1
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Zhang H, Zheng Y, Wang Z, Dong L, Xue L, Tian X, Deng H, Xue Q, Gao S, Gao Y, Li C, He J. KLF12 interacts with TRIM27 to affect cisplatin resistance and cancer metastasis in esophageal squamous cell carcinoma by regulating L1CAM expression. Drug Resist Updat 2024; 76:101096. [PMID: 38924996 DOI: 10.1016/j.drup.2024.101096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 05/20/2024] [Accepted: 05/21/2024] [Indexed: 06/28/2024]
Abstract
Krüppel-like factor 12 (KLF12) has been characterized as a transcriptional repressor, and previous studies have unveiled its roles in angiogenesis, neural tube defect, and natural killer (NK) cell proliferation. However, the contribution of KLF12 to cancer treatment remains undefined. Here, we show that KLF12 is downregulated in various cancer types, and KLF12 downregulation promotes cisplatin resistance and cancer metastasis in esophageal squamous cell carcinoma (ESCC). Mechanistically, KLF12 binds to the promoters of L1 Cell Adhesion Molecule (L1CAM) and represses its expression. Depletion of L1CAM abrogates cisplatin resistance and cancer metastasis caused by KLF12 loss. Moreover, the E3 ubiquitin ligase tripartite motif-containing 27 (TRIM27) binds to the N-terminal region of KLF12 and ubiquitinates KLF12 at K326 via K33-linked polyubiquitination. Notably, TRIM27 depletion enhances the transcriptional activity of KLF12 and consequently inhibits L1CAM expression. Overall, our study elucidated a novel regulatory mechanism involving TRIM27, KLF12 and L1CAM, which plays a substantial role in cisplatin resistance and cancer metastasis in ESCC. Targeting these genes could be a promising approach for ESCC treatment.
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Affiliation(s)
- Hao Zhang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yujia Zheng
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Zhen Wang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lin Dong
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Liyan Xue
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiaolin Tian
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
| | - Haiteng Deng
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
| | - Qi Xue
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shugeng Gao
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yibo Gao
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Laboratory of Translational Medicine, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China; State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China; Central Laboratory & Shenzhen Key Laboratory of Epigenetics and Precision Medicine for Cancers, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen 518116, China.
| | - Chunxiang Li
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Jie He
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
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Hume AJ, Olejnik J, White MR, Huang J, Turcinovic J, Heiden B, Bawa PS, Williams CJ, Gorham NG, Alekseyev YO, Connor JH, Kotton DN, Mühlberger E. Heat Inactivation of Nipah Virus for Downstream Single-Cell RNA Sequencing Does Not Interfere with Sample Quality. Pathogens 2024; 13:62. [PMID: 38251369 PMCID: PMC10818917 DOI: 10.3390/pathogens13010062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/04/2024] [Accepted: 01/05/2024] [Indexed: 01/23/2024] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) technologies are instrumental to improving our understanding of virus-host interactions in cell culture infection studies and complex biological systems because they allow separating the transcriptional signatures of infected versus non-infected bystander cells. A drawback of using biosafety level (BSL) 4 pathogens is that protocols are typically developed without consideration of virus inactivation during the procedure. To ensure complete inactivation of virus-containing samples for downstream analyses, an adaptation of the workflow is needed. Focusing on a commercially available microfluidic partitioning scRNA-seq platform to prepare samples for scRNA-seq, we tested various chemical and physical components of the platform for their ability to inactivate Nipah virus (NiV), a BSL-4 pathogen that belongs to the group of nonsegmented negative-sense RNA viruses. The only step of the standard protocol that led to NiV inactivation was a 5 min incubation at 85 °C. To comply with the more stringent biosafety requirements for BSL-4-derived samples, we included an additional heat step after cDNA synthesis. This step alone was sufficient to inactivate NiV-containing samples, adding to the necessary inactivation redundancy. Importantly, the additional heat step did not affect sample quality or downstream scRNA-seq results.
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Affiliation(s)
- Adam J. Hume
- Department of Virology, Immunology and Microbiology, Chobanian & Avedisian School of Medicine, Boston University, Boston, MA 02118, USA; (A.J.H.); (J.O.); (M.R.W.); (J.T.); (B.H.); (J.H.C.)
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02218, USA
| | - Judith Olejnik
- Department of Virology, Immunology and Microbiology, Chobanian & Avedisian School of Medicine, Boston University, Boston, MA 02118, USA; (A.J.H.); (J.O.); (M.R.W.); (J.T.); (B.H.); (J.H.C.)
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02218, USA
| | - Mitchell R. White
- Department of Virology, Immunology and Microbiology, Chobanian & Avedisian School of Medicine, Boston University, Boston, MA 02118, USA; (A.J.H.); (J.O.); (M.R.W.); (J.T.); (B.H.); (J.H.C.)
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02218, USA
| | - Jessie Huang
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA; (J.H.); (P.S.B.); (D.N.K.)
- The Pulmonary Center and Department of Medicine, Chobanian & Avedisian School of Medicine, Boston University, Boston, MA 02118, USA
| | - Jacquelyn Turcinovic
- Department of Virology, Immunology and Microbiology, Chobanian & Avedisian School of Medicine, Boston University, Boston, MA 02118, USA; (A.J.H.); (J.O.); (M.R.W.); (J.T.); (B.H.); (J.H.C.)
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02218, USA
| | - Baylee Heiden
- Department of Virology, Immunology and Microbiology, Chobanian & Avedisian School of Medicine, Boston University, Boston, MA 02118, USA; (A.J.H.); (J.O.); (M.R.W.); (J.T.); (B.H.); (J.H.C.)
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02218, USA
| | - Pushpinder S. Bawa
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA; (J.H.); (P.S.B.); (D.N.K.)
| | - Christopher J. Williams
- Department of Medicine, Single Cell Sequencing Core Facility, Chobanian & Avedisian School of Medicine, Boston University, Boston, MA 02118, USA;
| | - Nickolas G. Gorham
- Microarray and Sequencing Resource Core Facility, Chobanian & Avedisian School of Medicine, Boston University, Boston, MA 02118, USA;
| | - Yuriy O. Alekseyev
- Department of Pathology and Laboratory Medicine, Chobanian & Avedisian School of Medicine, Boston University, Boston, MA 02118, USA;
| | - John H. Connor
- Department of Virology, Immunology and Microbiology, Chobanian & Avedisian School of Medicine, Boston University, Boston, MA 02118, USA; (A.J.H.); (J.O.); (M.R.W.); (J.T.); (B.H.); (J.H.C.)
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02218, USA
| | - Darrell N. Kotton
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA; (J.H.); (P.S.B.); (D.N.K.)
- The Pulmonary Center and Department of Medicine, Chobanian & Avedisian School of Medicine, Boston University, Boston, MA 02118, USA
| | - Elke Mühlberger
- Department of Virology, Immunology and Microbiology, Chobanian & Avedisian School of Medicine, Boston University, Boston, MA 02118, USA; (A.J.H.); (J.O.); (M.R.W.); (J.T.); (B.H.); (J.H.C.)
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02218, USA
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3
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Pan X, Zhang W, Wang L, Guo H, Zheng M, Wu H, Weng Q, He Q, Ding L, Yang B. KLF12 transcriptionally regulates PD-L1 expression in non-small cell lung cancer. Mol Oncol 2023; 17:2659-2674. [PMID: 37606530 DOI: 10.1002/1878-0261.13512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 06/30/2023] [Accepted: 08/17/2023] [Indexed: 08/23/2023] Open
Abstract
Recent studies have pointed to the role of Krüpple-like factor 12 (KLF12) in cancer-associated processes, including cancer proliferation, apoptosis, and metastasis. However, the role of KLF12 in tumor immunity remains obscure. Here, we found that KLF12 expression was significantly higher in non-small cell lung cancer (NSCLC) cells with higher programmed death-ligand 1 (PD-L1) expression. Additionally, a positive correlation between KLF12 and PD-L1 was observed in clinical patient tumor tissues. By chromatin immunoprecipitation (ChIP) analysis, KLF12 was identified to bind to the CACCC motif of the PD-L1 promoter. Overexpression of KLF12 promoted PD-L1 transcription, whereas silencing of KLF12 inhibited PD-L1 transcription. Furthermore, signal transducer and activator of transcription 1 (STAT1)- and STAT3-triggered PD-L1 transcription was abolished in the absence of KLF12, and KLF12 knockdown weakened the binding of STAT1 and STAT3 to the PD-L1 promoter. Mechanistically, KLF12 physically interacted with P300, a histone acetyltransferase. In addition, KLF12 silencing reduced P300 binding to the PD-L1 promoter, which subsequently caused decreased acetylation of histone H3. PD-L1 transcription driven by KLF12 overexpression was eliminated by EP300 silencing. In immunocompetent mice, KLF12 knockout inhibited tumor growth and promoted infiltration of CD8+ T cells. However, this phenomenon was not observed in immunodeficient mice. Overall, this study reveals KLF12-mediated transcriptional regulation of PD-L1 in NSCLC; targeting KLF12 may be a potential therapeutic strategy for NSCLC.
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Affiliation(s)
- Xiaohui Pan
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
- School of Pharmaceutical Science, Wenzhou Medical University, China
| | - Wenxin Zhang
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
- School of Pharmaceutical Science, Wenzhou Medical University, China
| | - Longsheng Wang
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Hongjie Guo
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Mingming Zheng
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Honghai Wu
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Qinjie Weng
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Qiaojun He
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
- The Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou, China
- Cancer Center of Zhejiang University, Hangzhou, China
| | - Ling Ding
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Bo Yang
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, Institute of Pharmacology and Toxicology, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
- The Innovation Institute for Artificial Intelligence in Medicine, Zhejiang University, Hangzhou, China
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4
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Ling X, Wang Q, Zhang J, Zhang G. Genome-Wide Analysis of the KLF Gene Family in Chicken: Characterization and Expression Profile. Animals (Basel) 2023; 13:ani13091429. [PMID: 37174466 PMCID: PMC10177326 DOI: 10.3390/ani13091429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/08/2023] [Accepted: 04/20/2023] [Indexed: 05/15/2023] Open
Abstract
The kruppel-like factor (KLF) gene family is a group of transcription factors containing highly conserved zinc-finger motifs, which play a crucial role in cell proliferation and differentiation. Chicken has been widely used as a model animal for analyzing gene function, however, little is known about the function of the KLF gene family in chickens. In this study, we performed genome-wide studies of chicken KLF genes and analyzed their biological and expression characteristics. We identified 13 KLF genes from chickens. Our phylogenetic, motif, and conserved domain analyses indicate that the KLF gene family has remained conserved through evolution. Synteny analysis showed the collinear relationship among KLFs, which indicated that they had related biomolecular functions. Interaction network analysis revealed that KLFs worked with 20 genes in biological processes. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that KLF2 was involved in Apelin and Forkhead Box O (FOXO) signaling pathways. Moreover, qPCR showed that 13 KLF genes were expressed in the nine selected tissues and displayed various gene expression patterns in chickens. RNA-seq showed that KLF3 and KLF10 genes were differentially expressed in the normal and high-fat diet fed groups, and KLF4, KLF5, KLF6, KLF7, KLF9, KLF12, and KLF13 genes were differentially expressed between undifferentiated and differentiated chicken preadipocytes. Besides, RNA-seq also showed that KLF genes displayed different expression patterns in muscle at 11 and 16 embryonic days old, and in 1-day-old chickens. These results indicated that the KLF genes were involved in the development of muscle and fat in chickens. Our findings provide some valuable reference points for the subsequent study of the function of KLF genes.
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Affiliation(s)
- Xuanze Ling
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225000, China
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou 225000, China
| | - Qifan Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225000, China
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou 225000, China
| | - Jin Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225000, China
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou 225000, China
| | - Genxi Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225000, China
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou 225000, China
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5
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Mahmoudian RA, Akhlaghipour I, Lotfi M, Shahidsales S, Moghbeli M. Circular RNAs as the pivotal regulators of epithelial-mesenchymal transition in gastrointestinal tumor cells. Pathol Res Pract 2023; 245:154472. [PMID: 37087995 DOI: 10.1016/j.prp.2023.154472] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/11/2023] [Accepted: 04/18/2023] [Indexed: 04/25/2023]
Abstract
Gastrointestinal (GI) cancers, as the most common human malignancies are always considered one of the most important health challenges in the world. Late diagnosis in advanced tumor stages is one of the main reasons for the high mortality rate and treatment failure in these patients. Therefore, investigating the molecular pathways involved in GI tumor progression is required to introduce the efficient markers for the early tumor diagnosis. Epithelial-mesenchymal transition (EMT) is one of the main cellular mechanisms involved in the GI tumor metastasis. Non-coding RNAs (ncRNAs) are one of the main regulatory factors in EMT process. Circular RNAs (circRNAs) are a group of covalently closed loop ncRNAs that have higher stability in body fluids compared with other ncRNAs. Considering the importance of circRNAs in regulation of EMT process, in the present review we discussed the role of circRNAs in EMT process during GI tumor invasion. It has been reported that circRNAs mainly affect the EMT process through the regulation of EMT-specific transcription factors and signaling pathways such as WNT, PI3K/AKT, TGF-β, and MAPK. This review can be an effective step in introducing a circRNA/EMT based diagnostic panel marker for the early tumor detection among GI cancer patients.
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Affiliation(s)
- Reihaneh Alsadat Mahmoudian
- Basic Sciences Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Cancer Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Iman Akhlaghipour
- Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Malihe Lotfi
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Meysam Moghbeli
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
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Olejnik J, Leon J, Michelson D, Chowdhary K, Galvan-Pena S, Benoist C, Mühlberger E, Hume AJ. Establishment of an Inactivation Method for Ebola Virus and SARS-CoV-2 Suitable for Downstream Sequencing of Low Cell Numbers. Pathogens 2023; 12:342. [PMID: 36839614 PMCID: PMC9958562 DOI: 10.3390/pathogens12020342] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 02/06/2023] [Accepted: 02/15/2023] [Indexed: 02/22/2023] Open
Abstract
Technologies that facilitate the bulk sequencing of small numbers of cells as well as single-cell RNA sequencing (scRNA-seq) have aided greatly in the study of viruses as these analyses can be used to differentiate responses from infected versus bystander cells in complex systems, including in organoid or animal studies. While protocols for these analyses are typically developed with biosafety level 2 (BSL-2) considerations in mind, such analyses are equally useful for the study of viruses that require higher biosafety containment levels. Many of these workstreams, however, are not directly compatible with the more stringent biosafety regulations of BSL-3 and BSL-4 laboratories ensuring virus inactivation and must therefore be modified. Here we show that TCL buffer (Qiagen), which was developed for bulk sequencing of small numbers of cells and also facilitates scRNA-seq, inactivates both Ebola virus (EBOV) and SARS-CoV-2, BSL-4 and BSL-3 viruses, respectively. We show that additional heat treatment, necessary for the more stringent biosafety concerns for BSL-4-derived samples, was additionally sufficient to inactivate EBOV-containing samples. Critically, this heat treatment had minimal effects on extracted RNA quality and downstream sequencing results.
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Affiliation(s)
- Judith Olejnik
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02118, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02218, USA
| | - Juliette Leon
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
- INSERM UMR 1163, Institut Imagine, University of Paris, 75015 Paris, France
| | - Daniel Michelson
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Kaitavjeet Chowdhary
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Silvia Galvan-Pena
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Christophe Benoist
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Elke Mühlberger
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02118, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02218, USA
| | - Adam J. Hume
- Department of Microbiology, Boston University School of Medicine, Boston, MA 02118, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02218, USA
- Center for Emerging Infectious Diseases Policy & Research, Boston University, Boston, MA 02118, USA
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7
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Santosa EK, Lau CM, Sahin M, Leslie CS, Sun JC. 3D Chromatin Dynamics during Innate and Adaptive Immune Memory Acquisition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.16.524322. [PMID: 36711541 PMCID: PMC9882143 DOI: 10.1101/2023.01.16.524322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Immune cells responding to pathogens undergo molecular changes that are intimately linked to genome organization. Recent work has demonstrated that natural killer (NK) and CD8 + T cells experience substantial transcriptomic and epigenetic rewiring during their differentiation from naïve to effector to memory cells. Whether these molecular adaptations are accompanied by changes in three-dimensional (3D) chromatin architecture is unknown. In this study, we combine histone profiling, ATAC-seq, RNA-seq and high-throughput chromatin capture (HiC) assay to investigate the dynamics of one-dimensional (1D) and 3D chromatin during the differentiation of innate and adaptive lymphocytes. To this end, we discovered a coordinated 1D and 3D epigenetic remodeling during innate immune memory differentiation, and demonstrate that effector CD8 + T cells adopt an NK-like architectural program that is maintained in memory cells. Altogether, our study reveals the dynamic nature of the 1D and 3D genome during the formation of innate and adaptive immunological memory.
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Li Y, Ge J, Zhao X, Xu M, Gou M, Xie B, Huang J, Sun Q, Sun L, Bai X, Tan S, Wang X, Dong C. Cell autonomous expression of BCL6 is required to maintain lineage identity of mouse CCR6+ ILC3s. J Exp Med 2023; 220:213808. [PMID: 36651876 PMCID: PMC9856750 DOI: 10.1084/jem.20220440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 11/04/2022] [Accepted: 01/03/2023] [Indexed: 01/19/2023] Open
Abstract
Innate lymphoid cells (ILC) are similar to T helper (Th) cells in expression of cytokines and transcription factors. For example, RORγt is the lineage-specific transcription factor for both ILC3 and Th17 cells. However, the ILC counterpart for BCL6-expressing T follicular helper (Tfh) cells has not been defined. Here, we report that in the ILC compartment, BCL6 is selectively co-expressed with not only CXCR5 but also RORγt and CCR6 in ILC3 from multiple tissues. BCL6-deficient ILC3 produces enhanced levels of IL-17A and IL-22. More importantly, phenotypic and single-cell ATAC-seq analysis show that absence of BCL6 in mature ILC3 increases the numbers of ILC1 and transitional cells co-expressing ILC3 and ILC1 marker genes. A lineage-tracing experiment further reveals BCL6+ ILC3 to ILC1 trans-differentiation under steady state. Finally, microbiota promote BCL6 expression in colonic CCR6+ ILC3 and thus reinforce their stability. Collectively, our data have demonstrated that CCR6+ ILC3 have both Th17 and Tfh programs and that BCL6 expression in these cells functions to maintain their lineage identity.
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Affiliation(s)
- Yuling Li
- Institute for Immunology and School of Medicine, Tsinghua University, Beijing, China,Tsinghua University-Peking University Center for Life Sciences, Tsinghua University, Beijing, China
| | - Jing Ge
- Shanghai Immune Therapy Institute, Shanghai Jiao Tong University School of Medicine-Affiliated Renji Hospital, Shanghai, China
| | - Xiaohong Zhao
- Institute for Immunology and School of Medicine, Tsinghua University, Beijing, China
| | - Miao Xu
- Broad institute of MIT and Harvard, Cambridge, MA, USA
| | - Mengting Gou
- Shanghai Immune Therapy Institute, Shanghai Jiao Tong University School of Medicine-Affiliated Renji Hospital, Shanghai, China
| | - Bowen Xie
- Institute for Immunology and School of Medicine, Tsinghua University, Beijing, China
| | - Jinling Huang
- Institute for Immunology and School of Medicine, Tsinghua University, Beijing, China
| | - Qinli Sun
- Institute for Immunology and School of Medicine, Tsinghua University, Beijing, China
| | - Lin Sun
- Shanghai Immune Therapy Institute, Shanghai Jiao Tong University School of Medicine-Affiliated Renji Hospital, Shanghai, China
| | - Xue Bai
- Institute for Immunology and School of Medicine, Tsinghua University, Beijing, China
| | - Sangnee Tan
- Institute for Immunology and School of Medicine, Tsinghua University, Beijing, China
| | - Xiaohu Wang
- Institute for Immunology and School of Medicine, Tsinghua University, Beijing, China
| | - Chen Dong
- Institute for Immunology and School of Medicine, Tsinghua University, Beijing, China,Tsinghua University-Peking University Center for Life Sciences, Tsinghua University, Beijing, China,Shanghai Immune Therapy Institute, Shanghai Jiao Tong University School of Medicine-Affiliated Renji Hospital, Shanghai, China,Research Unit of Immune Regulation and Immune Diseases of Chinese Academy of Medical Sciences, Shanghai Jiao Tong University School of Medicine-Affiliated Renji Hospital, Shanghai, China,Correspondence to Chen Dong:
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9
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Bonaguro L, Schulte-Schrepping J, Carraro C, Sun LL, Reiz B, Gemünd I, Saglam A, Rahmouni S, Georges M, Arts P, Hoischen A, Joosten LA, van de Veerdonk FL, Netea MG, Händler K, Mukherjee S, Ulas T, Schultze JL, Aschenbrenner AC. Human variation in population-wide gene expression data predicts gene perturbation phenotype. iScience 2022; 25:105328. [PMID: 36310583 PMCID: PMC9614568 DOI: 10.1016/j.isci.2022.105328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 07/13/2022] [Accepted: 10/07/2022] [Indexed: 11/24/2022] Open
Abstract
Population-scale datasets of healthy individuals capture genetic and environmental factors influencing gene expression. The expression variance of a gene of interest (GOI) can be exploited to set up a quasi loss- or gain-of-function "in population" experiment. We describe here an approach, huva (human variation), taking advantage of population-scale multi-layered data to infer gene function and relationships between phenotypes and expression. Within a reference dataset, huva derives two experimental groups with LOW or HIGH expression of the GOI, enabling the subsequent comparison of their transcriptional profile and functional parameters. We demonstrate that this approach robustly identifies the phenotypic relevance of a GOI allowing the stratification of genes according to biological functions, and we generalize this concept to almost 16,000 genes in the human transcriptome. Additionally, we describe how huva predicts monocytes to be the major cell type in the pathophysiology of STAT1 mutations, evidence validated in a clinical cohort.
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Affiliation(s)
- Lorenzo Bonaguro
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), 53127 Bonn, Germany
- Genomics and Immunoregulation, Life and Medical Sciences (LIMES) Institute, University of Bonn, 53113 Bonn, Germany
| | - Jonas Schulte-Schrepping
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), 53127 Bonn, Germany
- Genomics and Immunoregulation, Life and Medical Sciences (LIMES) Institute, University of Bonn, 53113 Bonn, Germany
| | - Caterina Carraro
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), 53127 Bonn, Germany
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, 35131 Padova, Italy
| | - Laura L. Sun
- Genomics and Immunoregulation, Life and Medical Sciences (LIMES) Institute, University of Bonn, 53113 Bonn, Germany
| | | | - Ioanna Gemünd
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), 53127 Bonn, Germany
- Genomics and Immunoregulation, Life and Medical Sciences (LIMES) Institute, University of Bonn, 53113 Bonn, Germany
- Department of Microbiology and Immunology, the University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Parkville, 3010 VIC, Australia
| | - Adem Saglam
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), 53127 Bonn, Germany
| | - Souad Rahmouni
- Unit of Animal Genomics, GIGA-Institute, University of Liège, 4000 Liège, Belgium
| | - Michel Georges
- Unit of Animal Genomics, GIGA-Institute, University of Liège, 4000 Liège, Belgium
| | - Peer Arts
- Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 Nijmegen, the Netherlands
- Department of Genetics and Molecular Pathology, Centre for Cancer Biology, SA Pathology and the University of South Australia, Adelaide, 5000 SA, Australia
| | - Alexander Hoischen
- Department of Human Genetics and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 Nijmegen, the Netherlands
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, 6525 Nijmegen, the Netherlands
| | - Leo A.B. Joosten
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, 6525 Nijmegen, the Netherlands
- Department of Medical Genetics, “Iuliu Hatieganu” University of Medicine and Pharmacy, 400012 Cluj-Napoca, Romania
| | - Frank L. van de Veerdonk
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, 6525 Nijmegen, the Netherlands
| | - Mihai G. Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, 6525 Nijmegen, the Netherlands
- Immunology and Metabolism, Life and Medical Sciences (LIMES) Institute, University of Bonn, 53113 Bonn, Germany
| | - Kristian Händler
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), 53127 Bonn, Germany
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), PRECISE Platform for Genomics and Epigenomics at DZNE and University of Bonn, 53127 Bonn, Germany
| | - Sach Mukherjee
- Statistics and Machine Learning, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), 53127 Bonn, Germany
- MRC Biostatistics Unit, University of Cambridge, Cambridge CB2 0SR, UK
| | - Thomas Ulas
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), 53127 Bonn, Germany
- Genomics and Immunoregulation, Life and Medical Sciences (LIMES) Institute, University of Bonn, 53113 Bonn, Germany
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), PRECISE Platform for Genomics and Epigenomics at DZNE and University of Bonn, 53127 Bonn, Germany
| | - Joachim L. Schultze
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), 53127 Bonn, Germany
- Genomics and Immunoregulation, Life and Medical Sciences (LIMES) Institute, University of Bonn, 53113 Bonn, Germany
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), PRECISE Platform for Genomics and Epigenomics at DZNE and University of Bonn, 53127 Bonn, Germany
| | - Anna C. Aschenbrenner
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), 53127 Bonn, Germany
- Genomics and Immunoregulation, Life and Medical Sciences (LIMES) Institute, University of Bonn, 53113 Bonn, Germany
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, 6525 Nijmegen, the Netherlands
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10
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The RNA helicase DHX15 is a critical regulator of natural killer-cell homeostasis and functions. Cell Mol Immunol 2022; 19:687-701. [PMID: 35322175 DOI: 10.1038/s41423-022-00852-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 02/28/2022] [Indexed: 11/08/2022] Open
Abstract
The RNA helicase DHX15 is widely expressed in immune cells and traditionally thought to be an RNA splicing factor or a viral RNA sensor. However, the role of DHX15 in NK-cell activities has not been studied thus far. Here, we generated Dhx15-floxed mice and found that conditional deletion of Dhx15 in NK cells (Ncr1CreDhx15fl/fl mice) resulted in a marked reduction in NK cells in the periphery and that the remaining Dhx15-deleted NK cells failed to acquire a mature phenotype. As a result, Dhx15-deleted NK cells exhibited profound defects in their cytolytic functions. We also found that deletion of Dhx15 in NK cells abrogated their responsiveness to IL-15, which was associated with inhibition of IL-2/IL-15Rβ (CD122) expression and IL-15R signaling. The defects in Dhx15-deleted NK cells were rescued by ectopic expression of a constitutively active form of STAT5. Mechanistically, DHX15 did not affect CD122 mRNA splicing and stability in NK cells but instead facilitated the surface expression of CD122, likely through interaction with its 3'UTR, which was dependent on the ATPase domain of DHX15 rather than its splicing domain. Collectively, our data identify a key role for DHX15 in regulating NK-cell activities and provide novel mechanistic insights into how DHX15 regulates the IL-15 signaling pathway in NK cells.
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11
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Chen C, Man N, Liu F, Martin GM, Itonaga H, Sun J, Nimer SD. Epigenetic and transcriptional regulation of innate immunity in cancer. Cancer Res 2022; 82:2047-2056. [PMID: 35320354 DOI: 10.1158/0008-5472.can-21-3503] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 02/16/2022] [Accepted: 03/17/2022] [Indexed: 11/16/2022]
Abstract
Innate immune cells participate in the detection of tumor cells via complex signaling pathways mediated by pattern-recognition receptors, such as Toll-like receptors (TLR) and NOD-like receptors (NLR). These pathways are finely tuned via multiple mechanisms, including epigenetic regulation. It is well established that hematopoietic progenitors generate innate immune cells that can regulate cancer cell behavior, and the disruption of normal hematopoiesis in pathologic states may lead to altered immunity and the development of cancer. In this review, we discuss the epigenetic and transcriptional mechanisms that underlie the initiation and amplification of innate immune signaling in cancer. We also discuss new targeting possibilities for cancer control that exploit innate immune cells and signaling molecules, potentially heralding the next generation of immunotherapy.
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Affiliation(s)
- Chuan Chen
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida
| | - Na Man
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida
| | - Fan Liu
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, Florida
| | - Gloria Mas Martin
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida
| | - Hidehiro Itonaga
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida
| | - Jun Sun
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida
| | - Stephen D Nimer
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida
- Department of Medicine, University of Miami Miller School of Medicine, Miami, Florida
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12
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Liu Y, Yuan Q, Wang Z, Ding L, Kong N, Liu J, Hu Y, Zhang Y, Li C, Yan G, Jiang Y, Sun H. A high level of KLF12 causes folic acid-resistant neural tube defects by activating the Shh signalling pathway in mice. Biol Reprod 2021; 105:837-845. [PMID: 34104947 DOI: 10.1093/biolre/ioab111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/26/2021] [Accepted: 06/02/2021] [Indexed: 11/13/2022] Open
Abstract
Although adequate periconceptional folic acid (FA) supplementation has reduced the occurrence of pregnancies affected by neural tube defects (NTDs), the mechanisms underlying FA-resistant NTDs are poorly understood, and thus NTDs still remain a global public health concern. A high level of Krüppel-like factor 12 (KLF12) exerts deleterious effects on heath in most cases, but evidence for its roles in development has not been published. We observed KLF12-overexpressing mice showed disturbed neural tube development. KLF12-overexpressing foetuses died in utero at approximately 10.5 days post coitus, with 100% presenting cranial NTDs. Neither FA nor formate promoted normal neural tube closure in mutant foetuses. The RNA-seq results showed that a high level of KLF12 caused NTDs in mice via overactivating the sonic hedgehog (Shh) signalling pathway, leading to the upregulation of patched 1, GLI-Krüppel family member GLI1, hedgehog-interacting protein, etc., while FA metabolism-related enzymes did not express differently. PF-5274857, an antagonist of the Shh signalling pathway, significantly promoted dorsolateral hinge point formation and partially rescued the NTDs. The regulatory hierarchy between a high level of KLF12 and FA-resistant NTDs might provide new insights into the diagnosis and treatment of unexplained NTDs in the future.
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Affiliation(s)
- Yang Liu
- Reproductive Medicine Center, the Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing 210008, Jiangsu, People's Republic of China.,Center for Molecular Reproductive Medicine, Nanjing University, Nanjing 210008, Jiangsu, People's Republic of China
| | - Qiong Yuan
- Department of Obstetrics and Gynecology, the Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing 210008, Jiangsu, People's Republic of China
| | - Zhilong Wang
- Reproductive Medicine Center, the Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing 210008, Jiangsu, People's Republic of China.,Center for Molecular Reproductive Medicine, Nanjing University, Nanjing 210008, Jiangsu, People's Republic of China
| | - Lijun Ding
- Reproductive Medicine Center, the Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing 210008, Jiangsu, People's Republic of China
| | - Na Kong
- Reproductive Medicine Center, the Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing 210008, Jiangsu, People's Republic of China
| | - Jingyu Liu
- Reproductive Medicine Center, the Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing 210008, Jiangsu, People's Republic of China
| | - Yali Hu
- Reproductive Medicine Center, the Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing 210008, Jiangsu, People's Republic of China
| | - Yang Zhang
- Reproductive Medicine Center, the Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing 210008, Jiangsu, People's Republic of China
| | - Chaojun Li
- Reproductive Medicine Center, the Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing 210008, Jiangsu, People's Republic of China
| | - Guijun Yan
- Reproductive Medicine Center, the Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing 210008, Jiangsu, People's Republic of China.,Center for Molecular Reproductive Medicine, Nanjing University, Nanjing 210008, Jiangsu, People's Republic of China
| | - Yue Jiang
- Reproductive Medicine Center, the Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing 210008, Jiangsu, People's Republic of China
| | - Haixiang Sun
- Reproductive Medicine Center, the Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing 210008, Jiangsu, People's Republic of China.,Center for Molecular Reproductive Medicine, Nanjing University, Nanjing 210008, Jiangsu, People's Republic of China.,State Key Laboratory of Pharmaceutical Biotechnology, Department of Reproductive Medicine Center, the Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing 210008, Jiangsu, People's Republic of China
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13
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Fan Y, Liu M, Liu A, Cui N, Chen Z, Yang Q, Su A. Depletion of Circular RNA circ_CORO1C Suppresses Gastric Cancer Development by Modulating miR-138-5p/KLF12 Axis. Cancer Manag Res 2021; 13:3789-3801. [PMID: 34007212 PMCID: PMC8123969 DOI: 10.2147/cmar.s290629] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 02/05/2021] [Indexed: 12/24/2022] Open
Abstract
Background Gastric cancer (GC) is a common and deadly malignancy in the world. CircRNAs have emerged as important regulators in human diseases, including GC. In this work, we intended to explore the role of circ_CORO1C in GC progression and potential mechanism. Methods Quantitative real-time PCR (qRT-PCR) or Western blot assay was performed to examine the expression of circRNA coronin-like actin-binding protein 1C (circ_CORO1C), microRNA (miR)-138-5p and Krueppel-like factor 12 (KLF12) in clinical samples and cells. Cell colony formation ability and viability were measured by colony formation assay and methyl thiazolyl tetrazolium (MTT) assay, respectively. Expression of cell proliferation and epithelia-mesenchymal transition (EMT) biomarker was detected by Western blot analysis. And cell metastasis, including migration and invasion, and apoptosis were analyzed via Transwell assay and flow cytometry, respectively. Target relationship among circ_CORO1C, miR-138-5p and KLF12 was validated by dual-luciferase reporter assay. The in vivo role of circ_CORO1C was investigated by tumor xenograft assay. Results Circ_CORO1C and KLF12 were upregulated, while miR-138-5p was downregulated in GC tissues and cells. Circ_CORO1C knockdown suppressed colony formation ability, viability, migration, invasion and EMT in GC cells, while promoted cell apoptosis in vitro. Circ_CORO1C targeted miR-138-5p, the inhibition of which could attenuate silenced circ_CORO1C-induced inhibitory effects on GC progression. MiR-138-5p repressed the aggressive malignant behaviors of GC cells by directly targeting KLF12. Circ_CORO1C deficiency inhibited GC tumor growth in vivo. Conclusion Depletion of circ_CORO1C suppressed GC progression by regulating miR-138-5p/KLF12 axis, offering a potential molecular target for GC therapy.
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Affiliation(s)
- Yongqiang Fan
- Department of Gastroenterology, Sunshine Union Hospital, Weifang City, Shandong Province, People's Republic of China
| | - Min Liu
- Department of Gastroenterology, Sunshine Union Hospital, Weifang City, Shandong Province, People's Republic of China
| | - Anquan Liu
- Department of Gastroenterology, Sunshine Union Hospital, Weifang City, Shandong Province, People's Republic of China
| | - Nailing Cui
- Department of Gastroenterology, Weifang Medical University, Weifang City, Shandong Province, People's Republic of China
| | - Zhimei Chen
- Department of Gastroenterology, Sunshine Union Hospital, Weifang City, Shandong Province, People's Republic of China
| | - Qian Yang
- Department of Gastroenterology, Sunshine Union Hospital, Weifang City, Shandong Province, People's Republic of China
| | - Aihua Su
- Department of Emergency, Affiliated Hospital of Weifang Medical University, Weifang City, Shandong Province, People's Republic of China
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14
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Leylek R, Alcántara-Hernández M, Granja JM, Chavez M, Perez K, Diaz OR, Li R, Satpathy AT, Chang HY, Idoyaga J. Chromatin Landscape Underpinning Human Dendritic Cell Heterogeneity. Cell Rep 2021; 32:108180. [PMID: 32966789 PMCID: PMC7546547 DOI: 10.1016/j.celrep.2020.108180] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 06/18/2020] [Accepted: 09/01/2020] [Indexed: 12/16/2022] Open
Abstract
Human dendritic cells (DCs) comprise subsets with distinct phenotypic and functional characteristics, but the transcriptional programs that dictate their identity remain elusive. Here, we analyze global chromatin accessibility profiles across resting and stimulated human DC subsets by means of the assay for transposase-accessible chromatin using sequencing (ATAC-seq). We uncover specific regions of chromatin accessibility for each subset and transcriptional regulators of DC function. By comparing plasmacytoid DC responses to IFN-I-producing and non-IFN-I-producing conditions, we identify genetic programs related to their function. Finally, by intersecting chromatin accessibility with genome-wide association studies, we recognize DC subset-specific enrichment of heritability in autoimmune diseases. Our results unravel the basis of human DC subset heterogeneity and provide a framework for their analysis in disease pathogenesis. Human dendritic cells (DCs) orchestrate immune responses by a division of labor between functionally specialized subsets; however, the transcriptional basis of this heterogeneity is poorly understood. Using ATAC-seq, Leylek et al. profile the chromatin landscape of human DC subsets, providing insight into the underlying regulatory mechanisms that modulate their function.
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Affiliation(s)
- Rebecca Leylek
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Immunology Program, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Marcela Alcántara-Hernández
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Immunology Program, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jeffrey M Granja
- Biophysics Program, Stanford University School of Medicine, Stanford, CA 94305, USA; Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Michael Chavez
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Kimberly Perez
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Immunology Program, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Oscar R Diaz
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Rui Li
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ansuman T Satpathy
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Juliana Idoyaga
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA; Immunology Program, Stanford University School of Medicine, Stanford, CA 94305, USA.
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15
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Abstract
Natural killer (NK) cells are innate lymphocytes that provide critical host defense against pathogens and cancer. Originally heralded for their early and rapid effector activity, NK cells have been recognized over the last decade for their ability to undergo adaptive immune processes, including antigen-driven clonal expansion and generation of long-lived memory. This review presents an overview of how NK cells lithely partake in both innate and adaptive responses and how this versatility is manifest in human NK cell-mediated immunity.
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Affiliation(s)
- Adriana M Mujal
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA;
| | - Rebecca B Delconte
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA;
| | - Joseph C Sun
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; .,Department of Immunology and Microbial Pathogenesis, Weill Cornell Medical College, New York, NY 10065, USA
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16
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Zhang S, Zheng W, Jiang D, Xiong H, Liao G, Yang X, Ma H, Li J, Qiu M, Li B, Sun C, Zhao J, Wang L, Pang J. Systematic Chromatin Accessibility Analysis Based on Different Immunological Subtypes of Clear Cell Renal Cell Carcinoma. Front Oncol 2021; 11:575425. [PMID: 33937014 PMCID: PMC8085385 DOI: 10.3389/fonc.2021.575425] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 03/23/2021] [Indexed: 01/14/2023] Open
Abstract
Background Recent research of clear cell renal cell carcinoma (ccRCC) is focused on the tumor immune microenvironment (TIME). Chromatin accessibility is critical for regulation of gene expression. However, its role in different immunological subtypes of ccRCC based on immune cell infiltration has not been systematically studied. Methods Five hundred thirty patient data from The Cancer Genome Atlas Kidney Renal Clear Cell Carcinoma (TCGA-KIRC) were adopted to estimate immune cell infiltration. Twenty-four types of immune cells were evaluated with single-sample Gene Set Enrichment Analysis (ssGSEA). Patients were divided into two clusters based on immune cell infiltration. Systematic chromatin accessibility analysis was conducted based on the two clusters. Results We compared the relative expression of the immune gene signatures among 530 patients of TCGA-KIRC using ssGSEA. Overall survival (OS) analysis revealed 10 types of immune cells were significantly associated with prognosis. Patients were divided into two clusters based on 24 types of immune cell infiltration. Immune cell signals as well as PD-1/PD-L1 signal were higher in cluster 1. Among the two clusters, 2,400 differential peaks were found in TCGA-KIRC Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq) data. The distribution of differential peaks and prognosis-related immune cells in 23 chromosomes are essentially the same. There is no peak distribution downstream. The proportion of peaks upstream of the 5’ transcription start site decreases, and both sides of binding regions of the TSS 0.1-1 kb becomes smaller. Enrichment analysis of GO and KEGG of these differential peaks showed that they are remarkably related to the immune regulation in tumor microenvironment. Known motifs and de novo motifs were found by linking motif annotations to different peaks. Survival analysis of related motif transcription factors were prognostic. The GSEA enrichment analysis showed that high SP1 expression positively correlates with TGF-beta signaling and inflammatory response, while negatively correlates with TNF-alpha signaling via NFKB. High KLF12 expression negatively correlates with interferon gamma response, IL2-STAT5 signaling, TNF-alpha signaling via NFKB, IL6-JAK-STAT3 signaling. Conclusion The abnormality of chromatin accessibility may play an important regulatory role in ccRCC immunity.
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Affiliation(s)
- Shiqiang Zhang
- Department of Urology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Wenzhong Zheng
- Department of Urology, Fujian Medical University Union Hospital, Fuzhou, China
| | - Donggen Jiang
- Department of Urology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Haiyun Xiong
- Department of Urology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Guolong Liao
- Department of Urology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Xiangwei Yang
- Department of Urology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - He Ma
- Department of Urology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Jun Li
- Department of Urology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Miaojuan Qiu
- Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Binbin Li
- Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Chunhui Sun
- Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Jing Zhao
- Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Liling Wang
- Maternal and Child Health Research Institute, Baoan Women's and Children's Hospital, Jinan University, Shenzhen, China
| | - Jun Pang
- Department of Urology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
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17
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Beaulieu AM. Transcriptional and epigenetic regulation of memory NK cell responses. Immunol Rev 2021; 300:125-133. [PMID: 33491231 DOI: 10.1111/imr.12947] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 12/28/2020] [Accepted: 12/31/2020] [Indexed: 12/14/2022]
Abstract
Natural killer (NK) cells are cytotoxic innate lymphocytes with key roles in host protection against viruses and malignancy. Notwithstanding their historical classification as innate immune cells, NK cells are now understood to have some capacity to mount memory or memory-like immune responses in which effector cells undergo antigen-driven expansion and give rise to long-lived memory cells with enhanced functionality. Understanding how antigen-specific effector and memory NK responses are regulated is an important and active area of research in the field. Here, we discuss key transcription factors and epigenetic processes involved in antigen-specific effector and memory NK cell differentiation.
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Affiliation(s)
- Aimee M Beaulieu
- Center for Immunity and Inflammation, New Jersey Medical School, Rutgers Biomedical and Health Sciences, Rutgers - The State University of New Jersey, Newark, NJ, USA.,Department of Microbiology, Biochemistry, and Molecular Genetics, New Jersey Medical School, Rutgers Biomedical and Health Sciences, Rutgers - The State University of New Jersey, Newark, NJ, USA
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18
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Meta-Analysis of Transcriptome Data Detected New Potential Players in Response to Dioxin Exposure in Humans. Int J Mol Sci 2020; 21:ijms21217858. [PMID: 33113971 PMCID: PMC7672605 DOI: 10.3390/ijms21217858] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 10/18/2020] [Accepted: 10/21/2020] [Indexed: 12/26/2022] Open
Abstract
Dioxins are one of the most potent anthropogenic poisons, causing systemic disorders in embryonic development and pathologies in adults. The mechanism of dioxin action requires an aryl hydrocarbon receptor (AhR), but the downstream mechanisms are not yet precisely clear. Here, we performed a meta-analysis of all available transcriptome datasets taken from human cell cultures exposed to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). Differentially expressed genes from different experiments overlapped partially, but there were a number of those genes that were systematically affected by TCDD. Some of them have been linked to toxic dioxin effects, but we also identified other attractive targets. Among the genes that were affected by TCDD, there are functionally related gene groups that suggest an interplay between retinoic acid, AhR, and Wnt signaling pathways. Next, we analyzed the upstream regions of differentially expressed genes and identified potential transcription factor (TF) binding sites overrepresented in the genes responding to TCDD. Intriguingly, the dioxin-responsive element (DRE), the binding site of AhR, was not overrepresented as much as other cis-elements were. Bioinformatics analysis of the AhR binding profile unveils potential cooperation of AhR with E2F2, CTCFL, and ZBT14 TFs in the dioxin response. We discuss the potential implication of these predictions for further dioxin studies.
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19
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García M, López-Fernández L, Mínguez P, Morón-López S, Restrepo C, Navarrete-Muñoz MA, López-Bernaldo JC, Benguría A, García MI, Cabello A, Fernández-Guerrero M, De la Hera FJ, Estrada V, Barros C, Martínez-Picado J, Górgolas M, Benito JM, Rallón N. Transcriptional signature of resting-memory CD4 T cells differentiates spontaneous from treatment-induced HIV control. J Mol Med (Berl) 2020; 98:1093-1105. [PMID: 32556382 DOI: 10.1007/s00109-020-01930-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 05/04/2020] [Accepted: 05/25/2020] [Indexed: 01/29/2023]
Abstract
The HIV reservoir is the main barrier to eradicating HIV infection, and resting memory CD4 T (Trm) cells are one of the most relevant cellular component harboring latent proviruses. This is the first study analyzing the transcriptional profile of Trm cells, in two well-characterized groups of HIV patients with distinct mechanisms of viral replication control (spontaneous versus treatment-induced). We use a systems biology approach to unravel subtle but important differences in the molecular mechanisms operating at the cellular level that could be associated with the host's ability to control virus replication and persistence. Despite the absence of significant differences in the transcriptome of Trm cells between Elite Controllers (ECs) and cART-treated (TX) patients at the single gene level, we found 353 gene ontology (GO) categories upregulated in EC compared with TX. Our results suggest the existence of mechanisms at two different levels: first boosting both adaptive and innate immune responses, and second promoting active viral replication and halting HIV latency in the Trm cell compartment of ECs as compared with TX patients. These differences in the transcriptional profile of Trm cells could be involved in the lower HIV reservoir observed in ECs compared with TX individuals, although mechanistic studies are needed to confirm this hypothesis. Combining transcriptome analysis and systems biology methods is likely to provide important findings to help us in the design of therapeutic strategies aimed at purging the HIV reservoir. KEY MESSAGES: HIV-elite controllers have the lowest HIV-DNA content in resting memory CD4 T cells. HIV-ECs show a particular transcriptional profile in resting memory CD4 T cells. Molecular mechanisms of enhanced adaptative and innate immune response in HIV-ECs. High viral replication and low viral latency establishment associate to the EC status.
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Affiliation(s)
- Marcial García
- HIV and Viral Hepatitis Research Laboratory, Instituto de Investigación Sanitaria Fundación Jiménez Díaz, Universidad Autónoma de Madrid (IIS-FJD, UAM), Av. Reyes Católicos, 2, 28040, Madrid, Spain.,Hospital Universitario Rey Juan Carlos, Móstoles, Spain
| | - Luis López-Fernández
- Pharmacy Department, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Pablo Mínguez
- Bioinformatics Unit, Genetics Department, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD), Madrid, Spain
| | | | - Clara Restrepo
- HIV and Viral Hepatitis Research Laboratory, Instituto de Investigación Sanitaria Fundación Jiménez Díaz, Universidad Autónoma de Madrid (IIS-FJD, UAM), Av. Reyes Católicos, 2, 28040, Madrid, Spain.,Hospital Universitario Rey Juan Carlos, Móstoles, Spain
| | - María A Navarrete-Muñoz
- HIV and Viral Hepatitis Research Laboratory, Instituto de Investigación Sanitaria Fundación Jiménez Díaz, Universidad Autónoma de Madrid (IIS-FJD, UAM), Av. Reyes Católicos, 2, 28040, Madrid, Spain.,Hospital Universitario Rey Juan Carlos, Móstoles, Spain
| | | | - Alberto Benguría
- Genomics Unit, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - María Isabel García
- Pharmacy Department, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Alfonso Cabello
- Hospital Universitario Fundación Jiménez Díaz, Madrid, Spain
| | | | | | | | | | - Javier Martínez-Picado
- irsiCaixa AIDS Research Institute, Badalona, Spain.,University of Vic-Central University of Catalonia (UVic-UCC), Vic, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Miguel Górgolas
- Hospital Universitario Fundación Jiménez Díaz, Madrid, Spain
| | - José M Benito
- HIV and Viral Hepatitis Research Laboratory, Instituto de Investigación Sanitaria Fundación Jiménez Díaz, Universidad Autónoma de Madrid (IIS-FJD, UAM), Av. Reyes Católicos, 2, 28040, Madrid, Spain. .,Hospital Universitario Rey Juan Carlos, Móstoles, Spain.
| | - Norma Rallón
- HIV and Viral Hepatitis Research Laboratory, Instituto de Investigación Sanitaria Fundación Jiménez Díaz, Universidad Autónoma de Madrid (IIS-FJD, UAM), Av. Reyes Católicos, 2, 28040, Madrid, Spain. .,Hospital Universitario Rey Juan Carlos, Móstoles, Spain.
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20
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Abstract
One of the hallmarks of the vertebrate adaptive immune system is the prolific expansion of individual cell clones that encounter their cognate antigen. More recently, however, there is growing evidence for the clonal expansion of innate lymphocytes, particularly in the context of pathogen challenge. Clonal expansion not only serves to amplify the number of specific lymphocytes to mount a robust protective response to the pathogen at hand but also results in selection and differentiation of the responding lymphocytes to generate a multitude of cell fates. Here, we summarize the evidence for clonal expansion in innate lymphocytes, which has primarily been observed in natural killer (NK) cells responding to cytomegalovirus infection, and consider the requirements for such a response in NK cells in light of those for T cells. Furthermore, we discuss multiple aspects of heterogeneity that both contribute to and result from the fundamental immunological process of clonal expansion, highlighting the parallels between innate and adaptive lymphocytes, with a particular focus on NK cells and CD8+ T cells.
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21
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Corrigan JK, Ramachandran D, He Y, Palmer CJ, Jurczak MJ, Chen R, Li B, Friedline RH, Kim JK, Ramsey JJ, Lantier L, McGuinness OP, Banks AS. A big-data approach to understanding metabolic rate and response to obesity in laboratory mice. eLife 2020; 9:e53560. [PMID: 32356724 PMCID: PMC7274785 DOI: 10.7554/elife.53560] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 04/30/2020] [Indexed: 12/21/2022] Open
Abstract
Maintaining a healthy body weight requires an exquisite balance between energy intake and energy expenditure. To understand the genetic and environmental factors that contribute to the regulation of body weight, an important first step is to establish the normal range of metabolic values and primary sources contributing to variability. Energy metabolism is measured by powerful and sensitive indirect calorimetry devices. Analysis of nearly 10,000 wild-type mice from two large-scale experiments revealed that the largest variation in energy expenditure is due to body composition, ambient temperature, and institutional site of experimentation. We also analyze variation in 2329 knockout strains and establish a reference for the magnitude of metabolic changes. Based on these findings, we provide suggestions for how best to design and conduct energy balance experiments in rodents. These recommendations will move us closer to the goal of a centralized physiological repository to foster transparency, rigor and reproducibility in metabolic physiology experimentation.
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Affiliation(s)
- June K Corrigan
- Division of Endocrinology, Diabetes and Metabolism, Beth Israel Deaconess Medical Center and Harvard Medical SchoolBostonUnited States
| | - Deepti Ramachandran
- Division of Endocrinology, Diabetes and Metabolism, Beth Israel Deaconess Medical Center and Harvard Medical SchoolBostonUnited States
| | - Yuchen He
- Division of Endocrinology, Diabetes and Metabolism, Beth Israel Deaconess Medical Center and Harvard Medical SchoolBostonUnited States
| | - Colin J Palmer
- Division of Endocrinology, Diabetes and Metabolism, Beth Israel Deaconess Medical Center and Harvard Medical SchoolBostonUnited States
| | - Michael J Jurczak
- Division of Endocrinology, Yale University School of MedicineNew HavenUnited States
| | - Rui Chen
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of MedicineNashvilleUnited States
| | - Bingshan Li
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of MedicineNashvilleUnited States
| | - Randall H Friedline
- Program in Molecular Medicine, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Jason K Kim
- Program in Molecular Medicine, University of Massachusetts Medical SchoolWorcesterUnited States
- Division of Endocrinology, Metabolism, and Diabetes, Department of Medicine, University of Massachusetts Medical SchoolWorcesterUnited States
| | - Jon J Ramsey
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, DavisDavisUnited States
| | - Louise Lantier
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of MedicineNashvilleUnited States
| | - Owen P McGuinness
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of MedicineNashvilleUnited States
| | - Mouse Metabolic Phenotyping Center Energy Balance Working Group
- Division of Endocrinology, Diabetes and Metabolism, Beth Israel Deaconess Medical Center and Harvard Medical SchoolBostonUnited States
- Division of Endocrinology, Yale University School of MedicineNew HavenUnited States
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of MedicineNashvilleUnited States
- Program in Molecular Medicine, University of Massachusetts Medical SchoolWorcesterUnited States
- Division of Endocrinology, Metabolism, and Diabetes, Department of Medicine, University of Massachusetts Medical SchoolWorcesterUnited States
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, DavisDavisUnited States
| | - Alexander S Banks
- Division of Endocrinology, Diabetes and Metabolism, Beth Israel Deaconess Medical Center and Harvard Medical SchoolBostonUnited States
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22
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Netea MG, Domínguez-Andrés J, Barreiro LB, Chavakis T, Divangahi M, Fuchs E, Joosten LAB, van der Meer JWM, Mhlanga MM, Mulder WJM, Riksen NP, Schlitzer A, Schultze JL, Stabell Benn C, Sun JC, Xavier RJ, Latz E. Defining trained immunity and its role in health and disease. Nat Rev Immunol 2020; 20:375-388. [PMID: 32132681 PMCID: PMC7186935 DOI: 10.1038/s41577-020-0285-6] [Citation(s) in RCA: 1228] [Impact Index Per Article: 307.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/24/2020] [Indexed: 12/14/2022]
Abstract
Immune memory is a defining feature of the acquired immune system, but activation of the innate immune system can also result in enhanced responsiveness to subsequent triggers. This process has been termed ‘trained immunity’, a de facto innate immune memory. Research in the past decade has pointed to the broad benefits of trained immunity for host defence but has also suggested potentially detrimental outcomes in immune-mediated and chronic inflammatory diseases. Here we define ‘trained immunity’ as a biological process and discuss the innate stimuli and the epigenetic and metabolic reprogramming events that shape the induction of trained immunity. Here a group of leaders in the field define our current understanding of ‘trained immunity’, which refers to the memory-type responses that occur in the innate immune system. The authors discuss our current understanding of the key epigenetic and metabolic processes involved in trained immunity and consider its relevance in immune-mediated diseases and cancer.
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Affiliation(s)
- Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands. .,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands. .,Department of Genomics and Immunoregulation, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany.
| | - Jorge Domínguez-Andrés
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands.,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Luis B Barreiro
- Department of Genetics, CHU Sainte-Justine Research Centre, Montreal, QC, Canada.,Department of Pediatrics, University of Montreal, Montreal, QC, Canada.,Genetics Section, Department of Medicine, The University of Chicago, Chicago, IL, USA
| | - Triantafyllos Chavakis
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital and Faculty of Medicine Carl Gustav Carus of TU Dresden, Dresden, Germany.,Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Maziar Divangahi
- Meakins-Christie Laboratories, Department of Medicine, McGill University Health Centre, Montreal, QC, Canada.,Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada.,McGill International TB Centre, McGill University Health Centre, Montreal, QC, Canada
| | - Elaine Fuchs
- Howard Hughes Medical Institute, Robin Chemers Laboratory of Mammalian Cell Biology and Development, The Rockefeller University, New York, NY, USA
| | - Leo A B Joosten
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands.,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Jos W M van der Meer
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands.,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Musa M Mhlanga
- Division of Chemical and Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.,Gene Expression and Biophysics Unit, Instituto de Medicina Molecular, Faculdade de Medicina Universidade de Lisboa, Lisbon, Portugal
| | - Willem J M Mulder
- Translational and Molecular Imaging Institute, Department of Radiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, Netherlands
| | - Niels P Riksen
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, Netherlands.,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Andreas Schlitzer
- Myeloid Cell Biology, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - Joachim L Schultze
- Department of Genomics and Immunoregulation, Life and Medical Sciences Institute, University of Bonn, Bonn, Germany
| | - Christine Stabell Benn
- Bandim Health Project, OPEN, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Joseph C Sun
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Immunology and Microbial Pathogenesis, Weill Cornell Medical College, New York, NY, USA
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Eicke Latz
- Institute of Innate Immunity, University Hospital, University of Bonn, Bonn, Germany. .,Division of Infectious Diseases and Immunology, University of Massachusetts Medical School, Worcester, MA, USA. .,German Center for Neurodegenerative Diseases, Bonn, Germany.
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