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Lee S, Lee KY, Park JH, Kim DW, Oh HK, Oh ST, Jeon J, Lee D, Joe S, Chu HBK, Kang J, Lee JY, Cho S, Shim H, Kim SC, Lee HS, Kim YJ, Yang JO, Lee J, Kang SB. Exploring the DNA methylome of Korean patients with colorectal cancer consolidates the clinical implications of cancer-associated methylation markers. BMB Rep 2024; 57:161-166. [PMID: 37964634 PMCID: PMC10979344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/26/2023] [Accepted: 11/13/2023] [Indexed: 11/16/2023] Open
Abstract
Aberrant DNA methylation plays a critical role in the development and progression of colorectal cancer (CRC), which has high incidence and mortality rates in Korea. Various CRC-associated methylation markers for cancer diagnosis and prognosis have been developed; however, they have not been validated for Korean patients owing to the lack of comprehensive clinical and methylome data. Here, we obtained reliable methylation profiles for 228 tumor, 103 adjacent normal, and two unmatched normal colon tissues from Korean patients with CRC using an Illumina Infinium EPIC array; the data were corrected for biological and experiment biases. A comparative methylome analysis confirmed the previous findings that hypermethylated positions in the tumor were highly enriched in CpG island and promoter, 5' untranslated, and first exon regions. However, hypomethylated positions were enriched in the open-sea regions considerably distant from CpG islands. After applying a CpG island methylator phenotype (CIMP) to the methylome data of tumor samples to stratify the CRC patients, we consolidated the previously established clinicopathological findings that the tumors with high CIMP signatures were significantly enriched in the right colon. The results showed a higher prevalence of microsatellite instability status and MLH1 methylation in tumors with high CMP signatures than in those with low or non-CIMP signatures. Therefore, our methylome analysis and dataset provide insights into applying CRC-associated methylation markers for Korean patients regarding cancer diagnosis and prognosis. [BMB Reports 2024; 57(3): 161-166].
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Affiliation(s)
- Sejoon Lee
- Precision Medicine Center, Seoul National University Bundang Hospital, Seongnam 13620, Korea
| | - Kil-yong Lee
- Department of Surgery, Uijeongbu St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Uijeongbu 11765, Korea
| | - Ji-Hwan Park
- Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
- Department of Bioscience, University of Science and Technology (UST), Daejeon 34113, Korea
| | - Duck-Woo Kim
- Department of Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam 13620, Korea
| | - Heung-Kwon Oh
- Department of Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam 13620, Korea
| | - Seong-Taek Oh
- Department of Surgery, Uijeongbu St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Uijeongbu 11765, Korea
| | - Jongbum Jeon
- Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
| | - Dongyoon Lee
- Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
| | - Soobok Joe
- Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
| | - Hoang Bao Khanh Chu
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Jisun Kang
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Jin-Young Lee
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Sheehyun Cho
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Hyeran Shim
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Si-Cho Kim
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Hong Seok Lee
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Young-Joon Kim
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Jin Ok Yang
- Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
| | - Jaeim Lee
- Department of Surgery, Uijeongbu St. Mary’s Hospital, College of Medicine, The Catholic University of Korea, Uijeongbu 11765, Korea
| | - Sung-Bum Kang
- Department of Surgery, Seoul National University Bundang Hospital, Seoul National University College of Medicine, Seongnam 13620, Korea
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2
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Shim H, Jang K, Bang YH, Chu HBK, Kang J, Lee JY, Cho S, Lee HS, Jeon J, Hwang T, Joe S, Lim J, Choi JH, Joo EH, Park K, Moon JH, Han KY, Hong Y, Lee WY, Kim HC, Yun SH, Cho YB, Park YA, Huh JW, Shin JK, Pyo DH, Hong H, Lee HO, Park WY, Yang JO, Kim YJ. Comprehensive profiling of DNA methylation in Korean patients with colorectal cancer. BMB Rep 2024; 57:110-115. [PMID: 37605617 PMCID: PMC10910091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 06/27/2023] [Accepted: 08/21/2023] [Indexed: 08/23/2023] Open
Abstract
Alterations in DNA methylation play an important pathophysiological role in the development and progression of colorectal cancer. We comprehensively profiled DNA methylation alterations in 165 Korean patients with colorectal cancer (CRC), and conducted an in-depth investigation of cancer-specific methylation patterns. Our analysis of the tumor samples revealed a significant presence of hypomethylated probes, primarily within the gene body regions; few hypermethylated sites were observed, which were mostly enriched in promoter-like and CpG island regions. The CpG Island Methylator PhenotypeHigh (CIMP-H) exhibited notable enrichment of microsatellite instability-high (MSI-H). Additionally, our findings indicated a significant correlation between methylation of the MLH1 gene and MSI-H status. Furthermore, we found that the CIMP-H had a higher tendency to affect the right-side of the colon tissues and was slightly more prevalent among older patients. Through our methylome profile analysis, we successfully verified the thylation patterns and clinical characteristics of Korean patients with CRC. This valuable dataset lays a strong foundation for exploring novel molecular insights and potential therapeutic targets for the treatment of CRC. [BMB Reports 2024; 57(2): 110-115].
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Affiliation(s)
- Hyeran Shim
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Kiwon Jang
- Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
| | - Yeong Hak Bang
- Department of Digital Health, Samsung Advanced Institute for Health Science & Technology (SAIHST), Sungkyunkwan University, Seoul 06355, Korea
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea
| | - Hoang Bao Khanh Chu
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Jisun Kang
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Jin-Young Lee
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Sheehyun Cho
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Hong Seok Lee
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Jongbum Jeon
- Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
| | - Taeyeon Hwang
- Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
| | - Soobok Joe
- Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
| | - Jinyeong Lim
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul 06355, Korea
| | - Ji-Hye Choi
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul 06355, Korea
| | - Eun Hye Joo
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul 06355, Korea
| | - Kyunghee Park
- Samsung Genome Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea, Seoul 04779, Korea
| | - Ji Hwan Moon
- Samsung Genome Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea, Seoul 04779, Korea
| | - Kyung Yeon Han
- Samsung Genome Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea, Seoul 04779, Korea
| | - Yourae Hong
- Department of Oncology, Katholieke Universiteit Leuven, B-3000 Leuven, Belgium, Seoul 04779, Korea
| | - Woo Yong Lee
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea
| | - Hee Cheol Kim
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea
| | - Seong Hyeon Yun
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea
| | - Yong Beom Cho
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea
| | - Yoon Ah Park
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea
| | - Jung Wook Huh
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea
| | - Jung Kyong Shin
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea
| | - Dae Hee Pyo
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea
| | - Hyekyung Hong
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea
| | - Hae-Ock Lee
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
- Department of Biomedicine and Health Sciences, Graduate School, The Catholic University of Korea, Seoul 06591, Korea
| | - Woong-Yang Park
- Department of Digital Health, Samsung Advanced Institute for Health Science & Technology (SAIHST), Sungkyunkwan University, Seoul 06355, Korea
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul 06355, Korea
- Samsung Genome Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, Korea, Seoul 04779, Korea
| | - Jin Ok Yang
- Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
| | - Young-Joon Kim
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
- LepiDyne Co., Ltd., Seoul 04779, Korea
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3
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Golob JL, Oskotsky TT, Tang AS, Roldan A, Chung V, Ha CWY, Wong RJ, Flynn KJ, Parraga-Leo A, Wibrand C, Minot SS, Oskotsky B, Andreoletti G, Kosti I, Bletz J, Nelson A, Gao J, Wei Z, Chen G, Tang ZZ, Novielli P, Romano D, Pantaleo E, Amoroso N, Monaco A, Vacca M, De Angelis M, Bellotti R, Tangaro S, Kuntzleman A, Bigcraft I, Techtmann S, Bae D, Kim E, Jeon J, Joe S, Theis KR, Ng S, Lee YS, Diaz-Gimeno P, Bennett PR, MacIntyre DA, Stolovitzky G, Lynch SV, Albrecht J, Gomez-Lopez N, Romero R, Stevenson DK, Aghaeepour N, Tarca AL, Costello JC, Sirota M. Microbiome preterm birth DREAM challenge: Crowdsourcing machine learning approaches to advance preterm birth research. Cell Rep Med 2024; 5:101350. [PMID: 38134931 PMCID: PMC10829755 DOI: 10.1016/j.xcrm.2023.101350] [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: 03/28/2023] [Revised: 09/15/2023] [Accepted: 12/01/2023] [Indexed: 12/24/2023]
Abstract
Every year, 11% of infants are born preterm with significant health consequences, with the vaginal microbiome a risk factor for preterm birth. We crowdsource models to predict (1) preterm birth (PTB; <37 weeks) or (2) early preterm birth (ePTB; <32 weeks) from 9 vaginal microbiome studies representing 3,578 samples from 1,268 pregnant individuals, aggregated from public raw data via phylogenetic harmonization. The predictive models are validated on two independent unpublished datasets representing 331 samples from 148 pregnant individuals. The top-performing models (among 148 and 121 submissions from 318 teams) achieve area under the receiver operator characteristic (AUROC) curve scores of 0.69 and 0.87 predicting PTB and ePTB, respectively. Alpha diversity, VALENCIA community state types, and composition are important features in the top-performing models, most of which are tree-based methods. This work is a model for translation of microbiome data into clinically relevant predictive models and to better understand preterm birth.
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Affiliation(s)
- Jonathan L Golob
- Division of Infectious Disease, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA; March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA, USA.
| | - Tomiko T Oskotsky
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA, USA; Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA; Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA.
| | - Alice S Tang
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA, USA; Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA; Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Alennie Roldan
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA, USA; Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA; Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | | | - Connie W Y Ha
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Ronald J Wong
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA; March of Dimes Prematurity Research Center at Stanford University, Stanford, CA, USA
| | | | - Antonio Parraga-Leo
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA; Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA; Department of Pediatrics, Obstetrics and Gynaecology, Universidad de Valencia, Valencia, Spain; IVIRMA Global Research Alliance, IVI Foundation, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain
| | - Camilla Wibrand
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA; Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Samuel S Minot
- Data Core, Shared Resources, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Boris Oskotsky
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA
| | - Gaia Andreoletti
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA, USA; Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA; Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Idit Kosti
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA, USA; Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA; Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | | | | | - Jifan Gao
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, USA
| | - Zhoujingpeng Wei
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, USA
| | - Guanhua Chen
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, USA
| | - Zheng-Zheng Tang
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, USA
| | - Pierfrancesco Novielli
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, Università degli Studi di Bari Aldo Moro, Bari, Italy; Istituto Nazionale di Fisica Nucleare, Sezione di Bari, Bari, Italy
| | - Donato Romano
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, Università degli Studi di Bari Aldo Moro, Bari, Italy; Istituto Nazionale di Fisica Nucleare, Sezione di Bari, Bari, Italy
| | - Ester Pantaleo
- Istituto Nazionale di Fisica Nucleare, Sezione di Bari, Bari, Italy; Dipartimento Interateneo di Fisica "M, Merlin", Università degli Studi di Bari Aldo Moro, Bari, Italy
| | - Nicola Amoroso
- Istituto Nazionale di Fisica Nucleare, Sezione di Bari, Bari, Italy; Dipartimento di Farmacia - Scienze del Farmaco, Università degli Studi di Bari Aldo Moro, Bari, Italy
| | - Alfonso Monaco
- Istituto Nazionale di Fisica Nucleare, Sezione di Bari, Bari, Italy; Dipartimento Interateneo di Fisica "M, Merlin", Università degli Studi di Bari Aldo Moro, Bari, Italy
| | - Mirco Vacca
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, Università degli Studi di Bari Aldo Moro, Bari, Italy
| | - Maria De Angelis
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, Università degli Studi di Bari Aldo Moro, Bari, Italy
| | - Roberto Bellotti
- Istituto Nazionale di Fisica Nucleare, Sezione di Bari, Bari, Italy; Dipartimento Interateneo di Fisica "M, Merlin", Università degli Studi di Bari Aldo Moro, Bari, Italy
| | - Sabina Tangaro
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, Università degli Studi di Bari Aldo Moro, Bari, Italy; Istituto Nazionale di Fisica Nucleare, Sezione di Bari, Bari, Italy
| | - Abigail Kuntzleman
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, USA
| | - Isaac Bigcraft
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, USA
| | - Stephen Techtmann
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, USA
| | - Daehun Bae
- School of Electrical Engineering and Computer Science, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Eunyoung Kim
- School of Electrical Engineering and Computer Science, Gwangju Institute of Science and Technology (GIST), Gwangju, Republic of Korea
| | - Jongbum Jeon
- Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
| | - Soobok Joe
- Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
| | - Kevin R Theis
- Department of Biochemistry, Microbiology and Immunology, Wayne State University, Detroit, MI, USA
| | - Sherrianne Ng
- Imperial College Parturition Research Group, Division of the Institute of Reproductive and Developmental Biology, Imperial College London, London, UK; March of Dimes Prematurity Research Centre at Imperial College London, London, UK
| | - Yun S Lee
- Imperial College Parturition Research Group, Division of the Institute of Reproductive and Developmental Biology, Imperial College London, London, UK; March of Dimes Prematurity Research Centre at Imperial College London, London, UK
| | - Patricia Diaz-Gimeno
- IVIRMA Global Research Alliance, IVI Foundation, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain
| | - Phillip R Bennett
- Imperial College Parturition Research Group, Division of the Institute of Reproductive and Developmental Biology, Imperial College London, London, UK; March of Dimes Prematurity Research Centre at Imperial College London, London, UK
| | - David A MacIntyre
- Imperial College Parturition Research Group, Division of the Institute of Reproductive and Developmental Biology, Imperial College London, London, UK; March of Dimes Prematurity Research Centre at Imperial College London, London, UK
| | - Gustavo Stolovitzky
- Center for Computational Biology and Bioinformatics, Columbia University, New York, NY, USA; Thomas J. Watson Research Center, IBM, Yorktown Heights, NY, USA; Sema4, Stamford, CT, USA
| | - Susan V Lynch
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA; Division of Gastroenterology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | | | - Nardhy Gomez-Lopez
- Department of Biochemistry, Microbiology and Immunology, Wayne State University, Detroit, MI, USA; Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, US Department of Health and Human Services, Detroit, MI, USA
| | - Roberto Romero
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, US Department of Health and Human Services, Detroit, MI, USA; Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI, USA; Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI, USA; Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA; Detroit Medical Center, Detroit, MI, USA; Department of Obstetrics and Gynecology, Florida International University, Miami, FL, USA
| | - David K Stevenson
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA; Center for Academic Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Nima Aghaeepour
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA; Department of Anesthesiology, Perioperative, and Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA; Department of Biomedical Data Sciences, Stanford University School of Medicine, Stanford, CA, USA
| | - Adi L Tarca
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, US Department of Health and Human Services, Detroit, MI, USA; Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, USA; Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA; Department of Computer Science, Wayne State University College of Engineering, Detroit, MI, USA
| | - James C Costello
- Department of Pharmacology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Marina Sirota
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA, USA; Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA; Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA.
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4
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Jeon S, Choi H, Jeon Y, Choi WH, Choi H, An K, Ryu H, Bhak J, Lee H, Kwon Y, Ha S, Kim YJ, Blazyte A, Kim C, Kim Y, Kang Y, Woo YJ, Lee C, Seo J, Yoon C, Bolser D, Biro O, Shin ES, Kim BC, Kim SY, Park JH, Jeon J, Jung D, Lee S, Bhak J. Korea4K: whole genome sequences of 4,157 Koreans with 107 phenotypes derived from extensive health check-ups. Gigascience 2024; 13:giae014. [PMID: 38626723 PMCID: PMC11020240 DOI: 10.1093/gigascience/giae014] [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: 04/24/2023] [Revised: 11/28/2023] [Accepted: 03/15/2024] [Indexed: 04/18/2024] Open
Abstract
BACKGROUND Phenome-wide association studies (PheWASs) have been conducted on Asian populations, including Koreans, but many were based on chip or exome genotyping data. Such studies have limitations regarding whole genome-wide association analysis, making it crucial to have genome-to-phenome association information with the largest possible whole genome and matched phenome data to conduct further population-genome studies and develop health care services based on population genomics. RESULTS Here, we present 4,157 whole genome sequences (Korea4K) coupled with 107 health check-up parameters as the largest genomic resource of the Korean Genome Project. It encompasses most of the variants with allele frequency >0.001 in Koreans, indicating that it sufficiently covered most of the common and rare genetic variants with commonly measured phenotypes for Koreans. Korea4K provides 45,537,252 variants, and half of them were not present in Korea1K (1,094 samples). We also identified 1,356 new genotype-phenotype associations that were not found by the Korea1K dataset. Phenomics analyses further revealed 24 significant genetic correlations, 14 pleiotropic associations, and 127 causal relationships based on Mendelian randomization among 37 traits. In addition, the Korea4K imputation reference panel, the largest Korean variants reference to date, showed a superior imputation performance to Korea1K across all allele frequency categories. CONCLUSIONS Collectively, Korea4K provides not only the largest Korean genome data but also corresponding health check-up parameters and novel genome-phenome associations. The large-scale pathological whole genome-wide omics data will become a powerful set for genome-phenome level association studies to discover causal markers for the prediction and diagnosis of health conditions in future studies.
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Affiliation(s)
- Sungwon Jeon
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Clinomics, Inc., Ulsan 44919, Republic of Korea
| | - Hansol Choi
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Yeonsu Jeon
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Clinomics, Inc., Ulsan 44919, Republic of Korea
| | - Whan-Hyuk Choi
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Mathematics, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Hyunjoo Choi
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Kyungwhan An
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Hyojung Ryu
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Clinomics, Inc., Ulsan 44919, Republic of Korea
| | - Jihun Bhak
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Hyeonjae Lee
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Yoonsung Kwon
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Sukyeon Ha
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Computer Science & Engineering (CSE), College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Yeo Jin Kim
- Clinomics, Inc., Ulsan 44919, Republic of Korea
| | - Asta Blazyte
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Lee Gil Ya Cancer and Diabetes Institute, Gachon University, Incheon 21999, Republic of Korea
| | | | | | - Younghui Kang
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Clinomics, Inc., Ulsan 44919, Republic of Korea
| | | | - Chanyoung Lee
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Jeongwoo Seo
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Changhan Yoon
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Dan Bolser
- Geromics Ltd., Cambridge CB1 3NF, United Kingdom
| | | | - Eun-Seok Shin
- Department of Cardiology, Ulsan University Hospital, University of Ulsan College of Medicine, Ulsan 44033, Republic of Korea
| | | | - Seon-Young Kim
- Korea Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Ji-Hwan Park
- Korea Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Jongbum Jeon
- Korea Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Dooyoung Jung
- Department of Biomedical Engineering, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Semin Lee
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Jong Bhak
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Clinomics, Inc., Ulsan 44919, Republic of Korea
- Department of Biomedical Engineering, College of Information-Bio Convergence Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
- Personal Genomics Institute (PGI), Genome Research Foundation (GRF), Osong 28160, Republic of Korea
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5
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Joe S, Kim J, Lee JY, Jeon J, Byeon I, Han SW, Ryoo SB, Park KJ, Song SH, Cho S, Shim H, Chu HBK, Kang J, Lee HS, Kim D, Kim YJ, Kim TY, Kim SY. Epigenetic insights into colorectal cancer: comprehensive genome-wide DNA methylation profiling of 294 patients in Korea. BMB Rep 2023; 56:563-568. [PMID: 37574809 PMCID: PMC10618077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 06/20/2023] [Accepted: 08/14/2023] [Indexed: 08/15/2023] Open
Abstract
DNA methylation regulates gene expression and contributes to tumorigenesis in the early stages of cancer. In colorectal cancer (CRC), CpG island methylator phenotype (CIMP) is recognized as a distinct subset that is associated with specific molecular and clinical features. In this study, we investigated the genomewide DNA methylation patterns among patients with CRC. The methylation data of 1 unmatched normal, 142 adjacent normal, and 294 tumor samples were analyzed. We identified 40,003 differentially methylated positions with 6,933 (79.8%) hypermethylated and 16,145 (51.6%) hypomethylated probes in the genic region. Hypermethylated probes were predominantly found in promoter-like regions, CpG islands, and N shore sites; hypomethylated probes were enriched in open-sea regions. CRC tumors were categorized into three CIMP subgroups, with 90 (30.6%) in the CIMP-high (CIMP-H), 115 (39.1%) in the CIMP-low (CIMP-L), and 89 (30.3%) in the non-CIMP group. The CIMP-H group was associated with microsatellite instabilityhigh tumors, hypermethylation of MLH1, older age, and rightsided tumors. Our results showed that genome-wide methylation analyses classified patients with CRC into three subgroups according to CIMP levels, with clinical and molecular features consistent with previous data. [BMB Reports 2023; 56(10): 563-568].
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Affiliation(s)
- Soobok Joe
- Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
| | - Jinyong Kim
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Jin-Young Lee
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Jongbum Jeon
- Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
| | - Iksu Byeon
- Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
| | - Sae-Won Han
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul 03080, Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Seung-Bum Ryoo
- Department of Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Kyu Joo Park
- Department of Surgery, Seoul National University Hospital, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Sang-Hyun Song
- Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, Korea
| | - Sheehyun Cho
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Hyeran Shim
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Hoang Bao Khanh Chu
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Jisun Kang
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | - Hong Seok Lee
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
| | | | - Young-Joon Kim
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea
- LepiDyne Co., Ltd., Seoul 04779, Korea
| | - Tae-You Kim
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul 03080, Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul 03080, Korea
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 08826, Korea
- IMBdx, Inc., Seoul 08506, Korea
| | - Seon-Young Kim
- Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea
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6
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Golob JL, Oskotsky TT, Tang AS, Roldan A, Chung V, Ha CWY, Wong RJ, Flynn KJ, Parraga-Leo A, Wibrand C, Minot SS, Andreoletti G, Kosti I, Bletz J, Nelson A, Gao J, Wei Z, Chen G, Tang ZZ, Novielli P, Romano D, Pantaleo E, Amoroso N, Monaco A, Vacca M, De Angelis M, Bellotti R, Tangaro S, Kuntzleman A, Bigcraft I, Techtmann S, Bae D, Kim E, Jeon J, Joe S, Theis KR, Ng S, Lee Li YS, Diaz-Gimeno P, Bennett PR, MacIntyre DA, Stolovitzky G, Lynch SV, Albrecht J, Gomez-Lopez N, Romero R, Stevenson DK, Aghaeepour N, Tarca AL, Costello JC, Sirota M. Microbiome Preterm Birth DREAM Challenge: Crowdsourcing Machine Learning Approaches to Advance Preterm Birth Research. medRxiv 2023:2023.03.07.23286920. [PMID: 36945505 PMCID: PMC10029035 DOI: 10.1101/2023.03.07.23286920] [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] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
Globally, every year about 11% of infants are born preterm, defined as a birth prior to 37 weeks of gestation, with significant and lingering health consequences. Multiple studies have related the vaginal microbiome to preterm birth. We present a crowdsourcing approach to predict: (a) preterm or (b) early preterm birth from 9 publicly available vaginal microbiome studies representing 3,578 samples from 1,268 pregnant individuals, aggregated from raw sequences via an open-source tool, MaLiAmPi. We validated the crowdsourced models on novel datasets representing 331 samples from 148 pregnant individuals. From 318 DREAM challenge participants we received 148 and 121 submissions for our two separate prediction sub-challenges with top-ranking submissions achieving bootstrapped AUROC scores of 0.69 and 0.87, respectively. Alpha diversity, VALENCIA community state types, and composition (via phylotype relative abundance) were important features in the top performing models, most of which were tree based methods. This work serves as the foundation for subsequent efforts to translate predictive tests into clinical practice, and to better understand and prevent preterm birth.
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Affiliation(s)
- Jonathan L Golob
- Division of Infectious Disease. Department of Internal Medicine. University of Michigan. Ann Arbor, MI. USA
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
| | - Tomiko T Oskotsky
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
| | - Alice S Tang
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
| | - Alennie Roldan
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
| | | | - Connie W Y Ha
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA
| | - Ronald J Wong
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
- March of Dimes Prematurity Research Center at Stanford University, Stanford, CA USA
| | | | - Antonio Parraga-Leo
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
| | - Camilla Wibrand
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
| | - Samuel S Minot
- Data Core, Shared Resources, Fred Hutchinson Cancer Center. Seattle, WA. USA
| | - Gaia Andreoletti
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
| | - Idit Kosti
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
| | | | | | - Jifan Gao
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | - Zhoujingpeng Wei
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | - Guanhua Chen
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | - Zheng-Zheng Tang
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | - Pierfrancesco Novielli
- Division of Infectious Disease. Department of Internal Medicine. University of Michigan. Ann Arbor, MI. USA
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
- Sage Bionetworks, Seattle, WA. USA
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
- March of Dimes Prematurity Research Center at Stanford University, Stanford, CA USA
- Data Core, Shared Resources, Fred Hutchinson Cancer Center. Seattle, WA. USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | - Donato Romano
- Division of Infectious Disease. Department of Internal Medicine. University of Michigan. Ann Arbor, MI. USA
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
- Sage Bionetworks, Seattle, WA. USA
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
- March of Dimes Prematurity Research Center at Stanford University, Stanford, CA USA
- Data Core, Shared Resources, Fred Hutchinson Cancer Center. Seattle, WA. USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | - Ester Pantaleo
- Division of Infectious Disease. Department of Internal Medicine. University of Michigan. Ann Arbor, MI. USA
| | - Nicola Amoroso
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
| | - Alfonso Monaco
- Division of Infectious Disease. Department of Internal Medicine. University of Michigan. Ann Arbor, MI. USA
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
- Sage Bionetworks, Seattle, WA. USA
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
- March of Dimes Prematurity Research Center at Stanford University, Stanford, CA USA
- Data Core, Shared Resources, Fred Hutchinson Cancer Center. Seattle, WA. USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | - Mirco Vacca
- Division of Infectious Disease. Department of Internal Medicine. University of Michigan. Ann Arbor, MI. USA
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
- Sage Bionetworks, Seattle, WA. USA
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
- March of Dimes Prematurity Research Center at Stanford University, Stanford, CA USA
- Data Core, Shared Resources, Fred Hutchinson Cancer Center. Seattle, WA. USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | - Maria De Angelis
- Division of Infectious Disease. Department of Internal Medicine. University of Michigan. Ann Arbor, MI. USA
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
- Sage Bionetworks, Seattle, WA. USA
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
- March of Dimes Prematurity Research Center at Stanford University, Stanford, CA USA
- Data Core, Shared Resources, Fred Hutchinson Cancer Center. Seattle, WA. USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | - Roberto Bellotti
- Division of Infectious Disease. Department of Internal Medicine. University of Michigan. Ann Arbor, MI. USA
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
- Sage Bionetworks, Seattle, WA. USA
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
- March of Dimes Prematurity Research Center at Stanford University, Stanford, CA USA
- Data Core, Shared Resources, Fred Hutchinson Cancer Center. Seattle, WA. USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | - Sabina Tangaro
- Division of Infectious Disease. Department of Internal Medicine. University of Michigan. Ann Arbor, MI. USA
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
- Sage Bionetworks, Seattle, WA. USA
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
- March of Dimes Prematurity Research Center at Stanford University, Stanford, CA USA
- Data Core, Shared Resources, Fred Hutchinson Cancer Center. Seattle, WA. USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | - Abigail Kuntzleman
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
| | - Isaac Bigcraft
- Division of Infectious Disease. Department of Internal Medicine. University of Michigan. Ann Arbor, MI. USA
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
- Sage Bionetworks, Seattle, WA. USA
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
- March of Dimes Prematurity Research Center at Stanford University, Stanford, CA USA
- Data Core, Shared Resources, Fred Hutchinson Cancer Center. Seattle, WA. USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | - Stephen Techtmann
- Division of Infectious Disease. Department of Internal Medicine. University of Michigan. Ann Arbor, MI. USA
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
- Sage Bionetworks, Seattle, WA. USA
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
- March of Dimes Prematurity Research Center at Stanford University, Stanford, CA USA
- Data Core, Shared Resources, Fred Hutchinson Cancer Center. Seattle, WA. USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | - Daehun Bae
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
| | - Eunyoung Kim
- Division of Infectious Disease. Department of Internal Medicine. University of Michigan. Ann Arbor, MI. USA
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
- Sage Bionetworks, Seattle, WA. USA
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
- March of Dimes Prematurity Research Center at Stanford University, Stanford, CA USA
- Data Core, Shared Resources, Fred Hutchinson Cancer Center. Seattle, WA. USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | | | - Soobok Joe
- Division of Infectious Disease. Department of Internal Medicine. University of Michigan. Ann Arbor, MI. USA
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
- Sage Bionetworks, Seattle, WA. USA
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
- March of Dimes Prematurity Research Center at Stanford University, Stanford, CA USA
- Data Core, Shared Resources, Fred Hutchinson Cancer Center. Seattle, WA. USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | - Kevin R Theis
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA
| | - Sherrianne Ng
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
- March of Dimes Prematurity Research Center at Stanford University, Stanford, CA USA
| | - Yun S Lee Li
- Division of Infectious Disease. Department of Internal Medicine. University of Michigan. Ann Arbor, MI. USA
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
- Sage Bionetworks, Seattle, WA. USA
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
- March of Dimes Prematurity Research Center at Stanford University, Stanford, CA USA
- Data Core, Shared Resources, Fred Hutchinson Cancer Center. Seattle, WA. USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | - Patricia Diaz-Gimeno
- Division of Infectious Disease. Department of Internal Medicine. University of Michigan. Ann Arbor, MI. USA
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
- Sage Bionetworks, Seattle, WA. USA
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
- March of Dimes Prematurity Research Center at Stanford University, Stanford, CA USA
- Data Core, Shared Resources, Fred Hutchinson Cancer Center. Seattle, WA. USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | - Phillip R Bennett
- Division of Infectious Disease. Department of Internal Medicine. University of Michigan. Ann Arbor, MI. USA
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
- Sage Bionetworks, Seattle, WA. USA
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
- March of Dimes Prematurity Research Center at Stanford University, Stanford, CA USA
- Data Core, Shared Resources, Fred Hutchinson Cancer Center. Seattle, WA. USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | - David A MacIntyre
- Division of Infectious Disease. Department of Internal Medicine. University of Michigan. Ann Arbor, MI. USA
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
- Sage Bionetworks, Seattle, WA. USA
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
- March of Dimes Prematurity Research Center at Stanford University, Stanford, CA USA
- Data Core, Shared Resources, Fred Hutchinson Cancer Center. Seattle, WA. USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | - Gustavo Stolovitzky
- Data Core, Shared Resources, Fred Hutchinson Cancer Center. Seattle, WA. USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | - Susan V Lynch
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA
| | | | - Nardhy Gomez-Lopez
- Division of Infectious Disease. Department of Internal Medicine. University of Michigan. Ann Arbor, MI. USA
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
- Sage Bionetworks, Seattle, WA. USA
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
- March of Dimes Prematurity Research Center at Stanford University, Stanford, CA USA
- Data Core, Shared Resources, Fred Hutchinson Cancer Center. Seattle, WA. USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | - Roberto Romero
- Division of Infectious Disease. Department of Internal Medicine. University of Michigan. Ann Arbor, MI. USA
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
- Sage Bionetworks, Seattle, WA. USA
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
- March of Dimes Prematurity Research Center at Stanford University, Stanford, CA USA
- Data Core, Shared Resources, Fred Hutchinson Cancer Center. Seattle, WA. USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | - David K Stevenson
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
| | - Nima Aghaeepour
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
| | - Adi L Tarca
- Division of Infectious Disease. Department of Internal Medicine. University of Michigan. Ann Arbor, MI. USA
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
- Sage Bionetworks, Seattle, WA. USA
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
- March of Dimes Prematurity Research Center at Stanford University, Stanford, CA USA
- Data Core, Shared Resources, Fred Hutchinson Cancer Center. Seattle, WA. USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | - James C Costello
- Division of Infectious Disease. Department of Internal Medicine. University of Michigan. Ann Arbor, MI. USA
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
- Sage Bionetworks, Seattle, WA. USA
- Benioff Center for Microbiome Medicine, Department of Medicine, University of California, San Francisco, CA. USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA. USA
- March of Dimes Prematurity Research Center at Stanford University, Stanford, CA USA
- Data Core, Shared Resources, Fred Hutchinson Cancer Center. Seattle, WA. USA
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI. USA
| | - Marina Sirota
- March of Dimes Prematurity Research Center at the University of California San Francisco, San Francisco, CA USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA. USA
- Department of Pediatrics. University of California San Francisco, San Francisco, CA. USA
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7
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Lee B, Hwang S, Kim PG, Ko G, Jang K, Kim S, Kim JH, Jeon J, Kim H, Jung J, Yoon BH, Byeon I, Jang I, Song W, Choi J, Kim SY. Introduction of the Korea BioData Station (K-BDS) for sharing biological data. Genomics Inform 2023; 21:e12. [PMID: 37037470 PMCID: PMC10085736 DOI: 10.5808/gi.22073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 03/06/2023] [Indexed: 04/03/2023] Open
Abstract
A wave of new technologies has created opportunities for the cost-effective generation of high-throughput profiles of biological systems, foreshadowing a "data-driven science" era. The large variety of data available from biological research is also a rich resource that can be used for innovative endeavors. However, we are facing considerable challenges in big data deposition, integration, and translation due to the complexity of biological data and its production at unprecedented exponential rates. To address these problems, in 2020, the Korean government officially announced a national strategy to collect and manage the biological data produced through national R&D fund allocations and provide the collected data to researchers. To this end, the Korea Bioinformation Center (KOBIC) developed a new biological data repository, the Korea BioData Station (K-BDS), for sharing data from individual researchers and research programs to create a data-driven biological study environment. The K-BDS is dedicated to providing free open access to a suite of featured data resources in support of worldwide activities in both academia and industry.
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8
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Baek Y, Kwak E, Kim Y, Kim A, Song H, Jeon J. 088 Periodontal disease does not increase the risk of subsequent psoriasis: a nationwide population-based cohort study in Korea. J Invest Dermatol 2022. [DOI: 10.1016/j.jid.2022.09.098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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9
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Vaz-Luis I, Masiero M, Cavaletti G, Cervantes A, Chlebowski RT, Curigliano G, Felip E, Ferreira AR, Ganz PA, Hegarty J, Jeon J, Johansen C, Joly F, Jordan K, Koczwara B, Lagergren P, Lambertini M, Lenihan D, Linardou H, Loprinzi C, Partridge AH, Rauh S, Steindorf K, van der Graaf W, van de Poll-Franse L, Pentheroudakis G, Peters S, Pravettoni G. ESMO Expert Consensus Statements on Cancer Survivorship: promoting high-quality survivorship care and research in Europe. Ann Oncol 2022; 33:1119-1133. [PMID: 35963481 DOI: 10.1016/j.annonc.2022.07.1941] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 07/26/2022] [Accepted: 07/29/2022] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The increased number of cancer survivors and the recognition of physical and psychosocial challenges, present from cancer diagnosis through active treatment and beyond, led to the discipline of cancer survivorship. DESIGN AND METHODS Herein, we reflected on the different components of survivorship care, existing models and priorities, in order to facilitate the promotion of high-quality European survivorship care and research. RESULTS We identified five main components of survivorship care: (i) physical effects of cancer and chronic medical conditions; (ii) psychological effects of cancer; (iii) social, work and financial effects of cancer; (iv) surveillance for recurrences and second cancers; and (v) cancer prevention and overall health and well-being promotion. Survivorship care can be delivered by structured care models including but not limited to shared models integrating primary care and oncology services. The choice of the care model to be implemented has to be adapted to local realities. High-quality care should be expedited by the generation of: (i) focused and shared European recommendations, (ii) creation of tools to facilitate implementation of coordinated care and (iii) survivorship educational programs for health care teams and patients. The research agenda should be defined with the participation of health care providers, researchers, policy makers, patients and caregivers. The following patient-centered survivorship research areas were highlighted: (i) generation of a big data platform to collect long-term real-world data in survivors and healthy controls to (a) understand the resources, needs and preferences of patients with cancer, and (b) understand biological determinants of survivorship issues, and (ii) develop innovative effective interventions focused on the main components of survivorship care. CONCLUSIONS The European Society for Medical Oncology (ESMO) can actively contribute in the efforts of the oncology community toward (a) promoting the development of high-quality survivorship care programs, (b) providing educational material and (c) aiding groundbreaking research by reflecting on priorities and by supporting research networking.
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Affiliation(s)
- I Vaz-Luis
- Breast Cancer Unit, Medical Oncology Department, Gustave Roussy-Cancer Campus, Villejuif; UMR 981, Prédicteurs moléculaires et nouvelles cibles en oncologie, Gustave Roussy-Cancer Campus, Villejuif, France.
| | - M Masiero
- Department of Oncology and Hemato-Oncology, University of Milano, Milan; Applied Research Division for Cognitive and Psychological Science, Istituto Europeo di Oncologia, Milan
| | - G Cavaletti
- Experimental Neurology Unit, School of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - A Cervantes
- Department of Medical Oncology, INCLIVA, Biomedical Research Institute, University of Valencia, Valencia; CIBERONC, Instituto de Salud Carlos III, Madrid, Spain
| | | | - G Curigliano
- Department of Oncology and Hemato-Oncology, University of Milano, Milan; Division of Early Drug Development, Istituto Europeo di Oncologia, IRCCS, Milan, Italy
| | - E Felip
- Vall d'Hebron University Hospital, Barcelona, Spain
| | - A R Ferreira
- Breast Unit, Champalimaud Clinical Center, Champalimaud Foundation, Lisbon; Catolica Medical School, Universidade Católica Portuguesa, Lisbon, Portugal
| | - P A Ganz
- UCLA Jonsson Comprehensive Cancer Center and UCLA Fielding School of Public Health, Los Angeles, USA
| | - J Hegarty
- School of Nursing and Midwifery, University College Cork, Cork, Ireland
| | - J Jeon
- Exercise Medicine Center for Cancer and Diabetes Patients (ICONS), Department of Sport Industry, Cancer Prevention Center, Yonsei Cancer Center, Shinchon Severance Hospital, Yonsei University College of Medicine, Yonsei University, Seoul, Korea
| | - C Johansen
- Centre for Cancer Late Effect Research (CASTLE), Department of Oncology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - F Joly
- Department of Medical Oncology, Centre François Baclesse, U1086 Anticipe, Unicaen Normandy Universtity, Caen, France
| | - K Jordan
- Department for Hematology, Oncology and Palliative Medicine, Ernst von Bergmann Hospital, Potsdam; Department of Medicine V, Hematology, Oncology and Rheumatology, University of Heidelberg, Heidelberg, Germany
| | - B Koczwara
- Flinders Medical Centre and Flinders University, Adelaide, Australia
| | - P Lagergren
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; Department of Surgery and Cancer, Imperial College London, London, UK
| | - M Lambertini
- Department of Medical Oncology, U.O. Clinica di Oncologia Medica, IRCCS Ospedale Policlinico San Martino, Genova; Department of Internal Medicine and Medical Specialties (DiMI), School of Medicine, University of Genova, Genova, Italy
| | - D Lenihan
- International Cardio-Oncology Society, Tampa, USA
| | - H Linardou
- Fourth Oncology Department & Comprehensive Clinical Trials Center, Metropolitan Hospital, Athens, Greece
| | | | - A H Partridge
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, USA
| | - S Rauh
- Department of Medical Oncology, Centre Hospitalier Emile Mayrisch, Esch, Luxembourg
| | - K Steindorf
- Division of Physical Activity, Prevention and Cancer, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - W van der Graaf
- Department of Medical Oncology, Netherlands Cancer Institute, Amsterdam; Department of Medical Oncology, Erasmus MC Cancer institute, Erasmus University Medical Center, Rotterdam
| | - L van de Poll-Franse
- Division of Psychosocial Research & Epidemiology, Department of Psycological Research, The Netherlands Cancer Institute, Amsterdam; Department of Research & Development, Netherlands Comprehensive Cancer Organisation (IKNL), Utrecht; CoRPS-Center of Research on Psychology in Somatic diseases, Department of Medical and Clinical Psychology, Tilburg University, Tilburg, The Netherlands
| | - G Pentheroudakis
- European Society for Medical Oncology (ESMO), Lugano, Switzerland
| | - S Peters
- European Society for Medical Oncology (ESMO), Lugano, Switzerland
| | - G Pravettoni
- Department of Oncology and Hemato-Oncology, University of Milano, Milan; Applied Research Division for Cognitive and Psychological Science, Istituto Europeo di Oncologia, Milan
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10
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Kim H, Kim H, Jeon J, Choi S, Ahn J, Beom SH, Shin S, Park S, Ahn J. 324P Effects of screening and treatment improvement on colon cancer survival over 20 years in Korea. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.07.462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
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11
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Kim H, Jeon J, Lee KK, Lee YH. Longitudinal transmission of bacterial and fungal communities from seed to seed in rice. Commun Biol 2022; 5:772. [PMID: 35915150 PMCID: PMC9343636 DOI: 10.1038/s42003-022-03726-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 07/14/2022] [Indexed: 12/22/2022] Open
Abstract
Vertical transmission of microbes is crucial for the persistence of host-associated microbial communities. Although vertical transmission of seed microbes has been reported from diverse plants, ecological mechanisms and dynamics of microbial communities from parent to progeny remain scarce. Here we reveal the veiled ecological mechanism governing transmission of bacterial and fungal communities in rice across two consecutive seasons. We identify 29 bacterial and 34 fungal members transmitted across generations. Abundance-based regression models allow to classify colonization types of the microbes. We find that they are late colonizers dominating each community at the ripening stage. Ecological models further show that the observed temporal colonization patterns are affected by niche change and neutrality. Source-sink modeling reveals that parental seeds and stem endosphere are major origins of progeny seed microbial communities. This study gives empirical evidence for ecological mechanism and dynamics of bacterial and fungal communities as an ecological continuum during seed-to-seed transmission.
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Affiliation(s)
- Hyun Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jongbum Jeon
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, Republic of Korea.,Korea Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Kiseok Kieth Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Republic of Korea.,Department of Ecology and Evolution, The University of Chicago, 1101 East 57th Street, Chicago, IL, 60637, USA
| | - Yong-Hwan Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Republic of Korea. .,Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, Republic of Korea. .,Center for Plant Microbiome Research, Seoul National University, Seoul, 08826, Republic of Korea. .,Plant Immunity Research Center, Seoul National University, Seoul, 08826, Republic of Korea. .,Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
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12
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Jeon J, Ha N, Kim T, Song A. T119 Current status and future at GCMS immunodiagnostics platform (quantum dot). Clin Chim Acta 2022. [DOI: 10.1016/j.cca.2022.04.587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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13
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Jeon J, Kim KT, Choi J, Cheong K, Ko J, Choi G, Lee H, Lee GW, Park SY, Kim S, Kim ST, Min CW, Kang S, Lee YH. Alternative splicing diversifies the transcriptome and proteome of the rice blast fungus during host infection. RNA Biol 2022; 19:373-385. [PMID: 35311472 PMCID: PMC8942408 DOI: 10.1080/15476286.2022.2043040] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Alternative splicing (AS) contributes to diversifying and regulating cellular responses to environmental conditions and developmental cues by differentially producing multiple mRNA and protein isoforms from a single gene. Previous studies on AS in pathogenic fungi focused on profiling AS isoforms under a limited number of conditions. We analysed AS profiles in the rice blast fungus Magnaporthe oryzae, a global threat to rice production, using high-quality transcriptome data representing its vegetative growth (mycelia) and multiple host infection stages. We identified 4,270 AS isoforms derived from 2,413 genes, including 499 genes presumably regulated by infection-specific AS. AS appears to increase during infection, with 32.7% of the AS isoforms being produced during infection but absent in mycelia. Analysis of the isoforms observed at each infection stage showed that 636 AS isoforms were more abundant than corresponding annotated mRNAs, especially after initial hyphal penetration into host cell. Many such dominant isoforms were predicted to encode regulatory proteins such as transcription factors and phospho-transferases. We also identified the genes encoding distinct proteins via AS and confirmed the translation of some isoforms via a proteomic analysis, suggesting potential AS-mediated neo-functionalization of some genes during infection. Comprehensive profiling of the pattern of genome-wide AS during multiple stages of rice-M. oryzae interaction established a foundational resource that will help investigate the role and regulation of AS during rice infection.
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Affiliation(s)
- Jongbum Jeon
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, Korea
- Plant Immunity Research Center, Seoul National University, Seoul, Korea
- Korea Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
| | - Ki-Tae Kim
- Department of Agricultural Life Science, Sunchon National University, Suncheon, Korea
| | - Jaeyoung Choi
- Smart Farm Research Center, Korea Institute of Science and Technology, Gangneung, Korea
| | - Kyeongchae Cheong
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, Korea
| | - Jaeho Ko
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
| | - Gobong Choi
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, Korea
| | - Hyunjun Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
| | | | - Sook-Young Park
- Department of Agricultural Life Science, Sunchon National University, Suncheon, Korea
| | - Seongbeom Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
| | - Sun Tae Kim
- Department of Plant Bioscience, Pusan National University, Miryang, Korea
- Life and Energy Convergence Research Institute, Pusan National University, Miryang, Korea
| | - Cheol Woo Min
- Department of Plant Bioscience, Pusan National University, Miryang, Korea
| | - Seogchan Kang
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA USA
| | - Yong-Hwan Lee
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, Korea
- Plant Immunity Research Center, Seoul National University, Seoul, Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea
- Center for Fungal Genetic Resources, Seoul National University, Seoul, Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
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14
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Choi G, Jeon J, Lee H, Zhou S, Lee YH. Genome-wide profiling of long non-coding RNA of the rice blast fungus Magnaporthe oryzae during infection. BMC Genomics 2022; 23:132. [PMID: 35168559 PMCID: PMC8845233 DOI: 10.1186/s12864-022-08380-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 02/09/2022] [Indexed: 12/05/2022] Open
Abstract
Background Long non-coding RNAs (lncRNAs) play essential roles in developmental processes and disease development at the transcriptional and post-transcriptional levels across diverse taxa. However, only few studies have profiled fungal lncRNAs in a genome-wide manner during host infection. Results Infection-associated lncRNAs were identified using lncRNA profiling over six stages of host infection (e.g., vegetative growth, pre-penetration, biotrophic, and necrotrophic stages) in the model pathogenic fungus, Magnaporthe oryzae. We identified 2,601 novel lncRNAs, including 1,286 antisense lncRNAs and 980 intergenic lncRNAs. Among the identified lncRNAs, 755 were expressed in a stage-specific manner and 560 were infection-specifically expressed lncRNAs (ISELs). To decipher the potential roles of lncRNAs during infection, we identified 365 protein-coding genes that were associated with 214 ISELs. Analysis of the predicted functions of these associated genes suggested that lncRNAs regulate pathogenesis-related genes, including xylanases and effectors. Conclusions The ISELs and their associated genes provide a comprehensive view of lncRNAs during fungal pathogen-plant interactions. This study expands new insights into the role of lncRNAs in the rice blast fungus, as well as other plant pathogenic fungi. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08380-4.
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Affiliation(s)
- Gobong Choi
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, Korea
| | - Jongbum Jeon
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, Korea.,Plant Immunity Research Center, Seoul National University, Seoul, 08826, Korea.,Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Korea
| | - Hyunjun Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Korea
| | - Shenxian Zhou
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Korea
| | - Yong-Hwan Lee
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, Korea. .,Plant Immunity Research Center, Seoul National University, Seoul, 08826, Korea. .,Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Korea. .,Center for Plant Microbiome Research, Center for Fungal Genetic Resources, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Korea.
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15
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Kim H, Jeon J, Lee KK, Lee YH. Compositional Shift of Bacterial, Archaeal, and Fungal Communities Is Dependent on Trophic Lifestyles in Rice Paddy Soil. Front Microbiol 2021; 12:719486. [PMID: 34539610 PMCID: PMC8440912 DOI: 10.3389/fmicb.2021.719486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 08/16/2021] [Indexed: 11/29/2022] Open
Abstract
The soil environment determines plants’ health and performance during their life cycle. Therefore, ecological understanding on variations in soil environments, including physical, chemical, and biological properties, is crucial for managing agricultural fields. Here, we present a comprehensive and extensive blueprint of the bacterial, archaeal, and fungal communities in rice paddy soils with differing soil types and chemical properties. We discovered that natural variations of soil nutrients are important factors shaping microbial diversity. The responses of microbial diversity to soil nutrients were related to the distribution of microbial trophic lifestyles (oligotrophy and copiotrophy) in each community. The compositional changes of bacterial and archaeal communities in response to soil nutrients were mainly governed by oligotrophs, whereas copiotrophs were mainly involved in fungal compositional changes. Compositional shift of microbial communities by fertilization is linked to switching of microbial trophic lifestyles. Random forest models demonstrated that depletion of prokaryotic oligotrophs and enrichment of fungal copiotrophs are the dominant responses to fertilization in low-nutrient conditions, whereas enrichment of putative copiotrophs was important in high-nutrient conditions. Network inference also revealed that trophic lifestyle switching appertains to decreases in intra- and inter-kingdom microbial associations, diminished network connectivity, and switching of hub nodes from oligotrophs to copiotrophs. Our work provides ecological insight into how soil nutrient-driven variations in microbial communities affect soil health in modern agricultural systems.
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Affiliation(s)
- Hyun Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
| | - Jongbum Jeon
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, South Korea
| | - Kiseok Keith Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
| | - Yong-Hwan Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea.,Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, South Korea.,Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea.,Center for Fungal Genetic Resources, Seoul National University, Seoul, South Korea.,Plant Genomics and Breeding Institute, Seoul National University, Seoul, South Korea.,Plant Immunity Research Center, Seoul National University, Seoul, South Korea
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16
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Lee DY, Jeon J, Kim KT, Cheong K, Song H, Choi G, Ko J, Opiyo SO, Correll JC, Zuo S, Madhav S, Wang GL, Lee YH. Correction to: Comparative genome analyses of four rice-infecting Rhizoctonia solani isolates reveal extensive enrichment of homogalacturonan modification genes. BMC Genomics 2021; 22:306. [PMID: 33906599 PMCID: PMC8080325 DOI: 10.1186/s12864-021-07631-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Da-Young Lee
- Department of Plant Pathology, The Ohio State University, Columbus, OH, 43210, USA
| | - Jongbum Jeon
- Fungal Bioinformatics Laboratory, Seoul National University, Seoul, 08826, South Korea.,Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea
| | - Ki-Tae Kim
- Department of Agricultural Life Science, Sunchon National University, Suncheon, 57922, South Korea
| | - Kyeongchae Cheong
- Fungal Bioinformatics Laboratory, Seoul National University, Seoul, 08826, South Korea.,Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea
| | - Hyeunjeong Song
- Fungal Bioinformatics Laboratory, Seoul National University, Seoul, 08826, South Korea.,Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea
| | - Gobong Choi
- Fungal Bioinformatics Laboratory, Seoul National University, Seoul, 08826, South Korea.,Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea
| | - Jaeho Ko
- Fungal Bioinformatics Laboratory, Seoul National University, Seoul, 08826, South Korea.,Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, South Korea
| | - Stephen O Opiyo
- Ohio Agricultural Research and Development Center (OARDC) Molecular & Cellular Imaging Center (MCIC)-Columbus, The Ohio State University, Columbus, OH, 43210, USA
| | - James C Correll
- Department of Entomology & Plant Pathology, University of Arkansas, Fayetteville, AK, 72701, USA
| | - Shimin Zuo
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China
| | - Sheshu Madhav
- Indian Council of Agricultural Research-Indian Institute of Rice Research (ICAR-IIRR), Hyderabad, Telangana, 500030, India
| | - Guo-Liang Wang
- Department of Plant Pathology, The Ohio State University, Columbus, OH, 43210, USA.
| | - Yong-Hwan Lee
- Fungal Bioinformatics Laboratory, Seoul National University, Seoul, 08826, South Korea. .,Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea. .,Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, South Korea. .,Center for Fungal Genetic Resources, Plant Immunity Research Center, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea.
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17
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Park SY, Jeon J, Kim JA, Jeon MJ, Yu NH, Kim S, Park AR, Kim JC, Lee Y, Kim Y, Choi ED, Jeong MH, Lee YH, Kim S. Draft Genome Sequence of Xylaria grammica EL000614, a Strain Producing Grammicin, a Potent Nematicidal Compound. Mycobiology 2021; 49:294-296. [PMID: 34290553 PMCID: PMC8259839 DOI: 10.1080/12298093.2021.1914360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/02/2021] [Accepted: 04/05/2021] [Indexed: 06/13/2023]
Abstract
An endolichenic fungus, Xylaria grammica strain EL000614, showed strong nematicidal effects against plant pathogenic nematode, Meloidogyne incognita by producing grammicin. We report genome assembly of X. grammica EL000614 comprised of 25 scaffolds with a total length of 54.73 Mb, N50 of 4.60 Mb, and 99.8% of BUSCO completeness. GC contents of this genome were 44.02%. Gene families associated with biosynthesis of secondary metabolites or regulatory proteins were identified out of 13,730 gene models predicted.
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Affiliation(s)
- Sook-Young Park
- Department of Plant Medicine, Sunchon National University, Suncheon, Korea
| | - Jongbum Jeon
- Department of Agricultural Biotechnology, Interdisciplinary Program in Agricultural Genomics, Center for Fungal Genetic Resources, and Center for Fungal Pathogenesis, Seoul National University, Seoul, Korea
| | - Jung A Kim
- Animal Resources Division, National Institute of Biological Resources, Incheon, Korea
| | - Mi Jin Jeon
- Microorganism Resources Division, National Institute of Biological Resources, Incheon, Korea
| | - Nan Hee Yu
- Department of Agricultural Chemistry, Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju, Korea
| | - Seulbi Kim
- Department of Agricultural Chemistry, Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju, Korea
| | - Ae Ran Park
- Department of Agricultural Chemistry, Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju, Korea
| | - Jin-Cheol Kim
- Department of Agricultural Chemistry, Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju, Korea
| | - Yerim Lee
- Department of Plant Medicine, Sunchon National University, Suncheon, Korea
| | - Youngmin Kim
- Department of Plant Medicine, Sunchon National University, Suncheon, Korea
| | - Eu Ddeum Choi
- Department of Plant Medicine, Sunchon National University, Suncheon, Korea
| | - Min-Hye Jeong
- Department of Plant Medicine, Sunchon National University, Suncheon, Korea
| | - Yong-Hwan Lee
- Department of Agricultural Biotechnology, Interdisciplinary Program in Agricultural Genomics, Center for Fungal Genetic Resources, and Center for Fungal Pathogenesis, Seoul National University, Seoul, Korea
| | - Soonok Kim
- Microorganism Resources Division, National Institute of Biological Resources, Incheon, Korea
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Lee DY, Jeon J, Kim KT, Cheong K, Song H, Choi G, Ko J, Opiyo SO, Correll JC, Zuo S, Madhav S, Wang GL, Lee YH. Comparative genome analyses of four rice-infecting Rhizoctonia solani isolates reveal extensive enrichment of homogalacturonan modification genes. BMC Genomics 2021; 22:242. [PMID: 33827423 PMCID: PMC8028249 DOI: 10.1186/s12864-021-07549-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 03/23/2021] [Indexed: 11/24/2022] Open
Abstract
Background Plant pathogenic isolates of Rhizoctonia solani anastomosis group 1-intraspecific group IA (AG1-IA) infect a wide range of crops causing diseases such as rice sheath blight (ShB). ShB has become a serious disease in rice production worldwide. Additional genome sequences of the rice-infecting R. solani isolates from different geographical regions will facilitate the identification of important pathogenicity-related genes in the fungus. Results Rice-infecting R. solani isolates B2 (USA), ADB (India), WGL (India), and YN-7 (China) were selected for whole-genome sequencing. Single-Molecule Real-Time (SMRT) and Illumina sequencing were used for de novo sequencing of the B2 genome. The genomes of the other three isolates were then sequenced with Illumina technology and assembled using the B2 genome as a reference. The four genomes ranged from 38.9 to 45.0 Mbp in size, contained 9715 to 11,505 protein-coding genes, and shared 5812 conserved orthogroups. The proportion of transposable elements (TEs) and average length of TE sequences in the B2 genome was nearly 3 times and 2 times greater, respectively, than those of ADB, WGL and YN-7. Although 818 to 888 putative secreted proteins were identified in the four isolates, only 30% of them were predicted to be small secreted proteins, which is a smaller proportion than what is usually found in the genomes of cereal necrotrophic fungi. Despite a lack of putative secondary metabolite biosynthesis gene clusters, the rice-infecting R. solani genomes were predicted to contain the most carbohydrate-active enzyme (CAZyme) genes among all 27 fungal genomes used in the comparative analysis. Specifically, extensive enrichment of pectin/homogalacturonan modification genes were found in all four rice-infecting R. solani genomes. Conclusion Four R. solani genomes were sequenced, annotated, and compared to other fungal genomes to identify distinctive genomic features that may contribute to the pathogenicity of rice-infecting R. solani. Our analyses provided evidence that genomic conservation of R. solani genomes among neighboring AGs was more diversified than among AG1-IA isolates and the presence of numerous predicted pectin modification genes in the rice-infecting R. solani genomes that may contribute to the wide host range and virulence of this necrotrophic fungal pathogen. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07549-7.
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Affiliation(s)
- Da-Young Lee
- Department of Plant Pathology, The Ohio State University, Columbus, OH, 43210, USA
| | - Jongbum Jeon
- Fungal Bioinformatics Laboratory, Seoul National University, Seoul, 08826, South Korea.,Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea
| | - Ki-Tae Kim
- Department of Agricultural Life Science, Sunchon National University, Suncheon, 57922, South Korea
| | - Kyeongchae Cheong
- Fungal Bioinformatics Laboratory, Seoul National University, Seoul, 08826, South Korea.,Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea
| | - Hyeunjeong Song
- Fungal Bioinformatics Laboratory, Seoul National University, Seoul, 08826, South Korea.,Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea
| | - Gobong Choi
- Fungal Bioinformatics Laboratory, Seoul National University, Seoul, 08826, South Korea.,Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea
| | - Jaeho Ko
- Fungal Bioinformatics Laboratory, Seoul National University, Seoul, 08826, South Korea.,Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, South Korea
| | - Stephen O Opiyo
- Ohio Agricultural Research and Development Center (OARDC) Molecular & Cellular Imaging Center (MCIC)-Columbus, The Ohio State University, Columbus, OH, 43210, USA
| | - James C Correll
- Department of Entomology & Plant Pathology, University of Arkansas, Fayetteville, AK, 72701, USA
| | - Shimin Zuo
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China
| | - Sheshu Madhav
- Indian Council of Agricultural Research-Indian Institute of Rice Research (ICAR-IIRR), Hyderabad, 500030, Telangana, India
| | - Guo-Liang Wang
- Department of Plant Pathology, The Ohio State University, Columbus, OH, 43210, USA.
| | - Yong-Hwan Lee
- Fungal Bioinformatics Laboratory, Seoul National University, Seoul, 08826, South Korea. .,Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea. .,Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, South Korea. .,Center for Fungal Genetic Resources, Plant Immunity Research Center, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National University, 08826, Seoul, South Korea.
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19
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Bae S, Lim D, Kim D, Jeon J, Oh T. In vitro antibacterial effects of non-thermal atmospheric plasma irradiation on Staphylococcus pseudintermedius and Pseudomonas aeruginosa. Pol J Vet Sci 2021; 23:13-19. [PMID: 32233288 DOI: 10.24425/pjvs.2019.131414] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
In the last decade, atmospheric plasma has been used to treating bacterial infections in humans due to its bactericidal effects; however, its efficacy in dogs is unclear. This study evaluated the in vitro bactericidal efficacy of atmospheric plasma on Staphylococcus pseudinter- medius and Pseudomonas aeruginosa, two of the most important bacterial agents isolated from canine pyodermas. Three isolates each of S. pseudintermedius and P. aeruginosa obtained from dogs with pyoderma were subjected to atmospheric plasma. The isolates from the control group were not exposed to plasma, while those from the treatment groups were exposed to plasma for 15 (7.5 J/cm2), 30 (15 J/cm2), 60 (30 J/cm2), or 90 (45 J/cm2) seconds. After each treatment, a reduction in colony formation was observed. Bacterial viability was evaluated using the LIVE/ DEAD® BacLight™ Bacterial Viability Kit. The antibacterial effects were evaluated with Image J software and significance was assessed statistically in comparison to the control group. The bactericidal effect of atmospheric plasma against both bacteria increased significantly in a time-dependent manner. These results demonstrate the bactericidal capacity of atmospheric plasma, and suggest that it could serve as an alternative treatment method for canine pyoderma. Further studies are needed to evaluate the safety and efficacy of atmospheric plasma in dogs.
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Affiliation(s)
- S Bae
- Department of Veterinary Internal Medicine, College of Veterinary Medicine, Kyungpook National University, Daegu 41566, Republic of Korea
| | - D Lim
- Department of Veterinary Internal Medicine, College of Veterinary Medicine, Kyungpook National University, Daegu 41566, Republic of Korea
| | - D Kim
- Department of Veterinary Internal Medicine, College of Veterinary Medicine, Kyungpook National University, Daegu 41566, Republic of Korea
| | - J Jeon
- Department of Veterinary Internal Medicine, College of Veterinary Medicine, Kyungpook National University, Daegu 41566, Republic of Korea
| | - T Oh
- Department of Veterinary Internal Medicine, College of Veterinary Medicine, Kyungpook National University, Daegu 41566, Republic of Korea
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20
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Pearce K, Gray N, Gaur P, Jeon J, Suarez A, Shannahan J, Pappas RS, Watson-Wright C. Toxicological analysis of aerosols derived from three electronic nicotine delivery systems using normal human bronchial epithelial cells. Toxicol In Vitro 2020; 69:104997. [PMID: 32896591 DOI: 10.1016/j.tiv.2020.104997] [Citation(s) in RCA: 12] [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: 03/20/2020] [Revised: 07/21/2020] [Accepted: 09/03/2020] [Indexed: 12/19/2022]
Abstract
Electronic nicotine delivery systems (ENDS) are a rapidly growing global market advertised as a safer alternative to combustible cigarettes. However, comprehensive investigations of END aerosol physicochemical and toxicological properties have not been fully explored across brands to assess relative safety. In this study, we evaluated aerosols collected from three ENDS - Juul Fruit Medley (5% nicotine), Logic Power (2.4% nicotine), and Mistic (1.8% nicotine). ENDS aerosols were generated using standard machine puffing regimen and collected with a novel fluoropolymer condensation trap. Triple quadrupole-inductively coupled plasma-mass determined the presence of heavy metals in collected aerosols. The toxicological effects of ENDS aerosols on normal human bronchial epithelial cells (NHBE) were investigated using cellular viability, reactive oxygen species, oxidative stress assays, along with DNA damage assessments using the CometChip©. Results indicated the total metal concentrations within collected ENDS aerosols were higher for Mistic and Logic compared to Juul. Logic Power aerosols elicited higher reactive oxygen species levels than Mistic and Juul in NHBE after 24-h exposure. Similar dose-dependent reductions of cellular viability and total glutathione were found for each exposure. However, Logic and Juul aerosols caused greater single stranded DNA damage compared to Mistic. Our study indicates that regardless of brand, ENDS aerosols are toxic to upper airway epithelial cells and may pose a potential respiratory hazard to occasional and frequent users.
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Affiliation(s)
- K Pearce
- School of Public Health, Georgia State University, Atlanta, GA 30030, United States of America
| | - N Gray
- Tobacco Inorganics Group, Centers for Disease Control and Prevention, Atlanta, GA 30341, United States of America
| | - P Gaur
- School of Public Health, Georgia State University, Atlanta, GA 30030, United States of America
| | - J Jeon
- School of Public Health, Georgia State University, Atlanta, GA 30030, United States of America
| | - A Suarez
- School of Public Health, Georgia State University, Atlanta, GA 30030, United States of America
| | - J Shannahan
- School of Health Sciences, Purdue University, West Lafayette, IN 47907, United States of America
| | - R S Pappas
- Tobacco Inorganics Group, Centers for Disease Control and Prevention, Atlanta, GA 30341, United States of America
| | - C Watson-Wright
- School of Public Health, Georgia State University, Atlanta, GA 30030, United States of America.
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21
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Kim S, Cheong K, Park J, Kim M, Kim J, Seo M, Chae GY, Jang MJ, Mang H, Kwon S, Kim Y, Koo N, Min CW, Kim K, Oh N, Kim K, Jeon J, Kim H, Lee Y, Sohn KH, McCann HC, Ye S, Kim ST, Park K, Lee Y, Choi D. TGFam-Finder: a novel solution for target-gene family annotation in plants. New Phytol 2020; 227:1568-1581. [PMID: 32392385 PMCID: PMC7496378 DOI: 10.1111/nph.16645] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 04/21/2020] [Indexed: 05/26/2023]
Abstract
Whole-genome annotation error that omits essential protein-coding genes hinders further research. We developed Target Gene Family Finder (TGFam-Finder), an alternative tool for the structural annotation of protein-coding genes containing target domain(s) of interest in plant genomes. TGFam-Finder took considerably reduced annotation run-time and improved accuracy compared to conventional annotation tools. Large-scale re-annotation of 50 plant genomes identified an average of 150, 166 and 86 additional far-red-impaired response 1, nucleotide-binding and leucine-rich-repeat, and cytochrome P450 genes, respectively, that were missed in previous annotations. We detected significantly higher number of translated genes in the new annotations using mass spectrometry data from seven plant species compared to previous annotations. TGFam-Finder along with the new gene models can provide an optimized platform for comprehensive functional, comparative, and evolutionary studies in plants.
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Affiliation(s)
- Seungill Kim
- Department of Plant SciencePlant Immunity Research CenterPlant Genomics and Breeding InstituteResearch Institute for Agriculture and Life SciencesSeoul National UniversitySeoul08826Korea
- Department of Environmental HorticultureUniversity of SeoulSeoul02504Korea
| | - Kyeongchae Cheong
- Interdisciplinary Program in Agricultural GenomicsSeoul National UniversitySeoul08826Korea
| | - Jieun Park
- Department of Plant SciencePlant Immunity Research CenterPlant Genomics and Breeding InstituteResearch Institute for Agriculture and Life SciencesSeoul National UniversitySeoul08826Korea
| | - Myung‐Shin Kim
- Department of Plant SciencePlant Immunity Research CenterPlant Genomics and Breeding InstituteResearch Institute for Agriculture and Life SciencesSeoul National UniversitySeoul08826Korea
- Interdisciplinary Program in Agricultural GenomicsSeoul National UniversitySeoul08826Korea
| | - Jihyun Kim
- Department of Plant SciencePlant Immunity Research CenterPlant Genomics and Breeding InstituteResearch Institute for Agriculture and Life SciencesSeoul National UniversitySeoul08826Korea
| | - Min‐Ki Seo
- Department of Plant SciencePlant Immunity Research CenterPlant Genomics and Breeding InstituteResearch Institute for Agriculture and Life SciencesSeoul National UniversitySeoul08826Korea
| | - Geun Young Chae
- Department of Environmental HorticultureUniversity of SeoulSeoul02504Korea
| | - Min Jeong Jang
- Department of Environmental HorticultureUniversity of SeoulSeoul02504Korea
| | - Hyunggon Mang
- Department of Plant SciencePlant Immunity Research CenterPlant Genomics and Breeding InstituteResearch Institute for Agriculture and Life SciencesSeoul National UniversitySeoul08826Korea
| | - Sun‐Ho Kwon
- Department of PharmacologySeoul National University College of MedicineSeoul03080Korea
| | - Yong‐Min Kim
- Korean Bioinformation CenterKorea Research Institute of Bioscience and BiotechnologyDaejeon34141Korea
| | - Namjin Koo
- Korean Bioinformation CenterKorea Research Institute of Bioscience and BiotechnologyDaejeon34141Korea
| | - Cheol Woo Min
- Department of Plant BioscienceLife and Energy Convergence Research InstitutePusan National UniversityMiryang627‐706Korea
| | - Kwang‐Soo Kim
- Department of Biomedical ScienceCollege of Life ScienceCHA UniversitySeongnam13488Korea
| | - Nuri Oh
- Department of Biomedical ScienceCollege of Life ScienceCHA UniversitySeongnam13488Korea
| | - Ki‐Tae Kim
- Department of Agricultural BiotechnologySeoul National UniversitySeoul08826Korea
| | - Jongbum Jeon
- Interdisciplinary Program in Agricultural GenomicsSeoul National UniversitySeoul08826Korea
| | - Hyunbin Kim
- Interdisciplinary Program in Agricultural GenomicsSeoul National UniversitySeoul08826Korea
| | - Yoon‐Young Lee
- Department of Life SciencesPohang University of Science and TechnologyPohangGyeongbuk37673Korea
| | - Kee Hoon Sohn
- Department of Life SciencesPohang University of Science and TechnologyPohangGyeongbuk37673Korea
- School of Interdisciplinary Bioscience and BioengineeringPohang University of Science and TechnologyPohangGyeongbuk37673Korea
| | - Honour C. McCann
- New Zealand Institute for Advanced StudyMassey University AucklandAuckland0632New Zealand
| | - Sang‐Kyu Ye
- Department of PharmacologySeoul National University College of MedicineSeoul03080Korea
| | - Sun Tae Kim
- Department of Plant BioscienceLife and Energy Convergence Research InstitutePusan National UniversityMiryang627‐706Korea
| | - Kyung‐Soon Park
- Department of Biomedical ScienceCollege of Life ScienceCHA UniversitySeongnam13488Korea
| | - Yong‐Hwan Lee
- Interdisciplinary Program in Agricultural GenomicsSeoul National UniversitySeoul08826Korea
- Department of Agricultural BiotechnologySeoul National UniversitySeoul08826Korea
| | - Doil Choi
- Department of Plant SciencePlant Immunity Research CenterPlant Genomics and Breeding InstituteResearch Institute for Agriculture and Life SciencesSeoul National UniversitySeoul08826Korea
- Interdisciplinary Program in Agricultural GenomicsSeoul National UniversitySeoul08826Korea
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22
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Lee M, Lee K, Lee H, Kim N, Jeon J, Jeon S, Oh S, Kim S, Kim S, Lee Y. 0455 Role of Interaction Between Anterior Insula Response to Sleep-Related Pictures and Stress Levels on Sleep Disturbance. Sleep 2020. [DOI: 10.1093/sleep/zsaa056.452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Introduction
Literature suggests that stress may play an important role in sleep disturbance. Individuals with higher stress levels often showed hyperarousal to stressful events, possibly leading to sleep disturbance. Hyperarousal is also one of features of stress-related sleep disturbance. Here, we examined the extent to which stress levels interact with neural activity in response to sleep-related information to predict sleep disturbance.
Methods
Forty eight healthy adults (26 females, age = 35.7 ± 10.5) without sleep disorders based on nocturnal polysomnography participated in this study. They were viewing sleep-related pictures (e.g., bedroom and sunset) and non-sleep related, neutral pictures (e.g., kitchen and landscape) during fMRI scanning. They also completed questionnaires assessing stress levels and sleep disturbance using Life Experience Survey (LES) and Pittsburgh Sleep Quality Index (PSQI), respectively. Activity in response to sleep-related pictures compared to neutral pictures was extracted from our region-of-interest (ROI), the anterior insula, and entered into our moderation models. The SPSS macro PROCESS (Hayes, 2013) was used to conduct moderation analyses. Given a significant correlation between age and PSQI scores, age was included as a covariate.
Results
Our moderation analyses showed that interactions between stress levels and anterior insula response to sleep-related pictures significantly predicted sleep disturbance. Simple slope analyses showed that at higher anterior insula response, higher stress levels were associated with greater sleep disturbance, but at lower anterior insula response, stress was not significantly associated with sleep disturbance. These results indicate that individuals with high levels of stress were more likely to experience sleep disturbance if they showed greater anterior insula response to sleep-related pictures (i.e., hyperarousal in response to sleep-related information).
Conclusion
The current findings suggest that interactions between stress levels and neural substrates of hyperarousal, particularly the anterior insula, may play a critical role in sleep disturbance.
Support
Brain Research Program through the National Research Foundation of Korea funded by the Ministry of Science, ICT & Future Planning (Study No.: 2016M3C7A1904338 and NRF-2018R1D1A1B07049704).
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Affiliation(s)
- M Lee
- Seoul National University Hospital, Seoul, KOREA, REPUBLIC OF
| | - K Lee
- Seoul National University Hospital, Seoul, KOREA, REPUBLIC OF
| | - H Lee
- Seoul National University Hospital, Seoul, KOREA, REPUBLIC OF
| | - N Kim
- Neuroscience Research Institute, Gachon University, Incheon, KOREA, REPUBLIC OF
| | - J Jeon
- Seoul National University Hospital, Seoul, KOREA, REPUBLIC OF
| | - S Jeon
- Department of Psychiatry, Sungkyunkwan University College of Medicine, Samsung Medical Center, Seoul, KOREA, REPUBLIC OF
| | - S Oh
- Department of Psychiatry, Dongguk University Ilsan Hospital, Ilsan, KOREA, REPUBLIC OF
| | - S Kim
- Department of Neurology, Gangneung, Gangneung Asan Hospital,, Gangneung, KOREA, REPUBLIC OF
| | - S Kim
- Department of Psychiatry, Sungkyunkwan University College of Medicine, Samsung Medical Center, Seoul, KOREA, REPUBLIC OF
| | - Y Lee
- Seoul National University Hospital, Seoul, KOREA, REPUBLIC OF
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23
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Lee K, Lee H, Jeon J, Jeon S, Kim N, Oh S, Lee M, Kim S, Lee Y. 0064 Heightened Neural Responses to Negative Words in Shift Workers Using the Stroop Task. Sleep 2020. [DOI: 10.1093/sleep/zsaa056.062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Introduction
Shift work is known to have a negative impact on a wide range of health problems such as sleep disturbance, cognitive impairment, and emotional disorders (e.g., anxiety and depression). It is important to understand underlying mechanisms for negative impact of shift work on health problems. This study aimed to investigate psychological and neural mechanisms associated with shift work.
Methods
Thirty six shift workers (28 females, age = 29.9 ± 7.4) and 35 non-shift workers (20 females, age = 30.5 ± 5.5) participated in this study. They were performing the word Stroop task during fMRI scanning. This task included sleep-related words and negative words to investigate neural substrates associated with sleep-related information and emotional information processing. Neutral words were included as control stimuli. The participants also completed questionnaires assessing sleep-related problems such as Pittsburgh Sleep Quality Index (PSQI) and Epworth Sleepiness Scale, and emotion-related problems such as Beck Depression Inventory and Beck Anxiety Inventory. Two-sample t-tests were conducted to find group differences in self-report measures and neural response to sleep-related words and negative words compared to neutral words.
Results
Relative to non-shift workers, shift workers showed greater sleep disturbance (i.e., higher PSQI), but they did not show any evidence of emotion-related problems. Shift workers also demonstrated greater neural response to negative words (vs. neutral words) in several prefrontal regions (e.g., dorsal anterior cingulate cortex and dorsolateral prefrontal cortex), anterior insula and caudate compared to non-shift workers. However, shift workers did not show significantly different neural response to sleep-related words (vs. neutral words) compared to non-shift workers.
Conclusion
The result from this study provides supporting evidence that shift work is associated with subjective sleep disturbance. Shift workers’ heightened neural response to negative information may reflect their increased sensitivity to negative information, that may contribute to sleep disturbance.
Support
Brain Research Program through the National Research Foundation of Korea funded by the Ministry of Science, ICT & Future Planning (Study No.: 2016M3C7A1904338 and NRF-2018R1D1A1B07049704).
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Affiliation(s)
- K Lee
- Department of Psychiatry and Center for Sleep and Chronobiology, Seoul National University, College of Medicine and Hospital, Seoul, KOREA, REPUBLIC OF
| | - H Lee
- Department of Psychiatry and Center for Sleep and Chronobiology, Seoul National University, College of Medicine and Hospital, Seoul, KOREA, REPUBLIC OF
| | - J Jeon
- Department of Psychiatry and Center for Sleep and Chronobiology, Seoul National University, College of Medicine and Hospital, Seoul, KOREA, REPUBLIC OF
| | - S Jeon
- Sungkyunkwan University College of Medicine, Seoul, KOREA, REPUBLIC OF
| | - N Kim
- Gachon University, Incheon, KOREA, REPUBLIC OF
| | - S Oh
- Department of Psychiatry, Dongguk University Ilsan Hospital, Ilsan, KOREA, REPUBLIC OF
| | - M Lee
- Department of Psychiatry and Center for Sleep and Chronobiology, Seoul National University, College of Medicine and Hospital, Seoul, KOREA, REPUBLIC OF
| | - S Kim
- Sungkyunkwan University College of Medicine, Seoul, KOREA, REPUBLIC OF
| | - Y Lee
- Department of Psychiatry and Center for Sleep and Chronobiology, Seoul National University, College of Medicine and Hospital, Seoul, KOREA, REPUBLIC OF
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Park SY, Jeon J, Kim JA, Jeon MJ, Jeong MH, Kim Y, Lee Y, Chung H, Lee YH, Kim S. Draft Genome Sequence of Alternaria alternata JS-1623, a Fungal Endophyte of Abies koreana. Mycobiology 2020; 48:240-244. [PMID: 37970559 PMCID: PMC10635108 DOI: 10.1080/12298093.2020.1756134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 03/31/2020] [Accepted: 04/08/2020] [Indexed: 11/17/2023]
Abstract
Alternaria alternata JS-1623 is an endophytic fungus isolated from a stem tissue of Korean fir, Abies koreana. Ethyl acetate extracts of culture filtrates exhibited anti-inflammatory activity in LPS induced microglia BV-2 cell without cytotoxicity. Here we report a 33.67 Mb sized genome assembly of JS-1623 comprised of 13 scaffolds with N50 of 4.96 Mb, and 92.41% of BUSCO completeness. GC contents were 50.97%. Of the 11,197 genes annotated, gene families related to the biosynthesis of secondary metabolites or transcription factors were identified.
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Affiliation(s)
- Sook-Young Park
- Department of Plant Medicine, Sunchon National University, Suncheon, Korea
| | - Jongbum Jeon
- Department of Agricultural Biotechnology, Interdisciplinary Program in Agricultural Genomics, Center for Fungal Genetic Resources, and Center for Fungal Pathogenesis, Seoul National University, Seoul, Korea
| | - Jung A. Kim
- Microbiology Resources Division, National Institute of Biological Resources, Incheon, Korea
| | - Mi Jin Jeon
- Microbiology Resources Division, National Institute of Biological Resources, Incheon, Korea
| | - Min-Hye Jeong
- Department of Plant Medicine, Sunchon National University, Suncheon, Korea
| | - Youngmin Kim
- Department of Plant Medicine, Sunchon National University, Suncheon, Korea
| | - Yerim Lee
- Department of Plant Medicine, Sunchon National University, Suncheon, Korea
| | - Hyunjung Chung
- Department of Agricultural Biotechnology, Interdisciplinary Program in Agricultural Genomics, Center for Fungal Genetic Resources, and Center for Fungal Pathogenesis, Seoul National University, Seoul, Korea
| | - Yong-Hwan Lee
- Department of Agricultural Biotechnology, Interdisciplinary Program in Agricultural Genomics, Center for Fungal Genetic Resources, and Center for Fungal Pathogenesis, Seoul National University, Seoul, Korea
| | - Soonok Kim
- Microbiology Resources Division, National Institute of Biological Resources, Incheon, Korea
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25
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Kim H, Lee KK, Jeon J, Harris WA, Lee YH. Domestication of Oryza species eco-evolutionarily shapes bacterial and fungal communities in rice seed. Microbiome 2020; 8:20. [PMID: 32059747 PMCID: PMC7023700 DOI: 10.1186/s40168-020-00805-0] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 02/10/2020] [Indexed: 05/23/2023]
Abstract
BACKGROUND Plant-associated microbiomes, which are shaped by host and environmental factors, support their hosts by providing nutrients and attenuating abiotic and biotic stresses. Although host genetic factors involved in plant growth and immunity are known to shape compositions of microbial communities, the effects of host evolution on microbial communities are not well understood. RESULTS We show evidence that both host speciation and domestication shape seed bacterial and fungal community structures. Genome types of rice contributed to compositional variations of both communities, showing a significant phylosymbiosis with microbial composition. Following the domestication, abundance inequality of bacterial and fungal communities also commonly increased. However, composition of bacterial community was relatively conserved, whereas fungal membership was dramatically changed. These domestication effects were further corroborated when analyzed by a random forest model. With these changes, hub taxa of inter-kingdom networks were also shifted from fungi to bacteria by domestication. Furthermore, maternal inheritance of microbiota was revealed as a major path of microbial transmission across generations. CONCLUSIONS Our findings show that evolutionary processes stochastically affect overall composition of microbial communities, whereas dramatic changes in environments during domestication contribute to assembly of microbiotas in deterministic ways in rice seed. This study further provides new insights on host evolution and microbiome, the starting point of the holobiome of plants, microbial communities, and surrounding environments.
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Affiliation(s)
- Hyun Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Korea
| | - Kiseok Keith Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Korea
| | - Jongbum Jeon
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, Korea
| | - William Anthony Harris
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Korea
| | - Yong-Hwan Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Korea.
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, Korea.
- Center for Fungal Genetic Resources, Seoul National University, Seoul, 08826, Korea.
- Plant Immunity Research Center, Seoul National University, Seoul, 08826, Korea.
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Korea.
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26
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Jeon J, Lee GW, Kim KT, Park SY, Kim S, Kwon S, Huh A, Chung H, Lee DY, Kim CY, Lee YH. Transcriptome Profiling of the Rice Blast Fungus Magnaporthe oryzae and Its Host Oryza sativa During Infection. Mol Plant Microbe Interact 2020; 33:141-144. [PMID: 31634040 DOI: 10.1094/mpmi-07-19-0207-a] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
The rice blast (fungal pathogen: Magnaporthe oryzae and host: Oryza sativa) is one of the most important model pathosystems for understanding plant-microbe interactions. Although both genome sequences were published as the first cases of pathogen and host, only a few in planta transcriptome data during infection are available. Due to technical difficulties, previously reported fungal transcriptome data are not highly qualified to comprehensively profile the expression of fungal genes during infection. Here, we report the high-quality transcriptomes of M. oryzae and rice during infection using a sheath infection-based RNA sequencing approach. This comprehensive expression profiling of the fungal pathogen and its host will provide a better platform for understanding the plant-microbe interactions at the genomic level and serve as a valuable resource for the research community.
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Affiliation(s)
- Jongbum Jeon
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea
| | - Gir-Won Lee
- Department of Agricultural Biotechnology, Seoul National University
| | - Ki-Tae Kim
- Department of Agricultural Biotechnology, Seoul National University
| | - Sook-Young Park
- Department of Plant Medicine, College of Life Science and Natural Resources, Sunchon National University, Suncheon, 57922, South Korea
| | - Seongbeom Kim
- Department of Agricultural Biotechnology, Seoul National University
| | - Seomun Kwon
- Department of Agricultural Biotechnology, Seoul National University
| | - Aram Huh
- Department of Agricultural Biotechnology, Seoul National University
| | - Hyunjung Chung
- Department of Agricultural Biotechnology, Seoul National University
| | - Da-Young Lee
- Department of Agricultural Biotechnology, Seoul National University
| | - Chi-Yeol Kim
- Department of Agricultural Biotechnology, Seoul National University
| | - Yong-Hwan Lee
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea
- Department of Agricultural Biotechnology, Seoul National University
- Center for Fungal Genetic Resources, Plant Immunity Research Center, and Research Institute of Agriculture and Life Sciences, Seoul National University
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Jeon J, Matei N, Marchbank N, Sayer C, Myerson J, Messenger J, Routledge T, Pencharz D. Reducing unnecessary EBUS: use of SUVmax ratios in PET-CT can accurately classify some nodes as benign, even when enlarged. Lung Cancer 2020. [DOI: 10.1016/s0169-5002(20)30072-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Kim KT, Ko J, Song H, Choi G, Kim H, Jeon J, Cheong K, Kang S, Lee YH. Evolution of the Genes Encoding Effector Candidates Within Multiple Pathotypes of Magnaporthe oryzae. Front Microbiol 2019; 10:2575. [PMID: 31781071 PMCID: PMC6851232 DOI: 10.3389/fmicb.2019.02575] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 10/24/2019] [Indexed: 01/08/2023] Open
Abstract
Magnaporthe oryzae infects rice, wheat, and many grass species in the Poaceae family by secreting protein effectors. Here, we analyzed the distribution, sequence variation, and genomic context of effector candidate (EFC) genes in 31 isolates that represent five pathotypes of M. oryzae, three isolates of M. grisea, a sister species of M. oryzae, and one strain each for eight species in the family Magnaporthaceae to investigate how the host range expansion of M. oryzae has likely affected the evolution of effectors. We used the EFC genes of M. oryzae strain 70-15, whose genome has served as a reference for many comparative genomics analyses, to identify their homologs in these strains. We also analyzed the previously characterized avirulence (AVR) genes and single-copy orthologous (SCO) genes in these strains, which showed that the EFC and AVR genes evolved faster than the SCO genes. The EFC and AVR repertoires among M. oryzae pathotypes varied widely probably because adaptation to individual hosts exerted different types of selection pressure. Repetitive DNA elements appeared to have caused the variation of some EFC genes. Lastly, we analyzed expression patterns of the AVR and EFC genes to test the hypothesis that such genes are preferentially expressed during host infection. This comprehensive dataset serves as a foundation for future studies on the genetic basis of the evolution and host specialization in M. oryzae.
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Affiliation(s)
- Ki-Tae Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
| | - Jaeho Ko
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
| | - Hyeunjeong Song
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, South Korea
| | - Gobong Choi
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, South Korea
| | - Hyunbin Kim
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, South Korea
| | - Jongbum Jeon
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, South Korea
| | - Kyeongchae Cheong
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, South Korea
| | - Seogchan Kang
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, State College, PA, United States
| | - Yong-Hwan Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea.,Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, South Korea.,Center for Fungal Genetic Resources, Seoul National University, Seoul, South Korea.,Plant Immunity Research Center, Seoul National University, Seoul, South Korea.,Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
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Jeon J, Kim J, Kim K. Perception and satisfaction of cancer patients in clinical trials. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz423.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Kim T, Jeon J, Jung K, Kim H, Oh J, Jee S, Lee M. 100 The risk of psychiatric disorders among patients with psoriasis in Korea: a 12-year nationwide population-based cohort study. J Invest Dermatol 2019. [DOI: 10.1016/j.jid.2019.07.104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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El-Rabbany M, Caminiti M, Jeon J, Bradley G. Low Recurrence Rate Using 5-Fluorouracil in Managing Odontogenic Keratocysts: An Initial Report. J Oral Maxillofac Surg 2019. [DOI: 10.1016/j.joms.2019.06.140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Kwon HJ, Jeon J, Kim DH, Jang HR, Sung HH, Han DH, Park JB, Lee JE, Huh W, Kim SJ, Kim YG, Kim DJ, Oh HY. Clinical Impact of a Protocolized Kidney Donor Follow-up System. Transplant Proc 2019; 51:692-700. [PMID: 30979452 DOI: 10.1016/j.transproceed.2018.10.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Accepted: 10/23/2018] [Indexed: 10/27/2022]
Abstract
BACKGROUND Adequate kidney donor management after donation is increasingly emphasized due to concerns of renal function impairment after nephrectomy with increasing life expectancy. In this study, the clinical impact of a protocolized kidney donor follow-up system by nephrologists was evaluated. METHODS A total of 427 living kidney donors underwent nephrectomy from January 2010 to December 2014 and were followed for at least 2 years at the Samsung Medical Center. Donors were followed-up by nephrologists after the establishment of a donor clinic with systemized protocols in January 2013. The primary outcomes were incidence of post-donation low estimated glomerular filtration rate (eGFR) and renal function adaptability. Secondary outcomes were changes in compliance and incidence of hyperuricemia and microalbuminuria. RESULTS The patients were divided into 2 groups according to the time of nephrectomy: the pre-donor clinic period (n = 182) and the donor clinic period (n = 172). Preoperative eGFR in patients in the pre-donor clinic period was higher than that in patients in the donor clinic period. After donation, poor renal adaptation was less frequent in the donor clinic period compared to the pre-donor clinic period. Low eGFR tended to be less common during the donor clinic period. Shorter mean outpatient clinic visit intervals with more visits within 6 months after donation and earlier detection of de novo hyperuricemia were found during the donor clinic period. CONCLUSION A protocolized donor clinic run by nephrologists may improve post-nephrectomy renal outcomes and compliance and facilitate better management of potential risk factors of chronic kidney disease in donors.
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Affiliation(s)
- H J Kwon
- Division of Nephrology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - J Jeon
- Division of Nephrology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - D H Kim
- Division of Nephrology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - H R Jang
- Division of Nephrology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.
| | - H H Sung
- Department of Urology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - D H Han
- Department of Urology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - J B Park
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - J E Lee
- Division of Nephrology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - W Huh
- Division of Nephrology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - S J Kim
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Y G Kim
- Division of Nephrology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - D J Kim
- Division of Nephrology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - H Y Oh
- Division of Nephrology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
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Kim KD, Jung HY, Ryu HG, Kim B, Jeon J, Yoo HY, Park CH, Choi BH, Hyun CK, Kim KT, Fang S, Yang SH, Kim JB. Betulinic acid inhibits high-fat diet-induced obesity and improves energy balance by activating AMPK. Nutr Metab Cardiovasc Dis 2019; 29:409-420. [PMID: 30799179 DOI: 10.1016/j.numecd.2018.12.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 12/05/2018] [Accepted: 12/05/2018] [Indexed: 12/18/2022]
Abstract
BACKGROUND AND AIM Metabolic syndromes are prevalent worldwide and result in various complications including obesity, cardiovascular disease and type II diabetes. Betulinic acid (BA) is a naturally occurring triterpenoid that has anti-inflammatory properties. We hypothesized that treatment with BA may result in decreased body weight gain, adiposity and hepatic steatosis in a diet-induced mouse model of obesity. METHODS AND RESULTS Mice fed a high-fat diet and treated with BA showed less weight gain and tissue adiposity without any change in calorie intake. Gene expression profiling of mouse tissues and cell lines revealed that BA treatment increased expression of lipid oxidative genes and decreased that of lipogenesis-related genes. This modulation was mediated by increased AMP-activated protein kinase (AMPK) phosphorylation, which facilitates energy expenditure, lipid oxidation and thermogenic capacity and exerts protective effects against obesity and nonalcoholic fatty liver disease. Overall, BA markedly inhibited the development of obesity and nonalcoholic fatty liver disease in mice fed a high-fat diet, and AMPK activation in various tissues and enhanced thermogenesis are two possible mechanisms underlying the antiobesity and antisteatogenic effects of BA. CONCLUSIONS The current findings suggest that treatment with BA is a potential dietary strategy for preventing obesity and nonalcoholic fatty liver disease.
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Affiliation(s)
- K-D Kim
- School of Life Science, Handong Global University, Pohang, Gyungbuk, South Korea
| | - H-Y Jung
- Division of Integrative Biosciences and Biotechnology, POSTECH, Pohang, Gyungbuk, South Korea; R&D Center, NovMetaPharma Co., Ltd., Pohang, Gyungbuk, South Korea
| | - H G Ryu
- Department of Life Sciences, POSTECH, Pohang, Gyungbuk, South Korea
| | - B Kim
- School of Life Science, Handong Global University, Pohang, Gyungbuk, South Korea; R&D Center, NovMetaPharma Co., Ltd., Pohang, Gyungbuk, South Korea
| | - J Jeon
- Division of Integrative Biosciences and Biotechnology, POSTECH, Pohang, Gyungbuk, South Korea; R&D Center, NovMetaPharma Co., Ltd., Pohang, Gyungbuk, South Korea
| | - H Y Yoo
- Division of Integrative Biosciences and Biotechnology, POSTECH, Pohang, Gyungbuk, South Korea
| | - C H Park
- Mistle Biotech Co., Ltd., Pohang, Gyungbuk, South Korea
| | - B-H Choi
- Advanced Bio Convergence Center, Pohang Technopark, Pohang, Gyungbuk, South Korea
| | - C-K Hyun
- School of Life Science, Handong Global University, Pohang, Gyungbuk, South Korea
| | - K-T Kim
- Division of Integrative Biosciences and Biotechnology, POSTECH, Pohang, Gyungbuk, South Korea; Department of Life Sciences, POSTECH, Pohang, Gyungbuk, South Korea
| | - S Fang
- Severance Biomedical Science Institute, BK21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, South Korea
| | - S H Yang
- Kidney Research Institute, Seoul National University College of Medicine, Seoul, South Korea; Seoul National University Biomedical Research Institute, Seoul, South Korea
| | - J-B Kim
- School of Life Science, Handong Global University, Pohang, Gyungbuk, South Korea; Mistle Biotech Co., Ltd., Pohang, Gyungbuk, South Korea.
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Kim K, Han N, Ji E, Jeon J, Park J, Lee H, Baek J, Han NY, Ji E, Jeon J, Park JM, Lee H, Baek JH. Biomarker discovery of tumor response to neoadjuvant chemoradiotherapy in locally advanced rectal cancer by quantitative proteomic analysis. Eur J Surg Oncol 2019. [DOI: 10.1016/j.ejso.2018.10.186] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Huang L, Kim KT, Yang JY, Song H, Choi G, Jeon J, Cheong K, Ko J, Xu H, Lee YH. A High-Quality Draft Genome Sequence of Colletotrichum gloeosporioides sensu stricto SMCG1#C, a Causal Agent of Anthracnose on Cunninghamia lanceolata in China. Mol Plant Microbe Interact 2019; 32:139-141. [PMID: 30019989 DOI: 10.1094/mpmi-05-18-0144-a] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Colletotrichum has a broad host range and causes major yield losses of crops. The fungus Colletotrichum gloeosporioides is associated with anthracnose on Chinese fir. In this study, we present a high-quality draft genome sequence of C. gloeosporioides sensu stricto SMCG1#C, providing a reference genomic data for further research on anthracnose of Chinese fir and other hosts.
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Affiliation(s)
- Lin Huang
- 1 Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Ki-Tae Kim
- 2 Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
| | - Ji-Yun Yang
- 1 Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, Jiangsu 210037, China
| | - Hyeunjeong Song
- 3 Interdisciplinary Program in Agricultural Genomics, Seoul National University
| | - Gobong Choi
- 3 Interdisciplinary Program in Agricultural Genomics, Seoul National University
| | - Jongbum Jeon
- 3 Interdisciplinary Program in Agricultural Genomics, Seoul National University
| | - Kyeongchae Cheong
- 3 Interdisciplinary Program in Agricultural Genomics, Seoul National University
| | - Jaeho Ko
- 2 Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
| | - Haibin Xu
- 4 College of Biology and the Environment, Nanjing Forestry University; and
| | - Yong-Hwan Lee
- 2 Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Korea
- 3 Interdisciplinary Program in Agricultural Genomics, Seoul National University
- 5 Center for Fungal Genetic Resources, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National University
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Ibarra Caballero JR, Jeon J, Lee YH, Fraedrich S, Klopfenstein NB, Kim MS, Stewart JE. Genomic comparisons of the laurel wilt pathogen, Raffaelea lauricola, and related tree pathogens highlight an arsenal of pathogenicity related genes. Fungal Genet Biol 2019; 125:84-92. [PMID: 30716558 DOI: 10.1016/j.fgb.2019.01.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 01/09/2019] [Accepted: 01/31/2019] [Indexed: 12/15/2022]
Abstract
Raffaelea lauricola is an invasive fungal pathogen and symbiont of the redbay ambrosia beetle (Xyleborus glabratus) that has caused widespread mortality to redbay (Persea borbonia) and other Lauraceae species in the southeastern USA. We compare two genomes of R. lauricola (C2646 and RL570) to seven other related Ophiostomatales species including R. aguacate (nonpathogenic close relative of R. lauricola), R. quercus-mongolicae (associated with mortality of oaks in Korea), R. quercivora (associated with mortality of oaks in Japan), Grosmannia clavigera (cause of blue stain in conifers), Ophiostoma novo-ulmi (extremely virulent causal agent of Dutch elm disease), O. ulmi (moderately virulent pathogen that cause of Dutch elm disease), and O. piceae (blue-stain saprophyte of conifer logs and lumber). Structural and functional annotations were performed to determine genes that are potentially associated with disease development. Raffaelea lauricola and R. aguacate had the largest genomes, along with the largest number of protein-coding genes, genes encoding secreted proteins, small-secreted proteins, ABC transporters, cytochrome P450 enzymes, CAZYmes, and proteases. Our results indicate that this large genome size was not related to pathogenicity but was likely lineage specific, as the other pathogens in Raffaelea (R. quercus-mongolicae and R. quercivora) had similar genome characteristics to the Ophiostoma species. A diverse repertoire of wood-decaying enzymes were identified in each of the genomes, likely used for toxin neutralization rather than wood degradation. Lastly, a larger number of species-specific, secondary metabolite, synthesis clusters were identified in R. lauricola suggesting that it is well equipped as a pathogen, which could explain its success as a pathogen of a wide range of lauraceous hosts.
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Affiliation(s)
- Jorge R Ibarra Caballero
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523, USA
| | - Jongbum Jeon
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Yong-Hwan Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Stephen Fraedrich
- USDA Forest Service, Southern Research Station, Athens, GA 30602, USA
| | - Ned B Klopfenstein
- USDA Forest Service, Rocky Mountain Research Station, Moscow, ID 83843, USA
| | - Mee-Sook Kim
- USDA Forest Service, Pacific Northwest Research Station, Corvallis, OR 97331, USA
| | - Jane E Stewart
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523, USA.
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Baek YS, Seo JY, Song JY, Lee SY, Kim A, Jeon J. Li-Fraumeni syndrome presenting as cutaneous melanoma in a child: case report and review of literature. J Eur Acad Dermatol Venereol 2019; 33:e174-e175. [PMID: 30653764 DOI: 10.1111/jdv.15430] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Y S Baek
- Department of Dermatology, College of Medicine, Korea University, 148 Gurodong-ro, Guro-gu, Seoul, 08308, Korea
| | - J Y Seo
- Department of Dermatology, College of Medicine, Korea University, 148 Gurodong-ro, Guro-gu, Seoul, 08308, Korea
| | - J Y Song
- Department of Dermatology, College of Medicine, Korea University, 148 Gurodong-ro, Guro-gu, Seoul, 08308, Korea
| | - S-Y Lee
- Division of Oncology/Hematology, Department of Internal Medicine, College of Medicine, Korea University, 148 Gurodong-ro, Guro-gu, Seoul, 08308, Korea
| | - A Kim
- Department of Pathology, College of Medicine, Korea University, 148 Gurodong-ro, Guro-gu, Seoul, 08308, Korea
| | - J Jeon
- Department of Dermatology, College of Medicine, Korea University, 148 Gurodong-ro, Guro-gu, Seoul, 08308, Korea
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Kwon S, Lee J, Jeon J, Kim S, Park SY, Jeon J, Lee YH. Role of the Histone Acetyltransferase Rtt109 in Development and Pathogenicity of the Rice Blast Fungus. Mol Plant Microbe Interact 2018; 31:1200-1210. [PMID: 29856240 DOI: 10.1094/mpmi-01-18-0015-r] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Acetylation of histone H3 lysine 56 (H3K56) by the fungal-specific histone acetyltransferase Rtt109 plays important roles in maintaining genome integrity and surviving DNA damage. Here, we investigated the implications of Rtt109-mediated response to DNA damage on development and pathogenesis of the rice blast fungus Magnaporthe oryzae (anamorph: Pyricularia oryzae). The ortholog of Rtt109 in M. oryzae (MoRtt109) was found via sequence homology and its functionality was confirmed by phenotypic complementation of the Saccharomyces cerevisiae Rtt109 deletion strain. Targeted deletion of MoRtt109 resulted in a significant reduction in acetylation of H3K56 and rendered the fungus defective in hyphal growth and asexual reproduction. Furthermore, the deletion mutant displayed hypersensitivity to genotoxic agents, confirming the conserved importance of Rtt109 in genome integrity maintenance and genotoxic stress tolerance. Elevated expression of DNA repair genes and the results of the comet assay were consistent with constitutive endogenous DNA damage. Although the conidia produced from the mutant were not impaired in germination and appressorium morphogenesis, the mutant was significantly less pathogenic on rice leaves. Transcriptomic analysis provided insight into the factors underlying phenotypic defects that are associated with deficiency of H3K56 acetylation. Overall, our results indicate that MoRtt109 is a conserved histone acetyltransferase that affects proliferation and asexual fecundity of M. oryzae through maintenance of genome integrity and response to DNA damage.
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Affiliation(s)
- Seomun Kwon
- 1 Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Jaejoon Lee
- 2 Department of Biotechnology, College of Life and Applied Sciences, Yeungnam University, Gyeongsan, Gyeongbuk 38541, Korea; and
| | - Jongbum Jeon
- 1 Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Seongbeom Kim
- 1 Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Sook-Young Park
- 3 Department of Plant Medicine, Sunchon National University, Suncheon 57922, Korea
| | - Junhyun Jeon
- 2 Department of Biotechnology, College of Life and Applied Sciences, Yeungnam University, Gyeongsan, Gyeongbuk 38541, Korea; and
| | - Yong-Hwan Lee
- 1 Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
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Cho J, Kim B, Jeon J, Park S. INFORMATION AND COMMUNICATION TECHNOLOGY (ICT) CONFIDENCE AND LATER YEAR VOLUNTEERING. Innov Aging 2018. [DOI: 10.1093/geroni/igy023.2505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
| | - B Kim
- University of New Hampshire
| | - J Jeon
- Eastern Connecticut State University
| | - S Park
- Washington University in Saint Louis
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Jeon J, Meza R, Rozek L, Sriplung H. Trends of Colorectal Cancer Incidence in Thailand by Age, Gender, and Region. J Glob Oncol 2018. [DOI: 10.1200/jgo.18.73800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background: Colorectal cancer (CRC) is the third most common cancer in the world. While CRC incidence has decreased in many western countries over the last decades, largely thanks to screening, it is increasing in low and middle-income countries, including Thailand. However, it is unclear if these increases are consistent across different regions, gender and age groups. Aim: To understand the age-, gender- and region-specific temporal variation in CRC incidence in Thailand since the 1990s. Methods: We analyzed CRC incidence data from the Thailand National Cancer Network (TCIN) cancer registries, which include Chiang Mai (1990-2012), Lampang (1993-2014), Lopburi (2000-2014), Khon Kaen (1990-2014) and Songkhla (1990-2014) cancer registries. Trends in age-adjusted incidence (measured by annual percentage change (APC)) were assessed using Joinpoint regression. Trends by birth-year and calendar-year were assessed using age-period-cohort models. All analyses were done by region, gender, and age group (30-49, 50-84, 30-84). Results: CRC incidence has been increasing significantly in all regions, gender, and age groups; Overall, the APC was 3.82 for men and 3.84 for women (Chiang Mai, 4.34 for men & 3.26 for women; Khon Kaen, 2.69 for men & 3.68 for women; Lampang, 2.13 for men & 3.37 for women; Lopburi, 5.31 for men & 4.67 for women; Songkhla, 4.67 for men & 4.32 for women). The increase in incidence was higher for ages 50-84 (APC = 3.99 for men & 4.04 for women) compared with ages 30-49 (APC=2.97 for men & 3.09 for women). Test of parallelism suggests that increases are consistent between gender (P-value=0.97). The age-period-cohort analysis suggests that both calendar-year and birth-year are strongly correlated with CRC incidence trends, with a stronger relationship with birth-year than calendar-year for both genders. Conclusion: In contrast to western countries such as the US, CRC incidence is increasing across all age groups in Thailand, with faster increase in older ages. This highlights the needs for establishing population-wide screening programs to reduce the burden and stop the rise of CRC in Thailand and low-middle income countries.
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Affiliation(s)
- J. Jeon
- University of Michigan, Epidemiology, Ann Arbor, MI
| | - R. Meza
- University of Michigan, Epidemiology, Ann Arbor, MI
| | - L. Rozek
- University of Michigan, Environment Sciences, Ann Arbor, MI
| | - H. Sriplung
- Prince of Songkla University, Epidemiology Unit, Hat Yai, Thailand
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41
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Yoon N, Jeon J. Comparing clonality between components of combined hepatocellular carcinoma and cholangiocarcinoma by targeted sequencing. Ann Oncol 2018. [DOI: 10.1093/annonc/mdy314.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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42
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Bang C, Jeon J, Lee J, Lee S, Park Y, Lee J. 578 Acne severity scoring using deep learning. J Invest Dermatol 2018. [DOI: 10.1016/j.jid.2018.03.586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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43
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Kim J, Lee J, Kim A, Jeon J, Oh C, Seo S, Kim I, Krueger J. 888 β-Defensin 103 characterizes a distinct molecular phenotype of human acral melanoma, by its correlated expression with IL-17A & IFNγ-mediated immune genes, as well as MC1R-mediated pigmentation signatures. J Invest Dermatol 2018. [DOI: 10.1016/j.jid.2018.03.900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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44
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Choe JH, Jeon J, Lee ME, Wie JJ, Jin HJ, Yun YS. Nanoconfinement effects of chemically reduced graphene oxide nanoribbons on poly(vinyl chloride). Nanoscale 2018; 10:2025-2033. [PMID: 29322142 DOI: 10.1039/c7nr07098e] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Polymeric nanocomposites with graphene-based nanocarbons (GNCs) have been extensively studied with emphasis on the percolation of nanofillers toward electrical, rheological, and mechanical reinforcement. In this study, we report an unusual indirect reinforcing phenomenon of highly defective GNCs dispersed in the poly(vinyl chloride) (PVC) matrix via densification of the polymer packing originating from nanoscale confinement. Herein, chemically reduced graphene oxide nanoribbons (C-rGONRs) are employed as a nanofiller. The inclusion of defective and oxygen-functionalized C-rGONRs resulted in a dramatic densification of the PVC host with extremely low C-rGONR loading, largely exceeding the theoretical calculation from a rule of mixture. Along with the densification, the glass transition temperature of PVC also increased by 28.6 °C at 0.1 wt% filler loading. Remarkably, the oxygen barrier property and mechanical toughness under tension for the PVC/C-rGONR nanocomposite were the maximum when the greatest densification occurred. The structure-property relationship of the nanocomposites has been discussed with an emphasis on the nanoscale confinement phenomenon.
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Affiliation(s)
- J H Choe
- Department of Polymer Science and Engineering, Inha University, Incheon 22212, South Korea.
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45
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Jeon J, Jung J, Chow KH. Electron beam induced tunneling magnetoresistance in spatially confined manganite bridges. Nanoscale 2017; 9:19304-19309. [PMID: 29192923 DOI: 10.1039/c7nr04232a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Certain manganites exhibit rich and technologically relevant transport properties which can often be attributed to the existence and changes of the intrinsic electronic phase competition within these materials. Here we demonstrate that a scanning electron beam can be used to artificially create domain configurations within La0.3Pr0.4Ca0.3MnO3 thin film microbridges that results in novel magneto-transport effects. In particular, the electron beam preferentially produces insulating regions within the narrow film and can be used to create a configuration consisting of ferromagnetic metallic domains separated by a potential barrier. This arrangement enables the spin-dependent tunneling of charge carriers and can produce large switching tunneling magnetoresistance effects which were initially absent. Hence, this work describes a new and potentially powerful method for engineering the electronic phase domains in manganites to generate functional transport properties that are important for spintronic devices.
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Affiliation(s)
- J Jeon
- Department of Physics, University of Alberta, Edmonton T6G 2E1, Canada.
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46
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Kim S, Park J, Yeom SI, Kim YM, Seo E, Kim KT, Kim MS, Lee JM, Cheong K, Shin HS, Kim SB, Han K, Lee J, Park M, Lee HA, Lee HY, Lee Y, Oh S, Lee JH, Choi E, Choi E, Lee SE, Jeon J, Kim H, Choi G, Song H, Lee J, Lee SC, Kwon JK, Lee HY, Koo N, Hong Y, Kim RW, Kang WH, Huh JH, Kang BC, Yang TJ, Lee YH, Bennetzen JL, Choi D. New reference genome sequences of hot pepper reveal the massive evolution of plant disease-resistance genes by retroduplication. Genome Biol 2017; 18:210. [PMID: 29089032 PMCID: PMC5664825 DOI: 10.1186/s13059-017-1341-9] [Citation(s) in RCA: 152] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 10/06/2017] [Indexed: 01/08/2023] Open
Abstract
Background Transposable elements are major evolutionary forces which can cause new genome structure and species diversification. The role of transposable elements in the expansion of nucleotide-binding and leucine-rich-repeat proteins (NLRs), the major disease-resistance gene families, has been unexplored in plants. Results We report two high-quality de novo genomes (Capsicum baccatum and C. chinense) and an improved reference genome (C. annuum) for peppers. Dynamic genome rearrangements involving translocations among chromosomes 3, 5, and 9 were detected in comparison between C. baccatum and the two other peppers. The amplification of athila LTR-retrotransposons, members of the gypsy superfamily, led to genome expansion in C. baccatum. In-depth genome-wide comparison of genes and repeats unveiled that the copy numbers of NLRs were greatly increased by LTR-retrotransposon-mediated retroduplication. Moreover, retroduplicated NLRs are abundant across the angiosperms and, in most cases, are lineage-specific. Conclusions Our study reveals that retroduplication has played key roles for the massive emergence of NLR genes including functional disease-resistance genes in pepper plants. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1341-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Seungill Kim
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Jieun Park
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea.,Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea
| | - Seon-In Yeom
- Department of Agricultural Plant Science, Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, 52828, South Korea
| | - Yong-Min Kim
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejon, 34141, South Korea
| | - Eunyoung Seo
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Ki-Tae Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, South Korea
| | - Myung-Shin Kim
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Je Min Lee
- Department of Horticultural Science, Kyungpook National University, Daegu, 41566, South Korea
| | - Kyeongchae Cheong
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea.,Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, South Korea
| | - Ho-Sub Shin
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Saet-Byul Kim
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Koeun Han
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea.,Vegetable Breeding Research Center, Seoul National University, Seoul, 08826, South Korea
| | - Jundae Lee
- Department of Horticulture, Chonbuk National University, Jeonju, 54896, South Korea
| | - Minkyu Park
- Department of Genetics, University of Georgia, Athens, GA, 30602-7223, USA
| | - Hyun-Ah Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Hye-Young Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Youngsill Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Soohyun Oh
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Joo Hyun Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Eunhye Choi
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Eunbi Choi
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - So Eui Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Jongbum Jeon
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea
| | - Hyunbin Kim
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea
| | - Gobong Choi
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea
| | - Hyeunjeong Song
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea
| | - JunKi Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Sang-Choon Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Jin-Kyung Kwon
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea.,Vegetable Breeding Research Center, Seoul National University, Seoul, 08826, South Korea
| | - Hea-Young Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea.,Vegetable Breeding Research Center, Seoul National University, Seoul, 08826, South Korea
| | - Namjin Koo
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejon, 34141, South Korea
| | - Yunji Hong
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejon, 34141, South Korea
| | - Ryan W Kim
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejon, 34141, South Korea
| | - Won-Hee Kang
- Department of Agricultural Plant Science, Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, 52828, South Korea
| | - Jin Hoe Huh
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Byoung-Cheorl Kang
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea.,Vegetable Breeding Research Center, Seoul National University, Seoul, 08826, South Korea
| | - Tae-Jin Yang
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Yong-Hwan Lee
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea.,Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, South Korea
| | | | - Doil Choi
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea.
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47
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Kim S, Park J, Yeom SI, Kim YM, Seo E, Kim KT, Kim MS, Lee JM, Cheong K, Shin HS, Kim SB, Han K, Lee J, Park M, Lee HA, Lee HY, Lee Y, Oh S, Lee JH, Choi E, Choi E, Lee SE, Jeon J, Kim H, Choi G, Song H, Lee J, Lee SC, Kwon JK, Lee HY, Koo N, Hong Y, Kim RW, Kang WH, Huh JH, Kang BC, Yang TJ, Lee YH, Bennetzen JL, Choi D. New reference genome sequences of hot pepper reveal the massive evolution of plant disease-resistance genes by retroduplication. Genome Biol 2017; 18:210. [PMID: 29089032 DOI: 10.1007/s13580-019-00157-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 06/19/2019] [Accepted: 10/06/2017] [Indexed: 05/24/2023] Open
Abstract
BACKGROUND Transposable elements are major evolutionary forces which can cause new genome structure and species diversification. The role of transposable elements in the expansion of nucleotide-binding and leucine-rich-repeat proteins (NLRs), the major disease-resistance gene families, has been unexplored in plants. RESULTS We report two high-quality de novo genomes (Capsicum baccatum and C. chinense) and an improved reference genome (C. annuum) for peppers. Dynamic genome rearrangements involving translocations among chromosomes 3, 5, and 9 were detected in comparison between C. baccatum and the two other peppers. The amplification of athila LTR-retrotransposons, members of the gypsy superfamily, led to genome expansion in C. baccatum. In-depth genome-wide comparison of genes and repeats unveiled that the copy numbers of NLRs were greatly increased by LTR-retrotransposon-mediated retroduplication. Moreover, retroduplicated NLRs are abundant across the angiosperms and, in most cases, are lineage-specific. CONCLUSIONS Our study reveals that retroduplication has played key roles for the massive emergence of NLR genes including functional disease-resistance genes in pepper plants.
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Affiliation(s)
- Seungill Kim
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Jieun Park
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea
| | - Seon-In Yeom
- Department of Agricultural Plant Science, Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, 52828, South Korea
| | - Yong-Min Kim
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejon, 34141, South Korea
| | - Eunyoung Seo
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Ki-Tae Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, South Korea
| | - Myung-Shin Kim
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Je Min Lee
- Department of Horticultural Science, Kyungpook National University, Daegu, 41566, South Korea
| | - Kyeongchae Cheong
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, South Korea
| | - Ho-Sub Shin
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Saet-Byul Kim
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Koeun Han
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
- Vegetable Breeding Research Center, Seoul National University, Seoul, 08826, South Korea
| | - Jundae Lee
- Department of Horticulture, Chonbuk National University, Jeonju, 54896, South Korea
| | - Minkyu Park
- Department of Genetics, University of Georgia, Athens, GA, 30602-7223, USA
| | - Hyun-Ah Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Hye-Young Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Youngsill Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Soohyun Oh
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Joo Hyun Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Eunhye Choi
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Eunbi Choi
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - So Eui Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Jongbum Jeon
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea
| | - Hyunbin Kim
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea
| | - Gobong Choi
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea
| | - Hyeunjeong Song
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea
| | - JunKi Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Sang-Choon Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Jin-Kyung Kwon
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
- Vegetable Breeding Research Center, Seoul National University, Seoul, 08826, South Korea
| | - Hea-Young Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
- Vegetable Breeding Research Center, Seoul National University, Seoul, 08826, South Korea
| | - Namjin Koo
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejon, 34141, South Korea
| | - Yunji Hong
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejon, 34141, South Korea
| | - Ryan W Kim
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejon, 34141, South Korea
| | - Won-Hee Kang
- Department of Agricultural Plant Science, Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, 52828, South Korea
| | - Jin Hoe Huh
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Byoung-Cheorl Kang
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
- Vegetable Breeding Research Center, Seoul National University, Seoul, 08826, South Korea
| | - Tae-Jin Yang
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Yong-Hwan Lee
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, South Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, South Korea
| | | | - Doil Choi
- Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea.
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48
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Choi J, Lee GW, Kim KT, Jeon J, Détry N, Kuo HC, Sun H, Asiegbu FO, Lee YH. Comparative analysis of genome sequences of the conifer tree pathogen, Heterobasidion annosum s.s. Genom Data 2017; 14:106-113. [PMID: 29085779 PMCID: PMC5654758 DOI: 10.1016/j.gdata.2017.10.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 09/21/2017] [Accepted: 10/15/2017] [Indexed: 01/09/2023]
Abstract
The causal agent of root and butt rot of conifer trees, Heterobasidion annosum, is widespread in boreal forests and economically responsible for annual loss of approximately 50 million euros to forest industries in Finland alone and much more at European level. In order to further understand the pathobiology of this fungus at the genome level, a Finnish isolate of H. annosum sensu stricto (isolate 03012) was sequenced and analyzed with the genome sequences of 23 white-rot and 13 brown-rot fungi. The draft genome assembly of H. annosum has a size of 31.01 Mb, containing 11,453 predicted genes. Whole genome alignment showed that 84.38% of H. annosum genome sequences were aligned with those of previously sequenced H. irregulare TC 32-1 counterparts. The result is further supported by the protein sequence clustering analysis which revealed that the two genomes share 6719 out of 8647 clusters. When sequencing reads of H. annosum were aligned against the genome sequences of H. irregulare, six single nucleotide polymorphisms were found in every 1 kb, on average. In addition, 98.68% of SNPs were found to be homo-variants, suggesting that the two species have long evolved from different niches. Gene family analysis revealed that most of the white-rot fungi investigated had more gene families involved in lignin degradation or modification, including laccases and peroxidase. Comparative analysis of the two Heterobasidion spp. as well as white-/brown-rot fungi would provide new insights for understanding the pathobiology of the conifer tree pathogen.
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Affiliation(s)
- Jaeyoung Choi
- Department of Forest Sciences, University of Helsinki, 00014 Helsinki, Finland
| | - Gir-Won Lee
- National Instrumentation Center for Environmental Management, Seoul National University, Seoul 08826, Republic of Korea
| | - Ki-Tae Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea
| | - Jongbum Jeon
- Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea
| | - Nicolas Détry
- Department of Forest Sciences, University of Helsinki, 00014 Helsinki, Finland
| | - Hsiao-Che Kuo
- Department of Forest Sciences, University of Helsinki, 00014 Helsinki, Finland
| | - Hui Sun
- Department of Forest Sciences, University of Helsinki, 00014 Helsinki, Finland
| | - Fred O Asiegbu
- Department of Forest Sciences, University of Helsinki, 00014 Helsinki, Finland
| | - Yong-Hwan Lee
- Department of Forest Sciences, University of Helsinki, 00014 Helsinki, Finland.,Department of Agricultural Biotechnology, Seoul National University, Seoul 08826, Republic of Korea.,Center for Fungal Genetic Resources, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
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49
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Jeon J, Kim B, Cox K, Kimura M. THE INFORMATION AND COMMUNICATION TECHNOLOGIES UTILIZATION PATTERNS AND CHANGES IN SELF-RATED HEALTH. Innov Aging 2017. [DOI: 10.1093/geroni/igx004.4321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- J. Jeon
- Eastern Connecticut State University, Willimantic, Connecticut,
| | - B. Kim
- University of New Hampshire, Durham, New Hampshire
| | - K. Cox
- University of New Hampshire, Durham, New Hampshire
| | - M. Kimura
- University of New Hampshire, Durham, New Hampshire
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50
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Jeon J, D'Souza R, Pinto N, Ryu C, Park J, Yong D, Lee K. Characterization and complete genome sequence analysis of two
Myoviral
bacteriophages infecting clinical carbapenem‐resistant
Acinetobacter baumannii
isolates. J Appl Microbiol 2016; 121:68-77. [DOI: 10.1111/jam.13134] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 02/16/2016] [Accepted: 03/03/2016] [Indexed: 12/25/2022]
Affiliation(s)
- J. Jeon
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance Yonsei University College of Medicine Seoul Korea
| | - R. D'Souza
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance Yonsei University College of Medicine Seoul Korea
| | - N. Pinto
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance Yonsei University College of Medicine Seoul Korea
| | - C.‐M. Ryu
- Molecular Phytobacteriology Laboratory KRIBB Daejeon Korea
- Biosystems and Bioengineering Program School of Science University of Science and Technology (UST) Daejeon Korea
| | - J. Park
- Laboratory Animal Medicine College of Veterinary Medicine Chonnam National University Gwang‐ju Korea
| | - D. Yong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance Yonsei University College of Medicine Seoul Korea
| | - K. Lee
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance Yonsei University College of Medicine Seoul Korea
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