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Paralkar VR. Transcription factor regulation of ribosomal RNA in hematopoiesis. Curr Opin Hematol 2024:00062752-990000000-00069. [PMID: 38568093 DOI: 10.1097/moh.0000000000000816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
PURPOSE OF REVIEW Ribosomal RNAs (rRNAs) are transcribed within nucleoli from rDNA repeats by RNA Polymerase I (Pol I). There is variation in rRNA transcription rates across the hematopoietic tree, and leukemic blast cells have prominent nucleoli, indicating abundant ribosome biogenesis. The mechanisms underlying these variations are poorly understood. The purpose of this review is to summarize findings of rDNA binding and Pol I regulation by hematopoietic transcription factors. RECENT FINDINGS Our group recently used custom genome assemblies optimized for human and mouse rDNA mapping to map nearly 2200 ChIP-Seq datasets for nearly 250 factors to rDNA, allowing us to identify conserved occupancy patterns for multiple transcription factors. We confirmed known rDNA occupancy of MYC and RUNX factors, and identified new binding sites for CEBP factors, IRF factors, and SPI1 at canonical motif sequences. We also showed that CEBPA degradation rapidly leads to reduced Pol I occupancy and nascent rRNA in mouse myeloid cells. SUMMARY We propose that a number of hematopoietic transcription factors bind rDNA and potentially regulate rRNA transcription. Our model has implications for normal and malignant hematopoiesis. This review summarizes the literature, and outlines experimental considerations to bear in mind while dissecting transcription factor roles on rDNA.
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Affiliation(s)
- Vikram R Paralkar
- Division of Hematology and Oncology, Department of Medicine
- Department of Cell and Developmental Biology
- Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
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2
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Kleuskens MTA, Haasnoot ML, Garssen J, Bredenoord AJ, van Esch BCAM, Redegeld FA. Transcriptomic profiling of the acute mucosal response to local food injections in adults with eosinophilic esophagitis. J Allergy Clin Immunol 2024; 153:780-792. [PMID: 37972740 DOI: 10.1016/j.jaci.2023.10.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 10/12/2023] [Accepted: 10/27/2023] [Indexed: 11/19/2023]
Abstract
BACKGROUND Exposure of the esophageal mucosa to food allergens can cause acute mucosal responses in patients with eosinophilic esophagitis (EoE), but the underlying local immune mechanisms driving these acute responses are not well understood. OBJECTIVE We sought to gain insight into the early transcriptomic changes that occur during an acute mucosal response to food allergens in EoE. METHODS Bulk RNA sequencing was performed on esophageal biopsy specimens from adult patients with EoE (n = 5) collected before and 20 minutes after intramucosal injection of various food extracts in the esophagus. Baseline biopsy specimens from control subjects without EoE (n = 5) were also included. RESULTS At baseline, the transcriptome of the patients with EoE showed increased expression of genes related to an EoE signature. After local food injection, we identified 40 genes with a potential role in the early immune response to food allergens (most notably CEBPB, IL1B, TNFSF18, PHLDA2, and SLC15A3). These 40 genes were enriched in processes related to immune activation, such as the acute-phase response, cellular responses to external stimuli, and cell population proliferation. TNFSF18 (also called GITRL), a member of the TNF superfamily that is best studied for its costimulatory effect on T cells, was the most dysregulated early EoE gene, showing a 12-fold increase compared with baseline and an 18-fold increase compared with a negative visual response. Further experiments showed that the esophageal epithelium may be an important source of TNFSF18 in EoE, which was rapidly induced by costimulating esophageal epithelial cells with the EoE-relevant cytokines IL-13 and TNF-α. CONCLUSIONS Our data provide unprecedented insight into the transcriptomic changes that mediate the acute mucosal immune response to food allergens in EoE and suggest that TNFSF18 may be an important effector molecule in this response.
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Affiliation(s)
- Mirelle T A Kleuskens
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Maria L Haasnoot
- Department of Gastroenterology and Hepatology, Amsterdam UMC, Amsterdam, The Netherlands
| | - Johan Garssen
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, The Netherlands; Danone Nutricia Research, Utrecht, The Netherlands
| | - Albert J Bredenoord
- Department of Gastroenterology and Hepatology, Amsterdam UMC, Amsterdam, The Netherlands
| | - Betty C A M van Esch
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, The Netherlands; Danone Nutricia Research, Utrecht, The Netherlands.
| | - Frank A Redegeld
- Division of Pharmacology, Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, The Netherlands.
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3
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Begg LR, Orriols AM, Zannikou M, Yeh C, Vadlamani P, Kanojia D, Bolin R, Dunne SF, Balakrishnan S, Camarda R, Roth D, Zielinski-Mozny NA, Yau C, Vassilopoulos A, Huang TH, Kim KYA, Horiuchi D. S100A8/A9 predicts response to PIM kinase and PD-1/PD-L1 inhibition in triple-negative breast cancer mouse models. Commun Med (Lond) 2024; 4:22. [PMID: 38378783 PMCID: PMC10879183 DOI: 10.1038/s43856-024-00444-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 01/29/2024] [Indexed: 02/22/2024] Open
Abstract
BACKGROUND Understanding why some triple-negative breast cancer (TNBC) patients respond poorly to existing therapies while others respond well remains a challenge. This study aims to understand the potential underlying mechanisms distinguishing early-stage TNBC tumors that respond to clinical intervention from non-responders, as well as to identify clinically viable therapeutic strategies, specifically for TNBC patients who may not benefit from existing therapies. METHODS We conducted retrospective bioinformatics analysis of historical gene expression datasets to identify a group of genes whose expression levels in early-stage tumors predict poor clinical outcomes in TNBC. In vitro small-molecule screening, genetic manipulation, and drug treatment in syngeneic mouse models of TNBC were utilized to investigate potential therapeutic strategies and elucidate mechanisms of drug action. RESULTS Our bioinformatics analysis reveals a robust association between increased expression of immunosuppressive cytokine S100A8/A9 in early-stage tumors and subsequent disease progression in TNBC. A targeted small-molecule screen identifies PIM kinase inhibitors as capable of decreasing S100A8/A9 expression in multiple cell types, including TNBC and immunosuppressive myeloid cells. Combining PIM inhibition and immune checkpoint blockade induces significant antitumor responses, especially in otherwise resistant S100A8/A9-high PD-1/PD-L1-positive tumors. Notably, serum S100A8/A9 levels mirror those of tumor S100A8/A9 in a syngeneic mouse model of TNBC. CONCLUSIONS Our data propose S100A8/A9 as a potential predictive and pharmacodynamic biomarker in clinical trials evaluating combination therapy targeting PIM and immune checkpoints in TNBC. This work encourages the development of S100A8/A9-based liquid biopsy tests for treatment guidance.
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Affiliation(s)
- Lauren R Begg
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Adrienne M Orriols
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- University of Florida College of Medicine, Gainesville, FL, USA
| | - Markella Zannikou
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Chen Yeh
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Biostatistics Collaboration Center, Northwestern University, Chicago, IL, USA
- Rush University Medical Center, Chicago, IL, USA
| | | | - Deepak Kanojia
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Mythic Therapeutics, Waltham, MA, USA
| | - Rosemary Bolin
- Center for Comparative Medicine, Northwestern University, Chicago, IL, USA
- Pennington Biomedical Research Center, Baton Rouge, LA, USA
| | - Sara F Dunne
- High Throughput Analysis Laboratory, Northwestern University, Evanston, IL, USA
| | - Sanjeev Balakrishnan
- University of California, San Francisco, San Francisco, CA, USA
- Pulze.ai, San Francisco, CA, USA
| | - Roman Camarda
- University of California, San Francisco, San Francisco, CA, USA
- Novo Ventures US, Inc., San Francisco, CA, USA
| | - Diane Roth
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Nicolette A Zielinski-Mozny
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Center for Comparative Medicine, Northwestern University, Chicago, IL, USA
| | - Christina Yau
- University of California, San Francisco, San Francisco, CA, USA
| | - Athanassios Vassilopoulos
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA
- AbbVie, Inc., North Chicago, IL, USA
| | - Tzu-Hsuan Huang
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Kwang-Youn A Kim
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Biostatistics Collaboration Center, Northwestern University, Chicago, IL, USA
| | - Dai Horiuchi
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA.
- Center for Human Immunobiology, Northwestern University, Chicago, IL, USA.
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Liu L, Ma L, Yu Y, Ma Z, Yin Y, Zhou S, Yu Y, Cui N, Meng X, Fan H. Cucumis sativus CsbZIP90 suppresses Podosphaera xanthii resistance by modulating reactive oxygen species. Plant Sci 2024; 339:111945. [PMID: 38061503 DOI: 10.1016/j.plantsci.2023.111945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/19/2023] [Accepted: 12/02/2023] [Indexed: 01/13/2024]
Abstract
Resistance to disease in plants requires the coordinated action of multiple functionally related genes, as it is difficult to improve disease resistance with a single functional gene. Therefore, the use of transcription factors to regulate the expression of multiple resistance genes to improve disease resistance has become a recent focus in the field of gene research. The basic leucine zipper (bZIP) transcription factor family plays vital regulatory roles in processes, such as plant growth and development and the stress response. In our previous study, CsbZIP90 (Cucsa.134370) was involved in the defense response of cucumber to Podosphaera xanthii, but the relationship between cucumber and resistance to powdery mildew remained unclear. Herein, we detected the function of CsbZIP90 in response to P. xanthii. CsbZIP90 was localized to the cytoplasm and nucleus, and its expression was significantly induced during P. xanthii attack. Transient overexpression of CsbZIP90 in cucumber cotyledons resulted in decreased resistance to P. xanthii, while silencing CsbZIP90 increased resistance to P. xanthii. CsbZIP90 negatively regulated the expression of reactive oxygen species (ROS)-related genes and activities of ROS-related kinases. Taken together, our results show that CsbZIP90 suppresses P. xanthi resistance by modulating ROS. This study will provide target genes for breeding cucumbers resistant to P. xanthii.
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Affiliation(s)
- Linghao Liu
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Lifeng Ma
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Yongbo Yu
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Zhangtong Ma
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Yunhan Yin
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Shuang Zhou
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Yang Yu
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China; Key Laboratory of Fruit and Vegetable Biology and Germplasm Enhancement, Shenyang Agricultural University, Shenyang 110866, China; Key Laboratory of Protected Horticulture of Ministry of Education, Shenyang Agricultural University, Shenyang 110866, China
| | - Na Cui
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China; Key Laboratory of Fruit and Vegetable Biology and Germplasm Enhancement, Shenyang Agricultural University, Shenyang 110866, China; Key Laboratory of Protected Horticulture of Ministry of Education, Shenyang Agricultural University, Shenyang 110866, China
| | - Xiangnan Meng
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China; Key Laboratory of Fruit and Vegetable Biology and Germplasm Enhancement, Shenyang Agricultural University, Shenyang 110866, China; Key Laboratory of Protected Horticulture of Ministry of Education, Shenyang Agricultural University, Shenyang 110866, China.
| | - Haiyan Fan
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China; Key Laboratory of Fruit and Vegetable Biology and Germplasm Enhancement, Shenyang Agricultural University, Shenyang 110866, China; Key Laboratory of Protected Horticulture of Ministry of Education, Shenyang Agricultural University, Shenyang 110866, China.
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5
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Vishnevsky OV, Bocharnikov AV, Ignatieva EV. Peak Scores Significantly Depend on the Relationships between Contextual Signals in ChIP-Seq Peaks. Int J Mol Sci 2024; 25:1011. [PMID: 38256085 PMCID: PMC10816497 DOI: 10.3390/ijms25021011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/13/2023] [Accepted: 01/09/2024] [Indexed: 01/24/2024] Open
Abstract
Chromatin immunoprecipitation followed by massively parallel DNA sequencing (ChIP-seq) is a central genome-wide method for in vivo analyses of DNA-protein interactions in various cellular conditions. Numerous studies have demonstrated the complex contextual organization of ChIP-seq peak sequences and the presence of binding sites for transcription factors in them. We assessed the dependence of the ChIP-seq peak score on the presence of different contextual signals in the peak sequences by analyzing these sequences from several ChIP-seq experiments using our fully enumerative GPU-based de novo motif discovery method, Argo_CUDA. Analysis revealed sets of significant IUPAC motifs corresponding to the binding sites of the target and partner transcription factors. For these ChIP-seq experiments, multiple regression models were constructed, demonstrating a significant dependence of the peak scores on the presence in the peak sequences of not only highly significant target motifs but also less significant motifs corresponding to the binding sites of the partner transcription factors. A significant correlation was shown between the presence of the target motifs FOXA2 and the partner motifs HNF4G, which found experimental confirmation in the scientific literature, demonstrating the important contribution of the partner transcription factors to the binding of the target transcription factor to DNA and, consequently, their important contribution to the peak score.
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Affiliation(s)
- Oleg V. Vishnevsky
- Institute of Cytology and Genetics, 630090 Novosibirsk, Russia;
- Department of Natural Science, Novosibirsk State University, 630090 Novosibirsk, Russia;
| | - Andrey V. Bocharnikov
- Department of Natural Science, Novosibirsk State University, 630090 Novosibirsk, Russia;
| | - Elena V. Ignatieva
- Institute of Cytology and Genetics, 630090 Novosibirsk, Russia;
- Department of Natural Science, Novosibirsk State University, 630090 Novosibirsk, Russia;
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6
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Arai H, Matsui H, Chi S, Utsu Y, Masuda S, Aotsuka N, Minami Y. Germline Variants and Characteristic Features of Hereditary Hematological Malignancy Syndrome. Int J Mol Sci 2024; 25:652. [PMID: 38203823 PMCID: PMC10779750 DOI: 10.3390/ijms25010652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/25/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
Due to the proliferation of genetic testing, pathogenic germline variants predisposing to hereditary hematological malignancy syndrome (HHMS) have been identified in an increasing number of genes. Consequently, the field of HHMS is gaining recognition among clinicians and scientists worldwide. Patients with germline genetic abnormalities often have poor outcomes and are candidates for allogeneic hematopoietic stem cell transplantation (HSCT). However, HSCT using blood from a related donor should be carefully considered because of the risk that the patient may inherit a pathogenic variant. At present, we now face the challenge of incorporating these advances into clinical practice for patients with myelodysplastic syndrome (MDS) or acute myeloid leukemia (AML) and optimizing the management and surveillance of patients and asymptomatic carriers, with the limitation that evidence-based guidelines are often inadequate. The 2016 revision of the WHO classification added a new section on myeloid malignant neoplasms, including MDS and AML with germline predisposition. The main syndromes can be classified into three groups. Those without pre-existing disease or organ dysfunction; DDX41, TP53, CEBPA, those with pre-existing platelet disorders; ANKRD26, ETV6, RUNX1, and those with other organ dysfunctions; SAMD9/SAMD9L, GATA2, and inherited bone marrow failure syndromes. In this review, we will outline the role of the genes involved in HHMS in order to clarify our understanding of HHMS.
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Affiliation(s)
- Hironori Arai
- Department of Hematology, National Cancer Center Hospital East, Kashiwa 277-8577, Japan; (H.A.); (S.C.)
- Department of Hematology and Oncology, Japanese Red Cross Narita Hospital, Iidacho, Narita 286-0041, Japan; (Y.U.); (S.M.); (N.A.)
| | - Hirotaka Matsui
- Department of Laboratory Medicine, National Cancer Center Hospital, Tsukiji, Chuoku 104-0045, Japan;
- Department of Medical Oncology and Translational Research, Graduate School of Medical Sciences, Kumamoto University, Kumamoto 860-8665, Japan
| | - SungGi Chi
- Department of Hematology, National Cancer Center Hospital East, Kashiwa 277-8577, Japan; (H.A.); (S.C.)
| | - Yoshikazu Utsu
- Department of Hematology and Oncology, Japanese Red Cross Narita Hospital, Iidacho, Narita 286-0041, Japan; (Y.U.); (S.M.); (N.A.)
| | - Shinichi Masuda
- Department of Hematology and Oncology, Japanese Red Cross Narita Hospital, Iidacho, Narita 286-0041, Japan; (Y.U.); (S.M.); (N.A.)
| | - Nobuyuki Aotsuka
- Department of Hematology and Oncology, Japanese Red Cross Narita Hospital, Iidacho, Narita 286-0041, Japan; (Y.U.); (S.M.); (N.A.)
| | - Yosuke Minami
- Department of Hematology, National Cancer Center Hospital East, Kashiwa 277-8577, Japan; (H.A.); (S.C.)
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Abstract
Transcription factors (TFs) play a pivotal role as regulators of gene expression, orchestrating the formation and maintenance of diverse animal body plans and innovations. However, the precise contributions of TFs and the underlying mechanisms driving the origin of basal metazoan body plans, particularly in ctenophores, remain elusive. Here, we present a comprehensive catalog of TFs in 2 ctenophore species, Pleurobrachia bachei and Mnemiopsis leidyi, revealing 428 and 418 TFs in their respective genomes. In contrast, morphologically simpler metazoans have a reduced TF representation compared to ctenophores, cnidarians, and bilaterians: the sponge Amphimedon encodes 277 TFs, and the placozoan Trichoplax adhaerens encodes 274 TFs. The emergence of complex ctenophore tissues and organs coincides with significant lineage-specific diversification of the zinc finger C2H2 (ZF-C2H2) and homeobox superfamilies of TFs. Notable, the lineages leading to Amphimedon and Trichoplax exhibit independent expansions of leucine zipper (BZIP) TFs. Some lineage-specific TFs may have evolved through the domestication of mobile elements, thereby supporting alternative mechanisms of parallel TF evolution and body plan diversification across the Metazoa.
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Affiliation(s)
- Krishanu Mukherjee
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, USA.
| | - Leonid L Moroz
- Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, USA.
- Department of Neuroscience and McKnight Brain Institute, University of Florida, Gainesville, FL, USA.
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Wang Q, Jia D, He J, Sun Y, Qian Y, Ge Q, Qi Y, Wang Q, Hu Y, Wang L, Fang Y, He H, Luo M, Feng L, Si J, Song Z, Wang L, Chen S. Lactobacillus Intestinalis Primes Epithelial Cells to Suppress Colitis-Related Th17 Response by Host-Microbe Retinoic Acid Biosynthesis. Adv Sci (Weinh) 2023; 10:e2303457. [PMID: 37983567 PMCID: PMC10754072 DOI: 10.1002/advs.202303457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 10/24/2023] [Indexed: 11/22/2023]
Abstract
Gut microbiome is integral to the pathogenesis of ulcerative colitis. A novel probiotic Lactobacillus intestinalis (L. intestinalis) exerts a protective effect against dextran sodium sulfate-induced colitis in mice. Based on flow cytometry, colitis-associated Th17 cells are the target of L. intestinalis, which is supported by the lack of protective effects of L. intestinalis in T cell-null Rag1-/- mice or upon anti-IL-17-A antibody-treated mice. Although L. intestinalis exerts no direct effect on T cell differentiation, it decreases C/EBPA-driven gut epithelial SAA1 and SAA2 production, which in turn impairs Th17 cell differentiation. Cometabolism of L. intestinalis ALDH and host ALDH1A2 contributed to elevated biosynthesis of retinoic acid (RA), which accounts for the anti-colitis effect in RAR-α -mediated way. In a cohort of ulcerative colitis patients, it is observed that fecal abundance of L. intestinalis is negatively associated with the C/EBPA-SAA1/2-Th17 axis. Finally, L. intestinalis has a synergistic effect with mesalazine in alleviating murine colitis. In conclusion, L. intestinalis and associated metabolites, RA, have potential therapeutic effects for suppressing colonic inflammation by modulating the crosstalk between intestinal epithelia and immunity.
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Affiliation(s)
- Qi‐Wen Wang
- Department of GastroenterologySir Run Run Shaw HospitalZhejiang UniversityHangzhouZhejiang310058China
| | - Ding‐Jia‐Cheng Jia
- Department of GastroenterologySecond Affiliated Hospital of Zhejiang University School of MedicineHangzhouZhejiang310058China
| | - Jia‐Min He
- Department of GastroenterologySir Run Run Shaw HospitalZhejiang UniversityHangzhouZhejiang310058China
| | - Yong Sun
- Department of GastroenterologySecond Affiliated Hospital of Zhejiang University School of MedicineHangzhouZhejiang310058China
| | - Yun Qian
- Department of Gastroenterology and HepatologyShenzhen University General HospitalShenzhenGuangdong518055China
| | - Qi‐Wei Ge
- Department of GastroenterologySecond Affiliated Hospital of Zhejiang University School of MedicineHangzhouZhejiang310058China
| | - Ya‐Dong Qi
- Department of GastroenterologySir Run Run Shaw HospitalZhejiang UniversityHangzhouZhejiang310058China
| | - Qing‐Yi Wang
- Department of GastroenterologySir Run Run Shaw HospitalZhejiang UniversityHangzhouZhejiang310058China
| | - Ying‐Ying Hu
- Department of GastroenterologySir Run Run Shaw HospitalZhejiang UniversityHangzhouZhejiang310058China
| | - Lan Wang
- Department of GastroenterologySir Run Run Shaw HospitalZhejiang UniversityHangzhouZhejiang310058China
| | - Yan‐Fei Fang
- Department of GastroenterologySir Run Run Shaw HospitalZhejiang UniversityHangzhouZhejiang310058China
| | - Hui‐Qin He
- Department of GastroenterologySir Run Run Shaw HospitalZhejiang UniversityHangzhouZhejiang310058China
| | - Man Luo
- Department of NutritionSir Run Run Shaw HospitalZhejiang UniversityHangzhouZhejiang310058China
| | - Li‐Jun Feng
- Department of NutritionSir Run Run Shaw HospitalZhejiang UniversityHangzhouZhejiang310058China
| | - Jian‐Min Si
- Department of GastroenterologySir Run Run Shaw HospitalZhejiang UniversityHangzhouZhejiang310058China
- Institution of GastroenterologyZhejiang UniversityHangzhouZhejiang310058China
- Prevention and Treatment Research Center of Senescent DiseaseZhejiang University School of MedicineHangzhouZhejiang310058China
| | - Zhang‐Fa Song
- Department of Colorectal SurgerySir Run Run Shaw HospitalZhejiang UniversityHangzhouZhejiang310058China
| | - Liang‐Jing Wang
- Department of GastroenterologySecond Affiliated Hospital of Zhejiang University School of MedicineHangzhouZhejiang310058China
- Institution of GastroenterologyZhejiang UniversityHangzhouZhejiang310058China
- Prevention and Treatment Research Center of Senescent DiseaseZhejiang University School of MedicineHangzhouZhejiang310058China
| | - Shu‐Jie Chen
- Department of GastroenterologySir Run Run Shaw HospitalZhejiang UniversityHangzhouZhejiang310058China
- Institution of GastroenterologyZhejiang UniversityHangzhouZhejiang310058China
- Prevention and Treatment Research Center of Senescent DiseaseZhejiang University School of MedicineHangzhouZhejiang310058China
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Zhou X, Tan B, Gui W, Zhou C, Zhao H, Lin X, Li H. IGF2 deficiency promotes liver aging through mitochondrial dysfunction and upregulated CEBPB signaling in D-galactose-induced aging mice. Mol Med 2023; 29:161. [PMID: 38017373 PMCID: PMC10685569 DOI: 10.1186/s10020-023-00752-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 11/01/2023] [Indexed: 11/30/2023] Open
Abstract
BACKGROUND Liver aging, marked by cellular senescence and low-grade inflammation, heightens susceptibility to chronic liver disease and worsens its prognosis. Insulin-like growth factor 2 (IGF2) has been implicated in numerous aging-related diseases. Nevertheless, its role and underlying molecular mechanisms in liver aging remain largely unexplored. METHODS The expression of IGF2 was examined in the liver of young (2-4 months), middle-aged (9-12 months), and old (24-26 months) C57BL/6 mice. In vivo, we used transgenic IGF2f/f; Alb-Cre mice and D-galactose-induced aging model to explore the role of IGF2 in liver aging. In vitro, we used specific short hairpin RNA against IGF2 to knock down IGF2 in AML12 cells. D-galactose and hydrogen peroxide treatment were used to induce AML12 cell senescence. RESULTS We observed a significant reduction of IGF2 levels in the livers of aged mice. Subsequently, we demonstrated that IGF2 deficiency promoted senescence phenotypes and senescence-associated secretory phenotypes (SASPs), both in vitro and in vivo aging models. Moreover, IGF2 deficiency impaired mitochondrial function, reducing mitochondrial respiratory capacity, mitochondrial membrane potential, and nicotinamide adenine dinucleotide (NAD)+/NADH ratio, increasing intracellular and mitochondrial reactive oxygen species levels, and disrupting mitochondrial membrane structure. Additionally, IGF2 deficiency markedly upregulated CCAAT/enhancer-binding protein beta (CEBPB). Notably, inhibiting CEBPB reversed the senescence phenotypes and reduced SASPs induced by IGF2 deficiency. CONCLUSIONS In summary, our findings strongly suggest that IGF2 deficiency promotes liver aging through mitochondrial dysfunction and upregulated CEBPB signaling. These results provide compelling evidence for considering IGF2 as a potential target for interventions aimed at slowing down the process of liver aging.
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Affiliation(s)
- Xiaohai Zhou
- Department of Endocrinology, the Affiliated Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Bowen Tan
- Department of Endocrinology, the Affiliated Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Weiwei Gui
- Department of Endocrinology, the Affiliated Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Caiping Zhou
- Department of Endocrinology, the Affiliated Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Hanxin Zhao
- Department of Endocrinology, the Affiliated Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xihua Lin
- Department of Endocrinology, the Affiliated Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China.
| | - Hong Li
- Department of Endocrinology, the Affiliated Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, China.
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10
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An M, Lim YH. Surface-exposed chaperonin 60 derived from Propionibacterium freudenreichii MJ2 inhibits adipogenesis by decreasing the expression of C/EBPα/PPARγ. Sci Rep 2023; 13:19251. [PMID: 37935755 PMCID: PMC10630399 DOI: 10.1038/s41598-023-46436-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 11/01/2023] [Indexed: 11/09/2023] Open
Abstract
Recent studies have shown that the health benefits of probiotics are not limited to those offered by living bacteria. It was reported that both live and killed cells of Propionibacterium freudenreichii MJ2 (MJ2) isolated from raw milk showed antiobesity activity in 3T3-L1 cells and high-fat diet-induced obese mice. This study was aimed at identifying the active component(s) responsible for the antiadipogenic activity of MJ2. Cell wall, surface protein, and cytoplasmic fractions of MJ2 were investigated for their inhibitory effects on adipogenesis in 3T3-L1 cells. Adipocytes treated with the surface protein fraction showed significantly lower lipid accumulation. Using the MASCOT algorithm following LC-MS/MS analysis, 131 surface proteins were identified and they were principally classified into three categories (network clusters related to ribosomes, carbon metabolism, and chaperones). Among them, chaperonin 60 (Cpn60) was selected as a potential candidate protein. Cpn60 inhibited lipid accumulation and adipogenesis during the early period of differentiation (days 0-2) and decreased expression of genes related to adipogenesis (Pparg and Cebpa) and lipogenesis (Fas and Scd1). The expression of Gata2/3, which suppresses adipogenesis, significantly increased in Cpn60-treated cells. Moreover, the nuclear translocation of C/EBPβ was inhibited by Cpn60 treatment. In conclusion, Cpn60, a surface protein in MJ2, shows antiadipogenic activity by reducing the expression of C/EBPβ through the upregulation of Gata2/3 expression followed by downregulation of Pparg and Cebpa expression.
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Affiliation(s)
- Mirae An
- Department of Healthcare Sciences, Graduate School, Korea University, Seoul, 02841, Republic of Korea
| | - Young-Hee Lim
- Department of Healthcare Sciences, Graduate School, Korea University, Seoul, 02841, Republic of Korea.
- School of Biosystems and Biomedical Sciences, Korea University, Seoul, 02841, Republic of Korea.
- Department of Laboratory Medicine, Korea University Guro Hospital, Seoul, 08308, Republic of Korea.
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11
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Begg LR, Orriols AM, Zannikou M, Yeh C, Vadlamani P, Kanojia D, Bolin R, Dunne SF, Balakrishnan S, Camarda R, Roth D, Zielinski-Mozny NA, Yau C, Vassilopoulos A, Huang TH, Kim KYA, Horiuchi D. S100A8/A9 predicts triple-negative breast cancer response to PIM kinase and PD-1/PD-L1 inhibition. bioRxiv 2023:2023.09.21.558870. [PMID: 37790346 PMCID: PMC10542194 DOI: 10.1101/2023.09.21.558870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
It remains elusive why some triple-negative breast cancer (TNBC) patients respond poorly to existing therapies while others respond well. Our retrospective analysis of historical gene expression datasets reveals that increased expression of immunosuppressive cytokine S100A8/A9 in early-stage tumors is robustly associated with subsequent disease progression in TNBC. Although it has recently gained recognition as a potential anticancer target, S100A8/A9 has not been integrated into clinical study designs evaluating molecularly targeted therapies. Our small molecule screen has identified PIM kinase inhibitors as capable of decreasing S100A8/A9 expression in multiple cell types, including TNBC and immunosuppressive myeloid cells. Furthermore, combining PIM inhibition and immune checkpoint blockade induces significant antitumor responses, especially in otherwise resistant S100A8/A9-high PD-1/PD-L1-positive tumors. Importantly, serum S100A8/A9 levels mirror those of tumor S100A8/A9 in a syngeneic mouse model of TNBC. Thus, our data suggest that S100A8/A9 could be a predictive and pharmacodynamic biomarker in clinical trials evaluating combination therapy targeting PIM and immune checkpoints in TNBC and encourage the development of S100A8/A9-based liquid biopsy tests.
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12
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Arora R, Sharma R, Ahlawat S, Chhabra P, Kumar A, Kaur M, Vijh RK, Lal SB, Mishra DC, Farooqi MS, Srivastava S. Transcriptomics reveals key genes responsible for functional diversity in pectoralis major muscles of native black Kadaknath and broiler chicken. 3 Biotech 2023; 13:253. [PMID: 37396468 PMCID: PMC10310660 DOI: 10.1007/s13205-023-03682-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 06/21/2023] [Indexed: 07/04/2023] Open
Abstract
RNA sequencing-based expression profiles from pectoralis major muscles of black meat (Kadaknath) and white meat (broiler) chicken were compared to identify differentially expressed genes. A total of 156 genes with log2 fold change ≥ ± 2.0 showed higher expression in Kadaknath and 68 genes were expressed at a lower level in comparison to broiler. Significantly enriched biological functions of up-regulated genes in Kadaknath were skeletal muscle cell differentiation, regulation of response to reactive oxygen, positive regulation of fat cell differentiation and melanosome. Significant ontology terms up-regulated in broiler included DNA replication origin binding, G-protein coupled receptor signaling pathway and chemokine activity. Highly inter-connected differentially expressed genes in Kadaknath (ATFs, C/EPDs) were observed to be important regulators of cellular adaptive functions, while in broiler, the hub genes were involved in cell cycle progression and DNA replication. The study is an attempt to get an insight into the transcript diversity of pectoralis major muscles of Kadaknath and broiler chicken. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03682-0.
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Affiliation(s)
- Reena Arora
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
- Animal Biotechnology Division, G T Road By-Pass, P O Box 129, Karnal, Haryana 132001 India
| | - Rekha Sharma
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Sonika Ahlawat
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Pooja Chhabra
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Ashish Kumar
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Mandeep Kaur
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | | | - Shashi Bhushan Lal
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | | | - Md. Samir Farooqi
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Sudhir Srivastava
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
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13
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Hartl L, Duitman J, Maarten FB, Spek CA. The Dual Role of C/EBPδ in Cancer. Crit Rev Oncol Hematol 2023; 185:103983. [PMID: 37024021 DOI: 10.1016/j.critrevonc.2023.103983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/31/2023] [Accepted: 04/01/2023] [Indexed: 04/08/2023] Open
Abstract
CCAAT/Enhancer-Binding Protein delta (C/EBPδ) is a transcription factor involved in differentiation and inflammation. While sparsely expressed in adult tissues, aberrant expression of C/EBPδ has been associated with different cancers. Initially, re-expression of C/EBPδ in cell cultures limited tumor cell proliferation, assigning it a tumor suppressor role. However, opposing observations were made in pre-clinical models and patients, suggesting that C/EBPδ not only mediates cell proliferation but dictates a broader spectrum of tumorigenesis-related effects. It is now widely accepted that C/EBPδ contributes to an inflammatory, tumor-promoting microenvironment, aids hypoxia adaption and contributes to the recruitment of blood vessels for improved nutrient supply to tumor cells and facilitated extravasation. This review summarizes the work published on this transcription factor in the field of cancer over the past decade. It points out areas in which a consensus on C/EBPδ's role appears to emerge and seek to explain seemingly contradictory results.
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Affiliation(s)
- Leonie Hartl
- Amsterdam UMC Location University of Amsterdam, Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, 1105 AZ Amsterdam, the Netherlands; Cancer Center Amsterdam, Cancer Biology and Immunology, 1081 HV Amsterdam, the Netherlands.
| | - JanWillem Duitman
- Amsterdam UMC Location University of Amsterdam, Department of Pulmonary Medicine, 1105 AZ Amsterdam, the Netherlands; Amsterdam UMC Location University of Amsterdam, Department of Experimental Immunology, 1105 AZ Amsterdam, the Netherlands; Amsterdam Infection & Immunity, Inflammatory Diseases, 1105 AZ Amsterdam, the Netherlands
| | - F Bijlsma Maarten
- Amsterdam UMC Location University of Amsterdam, Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, 1105 AZ Amsterdam, the Netherlands; Cancer Center Amsterdam, Cancer Biology and Immunology, 1081 HV Amsterdam, the Netherlands
| | - C Arnold Spek
- Amsterdam UMC Location University of Amsterdam, Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, 1105 AZ Amsterdam, the Netherlands; Cancer Center Amsterdam, Cancer Biology and Immunology, 1081 HV Amsterdam, the Netherlands
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14
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Wang C, Zhang H, Zhu J, Liu H, Yang Y, Sun B, Wu T, Zhang Y, Yao D. The transcription factor CEBP homolog of Penaeus vannamei contributes to WSSV replication. Fish Shellfish Immunol 2023; 134:108571. [PMID: 36736844 DOI: 10.1016/j.fsi.2023.108571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/19/2023] [Accepted: 01/26/2023] [Indexed: 06/18/2023]
Abstract
The cellular transcription factors are known to play important roles in virus infection. The present study cloned and characterized a transcription factor CCAAT/Enhancer-binding protein homolog from the shrimp Penaeus vannamei (designates as PvCEBP), and explored its potential functions in white spot syndrome virus (WSSV) infection. PvCEBP has an open reading frame (ORF) of 864 bp encoding a putative protein of 287 amino acids, which contained a highly C-terminal conserved bZIP domain. Phylogenetic tree analysis showed that PvCEBP was evolutionarily clustered with invertebrate CEBPs and closely related to the CEBP of Homarus americanus. Quantitative real-time PCR (qPCR) analysis revealed that PvCEBP was expressed in all examined shrimp tissues, with transcript levels increased in shrimp hemocytes and gill upon WSSV challenge. Furthermore, knockdown of PvCEBP mediated by RNA interference significantly decreased the expression of WSSV genes and viral loads, while enhanced the shrimp survival rate under WSSV challenge. In silico prediction and reporter gene assays demonstrated that PvCEBP could activate the promoter activity of the viral immediate-early gene ie1. Collectively, our findings suggest that PvCEBP is annexed by WSSV to promote its propagation by enhancing the expression of viral immediate-early genes.
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Affiliation(s)
- Chuanqi Wang
- Institute of Marine Sciences and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China
| | - Huimin Zhang
- Institute of Marine Sciences and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China
| | - Jinghua Zhu
- Institute of Marine Sciences and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China
| | - Haiping Liu
- Institute of Marine Sciences and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China
| | - Yiqing Yang
- Institute of Marine Sciences and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China
| | - Bingbing Sun
- Institute of Marine Sciences and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China
| | - Tingchu Wu
- Institute of Marine Sciences and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China
| | - Yueling Zhang
- Institute of Marine Sciences and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China; STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China
| | - Defu Yao
- Institute of Marine Sciences and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China; STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China.
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15
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House JS, Gray S, Owen JR, Jima DD, Smart RC, Hall JR. C/EBPβ deficiency enhances the keratinocyte innate immune response to direct activators of cytosolic pattern recognition receptors. Innate Immun 2023; 29:14-24. [PMID: 37094088 PMCID: PMC10164275 DOI: 10.1177/17534259231162192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 01/10/2023] [Accepted: 02/08/2023] [Indexed: 04/26/2023] Open
Abstract
The skin is the first line of defense to cutaneous microbes and viruses, and epidermal keratinocytes play a critical role in preventing infection by viruses and pathogens through activation of the type I interferon (IFN) response. Using RNAseq analysis, here we report that the conditional deletion of C/EBPβ transcription factor in mouse epidermis (CKOβ mice) resulted in the upregulation of IFNβ and numerous keratinocyte interferon-stimulated genes (ISGs). The expression of cytosolic pattern recognition receptors (cPRRs), that recognize viral RNA and DNA, were significantly increased, and enriched in the RNAseq data set. cPRRs stimulate a type I IFN response that can trigger cell death to eliminate infected cells. To determine if the observed increases in cPRRs had functional consequences, we transfected CKOβ primary keratinocytes with the pathogen and viral mimics poly(I:C) (dsRNA) or poly(dA:dT) (synthetic B-DNA) that directly activate PRRs. Transfected CKOβ primary keratinocytes displayed an amplified type I IFN response which was accompanied by increased activation of IRF3, enhanced ISG expression, enhanced activation of caspase-8, caspase-3 and increased apoptosis. Our results identify C/EBPβ as a critical repressor of the keratinocyte type I IFN response, and demonstrates that the loss of C/EBPβ primes keratinocytes to the activation of cytosolic PRRs by pathogen RNA and DNA to induce cell death mediated by caspase-8 and caspase-3.
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Affiliation(s)
- John S. House
- Center of Human Health and the Environment, North Carolina State University, Raleigh, NC, 27695, USA
- Toxicology Graduate Program, North Carolina State University, Raleigh, NC, 27695, USA
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, Durham, NC 27709, USA
| | - Sophia Gray
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, 27695, USA
| | - Jennifer R. Owen
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, 27695, USA
| | - Dereje D. Jima
- Center of Human Health and the Environment, North Carolina State University, Raleigh, NC, 27695, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, 27695, USA
| | - Robert C. Smart
- Center of Human Health and the Environment, North Carolina State University, Raleigh, NC, 27695, USA
- Toxicology Graduate Program, North Carolina State University, Raleigh, NC, 27695, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, 27695, USA
| | - Jonathan R. Hall
- Center of Human Health and the Environment, North Carolina State University, Raleigh, NC, 27695, USA
- Toxicology Graduate Program, North Carolina State University, Raleigh, NC, 27695, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, 27695, USA
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16
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Holland SD, Ramer MS. Microglial activating transcription factor 3 upregulation: An indirect target to attenuate inflammation in the nervous system. Front Mol Neurosci 2023; 16:1150296. [PMID: 37033378 PMCID: PMC10076742 DOI: 10.3389/fnmol.2023.1150296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 03/09/2023] [Indexed: 04/11/2023] Open
Abstract
Activating Transcription Factor 3 (ATF3) is upregulated in reaction to several cellular stressors found in a wide range of pathological conditions to coordinate a transcriptional response. ATF3 was first implicated in the transcriptional reaction to axotomy when its massive upregulation was measured in sensory and motor neuron cell bodies following peripheral nerve injury. It has since been shown to be critical for successful axon regeneration in the peripheral nervous system and a promising target to mitigate regenerative failure in the central nervous system. However, much of the research to date has focused on ATF3's function in neurons, leaving the expression, function, and therapeutic potential of ATF3 in glia largely unexplored. In the immunology literature ATF3 is seen as a master regulator of the innate immune system. Specifically, in macrophages following pathogen or damage associated molecular pattern receptor activation and subsequent cytokine release, ATF3 upregulation abrogates the inflammatory response. Importantly, ATF3 upregulation is not exclusively due to cellular stress exposure but has been achieved by the administration of several small molecules. In the central nervous system, microglia represent the resident macrophage population and are therefore of immediate interest with respect to ATF3 induction. It is our perspective that the potential of inducing ATF3 expression to dampen inflammatory microglial phenotype represents an unexplored therapeutic target and may have synergistic benefits when paired with concomitant neuronal ATF3 upregulation. This would be of particular benefit in pathologies that involve both detrimental inflammation and neuronal damage including spinal cord injury, multiple sclerosis, and stroke.
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17
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Lau KH, Waldhart AN, Dykstra H, Avequin T, Wu N. PPARγ and C/EBPα response to acute cold stress in brown adipose tissue. iScience 2022; 26:105848. [PMID: 36624847 PMCID: PMC9823219 DOI: 10.1016/j.isci.2022.105848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/14/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Brown adipose tissue (BAT) has the ability to burn calories as heat. Utilizing BAT thermogenesis is thus an attractive way to combat obesity. However, the transcriptional network resulting in the lipid synthesis to oxidation shift during thermogenesis is not completely understood. Here, we report the regulation of two master regulators of adipogenesis, peroxisome proliferator-activated receptor gamma (PPARγ) and CCAAT/enhancer-binding protein alpha (C/EBPα), during acute cold stress in BAT. We found PPARγ dissociates from DNA in a fifth of its binding sites and these include Cebpa enhancers, leading to decreased C/EBPα expression. This dissociation requires PPARγ binding to activating ligands and is thus modulated by diet. Meanwhile, PPARα also detaches from DNA, and co-activator PGC1α associates with ERRα as part of a transcriptional network regulating lipid metabolism. Subsequent global replacement of C/EBPα by C/EBPβ and its associated transcriptional machinery is required for upregulation of structural lipid synthesis despite general upregulation of fatty acid oxidation.
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Affiliation(s)
- Kin H. Lau
- Van Andel Institute, Grand Rapids, MI 49503, USA
| | | | | | | | - Ning Wu
- Van Andel Institute, Grand Rapids, MI 49503, USA,Corresponding author
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18
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Jiang R, Lönnerdal B. Milk-Derived miR-22-3p Promotes Proliferation of Human Intestinal Epithelial Cells (HIECs) by Regulating Gene Expression. Nutrients 2022; 14. [PMID: 36432587 DOI: 10.3390/nu14224901] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/09/2022] [Accepted: 11/15/2022] [Indexed: 11/22/2022] Open
Abstract
MicroRNA (miRNA) is small non-coding RNA involved in gene silencing and post-transcriptional regulation of gene expression. Milk exosomes are microvesicles containing microRNAs (miRNAs). miR-22-3p (miR-22) is plentiful in human milk exosomes and may contribute to intestinal development since milk exosomes and microRNAs are resistant to gastrointestinal digestion in infants. After miR-22 mimics were transfected to human intestinal crypt-like epithelial cells (HIECs) using Lipofectamine for 24 h, RNA was isolated for microarray assay. Microarray results show that miR-22 markedly regulates gene expression, and the roles of miR-22 include promotion of proliferation, regulation of immune functions, and inhibition of apoptosis. Based on the microarray results and miR-22 predicted target genes, CCAAT/enhancer-binding protein δ (C/EBPδ) may be an important direct target of miR-22. C/EBPδ is a transcription factor that regulates numerous biological processes including cell proliferation. In miR-22 transfected HIECs, expression of the C/EBPδ gene was significantly inhibited. Silencing of the C/EBPδ gene by siRNA resulted in increased proliferation of HIECs. A luciferase assay showed that miR-22 specifically binds to the 3'-untranslated region of C/EBPδ mRNA. In summary, milk-derived miR-22 promotes intestinal proliferation by modifying gene expression, and C/EBPδ may be an important target for miR-22 involved in this effect.
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19
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Moshkovits I, Kaminitz A, Reuveni D, Pasmanik‐Chor M, Brazowski E, Mildner A, Leutz A, Zigmond E. Immune cell C/EBPβ deficiency is associated with hepatic mononuclear defects and spontaneous hepatitis but not steatohepatitis induced liver fibrosis. Immun Inflamm Dis 2022; 10:e728. [PMID: 36301029 PMCID: PMC9609438 DOI: 10.1002/iid3.728] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 09/20/2022] [Accepted: 10/12/2022] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND CCAAT/enhancer-binding protein β (C/EBPβ) is a transcription factor known to be involved in macrophage differentiation and function, steatohepatitis and liver fibrosis. METHODS Immune restricted C/EBPβ deficient and control mice were investigated in steady-state and in the CDA-HFD steatohepatitis model. Mice were assessed for weight change, liver biochemical profile, histology and hepatic phagocytes composition. RESULTS Flow cytometry analysis of hepatic nonparenchymal cells revealed reduced numbers of hepatic monocytes and Kupffer cells and an increase in hepatic MHC class II positive myeloid cells in immune cells restricted C/EBPβ deficient mice. Immune-restricted C/EBPβ deficiency resulted in decreased weight gain and appearance of mild spontaneous liver inflammation. Nevertheless, In the CDA-HFD steatohepatitis model, immune restricted C/EBPβ deficient and proficient mice exhibit similar grade of hepatic steatosis, liver enzymes levels and fibrosis stage. CONCLUSIONS Immune-restricted C/EBPβ deficiency leads to significant alteration in hepatic mononuclear phagocytes composition associated with spontaneous mild hepatitis. Steatohepatitis associated fibrosis is not dependent on C/EBPβ expression by immune cells.
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Affiliation(s)
- Itay Moshkovits
- Research Center for Digestive DiseasesTel Aviv Sourasky Medical CenterTel AvivIsrael,Sackler Faculty of MedicineTel Aviv UniversityTel AvivIsrael
| | - Ayelet Kaminitz
- Research Center for Digestive DiseasesTel Aviv Sourasky Medical CenterTel AvivIsrael,Sackler Faculty of MedicineTel Aviv UniversityTel AvivIsrael
| | - Debby Reuveni
- Research Center for Digestive DiseasesTel Aviv Sourasky Medical CenterTel AvivIsrael,Sackler Faculty of MedicineTel Aviv UniversityTel AvivIsrael,Center for Autoimmune Liver DiseasesTel Aviv Sourasky Medical CenterTel AvivIsrael
| | - Metsada Pasmanik‐Chor
- Bioinformatics Unit, George‐S. Wise Faculty of Life ScienceTel Aviv UniversityTel AvivIsrael
| | - Eli Brazowski
- Sackler Faculty of MedicineTel Aviv UniversityTel AvivIsrael,Department of PathologyTel Aviv Sourasky Medical CenterTel AvivIsrael
| | | | - Achim Leutz
- Max Delbrück Center for Molecular MedicineBerlinGermany
| | - Ehud Zigmond
- Research Center for Digestive DiseasesTel Aviv Sourasky Medical CenterTel AvivIsrael,Sackler Faculty of MedicineTel Aviv UniversityTel AvivIsrael,Center for Autoimmune Liver DiseasesTel Aviv Sourasky Medical CenterTel AvivIsrael
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20
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Antony C, George SS, Blum J, Somers P, Thorsheim CL, Wu-Corts DJ, Ai Y, Gao L, Lv K, Tremblay MG, Moss T, Tan K, Wilusz JE, Ganley ARD, Pimkin M, Paralkar VR. Control of ribosomal RNA synthesis by hematopoietic transcription factors. Mol Cell 2022; 82:3826-3839.e9. [PMID: 36113481 PMCID: PMC9588704 DOI: 10.1016/j.molcel.2022.08.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 06/23/2022] [Accepted: 08/23/2022] [Indexed: 11/19/2022]
Abstract
Ribosomal RNAs (rRNAs) are the most abundant cellular RNAs, and their synthesis from rDNA repeats by RNA polymerase I accounts for the bulk of all transcription. Despite substantial variation in rRNA transcription rates across cell types, little is known about cell-type-specific factors that bind rDNA and regulate rRNA transcription to meet tissue-specific needs. Using hematopoiesis as a model system, we mapped about 2,200 ChIP-seq datasets for 250 transcription factors (TFs) and chromatin proteins to human and mouse rDNA and identified robust binding of multiple TF families to canonical TF motifs on rDNA. Using a 47S-FISH-Flow assay developed for nascent rRNA quantification, we demonstrated that targeted degradation of C/EBP alpha (CEBPA), a critical hematopoietic TF with conserved rDNA binding, caused rapid reduction in rRNA transcription due to reduced RNA Pol I occupancy. Our work identifies numerous potential rRNA regulators and provides a template for dissection of TF roles in rRNA transcription.
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Affiliation(s)
- Charles Antony
- Division of Hematology and Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Subin S George
- Institute for Biomedical Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Justin Blum
- The College of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Patrick Somers
- Division of Hematology and Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Chelsea L Thorsheim
- Cardiovascular Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Dexter J Wu-Corts
- The College of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yuxi Ai
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Long Gao
- Beijing Advanced Innovation Center for Genomics (ICG) & Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing 100871, China
| | - Kaosheng Lv
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Michel G Tremblay
- Laboratory of Growth and Development, St Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre (CRCHU de Québec-Université Laval), Québec, QC G1R 3S3, Canada
| | - Tom Moss
- Laboratory of Growth and Development, St Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre (CRCHU de Québec-Université Laval), Québec, QC G1R 3S3, Canada; Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University, Québec, QC G1V 0A6, Canada
| | - Kai Tan
- Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Jeremy E Wilusz
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Austen R D Ganley
- School of Biological Sciences, University of Auckland, Auckland 0623, New Zealand; Digital Life Institute, University of Auckland, Auckland 0632, New Zealand
| | - Maxim Pimkin
- Cancer and Blood Disorders Center, Dana-Farber Cancer Institute and Boston Children's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Vikram R Paralkar
- Division of Hematology and Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Abramson Family Cancer Research Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
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21
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Wang L, Feng J, Deng Y, Yang Q, Wei Q, Ye D, Rong X, Guo J. CCAAT/Enhancer-Binding Proteins in Fibrosis: Complex Roles Beyond Conventional Understanding. Research (Wash D C) 2022; 2022:9891689. [PMID: 36299447 PMCID: PMC9575473 DOI: 10.34133/2022/9891689] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 09/18/2022] [Indexed: 07/29/2023]
Abstract
CCAAT/enhancer-binding proteins (C/EBPs) are a family of at least six identified transcription factors that contain a highly conserved basic leucine zipper domain and interact selectively with duplex DNA to regulate target gene expression. C/EBPs play important roles in various physiological processes, and their abnormal function can lead to various diseases. Recently, accumulating evidence has demonstrated that aberrant C/EBP expression or activity is closely associated with the onset and progression of fibrosis in several organs and tissues. During fibrosis, various C/EBPs can exert distinct functions in the same organ, while the same C/EBP can exert distinct functions in different organs. Modulating C/EBP expression or activity could regulate various molecular processes to alleviate fibrosis in multiple organs; therefore, novel C/EBPs-based therapeutic methods for treating fibrosis have attracted considerable attention. In this review, we will explore the features of C/EBPs and their critical functions in fibrosis in order to highlight new avenues for the development of novel therapies targeting C/EBPs.
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Affiliation(s)
- Lexun Wang
- Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine, China
- Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education of China, China
- Guangdong Key Laboratory of Metabolic Disease Prevention and Treatment of Traditional Chinese Medicine, China
- Institute of Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, China
| | - Jiaojiao Feng
- Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine, China
- Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education of China, China
- Guangdong Key Laboratory of Metabolic Disease Prevention and Treatment of Traditional Chinese Medicine, China
- Institute of Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, China
| | - Yanyue Deng
- Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine, China
- Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education of China, China
- Guangdong Key Laboratory of Metabolic Disease Prevention and Treatment of Traditional Chinese Medicine, China
- Institute of Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, China
| | - Qianqian Yang
- Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine, China
- Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education of China, China
- Guangdong Key Laboratory of Metabolic Disease Prevention and Treatment of Traditional Chinese Medicine, China
- Institute of Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, China
| | - Quxing Wei
- Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine, China
- Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education of China, China
- Guangdong Key Laboratory of Metabolic Disease Prevention and Treatment of Traditional Chinese Medicine, China
- Institute of Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, China
| | - Dewei Ye
- Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine, China
- Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education of China, China
- Guangdong Key Laboratory of Metabolic Disease Prevention and Treatment of Traditional Chinese Medicine, China
- Institute of Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, China
| | - Xianglu Rong
- Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine, China
- Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education of China, China
- Guangdong Key Laboratory of Metabolic Disease Prevention and Treatment of Traditional Chinese Medicine, China
- Institute of Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, China
| | - Jiao Guo
- Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine, China
- Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education of China, China
- Guangdong Key Laboratory of Metabolic Disease Prevention and Treatment of Traditional Chinese Medicine, China
- Institute of Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, China
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22
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Naranjo-Galvis CA, Cardona-Londoño KY, Orrego-Cardozo M, Elcoroaristizabal-Martín X. Toxoplasma gondii infection and peripheral-blood gene expression profiling of older people reveals dysregulation of cytokines and identifies hub genes as potential therapeutic targets. Heliyon 2022; 8:e10576. [PMID: 36119857 PMCID: PMC9478394 DOI: 10.1016/j.heliyon.2022.e10576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 11/12/2021] [Accepted: 09/02/2022] [Indexed: 11/21/2022] Open
Abstract
Infections of humans with the protozoan parasite Toxoplasma gondii (T. gondii) can lead to the disease's development, even in an asymptomatic status. However, the mechanisms that result in these clinical outcomes after infection are poorly understood. This study aimed to explore the molecular pathogenesis of toxoplasmosis-related inflammation through next-generation sequencing, to assess RNA expression profiles in peripheral blood from 5 female patients with chronic toxoplasmosis and 5 healthy female controls. All plasma samples were analyzed for anti-Toxoplasma IgG and IgM antibody titers by using electrochemiluminescence. Detection of acute and chronic toxoplasmosis was carried out using the ELISA IgG avidity. We evaluated the levels of INF-γ, IL-2, IL-12, TNF-α, IL-10, and IL-1β in culture supernatants of Peripheral Blood Mononuclear Cells infected with Toxoplasma lysate antigen (TLA) prepared with tachyzoites of strain T. gondii RH. Differential expression analysis was performed using DESeq2, pathway and enrichment analysis of DEGs was done on WEB-based Gene SeT AnaLysis Toolkit (WebGestalt) and Protein-protein interaction was carried out using NetworkAnalyst with STRING. In older people with chronic asymptomatic infection, a significant difference in the levels of inflammatory cytokines INF-γ and IL-2 was observed compared to seronegative individuals. Our results revealed differences in the regulation of critical biological processes involved in host responses to chronic T. gondii infection. Gene ontology analysis revealed several biologically relevant inflammatory and immune-related pathways.
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Affiliation(s)
- Carlos A Naranjo-Galvis
- Facultad de Salud, Universidad Autónoma de Manizales, Antigua Estación Del Ferrocarril, Manizales, Caldas, Colombia
| | - Kelly Y Cardona-Londoño
- Facultad de Salud, Universidad Autónoma de Manizales, Antigua Estación Del Ferrocarril, Manizales, Caldas, Colombia
| | - Mary Orrego-Cardozo
- Facultad de Salud, Universidad Autónoma de Manizales, Antigua Estación Del Ferrocarril, Manizales, Caldas, Colombia
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23
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Boštjančić LL, Francesconi C, Rutz C, Hoffbeck L, Poidevin L, Kress A, Jussila J, Makkonen J, Feldmeyer B, Bálint M, Schwenk K, Lecompte O, Theissinger K. Host-pathogen coevolution drives innate immune response to Aphanomyces astaci infection in freshwater crayfish: transcriptomic evidence. BMC Genomics 2022; 23:600. [PMID: 35989333 PMCID: PMC9394032 DOI: 10.1186/s12864-022-08571-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 04/20/2022] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND For over a century, scientists have studied host-pathogen interactions between the crayfish plague disease agent Aphanomyces astaci and freshwater crayfish. It has been hypothesised that North American crayfish hosts are disease-resistant due to the long-lasting coevolution with the pathogen. Similarly, the increasing number of latent infections reported in the historically sensitive European crayfish hosts seems to indicate that similar coevolutionary processes are occurring between European crayfish and A. astaci. Our current understanding of these host-pathogen interactions is largely focused on the innate immunity processes in the crayfish haemolymph and cuticle, but the molecular basis of the observed disease-resistance and susceptibility remain unclear. To understand how coevolution is shaping the host's molecular response to the pathogen, susceptible native European noble crayfish and invasive disease-resistant marbled crayfish were challenged with two A. astaci strains of different origin: a haplogroup A strain (introduced to Europe at least 50 years ago, low virulence) and a haplogroup B strain (signal crayfish in lake Tahoe, USA, high virulence). Here, we compare the gene expression profiles of the hepatopancreas, an integrated organ of crayfish immunity and metabolism. RESULTS We characterised several novel innate immune-related gene groups in both crayfish species. Across all challenge groups, we detected 412 differentially expressed genes (DEGs) in the noble crayfish, and 257 DEGs in the marbled crayfish. In the noble crayfish, a clear immune response was detected to the haplogroup B strain, but not to the haplogroup A strain. In contrast, in the marbled crayfish we detected an immune response to the haplogroup A strain, but not to the haplogroup B strain. CONCLUSIONS We highlight the hepatopancreas as an important hub for the synthesis of immune molecules in the response to A. astaci. A clear distinction between the innate immune response in the marbled crayfish and the noble crayfish is the capability of the marbled crayfish to mobilise a higher variety of innate immune response effectors. With this study we outline that the type and strength of the host immune response to the pathogen is strongly influenced by the coevolutionary history of the crayfish with specific A. astaci strains.
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Affiliation(s)
- Ljudevit Luka Boštjančić
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325, Frankfurt am Main, Germany
| | - Caterina Francesconi
- Institute for Environmental Sciences, University of Koblenz-Landau, Fortstrasse 7, 76829, Landau, Germany.
| | - Christelle Rutz
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Centre de Recherche en Biomédecine de Strasbourg, Rue Eugène Boeckel 1, 67000, Strasbourg, France
| | - Lucien Hoffbeck
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Centre de Recherche en Biomédecine de Strasbourg, Rue Eugène Boeckel 1, 67000, Strasbourg, France
| | - Laetitia Poidevin
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Centre de Recherche en Biomédecine de Strasbourg, Rue Eugène Boeckel 1, 67000, Strasbourg, France
| | - Arnaud Kress
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Centre de Recherche en Biomédecine de Strasbourg, Rue Eugène Boeckel 1, 67000, Strasbourg, France
| | - Japo Jussila
- Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box 1627, 70210, Kuopio, Finland
| | - Jenny Makkonen
- Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box 1627, 70210, Kuopio, Finland
- Present address: BioSafe - Biological Safety Solutions, Microkatu 1, 70210, Kuopio, Finland
| | - Barbara Feldmeyer
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325, Frankfurt am Main, Germany
| | - Miklós Bálint
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325, Frankfurt am Main, Germany
| | - Klaus Schwenk
- Institute for Environmental Sciences, University of Koblenz-Landau, Fortstrasse 7, 76829, Landau, Germany
| | - Odile Lecompte
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Centre de Recherche en Biomédecine de Strasbourg, Rue Eugène Boeckel 1, 67000, Strasbourg, France
| | - Kathrin Theissinger
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325, Frankfurt am Main, Germany
- Institute for Environmental Sciences, University of Koblenz-Landau, Fortstrasse 7, 76829, Landau, Germany
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Zhang L, Wang J. Sinomenine alleviates glomerular endothelial permeability by activating the C/EBP-α/claudin-5 signaling pathway. Hum Cell 2022; 35:1453-1463. [PMID: 35854195 DOI: 10.1007/s13577-022-00750-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 07/09/2022] [Indexed: 11/29/2022]
Abstract
Diabetic nephropathy (DN) is one of the main complications of diabetes. It is closely associated with the dysfunction of glomerular endothelial cells (GECs) under hyperglycemia. Severe inflammation is an important inducer for the development of GECs dysfunction, and it contributes to the disruption of tight junctions in GECs and the increased endothelial permeability. Sinomenine, an alkaloid monomer extracted from the rhizome of Sinomenium acutum, is recognized for its multiple pharmacological functions, including an anti-DN property. The present study aimed to explore the potential functional mechanism of Sinomenine against DN. Animals were randomly divided into Sham, DN, DN + Sinomenine (20 mg/kg), and DN + Sinomenine (40 mg/kg) groups. The Sinomenine or vehicle was administered every day for 6 weeks, followed by collecting renal tissues for further detection. Increased body weights, elevated blood glucose levels and UAE values, aggravated renal tissue pathology, higher concentrations of IL-18 and IL-1β in renal tissues, and reduced claudin-5 expression were observed in DN rats. However, the administration of Sinomenine significantly alleviated all these DN-related changes. Furthermore, human renal glomerular endothelial cells (HrGECs) were treated with high glucose (HG, 30 mM) with or without Sinomenine (50, 100 μM) for 24 h. We found that Sinomenine treatment ameliorated the elevated production of IL-18 and IL-1β, increased fluorescence intensity of FITC-dextran, declined trans-endothelial electrical resistance (TEER) value, and reduction of claudin-5 and C/EBP-α in HG-treated HrGECs. Moreover, the regulatory effect of Sinomenine on endothelial monolayer permeability in HG-treated HrGECs was abolished by the knockdown of C/EBP-α, indicating C/EBP-α is required for the effect of Sinomenine. We concluded that Sinomenine alleviated diabetic nephropathy-induced renal glomerular endothelial dysfunction via activating the C/EBP-α/claudin-5 axis.
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Affiliation(s)
- Li Zhang
- Department of Nephrology, The First Affiliated Hospital of Henan University of Science and Technology, No. 24 Jinghua Road, Jianxi Distract, Luoyang, 471003, Henan, China
| | - Junxia Wang
- Department of Nephrology, The First Affiliated Hospital of Henan University of Science and Technology, No. 24 Jinghua Road, Jianxi Distract, Luoyang, 471003, Henan, China.
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25
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Lang Kuhs KA, Faden DL, Chen L, Smith DK, Pinheiro M, Wood CB, Davis S, Yeager M, Boland JF, Cullen M, Steinberg M, Bass S, Wang X, Liu P, Mehrad M, Tucker T, Lewis JS, Ferris RL, Mirabello L. Genetic variation within the human papillomavirus type 16 genome is associated with oropharyngeal cancer prognosis. Ann Oncol 2022; 33:638-648. [PMID: 35306154 PMCID: PMC9350957 DOI: 10.1016/j.annonc.2022.03.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/08/2022] [Accepted: 03/11/2022] [Indexed: 01/02/2023] Open
Abstract
PURPOSE A significant barrier to adoption of de-escalated treatment protocols for human papillomavirus-driven oropharyngeal cancer (HPV-OPC) is that few predictors of poor prognosis exist. We conducted the first large whole-genome sequencing (WGS) study to characterize the genetic variation of the HPV type 16 (HPV16) genome and to evaluate its association with HPV-OPC patient survival. PATIENTS AND METHODS A total of 460 OPC tumor specimens from two large United States medical centers (1980-2017) underwent HPV16 whole-genome sequencing. Site-specific variable positions [single nucleotide polymorphisms (SNPs)] across the HPV16 genome were identified. Cox proportional hazards model estimated hazard ratios (HRs) and 95% confidence intervals (CIs) for overall survival by HPV16 SNPs. Harrell C-index and time-dependent positive predictive value (PPV) curves and areas under the PPV curves were used to evaluate the predictive accuracy of HPV16 SNPs for overall survival. RESULTS A total of 384 OPC tumor specimens (83.48%) passed quality control filters with sufficient depth and coverage of HPV16 genome sequencing to be analyzed. Some 284 HPV16 SNPs with a minor allele frequency ≥1% were identified. Eight HPV16 SNPs were significantly associated with worse survival after false discovery rate correction (individual prevalence: 1.0%-5.5%; combined prevalence: 15.10%); E1 gene position 1053 [HR for overall survival (HRos): 3.75, 95% CI 1.77-7.95; Pfdr = 0.0099]; L2 gene positions 4410 (HRos: 5.32, 95% CI 1.91-14.81; Pfdr = 0.0120), 4539 (HRos: 6.54, 95% CI 2.03-21.08; Pfdr = 0.0117); 5050 (HRos: 6.53, 95% CI 2.34-18.24; Pfdr = 0.0030), and 5254 (HRos: 7.76, 95% CI 2.41-24.98; Pfdr = 0.0030); and L1 gene positions 5962 (HRos: 4.40, 95% CI 1.88-10.31; Pfdr = 0.0110) and 6025 (HRos: 5.71, 95% CI 2.43-13.41; Pfdr = 0.0008) and position 7173 within the upstream regulatory region (HRos: 9.90, 95% CI 3.05-32.12; Pfdr = 0.0007). Median survival time for patients with ≥1 high-risk HPV16 SNPs was 3.96 years compared with 18.67 years for patients without a high-risk SNP; log-rank test P < 0.001. HPV16 SNPs significantly improved the predictive accuracy for overall survival above traditional factors (age, smoking, stage, treatment); increase in C-index was 0.069 (95% CI 0.019-0.119, P < 0.001); increase in area under the PPV curve for predicting 5-year survival was 0.068 (95% CI 0.015-0.111, P = 0.008). CONCLUSIONS HPV16 genetic variation is associated with HPV-OPC prognosis and can improve prognostic accuracy.
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Affiliation(s)
- K A Lang Kuhs
- Department of Epidemiology, College of Public Health, University of Kentucky, Lexington, USA; Department of Medicine, Vanderbilt University Medical Cancer, Nashville, USA.
| | - D L Faden
- Department of Otolaryngology, Massachusetts Eye and Ear, Massachusetts General Hospital, Harvard Medical School, Boston, USA; Broad Institute of MIT and Harvard, Cambridge, USA
| | - L Chen
- Division of Cancer Biostatistics, Department of Internal Medicine and Biostatistics and Bioinformatics Shared Resource Facility, Markey Cancer Center, University of Kentucky, Lexington, USA
| | - D K Smith
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, USA
| | - M Pinheiro
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, USA
| | - C B Wood
- Department of Otolaryngology - Head and Neck Surgery, Vanderbilt University Medical Center, Nashville, USA; Department of Otolaryngology - Head and Neck Surgery, University of Tennessee Health Science Center, Memphis, USA
| | - S Davis
- Department of Otolaryngology - Head and Neck Surgery, Vanderbilt University Medical Center, Nashville, USA
| | - M Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, USA; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, USA
| | - J F Boland
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, USA; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, USA
| | - M Cullen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, USA; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, USA
| | - M Steinberg
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, USA; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, USA
| | - S Bass
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, USA; Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick, USA
| | - X Wang
- Department of Pharmacology and Regenerative Medicine, The University of Illinois at Chicago, Chicago, USA
| | - P Liu
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, USA
| | - M Mehrad
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, USA
| | - T Tucker
- Department of Epidemiology, College of Public Health, University of Kentucky, Lexington, USA
| | - J S Lewis
- Department of Otolaryngology - Head and Neck Surgery, Vanderbilt University Medical Center, Nashville, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, USA
| | - R L Ferris
- University of Pittsburgh Medical Center Hillman Cancer Center, Pittsburgh, USA; Department of Otolaryngology-Head and Neck Surgery, University of Pittsburgh Medical Center, Pittsburgh, USA
| | - L Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, USA
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26
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Zullow HJ, Sankar A, Ingram DR, Guerra DDS, D’Avino AR, Collings CK, Segura RNL, Yang WL, Liang Y, Qi J, Lazar A, Kadoch C. The FUS::DDIT3 fusion oncoprotein inhibits BAF complex targeting and activity in myxoid liposarcoma. Mol Cell 2022; 82:1737-1750.e8. [PMID: 35390276 PMCID: PMC9465545 DOI: 10.1016/j.molcel.2022.03.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 12/30/2021] [Accepted: 03/11/2022] [Indexed: 12/13/2022]
Abstract
Mammalian SWI/SNF (mSWI/SNF or BAF) ATP-dependent chromatin remodeling complexes play critical roles in governing genomic architecture and gene expression and are frequently perturbed in human cancers. Transcription factors (TFs), including fusion oncoproteins, can bind to BAF complex surfaces to direct chromatin targeting and accessibility, often activating oncogenic gene loci. Here, we demonstrate that the FUS::DDIT3 fusion oncoprotein hallmark to myxoid liposarcoma (MLPS) inhibits BAF complex-mediated remodeling of adipogenic enhancer sites via sequestration of the adipogenic TF, CEBPB, from the genome. In mesenchymal stem cells, small-molecule inhibition of BAF complex ATPase activity attenuates adipogenesis via failure of BAF-mediated DNA accessibility and gene activation at CEBPB target sites. BAF chromatin occupancy and gene expression profiles of FUS::DDIT3-expressing cell lines and primary tumors exhibit similarity to SMARCB1-deficient tumor types. These data present a mechanism by which a fusion oncoprotein generates a BAF complex loss-of-function phenotype, independent of deleterious subunit mutations.
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Affiliation(s)
- Hayley J. Zullow
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, 02215 USA,Broad Institute of MIT and Harvard, Cambridge, MA, USA,Medical Scientist Training Program, Harvard Medical School, Cambridge, MA USA
| | - Akshay Sankar
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, 02215 USA,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Davis R. Ingram
- Department of Pathology, MD Anderson Cancer Center, Houston, TX, USA
| | - Daniel D. Same Guerra
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, 02215 USA,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Andrew R. D’Avino
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, 02215 USA,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Clayton K. Collings
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, 02215 USA,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - We-Lien Yang
- Department of Pathology, MD Anderson Cancer Center, Houston, TX, USA
| | - Yu Liang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jun Qi
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Alexander Lazar
- Department of Pathology, MD Anderson Cancer Center, Houston, TX, USA
| | - Cigall Kadoch
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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27
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Renfro Z, White BE, Stephens KE. CCAAT enhancer binding protein gamma (C/EBP-γ): An understudied transcription factor. Adv Biol Regul 2022; 84:100861. [PMID: 35121409 PMCID: PMC9376885 DOI: 10.1016/j.jbior.2022.100861] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/10/2022] [Accepted: 01/24/2022] [Indexed: 05/03/2023]
Abstract
The CCAAT enhancer binding protein (C/EBP) family of transcription factors are important transcriptional mediators of a wide range of physiologic processes. C/EBP-γ is the shortest C/EBP protein and lacks a canonical activation domain for the recruitment of transcriptional machinery. Despite its ubiquitous expression and ability to dimerize with other C/EBP proteins, C/EBP-γ has been studied far less than other C/EBP proteins, and, to our knowledge, no review of its functions has been written. This review seeks to integrate the current knowledge about C/EBP-γ and its physiologic roles, especially in cell proliferation, the integrated stress response, oncogenesis, hematopoietic and nervous system development, and metabolism, as well as to identify areas for future research.
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Affiliation(s)
- Zachary Renfro
- Department of Pediatrics, Division of Infectious Diseases, College of Medicine, University of Arkansas for Medical Sciences, USA; Arkansas Children's Research Institute, 13 Children's Way, Mail slot 512-47, Little Rock, AR, 72202, USA.
| | - Bryan E White
- Department of Pediatrics, Division of Infectious Diseases, College of Medicine, University of Arkansas for Medical Sciences, USA; Arkansas Children's Research Institute, 13 Children's Way, Mail slot 512-47, Little Rock, AR, 72202, USA.
| | - Kimberly E Stephens
- Department of Pediatrics, Division of Infectious Diseases, College of Medicine, University of Arkansas for Medical Sciences, USA; Arkansas Children's Research Institute, 13 Children's Way, Mail slot 512-47, Little Rock, AR, 72202, USA.
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28
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Kiparaki M, Khan C, Folgado-Marco V, Chuen J, Moulos P, Baker NE. The transcription factor Xrp1 orchestrates both reduced translation and cell competition upon defective ribosome assembly or function. eLife 2022; 11:e71705. [PMID: 35179490 PMCID: PMC8933008 DOI: 10.7554/elife.71705] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 02/09/2022] [Indexed: 11/26/2022] Open
Abstract
Ribosomal Protein (Rp) gene haploinsufficiency affects translation rate, can lead to protein aggregation, and causes cell elimination by competition with wild type cells in mosaic tissues. We find that the modest changes in ribosomal subunit levels observed were insufficient for these effects, which all depended on the AT-hook, bZip domain protein Xrp1. Xrp1 reduced global translation through PERK-dependent phosphorylation of eIF2α. eIF2α phosphorylation was itself sufficient to enable cell competition of otherwise wild type cells, but through Xrp1 expression, not as the downstream effector of Xrp1. Unexpectedly, many other defects reducing ribosome biogenesis or function (depletion of TAF1B, eIF2, eIF4G, eIF6, eEF2, eEF1α1, or eIF5A), also increased eIF2α phosphorylation and enabled cell competition. This was also through the Xrp1 expression that was induced in these depletions. In the absence of Xrp1, translation differences between cells were not themselves sufficient to trigger cell competition. Xrp1 is shown here to be a sequence-specific transcription factor that regulates transposable elements as well as single-copy genes. Thus, Xrp1 is the master regulator that triggers multiple consequences of ribosomal stresses and is the key instigator of cell competition.
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Affiliation(s)
- Marianthi Kiparaki
- Department of Genetics, Albert Einstein College of MedicineThe BronxUnited States
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center "Alexander Fleming”VariGreece
| | - Chaitali Khan
- Department of Genetics, Albert Einstein College of MedicineThe BronxUnited States
| | | | - Jacky Chuen
- Department of Genetics, Albert Einstein College of MedicineThe BronxUnited States
| | - Panagiotis Moulos
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center "Alexander Fleming”VariGreece
| | - Nicholas E Baker
- Department of Genetics, Albert Einstein College of MedicineThe BronxUnited States
- Department of Developmental and Molecular Biology, Albert Einstein College of MedicineThe BronxUnited States
- Department of Opthalmology and Visual Sciences, Albert Einstein College of MedicineThe BronxUnited States
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Zheng X, Xu L, Ye M, Gu T, Yao YL, Lv LB, Yu D, Yao YG. Characterizing the role of Tupaia DNA damage inducible transcript 3 (DDIT3) gene in viral infections. Dev Comp Immunol 2022; 127:104307. [PMID: 34748795 DOI: 10.1016/j.dci.2021.104307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 11/01/2021] [Accepted: 11/01/2021] [Indexed: 06/13/2023]
Abstract
DNA damage inducible transcript 3 (DDIT3, also known as CHOP) belongs to the CCAAT/enhancer-binding protein (C/EBP) family and plays an essential role in endoplasmic reticulum stress. Here, we characterized the potential role of the Chinese tree shrew (Tupaia belangeri chinensis) DDIT3 (tDDIT3) in viral infections. The tDDIT3 protein is highly conserved and has a species-specific insertion of the SQSS repeat upstream of the C-terminal basic-leucine zipper (bZIP) domain. Phylogenetic analysis of DDIT3 protein sequences of tree shrew and related mammals indicated a closer genetic affinity between tree shrew and primates than between tree shrew and rodents. Three positively selected sites (PSSs: Glu83, Pro93, and Ser172) were identified in tDDIT3 based on the branch-site model. Expression analysis of tDDIT3 showed a constitutively expressed level in different tissues and a significantly increased level in tree shrew cells upon herpes simplex virus type 1 (HSV-1) and Newcastle disease virus (NDV) infections. Overexpression of tDDIT3 significantly increased the production of HSV-1 and vesicular stomatitis virus (VSV) in tree shrew primary renal cells (TSPRCs), whereas tDDIT3 knockout in tree shrew stable cell line (TSR6 cells) had an inhibitory effect on virus production. The enhanced effect on viral infection by tDDIT3 was not associated with the three PSSs. Mechanistically, tDDIT3 overexpression inhibited type I IFN signaling. tDDIT3 interacted with tMAVS through CARD and PRR domains, but not with other immune-related factors such as tMDA5, tSTING and tTBK1. Collectively, our results revealed tDDIT3 as a negative regulator for virus infection.
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Affiliation(s)
- Xiao Zheng
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230026, China; Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650204, China
| | - Ling Xu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650204, China; KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650204, China; National Resource Center for Non-Human Primates, National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650107, China
| | - Maosen Ye
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650204, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, 650204, China
| | - Tianle Gu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650204, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, 650204, China
| | - Yu-Lin Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650204, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, 650204, China
| | - Long-Bao Lv
- National Resource Center for Non-Human Primates, National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650107, China
| | - Dandan Yu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650204, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, 650204, China; National Resource Center for Non-Human Primates, National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650107, China.
| | - Yong-Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650204, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, 650204, China; KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650204, China; National Resource Center for Non-Human Primates, National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, 650107, China.
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30
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AlSudais H, Rajgara R, Saleh A, Wiper-Bergeron N. C/EBPβ promotes the expression of atrophy-inducing factors by tumours and is a central regulator of cancer cachexia. J Cachexia Sarcopenia Muscle 2022; 13:743-757. [PMID: 35014202 PMCID: PMC8818591 DOI: 10.1002/jcsm.12909] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 10/27/2021] [Accepted: 11/29/2021] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND CCAAT/enhancer-binding protein β (C/EBPβ) is a transcription factor whose high expression in human cancers is associated with tumour aggressiveness and poor outcomes. Most advanced cancer patients will develop cachexia, characterized by loss of skeletal muscle mass. In response to secreted factors from cachexia-inducing tumours, C/EBPβ is stimulated in muscle, leading to both myofibre atrophy and the inhibition of muscle regeneration. Involved in the regulation of immune responses, C/EBPβ induces the expression of many secreted factors, including cytokines. Because tumour-secreted factors drive cachexia and aggressive tumours have higher expression of C/EBPβ, we examined a potential role for C/EBPβ in the expression of tumour-derived cachexia-inducing factors. METHODS We used gain-of-function and loss-of-function approaches in vitro and in vivo to evaluate the role of tumour C/EBPβ expression on the secretion of cachexia-inducing factors. RESULTS We report that C/EBPβ overexpression up-regulates the expression of 260 secreted protein genes, resulting in a secretome that inhibits myogenic differentiation (-31%, P < 0.05) and myotube maturation [-38% (fusion index) and -25% (myotube diameter), P < 0.05]. We find that knockdown of C/EBPβ in cachexia-inducing Lewis lung carcinoma cells restores myogenic differentiation (+25%, P < 0.0001) and myotube diameter (+90%, P < 0.0001) in conditioned medium experiments and, in vivo, prevents muscle wasting (-51% for small myofibres vs. controls, P < 0.01; +140% for large myofibres, P < 0.01). Conversely, overexpression of C/EBPβ in non-cachectic tumours converts their secretome into a cachexia-inducing one, resulting in reduced myotube diameter (-41%, P < 0.0001, EL4 model) and inhibition of differentiation in culture (-26%, P < 0.01, EL4 model) and muscle wasting in vivo (+98% small fibres, P < 0.001; -76% large fibres, P < 0.001). Comparison of the differently expressed transcripts coding for secreted proteins in C/EBPβ-overexpressing myoblasts with the secretome from 27 different types of human cancers revealed ~18% similarity between C/EBPβ-regulated secreted proteins and those secreted by highly cachectic tumours (brain, pancreatic, and stomach cancers). At the protein level, we identified 16 novel secreted factors that are present in human cancer secretomes and are up-regulated by C/EBPβ. Of these, we tested the effect of three factors (SERPINF1, TNFRSF11B, and CD93) on myotubes and found that all had atrophic potential (-33 to -36% for myotube diameter, P < 0.01). CONCLUSIONS We find that C/EBPβ is necessary and sufficient to induce the secretion of cachexia-inducing factors by cancer cells and loss of C/EBPβ in tumours attenuates muscle atrophy in an animal model of cancer cachexia. Our findings establish C/EBPβ as a central regulator of cancer cachexia and an important therapeutic target.
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Affiliation(s)
- Hamood AlSudais
- Graduate Program in Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Rashida Rajgara
- Graduate Program in Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Aisha Saleh
- Graduate Program in Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Nadine Wiper-Bergeron
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
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Wang L, Wang P, Xu S, Li Z, Duan DD, Ye J, Li J, Ding Y, Zhang W, Lu J, Liu P. The cross-talk between PARylation and SUMOylation in C/EBPβ at K134 site participates in pathological cardiac hypertrophy. Int J Biol Sci 2022; 18:783-799. [PMID: 35002525 PMCID: PMC8741850 DOI: 10.7150/ijbs.65211] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 11/13/2021] [Indexed: 12/23/2022] Open
Abstract
Poly(ADP-ribosyl)ation (PARylation) and SUMO modification (SUMOylation) are novel post-translational modifications (PTMs) mainly induced by PARP1 and SUMO1. Growing evidence has revealed that C/EBPβ plays multiple roles in biological processes and participates in cardiovascular diseases. However, the cross-talk between C/EBPβ PARylation and SUMOylation during cardiovascular diseases is unknown. This study aims to investigate the effects of C/EBPβ PTMs on cardiac hypertrophy and its underlying mechanism. Abdominal aortic constriction (AAC) and phenylephrine (PE) were conducted to induce cardiac hypertrophy. Intramyocardial delivery of recombinant adenovirus (Ad-PARP1) was taken to induce PARP1 overexpression. In this study, we found C/EBPβ participates in PARP1-induced cardiac hypertrophy. C/EBPβ K134 residue could be both PARylated and SUMOylated individually by PARP1 and SUMO1. Moreover, the accumulation of PARylation on C/EBPβ at K134 site exhibits downregulation of C/EBPβ SUMOylation at the same site. Importantly, C/EBPβ K134 site SUMOylation could decrease C/EBPβ protein stability and participates in PARP1-induced cardiac hypertrophy. Taken together, these findings highlight the importance of the cross-talk between C/EBPβ PTMs at K134 site in determining its protein level and function, suggesting that multi-target pharmacological strategies inhibiting PARP1 and activating C/EBPβ SUMOylation would be potential for treating pathological cardiac hypertrophy.
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Affiliation(s)
- Luping Wang
- Department of Pharmacology and Toxicology, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangdong, China.,Laboratory of Hematopathology & Drug Discovery, School of Medicine, South China University of Technology, Guangdong, China
| | - Panxia Wang
- Department of Pharmacology and Toxicology, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangdong, China
| | - Suowen Xu
- Department of Endocrinology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Anhui, China
| | - Zhuoming Li
- Department of Pharmacology and Toxicology, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangdong, China
| | - Dayue Darrel Duan
- Center for Phenomics of Traditional Chinese Medicine/the Affiliated Hospital of Traditional Chinese Medicine, Southwest Medical University, Sichuan, China
| | - Jiantao Ye
- Department of Pharmacology and Toxicology, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangdong, China
| | - Jingyan Li
- Department of Pharmacology and Toxicology, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangdong, China
| | - Yanqing Ding
- Department of Pharmacology and Toxicology, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangdong, China
| | - Wenqing Zhang
- Laboratory of Hematopathology & Drug Discovery, School of Medicine, South China University of Technology, Guangdong, China
| | - Jing Lu
- Department of Pharmacology and Toxicology, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangdong, China
| | - Peiqing Liu
- Department of Pharmacology and Toxicology, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangdong, China.,National and Local United Engineering Lab of Druggability and New Drugs Evaluation, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangdong, China.,School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangdong, China
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32
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Liu H, Huang Q, Lv Y, Dong Y, Song D. CEBPB knockdown sensitizes nasopharyngeal carcinoma cells to cisplatin by promoting the expression of serine protease inhibitor Kazal-type 5. Anticancer Drugs 2022; 33:e327-e335. [PMID: 34387602 DOI: 10.1097/cad.0000000000001208] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Serine protease inhibitor Kazal-type 5 (SPINK5) has been indicated to act as a prognostic predictor for patients with head and neck squamous cell carcinoma. However, its specific role in nasopharyngeal carcinoma (NPC), a malignancy that has a high propensity for chemoresistance, remains largely obscure. We, thus, sought to investigate the importance of SPINK5 expression in regulating chemoresistance in NPC. Differentially expressed genes in NPC were screened using the cancer genome atlas-head and neck squamous cell carcinoma database and microarray analysis. SPINK5 was downregulated in NPC tissues and cells. After SPINK5 upregulation, the cells treated with cisplatin showed reduced cell survival and the ability to migrate, invade and metastasize. Mechanistically, the transcription factors regulating SPINK5 were queried through the JASPAR website, followed by dual-luciferase and Chromatin immunoprecipitation assay validation. CCAAT enhancer-binding protein (CEBP) beta (CEBPB) bound to the SPINK5 promoter region in NPC cells. The silencing of CEBPB enhanced the expression of SPINK5. CEBPB overexpression reversed the inhibitory effects of cisplatin on NPC cell malignant phenotype in the presence of SPINK5 overexpression. In conclusion, CEBPB silencing promoted chemoresistance of NPC cells via activating SPINK5, signifying that targeting CEBPB was a new approach to enhance the chemotherapy efficacy in NPC.
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Affiliation(s)
- Hong Liu
- Department of Oncology, Binzhou Central Hospital, Binzhou
| | - Qingli Huang
- Department of Otolaryngology, Liaocheng People's Hospital
| | - Yunxia Lv
- Department of Otolaryngology, Yanggu People's Hospital, Liaocheng
| | - Youwei Dong
- Department of Otolaryngology, Juxian people's Hospital, Rizhao
| | - Daoliang Song
- Department of Otorhinolargology Head and Neck Surgery, Zibo Central Hospital, Zibo, Shandong, People's Republic of China
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33
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Liu K, Shimbo T, Song X, Wade PA, Min J. Proteins That Read DNA Methylation. Advances in Experimental Medicine and Biology 2022. [DOI: 10.1007/978-3-031-11454-0_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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AlSudais H, Wiper-Bergeron N. From quiescence to repair: C/EBPβ as a regulator of muscle stem cell function in health and disease. FEBS J 2021; 289:6518-6530. [PMID: 34854237 DOI: 10.1111/febs.16307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 10/21/2021] [Accepted: 11/30/2021] [Indexed: 11/26/2022]
Abstract
CCAAT/Enhancer Binding protein beta (C/EBPβ) is a transcriptional regulator involved in numerous physiological processes. Herein, we describe a role for C/EBPβ as a regulator of skeletal muscle stem cell function. In particular, C/EBPβ is expressed in muscle stem cells in healthy muscle where it inhibits myogenic differentiation. Downregulation of C/EBPβ expression at the protein and transcriptional level allows for differentiation. Persistence of C/EBPβ promotes stem cell self-renewal and C/EBPβ expression is required for mitotic quiescence in this cell population. As a critical regulator of skeletal muscle homeostasis, C/EBPβ expression is stimulated in pathological conditions such as cancer cachexia, which perturbs muscle regeneration and promotes myofiber atrophy in the context of systemic inflammation. C/EBPβ is also an important regulator of cytokine expression and immune response genes, a mechanism by which it can influence muscle stem cell function. In this viewpoint, we describe a role for C/EBPβ in muscle stem cells and propose a functional intersection between C/EBPβ and NF-kB action in the regulation of cancer cachexia.
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Affiliation(s)
- Hamood AlSudais
- Graduate Program in Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Canada.,Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Saudi Arabia
| | - Nadine Wiper-Bergeron
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Canada
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Sahoo L, Das SP, Bit A, Patnaik S, Mohanty M, Das G, Das P. De novo assembly, transcriptome characterization and marker discovery in Indian major carp, Labeo rohita through pyrosequencing. Genetica 2021. [PMID: 34825293 DOI: 10.1007/s10709-021-00141-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 11/16/2021] [Indexed: 10/19/2022]
Abstract
Labeo rohita, one of the Indian major carps, is the most popular culture species in Indian subcontinent due to its consumer preference and delicacy. A selective breeding program for harvest body weight has resulted in an average genetic gain of 17% per generation. Transcriptome resource for this species is scanty. Here, we have characterized the liver and muscle transcriptomes of rohu using Roche 454 GS-FLX next generation sequencing platform. In total, 1.2 million reads were generated, de novo assembly and clustering resulted in 4171 transcripts. Out of these, 4171 had significant blast hit against NCBI nr database, and 2130 transcripts were successfully annotated. In total, 289 SSRs were identified with an identification rate of 5.8%, and dinucleotide repeat motifs were observed to be the most abundant SSRs. Further, 2231 putative SNPs were identified with high confidence. Validation of eight putative SNPs using Sanger sequencing resulted in 100% true SNPs. Significant allelic imbalance of M1, M4 and M5 loci between growth selected and control individual were observed. Furthermore, 13 transcription factors were identified in the present study belonging to six different transcription factor families. The present study demonstrated the utility of RNAseq to develop genomics resources in non-model fish species, and the marker resources developed would support the genetic improvement program of this species.
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Chen Y, Gao L, Lin T, Pei X, Gao Q, Chen J, Zhang Y, Wu X, Li Z, Zhang Z. C/EBPZ modulates the differentiation and proliferation of preadipocytes. Int J Obes (Lond) 2021. [PMID: 34789850 DOI: 10.1038/s41366-021-01020-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 10/24/2021] [Accepted: 11/01/2021] [Indexed: 11/09/2022]
Abstract
BACKGROUND/OBJECTIVES This study investigated the functions of CCAAT/enhancer-binding protein zeta (C/EBPZ; Gene ID: 10153) in adipose tissue. SUBJECTS/METHODS Bioinformatics analysis were used to study the expression pattern of C/EBPZ in human adipose tissue. The expression and function of C/EBPZ in adipose tissue were further studied using chicken as animal model in vivo and in vitro. RESULTS The human C/EBPZ transcripts were greater and more stable in subcutaneous adipose tissue than in visceral adipose tissue (P < 0.01), and they were increased with age in adipose tissue (P < 0.05). In addition, the chicken C/EBPZ transcripts (C/EBPZ /ACTB) of visceral (abdominal) adipose tissue were significantly different between fat and lean broilers and decreased with age during development (P < 0.01). RNA-seq analysis showed that the C/EBPZ overexpression associated with adipose tissue development and DNA replication in chicken preadipocytes (P < 0.05). Additionally, overexpression of chicken C/EBPZ inhibited preadipocytes differentiation and promoted preadipoytes proliferation in vitro (P < 0.05). In addition, C/EBPZ overexpression suppressed the promoter activities of PPARγ, C/EBPα, FASN and LPL, and promoted the promoter activities of GATA2 and FABP4 in chicken preadipocytes (P < 0.05). CONCLUSIONS C/EBPZ modulated the differentiation and proliferation of preadipocytes, and it might be a new negative regulator of adipogenesis.
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Jiang Y, Wu SY, Chen YL, Zhang ZM, Tao YF, Xie Y, Liao XM, Li XL, Li G, Wu D, Wang HR, Zuo R, Cao HB, Pan JJ, Yu JJ, Jia SQ, Zhang Z, Chu XR, Zhang YP, Feng CX, Wang JW, Hu SY, Li ZH, Pan J, Fang F, Lu J. CEBPG promotes acute myeloid leukemia progression by enhancing EIF4EBP1. Cancer Cell Int 2021; 21:598. [PMID: 34743716 PMCID: PMC8574011 DOI: 10.1186/s12935-021-02305-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 10/27/2021] [Indexed: 12/18/2022] Open
Abstract
Background Acute myeloid leukemia (AML) is a myeloid neoplasm accounts for 7.6% of hematopoietic malignancies. AML is a complex disease, and understanding its pathophysiology is contributing to the improvement in the treatment and prognosis of AML. In this study, we assessed the expression profile and molecular functions of CCAAT enhancer binding protein gamma (CEBPG), a gene implicated in myeloid differentiation and AML progression. Methods shRNA mediated gene interference was used to down-regulate the expression of CEBPG in AML cell lines, and knockdown efficiency was detected by RT-qPCR and western blotting. The effect of knockdown on the growth of AML cell lines was evaluated by CCK-8. Western blotting was used to detect PARP cleavage, and flow cytometry were used to determine the effect of knockdown on apoptosis of AML cells. Genes and pathways affected by knockdown of CEBPG were identified by gene expression analysis using RNA-seq. One of the genes affected by knockdown of CEBPG was Eukaryotic translation initiation factor 4E binding protein 1 (EIF4EBP1), a known repressor of translation. Knockdown of EIF4EBP1 was used to assess its potential role in AML progression downstream of CEBPG. Results We explored the ChIP-Seq data of AML cell lines and non-AML hematopoietic cells, and found CEBPG was activated through its distal enhancer in AML cell lines. Using the public transcriptomic dataset, the Cancer Cell Line Encyclopedia (CCLE) and western blotting, we also found CEBPG was overexpressed in AML. Moreover, we observed that CEBPG promotes AML cell proliferation by activating EIF4EBP1, thus contributing to the progression of AML. These findings indicate that CEBPG could act as a potential therapeutic target for AML patients. Conclusion In summary, we systematically explored the molecular characteristics of CEBPG in AML and identified CEBPG as a potential therapeutic target for AML patients. Our findings provide novel insights into the pathophysiology of AML and indicate a key role for CEBPG in promoting AML progression. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-021-02305-z.
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Affiliation(s)
- You Jiang
- Department of Hematology, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, 215003, Jiangsu, China
| | - Shui-Yan Wu
- Department of Hematology, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, 215003, Jiangsu, China.,Intensive Care Unit, Children's Hospital of Soochow University, Suzhou, 215003, China
| | - Yan-Ling Chen
- Institute of Pediatric Research, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, 215003, China.,School of Basic Medicine and Biological Sciences, Soochow University, Suzhou, 215003, China
| | - Zi-Mu Zhang
- Institute of Pediatric Research, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, 215003, China
| | - Yan-Fang Tao
- Department of Hematology, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, 215003, Jiangsu, China.,Institute of Pediatric Research, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, 215003, China
| | - Yi Xie
- Institute of Pediatric Research, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, 215003, China
| | - Xin-Mei Liao
- Institute of Pediatric Research, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, 215003, China
| | - Xiao-Lu Li
- Institute of Pediatric Research, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, 215003, China
| | - Gen Li
- Institute of Pediatric Research, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, 215003, China
| | - Di Wu
- Institute of Pediatric Research, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, 215003, China
| | - Hai-Rong Wang
- Institute of Pediatric Research, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, 215003, China
| | - Ran Zuo
- Institute of Pediatric Research, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, 215003, China
| | - Hai-Bo Cao
- Institute of Pediatric Research, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, 215003, China
| | - Jing-Jing Pan
- Department of Hematology, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, 215003, Jiangsu, China.,Institute of Pediatric Research, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, 215003, China
| | - Juan-Juan Yu
- Institute of Pediatric Research, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, 215003, China
| | - Si-Qi Jia
- Institute of Pediatric Research, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, 215003, China.,School of Basic Medicine and Biological Sciences, Soochow University, Suzhou, 215003, China
| | - Zheng Zhang
- Institute of Pediatric Research, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, 215003, China
| | - Xin-Ran Chu
- Department of Hematology, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, 215003, Jiangsu, China
| | - Yong-Ping Zhang
- Department of Hematology, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, 215003, Jiangsu, China
| | - Chen-Xi Feng
- Institute of Pediatric Research, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, 215003, China
| | - Jian-Wei Wang
- Institute of Pediatric Research, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, 215003, China
| | - Shao-Yan Hu
- Department of Hematology, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, 215003, Jiangsu, China.,Institute of Pediatric Research, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, 215003, China
| | - Zhi-Heng Li
- Institute of Pediatric Research, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, 215003, China
| | - Jian Pan
- Department of Hematology, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, 215003, Jiangsu, China. .,Institute of Pediatric Research, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, 215003, China.
| | - Fang Fang
- Institute of Pediatric Research, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, 215003, China.
| | - Jun Lu
- Department of Hematology, Children's Hospital of Soochow University, No.92 Zhongnan Street, SIP, Suzhou, 215003, Jiangsu, China.
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38
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Levi S, Ripamonti M, Dardi M, Cozzi A, Santambrogio P. Mitochondrial Ferritin: Its Role in Physiological and Pathological Conditions. Cells 2021; 10:1969. [PMID: 34440737 DOI: 10.3390/cells10081969] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 07/27/2021] [Accepted: 07/30/2021] [Indexed: 12/16/2022] Open
Abstract
In 2001, a new type of human ferritin was identified by searching for homologous sequences to H-ferritin in the human genome. After the demonstration that this ferritin is located specifically in the mitochondrion, it was called mitochondrial ferritin. Studies on the properties of this new type of ferritin have been limited by its very high homology with the cytosolic H-ferritin, which is expressed at higher levels in cells. This great similarity made it difficult to obtain specific antibodies against the mitochondrial ferritin devoid of cross-reactivity with cytosolic ferritin. Thus, the knowledge of the physiological role of mitochondrial ferritin is still incomplete despite 20 years of research. In this review, we summarize the literature on mitochondrial ferritin expression regulation and its physical and biochemical properties, with particular attention paid to the differences with cytosolic ferritin and its role in physiological condition. Until now, there has been no evidence that the alteration of the mitochondrial ferritin gene is causative of any disorder; however, the identified association of the mitochondrial ferritin with some disorders is discussed.
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Zapata RC, Chaudry BS, Valencia ML, Zhang D, Ochsner SA, McKenna NJ, Osborn O. Conserved immunomodulatory transcriptional networks underlie antipsychotic-induced weight gain. Transl Psychiatry 2021; 11:405. [PMID: 34294678 PMCID: PMC8296828 DOI: 10.1038/s41398-021-01528-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 06/05/2021] [Accepted: 07/07/2021] [Indexed: 12/20/2022] Open
Abstract
Although antipsychotics, such as olanzapine, are effective in the management of psychiatric conditions, some patients experience excessive antipsychotic-induced weight gain (AIWG). To illuminate pathways underlying AIWG, we compared baseline blood gene expression profiles in two cohorts of mice that were either prone (AIWG-P) or resistant (AIWG-R) to weight gain in response to olanzapine treatment for two weeks. We found that transcripts elevated in AIWG-P mice relative to AIWG-R are enriched for high-confidence transcriptional targets of numerous inflammatory and immunomodulatory signaling nodes. Moreover, these nodes are themselves enriched for genes whose disruption in mice is associated with reduced body fat mass and slow postnatal weight gain. In addition, we identified gene expression profiles in common between our mouse AIWG-P gene set and an existing human AIWG-P gene set whose regulation by immunomodulatory transcription factors is highly conserved between species. Finally, we identified striking convergence between mouse AIWG-P transcriptional regulatory networks and those associated with body weight and body mass index in humans. We propose that immunomodulatory transcriptional networks drive AIWG, and that these networks have broader conserved roles in whole body-metabolism.
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Affiliation(s)
- Rizaldy C. Zapata
- grid.266100.30000 0001 2107 4242Division of Endocrinology and Metabolism, School of Medicine, University of California San Diego, La Jolla, CA 92093 USA
| | - Besma S. Chaudry
- grid.266100.30000 0001 2107 4242Division of Endocrinology and Metabolism, School of Medicine, University of California San Diego, La Jolla, CA 92093 USA
| | - Mariela Lopez Valencia
- grid.266100.30000 0001 2107 4242Division of Endocrinology and Metabolism, School of Medicine, University of California San Diego, La Jolla, CA 92093 USA
| | - Dinghong Zhang
- grid.266100.30000 0001 2107 4242Division of Endocrinology and Metabolism, School of Medicine, University of California San Diego, La Jolla, CA 92093 USA
| | - Scott A. Ochsner
- grid.39382.330000 0001 2160 926XSignaling Pathways Project and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030 USA
| | - Neil J. McKenna
- grid.39382.330000 0001 2160 926XSignaling Pathways Project and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030 USA
| | - Olivia Osborn
- Division of Endocrinology and Metabolism, School of Medicine, University of California San Diego, La Jolla, CA, 92093, USA.
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40
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Bechara R, Amatya N, Bailey RD, Li Y, Aggor FEY, Li DD, Jawale CV, Coleman BM, Dai N, Gokhale NS, Taylor TC, Horner SM, Poholek AC, Bansal A, Biswas PS, Gaffen SL. The m 6A reader IMP2 directs autoimmune inflammation through an IL-17- and TNFα-dependent C/EBP transcription factor axis. Sci Immunol 2021; 6:eabd1287. [PMID: 34215679 PMCID: PMC8404281 DOI: 10.1126/sciimmunol.abd1287] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 04/02/2021] [Accepted: 06/03/2021] [Indexed: 12/15/2022]
Abstract
Excessive cytokine activity underlies many autoimmune conditions, particularly through the interleukin-17 (IL-17) and tumor necrosis factor-α (TNFα) signaling axis. Both cytokines activate nuclear factor κB, but appropriate induction of downstream effector genes requires coordinated activation of other transcription factors, notably, CCAAT/enhancer binding proteins (C/EBPs). Here, we demonstrate the unexpected involvement of a posttranscriptional "epitranscriptomic" mRNA modification [N6-methyladenosine (m6A)] in regulating C/EBPβ and C/EBPδ in response to IL-17A, as well as IL-17F and TNFα. Prompted by the observation that C/EBPβ/δ-encoding transcripts contain m6A consensus sites, we show that Cebpd and Cebpb mRNAs are subject to m6A modification. Induction of C/EBPs is enhanced by an m6A methylase "writer" and suppressed by a demethylase "eraser." The only m6A "reader" found to be involved in this pathway was IGF2BP2 (IMP2), and IMP2 occupancy of Cebpd and Cebpb mRNA was enhanced by m6A modification. IMP2 facilitated IL-17-mediated Cebpd mRNA stabilization and promoted translation of C/EBPβ/δ in response to IL-17A, IL-17F, and TNFα. RNA sequencing revealed transcriptome-wide IL-17-induced transcripts that are IMP2 influenced, and RNA immunoprecipitation sequencing identified the subset of mRNAs that are directly occupied by IMP2, which included Cebpb and Cebpd Lipocalin-2 (Lcn2), a hallmark of autoimmune kidney injury, was strongly dependent on IL-17, IMP2, and C/EBPβ/δ. Imp2-/- mice were resistant to autoantibody-induced glomerulonephritis (AGN), showing impaired renal expression of C/EBPs and Lcn2 Moreover, IMP2 deletion initiated only after AGN onset ameliorated disease. Thus, posttranscriptional regulation of C/EBPs through m6A/IMP2 represents a previously unidentified paradigm of cytokine-driven autoimmune inflammation.
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Affiliation(s)
- Rami Bechara
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Nilesh Amatya
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Rachel D Bailey
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yang Li
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Felix E Y Aggor
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh, Pittsburgh, PA, USA
| | - De-Dong Li
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Chetan V Jawale
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Bianca M Coleman
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ning Dai
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Nandan S Gokhale
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
| | - Tiffany C Taylor
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Stacy M Horner
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
- Department of Medicine, Duke University Medical Center, Durham, NC, USA
| | - Amanda C Poholek
- Division of Pediatrics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Anita Bansal
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Partha S Biswas
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Sarah L Gaffen
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh, Pittsburgh, PA, USA.
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41
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Cheng G, Raza SHA, Khan R, Wang H, Shater AF, Mohammedsaleh ZM, Wang L, Tian Y, Long F, Zan L. C/EBPβ converts bovine fibroblasts to adipocytes without hormone cocktail induction. ELECTRON J BIOTECHN 2021; 52:67-75. [DOI: 10.1016/j.ejbt.2021.04.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
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42
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Bajaffer A, Mineta K, Gojobori T. Evolution of memory system-related genes. FEBS Open Bio 2021; 11:3201-3210. [PMID: 34110105 PMCID: PMC8634864 DOI: 10.1002/2211-5463.13224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/25/2021] [Accepted: 06/09/2021] [Indexed: 11/29/2022] Open
Abstract
Memory has an essential function in human life as it helps individuals remember and recognize their surroundings. It is also the major form of cognition that controls behavior. As memory is a function that is highly characteristic of humans, how it was established is of particular interest. Recent progress in the field of neurosciences, together with the technological advancement of genome‐wide approaches, has led to the accumulation of evidence regarding the presence and similar/distinct mechanisms of memory among species. However, the understanding of the evolution of memory obtained utilizing these genome‐wide approaches remains unclear. The purpose of this review was to provide an overview of the literature on the evolution of the memory system among species and the genes involved in this process. This review also discusses possible approaches to study the evolution of memory systems to guide future research.
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Affiliation(s)
- Amal Bajaffer
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Katsuhiko Mineta
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Takashi Gojobori
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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43
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Ramberger E, Sapozhnikova V, Kowenz-Leutz E, Zimmermann K, Nicot N, Nazarov PV, Perez-Hernandez D, Reimer U, Mertins P, Dittmar G, Leutz A. PRISMA and BioID disclose a motifs-based interactome of the intrinsically disordered transcription factor C/EBPα. iScience 2021; 24:102686. [PMID: 34189442 PMCID: PMC8220391 DOI: 10.1016/j.isci.2021.102686] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 05/17/2021] [Accepted: 05/30/2021] [Indexed: 01/27/2023] Open
Abstract
C/EBPα represents a paradigm intrinsically disordered transcription factor containing short linear motifs and post-translational modifications (PTM). Unraveling C/EBPα protein interaction networks is a prerequisite for understanding the multi-modal functions of C/EBPα in hematopoiesis and leukemia. Here, we combined arrayed peptide matrix screening (PRISMA) with BioID to generate an in vivo validated and isoform specific interaction map of C/EBPα. The myeloid C/EBPα interactome comprises promiscuous and PTM-regulated interactions with protein machineries involved in gene expression, epigenetics, genome organization, DNA replication, RNA processing, and nuclear transport. C/EBPα interaction hotspots coincide with homologous conserved regions of the C/EBP family that also score as molecular recognition features. PTMs alter the interaction spectrum of C/EBP-motifs to configure a multi-valent transcription factor hub that interacts with multiple co-regulatory components, including BAF/SWI-SNF or Mediator complexes. Combining PRISMA and BioID is a powerful strategy to systematically explore the PTM-regulated interactomes of intrinsically disordered transcription factors. Combining peptide arrays and BioID refines the C/EBPα interactome Hotspots of protein interactions in C/EBPα mostly occur in conserved regions The interaction with the BAF/SWI-SNF complex is modulated by C/EBPα methylation Experimental design suits interactome studies of intrinsically disordered proteins
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Affiliation(s)
- Evelyn Ramberger
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Valeria Sapozhnikova
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Elisabeth Kowenz-Leutz
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Karin Zimmermann
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Nathalie Nicot
- Quantitative Biology Unit, Luxembourg Institute of Health, 1a Rue Thomas Edison, 1445 Strassen, Luxembourg
| | - Petr V Nazarov
- Quantitative Biology Unit, Luxembourg Institute of Health, 1a Rue Thomas Edison, 1445 Strassen, Luxembourg
| | - Daniel Perez-Hernandez
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Strasse 10, 13125 Berlin, Germany.,Quantitative Biology Unit, Luxembourg Institute of Health, 1a Rue Thomas Edison, 1445 Strassen, Luxembourg
| | - Ulf Reimer
- JPT Peptide Technologies GmbH, Volmerstrasse 5, 12489 Berlin, Germany
| | - Philipp Mertins
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Gunnar Dittmar
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Strasse 10, 13125 Berlin, Germany.,Quantitative Biology Unit, Luxembourg Institute of Health, 1a Rue Thomas Edison, 1445 Strassen, Luxembourg
| | - Achim Leutz
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Strasse 10, 13125 Berlin, Germany.,Institute of Biology, Humboldt University of Berlin, 10115 Berlin, Germany
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44
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Yang J, Horton JR, Akdemir KC, Li J, Huang Y, Kumar J, Blumenthal RM, Zhang X, Cheng X. Preferential CEBP binding to T:G mismatches and increased C-to-T human somatic mutations. Nucleic Acids Res 2021; 49:5084-5094. [PMID: 33877329 PMCID: PMC8136768 DOI: 10.1093/nar/gkab276] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 04/07/2021] [Indexed: 12/02/2022] Open
Abstract
DNA cytosine methylation in mammals modulates gene expression and chromatin accessibility. It also impacts mutation rates, via spontaneous oxidative deamination of 5-methylcytosine (5mC) to thymine. In most cases the resulting T:G mismatches are repaired, following T excision by one of the thymine DNA glycosylases, TDG or MBD4. We found that C-to-T mutations are enriched in the binding sites of CCAAT/enhancer binding proteins (CEBP). Within a CEBP site, the presence of a T:G mismatch increased CEBPβ binding affinity by a factor of >60 relative to the normal C:G base pair. This enhanced binding to a mismatch inhibits its repair by both TDG and MBD4 in vitro. Furthermore, repair of the deamination product of unmethylated cytosine, which yields a U:G DNA mismatch that is normally repaired via uracil DNA glycosylase, is also inhibited by CEBPβ binding. Passage of a replication fork over either a T:G or U:G mismatch, before repair can occur, results in a C-to-T mutation in one of the daughter duplexes. Our study thus provides a plausible mechanism for accumulation of C-to-T human somatic mutations.
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Affiliation(s)
- Jie Yang
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - John R Horton
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kadir C Akdemir
- Departments of Genomic Medicine and Neurosurgery, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jia Li
- Center for Epigenetics & Disease Prevention, Institute of Biosciences and Technology, College of Medicine, Texas A&M University, Houston, TX 77030, USA
| | - Yun Huang
- Center for Epigenetics & Disease Prevention, Institute of Biosciences and Technology, College of Medicine, Texas A&M University, Houston, TX 77030, USA
| | - Janani Kumar
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Robert M Blumenthal
- Department of Medical Microbiology and Immunology, and Program in Bioinformatics, The University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
| | - Xing Zhang
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xiaodong Cheng
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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45
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Torcal Garcia G, Graf T. The transcription factor code: a beacon for histone methyltransferase docking. Trends Cell Biol 2021:S0962-8924(21)00071-4. [PMID: 34016504 DOI: 10.1016/j.tcb.2021.04.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/30/2021] [Accepted: 04/08/2021] [Indexed: 12/19/2022]
Abstract
Histone methylation is required for the establishment and maintenance of gene expression patterns that determine cellular identity, and its perturbation often leads to aberrant development and disease. Recruitment of histone methyltransferases (HMTs) to gene regulatory elements (GREs) of developmental genes is important for the correct activation and silencing of these genes, but the drivers of this recruitment are largely unknown. Here we propose that lineage-instructive transcription factors (Lin-TFs) act as general recruiters of HMT complexes to cell type-specific GREs through protein-protein interactions. We also postulate that the specificity of these interactions is dictated by Lin-TF post-translational modifications (PTMs), which act as a 'transcription factor code' that can determine the directionality of cell fate decisions during differentiation and development.
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46
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Ullmann T, Luckhardt S, Wolf M, Parnham MJ, Resch E. High-Throughput Screening for CEBPD-Modulating Compounds in THP-1-Derived Reporter Macrophages Identifies Anti-Inflammatory HDAC and BET Inhibitors. Int J Mol Sci 2021; 22:ijms22063022. [PMID: 33809617 PMCID: PMC8002291 DOI: 10.3390/ijms22063022] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/07/2021] [Accepted: 03/11/2021] [Indexed: 12/25/2022] Open
Abstract
This study aimed to identify alternative anti-inflammatory compounds that modulate the activity of a relevant transcription factor, CCAAT/enhancer binding protein delta (C/EBPδ). C/EBPδ is a master regulator of inflammatory responses in macrophages (Mϕ) and is mainly regulated at the level of CEBPD gene transcription initiation. To screen for CEBPD-modulating compounds, we generated a THP-1-derived reporter cell line stably expressing secreted alkaline phosphatase (SEAP) under control of the defined CEBPD promoter (CEBPD::SEAP). A high-throughput screening of LOPAC®1280 and ENZO®774 libraries on LPS- and IFN-γ-activated THP-1 reporter Mϕ identified four epigenetically active hits: two bromodomain and extraterminal domain (BET) inhibitors, I-BET151 and Ro 11-1464, as well as two histone deacetylase (HDAC) inhibitors, SAHA and TSA. All four hits markedly and reproducibly upregulated SEAP secretion and CEBPD::SEAP mRNA expression, confirming screening assay reliability. Whereas BET inhibitors also upregulated the mRNA expression of the endogenous CEBPD, HDAC inhibitors completely abolished it. All hits displayed anti-inflammatory activity through the suppression of IL-6 and CCL2 gene expression. However, I-BET151 and HDAC inhibitors simultaneously upregulated the mRNA expression of pro-inflammatory IL-1ß. The modulation of CEBPD gene expression shown in this study contributes to our understanding of inflammatory responses in Mϕ and may offer an approach to therapy for inflammation-driven disorders.
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Affiliation(s)
- Tatjana Ullmann
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany; (S.L.); (M.J.P.); (E.R.)
- Correspondence:
| | - Sonja Luckhardt
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany; (S.L.); (M.J.P.); (E.R.)
| | - Markus Wolf
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Schnackenburgallee 114, 22525 Hamburg, Germany;
| | - Michael J. Parnham
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany; (S.L.); (M.J.P.); (E.R.)
- EpiEndo Pharmaceuticals ehf, Eiðistorg 13-15, 170 Seltjarnarnes, Iceland
| | - Eduard Resch
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany; (S.L.); (M.J.P.); (E.R.)
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47
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Bachhawat AK, Yadav S, Jainarayanan AK, Dubey P. Heart failure and the glutathione cycle: an integrated view. Biochem J 2020; 477:3123-30. [PMID: 32886767 DOI: 10.1042/BCJ20200429] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 08/07/2020] [Accepted: 08/11/2020] [Indexed: 12/15/2022]
Abstract
Heart failure results from the heart's inability to carryout ventricular contraction and relaxation, and has now become a worldwide problem. During the onset of heart failure, several signatures are observed in cardiomyocytes that includes fetal reprogramming of gene expression where adult genes are repressed and fetal genes turned on, endoplasmic reticulum stress and oxidative stress. In this short review and analysis, we examine these different phenomenon from the viewpoint of the glutathione cycle and the role of the recently discovered Chac1 enzyme. Chac1, which belongs to the family of γ-glutamylcyclotransferases, is a recently discovered member of the glutathione cycle, being involved in the cytosolic degradation of glutathione. This enzyme is induced during the Endoplasmic Stress response, but also in the developing heart. Owing to its exclusive action on reduced glutathione, its induction leads to an increase in the oxidative redox potential of the cell that also serves as signaling mechanism for calcium ions channel activation. The end product of Chac1 action is 5-oxoproline, and studies with 5-oxoprolinase (OPLAH), an enzyme of the glutathione cycle has revealed that down-regulation of OPLAH can lead to the accumulation of 5-oxproline which is an important factor in heart failure. With these recent findings, we have re-examined the roles and regulation of the enzymes in the glutathione cycle which are central to these responses. We present an integrated view of the glutathione cycle in the cellular response to heart failure.
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48
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Brown AL, Hahn CN, Scott HS. Secondary leukemia in patients with germline transcription factor mutations (RUNX1, GATA2, CEBPA). Blood 2020; 136:24-35. [PMID: 32430494 DOI: 10.1182/blood.2019000937] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 02/25/2020] [Indexed: 02/07/2023] Open
Abstract
Recognition that germline mutations can predispose individuals to blood cancers, often presenting as secondary leukemias, has largely been driven in the last 20 years by studies of families with inherited mutations in the myeloid transcription factors (TFs) RUNX1, GATA2, and CEBPA. As a result, in 2016, classification of myeloid neoplasms with germline predisposition for each of these and other genes was added to the World Health Organization guidelines. The incidence of germline mutation carriers in the general population or in various clinically presenting patient groups remains poorly defined for reasons including that somatic mutations in these genes are common in blood cancers, and our ability to distinguish germline (inherited or de novo) and somatic mutations is often limited by the laboratory analyses. Knowledge of the regulation of these TFs and their mutant alleles, their interaction with other genes and proteins and the environment, and how these alter the clinical presentation of patients and their leukemias is also incomplete. Outstanding questions that remain for patients with these germline mutations or their treating clinicians include: What is the natural course of the disease? What other symptoms may I develop and when? Can you predict them? Can I prevent them? and What is the best treatment? The resolution of many of the remaining clinical and biological questions and effective evidence-based treatment of patients with these inherited mutations will depend on worldwide partnerships among patients, clinicians, diagnosticians, and researchers to aggregate sufficient longitudinal clinical and laboratory data and integrate these data with model systems.
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49
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Johansson E, Martin LJ, He H, Chen X, Weirauch MT, Kroner JW, Khurana Hershey GK, Biagini JM. Second-hand smoke and NFE2L2 genotype interaction increases paediatric asthma risk and severity. Clin Exp Allergy 2021; 51:801-810. [PMID: 33382170 DOI: 10.1111/cea.13815] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 12/16/2020] [Accepted: 12/27/2020] [Indexed: 12/13/2022]
Abstract
BACKGROUND Second-hand smoke (SHS) exposure is associated with paediatric asthma, and oxidative stress is believed to play a role in mediating this association. The nuclear factor (erythroid-derived 2)-like 2 (NFE2L2) is important for the defence against oxidative stress. OBJECTIVE To explore interactions between NFE2L2 genotype and SHS exposure in paediatric asthma risk. METHODS We used a genotyped subset of patients of European ancestry (N = 669, median age at enrolment = 6.8 years) enrolled in the clinical cohort Greater Cincinnati Pediatric Clinic Repository as the study population, and a population-based paediatric cohort (N = 791) to replicate our findings. History of asthma diagnosis was obtained from medical records, and SHS exposure was obtained from questionnaires. Four NFE2L2 tagging SNPs were included in the analysis, and interactions between SHS and NFE2L2 genotype were evaluated using logistic regression. RESULTS Three of the analysed SNPs, rs10183914, rs1806649 and rs2886161, interacted significantly with SHS exposure to increase asthma risk (p ≤ .02). The interaction was replicated in an independent cohort for rs10183914 (p = .04). Interactions between SHS exposure and NFE2L2 genotype were also associated with an increased risk of hospitalization (p = .016). In stratified analyses, NFE2L2 genotype was associated with daily asthma symptoms in children with SHS exposure (OR = 3.1; p = .048). No association was found in children without SHS exposure. Examination of publicly available chromatin immunoprecipitation followed by sequencing (ChIP-seq) data sets confirmed the presence of active histone marks and binding sites for particular transcription factors overlapping the coordinates for the significantly associated SNPs. CONCLUSIONS AND CLINICAL RELEVANCE Our study provides evidence that NFE2L2 genotype interacts with SHS exposure to affect both asthma risk and severity in children and identifies a population of children at increased risk of asthma development.
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Affiliation(s)
- Elisabet Johansson
- Division of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Lisa J Martin
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Hua He
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Xiaoting Chen
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Matthew T Weirauch
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.,Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.,Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - John W Kroner
- Division of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Gurjit K Khurana Hershey
- Division of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Jocelyn M Biagini
- Division of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
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Wang L, Zhu P, Mo Q, Luo W, Du Z, Jiang J, Yang S, Zhao L, Gong Q, Wang Y. Comprehensive analysis of full-length transcriptomes of Schizothorax prenanti by single-molecule long-read sequencing. Genomics 2021; 114:456-464. [PMID: 33516848 DOI: 10.1016/j.ygeno.2021.01.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 01/12/2021] [Accepted: 01/20/2021] [Indexed: 01/01/2023]
Abstract
Schizothorax prenanti (S. prenanti) is one of the most important aquaculture species in the southwest of China. However, information of the full-length transcripts in S. prenanti remains unknown. In this study, single-molecule real-time (SMRT) sequencing was performed to generate full-length transcriptomes of S.prenanti. In total, 23.26 Gb of clean reads were generated. A total of 312,587 circular consensus sequences (CCS) were obtained with average lengths of 2634 bp and 84.16% (270,662) of CCS were full-length non-chimeric reads. After being corrected with Illumina library sequencing, 18,005 contigs were obtained, with 17,797 (98.81%) successfully annotated in eight public databases, including 15,839 complete open reading frames (ORFs) with an average length of 1330 bp. Furthermore, a total of 4152 alternative splicing (AS) events and 250 long non-coding RNA (lncRNA) transcripts were detected. Additionally, a total of 1129 putative transcription factors (TFs) members from 56 TF families and 11,660 simple sequence repeats (SSRs) were identified. This study provided a valuable resource of full-length transcripts for further research on S. prenanti.
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Affiliation(s)
- Linjie Wang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, Sichuan, PR China
| | - Peng Zhu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, Sichuan, PR China
| | - Qilang Mo
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, Sichuan, PR China
| | - Wei Luo
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, Sichuan, PR China
| | - Zongjun Du
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, Sichuan, PR China
| | - Jun Jiang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, Sichuan, PR China
| | - Song Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, Sichuan, PR China
| | - Liulan Zhao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, Sichuan, PR China
| | - Quan Gong
- Fisheries institute, Sichuan Academy of Agricultural Sciences, Chengdu 611713, Sichuan, PR China
| | - Yan Wang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, Sichuan, PR China.
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