Museum, Roskilde, Denmark
| | | | - Pasquale Favia
- Department of Humanities, University of Foggia, Foggia, Italy
| | - Per Holck
- Department of Molecular Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Sabine Sten
- Department of Archaeology and Ancient History, Uppsala University Campus Gotland, Visby, Sweden
| | - Símun V Arge
- Tjóðsavnið - Faroe Islands National Museum, Tórshavn, Faroe Islands
| | - Sturla Ellingvåg
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Vayacheslav Moiseyev
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Science, St Petersburg, Russia
| | | | | | - Ludovic Orlando
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Peter Pentz
- National Museum of Denmark, Copenhagen, Denmark
| | | | | | - Mark Collard
- Department of Archaeology, Simon Fraser University, Burnaby, British Colombia, Canada
| | - Daniel G Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Marie Louise Jørkov
- Department of Forensic Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Jette Arneborg
- National Museum of Denmark, Copenhagen, Denmark.,School of GeoSciences, University of Edinburgh, Edinburgh, UK
| | - Niels Lynnerup
- Department of Forensic Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Neil Price
- Department of Archaeology and Ancient History, Uppsala University, Uppsala, Sweden
| | - M Thomas P Gilbert
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Department of Natural History, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Morten E Allentoft
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, Western Australia, Australia
| | - Jan Bill
- Museum of Cultural History, University of Oslo, Oslo, Norway
| | - Søren M Sindbæk
- Centre for Urban Network Evolutions (UrbNet), School of Culture and Society, Aarhus University, Højbjerg, Denmark
| | - Lotte Hedeager
- Institute of Archaeology, Conservation and History, Oslo, Norway
| | | | - Rasmus Nielsen
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. .,Department of Integrative Biology, UC Berkeley, Berkeley, CA, USA. .,Department of Statistics, UC Berkeley, Berkeley, CA, USA.
| | - Thomas Werge
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. .,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark. .,Institute of Biological Psychiatry, Mental Health Services Copenhagen, Copenhagen, Denmark. .,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Copenhagen, Denmark.
| | - Eske Willerslev
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. .,Department of Zoology, University of Cambridge, Cambridge, UK. .,The Danish Institute for Advanced Study, University of Southern Denmark, Odense, Denmark. .,The Wellcome Trust Sanger Institute, Cambridge, UK.
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16
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Margaryan A, Lawson DJ, Sikora M, Racimo F, Rasmussen S, Moltke I, Cassidy LM, Jørsboe E, Ingason A, Pedersen MW, Korneliussen T, Wilhelmson H, Buś MM, de Barros Damgaard P, Martiniano R, Renaud G, Bhérer C, Moreno-Mayar JV, Fotakis AK, Allen M, Allmäe R, Molak M, Cappellini E, Scorrano G, McColl H, Buzhilova A, Fox A, Albrechtsen A, Schütz B, Skar B, Arcini C, Falys C, Jonson CH, Błaszczyk D, Pezhemsky D, Turner-Walker G, Gestsdóttir H, Lundstrøm I, Gustin I, Mainland I, Potekhina I, Muntoni IM, Cheng J, Stenderup J, Ma J, Gibson J, Peets J, Gustafsson J, Iversen KH, Simpson L, Strand L, Loe L, Sikora M, Florek M, Vretemark M, Redknap M, Bajka M, Pushkina T, Søvsø M, Grigoreva N, Christensen T, Kastholm O, Uldum O, Favia P, Holck P, Sten S, Arge SV, Ellingvåg S, Moiseyev V, Bogdanowicz W, Magnusson Y, Orlando L, Pentz P, Jessen MD, Pedersen A, Collard M, Bradley DG, Jørkov ML, Arneborg J, Lynnerup N, Price N, Gilbert MTP, Allentoft ME, Bill J, Sindbæk SM, Hedeager L, Kristiansen K, Nielsen R, Werge T, Willerslev E. Population genomics of the Viking world. Nature 2020; 585:390-396. [PMID: 32939067 DOI: 10.1038/s41586-020-2688-8] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 05/21/2020] [Indexed: 12/24/2022]
Abstract
The maritime expansion of Scandinavian populations during the Viking Age (about AD 750-1050) was a far-flung transformation in world history1,2. Here we sequenced the genomes of 442 humans from archaeological sites across Europe and Greenland (to a median depth of about 1×) to understand the global influence of this expansion. We find the Viking period involved gene flow into Scandinavia from the south and east. We observe genetic structure within Scandinavia, with diversity hotspots in the south and restricted gene flow within Scandinavia. We find evidence for a major influx of Danish ancestry into England; a Swedish influx into the Baltic; and Norwegian influx into Ireland, Iceland and Greenland. Additionally, we see substantial ancestry from elsewhere in Europe entering Scandinavia during the Viking Age. Our ancient DNA analysis also revealed that a Viking expedition included close family members. By comparing with modern populations, we find that pigmentation-associated loci have undergone strong population differentiation during the past millennium, and trace positively selected loci-including the lactase-persistence allele of LCT and alleles of ANKA that are associated with the immune response-in detail. We conclude that the Viking diaspora was characterized by substantial transregional engagement: distinct populations influenced the genomic makeup of different regions of Europe, and Scandinavia experienced increased contact with the rest of the continent.
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Affiliation(s)
- Ashot Margaryan
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Institute of Molecular Biology, National Academy of Sciences, Yerevan, Armenia.,Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Daniel J Lawson
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK.,School of Statistical Sciences, University of Bristol, Bristol, UK
| | - Martin Sikora
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Fernando Racimo
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Simon Rasmussen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ida Moltke
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Lara M Cassidy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Emil Jørsboe
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Andrés Ingason
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark.,Institute of Biological Psychiatry, Mental Health Services Copenhagen, Copenhagen, Denmark
| | - Mikkel W Pedersen
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Thorfinn Korneliussen
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,HSE University, Russian Federation National Research University Higher School of Economics, Moscow, Russia
| | - Helene Wilhelmson
- Department of Archaeology and Ancient History, Lund University, Lund, Sweden.,Sydsvensk Arkeologi AB, Kristianstad, Sweden
| | - Magdalena M Buś
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Peter de Barros Damgaard
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Rui Martiniano
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Gabriel Renaud
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Department of Health Technology, Section for Bioinformatics, Technical University of Denmark (DTU), Copenhagen, Denmark
| | - Claude Bhérer
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada
| | - J Víctor Moreno-Mayar
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,National Institute of Genomic Medicine (INMEGEN), Mexico City, Mexico
| | - Anna K Fotakis
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Marie Allen
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Raili Allmäe
- Archaeological Research Collection, Tallinn University, Tallinn, Estonia
| | - Martyna Molak
- Museum and Institute of Zoology, Polish Academy of Sciences, Warsaw, Poland
| | - Enrico Cappellini
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Gabriele Scorrano
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Hugh McColl
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Alexandra Buzhilova
- Anuchin Research Institute and Museum of Anthropology, Moscow State University, Moscow, Russia
| | - Allison Fox
- Manx National Heritage, Douglas, Isle of Man
| | - Anders Albrechtsen
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Birgitte Skar
- NTNU University Museum, Department of Archaeology and Cultural History, Trondheim, Norway
| | - Caroline Arcini
- The Archaeologists, National Historical Museums, Stockholm, Sweden
| | - Ceri Falys
- Thames Valley Archaeological Services (TVAS), Reading, UK
| | | | | | - Denis Pezhemsky
- Anuchin Research Institute and Museum of Anthropology, Moscow State University, Moscow, Russia
| | - Gordon Turner-Walker
- Department of Cultural Heritage Conservation, National Yunlin University of Science and Technology, Douliou, Taiwan
| | | | - Inge Lundstrøm
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Ingrid Gustin
- Department of Archaeology and Ancient History, Lund University, Lund, Sweden
| | - Ingrid Mainland
- UHI Archaeology Institute, University of the Highlands and Islands, Kirkwall, UK
| | - Inna Potekhina
- Department of Bioarchaeology, Institute of Archaeology of National Academy of Sciences of Ukraine, Kiev, Ukraine
| | - Italo M Muntoni
- Soprintendenza Archeologia, Belle Arti e Paesaggio per le Province di Barletta, Andria, Trani e Foggia, Foggia, Italy
| | - Jade Cheng
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Jesper Stenderup
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Jilong Ma
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Julie Gibson
- UHI Archaeology Institute, University of the Highlands and Islands, Kirkwall, UK
| | - Jüri Peets
- Archaeological Research Collection, Tallinn University, Tallinn, Estonia
| | | | - Katrine H Iversen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Health Technology, Section for Bioinformatics, Technical University of Denmark (DTU), Copenhagen, Denmark
| | | | - Lisa Strand
- NTNU University Museum, Department of Archaeology and Cultural History, Trondheim, Norway
| | - Louise Loe
- Heritage Burial Services, Oxford Archaeology, Oxford, UK
| | | | - Marek Florek
- Institute of Archaeology, Maria Curie-Sklodowska University in Lublin, Lublin, Poland
| | | | - Mark Redknap
- Department of History and Archaeology, Amgueddfa Cymru-National Museum Wales, Cardiff, UK
| | - Monika Bajka
- Trzy Epoki Archaeological Service, Klimontów, Poland
| | | | | | - Natalia Grigoreva
- Department of Slavic-Finnish Archaeology, Institute for the History of Material Culture, Russian Academy of Sciences, Saint Petersburg, Russia
| | | | - Ole Kastholm
- Department of Research and Heritage, Roskilde Museum, Roskilde, Denmark
| | | | - Pasquale Favia
- Department of Humanities, University of Foggia, Foggia, Italy
| | - Per Holck
- Department of Molecular Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Sabine Sten
- Department of Archaeology and Ancient History, Uppsala University Campus Gotland, Visby, Sweden
| | - Símun V Arge
- Tjóðsavnið - Faroe Islands National Museum, Tórshavn, Faroe Islands
| | - Sturla Ellingvåg
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Vayacheslav Moiseyev
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Science, St Petersburg, Russia
| | | | | | - Ludovic Orlando
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Peter Pentz
- National Museum of Denmark, Copenhagen, Denmark
| | | | | | - Mark Collard
- Department of Archaeology, Simon Fraser University, Burnaby, British Colombia, Canada
| | - Daniel G Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Marie Louise Jørkov
- Department of Forensic Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Jette Arneborg
- National Museum of Denmark, Copenhagen, Denmark.,School of GeoSciences, University of Edinburgh, Edinburgh, UK
| | - Niels Lynnerup
- Department of Forensic Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Neil Price
- Department of Archaeology and Ancient History, Uppsala University, Uppsala, Sweden
| | - M Thomas P Gilbert
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Department of Natural History, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Morten E Allentoft
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, Western Australia, Australia
| | - Jan Bill
- Museum of Cultural History, University of Oslo, Oslo, Norway
| | - Søren M Sindbæk
- Centre for Urban Network Evolutions (UrbNet), School of Culture and Society, Aarhus University, Højbjerg, Denmark
| | - Lotte Hedeager
- Institute of Archaeology, Conservation and History, Oslo, Norway
| | | | - Rasmus Nielsen
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. .,Department of Integrative Biology, UC Berkeley, Berkeley, CA, USA. .,Department of Statistics, UC Berkeley, Berkeley, CA, USA.
| | - Thomas Werge
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. .,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark. .,Institute of Biological Psychiatry, Mental Health Services Copenhagen, Copenhagen, Denmark. .,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Copenhagen, Denmark.
| | - Eske Willerslev
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. .,Department of Zoology, University of Cambridge, Cambridge, UK. .,The Danish Institute for Advanced Study, University of Southern Denmark, Odense, Denmark. .,The Wellcome Trust Sanger Institute, Cambridge, UK.
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17
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Yucesan E, Hatirnaz Ng O, Yalniz FF, Yilmaz H, Salihoglu A, Sudutan T, Eskazan AE, Ongoren S, Baslar Z, Soysal T, Ozbek U, Sayitoglu M, Ar MC. Copy-number variations in adult patients with chronic immune thrombocytopenia. Expert Rev Hematol 2020; 13:1277-1287. [PMID: 32885695 DOI: 10.1080/17474086.2020.1819786] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
OBJECTIVES Immune thrombocytopenia (ITP) is an autoimmune disease with heterogeneous background. FCGR2C mutations were defined in one third of the patients but genetic players have not been fully elucidated yet. Although childhood ITP present as benign, ITP in adulthood is chronic disease with treatment challenges. This study aimed to focus on adult ITP patients using a whole genome genotyping that is valuable approach to identify the responsible genomic regions for the disease. METHODS Herein 24 adult primary-refractory for ITP patients were evaluated using HumanCytoSNP12BeadChip,Illumina. Forty-six age and sex matched healthy individuals, and ptients awith nonhematological conditions were analyzed as controls. Identified CNV regions were verified by qRTPCR. T-cell receptor beta and delta (TCRB/TCRG) clonality were assessed by heteroduplex analysis in mosaic cases. RESULTS Several CNV losses and gains were defined (losses:2q,7q,17q,19p, and gains: 1q,2p,3q,4q,7q,10q,12p,13q,14q,15q,17p,20q,21p,22q,Xp). Mosaic changes of different sizes (0.2-17.77Mb) were identified in five patients and three of them showed clonality. CNV regions that were unique to ITP patients were identified for the first time and among these genes, those related to immune regulation, and cellular trafficking were noteworthy. Conclusion: Identified CNV regions harbor several candidate genes, the functions of which might shed light on the pathogenesis of chronic ITP.
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Affiliation(s)
- Emrah Yucesan
- Faculty of Medicine, Department of Medical Biology, Bezmialem Vakif University , Istanbul, Turkey
| | - Ozden Hatirnaz Ng
- Department of Genetics, Aziz Sancar Institute of Experimental Medicine, Istanbul University , Istanbul, Turkey
| | - Fevzi Firat Yalniz
- Cerrahpasa Faculty of Medicine, Division of Haematology, Department of Internal Medicine, Istanbul University-Cerrahpasa , Istanbul, Turkey
| | - Hulya Yilmaz
- Cerrahpasa Faculty of Medicine, Division of Haematology, Department of Internal Medicine, Istanbul University-Cerrahpasa , Istanbul, Turkey
| | - Ayse Salihoglu
- Cerrahpasa Faculty of Medicine, Division of Haematology, Department of Internal Medicine, Istanbul University-Cerrahpasa , Istanbul, Turkey
| | - Tugce Sudutan
- Department of Genetics, Aziz Sancar Institute of Experimental Medicine, Istanbul University , Istanbul, Turkey
| | - Ahmet Emre Eskazan
- Cerrahpasa Faculty of Medicine, Division of Haematology, Department of Internal Medicine, Istanbul University-Cerrahpasa , Istanbul, Turkey
| | - Seniz Ongoren
- Cerrahpasa Faculty of Medicine, Division of Haematology, Department of Internal Medicine, Istanbul University-Cerrahpasa , Istanbul, Turkey
| | - Zafer Baslar
- Cerrahpasa Faculty of Medicine, Division of Haematology, Department of Internal Medicine, Istanbul University-Cerrahpasa , Istanbul, Turkey
| | - Teoman Soysal
- Cerrahpasa Faculty of Medicine, Division of Haematology, Department of Internal Medicine, Istanbul University-Cerrahpasa , Istanbul, Turkey
| | - Ugur Ozbek
- Department of Medical Genetics, Acibadem Mehmet Ali Aydinlar University, School of Medicine , Istanbul, Turkey
| | - Muge Sayitoglu
- Department of Genetics, Aziz Sancar Institute of Experimental Medicine, Istanbul University , Istanbul, Turkey
| | - M Cem Ar
- Cerrahpasa Faculty of Medicine, Division of Haematology, Department of Internal Medicine, Istanbul University-Cerrahpasa , Istanbul, Turkey
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18
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Zhao T, Ma C, Xie B, Zhao B, Wang W, Liu J. Evaluation of Common Variants in the AKNA Gene and Susceptibility to Knee Osteoarthritis Among the Han Chinese. Genet Test Mol Biomarkers 2020; 24:425-430. [PMID: 32460535 DOI: 10.1089/gtmb.2020.0014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Background: Osteoarthritis (OA) is a complex degenerative joint disease that is associated with both genetic and environmental factors. The AKNA gene, located at 9q32, has recently been identified as being associated with knee osteoarthritis (KOA) in the Mexican population. Our aim was to investigate the relationship of common variants in this gene with the risk of KOA in a large Han Chinese population. Methods: A total of 2,500 Han Chinese subjects were recruited, consisting of 824 KOA patients and 1,676 controls. Eight tag single nucleotide polymorphisms (SNPs) located within the ANKA gene were selected for genotyping. Single marker-based association analyses were conducted using multiple modes of inheritance, including genotypic, allelic, dominant, and recessive. Haplotype-based association analyses were also performed. Plink was utilized for genetic association analyses. In addition, we examined the GTEx database to test the expression quantitative loci effects of the significant SNPs within the AKNA gene. Results: Among these eight SNPs evaluated we identified one, rs10817595, as being significantly associated with the risk of KOA. Compared to the CC genotype at this locus, the odds ratio (95% confidence interval) for KOA with the AA genotype was 1.58 (1.23-2.01)-fold greater. A linkage disequilibrium block that included this SNP was also determined to be significantly associated with the risk of KOA (χ2 = 25.08, p = 3.58 × 10-6). In general, the minor allele A of SNP rs10817595 was associated with an increased risk of KOA. Conclusion: This study is the first to present evidence for a potential link between the risk of KOA and an AKNA gene polymorphism among persons with a Han Chinese ancestry. Future functional analyses based on animal models and sequencing-based population studies are needed to elucidate the biological plausibility and genetic architecture of AKNA for KOA susceptibility.
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Affiliation(s)
- Tianyun Zhao
- Department of Orthopedics and The First Hospital of Tianshui City, Tianshui, China.,Department of Sports Medicine, The First Hospital of Tianshui City, Tianshui, China
| | - Chi Ma
- Department of Orthopedics and The First Hospital of Tianshui City, Tianshui, China
| | - Baopin Xie
- Department of Sports Medicine, The First Hospital of Tianshui City, Tianshui, China
| | - Bin Zhao
- Department of Sports Medicine, The First Hospital of Tianshui City, Tianshui, China
| | - Wei Wang
- Department of Sports Medicine, The First Hospital of Tianshui City, Tianshui, China
| | - Jibin Liu
- Department of Oncology Research, The Affiliated Oncology Hospital of Nantong University, Nantong, China
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19
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AKNA Is a Potential Prognostic Biomarker in Gastric Cancer and Function as a Tumor Suppressor by Modulating EMT-Related Pathways. BIOMED RESEARCH INTERNATIONAL 2020; 2020:6726759. [PMID: 32462010 PMCID: PMC7243015 DOI: 10.1155/2020/6726759] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 03/11/2020] [Accepted: 04/16/2020] [Indexed: 01/24/2023]
Abstract
The AT-hook transcription factor, AKNA, is a nuclear protein that affects a few physiological and pathological processes including cancer. Here, we investigated the role of AKNA in gastric cancer (GC). By using quantitative real-time polymerase chain reaction (qRT-PCR) and Western blot assays, AKNA was found deregulated in both GC cell lines and 32 paired GC tissues. Subsequently, Kaplan-Meier analysis and clinicopathological analysis were conducted using both 32 GC cases' data above and RNA-Seq data of AKNA in 354 GC patients and the corresponding clinical-pathological data obtained from The Cancer Genome Atlas (TCGA), and AKNA expression was found closely related to location, metastasis, and TNM staging of GC. Then, the potential molecular mechanisms of AKNA in GC were explored by gene set enrichment analysis (GSEA), qRT-PCR, and Western blot assays. AKNA was found to be a hub gene related to homotypic cell to cell adhesion, regulation of cell to cell adhesion, leukocyte cell to cell adhesion, and regulation of T cell proliferation in GC. GO analysis revealed that AKNA involved in the regulation of epithelial-mesenchymal transition (EMT)-related pathways including chemokine signaling pathway, cytokine to cytokine receptor interaction, cell adhesion molecules, and jak-stat signaling pathway in GC. To explore the regulation of AKNA expression, Targetscan and TargetMiner were used to predict the possible miRNA which targeted AKNA and found the expression of AKNA was negatively correlated to miR-762 which could be sponged by circTRNC18. In conclusion, AKNA could function as a tumor suppressor by modulating EMT-related pathways in GC. The expression of AKNA might be regulated by circTRNC18/miR-762 axis. AKNA could serve as a potential biomarker and an effective target for GC diagnosis and therapy.
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20
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Hug P, Anderegg L, Kehl A, Jagannathan V, Leeb T. AKNA Frameshift Variant in Three Dogs with Recurrent Inflammatory Pulmonary Disease. Genes (Basel) 2019; 10:E567. [PMID: 31357536 PMCID: PMC6723478 DOI: 10.3390/genes10080567] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 07/16/2019] [Accepted: 07/25/2019] [Indexed: 01/03/2023] Open
Abstract
We investigated three related Rough Collies with recurrent inflammatory pulmonary disease. The clinical symptoms were similar to primary ciliary dyskinesia (PCD). However, the affected dogs did not carry any known pathogenic PCD variants. Pedigree analysis suggested a recessive mode of inheritance. Combined linkage and homozygosity mapping in three cases and seven non-affected family members delineated 19 critical intervals on 10 chromosomes comprising a total of 99 Mb. The genome of one affected dog was sequenced and compared to 601 control genomes. We detected only a single private homozygous protein-changing variant in the critical intervals. The detected variant was a 4 bp deletion, c.2717_2720delACAG, in the AKNA gene encoding the AT-hook transcription factor. It causes a frame-shift introducing a premature stop codon and truncates 37% of the open reading frame, p.(Asp906Alafs*173). We genotyped 88 Rough Collies consisting of family members and unrelated individuals. All three available cases were homozygous for the mutant allele and all 85 non-affected dogs were either homozygous wildtype (n = 67) or heterozygous (n = 18). AKNA modulates inflammatory immune responses. Akna-/- knockout mice die shortly after birth due to systemic autoimmune inflammatory processes including lung inflammation that is accompanied by enhanced leukocyte infiltration and alveolar destruction. The perfect genotype-phenotype association and the comparative functional data strongly suggest that the detected AKNA:c.2717_2720delACAG variant caused the observed severe airway inflammation in the investigated dogs. Our findings enable genetic testing, which can be used to avoid the unintentional breeding of affected puppies.
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Affiliation(s)
- Petra Hug
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland
| | - Linda Anderegg
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland
| | | | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland.
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21
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Camargo Ortega G, Falk S, Johansson PA, Peyre E, Broix L, Sahu SK, Hirst W, Schlichthaerle T, De Juan Romero C, Draganova K, Vinopal S, Chinnappa K, Gavranovic A, Karakaya T, Steininger T, Merl-Pham J, Feederle R, Shao W, Shi SH, Hauck SM, Jungmann R, Bradke F, Borrell V, Geerlof A, Reber S, Tiwari VK, Huttner WB, Wilsch-Bräuninger M, Nguyen L, Götz M. The centrosome protein AKNA regulates neurogenesis via microtubule organization. Nature 2019; 567:113-117. [PMID: 30787442 DOI: 10.1038/s41586-019-0962-4] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 01/23/2019] [Indexed: 12/20/2022]
Abstract
The expansion of brain size is accompanied by a relative enlargement of the subventricular zone during development. Epithelial-like neural stem cells divide in the ventricular zone at the ventricles of the embryonic brain, self-renew and generate basal progenitors1 that delaminate and settle in the subventricular zone in enlarged brain regions2. The length of time that cells stay in the subventricular zone is essential for controlling further amplification and fate determination. Here we show that the interphase centrosome protein AKNA has a key role in this process. AKNA localizes at the subdistal appendages of the mother centriole in specific subtypes of neural stem cells, and in almost all basal progenitors. This protein is necessary and sufficient to organize centrosomal microtubules, and promote their nucleation and growth. These features of AKNA are important for mediating the delamination process in the formation of the subventricular zone. Moreover, AKNA regulates the exit from the subventricular zone, which reveals the pivotal role of centrosomal microtubule organization in enabling cells to both enter and remain in the subventricular zone. The epithelial-to-mesenchymal transition is also regulated by AKNA in other epithelial cells, demonstrating its general importance for the control of cell delamination.
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Affiliation(s)
- Germán Camargo Ortega
- Institute of Stem Cell Research, Helmholtz Center Munich, German Research Center for Environmental Health, Munich, Germany.,Physiological Genomics, Biomedical Center, Ludwig-Maximilians University, Munich, Germany.,Graduate School of Systemic Neurosciences, Biocenter, Ludwig-Maximilians University, Munich, Germany
| | - Sven Falk
- Institute of Stem Cell Research, Helmholtz Center Munich, German Research Center for Environmental Health, Munich, Germany.,Physiological Genomics, Biomedical Center, Ludwig-Maximilians University, Munich, Germany
| | - Pia A Johansson
- Institute of Stem Cell Research, Helmholtz Center Munich, German Research Center for Environmental Health, Munich, Germany.,Physiological Genomics, Biomedical Center, Ludwig-Maximilians University, Munich, Germany.,Laboratory of Molecular Neurogenetics, Lund University, Lund, Sweden
| | - Elise Peyre
- GIGA-Stem Cells, Molecular regulation of neurogenesis, University of Liège, Liège, Belgium
| | - Loïc Broix
- GIGA-Stem Cells, Molecular regulation of neurogenesis, University of Liège, Liège, Belgium
| | | | - William Hirst
- IRI for the Life Sciences, Humboldt University, Berlin, Germany.,Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Thomas Schlichthaerle
- Max Planck Institute of Biochemistry, Martinsried, Germany.,Department of Physics and Center for Nanoscience, Ludwig Maximilians University, Munich, Germany
| | - Camino De Juan Romero
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas and Universidad Miguel Hernández, Sant Joan d'Alacant, Spain
| | - Kalina Draganova
- Institute of Stem Cell Research, Helmholtz Center Munich, German Research Center for Environmental Health, Munich, Germany.,Physiological Genomics, Biomedical Center, Ludwig-Maximilians University, Munich, Germany
| | - Stanislav Vinopal
- Laboratory for Axon Growth and Regeneration, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Kaviya Chinnappa
- Institute of Stem Cell Research, Helmholtz Center Munich, German Research Center for Environmental Health, Munich, Germany.,Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas and Universidad Miguel Hernández, Sant Joan d'Alacant, Spain
| | - Anna Gavranovic
- Institute of Stem Cell Research, Helmholtz Center Munich, German Research Center for Environmental Health, Munich, Germany
| | - Tugay Karakaya
- Institute of Stem Cell Research, Helmholtz Center Munich, German Research Center for Environmental Health, Munich, Germany
| | - Thomas Steininger
- Institute of Stem Cell Research, Helmholtz Center Munich, German Research Center for Environmental Health, Munich, Germany
| | - Juliane Merl-Pham
- Research Unit Protein Science, Helmholtz Centre Munich, German Research Center for Environmental Health, Munich, Germany
| | - Regina Feederle
- Institute for Diabetes and Obesity, Monoclonal Antibody Core Facility, Helmholtz Center Munich, German Research Center for Environmental Health, Munich, Germany.,SYNERGY, Excellence Cluster of Systems Neurology, Biomedical Center, Ludwig-Maximilians University, Munich, Germany
| | - Wei Shao
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,BCMB Allied Graduate Program, Weill Cornell Medical College, New York, NY, USA
| | - Song-Hai Shi
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,BCMB Allied Graduate Program, Weill Cornell Medical College, New York, NY, USA
| | - Stefanie M Hauck
- Research Unit Protein Science, Helmholtz Centre Munich, German Research Center for Environmental Health, Munich, Germany
| | - Ralf Jungmann
- Max Planck Institute of Biochemistry, Martinsried, Germany.,Department of Physics and Center for Nanoscience, Ludwig Maximilians University, Munich, Germany
| | - Frank Bradke
- Laboratory for Axon Growth and Regeneration, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Victor Borrell
- Instituto de Neurociencias, Consejo Superior de Investigaciones Científicas and Universidad Miguel Hernández, Sant Joan d'Alacant, Spain
| | - Arie Geerlof
- Protein Expression and Purification Facility, Institute of Structural Biology, Helmholtz Center Munich, German Research Center for Environmental Health, Munich, Germany
| | - Simone Reber
- IRI for the Life Sciences, Humboldt University, Berlin, Germany.,University of Applied Sciences, Berlin, Germany
| | | | - Wieland B Huttner
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | | | - Laurent Nguyen
- GIGA-Stem Cells, Molecular regulation of neurogenesis, University of Liège, Liège, Belgium
| | - Magdalena Götz
- Institute of Stem Cell Research, Helmholtz Center Munich, German Research Center for Environmental Health, Munich, Germany. .,Physiological Genomics, Biomedical Center, Ludwig-Maximilians University, Munich, Germany. .,Max Planck Institute of Biochemistry, Martinsried, Germany. .,SYNERGY, Excellence Cluster of Systems Neurology, Biomedical Center, Ludwig-Maximilians University, Munich, Germany.
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22
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Manzo-Merino J, Lagunas-Martínez A, Contreras-Ochoa CO, Lizano M, Castro-Muñoz LJ, Calderón-Corona C, Torres-Poveda K, Román-Gonzalez A, Hernández-Pando R, Bahena-Román M, Madrid-Marina V. The Human Papillomavirus (HPV) E6 Oncoprotein Regulates CD40 Expression via the AT-Hook Transcription Factor AKNA. Cancers (Basel) 2018; 10:cancers10120521. [PMID: 30562965 PMCID: PMC6316281 DOI: 10.3390/cancers10120521] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 11/23/2018] [Accepted: 12/13/2018] [Indexed: 12/22/2022] Open
Abstract
Persistent infection with high-risk Human Papillomavirus (HR-HPV) is the main requisite for cervical cancer development. Normally, HPV is limited to the site of infection and regulates a plethora of cellular elements to avoid the immune surveillance by inducing an anti-inflammatory state, allowing the progress through the viral cycle and the carcinogenic process. Recent findings suggest that the AT-hook transcriptional factor AKNA could play a role in the development of cervical cancer. AKNA is strongly related to the expression of co-stimulatory molecules such CD40/CD40L to achieve an anti-tumoral immune response. To date, there is no evidence demonstrating the effect of the HPV E6 oncoprotein on the AT-hook factor AKNA. In this work, minimal expression of AKNA in cervical carcinoma compared to normal tissue was found. We show the ability of E6 from high-risk HPVs 16 and 18 to interact with and down-regulate AKNA as well as its co-stimulatory molecule CD40 in a proteasome dependent manner. We also found that p53 interacts with AKNA and promotes AKNA expression. Our results indicate that the de-regulation of CD40 and AKNA is induced by the HPV E6 oncoprotein, and this event involves the action of p53 suggesting that the axis E6/p53A/AKNA might play an important role in the de-regulation of the immune system during the carcinogenic process induced by HR-HPV.
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Affiliation(s)
- Joaquin Manzo-Merino
- CONACyT-Instituto Nacional de Cancerología, Mexico City 14080, Mexico.
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City 14080, Mexico.
- Chronic Infections and Cancer Division, Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública, Secretaría de Salud, Avenida Universidad 655, Col. Santa María Ahuacatitlan, Cuernavaca, Morelos 62100, Mexico.
| | - Alfredo Lagunas-Martínez
- Chronic Infections and Cancer Division, Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública, Secretaría de Salud, Avenida Universidad 655, Col. Santa María Ahuacatitlan, Cuernavaca, Morelos 62100, Mexico.
| | - Carla O Contreras-Ochoa
- Chronic Infections and Cancer Division, Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública, Secretaría de Salud, Avenida Universidad 655, Col. Santa María Ahuacatitlan, Cuernavaca, Morelos 62100, Mexico.
| | - Marcela Lizano
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City 14080, Mexico.
- Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico.
| | - Leonardo J Castro-Muñoz
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City 14080, Mexico.
| | - Crysele Calderón-Corona
- Chronic Infections and Cancer Division, Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública, Secretaría de Salud, Avenida Universidad 655, Col. Santa María Ahuacatitlan, Cuernavaca, Morelos 62100, Mexico.
| | - Kirvis Torres-Poveda
- Chronic Infections and Cancer Division, Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública, Secretaría de Salud, Avenida Universidad 655, Col. Santa María Ahuacatitlan, Cuernavaca, Morelos 62100, Mexico.
- CONACyT-Instituto Nacional de Salud Pública (INSP), Cuernavaca, Morelos 62100, Mexico.
| | - Alicia Román-Gonzalez
- Chronic Infections and Cancer Division, Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública, Secretaría de Salud, Avenida Universidad 655, Col. Santa María Ahuacatitlan, Cuernavaca, Morelos 62100, Mexico.
| | - Rogelio Hernández-Pando
- Section of Experimental Pathology, Department of Pathology, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City 14080, Mexico.
| | - Margarita Bahena-Román
- Chronic Infections and Cancer Division, Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública, Secretaría de Salud, Avenida Universidad 655, Col. Santa María Ahuacatitlan, Cuernavaca, Morelos 62100, Mexico.
| | - Vicente Madrid-Marina
- Chronic Infections and Cancer Division, Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública, Secretaría de Salud, Avenida Universidad 655, Col. Santa María Ahuacatitlan, Cuernavaca, Morelos 62100, Mexico.
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23
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Piulats JM, Vidal A, García-Rodríguez FJ, Muñoz C, Nadal M, Moutinho C, Martínez-Iniesta M, Mora J, Figueras A, Guinó E, Padullés L, Aytés À, Molleví DG, Puertas S, Martínez-Fernández C, Castillo W, Juliachs M, Moreno V, Muñoz P, Stefanovic M, Pujana MA, Condom E, Esteller M, Germà JR, Capella G, Farré L, Morales A, Viñals F, García-del-Muro X, Cerón J, Villanueva A. Orthoxenografts of Testicular Germ Cell Tumors Demonstrate Genomic Changes Associated with Cisplatin Resistance and Identify PDMP as a Resensitizing Agent. Clin Cancer Res 2018; 24:3755-3766. [DOI: 10.1158/1078-0432.ccr-17-1898] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 11/22/2017] [Accepted: 03/23/2018] [Indexed: 11/16/2022]
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24
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Savitski MM, Zinn N, Faelth-Savitski M, Poeckel D, Gade S, Becher I, Muelbaier M, Wagner AJ, Strohmer K, Werner T, Melchert S, Petretich M, Rutkowska A, Vappiani J, Franken H, Steidel M, Sweetman GM, Gilan O, Lam EYN, Dawson MA, Prinjha RK, Grandi P, Bergamini G, Bantscheff M. Multiplexed Proteome Dynamics Profiling Reveals Mechanisms Controlling Protein Homeostasis. Cell 2018; 173:260-274.e25. [PMID: 29551266 PMCID: PMC5871718 DOI: 10.1016/j.cell.2018.02.030] [Citation(s) in RCA: 150] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Revised: 12/01/2017] [Accepted: 02/09/2018] [Indexed: 02/07/2023]
Abstract
Protein degradation plays important roles in biological processes and is tightly regulated. Further, targeted proteolysis is an emerging research tool and therapeutic strategy. However, proteome-wide technologies to investigate the causes and consequences of protein degradation in biological systems are lacking. We developed “multiplexed proteome dynamics profiling” (mPDP), a mass-spectrometry-based approach combining dynamic-SILAC labeling with isobaric mass tagging for multiplexed analysis of protein degradation and synthesis. In three proof-of-concept studies, we uncover different responses induced by the bromodomain inhibitor JQ1 versus a JQ1 proteolysis targeting chimera; we elucidate distinct modes of action of estrogen receptor modulators; and we comprehensively classify HSP90 clients based on their requirement for HSP90 constitutively or during synthesis, demonstrating that constitutive HSP90 clients have lower thermal stability than non-clients, have higher affinity for the chaperone, vary between cell types, and change upon external stimuli. These findings highlight the potential of mPDP to identify dynamically controlled degradation mechanisms in cellular systems. Multiplexed proteome dynamics profiling, mPDP, measures changes in proteostasis JQ1-PROTAC degrades a key mRNA export factor and blocks protein synthesis Raloxifene induces TMEM97 degradation dysregulating cholesterol homeostasis Characterization of proteins dependent on HSP90 constitutively or during synthesis
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Affiliation(s)
- Mikhail M Savitski
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany; Genome Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
| | - Nico Zinn
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | | | - Daniel Poeckel
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Stephan Gade
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Isabelle Becher
- Genome Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Marcel Muelbaier
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Anne J Wagner
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Katrin Strohmer
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Thilo Werner
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Stephanie Melchert
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Massimo Petretich
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Anna Rutkowska
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Johanna Vappiani
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Holger Franken
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Michael Steidel
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Gavain M Sweetman
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Omer Gilan
- Cancer Research Division, Peter MacCallum Cancer Centre, East Melbourne, VIC 3002, Australia
| | - Enid Y N Lam
- Cancer Research Division, Peter MacCallum Cancer Centre, East Melbourne, VIC 3002, Australia
| | - Mark A Dawson
- Cancer Research Division, Peter MacCallum Cancer Centre, East Melbourne, VIC 3002, Australia
| | - Rab K Prinjha
- Epinova DPU, Immuno-Inflammation Centre of Excellence for Drug Discovery, GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, UK
| | - Paola Grandi
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Giovanna Bergamini
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
| | - Marcus Bantscheff
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
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25
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Lei J, Wu Z, Jiang Z, Li J, Zong L, Chen X, Duan W, Xu Q, Zhang L, Han L, Ma Q, Wang Z, Zhang D. Pancreatic carcinoma-specific immunotherapy using novel tumor specific cytotoxic T cells. Oncotarget 2018; 7:83601-83610. [PMID: 27876704 PMCID: PMC5347791 DOI: 10.18632/oncotarget.13469] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Accepted: 09/24/2016] [Indexed: 01/13/2023] Open
Abstract
Pancreatic cancer represents one of the most lethal human cancers. Investigation of the effective targeting to the tumor cells is essential for both primary tumors and metastases. Tumor specific cytotoxic T lymphocytes (CTLs) have recently been considered to be the attractive vehicles for delivering therapeutic agents toward various tumor diseases. This study was to explore the distribution pattern of CTL carrying the lentiviral vectors with the characteristic of adenoviral E1 gene under the control of the cell activation-dependent CD40 ligand promoter (Lenti/hCD40L/E1AB). Following transduction with adenoviral particles containing chimeric type 5 and type 35 fiber proteins (Ad5/35-TRAIL), these CTLs produced infectious virus when exposed to SW1990 cells. We found that the novel CTL harboring Lenti/hCD40L/E1AB and Ad5/35-TRAIL inhibited pancreatic cancer cell growth and angiogenesis in vitro and in vivo. Furthermore, Ad5/35-TRAIL transduced CTL induced significant apoptosis in pancreatic carcinoma cell lines and upregulated IFN-gamma (IFN-γ) secretion of CTLs. Importantly, Ad5/35-TRAIL transduced CTLs had no inhibitory effect on normal cells. Thus, the novel CTLs may be safe and feasible for the development of gene therapy approaches to pancreatic carcinoma.
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Affiliation(s)
- Jianjun Lei
- Department of Hepatobiliary and Pancreas Surgery, First Affiliated Hospital of Medical College, Xi'an Jiaotong University, Xi'an 710061, Shaanxi Province, China
| | - Zheng Wu
- Department of Hepatobiliary and Pancreas Surgery, First Affiliated Hospital of Medical College, Xi'an Jiaotong University, Xi'an 710061, Shaanxi Province, China
| | - Zhengdong Jiang
- Department of Hepatobiliary and Pancreas Surgery, First Affiliated Hospital of Medical College, Xi'an Jiaotong University, Xi'an 710061, Shaanxi Province, China
| | - Jiahui Li
- Department of Hepatobiliary and Pancreas Surgery, First Affiliated Hospital of Medical College, Xi'an Jiaotong University, Xi'an 710061, Shaanxi Province, China
| | - Liang Zong
- Department of Hepatobiliary and Pancreas Surgery, First Affiliated Hospital of Medical College, Xi'an Jiaotong University, Xi'an 710061, Shaanxi Province, China
| | - Xin Chen
- Department of Hepatobiliary and Pancreas Surgery, First Affiliated Hospital of Medical College, Xi'an Jiaotong University, Xi'an 710061, Shaanxi Province, China
| | - Wanxing Duan
- Department of Hepatobiliary and Pancreas Surgery, First Affiliated Hospital of Medical College, Xi'an Jiaotong University, Xi'an 710061, Shaanxi Province, China
| | - Qinhong Xu
- Department of Hepatobiliary and Pancreas Surgery, First Affiliated Hospital of Medical College, Xi'an Jiaotong University, Xi'an 710061, Shaanxi Province, China
| | - Lun Zhang
- Department of Hepatobiliary and Pancreas Surgery, First Affiliated Hospital of Medical College, Xi'an Jiaotong University, Xi'an 710061, Shaanxi Province, China
| | - Liang Han
- Department of Hepatobiliary and Pancreas Surgery, First Affiliated Hospital of Medical College, Xi'an Jiaotong University, Xi'an 710061, Shaanxi Province, China
| | - Qingyong Ma
- Department of Hepatobiliary and Pancreas Surgery, First Affiliated Hospital of Medical College, Xi'an Jiaotong University, Xi'an 710061, Shaanxi Province, China
| | - Zheng Wang
- Department of Hepatobiliary and Pancreas Surgery, First Affiliated Hospital of Medical College, Xi'an Jiaotong University, Xi'an 710061, Shaanxi Province, China
| | - Dong Zhang
- Department of Hepatobiliary and Pancreas Surgery, First Affiliated Hospital of Medical College, Xi'an Jiaotong University, Xi'an 710061, Shaanxi Province, China
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26
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The association of AKNA gene polymorphisms with knee osteoarthritis suggests the relevance of this immune response regulator in the disease genetic susceptibility. Mol Biol Rep 2018; 45:151-161. [PMID: 29368274 DOI: 10.1007/s11033-018-4148-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 01/16/2018] [Indexed: 12/20/2022]
Abstract
Recent studies have identified AKNA as a potential susceptibility gene for several inflammatory diseases. Here, we aimed to assess the potential association of AKNA polymorphisms with knee osteoarthritis (KOA) susceptibility in a Mexican population, following STREGA recommendations. From a DNA bank of 181 KOA patients and 140 healthy controls, two AKNA SNPs were genotyped using TaqMan probes. The association between KOA susceptibility and AKNA polymorphisms genotypes was evaluated by multivariated logistic regression analysis. Information regarding patients' inflammatory biomarkers levels was obtained and their association with AKNA polymorphisms genotypes was assessed by lineal regression. We found a positive association with the recessive inheritance model of both AKNA polymorphisms (A/A genotype for both) and KOA susceptibility adjusting by age, body mass index (BMI), gender and place of birth (OR = 2.48, 95% CI 1.09-5.65 for rs10817595 polymorphism; and OR = 4.96; 95% CI 2.421-10.2 for rs3748176 polymorphism). Additionally these associations were also seen after stratifying patients by KOA severity and age. Furthermore the total leukocyte count was positively associated with rs10817595 AKNA polymorphism (β = 1.39; 95% CI 0.44-2.34) adjusting by age, BMI, gender, place of birth and disease severity. We suggest that regulatory and coding polymorphisms of the inflammatory modulator gene AKNA can influence the development of KOA. Further structural and functional studies might reveal the role of AKNA in OA and other rheumatic diseases.
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27
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Direct anti-inflammatory effects of granulocyte colony-stimulating factor (G-CSF) on activation and functional properties of human T cell subpopulations in vitro. Cell Immunol 2018; 325:23-32. [PMID: 29357983 DOI: 10.1016/j.cellimm.2018.01.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Revised: 12/18/2017] [Accepted: 01/13/2018] [Indexed: 11/21/2022]
Abstract
We investigated the direct effects of human granulocyte colony-stimulating factor (G-CSF) on functionality of human T-cell subsets. CD3+ T-lymphocytes were isolated from blood of healthy donors by positive magnetic separation. T cell activation with particles conjugated with antibodies (Abs) to human CD3, CD28 and CD2 molecules increased the proportion of cells expressing G-CSF receptor (G-CSFR, CD114) in all T cell subpopulations studied (CD45RA+/CD197+ naive T cells, CD45RA-/CD197+ central memory T cells, CD45RA-/CD197- effector memory T cells and CD45RA+/CD197- terminally differentiated effector T cells). Upon T-cell activation in vitro, G-CSF (10.0 ng/ml) significantly and specifically enhanced the proportion of CD114+ T cells in central memory CD4+ T cell compartment. A dilution series of G-CSF (range, 0.1-10.0 ng/ml) was tested, with no effect on the expression of CD25 (interleukin-2 receptor α-chain) on activated T cells. Meanwhile, G-CSF treatment enhanced the proportion of CD38+ T cells in CD4+ naïve T cell, effector memory T cell and terminally differentiated effector T cell subsets, as well as in CD4- central memory T cells and terminally differentiated effector T cells. G-CSF did not affect IL-2 production by T cells; relatively low concentrations of G-CSF down-regulated INF-γ production, while high concentrations of this cytokine up-regulated IL-4 production in activated T cells. The data obtained suggests that G-CSF could play a significant role both in preventing the development of excessive and potentially damaging inflammatory reactivity, and in constraining the expansion of potentially cytodestructive T cells.
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28
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Liu X, Huang D, Guo P, Wu Q, Dai M, Cheng G, Hao H, Xie S, Yuan Z, Wang X. PKA/CREB and NF-κB pathway regulates AKNA transcription: A novel insight into T-2 toxin-induced inflammation and GH deficiency in GH3 cells. Toxicology 2017; 392:81-95. [DOI: 10.1016/j.tox.2017.10.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 10/14/2017] [Accepted: 10/22/2017] [Indexed: 12/22/2022]
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29
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Liu J, Kumar S, Dolzhenko E, Alvarado GF, Guo J, Lu C, Chen Y, Li M, Dessing MC, Parvez RK, Cippà PE, Krautzberger AM, Saribekyan G, Smith AD, McMahon AP. Molecular characterization of the transition from acute to chronic kidney injury following ischemia/reperfusion. JCI Insight 2017; 2:94716. [PMID: 28931758 PMCID: PMC5612583 DOI: 10.1172/jci.insight.94716] [Citation(s) in RCA: 188] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 08/10/2017] [Indexed: 12/16/2022] Open
Abstract
Though an acute kidney injury (AKI) episode is associated with an increased risk of chronic kidney disease (CKD), the mechanisms determining the transition from acute to irreversible chronic injury are not well understood. To extend our understanding of renal repair, and its limits, we performed a detailed molecular characterization of a murine ischemia/reperfusion injury (IRI) model for 12 months after injury. Together, the data comprising RNA-sequencing (RNA-seq) analysis at multiple time points, histological studies, and molecular and cellular characterization of targeted gene activity provide a comprehensive profile of injury, repair, and long-term maladaptive responses following IRI. Tubular atrophy, interstitial fibrosis, inflammation, and development of multiple renal cysts were major long-term outcomes of IRI. Progressive proximal tubular injury tracks with de novo activation of multiple Krt genes, including Krt20, a biomarker of renal tubule injury. RNA-seq analysis highlights a cascade of temporal-specific gene expression patterns related to tubular injury/repair, fibrosis, and innate and adaptive immunity. Intersection of these data with human kidney transplant expression profiles identified overlapping gene expression signatures correlating with different stages of the murine IRI response. The comprehensive characterization of incomplete recovery after ischemic AKI provides a valuable resource for determining the underlying pathophysiology of human CKD.
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Affiliation(s)
- Jing Liu
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Sanjeev Kumar
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA.,Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Egor Dolzhenko
- Molecular and Computational Biology, Division of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - Gregory F Alvarado
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Jinjin Guo
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Can Lu
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Yibu Chen
- Norris Medical Library, University of Southern California, Los Angeles, California
| | - Meng Li
- Norris Medical Library, University of Southern California, Los Angeles, California
| | - Mark C Dessing
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Riana K Parvez
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Pietro E Cippà
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - A Michaela Krautzberger
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Gohar Saribekyan
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Andrew D Smith
- Molecular and Computational Biology, Division of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - Andrew P McMahon
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
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30
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DNA methylation in demyelinated multiple sclerosis hippocampus. Sci Rep 2017; 7:8696. [PMID: 28821749 PMCID: PMC5562763 DOI: 10.1038/s41598-017-08623-5] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 07/10/2017] [Indexed: 12/21/2022] Open
Abstract
Multiple Sclerosis (MS) is an immune-mediated demyelinating disease of the human central nervous system (CNS). Memory impairments and hippocampal demyelination are common features in MS patients. Our previous data have shown that demyelination alters neuronal gene expression in the hippocampus. DNA methylation is a common epigenetic modifier of gene expression. In this study, we investigated whether DNA methylation is altered in MS hippocampus following demyelination. Our results show that mRNA levels of DNA methyltransferase were increased in demyelinated MS hippocampus, while de-methylation enzymes were decreased. Comparative methylation profiling identify hypo-methylation within upstream sequences of 6 genes and hyper-methylation of 10 genes in demyelinated MS hippocampus. Genes identified in the current study were also validated in an independent microarray dataset generated from MS hippocampus. Independent validation using RT-PCR revealed that DNA methylation inversely correlated with mRNA levels of the candidate genes. Queries across cell-specific databases revealed that a majority of the candidate genes are expressed by astrocytes and neurons in mouse and human CNS. Taken together, our results expands the list of genes previously identified in MS hippocampus and establish DNA methylation as a mechanism of altered gene expression in MS hippocampus.
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Yan Q, Yang C, Fu Q, Chen Z, Liu S, Fu D, Rahman RN, Nakazato R, Yoshioka K, Kung SKP, Ding G, Wang H. Scaffold protein JLP mediates TCR-initiated CD4 +T cell activation and CD154 expression. Mol Immunol 2017; 87:258-266. [PMID: 28521278 DOI: 10.1016/j.molimm.2017.05.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 04/27/2017] [Accepted: 05/06/2017] [Indexed: 11/16/2022]
Abstract
CD4+ T-cell activation and its subsequent induction of CD154 (CD40 ligand, CD40L) expression are pivotal in shaping both the humoral and cellular immune responses. Scaffold protein JLP regulates signal transduction pathways and molecular trafficking inside cells, thus represents a critical component in maintaining cellular functions. Its role in regulating CD4+ T-cell activation and CD154 expression, however, is unclear. Here, we demonstrated expression of JLP in mouse tissues of lymph nodes, thymus, spleen, and also CD4+ T cells. Using CD4+ T cells from jlp-deficient and jlp-wild-type mice, we demonstrated that JLP-deficiency impaired T-cell proliferation, IL-2 production, and CD154 induction upon TCR stimulations, but had no impacts on the expression of other surface molecules such as CD25, CD69, and TCR. These observed impaired T-cell functions in the jlp-/- CD4+ T cells were associated with defective NF-AT activation and Ca2+ influx, but not the MAPK, NF-κB, as well as AP-1 signaling pathways. Our findings indicated that, for the first time, JLP plays a critical role in regulating CD4+ T cells response to TCR stimulation partly by mediating the activation of TCR-initiated Ca2+/NF-AT.
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Affiliation(s)
- Qi Yan
- Department of Nephrology, Renmin hospital of Wuhan University, Wuhan, China
| | - Cheng Yang
- Department of Nephrology, Renmin hospital of Wuhan University, Wuhan, China
| | - Qiang Fu
- Department of Nephrology, Renmin hospital of Wuhan University, Wuhan, China
| | - Zhaowei Chen
- Department of Nephrology, Renmin hospital of Wuhan University, Wuhan, China
| | - Shan Liu
- Department of Nephrology, Renmin hospital of Wuhan University, Wuhan, China
| | - Dou Fu
- Department of Nephrology, Renmin hospital of Wuhan University, Wuhan, China
| | - Rahmat N Rahman
- Department of Immunology, Max Rady College of Medicine, University of Manitoba, Canada
| | - Ryota Nakazato
- Cancer Research Institute, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Katsuji Yoshioka
- Cancer Research Institute, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Sam K P Kung
- Department of Immunology, Max Rady College of Medicine, University of Manitoba, Canada
| | - Guohua Ding
- Department of Nephrology, Renmin hospital of Wuhan University, Wuhan, China.
| | - Huiming Wang
- Department of Nephrology, Renmin hospital of Wuhan University, Wuhan, China.
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HIF1A (rs11549465) and AKNA (rs10817595) Gene Polymorphisms Are Associated with Primary Sjögren's Syndrome. BIOMED RESEARCH INTERNATIONAL 2017; 2017:5845849. [PMID: 28484714 PMCID: PMC5397622 DOI: 10.1155/2017/5845849] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 03/06/2017] [Accepted: 03/23/2017] [Indexed: 11/29/2022]
Abstract
Objective. To evaluate the allele and genotype frequencies of polymorphic sites of HIF1A and ANKA genes in primary Sjögren's syndrome (pSS). Methods. We included 110 patients with pSS and 141 ethnically matched healthy controls. Three HIF1A gene polymorphisms (Pro582Ser, Ala588Thr, and C191T) and two AKNA gene polymorphisms (−1372C>A and Pro624Leu) were genotyped using TaqMan probes in a Real-Time PCR instrument. Associations between pSS and genotypes, alleles, and inheritance models of the SNPs of interest were evaluated by logistic regression adjusted by age and gender. Results. The C/T genotype and the T allele of the HIF1A Pro582Ser polymorphism protected against pSS (OR = 0.22; 95% CI = 0.09–0.52; P < 0.01; OR = 0.26; 95% CI = 0.12–0.58; P < 0.01, resp.), whereas under a recessive model adjusted by age and gender, the AKNA −1372C>A polymorphism A/A genotype was associated with an increased risk of pSS (OR = 2.60; 95% CI = 1.11–6.12; P = 0.03). Conclusions. We identified HIF1A Pro582Ser T allele and C/T genotype as well as AKNA −1372C>A polymorphism A/A genotype as genetic factors associated with pSS. Further studies in other populations are needed to validate our findings and research is warranted in order to shed some light on their functional implications across biological pathways in this disease.
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Filarsky M, Zillner K, Araya I, Villar-Garea A, Merkl R, Längst G, Németh A. The extended AT-hook is a novel RNA binding motif. RNA Biol 2016; 12:864-76. [PMID: 26156556 PMCID: PMC4615771 DOI: 10.1080/15476286.2015.1060394] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The AT-hook has been defined as a DNA binding peptide motif that contains a glycine-arginine-proline (G-R-P) tripeptide core flanked by basic amino acids. Recent reports documented variations in the sequence of AT-hooks and revealed RNA binding activity of some canonical AT-hooks, suggesting a higher structural and functional variability of this protein domain than previously anticipated. Here we describe the discovery and characterization of the extended AT-hook peptide motif (eAT-hook), in which basic amino acids appear symmetrical mainly at a distance of 12-15 amino acids from the G-R-P core. We identified 80 human and 60 mouse eAT-hook proteins and biochemically characterized the eAT-hooks of Tip5/BAZ2A, PTOV1 and GPBP1. Microscale thermophoresis and electrophoretic mobility shift assays reveal the nucleic acid binding features of this peptide motif, and show that eAT-hooks bind RNA with one order of magnitude higher affinity than DNA. In addition, cellular localization studies suggest a role for the N-terminal eAT-hook of PTOV1 in nucleocytoplasmic shuttling. In summary, our findings classify the eAT-hook as a novel nucleic acid binding motif, which potentially mediates various RNA-dependent cellular processes.
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Affiliation(s)
- Michael Filarsky
- a Biochemistry Center Regensburg ; University of Regensburg ; Regensburg , Germany
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Chen C, Bartenhagen C, Gombert M, Okpanyi V, Binder V, Röttgers S, Bradtke J, Teigler-Schlegel A, Harbott J, Ginzel S, Thiele R, Husemann P, Krell PF, Borkhardt A, Dugas M, Hu J, Fischer U. Next-generation-sequencing of recurrent childhood high hyperdiploid acute lymphoblastic leukemia reveals mutations typically associated with high risk patients. Leuk Res 2015; 39:990-1001. [DOI: 10.1016/j.leukres.2015.06.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 06/08/2015] [Accepted: 06/10/2015] [Indexed: 01/07/2023]
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Martínez-Nava GA, Torres-Poveda K, Lagunas-Martínez A, Bahena-Román M, Zurita-Díaz MA, Ortíz-Flores E, García-Carrancá A, Madrid-Marina V, Burguete-García AI. Cervical cancer-associated promoter polymorphism affects akna expression levels. Genes Immun 2014; 16:43-53. [PMID: 25373726 DOI: 10.1038/gene.2014.60] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 09/02/2014] [Accepted: 09/24/2014] [Indexed: 12/17/2022]
Abstract
Cervical cancer (CC) is responsible for >260,000 deaths worldwide each year. Efforts are being focused on identifying genetic susceptibility factors, especially in genes related to the immune response. Akna has been proposed to be one of them, but data regarding its functional role in the disease is scarce. Supporting the notion of akna as a CC susceptibility gene, we found two polymorphisms associated with squamous intraepithelial lesion (SIL) and CC; moreover, we identified an association between high akna expression levels and CC and SIL, but its direction differs in each disease stage. To show the potential existence of a cis-acting polymorphism, we assessed akna allelic expression imbalance for the alleles of the -1372C>A polymorphism. We found that, regardless of the study group, the number of transcripts derived from the A allele was significantly higher than those from the C allele. Our results support the hypothesis that akna is a CC susceptibility genetic factor and suggest that akna transcriptional regulation has a role in the disease. We anticipate our study to be a starting point for in vitro evaluation of akna transcriptional regulation and for the identification of transcription factors and cis-elements regulating AKNA function that are involved in carcinogenesis.
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Affiliation(s)
- G A Martínez-Nava
- 193;rea de Infecciones Crónicas y Cáncer, Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Mexico
| | - K Torres-Poveda
- 193;rea de Infecciones Crónicas y Cáncer, Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Mexico
| | - A Lagunas-Martínez
- 193;rea de Infecciones Crónicas y Cáncer, Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Mexico
| | - M Bahena-Román
- 193;rea de Infecciones Crónicas y Cáncer, Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Mexico
| | - M A Zurita-Díaz
- 193;rea de Infecciones Crónicas y Cáncer, Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Mexico
| | - E Ortíz-Flores
- 193;rea de Infecciones Crónicas y Cáncer, Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Mexico
| | - A García-Carrancá
- Unidad de Investigación Biomédica en Cáncer, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México and Instituto Nacional de Cancerología, Secretaría de Salud, Distrito Federal, Mexico
| | - V Madrid-Marina
- 193;rea de Infecciones Crónicas y Cáncer, Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Mexico
| | - A I Burguete-García
- 193;rea de Infecciones Crónicas y Cáncer, Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Mexico
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MacDonald KPA, Le Texier L, Zhang P, Morris H, Kuns RD, Lineburg KE, Leveque L, Don AL, Markey KA, Vuckovic S, Bagger FO, Boyle GM, Blazar BR, Hill GR. Modification of T cell responses by stem cell mobilization requires direct signaling of the T cell by G-CSF and IL-10. THE JOURNAL OF IMMUNOLOGY 2014; 192:3180-9. [PMID: 24585878 DOI: 10.4049/jimmunol.1302315] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The majority of allogeneic stem cell transplants are currently undertaken using G-CSF mobilized peripheral blood stem cells. G-CSF has diverse biological effects on a broad range of cells and IL-10 is a key regulator of many of these effects. Using mixed radiation chimeras in which the hematopoietic or nonhematopoietic compartments were wild-type, IL-10(-/-), G-CSFR(-/-), or combinations thereof we demonstrated that the attenuation of alloreactive T cell responses after G-CSF mobilization required direct signaling of the T cell by both G-CSF and IL-10. IL-10 was generated principally by radio-resistant tissue, and was not required to be produced by T cells. G-CSF mobilization significantly modulated the transcription profile of CD4(+)CD25(+) regulatory T cells, promoted their expansion in the donor and recipient and their depletion significantly increased graft-versus-host disease (GVHD). In contrast, stem cell mobilization with the CXCR4 antagonist AMD3100 did not alter the donor T cell's ability to induce acute GVHD. These studies provide an explanation for the effects of G-CSF on T cell function and demonstrate that IL-10 is required to license regulatory function but T cell production of IL-10 is not itself required for the attenuation GVHD. Although administration of CXCR4 antagonists is an efficient means of stem cell mobilization, this fails to evoke the immunomodulatory effects seen during G-CSF mobilization. These data provide a compelling rationale for considering the immunological benefits of G-CSF in selecting mobilization protocols for allogeneic stem cell transplantation.
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Affiliation(s)
- Kelli P A MacDonald
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4006, Australia
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37
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Suram S, Silveira LJ, Mahaffey S, Brown GD, Bonventre JV, Williams DL, Gow NAR, Bratton DL, Murphy RC, Leslie CC. Cytosolic phospholipase A(2)α and eicosanoids regulate expression of genes in macrophages involved in host defense and inflammation. PLoS One 2013; 8:e69002. [PMID: 23950842 PMCID: PMC3742295 DOI: 10.1371/journal.pone.0069002] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Accepted: 06/03/2013] [Indexed: 12/20/2022] Open
Abstract
The role of Group IVA cytosolic phospholipase A2 (cPLA2α)
activation in regulating macrophage transcriptional responses to
Candida
albicans infection was investigated.
cPLA2α releases arachidonic acid for the production of
eicosanoids. In mouse resident peritoneal macrophages, prostacyclin,
prostaglandin E2 and leukotriene C4 were produced within
minutes of C.
albicans addition before cyclooxygenase 2
expression. The production of TNFα was lower in C.
albicans-stimulated cPLA2α+/+
than cPLA2α-/- macrophages due to an autocrine effect of
prostaglandins that increased cAMP to a greater extent in
cPLA2α+/+ than cPLA2α-/-
macrophages. For global insight, differential gene expression in
C.
albicans-stimulated
cPLA2α+/+ and cPLA2α-/-
macrophages (3 h) was compared by microarray. cPLA2α+/+
macrophages expressed 86 genes at lower levels and 181 genes at higher levels
than cPLA2α-/- macrophages (≥2-fold, p<0.05). Several
pro-inflammatory genes were expressed at lower levels (Tnfα,
Cx3cl1, Cd40, Ccl5,
Csf1, Edn1, CxCr7, Irf1,
Irf4, Akna, Ifnγ, several IFNγ-inducible
GTPases). Genes that dampen inflammation (Socs3,
Il10, Crem, Stat3,
Thbd, Thbs1, Abca1) and
genes involved in host defense (Gja1, Csf3,
Trem1, Hdc) were expressed at higher
levels in cPLA2α+/+ macrophages. Representative genes
expressed lower in cPLA2α+/+ macrophages (Tnfα,
Csf1) were increased by treatment with a prostacyclin receptor
antagonist and protein kinase A inhibitor, whereas genes expressed at higher
levels (Crem, Nr4a2, Il10,
Csf3) were suppressed. The results suggest that
C.
albicans stimulates an autocrine loop in
macrophages involving cPLA2α, cyclooxygenase 1-derived prostaglandins
and increased cAMP that globally effects expression of genes involved in host
defense and inflammation.
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Affiliation(s)
- Saritha Suram
- Department of Pediatrics, National Jewish Health, Denver, Colorado,
United States of America
| | - Lori J. Silveira
- Division of Biostatistics and Bioinformatics, National Jewish Health,
Denver, Colorado, United States of America
| | - Spencer Mahaffey
- Department of Pediatrics, National Jewish Health, Denver, Colorado,
United States of America
| | - Gordon D. Brown
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, United
Kingdom
| | - Joseph V. Bonventre
- Renal Division, Brigham and Women’s Hospital, Boston, Massachusetts,
United States of America
| | - David L. Williams
- Department of Surgery, James H. Quillen College of Medicine, Johnson
City, Tennessee, United States of America
| | - Neil A. R. Gow
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, United
Kingdom
| | - Donna L. Bratton
- Department of Pediatrics, National Jewish Health, Denver, Colorado,
United States of America
| | - Robert C. Murphy
- Department of Pharmacology, University of Colorado Denver, Aurora,
Colorado, United States of America
| | - Christina C. Leslie
- Department of Pediatrics, National Jewish Health, Denver, Colorado,
United States of America
- Department of Pharmacology, University of Colorado Denver, Aurora,
Colorado, United States of America
- Department of Pathology, University of Colorado Denver, Aurora, Colorado,
United States of America
- * E-mail:
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38
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Wang Z, Li P, Xu Q, Xu J, Li X, Zhang X, Ma Q, Wu Z. Potent Antitumor Activity Generated by a Novel Tumor Specific Cytotoxic T Cell. PLoS One 2013; 8:e66659. [PMID: 23825554 PMCID: PMC3688986 DOI: 10.1371/journal.pone.0066659] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Accepted: 05/09/2013] [Indexed: 01/29/2023] Open
Abstract
Hepatocellular carcinoma is one of the most common malignant neoplasms in the world and is the main cause of death in patients with liver cirrhosis. Surgical intervention is not suitable for majority of hepatocellular carcinoma. Investigation of the effective targeting to the tumor cells is essential for both primary tumors and metastases. Tumor specific cytotoxic T lymphocytes (CTL) have been considered to be the attractive vehicles for delivering therapeutic agents toward various tumor diseases. This study was to explore the distribution pattern of CTL carrying the lentiviral vectors with the characteristic of adenoviral E1 gene under the control of the cell activation-dependent CD40 ligand promoter (Lenti/hCD40L/E1AB). Following transduction with adenoviral vectors containing chimeric type 5 and type 35 fiber proteins (Ad5/35-TRAIL), these CTLs produced infectious virus when exposed to HepG2 cells. We assessed the therapeutic ability of CTLs using MTT, Western blot and colony formation assay. The novel CTL harboring Lenti/hCD40L/E1AB and Ad5/35-TRAIL caused proliferation inhibition and significant apoptosis in hepatocellular carcinoma cell lines. Thus, the novel CTL may be useful for the development of gene therapy approaches to hepatocellular carcinoma.
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Affiliation(s)
- Zheng Wang
- Department of Hepatobiliary Surgery, First Affiliated Hospital of Medical College, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Pei Li
- Department of Hepatobiliary Surgery, First Affiliated Hospital of Medical College, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Qinhong Xu
- Department of Hepatobiliary Surgery, First Affiliated Hospital of Medical College, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Jun Xu
- Department of Hepatobiliary Surgery, First Affiliated Hospital of Medical College, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Xuqi Li
- Department of Hepatobiliary Surgery, First Affiliated Hospital of Medical College, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Xufeng Zhang
- Department of Hepatobiliary Surgery, First Affiliated Hospital of Medical College, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Qingyong Ma
- Department of Hepatobiliary Surgery, First Affiliated Hospital of Medical College, Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Zheng Wu
- Department of Hepatobiliary Surgery, First Affiliated Hospital of Medical College, Xi'an Jiaotong University, Xi'an, Shaanxi, China
- * E-mail:
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Papic N, Maxwell CI, Delker DA, Liu S, Heale BSE, Hagedorn CH. RNA-sequencing analysis of 5' capped RNAs identifies many new differentially expressed genes in acute hepatitis C virus infection. Viruses 2012; 4:581-612. [PMID: 22590687 PMCID: PMC3347324 DOI: 10.3390/v4040581] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Revised: 03/31/2012] [Accepted: 04/03/2012] [Indexed: 12/28/2022] Open
Abstract
We describe the first report of RNA sequencing of 5' capped (Pol II) RNAs isolated from acutely hepatitis C virus (HCV) infected Huh 7.5 cells that provides a general approach to identifying differentially expressed annotated and unannotated genes that participate in viral-host interactions. We identified 100, 684, and 1,844 significantly differentially expressed annotated genes in acutely infected proliferative Huh 7.5 cells at 6, 48, and 72 hours, respectively (fold change ≥ 1.5 and Bonferroni adjusted p-values < 0.05). Most of the differentially expressed genes (>80%) and biological pathways (such as adipocytokine, Notch, Hedgehog and NOD-like receptor signaling) were not identified by previous gene array studies. These genes are critical components of host immune, inflammatory and oncogenic pathways and provide new information regarding changes that may benefit the virus or mediate HCV induced pathology. RNAi knockdown studies of newly identified highly upregulated FUT1 and KLHDC7B genes provide evidence that their gene products regulate and facilitate HCV replication in hepatocytes. Our approach also identified novel Pol II unannotated transcripts that were upregulated. Results further identify new pathways that regulate HCV replication in hepatocytes and suggest that our approach will have general applications in studying viral-host interactions in model systems and clinical biospecimens.
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Affiliation(s)
- Neven Papic
- Department of Medicine, University of Utah, 30 N 1900 E #3C310, Salt Lake City, UT 84132, USA; (N.P.); (C.I.M.); (D.A.D.); (S.L.); (B.S.E.H.)
| | - Christopher I. Maxwell
- Department of Medicine, University of Utah, 30 N 1900 E #3C310, Salt Lake City, UT 84132, USA; (N.P.); (C.I.M.); (D.A.D.); (S.L.); (B.S.E.H.)
- Huntsman Cancer Institute, University of Utah, 30 N 1900 E #3C310, Salt Lake City, UT 84132, USA
| | - Don A. Delker
- Department of Medicine, University of Utah, 30 N 1900 E #3C310, Salt Lake City, UT 84132, USA; (N.P.); (C.I.M.); (D.A.D.); (S.L.); (B.S.E.H.)
| | - Shuanghu Liu
- Department of Medicine, University of Utah, 30 N 1900 E #3C310, Salt Lake City, UT 84132, USA; (N.P.); (C.I.M.); (D.A.D.); (S.L.); (B.S.E.H.)
| | - Bret S. E. Heale
- Department of Medicine, University of Utah, 30 N 1900 E #3C310, Salt Lake City, UT 84132, USA; (N.P.); (C.I.M.); (D.A.D.); (S.L.); (B.S.E.H.)
| | - Curt H. Hagedorn
- Department of Medicine, University of Utah, 30 N 1900 E #3C310, Salt Lake City, UT 84132, USA; (N.P.); (C.I.M.); (D.A.D.); (S.L.); (B.S.E.H.)
- Department of Experimental Pathology, University of Utah, 30 N 1900 E #3C310, Salt Lake City, UT 84132, USA
- Author to whom correspondence should be addressed; ; Tel.: +1-801-587-4619; Fax: +1-801-585-0187
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40
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Moliterno AR, Resar LMS. AKNA: another AT-hook transcription factor "hooking-up" with inflammation. Cell Res 2011; 21:1528-30. [PMID: 21670742 DOI: 10.1038/cr.2011.96] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Affiliation(s)
- Alison R Moliterno
- Division of Hematology, Johns Hopkins University, Baltimore, MD 21205, USA
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41
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Coordinate activation of inflammatory gene networks, alveolar destruction and neonatal death in AKNA deficient mice. Cell Res 2011; 21:1564-77. [PMID: 21606955 DOI: 10.1038/cr.2011.84] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Gene expression can be regulated by chromatin modifiers, transcription factors and proteins that modulate DNA architecture. Among the latter, AT-hook transcription factors have emerged as multifaceted regulators that can activate or repress broad A/T-rich gene networks. Thus, alterations of AT-hook genes could affect the transcription of multiple genes causing global cell dysfunction. Here we report that targeted deletions of mouse AKNA, a hypothetical AT-hook-like transcription factor, sensitize mice to pathogen-induced inflammation and cause sudden neonatal death. Compared with wild-type littermates, AKNA KO mice appeared weak, failed to thrive and most died by postnatal day 10. Systemic inflammation, predominantly in the lungs, was accompanied by enhanced leukocyte infiltration and alveolar destruction. Cytologic, immunohistochemical and molecular analyses revealed CD11b(+)Gr1(+) neutrophils as major tissue infiltrators, neutrophilic granule protein, cathelin-related antimicrobial peptide and S100A8/9 as neutrophil-specific chemoattracting factors, interleukin-1β and interferon-γ as proinflammatory mediators, and matrix metalloprotease 9 as a plausible proteolytic trigger of alveolar damage. AKNA KO bone marrow transplants in wild-type recipients reproduced the severe pathogen-induced reactions and confirmed the involvement of neutrophils in acute inflammation. Moreover, promoter/reporter experiments showed that AKNA could act as a gene repressor. Our results support the concept of coordinated pathway-specific gene regulation functions modulating the intensity of inflammatory responses, reveal neutrophils as prominent mediators of acute inflammation and suggest mechanisms underlying the triggering of acute and potentially fatal immune reactions.
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42
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Mao L, Yang P, Hou S, Li F, Kijlstra A. Label-free proteomics reveals decreased expression of CD18 and AKNA in peripheral CD4+ T cells from patients with Vogt-Koyanagi-Harada syndrome. PLoS One 2011; 6:e14616. [PMID: 21297967 PMCID: PMC3030555 DOI: 10.1371/journal.pone.0014616] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Accepted: 01/03/2011] [Indexed: 01/29/2023] Open
Abstract
Vogt-Koyanagi-Harada (VKH) syndrome is a systemic autoimmune disease. CD4+ T cells have been shown to be involved in autoimmune diseases including VKH syndrome. To screen aberrantly expressed membrane proteins in CD4+ T cell from patients with active VKH syndrome, blood samples were taken from five patients with active VKH syndrome and five healthy individuals. A label-free quantitative proteomic strategy was used to identify the differently expressed proteins between the two groups. The results revealed that the expression of 102 peptides was significantly altered (p<0.05) between two groups and matched amino acid sequences of proteins deposited in the international protein index (ipi.HUMAN.v3.36.fasta). The identified peptides corresponded to 64 proteins, in which 30 showed more than a 1.5-fold difference between the two groups. The decreased expression of CD18 and AKNA transcription factor (AKNA), both being three-fold lower than controls in expression identified by the label-free method, was further confirmed in an additional group of five active VKH patients and six normal individuals using the Western blot technique. A significantly decreased expression of CD18 and AKNA suggests a role for both proteins in the pathogenesis of this syndrome.
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Affiliation(s)
- Liming Mao
- Laboratory of Ophthalmology, Chongqing Eye Institute, The First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Peizeng Yang
- Laboratory of Ophthalmology, Chongqing Eye Institute, The First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
- * E-mail:
| | - Shengping Hou
- Laboratory of Ophthalmology, Chongqing Eye Institute, The First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Fuzhen Li
- Laboratory of Ophthalmology, Chongqing Eye Institute, The First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Aize Kijlstra
- The Department of Ophthalmology, University of Maastricht, Maastricht, The Netherlands
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Differential effect of pretransplant blood transfusions on immune effector and regulatory compartments in HLA-sensitized and nonsensitized recipients. Transplantation 2011; 90:1192-9. [PMID: 21166103 DOI: 10.1097/tp.0b013e3181fa943d] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
BACKGROUND Blood transfusion (BT) may elicit both harmful and beneficial immune responses against a subsequent organ graft. Immune parameters of a single, non leukocyte-depleted BT were investigated in two groups: non-human leukocyte antigen (HLA)-sensitized recipients with a one-HLA-DR matched donor (protocolled BT [PBT]) and females with previous exposure to HLA alloantigens through pregnancy (donor-specific transfusion [DST]). METHODS Thirty-five percent of DST recipients and 9.5% of PBT recipients developed HLA antibodies after BT.Phenotypic and functional analyses were performed in pre-BT, 2 weeks post-BT, and more than 10 weeks post-BT samples (PBT: n=10; DST: n=14). RESULT The number of donor-reactive interferon-γ-producing memory T cells increased 2 weeks post-BT, but only in the DST group, increased frequencies persisted beyond 10 weeks (P0.004). In the DST recipients, the proportion of natural killer cells (CD3(-)CD56(+)) significantly increased after BT (P=0.01), whereas in PBT recipients, the proportion of regulatoryT cells (CD4(+)CD25(+)Foxp3(+)CD127 low) significantly increased at 2 weeks post-BT (P=0.039). Microarray analysis confirmed increased activity of genes involved in function of natural killer cells,Tcells, and Bcells in DSTrecipients and increased expression of immune regulatory genes (galectin-1, Foxo3a, and follistatin-like 3) in PBT recipients. Galectin-1 expression by quantitative polymerase chain reaction was significantly enhanced in peripheral blood cells after PBT (P0.05). CONCLUSION Decreased immune effector mechanisms combined with an increased immune regulatory cell signature after HLA-DR-matched BT in nonsensitized patients is in line with clinical observations of improved outcome of a subsequent graft. Previous sensitization, however, may lead to HLA antibody formation and prolonged donor-specific memory T-cell reactivity after BT.
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Perales G, Burguete-García AI, Dimas J, Bahena-Román M, Bermúdez-Morales VH, Moreno J, Madrid-Marina V. A polymorphism in the AT-hook motif of the transcriptional regulatorAKNAis a risk factor for cervical cancer. Biomarkers 2010; 15:470-4. [DOI: 10.3109/1354750x.2010.485332] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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45
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Yoo JK, Lim JJ, Ko JJ, Lee DR, Kim JK. Expression profile of genes identified in human spermatogonial stem cell-like cells using suppression subtractive hybridization. J Cell Biochem 2010; 110:752-62. [DOI: 10.1002/jcb.22588] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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46
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A T-cell-specific CD154 transcriptional enhancer located just upstream of the promoter. Genes Immun 2008; 9:640-9. [PMID: 18719603 DOI: 10.1038/gene.2008.67] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
CD154 (CD40-ligand) is a critical immune regulator. CD154 expression is tightly regulated and largely restricted to activated CD4 T cells. Using DNase I hypersensitivity site (HSS) mapping, we identified two novel HSS mapping to the human CD154 promoter element and just upstream. Both HSS were activation independent and CD4 T-cell specific. Approximately 350 bp of DNA sequence flanking the upstream HSS site was highly conserved between mouse and man, and was rich in binding sites for GATA and NFAT proteins. Gel shift and chromatin immunoprecipitation assays demonstrated both NFAT1 and the Th2 factor, GATA-3, bound this enhancer element in vitro and in vivo, respectively. A PstI/XbaI 345 bp fragment of this region acted as a transcriptional enhancer of the CD154 promoter in primary human CD4 T cells. Overexpression of repressor of GATA and a dominant negative GATA-3 protein independently inhibited transcription, whereas overexpression of wild-type GATA-3 enhanced transcriptional activity, by this element in primary CD4 T cells. Moreover, more interleukin-4-producing CD4 T cells expressed CD154 following activation than interferon-gamma-producing CD4 T cells. Thus, we identified a novel T-cell-specific, GATA-3 responsive, CD154 transcriptional enhancer, which may contribute to increased propensity of Th2 cells to express CD154.
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Stewart R, Wei W, Challa A, Armitage RJ, Arrand JR, Rowe M, Young LS, Eliopoulos A, Gordon J. CD154 tone sets the signaling pathways and transcriptome generated in model CD40-pluricompetent L3055 Burkitt's lymphoma cells. THE JOURNAL OF IMMUNOLOGY 2007; 179:2705-12. [PMID: 17709483 DOI: 10.4049/jimmunol.179.5.2705] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Activated B cells reacting to small amounts of CD40L (CD154) maintain homeostasis by suppressing default apoptosis. Additional outcomes, particularly differentiation, demand higher CD40 occupancy. Here, focusing on survival, we compared changes in the transcriptome of pleiotropically competent, early passage L3055 Burkitt's lymphoma cells confronted with low (picomolar) and high (nanomolar) concentrations of CD154 to gain insight into how a single receptor sets these distinct phenotypes. Of 267 genes altering transcriptional activity in response to strong CD154 tone, only 25 changed coordinately on low receptor occupancy. Seven of the top nine common up-regulated genes were targets of NF-kappaB. Direct measurement and functional inhibition of the NF-kappaB pathway revealed it to be central to a CD40-dependent survival signature. Although the canonical NF-kappaB axis was engaged by both signaling strengths equally, robust alternative pathway activation was a feature selective to a strong CD40 signal. Discriminatory exploitation of the two separate arms of NF-kappaB activation may indicate a principle whereby a cell senses and reacts differentially to shifting ligand availability. Identifying components selectively coupling CD40 to each axis could indicate targets for disruption in B cell pathologies underpinned by ectopic and/or hyper-CD154 activity such as neoplasia and some autoimmunities.
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Affiliation(s)
- Ross Stewart
- MRC Centre for Immune Regulation, University of Birmingham Medical School, Birmingham, United Kingdom
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Kim SY, Kim YC, Seong ES, Lee YH, Park JM, Choi D. The chili pepper CaATL1: an AT-hook motif-containing transcription factor implicated in defence responses against pathogens. MOLECULAR PLANT PATHOLOGY 2007; 8:761-771. [PMID: 20507536 DOI: 10.1111/j.1364-3703.2007.00427.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
SUMMARY Using cDNA microarray analysis, we isolated a cDNA clone, CaATL1 (Capsicum annuum L. Bukang AT-hook-Like gene 1), from a chili pepper plant incompatibly interacting with bacterial pathogens. The deduced amino acid sequence has a potential nuclear localization sequence and an AT-hook DNA binding motif which can bind AT-rich sequence elements. Expression of CaATL1 was specifically induced in host- and non-host-resistant responses against bacterial and viral pathogens in pepper plants. In addition, CaATL1 transcripts also increased following salicylic acid and ethephone treatment but were only mildly induced by methyl-jasmonate treatment. CaATL1::smGFP (soluble-modified green fluorescent protein) fusion protein localized to nuclei in tobacco BY2 protoplasts. The C-terminal region of the CaATL1 protein fused to the LexA DNA binding domain was able to activate reporter gene expression in yeast. To analyse further the role of the CaATL1 in pathogen defence response, we generated CaATL1-over-expressing transgenic tomato plants. These transgenic plants showed enhanced disease resistance against bacterial and oomycete pathogens. Taken together, these results provide the first evidence of a role for a plant AT-hook motif-containing transcription factor in pathogen defence response.
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Affiliation(s)
- Soo-Yong Kim
- Plant Genome Research Center, KRIBB, PO Box 115, Yusung, Daejon 305-600, Republic of Korea
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Harhaj NS, Janic B, Ramos JC, Harrington WJ, Harhaj EW. Deregulated expression of CD40 ligand in HTLV-I infection: distinct mechanisms of downregulation in HTLV-I-transformed cell lines and ATL patients. Virology 2007; 362:99-108. [PMID: 17258259 PMCID: PMC1949045 DOI: 10.1016/j.virol.2006.12.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2006] [Revised: 11/09/2006] [Accepted: 12/18/2006] [Indexed: 10/23/2022]
Abstract
HTLV-I infection is associated with the development of adult T cell leukemia (ATL) and the neuroinflammatory disease HAM/TSP. There are quantitative and qualitative differences in the antiviral cytotoxic T cell (CTL) response in ATL and HAM/TSP although the underlying mechanisms are unclear. Here, we demonstrate that the HTLV-I Tax trans-activating protein is a transcriptional activator of CD40 ligand (CD40L), a critical regulator of dendritic cell maturation and adaptive immunity. Tax activates CD40L expression via a cyclosporin A insensitive pathway that is also independent of NF-kappaB. Although Tax upregulates CD40L gene expression, CD40L expression is absent in Tax-expressing HTLV-I-transformed cell lines via an epigenetic mechanism involving methylation. T lymphocytes cultured ex vivo from ATL patients, but not HAM/TSP or normal controls, exhibit a potent block in the induction of CD40L, but not CD69. However, the CD40L gene is not silenced by methylation in ATL patients, thus CD40L is downregulated by distinct mechanisms in HTLV-I-transformed cell lines and ATL patients.
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Affiliation(s)
- Nicole S Harhaj
- Department of Microbiology and Immunology, Sylvester Comprehensive Cancer Center, The University of Miami, Miller School of Medicine, 1550 NW 10 Avenue, Miami, FL 33136, USA
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Steiper ME, Parikh SJ, Zichello JM. Phylogenetic analysis of the promoter region of the CD40L gene in primates and other mammals. INFECTION GENETICS AND EVOLUTION 2006; 8:406-13. [PMID: 17275421 DOI: 10.1016/j.meegid.2006.12.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2006] [Revised: 12/12/2006] [Accepted: 12/14/2006] [Indexed: 11/15/2022]
Abstract
CD40L is a type II membrane protein comprised of 261 amino acids. CD40L plays a crucial role in the immune system where it is primarily expressed on activated T cells and triggers immunoglobulin class switching. The genetic disease X-linked hypergammaglobulinemia (HIGM1, XHIGM or XHIM) is caused by mutations in the CD40L gene. Individuals with HIGM1 are susceptible to recurrent infections to pathogens and a relationship has been shown to exist with malaria [Sabeti, P., Usen, S., Farhadian, S., Jallow, M., Doherty, T., Newport, M., Pinder, M., Ward, R., Kwiatkowski, D., 2002a. CD40L association with protection from severe malaria. Genes Immun. 3, 286-291]. In this paper, we phylogenetically examine the promoter region of CD40L in primates and other mammals via phylogenetic shadowing. This analysis revealed several regions of the CD40L promoter that were highly constrained and thereby inferred to be functional. These constrained regions confirmed many known regulatory sites. In addition, a novel, highly constrained upstream region was also identified which had an NF-AT recognition motif. These analyses also showed that the different mammal groups do not share an exactly similar set of promoter binding sites and taxon-specific promoters have evolved.
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Affiliation(s)
- Michael E Steiper
- Department of Anthropology, Hunter College of the City University of New York, New York, NY 10021, United States.
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