1
|
Lee SJ, Noh SE, Jo DH, Cho CS, Park KS, Kim JH. IL-10-induced modulation of macrophage polarization suppresses outer-blood-retinal barrier disruption in the streptozotocin-induced early diabetic retinopathy mouse model. FASEB J 2024; 38:e23638. [PMID: 38713098 DOI: 10.1096/fj.202400053r] [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: 01/10/2024] [Revised: 03/26/2024] [Accepted: 04/18/2024] [Indexed: 05/08/2024]
Abstract
Diabetic retinopathy (DR) is associated with ocular inflammation leading to retinal barrier breakdown, vascular leakage, macular edema, and vision loss. DR is not only a microvascular disease but also involves retinal neurodegeneration, demonstrating that pathological changes associated with neuroinflammation precede microvascular injury in early DR. Macrophage activation plays a central role in neuroinflammation. During DR, the inflammatory response depends on the polarization of retinal macrophages, triggering pro-inflammatory (M1) or anti-inflammatory (M2) activity. This study aimed to determine the role of macrophages in vascular leakage through the tight junction complexes of retinal pigment epithelium, which is the outer blood-retinal barrier (BRB). Furthermore, we aimed to assess whether interleukin-10 (IL-10), a representative M2-inducer, can decrease inflammatory macrophages and alleviate outer-BRB disruption. We found that modulation of macrophage polarization affects the structural and functional integrity of ARPE-19 cells in a co-culture system under high-glucose conditions. Furthermore, we demonstrated that intravitreal IL-10 injection induces an increase in the ratio of anti-inflammatory macrophages and effectively suppresses outer-BRB disruption and vascular leakage in a mouse model of early-stage streptozotocin-induced diabetes. Our results suggest that modulation of macrophage polarization by IL-10 administration during early-stage DR has a promising protective effect against outer-BRB disruption and vascular leakage. This finding provides valuable insights for early intervention in DR.
Collapse
Affiliation(s)
- Seok Jae Lee
- Fight against Angiogenesis-Related Blindness (FARB) Laboratory, Clinical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
- Global Excellence Center for Gene & Cell Therapy (GEC-GCT), Seoul National University Hospital, Seoul, Republic of Korea
| | - Sung-Eun Noh
- Fight against Angiogenesis-Related Blindness (FARB) Laboratory, Clinical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
- Global Excellence Center for Gene & Cell Therapy (GEC-GCT), Seoul National University Hospital, Seoul, Republic of Korea
| | - Dong Hyun Jo
- Global Excellence Center for Gene & Cell Therapy (GEC-GCT), Seoul National University Hospital, Seoul, Republic of Korea
- Department of Anatomy & Cell Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Chang Sik Cho
- Fight against Angiogenesis-Related Blindness (FARB) Laboratory, Clinical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
- Global Excellence Center for Gene & Cell Therapy (GEC-GCT), Seoul National University Hospital, Seoul, Republic of Korea
| | - Kyu-Sang Park
- Department of Physiology, Yonsei University Wonju College of Medicine, Wonju, Republic of Korea
| | - Jeong Hun Kim
- Fight against Angiogenesis-Related Blindness (FARB) Laboratory, Clinical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
- Global Excellence Center for Gene & Cell Therapy (GEC-GCT), Seoul National University Hospital, Seoul, Republic of Korea
- Department of Biomedical Sciences & Ophthalmology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Institute of Reproductive Medicine and Population, Seoul National University College of Medicine, Seoul, Republic of Korea
| |
Collapse
|
2
|
Park SJ, Ju S, Goh SH, Yoon BH, Park JL, Kim JH, Lee S, Lee SJ, Kwon Y, Lee W, Park KC, Lee GK, Park SY, Kim S, Kim SY, Han JY, Lee C. Proteogenomic Characterization Reveals Estrogen Signaling as a Target for Never-Smoker Lung Adenocarcinoma Patients without EGFR or ALK Alterations. Cancer Res 2024; 84:1491-1503. [PMID: 38607364 DOI: 10.1158/0008-5472.can-23-1551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 10/24/2023] [Accepted: 01/18/2024] [Indexed: 04/13/2024]
Abstract
Never-smoker lung adenocarcinoma (NSLA) is prevalent in Asian populations, particularly in women. EGFR mutations and anaplastic lymphoma kinase (ALK) fusions are major genetic alterations observed in NSLA, and NSLA with these alterations have been well studied and can be treated with targeted therapies. To provide insights into the molecular profile of NSLA without EGFR and ALK alterations (NENA), we selected 141 NSLA tissues and performed proteogenomic characterization, including whole genome sequencing (WGS), transcriptomic, methylation EPIC array, total proteomic, and phosphoproteomic analyses. Forty patients with NSLA harboring EGFR and ALK alterations and seven patients with NENA with microsatellite instability were excluded. Genome analysis revealed that TP53 (25%), KRAS (22%), and SETD2 (11%) mutations and ROS1 fusions (14%) were the most frequent genetic alterations in NENA patients. Proteogenomic impact analysis revealed that STK11 and ERBB2 somatic mutations had broad effects on cancer-associated genes in NENA. DNA copy number alteration analysis identified 22 prognostic proteins that influenced transcriptomic and proteomic changes. Gene set enrichment analysis revealed estrogen signaling as the key pathway activated in NENA. Increased estrogen signaling was associated with proteogenomic alterations, such as copy number deletions in chromosomes 14 and 21, STK11 mutation, and DNA hypomethylation of LLGL2 and ST14. Finally, saracatinib, an Src inhibitor, was identified as a potential drug for targeting activated estrogen signaling in NENA and was experimentally validated in vitro. Collectively, this study enhanced our understanding of NENA NSLA by elucidating the proteogenomic landscape and proposed saracatinib as a potential treatment for this patient population that lacks effective targeted therapies. SIGNIFICANCE The proteogenomic landscape in never-smoker lung cancer without known driver mutations reveals prognostic proteins and enhanced estrogen signaling that can be targeted as a potential therapeutic strategy to improve patient outcomes.
Collapse
Affiliation(s)
- Seung-Jin Park
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Department of Bioscience, University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Shinyeong Ju
- Chemical and Biological Integrative Research Center, Korea Institute of Science and Technology, Seoul, Republic of Korea
| | - Sung-Ho Goh
- National Cancer Center, Goyang, Republic of Korea
| | - Byoung-Ha Yoon
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Jong-Lyul Park
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Jeong-Hwan Kim
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Seonjeong Lee
- Chemical and Biological Integrative Research Center, Korea Institute of Science and Technology, Seoul, Republic of Korea
- Division of Bio-Medical Science and Technology, KIST School, University of Science and Technology, Seoul, Republic of Korea
| | - Sang-Jin Lee
- National Cancer Center, Goyang, Republic of Korea
| | - Yumi Kwon
- Chemical and Biological Integrative Research Center, Korea Institute of Science and Technology, Seoul, Republic of Korea
| | - Wonyeop Lee
- National Cancer Center, Goyang, Republic of Korea
| | - Kyung Chan Park
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Department of Bioscience, University of Science and Technology (UST), Daejeon, Republic of Korea
| | | | | | - Sunshin Kim
- National Cancer Center, Goyang, Republic of Korea
| | - Seon-Young Kim
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Department of Bioscience, University of Science and Technology (UST), Daejeon, Republic of Korea
- Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Ji-Youn Han
- National Cancer Center, Goyang, Republic of Korea
| | - Cheolju Lee
- Chemical and Biological Integrative Research Center, Korea Institute of Science and Technology, Seoul, Republic of Korea
- Division of Bio-Medical Science and Technology, KIST School, University of Science and Technology, Seoul, Republic of Korea
| |
Collapse
|
3
|
Seo Y, Rhim J, Kim JH. RNA-binding proteins and exoribonucleases modulating miRNA in cancer: the enemy within. Exp Mol Med 2024:10.1038/s12276-024-01224-z. [PMID: 38689093 DOI: 10.1038/s12276-024-01224-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 02/20/2024] [Accepted: 02/25/2024] [Indexed: 05/02/2024] Open
Abstract
Recent progress in the investigation of microRNA (miRNA) biogenesis and the miRNA processing machinery has revealed previously unknown roles of posttranscriptional regulation in gene expression. The molecular mechanistic interplay between miRNAs and their regulatory factors, RNA-binding proteins (RBPs) and exoribonucleases, has been revealed to play a critical role in tumorigenesis. Moreover, recent studies have shown that the proliferation of hepatocellular carcinoma (HCC)-causing hepatitis C virus (HCV) is also characterized by close crosstalk of a multitude of host RBPs and exoribonucleases with miR-122 and its RNA genome, suggesting the importance of the mechanistic interplay among these factors during the proliferation of HCV. This review primarily aims to comprehensively describe the well-established roles and discuss the recently discovered understanding of miRNA regulators, RBPs and exoribonucleases, in relation to various cancers and the proliferation of a representative cancer-causing RNA virus, HCV. These have also opened the door to the emerging potential for treating cancers as well as HCV infection by targeting miRNAs or their respective cellular modulators.
Collapse
Affiliation(s)
- Yoona Seo
- Cancer Molecular Biology Branch, Research Institute, National Cancer Center, Goyang, 10408, Korea
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, 10408, Korea
| | - Jiho Rhim
- Cancer Molecular Biology Branch, Research Institute, National Cancer Center, Goyang, 10408, Korea
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, 10408, Korea
| | - Jong Heon Kim
- Cancer Molecular Biology Branch, Research Institute, National Cancer Center, Goyang, 10408, Korea.
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, 10408, Korea.
| |
Collapse
|
4
|
Ko SR, Lee S, Koo H, Seo H, Yu J, Kim YM, Kwon SY, Shin AY. High-quality chromosome-level genome assembly of Nicotiana benthamiana. Sci Data 2024; 11:386. [PMID: 38627408 PMCID: PMC11021556 DOI: 10.1038/s41597-024-03232-0] [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: 12/18/2023] [Accepted: 04/05/2024] [Indexed: 04/19/2024] Open
Abstract
Nicotiana benthamiana is a fundamental model organism in plant research. Recent advancements in genomic sequencing have revealed significant intraspecific genetic variations. This study addresses the pressing need for a precise genome sequence specific to its geographic origin by presenting a comprehensive genome assembly of the N. benthamiana LAB strain from the Republic of Korea (NbKLAB). We compare this assembly with the widely used NbLAB360 strain, shedding light on essential genomic differences between them. The outcome is a high-quality, chromosome-level genome assembly comprising 19 chromosomes, spanning 2,762 Mb, with an N50 of 142.6 Mb. Comparative analyses revealed notable variations, including 46,215 protein-coding genes, with an impressive 99.5% BUSCO completeness score. Furthermore, the NbKLAB assembly substantially improved the QV from 33% for NbLAB360 to 49%. This refined chromosomal genome assembly for N. benthamiana, in conjunction with comparative insights, provides a valuable resource for genomics research and molecular biology. This accomplishment forms a strong foundation for in-depth exploration into the intricacies of plant genetics and genomics, improved precision, and a comparative framework.
Collapse
Affiliation(s)
- Seo-Rin Ko
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34113, Republic of Korea
| | - Sanghee Lee
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- Biosystems and Bioengineering Program, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), Daejeon, 34113, Korea
| | - Hyunjin Koo
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | | | | | - Yong-Min Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34113, Republic of Korea.
- Digital Biotech Innovation Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
| | - Suk-Yoon Kwon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
- Biosystems and Bioengineering Program, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), Daejeon, 34113, Korea.
| | - Ah-Young Shin
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34113, Republic of Korea.
| |
Collapse
|
5
|
Kang EJ, Kim JH, Kim YE, Lee H, Jung KB, Chang DH, Lee Y, Park S, Lee EY, Lee EJ, Kang HB, Rhyoo MY, Seo S, Park S, Huh Y, Go J, Choi JH, Choi YK, Lee IB, Choi DH, Seo YJ, Noh JR, Kim KS, Hwang JH, Jeong JS, Kwon HJ, Yoo HM, Son MY, Kim YG, Lee DH, Kim TY, Kwon HJ, Kim MH, Kim BC, Kim YH, Kang D, Lee CH. The secreted protein Amuc_1409 from Akkermansia muciniphila improves gut health through intestinal stem cell regulation. Nat Commun 2024; 15:2983. [PMID: 38582860 PMCID: PMC10998920 DOI: 10.1038/s41467-024-47275-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 03/26/2024] [Indexed: 04/08/2024] Open
Abstract
Akkermansia muciniphila has received great attention because of its beneficial roles in gut health by regulating gut immunity, promoting intestinal epithelial development, and improving barrier integrity. However, A. muciniphila-derived functional molecules regulating gut health are not well understood. Microbiome-secreted proteins act as key arbitrators of host-microbiome crosstalk through interactions with host cells in the gut and are important for understanding host-microbiome relationships. Herein, we report the biological function of Amuc_1409, a previously uncharacterised A. muciniphila-secreted protein. Amuc_1409 increased intestinal stem cell (ISC) proliferation and regeneration in ex vivo intestinal organoids and in vivo models of radiation- or chemotherapeutic drug-induced intestinal injury and natural aging with male mice. Mechanistically, Amuc_1409 promoted E-cadherin/β-catenin complex dissociation via interaction with E-cadherin, resulting in the activation of Wnt/β-catenin signaling. Our results demonstrate that Amuc_1409 plays a crucial role in intestinal homeostasis by regulating ISC activity in an E-cadherin-dependent manner and is a promising biomolecule for improving and maintaining gut health.
Collapse
Affiliation(s)
- Eun-Jung Kang
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- Department of Veterinary Pathology, College of Veterinary Medicine, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Jae-Hoon Kim
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- Livestock Products Analysis Division, Division of Animal health, Daejeon Metropolitan City Institute of Health and Environment, Daejeon, 34146, Republic of Korea
| | - Young Eun Kim
- Group for Biometrology, Korea Research Institute of Standards and Science (KRISS), Daejeon, 34113, Republic of Korea
- School of Earth Sciences & Environmental Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, 61005, Republic of Korea
| | - Hana Lee
- Stem Cell Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Kwang Bo Jung
- Stem Cell Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Dong-Ho Chang
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Youngjin Lee
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Shinhye Park
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Eun-Young Lee
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Eun-Ji Lee
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Ho Bum Kang
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Moon-Young Rhyoo
- Laboratory Animal Resource Center, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Seungwoo Seo
- School of Earth Sciences & Environmental Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, 61005, Republic of Korea
| | - Sohee Park
- Stem Cell Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- Department of Bio-Molecular Science, Korea Research Institute of Bioscience and Biotechnology (KRIBB) School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34141, Republic of Korea
| | - Yubin Huh
- Stem Cell Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- Department of Bio-Molecular Science, Korea Research Institute of Bioscience and Biotechnology (KRIBB) School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34141, Republic of Korea
| | - Jun Go
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Jung Hyeon Choi
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Young-Keun Choi
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - In-Bok Lee
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Dong-Hee Choi
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Yun Jeong Seo
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Jung-Ran Noh
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Kyoung-Shim Kim
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- Department of Functional Genomics, Korea Research Institute of Bioscience and Biotechnology (KRIBB) School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34141, Republic of Korea
| | - Jung Hwan Hwang
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- Department of Functional Genomics, Korea Research Institute of Bioscience and Biotechnology (KRIBB) School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34141, Republic of Korea
| | - Ji-Seon Jeong
- Group for Biometrology, Korea Research Institute of Standards and Science (KRISS), Daejeon, 34113, Republic of Korea
- Department of Measurement Science, Korea Research Institute of Standards and Science (KRISS) School of Precision Measurement, Korea University of Science and Technology (UST), Daejeon, 34113, Republic of Korea
| | - Ha-Jeong Kwon
- Group for Biometrology, Korea Research Institute of Standards and Science (KRISS), Daejeon, 34113, Republic of Korea
| | - Hee Min Yoo
- Group for Biometrology, Korea Research Institute of Standards and Science (KRISS), Daejeon, 34113, Republic of Korea
- Department of Measurement Science, Korea Research Institute of Standards and Science (KRISS) School of Precision Measurement, Korea University of Science and Technology (UST), Daejeon, 34113, Republic of Korea
| | - Mi-Young Son
- Stem Cell Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- Department of Bio-Molecular Science, Korea Research Institute of Bioscience and Biotechnology (KRIBB) School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34141, Republic of Korea
| | - Yeon-Gu Kim
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- Department of Applied Biological Engineering, Korea Research Institute of Bioscience and Biotechnology (KRIBB) School of Biotechnology, University of Science and Technology (UST), Daejeon, 34141, Republic of Korea
| | - Dae-Hee Lee
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- Department of Biosystems and Bioengineering, Korea Research Institute of Bioscience and Biotechnology (KRIBB) School of Biotechnology, University of Science and Technology (UST), Daejeon, 34141, Republic of Korea
| | - Tae-Young Kim
- School of Earth Sciences & Environmental Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, 61005, Republic of Korea
| | - Hyo-Jung Kwon
- Department of Veterinary Pathology, College of Veterinary Medicine, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Myung Hee Kim
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Byoung-Chan Kim
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- HealthBiome Inc., Daejeon, 34141, Republic of Korea
| | - Yong-Hoon Kim
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
- Department of Functional Genomics, Korea Research Institute of Bioscience and Biotechnology (KRIBB) School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34141, Republic of Korea.
| | - Dukjin Kang
- Group for Biometrology, Korea Research Institute of Standards and Science (KRISS), Daejeon, 34113, Republic of Korea.
| | - Chul-Ho Lee
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
- Department of Functional Genomics, Korea Research Institute of Bioscience and Biotechnology (KRIBB) School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34141, Republic of Korea.
| |
Collapse
|
6
|
Kim Y, You JH, Ryu Y, Park G, Lee U, Moon HE, Park HR, Song CW, Ku JL, Park SH, Paek SH. ELAVL2 loss promotes aggressive mesenchymal transition in glioblastoma. NPJ Precis Oncol 2024; 8:79. [PMID: 38548861 PMCID: PMC10978835 DOI: 10.1038/s41698-024-00566-1] [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: 05/16/2023] [Accepted: 03/08/2024] [Indexed: 04/01/2024] Open
Abstract
Glioblastoma (GBM), the most lethal primary brain cancer, exhibits intratumoral heterogeneity and molecular plasticity, posing challenges for effective treatment. Despite this, the regulatory mechanisms underlying such plasticity, particularly mesenchymal (MES) transition, remain poorly understood. In this study, we elucidate the role of the RNA-binding protein ELAVL2 in regulating aggressive MES transformation in GBM. We found that ELAVL2 is most frequently deleted in GBM compared to other cancers and associated with distinct clinical and molecular features. Transcriptomic analysis revealed that ELAVL2-mediated alterations correspond to specific GBM subtype signatures. Notably, ELAVL2 expression negatively correlated with epithelial-to-mesenchymal transition (EMT)-related genes, and its loss promoted MES process and chemo-resistance in GBM cells, whereas ELAVL2 overexpression exerted the opposite effect. Further investigation via tissue microarray analysis demonstrated that high ELAVL2 protein expression confers a favorable survival outcome in GBM patients. Mechanistically, ELAVL2 was shown to directly bind to the transcripts of EMT-inhibitory molecules, SH3GL3 and DNM3, modulating their mRNA stability, potentially through an m6A-dependent mechanism. In summary, our findings identify ELAVL2 as a critical tumor suppressor and mRNA stabilizer that regulates MES transition in GBM, underscoring its role in transcriptomic plasticity and glioma progression.
Collapse
Affiliation(s)
- Yona Kim
- Department of Neurosurgery, Cancer Research Institute and Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul, Korea
- Interdisciplinary Program in Neuroscience, Seoul National University College of Biological Sciences, Seoul, Korea
| | - Ji Hyeon You
- Department of Neurosurgery, Cancer Research Institute and Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul, Korea
- Interdisciplinary Program in Caner Biology, Seoul National University College of Medicine, Seoul, Korea
| | - Yeonjoo Ryu
- Department of Neurosurgery, Cancer Research Institute and Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul, Korea
- Interdisciplinary Program in Neuroscience, Seoul National University College of Biological Sciences, Seoul, Korea
| | - Gyuri Park
- Department of Neurosurgery, Cancer Research Institute and Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul, Korea
- Interdisciplinary Program in Caner Biology, Seoul National University College of Medicine, Seoul, Korea
| | - Urim Lee
- Department of Neurosurgery, Cancer Research Institute and Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul, Korea
- Interdisciplinary Program in Caner Biology, Seoul National University College of Medicine, Seoul, Korea
| | - Hyo Eun Moon
- Department of Neurosurgery, Cancer Research Institute and Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Hye Ran Park
- Department of Neurosurgery, Soonchunhyang University Seoul Hospital, Seoul, Korea
| | - Chang W Song
- Department of Radiation Oncology, University of Minnesota Medical School, Minneapolis, MN, 55455, USA
| | - Ja-Lok Ku
- Korean Cell Line Bank, Laboratory of Cell Biology, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Sung-Hye Park
- Department of Pathology, Seoul National University Hospital, Seoul, Korea
| | - Sun Ha Paek
- Department of Neurosurgery, Cancer Research Institute and Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul, Korea.
- Advanced Institute of Convergence Technology, Seoul National University, Suwon, Korea.
| |
Collapse
|
7
|
Chang S, Shin KS, Park B, Park S, Shin J, Park H, Jung IK, Kim JH, Bae SE, Kim JO, Baek SH, Kim G, Hong JJ, Seo H, Volz E, Kang CY. Strategy to develop broadly effective multivalent COVID-19 vaccines against emerging variants based on Ad5/35 platform. Proc Natl Acad Sci U S A 2024; 121:e2313681121. [PMID: 38408238 DOI: 10.1073/pnas.2313681121] [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: 08/18/2023] [Accepted: 01/28/2024] [Indexed: 02/28/2024] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron strain has evolved into highly divergent variants with several sub-lineages. These newly emerging variants threaten the efficacy of available COVID-19 vaccines. To mitigate the occurrence of breakthrough infections and re-infections, and more importantly, to reduce the disease burden, it is essential to develop a strategy for producing updated multivalent vaccines that can provide broad neutralization against both currently circulating and emerging variants. We developed bivalent vaccine AdCLD-CoV19-1 BA.5/BA.2.75 and trivalent vaccines AdCLD-CoV19-1 XBB/BN.1/BQ.1.1 and AdCLD-CoV19-1 XBB.1.5/BN.1/BQ.1.1 using an Ad5/35 platform-based non-replicating recombinant adenoviral vector. We compared immune responses elicited by the monovalent and multivalent vaccines in mice and macaques. We found that the BA.5/BA.2.75 bivalent and the XBB/BN.1/BQ.1.1 and XBB.1.5/BN.1/BQ.1.1 trivalent vaccines exhibited improved cross-neutralization ability compared to their respective monovalent vaccines. These data suggest that the developed multivalent vaccines enhance immunity against circulating Omicron subvariants and effectively elicit neutralizing antibodies across a broad spectrum of SARS-CoV-2 variants.
Collapse
Affiliation(s)
- Soojeong Chang
- Research & Development Center, Cellid Co., Ltd., Seoul 08826, Republic of Korea
| | - Kwang-Soo Shin
- Research & Development Center, Cellid Co., Ltd., Seoul 08826, Republic of Korea
| | - Bongju Park
- Research & Development Center, Cellid Co., Ltd., Seoul 08826, Republic of Korea
| | - Seowoo Park
- Research & Development Center, Cellid Co., Ltd., Seoul 08826, Republic of Korea
| | - Jieun Shin
- Research & Development Center, Cellid Co., Ltd., Seoul 08826, Republic of Korea
| | - Hyemin Park
- Research & Development Center, Cellid Co., Ltd., Seoul 08826, Republic of Korea
| | - In Kyung Jung
- Research & Development Center, Cellid Co., Ltd., Seoul 08826, Republic of Korea
| | - Jong Heon Kim
- Research & Development Center, Cellid Co., Ltd., Seoul 08826, Republic of Korea
| | - Seong Eun Bae
- Science Unit, International Vaccine Institute, Seoul 08826, Republic of Korea
| | - Jae-Ouk Kim
- Science Unit, International Vaccine Institute, Seoul 08826, Republic of Korea
| | - Seung Ho Baek
- National Primate Research Centre, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Chungcheongbuk 28116, Republic of Korea
| | - Green Kim
- National Primate Research Centre, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Chungcheongbuk 28116, Republic of Korea
| | - Jung Joo Hong
- National Primate Research Centre, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Chungcheongbuk 28116, Republic of Korea
- Korea Research Institute of Bioscience and Biotechnology School of Bioscience, Korea University of Science & Technology, Daejeon 34141, Republic of Korea
| | - Hyungseok Seo
- Laboratory of Cell & Gene Therapy, Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Erik Volz
- Department of Infectious Disease Epidemiology, Medical Research Council Centre for Global Infectious Disease Analysis, Imperial College London, London W2 1PG, United Kingdom
| | - Chang-Yuil Kang
- Research & Development Center, Cellid Co., Ltd., Seoul 08826, Republic of Korea
| |
Collapse
|
8
|
Im JY, Kim SJ, Park JL, Han TH, Kim WI, Kim I, Ko B, Chun SY, Kang MJ, Kim BK, Jeon SA, Kim SK, Ryu I, Kim SY, Nam KH, Hwang I, Ban HS, Won M. CYB5R3 functions as a tumor suppressor by inducing ER stress-mediated apoptosis in lung cancer cells via the PERK-ATF4 and IRE1α-JNK pathways. Exp Mol Med 2024; 56:235-249. [PMID: 38253797 PMCID: PMC10834511 DOI: 10.1038/s12276-024-01155-9] [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: 04/12/2023] [Revised: 09/04/2023] [Accepted: 11/06/2023] [Indexed: 01/24/2024] Open
Abstract
Cytochrome b5 reductase 3 (CYB5R3) is involved in various cellular metabolic processes, including fatty acid synthesis and drug metabolism. However, the role of CYB5R3 in cancer development remains poorly understood. Here, we show that CYB5R3 expression is downregulated in human lung cancer cell lines and tissues. Adenoviral overexpression of CYB5R3 suppresses lung cancer cell growth in vitro and in vivo. However, CYB5R3 deficiency promotes tumorigenesis and metastasis in mouse models. Transcriptome analysis revealed that apoptosis- and endoplasmic reticulum (ER) stress-related genes are upregulated in CYB5R3-overexpressing lung cancer cells. Metabolomic analysis revealed that CYB5R3 overexpression increased the production of nicotinamide adenine dinucleotide (NAD+) and oxidized glutathione (GSSG). Ectopic CYB5R3 is mainly localized in the ER, where CYB5R3-dependent ER stress signaling is induced via activation of protein kinase RNA-like ER kinase (PERK) and inositol-requiring enzyme 1 alpha (IRE1α). Moreover, NAD+ activates poly (ADP-ribose) polymerase16 (PARP16), an ER-resident protein, to promote ADP-ribosylation of PERK and IRE1α and induce ER stress. In addition, CYB5R3 induces the generation of reactive oxygen species and caspase-9-dependent intrinsic cell death. Our findings highlight the importance of CYB5R3 as a tumor suppressor for the development of CYB5R3-based therapeutics for lung cancer.
Collapse
Affiliation(s)
- Joo-Young Im
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
| | - Soo Jin Kim
- Chungnam National University Sejong Hospital (CNUSH), Sejong, 30099, Republic of Korea
| | - Jong-Lyul Park
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- Aging Convergence Research Center, KRIBB, Daejeon, 34141, Republic of Korea
| | - Tae-Hee Han
- Biotherapeutics Translational Research Center, KRIBB, Daejeon, 34141, Republic of Korea
- KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Woo-Il Kim
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Inhyub Kim
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Bomin Ko
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - So-Young Chun
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Mi-Jung Kang
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Bo-Kyung Kim
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- R&D Center, OneCureGEN Co., Ltd., Daejeon, 34141, Republic of Korea
| | - Sol A Jeon
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Seon-Kyu Kim
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- Aging Convergence Research Center, KRIBB, Daejeon, 34141, Republic of Korea
| | - Incheol Ryu
- YD Global Life Science Co., Ltd., Seongnam-si, Gyeonggi-do, 13207, Republic of Korea
| | - Seon-Young Kim
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Ki-Hoan Nam
- Laboratory Animal Resource & Research Center, KRIBB, Cheongju, Chungbuk, Republic of Korea
| | - Inah Hwang
- Graduate School of Pharmaceutical Sciences, College of Pharmacy, Ewha Womans University, Seoul, 03760, Republic of Korea
| | - Hyun Seung Ban
- Biotherapeutics Translational Research Center, KRIBB, Daejeon, 34141, Republic of Korea
- KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Misun Won
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
- KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon, 34113, Republic of Korea.
- R&D Center, OneCureGEN Co., Ltd., Daejeon, 34141, Republic of Korea.
| |
Collapse
|
9
|
Shin J, Liao S, Kuanyshev N, Xin Y, Kim C, Lu T, Jin YS. Compositional and temporal division of labor modulates mixed sugar fermentation by an engineered yeast consortium. Nat Commun 2024; 15:781. [PMID: 38278783 PMCID: PMC10817915 DOI: 10.1038/s41467-024-45011-w] [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: 08/31/2022] [Accepted: 01/11/2024] [Indexed: 01/28/2024] Open
Abstract
Synthetic microbial communities have emerged as an attractive route for chemical bioprocessing. They are argued to be superior to single strains through microbial division of labor (DOL), but the exact mechanism by which DOL confers advantages remains unclear. Here, we utilize a synthetic Saccharomyces cerevisiae consortium along with mathematical modeling to achieve tunable mixed sugar fermentation to overcome the limitations of single-strain fermentation. The consortium involves two strains with each specializing in glucose or xylose utilization for ethanol production. By controlling initial community composition, DOL allows fine tuning of fermentation dynamics and product generation. By altering inoculation delay, DOL provides additional programmability to parallelly regulate fermentation characteristics and product yield. Mathematical models capture observed experimental findings and further offer guidance for subsequent fermentation optimization. This study demonstrates the functional potential of DOL in bioprocessing and provides insight into the rational design of engineered ecosystems for various applications.
Collapse
Affiliation(s)
- Jonghyeok Shin
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
| | - Siqi Liao
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Nurzhan Kuanyshev
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Yongping Xin
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Chanwoo Kim
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Ting Lu
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| | - Yong-Su Jin
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
| |
Collapse
|
10
|
Jang H, Song J, Kim S, Byun JH, Lee KG, Park KH, Woo E, Lim EK, Jung J, Kang T. ANCA: artificial nucleic acid circuit with argonaute protein for one-step isothermal detection of antibiotic-resistant bacteria. Nat Commun 2023; 14:8033. [PMID: 38052830 DOI: 10.1038/s41467-023-43899-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 11/23/2023] [Indexed: 12/07/2023] Open
Abstract
Endonucleases have recently widely used in molecular diagnostics. Here, we report a strategy to exploit the properties of Argonaute (Ago) proteins for molecular diagnostics by introducing an artificial nucleic acid circuit with Ago protein (ANCA) method. The ANCA is designed to perform a continuous autocatalytic reaction through cross-catalytic cleavage of the Ago protein, enabling one-step, amplification-free, and isothermal DNA detection. Using the ANCA method, carbapenemase-producing Klebsiella pneumoniae (CPKP) are successfully detected without DNA extraction and amplification steps. In addition, we demonstrate the detection of carbapenem-resistant bacteria in human urine and blood samples using the method. We also demonstrate the direct identification of CPKP swabbed from surfaces using the ANCA method in conjunction with a three-dimensional nanopillar structure. Finally, the ANCA method is applied to detect CPKP in rectal swab specimens from infected patients, achieving sensitivity and specificity of 100% and 100%, respectively. The developed method can contribute to simple, rapid and accurate diagnosis of CPKP, which can help prevent nosocomial infections.
Collapse
Affiliation(s)
- Hyowon Jang
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Jayeon Song
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
- Center for Systems Biology, Massachusetts General Hospital Research Institute, 175 Cambridge Street, Boston, MA, 02114, USA
- Department of Radiology, Massachusetts General Hospital, Harvard Medical School, 55 Fruit Street, Boston, MA, 02114, USA
| | - Sunjoo Kim
- Department of Laboratory Medicine, Gyeongsang National University Hospital, Gyeongsang National University College of Medicine, 79 Gangnam-ro, Jinju-si, Gyeongsangnam-do, 52727, Republic of Korea
| | - Jung-Hyun Byun
- Department of Laboratory Medicine, Gyeongsang National University Hospital, Gyeongsang National University College of Medicine, 79 Gangnam-ro, Jinju-si, Gyeongsangnam-do, 52727, Republic of Korea
| | - Kyoung G Lee
- Division of Nano-Bio Sensors/Chips Development, National NanoFab Center (NNFC), 291 Daehak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Kwang-Hyun Park
- Disease Target Structure Research Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Euijeon Woo
- Disease Target Structure Research Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
- Department of Biomolecular Science, KRIBB School of Biotechnology, University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea
| | - Eun-Kyung Lim
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
- Department of Nanobiotechnology, KRIBB School of Biotechnology, UST, 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea
- School of Pharmacy, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon-si, Gyeongi-do, 16419, Republic of Korea
| | - Juyeon Jung
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
- School of Pharmacy, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon-si, Gyeongi-do, 16419, Republic of Korea
| | - Taejoon Kang
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.
- School of Pharmacy, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon-si, Gyeongi-do, 16419, Republic of Korea.
| |
Collapse
|
11
|
Cho MJ, Lee MR, Park JG. Aortic aneurysms: current pathogenesis and therapeutic targets. Exp Mol Med 2023; 55:2519-2530. [PMID: 38036736 PMCID: PMC10766996 DOI: 10.1038/s12276-023-01130-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/29/2023] [Accepted: 08/30/2023] [Indexed: 12/02/2023] Open
Abstract
Aortic aneurysm is a chronic disease characterized by localized expansion of the aorta, including the ascending aorta, arch, descending aorta, and abdominal aorta. Although aortic aneurysms are generally asymptomatic, they can threaten human health by sudden death due to aortic rupture. Aortic aneurysms are estimated to lead to 150,000 ~ 200,000 deaths per year worldwide. Currently, there are no effective drugs to prevent the growth or rupture of aortic aneurysms; surgical repair or endovascular repair is the only option for treating this condition. The pathogenic mechanisms and therapeutic targets for aortic aneurysms have been examined over the past decade; however, there are unknown pathogenic mechanisms involved in cellular heterogeneity and plasticity, the complexity of the transforming growth factor-β signaling pathway, inflammation, cell death, intramural neovascularization, and intercellular communication. This review summarizes the latest research findings and current pathogenic mechanisms of aortic aneurysms, which may enhance our understanding of aortic aneurysms.
Collapse
Affiliation(s)
- Min Ji Cho
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - Mi-Ran Lee
- Department of Biomedical Laboratory Science, Jungwon University, 85 Munmu-ro, Goesan-eup, Goesan-gun, Chungbuk, 28024, Republic of Korea
| | - Jong-Gil Park
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.
- Department of Bioscience, KRIBB School of Bioscience, Korea University of Science and Technology (UST), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.
| |
Collapse
|
12
|
Ranathunga L, Dodantenna N, Cha JW, Chathuranga K, Chathuranga WAG, Weerawardhana A, Subasinghe A, Haluwana DK, Gamage N, Lee JS. African swine fever virus B175L inhibits the type I interferon pathway by targeting STING and 2'3'-cGAMP. J Virol 2023; 97:e0079523. [PMID: 37902401 PMCID: PMC10688321 DOI: 10.1128/jvi.00795-23] [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: 05/26/2023] [Accepted: 10/11/2023] [Indexed: 10/31/2023] Open
Abstract
IMPORTANCE African swine fever virus (ASFV), the only known DNA arbovirus, is the causative agent of African swine fever (ASF), an acutely contagious disease in pigs. ASF has recently become a crisis in the pig industry in recent years, but there are no commercially available vaccines. Studying the immune evasion mechanisms of ASFV proteins is important for the understanding the pathogenesis of ASFV and essential information for the development of an effective live-attenuated ASFV vaccines. Here, we identified ASFV B175L, previously uncharacterized proteins that inhibit type I interferon signaling by targeting STING and 2'3'-cGAMP. The conserved B175L-zf-FCS motif specifically interacted with both cGAMP and the R238 and Y240 amino acids of STING. Consequently, this interaction interferes with the interaction of cGAMP and STING, thereby inhibiting downstream signaling of IFN-mediated antiviral responses. This novel mechanism of B175L opens a new avenue as one of the ASFV virulent genes that can contribute to the advancement of ASFV live-attenuated vaccines.
Collapse
Affiliation(s)
- Lakmal Ranathunga
- College of Veterinary Medicine, Chungnam National University, Daejeon, South Korea
| | - Niranjan Dodantenna
- College of Veterinary Medicine, Chungnam National University, Daejeon, South Korea
| | - Ji-Won Cha
- College of Veterinary Medicine, Chungnam National University, Daejeon, South Korea
| | - Kiramage Chathuranga
- College of Veterinary Medicine, Chungnam National University, Daejeon, South Korea
| | | | - Asela Weerawardhana
- College of Veterinary Medicine, Chungnam National University, Daejeon, South Korea
| | - Ashan Subasinghe
- College of Veterinary Medicine, Chungnam National University, Daejeon, South Korea
| | - D. K. Haluwana
- College of Veterinary Medicine, Chungnam National University, Daejeon, South Korea
| | - Nuwan Gamage
- College of Veterinary Medicine, Chungnam National University, Daejeon, South Korea
| | - Jong-Soo Lee
- College of Veterinary Medicine, Chungnam National University, Daejeon, South Korea
| |
Collapse
|
13
|
Yin J, Seo Y, Rhim J, Jin X, Kim TH, Kim SS, Hong JH, Gwak HS, Yoo H, Park JB, Kim JH. Cross-talk between PARN and EGFR-STAT3 Signaling Facilitates Self-Renewal and Proliferation of Glioblastoma Stem Cells. Cancer Res 2023; 83:3693-3709. [PMID: 37747775 DOI: 10.1158/0008-5472.can-22-3965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 07/19/2023] [Accepted: 09/21/2023] [Indexed: 09/26/2023]
Abstract
Glioblastoma is the most common type of malignant primary brain tumor and displays highly aggressive and heterogeneous phenotypes. The transcription factor STAT3 has been reported to play a key role in glioblastoma malignancy. Thus, discovering targets and functional downstream networks regulated by STAT3 that govern glioblastoma pathogenesis may lead to improved treatment strategies. In this study, we identified that poly(A)-specific ribonuclease (PARN), a key modulator of RNA metabolism, activates EGFR-STAT3 signaling to support glioblastoma stem cells (GSC). Functional integrative analysis of STAT3 found PARN as the top-scoring transcriptional target involved in RNA processing in patients with glioblastoma, and PARN expression was strongly correlated with poor patient survival and elevated malignancy. PARN positively regulated self-renewal and proliferation of GSCs through its 3'-5' exoribonuclease activity. EGFR was identified as a clinically relevant target of PARN in GSCs. PARN positively modulated EGFR by negatively regulating the EGFR-targeting miRNA miR-7, and increased EGFR expression created a positive feedback loop to increase STAT3 activation. PARN depletion in GSCs reduced infiltration and prolonged survival in orthotopic brain tumor xenografts; similar results were observed using siRNA nanocapsule-mediated PARN targeting. Pharmacological targeting of STAT3 also confirmed PARN regulation by STAT3 signaling. In sum, these results suggest that a STAT3-PARN regulatory network plays a pivotal role in tumor progression and thus may represent a target for glioblastoma therapeutics. SIGNIFICANCE A positive feedback loop comprising PARN and EGFR-STAT3 signaling supports self-renewal and proliferation of glioblastoma stem cells to drive tumor progression and can be targeted in glioblastoma therapeutics.
Collapse
Affiliation(s)
- Jinlong Yin
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea
- Henan-Macquarie University Joint Centre for Biomedical Innovation, School of Life Sciences, Henan University, Kaifeng, Henan, China
| | - Yoona Seo
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea
- Cancer Molecular Biology Branch, Research Institute, National Cancer Center, Goyang, Korea
| | - Jiho Rhim
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea
- Cancer Molecular Biology Branch, Research Institute, National Cancer Center, Goyang, Korea
| | - Xiong Jin
- Henan-Macquarie University Joint Centre for Biomedical Innovation, School of Life Sciences, Henan University, Kaifeng, Henan, China
| | - Tae Hoon Kim
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea
| | - Sung Soo Kim
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea
| | - Jun-Hee Hong
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea
| | - Ho-Shin Gwak
- Neuro-Oncology Clinic, National Cancer Center, Goyang, Korea
- Department of Cancer Control, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea
| | - Heon Yoo
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea
- Neuro-Oncology Clinic, National Cancer Center, Goyang, Korea
| | - Jong Bae Park
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea
| | - Jong Heon Kim
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea
- Cancer Molecular Biology Branch, Research Institute, National Cancer Center, Goyang, Korea
| |
Collapse
|
14
|
Lee EY, Hwang J, Kim MH. Phosphocode-dependent glutamyl-prolyl-tRNA synthetase 1 signaling in immunity, metabolism, and disease. Exp Mol Med 2023; 55:2116-2126. [PMID: 37779151 PMCID: PMC10618286 DOI: 10.1038/s12276-023-01094-x] [Citation(s) in RCA: 1] [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: 03/30/2023] [Revised: 07/10/2023] [Accepted: 07/11/2023] [Indexed: 10/03/2023] Open
Abstract
Ubiquitously expressed aminoacyl-tRNA synthetases play essential roles in decoding genetic information required for protein synthesis in every living species. Growing evidence suggests that they also function as crossover mediators of multiple biological processes required for homeostasis. In humans, eight cytoplasmic tRNA synthetases form a central machinery called the multi-tRNA synthetase complex (MSC). The formation of MSCs appears to be essential for life, although the role of MSCs remains unclear. Glutamyl-prolyl-tRNA synthetase 1 (EPRS1) is the most evolutionarily derived component within the MSC that plays a critical role in immunity and metabolism (beyond its catalytic role in translation) via stimulus-dependent phosphorylation events. This review focuses on the role of EPRS1 signaling in inflammation resolution and metabolic modulation. The involvement of EPRS1 in diseases such as cancer is also discussed.
Collapse
Affiliation(s)
- Eun-Young Lee
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
| | - Jungwon Hwang
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea
| | - Myung Hee Kim
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Korea.
| |
Collapse
|
15
|
Oh T, Kim G, Baek SH, Woo Y, Koo BS, Hwang EH, Shim K, An YJ, Kim Y, Won J, Lee Y, Lim KS, Park JH, Hong JJ. Spatial transcriptome atlas reveals pulmonary microstructure-specific COVID-19 gene signatures in cynomolgus macaques. Commun Biol 2023; 6:879. [PMID: 37640792 PMCID: PMC10462721 DOI: 10.1038/s42003-023-05253-8] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 08/17/2023] [Indexed: 08/31/2023] Open
Abstract
Characterizing the host response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) at the molecular level is necessary to understand viral pathogenesis and identify clinically relevant biomarkers. However, in humans, the pulmonary host response during disease onset remains poorly understood. Herein, we utilized a spatial transcriptome atlas to identify pulmonary microstructure-specific COVID-19 gene signatures during the acute phase of lung infection in cynomolgus macaques. The innate immune response to virus-induced cell death was primarily active in the alveolar regions involving activated macrophage infiltration. Inflamed vascular regions exhibited prominent upregulation of interferon and complement pathway genes that mediate antiviral activity and tissue damage response. Furthermore, known biomarker genes were significantly expressed in specific microstructures, and some of them were universally expressed across all microstructures. These findings underscore the importance of identifying key drivers of disease progression and clinically applicable biomarkers by focusing on pulmonary microstructures appearing during SARS-CoV-2 infection.
Collapse
Affiliation(s)
- Taehwan Oh
- National Primate Research Centre, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Chungcheongbuk, Republic of Korea
| | - Green Kim
- National Primate Research Centre, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Chungcheongbuk, Republic of Korea
| | - Seung Ho Baek
- National Primate Research Centre, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Chungcheongbuk, Republic of Korea
| | - YoungMin Woo
- National Primate Research Centre, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Chungcheongbuk, Republic of Korea
- KRIBB School of Bioscience, Korea University of Science & Technology (UST), Daejeon, Republic of Korea
| | - Bon-Sang Koo
- National Primate Research Centre, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Chungcheongbuk, Republic of Korea
| | - Eun-Ha Hwang
- National Primate Research Centre, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Chungcheongbuk, Republic of Korea
| | - Kyuyoung Shim
- National Primate Research Centre, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Chungcheongbuk, Republic of Korea
- KRIBB School of Bioscience, Korea University of Science & Technology (UST), Daejeon, Republic of Korea
| | - You Jung An
- National Primate Research Centre, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Chungcheongbuk, Republic of Korea
| | - Yujin Kim
- National Primate Research Centre, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Chungcheongbuk, Republic of Korea
| | - Jinyoung Won
- National Primate Research Centre, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Chungcheongbuk, Republic of Korea
| | - Youngjeon Lee
- National Primate Research Centre, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Chungcheongbuk, Republic of Korea
| | - Kyung Seob Lim
- Futuristic Animal Resource and Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Republic of Korea
| | - Jae-Hak Park
- Department of Laboratory Animal Medicine, College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea
| | - Jung Joo Hong
- National Primate Research Centre, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Chungcheongbuk, Republic of Korea.
- KRIBB School of Bioscience, Korea University of Science & Technology (UST), Daejeon, Republic of Korea.
| |
Collapse
|
16
|
Jeon SB, Koh H, Han AR, Kim J, Lee S, Lee JH, Im SS, Yoon YS, Lee JH, Lee JY. Ferric citrate and apo-transferrin enable erythroblast maturation with β-globin from hemogenic endothelium. NPJ Regen Med 2023; 8:46. [PMID: 37626061 PMCID: PMC10457393 DOI: 10.1038/s41536-023-00320-4] [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: 11/22/2022] [Accepted: 08/08/2023] [Indexed: 08/27/2023] Open
Abstract
Red blood cell (RBC) generation from human pluripotent stem cells (PSCs) offers potential for innovative cell therapy in regenerative medicine as well as developmental studies. Ex vivo erythropoiesis from PSCs is currently limited by the low efficiency of functional RBCs with β-globin expression in culture systems. During induction of β-globin expression, the absence of a physiological microenvironment, such as a bone marrow niche, may impair cell maturation and lineage specification. Here, we describe a simple and reproducible culture system that can be used to generate erythroblasts with β-globin expression. We prepared a two-dimensional defined culture with ferric citrate treatment based on definitive hemogenic endothelium (HE). Floating erythroblasts derived from HE cells were primarily CD45+CD71+CD235a+ cells, and their number increased remarkably upon Fe treatment. Upon maturation, the erythroblasts cultured in the presence of ferric citrate showed high transcriptional levels of β-globin and enrichment of genes associated with heme synthesis and cell cycle regulation, indicating functionality. The rapid maturation of these erythroblasts into RBCs was observed when injected in vivo, suggesting the development of RBCs that were ready to grow. Hence, induction of β-globin expression may be explained by the effects of ferric citrate that promote cell maturation by binding with soluble transferrin and entering the cells.Taken together, upon treatment with Fe, erythroblasts showed advanced maturity with a high transcription of β-globin. These findings can help devise a stable protocol for the generation of clinically applicable RBCs.
Collapse
Affiliation(s)
- Soo-Been Jeon
- CHA Advanced Research Institute, Bundang CHA Medical Center, CHA University, Seongnam, Kyunggi-do, 13488, South Korea
| | - Hyebin Koh
- Futuristic Animal Resource & Research Center (FARRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Republic of Korea
- Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, Republic of Korea
| | - A-Reum Han
- CHA Advanced Research Institute, Bundang CHA Medical Center, CHA University, Seongnam, Kyunggi-do, 13488, South Korea
| | - Jieun Kim
- National Primate Research Center (NPRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Republic of Korea
| | - Sunghun Lee
- CHA Advanced Research Institute, Bundang CHA Medical Center, CHA University, Seongnam, Kyunggi-do, 13488, South Korea
| | - Jae-Ho Lee
- Department of Physiology, Keimyung University School of Medicine, Daegu, 42601, Korea
| | - Seung-Soon Im
- Department of Physiology, Keimyung University School of Medicine, Daegu, 42601, Korea
| | - Young-Sup Yoon
- Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, Korea
- Department of Medicine, Emory University, Atlanta, USA
| | - Jong-Hee Lee
- Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, Republic of Korea.
- National Primate Research Center (NPRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Republic of Korea.
| | - Ji Yoon Lee
- CHA Advanced Research Institute, Bundang CHA Medical Center, CHA University, Seongnam, Kyunggi-do, 13488, South Korea.
- Department of Biomedical Science, CHA University, Seongnam, Kyunggi-do, 13488, South Korea.
- Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, Korea.
| |
Collapse
|
17
|
Kong HG, Son JS, Chung JH, Lee S, Kim JS, Ryu CM. Population Dynamics of Intestinal Enterococcus Modulate Galleria mellonella Metamorphosis. Microbiol Spectr 2023; 11:e0278022. [PMID: 37358445 PMCID: PMC10434003 DOI: 10.1128/spectrum.02780-22] [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: 07/20/2022] [Accepted: 05/24/2023] [Indexed: 06/27/2023] Open
Abstract
Microbes found in the digestive tracts of insects are known to play an important role in their host's behavior. Although Lepidoptera is one of the most varied insect orders, the link between microbial symbiosis and host development is still poorly understood. In particular, little is known about the role of gut bacteria in metamorphosis. Here, we explored gut microbial biodiversity throughout the life cycle of Galleria mellonella, using amplicon pyrosequencing with the V1 to V3 regions, and found that Enterococcus spp. were abundant in larvae, while Enterobacter spp. were predominant in pupae. Interestingly, eradication of Enterococcus spp. from the digestive system accelerated the larval-to-pupal transition. Furthermore, host transcriptome analysis demonstrated that immune response genes were upregulated in pupae, whereas hormone genes were upregulated in larvae. In particular, regulation of antimicrobial peptide production in the host gut correlated with developmental stage. Certain antimicrobial peptides inhibited the growth of Enterococcus innesii, a dominant bacterial species in the gut of G. mellonella larvae. Our study highlights the importance of gut microbiota dynamics on metamorphosis as a consequence of the active secretion of antimicrobial peptides in the G. mellonella gut. IMPORTANCE First, we demonstrated that the presence of Enterococcus spp. is a driving force for insect metamorphosis. RNA sequencing and peptide production subsequently revealed that antimicrobial peptides targeted against microorganisms in the gut of Galleria mellonella (wax moth) did not kill Enterobacteria species, but did kill Enterococcus species, when the moth was at a certain stage of growth, and this promoted moth pupation.
Collapse
Affiliation(s)
- Hyun Gi Kong
- Infection Disease Research Center, KRIBB, Daejeon, South Korea
- Department of Plant Medicine, Chungbuk National University, Cheongju, South Korea
| | - Jin-Soo Son
- Infection Disease Research Center, KRIBB, Daejeon, South Korea
| | - Joon-Hui Chung
- Infection Disease Research Center, KRIBB, Daejeon, South Korea
| | - Soohyun Lee
- Infection Disease Research Center, KRIBB, Daejeon, South Korea
| | - Jun-Seob Kim
- Department of Nano-Bioengineering, Incheon National University, Incheon, South Korea
| | - Choong-Min Ryu
- Infection Disease Research Center, KRIBB, Daejeon, South Korea
| |
Collapse
|
18
|
Jang HJ, Lee YH, Dao T, Jo Y, Khim KW, Eom HJ, Lee JE, Song YJ, Choi SS, Park K, Ji H, Chae YC, Myung K, Kim H, Ryu D, Park NH, Park SH, Choi JH. Thrap3 promotes nonalcoholic fatty liver disease by suppressing AMPK-mediated autophagy. Exp Mol Med 2023; 55:1720-1733. [PMID: 37524868 PMCID: PMC10474030 DOI: 10.1038/s12276-023-01047-4] [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: 10/02/2022] [Revised: 03/14/2023] [Accepted: 04/30/2023] [Indexed: 08/02/2023] Open
Abstract
Autophagy functions in cellular quality control and metabolic regulation. Dysregulation of autophagy is one of the major pathogenic factors contributing to the progression of nonalcoholic fatty liver disease (NAFLD). Autophagy is involved in the breakdown of intracellular lipids and the maintenance of healthy mitochondria in NAFLD. However, the mechanisms underlying autophagy dysregulation in NAFLD remain unclear. Here, we demonstrate that the hepatic expression level of Thrap3 was significantly increased in NAFLD conditions. Liver-specific Thrap3 knockout improved lipid accumulation and metabolic properties in a high-fat diet (HFD)-induced NAFLD model. Furthermore, Thrap3 deficiency enhanced autophagy and mitochondrial function. Interestingly, Thrap3 knockout increased the cytosolic translocation of AMPK from the nucleus and enhanced its activation through physical interaction. The translocation of AMPK was regulated by direct binding with AMPK and the C-terminal domain of Thrap3. Our results indicate a role for Thrap3 in NAFLD progression and suggest that Thrap3 is a potential target for NAFLD treatment.
Collapse
Affiliation(s)
- Hyun-Jun Jang
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, Naju, 58245, Republic of Korea
| | - Yo Han Lee
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Tam Dao
- Department of Molecular Cell Biology, Sungkyunkwan University (SKKU) School of Medicine, Suwon, 16419, Republic of Korea
| | - Yunju Jo
- Department of Molecular Cell Biology, Sungkyunkwan University (SKKU) School of Medicine, Suwon, 16419, Republic of Korea
| | - Keon Woo Khim
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Hye-Jin Eom
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Ju Eun Lee
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Yi Jin Song
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Sun Sil Choi
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Kieun Park
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Haneul Ji
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Young Chan Chae
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Kyungjae Myung
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, 44919, Republic of Korea
| | - Hongtae Kim
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Dongryeol Ryu
- Department of Molecular Cell Biology, Sungkyunkwan University (SKKU) School of Medicine, Suwon, 16419, Republic of Korea
| | - Neung Hwa Park
- Department of Internal Medicine, University of Ulsan College of Medicine, Ulsan University Hospital, Ulsan, 44033, Republic of Korea.
| | - Sung Ho Park
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.
| | - Jang Hyun Choi
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.
| |
Collapse
|
19
|
Lee S, Hwang N, Seok BG, Lee S, Lee SJ, Chung SW. Autophagy mediates an amplification loop during ferroptosis. Cell Death Dis 2023; 14:464. [PMID: 37491375 PMCID: PMC10368698 DOI: 10.1038/s41419-023-05978-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 06/09/2023] [Accepted: 07/11/2023] [Indexed: 07/27/2023]
Abstract
Ferroptosis, a programmed cell death, has been identified and associated with cancer and various other diseases. Ferroptosis is defined as a reactive oxygen species (ROS)-dependent cell death related to iron accumulation and lipid peroxidation, which is different from apoptosis, necrosis, autophagy, and other forms of cell death. However, accumulating evidence has revealed a link between autophagy and ferroptosis at the molecular level and has suggested that autophagy is involved in regulating the accumulation of iron-dependent lipid peroxidation and ROS during ferroptosis. Understanding the roles and pathophysiological processes of autophagy during ferroptosis may provide effective strategies for the treatment of ferroptosis-related diseases. In this review, we summarize the current knowledge regarding the regulatory mechanisms underlying ferroptosis, including iron and lipid metabolism, and its association with the autophagy pathway. In addition, we discuss the contribution of autophagy to ferroptosis and elucidate the role of autophagy as a ferroptosis enhancer during ROS-dependent ferroptosis.
Collapse
Affiliation(s)
- Seunghee Lee
- Department of Biological Sciences, College of Natural Sciences, University of Ulsan, 93 Daehak-ro, Nam-gu, Ulsan, 44610, South Korea
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, VA Palo Alto Health Care System and Stanford University School of Medicine, Palo Alto, CA, 94305, USA
| | - Narae Hwang
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Byeong Geun Seok
- Department of Biological Sciences, College of Natural Sciences, University of Ulsan, 93 Daehak-ro, Nam-gu, Ulsan, 44610, South Korea
| | - Sangguk Lee
- Department of Biological Sciences, College of Natural Sciences, University of Ulsan, 93 Daehak-ro, Nam-gu, Ulsan, 44610, South Korea
| | - Seon-Jin Lee
- Environmental Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Yuseong-gu, Daejeon, 34141, South Korea
| | - Su Wol Chung
- Department of Biological Sciences, College of Natural Sciences, University of Ulsan, 93 Daehak-ro, Nam-gu, Ulsan, 44610, South Korea.
- Basic-Clinical Convergence Research Institute, University of Ulsan, Ulsan, 44610, South Korea.
| |
Collapse
|
20
|
Park A, Kim KE, Park I, Lee SH, Park KY, Jung M, Li X, Sleiman MB, Lee SJ, Kim DS, Kim J, Lim DS, Woo EJ, Lee EW, Han BS, Oh KJ, Lee SC, Auwerx J, Mun JY, Rhee HW, Kim WK, Bae KH, Suh JM. Mitochondrial matrix protein LETMD1 maintains thermogenic capacity of brown adipose tissue in male mice. Nat Commun 2023; 14:3746. [PMID: 37353518 PMCID: PMC10290150 DOI: 10.1038/s41467-023-39106-z] [Citation(s) in RCA: 1] [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: 11/03/2021] [Accepted: 05/31/2023] [Indexed: 06/25/2023] Open
Abstract
Brown adipose tissue (BAT) has abundant mitochondria with the unique capability of generating heat via uncoupled respiration. Mitochondrial uncoupling protein 1 (UCP1) is activated in BAT during cold stress and dissipates mitochondrial proton motive force generated by the electron transport chain to generate heat. However, other mitochondrial factors required for brown adipocyte respiration and thermogenesis under cold stress are largely unknown. Here, we show LETM1 domain-containing protein 1 (LETMD1) is a BAT-enriched and cold-induced protein required for cold-stimulated respiration and thermogenesis of BAT. Proximity labeling studies reveal that LETMD1 is a mitochondrial matrix protein. Letmd1 knockout male mice display aberrant BAT mitochondria and fail to carry out adaptive thermogenesis under cold stress. Letmd1 knockout BAT is deficient in oxidative phosphorylation (OXPHOS) complex proteins and has impaired mitochondrial respiration. In addition, BAT-specific Letmd1 deficient mice exhibit phenotypes identical to those observed in Letmd1 knockout mice. Collectively, we demonstrate that the BAT-enriched mitochondrial matrix protein LETMD1 plays a tissue-autonomous role that is essential for BAT mitochondrial function and thermogenesis.
Collapse
Affiliation(s)
- Anna Park
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Kwang-Eun Kim
- Graduate School of Medical Science and Engineering, KAIST, Daejeon, 34141, Republic of Korea
- Department of Chemistry, Seoul National University, Seoul, 08826, Republic of Korea
| | - Isaac Park
- Department of Chemistry, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sang Heon Lee
- Graduate School of Medical Science and Engineering, KAIST, Daejeon, 34141, Republic of Korea
| | - Kun-Young Park
- Graduate School of Medical Science and Engineering, KAIST, Daejeon, 34141, Republic of Korea
| | - Minkyo Jung
- Neural Circuit Research Group, Korea Brain Research Institute, Daegu, 41068, Republic of Korea
| | - Xiaoxu Li
- Laboratory of Integrative Systems Physiology, École polytechnique fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Maroun Bou Sleiman
- Laboratory of Integrative Systems Physiology, École polytechnique fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Su Jeong Lee
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34141, Republic of Korea
| | - Dae-Soo Kim
- Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34141, Republic of Korea
- Digital Biotech Innovation Center, KRIBB, Daejeon, 34141, Republic of Korea
| | - Jaehoon Kim
- Department of Biological Sciences, KAIST, Daejeon, 34141, Republic of Korea
| | - Dae-Sik Lim
- National Creative Research Center for Cell Plasticity, KAIST Stem Cell Center, Department of Biological Sciences, KAIST, Daejeon, 34141, Republic of Korea
| | - Eui-Jeon Woo
- Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34141, Republic of Korea
- Disease Target Structure Research Center, KRIBB, Daejeon, 34141, Republic of Korea
| | - Eun Woo Lee
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34141, Republic of Korea
| | - Baek Soo Han
- Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34141, Republic of Korea
- Biodefense Research Center, KRIBB, Daejeon, 34141, Republic of Korea
| | - Kyoung-Jin Oh
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34141, Republic of Korea
| | - Sang Chul Lee
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Johan Auwerx
- Laboratory of Integrative Systems Physiology, École polytechnique fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Ji Young Mun
- Neural Circuit Research Group, Korea Brain Research Institute, Daegu, 41068, Republic of Korea
| | - Hyun-Woo Rhee
- Department of Chemistry, Seoul National University, Seoul, 08826, Republic of Korea
| | - Won Kon Kim
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
- Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34141, Republic of Korea.
- School of Medicine, Sungkyunkwan University, Suwon, 16419, Republic of Korea.
| | - Kwang-Hee Bae
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
- Department of Developmental and Cell Biology, School of Biological Sciences, University of California, Irvine, CA, 92697, USA.
| | - Jae Myoung Suh
- Graduate School of Medical Science and Engineering, KAIST, Daejeon, 34141, Republic of Korea.
| |
Collapse
|
21
|
Kim J, Kim BY, Lee JS, Jeong YM, Cho HJ, Park E, Kim D, Kim SS, Kim BT, Choi YJ, Won YY, Jin HS, Chung YS, Jeong SY. UBAP2 plays a role in bone homeostasis through the regulation of osteoblastogenesis and osteoclastogenesis. Nat Commun 2023; 14:3668. [PMID: 37339951 PMCID: PMC10281941 DOI: 10.1038/s41467-023-39448-8] [Citation(s) in RCA: 1] [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: 02/08/2021] [Accepted: 06/14/2023] [Indexed: 06/22/2023] Open
Abstract
Osteoporosis is a condition characterized by decreased bone mineral density (BMD) and reduced bone strength, leading to an increased risk of fractures. Here, to identify novel risk variants for susceptibility to osteoporosis-related traits, an exome-wide association study is performed with 6,485 exonic single nucleotide polymorphisms (SNPs) in 2,666 women of two Korean study cohorts. The rs2781 SNP in UBAP2 gene is suggestively associated with osteoporosis and BMD with p-values of 6.1 × 10-7 (odds ratio = 1.72) and 1.1 × 10-7 in the case-control and quantitative analyzes, respectively. Knockdown of Ubap2 in mouse cells decreases osteoblastogenesis and increases osteoclastogenesis, and knockdown of ubap2 in zebrafish reveals abnormal bone formation. Ubap2 expression is associated with E-cadherin (Cdh1) and Fra1 (Fosl1) expression in the osteclastogenesis-induced monocytes. UBAP2 mRNA levels are significantly reduced in bone marrow, but increased in peripheral blood, from women with osteoporosis compared to controls. UBAP2 protein level is correlated with the blood plasma level of the representative osteoporosis biomarker osteocalcin. These results suggest that UBAP2 has a critical role in bone homeostasis through the regulation of bone remodeling.
Collapse
Affiliation(s)
- Jeonghyun Kim
- Department of Medical Genetics, Ajou University School of Medicine, Suwon, Republic of Korea
- Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon, Republic of Korea
| | - Bo-Young Kim
- Division of Intractable Disease, Center for Biomedical Sciences, National Institute of Health, Korea Centers for Disease Control & Prevention, Cheongju, Republic of Korea
| | - Jeong-Soo Lee
- Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- KRIBB School, University of Science and Technology, Daejeon, Republic of Korea
| | - Yun-Mi Jeong
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Hyun-Ju Cho
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Eunkuk Park
- Department of Medical Genetics, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Dowan Kim
- Department of Medical Genetics, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Sung-Soo Kim
- Department of Biomedical Laboratory Science, College of Life and Health Sciences, Hoseo University, Asan, Republic of Korea
| | - Bom-Taeck Kim
- Department of Family Practice and Community Health, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Yong Jun Choi
- Department of Endocrinology and Metabolism, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Ye-Yeon Won
- Department of Orthopedic Surgery, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Hyun-Seok Jin
- Department of Biomedical Laboratory Science, College of Life and Health Sciences, Hoseo University, Asan, Republic of Korea.
| | - Yoon-Sok Chung
- Department of Endocrinology and Metabolism, Ajou University School of Medicine, Suwon, Republic of Korea.
| | - Seon-Yong Jeong
- Department of Medical Genetics, Ajou University School of Medicine, Suwon, Republic of Korea.
- Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon, Republic of Korea.
| |
Collapse
|
22
|
Im JY, Kang MJ, Kim BK, Won M. DDIAS, DNA damage-induced apoptosis suppressor, is a potential therapeutic target in cancer. Exp Mol Med 2023:10.1038/s12276-023-00974-6. [PMID: 37121974 DOI: 10.1038/s12276-023-00974-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 01/11/2023] [Accepted: 01/19/2023] [Indexed: 05/02/2023] Open
Abstract
Increasing evidence indicates that DNA damage-induced apoptosis suppressor (DDIAS) is an oncogenic protein that is highly expressed in a variety of cancers, including colorectal cancer, lung cancer, breast cancer, and hepatocellular carcinoma (HCC). The discovery of DDIAS as a novel therapeutic target and its role in human cancer biology is fascinating and noteworthy. Recent studies have shown that DDIAS is involved in tumorigenesis, metastasis, DNA repair and synthesis, and drug resistance and that it plays multiple roles with distinct binding partners in several human cancers. This review focuses on the function of DDIAS and its regulatory proteins in human cancer as potential targets for cancer therapy, as well as the development and future prospects of DDIAS inhibitors.
Collapse
Affiliation(s)
- Joo-Young Im
- Personalized Genomic Medicine Research Center, KRIBB, Daejeon, 34141, Republic of Korea.
| | - Mi-Jung Kang
- Personalized Genomic Medicine Research Center, KRIBB, Daejeon, 34141, Republic of Korea
| | - Bo-Kyung Kim
- Personalized Genomic Medicine Research Center, KRIBB, Daejeon, 34141, Republic of Korea
- University of Science and Technology (UST), Daejeon, 34113, Republic of Korea
- R&D Center, OneCureGEN Co., Ltd., Daejeon, 34141, Republic of Korea
| | - Misun Won
- Personalized Genomic Medicine Research Center, KRIBB, Daejeon, 34141, Republic of Korea.
- University of Science and Technology (UST), Daejeon, 34113, Republic of Korea.
- R&D Center, OneCureGEN Co., Ltd., Daejeon, 34141, Republic of Korea.
| |
Collapse
|
23
|
Choi YJ, Yoo JS, Jung K, Rice L, Kim D, Zlojutro V, Frimel M, Madden E, Choi UY, Foo SS, Choi Y, Jiang Z, Johnson H, Kwak MJ, Kang S, Hong B, Seo GJ, Kim S, Lee SA, Amini-Bavil-Olyaee S, Maazi H, Akbari O, Asosingh K, Jung JU. Lung-specific MCEMP1 functions as an adaptor for KIT to promote SCF-mediated mast cell proliferation. Nat Commun 2023; 14:2045. [PMID: 37041174 PMCID: PMC10090139 DOI: 10.1038/s41467-023-37873-3] [Citation(s) in RCA: 3] [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: 03/08/2022] [Accepted: 04/03/2023] [Indexed: 04/13/2023] Open
Abstract
Lung mast cells are important in host defense, and excessive proliferation or activation of these cells can cause chronic inflammatory disorders like asthma. Two parallel pathways induced by KIT-stem cell factor (SCF) and FcεRI-immunoglobulin E interactions are critical for the proliferation and activation of mast cells, respectively. Here, we report that mast cell-expressed membrane protein1 (MCEMP1), a lung-specific surface protein, functions as an adaptor for KIT, which promotes SCF-mediated mast cell proliferation. MCEMP1 elicits intracellular signaling through its cytoplasmic immunoreceptor tyrosine-based activation motif and forms a complex with KIT to enhance its autophosphorylation and activation. Consequently, MCEMP1 deficiency impairs SCF-induced peritoneal mast cell proliferation in vitro and lung mast cell expansion in vivo. Mcemp1-deficient mice exhibit reduced airway inflammation and lung impairment in chronic asthma mouse models. This study shows lung-specific MCEMP1 as an adaptor for KIT to facilitate SCF-mediated mast cell proliferation.
Collapse
Affiliation(s)
- Youn Jung Choi
- Department of Cancer Biology, Infection Biology Program, and Global Center for Pathogen and Human Health Research, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA.
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA.
| | - Ji-Seung Yoo
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
- School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, Kyungpook National University, Daegu, 41566, South Korea
| | - Kyle Jung
- Department of Cancer Biology, Infection Biology Program, and Global Center for Pathogen and Human Health Research, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Logan Rice
- Department of Cancer Biology, Infection Biology Program, and Global Center for Pathogen and Human Health Research, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Dokyun Kim
- Department of Cancer Biology, Infection Biology Program, and Global Center for Pathogen and Human Health Research, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Violetta Zlojutro
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Matthew Frimel
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Evan Madden
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Un Yung Choi
- Department of Cancer Biology, Infection Biology Program, and Global Center for Pathogen and Human Health Research, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Suan-Sin Foo
- Department of Cancer Biology, Infection Biology Program, and Global Center for Pathogen and Human Health Research, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Younho Choi
- Department of Cancer Biology, Infection Biology Program, and Global Center for Pathogen and Human Health Research, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
- Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL, 34987, USA
| | - Zhongyi Jiang
- Department of Cancer Biology, Infection Biology Program, and Global Center for Pathogen and Human Health Research, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Holly Johnson
- Department of Cancer Biology, Infection Biology Program, and Global Center for Pathogen and Human Health Research, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Mi-Jeong Kwak
- Department of Cancer Biology, Infection Biology Program, and Global Center for Pathogen and Human Health Research, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Seokmin Kang
- Department of Cancer Biology, Infection Biology Program, and Global Center for Pathogen and Human Health Research, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Brian Hong
- Department of Cancer Biology, Infection Biology Program, and Global Center for Pathogen and Human Health Research, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Gil Ju Seo
- Department of Cancer Biology, Infection Biology Program, and Global Center for Pathogen and Human Health Research, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Stephanie Kim
- Department of Cancer Biology, Infection Biology Program, and Global Center for Pathogen and Human Health Research, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Shin-Ae Lee
- Department of Cancer Biology, Infection Biology Program, and Global Center for Pathogen and Human Health Research, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Samad Amini-Bavil-Olyaee
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
- Biosafety Development Group, Cellular Sciences Department, Amgen Inc., One Amgen Center Drive, Thousand Oaks, CA, 91320, USA
| | - Hadi Maazi
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Omid Akbari
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Kewal Asosingh
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA
| | - Jae U Jung
- Department of Cancer Biology, Infection Biology Program, and Global Center for Pathogen and Human Health Research, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, 44195, USA.
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA.
- Florida Research and Innovation Center, Cleveland Clinic, Port Saint Lucie, FL, 34987, USA.
| |
Collapse
|
24
|
Kwon PS, Xu S, Oh H, Kwon SJ, Rodrigues AL, Feroz M, Fraser K, He P, Zhang F, Hong JJ, Linhardt RJ, Dordick JS. Suramin binds and inhibits infection of SARS-CoV-2 through both spike protein-heparan sulfate and ACE2 receptor interactions. Commun Biol 2023; 6:387. [PMID: 37031303 PMCID: PMC10082822 DOI: 10.1038/s42003-023-04789-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 03/31/2023] [Indexed: 04/10/2023] Open
Abstract
SARS-CoV-2 receptor binding domains (RBDs) interact with both the ACE2 receptor and heparan sulfate on the surface of host cells to enhance SARS-CoV-2 infection. We show that suramin, a polysulfated synthetic drug, binds to the ACE2 receptor and heparan sulfate binding sites on the RBDs of wild-type, Delta, and Omicron variants. Specifically, heparan sulfate and suramin had enhanced preferential binding for Omicron RBD, and suramin is most potent against the live SARS-CoV-2 Omicron variant (B.1.1.529) when compared to wild type and Delta (B.1.617.2) variants in vitro. These results suggest that inhibition of live virus infection occurs through dual SARS-CoV-2 targets of S-protein binding and previously reported RNA-dependent RNA polymerase inhibition and offers the possibility for this and other polysulfated molecules to be used as potential therapeutic and prophylactic options against COVID-19.
Collapse
Affiliation(s)
- Paul S Kwon
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY, USA
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA
| | - Shirley Xu
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Hanseul Oh
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Chungcheongbuk, Republic of Korea
- College of Veterinary Medicine, Chungbuk National University, Cheongju, Chungcheongbuk, Republic of Korea
| | - Seok-Joon Kwon
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Andre L Rodrigues
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Maisha Feroz
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Keith Fraser
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Peng He
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Fuming Zhang
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Jung Joo Hong
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Chungcheongbuk, Republic of Korea.
| | - Robert J Linhardt
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY, USA.
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA.
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, USA.
| | - Jonathan S Dordick
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA.
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, USA.
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY, USA.
| |
Collapse
|
25
|
Jeong KB, Ryu M, Kim JS, Kim M, Yoo J, Chung M, Oh S, Jo G, Lee SG, Kim HM, Lee MK, Chi SW. Single-molecule fingerprinting of protein-drug interaction using a funneled biological nanopore. Nat Commun 2023; 14:1461. [PMID: 37015934 PMCID: PMC10073129 DOI: 10.1038/s41467-023-37098-4] [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] [Received: 02/09/2022] [Accepted: 03/01/2023] [Indexed: 04/06/2023] Open
Abstract
In drug discovery, efficient screening of protein-drug interactions (PDIs) is hampered by the limitations of current biophysical approaches. Here, we develop a biological nanopore sensor for single-molecule detection of proteins and PDIs using the pore-forming toxin YaxAB. Using this YaxAB nanopore, we demonstrate label-free, single-molecule detection of interactions between the anticancer Bcl-xL protein and small-molecule drugs as well as the Bak-BH3 peptide. The long funnel-shaped structure and nanofluidic characteristics of the YaxAB nanopore enable the electro-osmotic trapping of diverse folded proteins and high-resolution monitoring of PDIs. Distinctive nanopore event distributions observed in the two-dimensional (ΔI/Io-versus-IN) plot illustrate the ability of the YaxAB nanopore to discriminate individual small-molecule drugs bound to Bcl-xL from non-binders. Taken together, our results present the YaxAB nanopore as a robust platform for label-free, ultrasensitive, single-molecule detection of PDIs, opening up a possibility for low-cost, highly efficient drug discovery against diverse drug targets.
Collapse
Affiliation(s)
- Ki-Baek Jeong
- Disease Target Structure Research Center, Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- Critical Diseases Diagnostics Convergence Research Center, KRIBB, Daejeon, 34141, Republic of Korea
| | - Minju Ryu
- Disease Target Structure Research Center, Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- Department of Proteome Structural Biology, KRIBB School of Bioscience, University of Science and Technology, Daejeon, 34113, Republic of Korea
| | - Jin-Sik Kim
- Disease Target Structure Research Center, Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
- Critical Diseases Diagnostics Convergence Research Center, KRIBB, Daejeon, 34141, Republic of Korea
| | - Minsoo Kim
- Department of Physics, Sungkyunkwan University, Suwon, Gyeonggi, 16419, Republic of Korea
| | - Jejoong Yoo
- Department of Physics, Sungkyunkwan University, Suwon, Gyeonggi, 16419, Republic of Korea
| | - Minji Chung
- Disease Target Structure Research Center, Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Sohee Oh
- Disease Target Structure Research Center, Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Gyunghee Jo
- Center for Biomolecular and Cellular Structure, Institute for Basic Science (IBS), Daejeon, 34126, Republic of Korea
| | - Seong-Gyu Lee
- Center for Biomolecular and Cellular Structure, Institute for Basic Science (IBS), Daejeon, 34126, Republic of Korea
| | - Ho Min Kim
- Center for Biomolecular and Cellular Structure, Institute for Basic Science (IBS), Daejeon, 34126, Republic of Korea
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Mi-Kyung Lee
- Disease Target Structure Research Center, Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
- Critical Diseases Diagnostics Convergence Research Center, KRIBB, Daejeon, 34141, Republic of Korea.
- Department of Proteome Structural Biology, KRIBB School of Bioscience, University of Science and Technology, Daejeon, 34113, Republic of Korea.
| | - Seung-Wook Chi
- Disease Target Structure Research Center, Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
- Department of Proteome Structural Biology, KRIBB School of Bioscience, University of Science and Technology, Daejeon, 34113, Republic of Korea.
- School of Pharmacy, Sungkyunkwan University, Suwon, Gyeonggi, 16419, Republic of Korea.
| |
Collapse
|
26
|
Kim DY, Chung Y, Lee Y, Jeong D, Park KH, Chin HJ, Lee JM, Park S, Ko S, Ko JH, Kim YS. Author Correction: Hypercompact adenine base editors based on a Cas12f variant guided by engineered RNA. Nat Chem Biol 2023; 19:389. [PMID: 36797406 DOI: 10.1038/s41589-023-01258-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Affiliation(s)
| | | | - Yujin Lee
- KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon, Republic of Korea
- Genome Editing Research Center, KRIBB, Daejeon, Republic of Korea
| | - Dongmin Jeong
- KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon, Republic of Korea
- Genome Editing Research Center, KRIBB, Daejeon, Republic of Korea
| | - Kwang-Hyun Park
- Genome Editing Research Center, KRIBB, Daejeon, Republic of Korea
| | - Hyun Jung Chin
- Genome Editing Research Center, KRIBB, Daejeon, Republic of Korea
| | - Jeong Mi Lee
- Genome Editing Research Center, KRIBB, Daejeon, Republic of Korea
| | | | - Sumin Ko
- GenKOre, Daejeon, Republic of Korea
| | - Jeong-Heon Ko
- KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon, Republic of Korea
- Genome Editing Research Center, KRIBB, Daejeon, Republic of Korea
| | - Yong-Sam Kim
- GenKOre, Daejeon, Republic of Korea.
- KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon, Republic of Korea.
- Genome Editing Research Center, KRIBB, Daejeon, Republic of Korea.
| |
Collapse
|
27
|
Lee SA, Chang LC, Jung W, Bowman JW, Kim D, Chen W, Foo SS, Choi YJ, Choi UY, Bowling A, Yoo JS, Jung JU. OASL phase condensation induces amyloid-like fibrillation of RIPK3 to promote virus-induced necroptosis. Nat Cell Biol 2023; 25:92-107. [PMID: 36604592 PMCID: PMC9859756 DOI: 10.1038/s41556-022-01039-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 11/01/2022] [Indexed: 01/07/2023]
Abstract
RIPK3-ZBP1-MLKL-mediated necroptosis is a proinflammatory cell death process that is crucial for antiviral host defence. RIPK3 self-oligomerization and autophosphorylation are prerequisites for executing necroptosis, yet the underlying mechanism of virus-induced RIPK3 activation remains elusive. Interferon-inducible 2'-5' oligoadenylate synthetase-like (OASL) protein is devoid of enzymatic function but displays potent antiviral activity. Here we describe a role of OASL as a virus-induced necroptosis promoter that scaffolds the RIPK3-ZBP1 non-canonical necrosome via liquid-like phase condensation. This liquid-like platform of OASL recruits RIPK3 and ZBP1 via protein-protein interactions to provide spatial segregation for RIPK3 nucleation. This process facilitates the amyloid-like fibril formation and activation of RIPK3 and thereby MLKL phosphorylation for necroptosis. Mice deficient in Oasl1 exhibit severely impaired necroptosis and attenuated inflammation after viral infection, resulting in uncontrolled viral dissemination and lethality. Our study demonstrates an interferon-induced innate response whereby OASL scaffolds RIPK3-ZBP1 assembly via its phase-separated liquid droplets to facilitate necroptosis-mediated antiviral immunity.
Collapse
Affiliation(s)
- Shin-Ae Lee
- Department of Cancer Biology, Infection Biology Program, and Global Center for Pathogen Research and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA.
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
| | - Lin-Chun Chang
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
- Immunology Program of the Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - WooRam Jung
- Department of Cancer Biology, Infection Biology Program, and Global Center for Pathogen Research and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - James W Bowman
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Dokyun Kim
- Department of Cancer Biology, Infection Biology Program, and Global Center for Pathogen Research and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Weiqiang Chen
- Department of Cancer Biology, Infection Biology Program, and Global Center for Pathogen Research and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Suan-Sin Foo
- Department of Cancer Biology, Infection Biology Program, and Global Center for Pathogen Research and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Youn Jung Choi
- Department of Cancer Biology, Infection Biology Program, and Global Center for Pathogen Research and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Un Yung Choi
- Department of Cancer Biology, Infection Biology Program, and Global Center for Pathogen Research and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Anna Bowling
- Department of Cancer Biology, Infection Biology Program, and Global Center for Pathogen Research and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Ji-Seung Yoo
- Center for Study of Emerging and Re-emerging Viruses, Korea Virus Research Institute, Institute for Basic Science, Daejeon, Republic of Korea
| | - Jae U Jung
- Department of Cancer Biology, Infection Biology Program, and Global Center for Pathogen Research and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA.
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
| |
Collapse
|
28
|
Whon TW, Kim HS, Shin NR, Sung H, Kim MS, Kim JY, Kang W, Kim PS, Hyun DW, Seong HJ, Sul WJ, Roh SW, Bae JW. Calf Diarrhea Caused by Prolonged Expansion of Autochthonous Gut Enterobacteriaceae and Their Lytic Bacteriophages. mSystems 2021; 6:e00816-20. [PMID: 33653940 PMCID: PMC8546982 DOI: 10.1128/msystems.00816-20] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Accepted: 02/03/2021] [Indexed: 01/04/2023] Open
Abstract
Neonatal calf diarrhea is a common disease leading to a major economic loss for cattle producers worldwide. Several infectious and noninfectious factors are implicated in calf diarrhea, but disease control remains problematic because of the multifactorial etiology of the disease. Here, we conducted diagnostic multiplex PCR assay and meta-omics analysis (16S rRNA gene-based metataxonomics and untargeted transcriptional profiling) of rectal content of normal and diarrheic beef calves (n = 111). In the diarrheic calf gut, we detected both microbial compositional dysbiosis (i.e., increased abundances of the family Enterobacteriaceae members and their lytic bacteriophages) and functional dysbiosis (i.e., elevated levels of aerobic respiration and virulence potential). The calf diarrheic transcriptome mirrored the gene expression of the bovine host and was enriched in cellular pathways of sulfur metabolism, innate immunity, and gut motility. We then isolated 12 nontoxigenic Enterobacteriaceae strains from the gut of diarrheic calves. Feeding a strain mixture to preweaning mice resulted in a significantly higher level of fecal moisture content, with decreased body weight gain and shortened colon length. The presented findings suggest that gut inflammation followed by a prolonged expansion of nontoxigenic autochthonous Enterobacteriaceae contributes to the onset of diarrhea in preweaning animals.IMPORTANCE Calf diarrhea is the leading cause of death of neonatal calves worldwide. Several infectious and noninfectious factors are implicated in calf diarrhea, but disease control remains problematic because of the multifactorial etiology of the disease. The major finding of the current study centers around the observation of microbial compositional and functional dysbiosis in rectal samples from diarrheic calves. These results highlight the notion that gut inflammation followed by a prolonged expansion of autochthonous Enterobacteriaceae contributes to the onset of calf diarrhea. Moreover, this condition possibly potentiates the risk of invasion of notorious enteric pathogens, including Salmonella spp., and the emergence of inflammation-resistant (or antibiotic-resistant) microbiota via active horizontal gene transfer mediated by lytic bacteriophages.
Collapse
Affiliation(s)
- Tae Woong Whon
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul, Republic of Korea
- Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju, Republic of Korea
| | - Hyun Sik Kim
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul, Republic of Korea
| | - Na-Ri Shin
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul, Republic of Korea
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup-si, Jeollabuk-do, Republic of Korea
| | - Hojun Sung
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul, Republic of Korea
| | - Min-Soo Kim
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul, Republic of Korea
- Department of Microbiology and Molecular Biology, Chungnam National University, Daejeon, Republic of Korea
| | - Joon Yong Kim
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul, Republic of Korea
- Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju, Republic of Korea
| | - Woorim Kang
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul, Republic of Korea
| | - Pil Soo Kim
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul, Republic of Korea
| | - Dong-Wook Hyun
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul, Republic of Korea
| | - Hoon Je Seong
- Department of Systems Biotechnology, Chung-Ang University, Anseong-si, Gyeonggi-do, Republic of Korea
| | - Woo Jun Sul
- Department of Systems Biotechnology, Chung-Ang University, Anseong-si, Gyeonggi-do, Republic of Korea
| | - Seong Woon Roh
- Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju, Republic of Korea
| | - Jin-Woo Bae
- Department of Life and Nanopharmaceutical Sciences and Department of Biology, Kyung Hee University, Seoul, Republic of Korea
| |
Collapse
|
29
|
Kim YI, Kim D, Yu KM, Seo HD, Lee SA, Casel MAB, Jang SG, Kim S, Jung W, Lai CJ, Choi YK, Jung JU. Development of Spike Receptor-Binding Domain Nanoparticles as a Vaccine Candidate against SARS-CoV-2 Infection in Ferrets. mBio 2021; 12:e00230-21. [PMID: 33653891 PMCID: PMC8092224 DOI: 10.1128/mbio.00230-21] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 02/01/2021] [Indexed: 12/31/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a causative agent of the CoV disease 2019 (COVID-19) pandemic, enters host cells via the interaction of its receptor-binding domain (RBD) of the spike protein with host angiotensin-converting enzyme 2 (ACE2). Therefore, the RBD is a promising vaccine target to induce protective immunity against SARS-CoV-2 infection. In this study, we report the development of an RBD protein-based vaccine candidate against SARS-CoV-2 using self-assembling Helicobacter pylori-bullfrog ferritin nanoparticles as an antigen delivery system. RBD-ferritin protein purified from mammalian cells efficiently assembled into 24-mer nanoparticles. Sixteen- to 20-month-old ferrets were vaccinated with RBD-ferritin nanoparticles (RBD nanoparticles) by intramuscular or intranasal inoculation. All vaccinated ferrets with RBD nanoparticles produced potent neutralizing antibodies against SARS-CoV-2. Strikingly, vaccinated ferrets demonstrated efficient protection from SARS-CoV-2 challenge, showing no fever, body weight loss, or clinical symptoms. Furthermore, vaccinated ferrets showed rapid clearance of infectious virus in nasal washes and lungs as well as of viral RNA in respiratory organs. This study demonstrates that spike RBD-nanoparticles are an effective protein vaccine candidate against SARS-CoV-2.
Collapse
Affiliation(s)
- Young-Il Kim
- College of Medicine, Chungbuk National University, Cheongju, Republic of Korea
- Medical Research Institute, Chungbuk National University, Cheongju, Republic of Korea
- Zoonotic Infectious Disease Research Center, Chungbuk National University, Cheongju, Republic of Korea
| | - Dokyun Kim
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
- Global Center for Pathogen Research and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Kwang-Min Yu
- College of Medicine, Chungbuk National University, Cheongju, Republic of Korea
- Medical Research Institute, Chungbuk National University, Cheongju, Republic of Korea
- Zoonotic Infectious Disease Research Center, Chungbuk National University, Cheongju, Republic of Korea
| | - Hogyu David Seo
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
- Global Center for Pathogen Research and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Shin-Ae Lee
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
- Global Center for Pathogen Research and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Mark Anthony B Casel
- College of Medicine, Chungbuk National University, Cheongju, Republic of Korea
- Medical Research Institute, Chungbuk National University, Cheongju, Republic of Korea
- Zoonotic Infectious Disease Research Center, Chungbuk National University, Cheongju, Republic of Korea
| | - Seung-Gyu Jang
- College of Medicine, Chungbuk National University, Cheongju, Republic of Korea
- Medical Research Institute, Chungbuk National University, Cheongju, Republic of Korea
- Zoonotic Infectious Disease Research Center, Chungbuk National University, Cheongju, Republic of Korea
| | - Stephanie Kim
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
- Global Center for Pathogen Research and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - WooRam Jung
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
- Global Center for Pathogen Research and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Chih-Jen Lai
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
- Global Center for Pathogen Research and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Young Ki Choi
- College of Medicine, Chungbuk National University, Cheongju, Republic of Korea
- Medical Research Institute, Chungbuk National University, Cheongju, Republic of Korea
- Zoonotic Infectious Disease Research Center, Chungbuk National University, Cheongju, Republic of Korea
| | - Jae U Jung
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
- Global Center for Pathogen Research and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| |
Collapse
|
30
|
Lee SM, Kong HG, Song GC, Ryu CM. Disruption of Firmicutes and Actinobacteria abundance in tomato rhizosphere causes the incidence of bacterial wilt disease. ISME J 2021; 15:330-347. [PMID: 33028974 PMCID: PMC7852523 DOI: 10.1038/s41396-020-00785-x] [Citation(s) in RCA: 122] [Impact Index Per Article: 40.7] [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] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 08/27/2020] [Accepted: 09/17/2020] [Indexed: 02/08/2023]
Abstract
Enrichment of protective microbiota in the rhizosphere facilitates disease suppression. However, how the disruption of protective rhizobacteria affects disease suppression is largely unknown. Here, we analyzed the rhizosphere microbial community of a healthy and diseased tomato plant grown <30-cm apart in a greenhouse at three different locations in South Korea. The abundance of Gram-positive Actinobacteria and Firmicutes phyla was lower in diseased rhizosphere soil (DRS) than in healthy rhizosphere soil (HRS) without changes in the causative Ralstonia solanacearum population. Artificial disruption of Gram-positive bacteria in HRS using 500-μg/mL vancomycin increased bacterial wilt occurrence in tomato. To identify HRS-specific and plant-protective Gram-positive bacteria species, Brevibacterium frigoritolerans HRS1, Bacillus niacini HRS2, Solibacillus silvestris HRS3, and Bacillus luciferensis HRS4 were selected from among 326 heat-stable culturable bacteria isolates. These four strains did not directly antagonize R. solanacearum but activated plant immunity. A synthetic community comprising these four strains displayed greater immune activation against R. solanacearum and extended plant protection by 4 more days in comparison with each individual strain. Overall, our results demonstrate for the first time that dysbiosis of the protective Gram-positive bacterial community in DRS promotes the incidence of disease.
Collapse
Affiliation(s)
- Sang-Moo Lee
- Molecular Phytobacteriology Laboratory, Infectious Disease Research Center, KRIBB, Daejeon, 34141, South Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, 34113, South Korea
| | - Hyun Gi Kong
- Molecular Phytobacteriology Laboratory, Infectious Disease Research Center, KRIBB, Daejeon, 34141, South Korea
- Crop Protection Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, 54875, South Korea
| | - Geun Cheol Song
- Molecular Phytobacteriology Laboratory, Infectious Disease Research Center, KRIBB, Daejeon, 34141, South Korea
| | - Choong-Min Ryu
- Molecular Phytobacteriology Laboratory, Infectious Disease Research Center, KRIBB, Daejeon, 34141, South Korea.
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, Daejeon, 34113, South Korea.
| |
Collapse
|
31
|
Abstract
Cpf1-linked base editors broaden the targeting scope of programmable cytidine deaminases by recognizing thymidine-rich protospacer-adjacent motifs (PAM) without inducing DNA double-strand breaks (DSBs). Here we present an unbiased in vitro method for identifying genome-wide off-target sites of Cpf1 base editors via whole genome sequencing. First, we treat human genomic DNA with dLbCpf1-BE ribonucleoprotein (RNP) complexes, which convert C-to-U at on-target and off-target sites and, then, with a mixture of E. coli uracil DNA glycosylase (UDG) and DNA glycosylase-lyase Endonuclease VIII, which removes uracil and produces single-strand breaks (SSBs) in vitro. Whole-genome sequencing of the resulting digested genome (Digenome-seq) reveals that, on average, dLbCpf1-BE induces 12 SSBs in vitro per crRNA in the human genome. Off-target sites with an editing frequency as low as 0.1% are successfully identified by this modified Digenome-seq method, demonstrating its high sensitivity. dLbCpf1-BEs and LbCpf1 nucleases often recognize different off-target sites, calling for independent analysis of each tool.
Collapse
Affiliation(s)
- Daesik Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea.
- Center for Genome Engineering, Institute for Basic Science (IBS), Daejeon, 34126, Republic of Korea.
| | - Kayeong Lim
- Center for Genome Engineering, Institute for Basic Science (IBS), Daejeon, 34126, Republic of Korea
- Department of Chemistry, Seoul National University, Seoul, 08826, Republic of Korea
| | - Da-Eun Kim
- Center for Genome Engineering, Institute for Basic Science (IBS), Daejeon, 34126, Republic of Korea
- Department of Chemistry, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jin-Soo Kim
- Center for Genome Engineering, Institute for Basic Science (IBS), Daejeon, 34126, Republic of Korea.
- Department of Chemistry, Seoul National University, Seoul, 08826, Republic of Korea.
| |
Collapse
|
32
|
Kwon PS, Oh H, Kwon SJ, Jin W, Zhang F, Fraser K, Hong JJ, Linhardt RJ, Dordick JS. Sulfated polysaccharides effectively inhibit SARS-CoV-2 in vitro. Cell Discov 2020; 6:50. [PMID: 32714563 PMCID: PMC7378085 DOI: 10.1038/s41421-020-00192-8] [Citation(s) in RCA: 193] [Impact Index Per Article: 48.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 07/10/2020] [Indexed: 12/31/2022] Open
Affiliation(s)
- Paul S. Kwon
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY USA
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY USA
| | - Hanseul Oh
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Chungcheongbuk Republic of Korea
| | - Seok-Joon Kwon
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY USA
| | - Weihua Jin
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY USA
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, 310014 China
| | - Fuming Zhang
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY USA
| | - Keith Fraser
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY USA
| | - Jung Joo Hong
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Chungcheongbuk Republic of Korea
| | - Robert J. Linhardt
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY USA
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY USA
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY USA
| | - Jonathan S. Dordick
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY USA
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY USA
| |
Collapse
|
33
|
Kang SH, Lee WJ, An JH, Lee JH, Kim YH, Kim H, Oh Y, Park YH, Jin YB, Jun BH, Hur JK, Kim SU, Lee SH. Prediction-based highly sensitive CRISPR off-target validation using target-specific DNA enrichment. Nat Commun 2020; 11:3596. [PMID: 32681048 PMCID: PMC7368065 DOI: 10.1038/s41467-020-17418-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [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: 02/01/2020] [Accepted: 06/22/2020] [Indexed: 11/09/2022] Open
Abstract
CRISPR effectors, which comprise a CRISPR-Cas protein and a guide (g)RNA derived from the bacterial immune system, are widely used for target-specific genome editing. When the gRNA recognizes genomic loci with sequences that are similar to the target, deleterious mutations can occur. Off-target mutations with a frequency below 0.5% remain mostly undetected by current genome-wide off-target detection techniques. Here we report a method to effectively detect extremely small amounts of mutated DNA based on predicted off-target-specific amplification. In this study, we used various genome editors to induce intracellular genome mutations, and the CRISPR amplification method detected off-target mutations at a significantly higher rate (1.6~984 fold increase) than an existing targeted amplicon sequencing method. In the near future, CRISPR amplification in combination with genome-wide off-target detection methods will allow detection of genome editor-induced off-target mutations with high sensitivity and in a non-biased manner.
Collapse
Affiliation(s)
- Seung-Hun Kang
- Department of Medicine, Graduate School, Kyung Hee University, Seoul, Republic of Korea
- Futuristic Animal Resource & Research Center (FARRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Republic of Korea
| | - Wi-Jae Lee
- Futuristic Animal Resource & Research Center (FARRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Republic of Korea
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, 143-701, Korea
| | - Ju-Hyun An
- Futuristic Animal Resource & Research Center (FARRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Republic of Korea
- Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, Korea
| | - Jong-Hee Lee
- National Primate Research Center (NPRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Korea
| | - Young-Hyun Kim
- Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, Korea
- National Primate Research Center (NPRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Korea
| | - Hanseop Kim
- Futuristic Animal Resource & Research Center (FARRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Republic of Korea
- School of Life Sciences and Biotechnology, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University, Daegu, Republic of Korea
| | - Yeounsun Oh
- Futuristic Animal Resource & Research Center (FARRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Republic of Korea
- Division of Biotechnology, College of Life Science and Biotechnology, Korea University, Seoul, 02841, Republic of Korea
| | - Young-Ho Park
- Futuristic Animal Resource & Research Center (FARRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Republic of Korea
| | - Yeung Bae Jin
- National Primate Research Center (NPRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Korea
| | - Bong-Hyun Jun
- Department of Bioscience and Biotechnology, Konkuk University, Seoul, 143-701, Korea
| | - Junho K Hur
- Department of Pathology, College of Medicine, Kyung Hee University, Seoul, Republic of Korea.
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul, Republic of Korea.
- Department of Medical Genetics, College of Medicine, Hanyang University, Seoul, Republic of Korea.
| | - Sun-Uk Kim
- Futuristic Animal Resource & Research Center (FARRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Republic of Korea.
- Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, Korea.
| | - Seung Hwan Lee
- National Primate Research Center (NPRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Cheongju, Korea.
| |
Collapse
|
34
|
Abstract
Salt stress causes rapid accumulation of nonexpressor of pathogenesis-related genes 1 (NPR1) protein, known as the redox-sensitive transcription coactivator, which in turn elicits many adaptive responses. The NPR1 protein transiently accumulates in chloroplast stroma under salt stress, which attenuates stress-triggered down-regulation of photosynthetic capability. We observed that oligomeric NPR1 in chloroplasts and cytoplasm had chaperone activity, whereas monomeric NPR1 in the nucleus did not. Additionally, NPR1 overexpression resulted in reinforcement of morning-phased and evening-phased circadian clock. NPR1 overexpression also enhanced antioxidant activity and reduced stress-induced reactive oxygen species (ROS) generation at early stage, followed with transcription levels for ROS detoxification. These results suggest a functional switch from a molecular chaperone to a transcriptional coactivator, which is dependent on subcellular localization. Our findings imply that dual localization of NPR1 is related to proteostasis and redox homeostasis in chloroplasts for emergency restoration as well as transcriptional coactivator in the nucleus for adaptation to stress.
Collapse
Affiliation(s)
- So Yeon Seo
- Department of Biology, Sunchon National University, Sunchon, Chonnam, Republic of Korea
| | - Soo Jin Wi
- Department of Biology, Sunchon National University, Sunchon, Chonnam, Republic of Korea
| | - Ky Young Park
- Department of Biology, Sunchon National University, Sunchon, Chonnam, Republic of Korea.
| |
Collapse
|
35
|
Noh JR, Kim YH, Kim DK, Hwang JH, Kim KS, Choi DH, Lee SJ, Lee HG, Lee TG, Weng HL, Dooley S, Choi HS, Lee CH. Small heterodimer partner negatively regulates C-X-C motif chemokine ligand 2 in hepatocytes during liver inflammation. Sci Rep 2018; 8:15222. [PMID: 30323351 PMCID: PMC6189097 DOI: 10.1038/s41598-018-33660-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 10/03/2018] [Indexed: 11/18/2022] Open
Abstract
Recently, we reported that orphan nuclear receptor small heterodimer partner (SHP) is involved in neutrophil recruitment through the regulation of C-X-C motif chemokine ligand 2 (CXCL2) expression in a concanavalin A (ConA)-induced hepatitis model. In the present study, we examined the mechanisms underlying CXCL2 regulation by SHP and the cell types involved in liver inflammation. To this end, either Shp knockout (KO) or wild-type (WT) bone marrow cells were transferred into sublethally-irradiated WT (KO → WT or WT → WT) or Shp KO (KO → KO or WT → KO) recipients, followed by intravenous injection of ConA (20-30 mg/kg) 8 weeks later. The KO recipient groups showed higher ConA-induced lethality than the WT recipient groups. Accordingly, plasma alanine aminotransferase (ALT) and aspartate aminotransferase (AST) levels, and inflammatory cytokine expressions were significantly higher in the KO recipients than in the WT recipients regardless of donor genotype. Massively increased hepatocyte death in KO recipients, as determined by H&E and TUNEL staining, was observed after ConA challenge. Bone marrow chimera experiments and in vitro chemotaxis assay also showed that SHP-deficient hepatocytes have an enhanced ability to recruit neutrophils to the injured liver. In vitro promoter assays showed that SHP is a negative regulator of Cxcl2 transcription by interfering with c-Jun binding to the AP-1 site within the Cxcl2 promoter. Collectively, SHP regulates Cxcl2 transcription in hepatocytes, playing a pivotal role in the recruitment of neutrophils. SHP-targeting strategies may represent alternative approaches to control fulminant hepatitis.
Collapse
Affiliation(s)
- Jung-Ran Noh
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, South Korea
| | - Yong-Hoon Kim
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, South Korea
- University of Science and Technology (UST), Daejeon, 34113, South Korea
| | - Don-Kyu Kim
- National Creative Research Initiatives Center for Nuclear Receptor Signals and Hormone Research Center, School of Biological Sciences and Technology, Chonnam National University, Gwangju, 61186, South Korea
| | - Jung Hwan Hwang
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, South Korea
- University of Science and Technology (UST), Daejeon, 34113, South Korea
| | - Kyoung-Shim Kim
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, South Korea
- University of Science and Technology (UST), Daejeon, 34113, South Korea
| | - Dong-Hee Choi
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, South Korea
| | - Seon-Jin Lee
- University of Science and Technology (UST), Daejeon, 34113, South Korea
- Immunotherapy Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Hee Gu Lee
- University of Science and Technology (UST), Daejeon, 34113, South Korea
- Immunotherapy Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Tae Geol Lee
- Center for Nano-Bio Measurement, Korea Research Institute of Standard and Science, 267 Gajeong-ro, Yuseong-gu, Daejeon, 34113, South Korea
| | - Hong-Lei Weng
- Department of Medicine II, Section Molecular Hepatology, Medical Faculty Mannheim, Heidelberg University, Theodor-Kutzer Ufer 1-3, 68167, Mannheim, Germany
| | - Steven Dooley
- Department of Medicine II, Section Molecular Hepatology, Medical Faculty Mannheim, Heidelberg University, Theodor-Kutzer Ufer 1-3, 68167, Mannheim, Germany
| | - Hueng-Sik Choi
- National Creative Research Initiatives Center for Nuclear Receptor Signals and Hormone Research Center, School of Biological Sciences and Technology, Chonnam National University, Gwangju, 61186, South Korea.
| | - Chul-Ho Lee
- Laboratory Animal Resource Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, South Korea.
- University of Science and Technology (UST), Daejeon, 34113, South Korea.
| |
Collapse
|
36
|
Noh JY, Jeong DG, Yoon SW, Kim JH, Choi YG, Kang SY, Kim HK. Isolation and characterization of novel bat paramyxovirus B16-40 potentially belonging to the proposed genus Shaanvirus. Sci Rep 2018; 8:12533. [PMID: 30135435 PMCID: PMC6105681 DOI: 10.1038/s41598-018-30319-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [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: 01/15/2018] [Accepted: 07/27/2018] [Indexed: 01/19/2023] Open
Abstract
The bat paramyxovirus B16-40 was first isolated in Korea in this study. Using the isolated virus, we could obtain not only genomic information, but also several biological characteristics of the virus. In the phylogenetic analysis, the virus was found to belong to the recently proposed genus Shaanvirus. Through sequence analyses and in vitro testing, the isolated virus was also found to have haemagglutinin-neuraminidase (HN) protein as one of the structural proteins. When mouse antiserum was generated against the isolated virus and tested, it was cross-reactive to human parainfluenza virus 1 in an indirect immunofluorescence assay but could not cross-neutralize human parainfluenza virus 1. In addition, the bat paramyxovirus B16-40 was not infectious in the mouse model. Collectively, this study provided basic information on further classification of the bat paramyxovirus B16-40 and related viruses in the proposed genus Shaanvirus.
Collapse
Affiliation(s)
- Ji Yeong Noh
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- College of Veterinary Medicine, Chungbuk National University, Cheongju, 28644, Republic of Korea
| | - Dae Gwin Jeong
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Bio-Analytical Science Division, University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Sun-Woo Yoon
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Bio-Analytical Science Division, University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Ji Hyung Kim
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Yong Gun Choi
- The Korean Institute of Biospeleology, Daejeon, Republic of Korea
| | - Shien-Young Kang
- College of Veterinary Medicine, Chungbuk National University, Cheongju, 28644, Republic of Korea.
| | - Hye Kwon Kim
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea.
| |
Collapse
|
37
|
Ramanan R, Tran QG, Cho DH, Jung JE, Kim BH, Shin SY, Choi SH, Liu KH, Kim DS, Lee SJ, Crespo JL, Lee HG, Oh HM, Kim HS. The Ancient Phosphatidylinositol 3-Kinase Signaling System Is a Master Regulator of Energy and Carbon Metabolism in Algae. Plant Physiol 2018; 177:1050-1065. [PMID: 29769325 PMCID: PMC6053016 DOI: 10.1104/pp.17.01780] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 05/02/2018] [Indexed: 05/08/2023]
Abstract
Algae undergo a complete metabolic transformation under stress by arresting cell growth, inducing autophagy and hyper-accumulating biofuel precursors such as triacylglycerols and starch. However, the regulatory mechanisms behind this stress-induced transformation are still unclear. Here, we use biochemical, mutational, and "omics" approaches to demonstrate that PI3K signaling mediates the homeostasis of energy molecules and influences carbon metabolism in algae. In Chlamydomonas reinhardtii, the inhibition and knockdown (KD) of algal class III PI3K led to significantly decreased cell growth, altered cell morphology, and higher lipid and starch contents. Lipid profiling of wild-type and PI3K KD lines showed significantly reduced membrane lipid breakdown under nitrogen starvation (-N) in the KD. RNA-seq and network analyses showed that under -N conditions, the KD line carried out lipogenesis rather than lipid hydrolysis by initiating de novo fatty acid biosynthesis, which was supported by tricarboxylic acid cycle down-regulation and via acetyl-CoA synthesis from glycolysis. Remarkably, autophagic responses did not have primacy over inositide signaling in algae, unlike in mammals and vascular plants. The mutant displayed a fundamental shift in intracellular energy flux, analogous to that in tumor cells. The high free fatty acid levels and reduced mitochondrial ATP generation led to decreased cell viability. These results indicate that the PI3K signal transduction pathway is the metabolic gatekeeper restraining biofuel yields, thus maintaining fitness and viability under stress in algae. This study demonstrates the existence of homeostasis between starch and lipid synthesis controlled by lipid signaling in algae and expands our understanding of such processes, with biotechnological and evolutionary implications.
Collapse
Affiliation(s)
- Rishiram Ramanan
- Department of Environmental Science, School of Earth Science Systems, Central University of Kerala, Tejaswini Hills, Periya, Kasaragod 671316, Kerala, India
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Quynh-Giao Tran
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong-gu, Daejeon 34141, Republic of Korea
- Department of Environmental Biotechnology, KRIBB School of Biotechnology, Korea University of Science and Technology, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Dae-Hyun Cho
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Jae-Eun Jung
- Genome Research Center, KRIBB, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Byung-Hyuk Kim
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Sang-Yoon Shin
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong-gu, Daejeon 34141, Republic of Korea
- Department of Environmental Biotechnology, KRIBB School of Biotechnology, Korea University of Science and Technology, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Sae-Hae Choi
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Kwang-Hyeon Liu
- College of Pharmacy, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Dae-Soo Kim
- Genome Research Center, KRIBB, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Seon-Jin Lee
- Biomedical Genomics Research Center, KRIBB, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - José L Crespo
- Instituto de Bioquimica Vegetal y Fotosintesis, Consejo Superior de Investigaciones Cientificas, Universidad de Sevilla, Seville 41092, Spain
| | - Hee-Gu Lee
- Biomedical Genomics Research Center, KRIBB, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Hee-Mock Oh
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong-gu, Daejeon 34141, Republic of Korea
- Department of Environmental Biotechnology, KRIBB School of Biotechnology, Korea University of Science and Technology, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Hee-Sik Kim
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Yuseong-gu, Daejeon 34141, Republic of Korea
- Department of Environmental Biotechnology, KRIBB School of Biotechnology, Korea University of Science and Technology, Yuseong-gu, Daejeon 34141, Republic of Korea
| |
Collapse
|