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Article: Validity of patient-derived xenograft mouse models for lung cancer based on exome sequencing data.

Kim, Jaewon / Rhee, Hwanseok / Kim, Jhingook / Lee, Sanghyuk

2020 Volume 18, Issue 1, Page(s) e3

Abstract: Patient-derived xenograft (PDX) mouse models are frequently used to test the drug efficacy in diverse types of cancer. They are known to recapitulate the patient characteristics faithfully, but a systematic survey with a large number of cases is yet ... ...

Abstract	Patient-derived xenograft (PDX) mouse models are frequently used to test the drug efficacy in diverse types of cancer. They are known to recapitulate the patient characteristics faithfully, but a systematic survey with a large number of cases is yet missing in lung cancer. Here we report the comparison of genomic characters between mouse and patient tumor tissues in lung cancer based on exome sequencing data. We established PDX mouse models for 132 lung cancer patients and performed whole exome sequencing for trio samples of tumor-normal-xenograft tissues. Then we computed the somatic mutations and copy number variations, which were used to compare the PDX and patient tumor tissues. Genomic and histological conclusions for validity of PDX models agreed in most cases, but we observed eight (~7%) discordant cases. We further examined the changes in mutations and copy number alterations in PDX model production and passage processes, which highlighted the clonal evolution in PDX mouse models. Our study shows that the genomic characterization plays complementary roles to the histological examination in cancer studies utilizing PDX mouse models.
Language	English
Publishing date	2020-03-31
Publishing country	Korea (South)
Document type	Journal Article
ZDB-ID	2802682-2
ISSN	2234-0742 ; 1598-866X
ISSN (online)	2234-0742
ISSN	1598-866X
DOI	10.5808/GI.2020.18.1.e3
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Erratum: Interleukin-34 Limits the Therapeutic Effects of Immune Checkpoint Blockade.

Hama, Naoki / Kobayashi, Takuto / Han, Nanumi / Kitagawa, Fumihito / Kajihara, Nabeel / Otsuka, Ryo / Wada, Haruka / Lee, Hee-Kyung / Rhee, Hwanseok / Hasegawa, Yoshinori / Yagita, Hideo / Baghdadi, Muhammad / Seino, Ken-Ichiro

iScience

2022 Volume 25, Issue 1, Page(s) 103713

Abstract: This corrects the article DOI: 10.1016/j.isci.2020.101584.]. ...

Abstract	[This corrects the article DOI: 10.1016/j.isci.2020.101584.].
Language	English
Publishing date	2022-01-05
Publishing country	United States
Document type	Published Erratum
ISSN	2589-0042
ISSN (online)	2589-0042
DOI	10.1016/j.isci.2021.103713
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Interleukin-34 Limits the Therapeutic Effects of Immune Checkpoint Blockade

Naoki Hama / Takuto Kobayashi / Nanumi Han / Fumihito Kitagawa / Nabeel Kajihara / Ryo Otsuka / Haruka Wada / Hee-kyung Lee / Hwanseok Rhee / Yoshinori Hasegawa / Hideo Yagita / Muhammad Baghdadi / Ken-ichiro Seino

iScience, Vol 25, Iss 1, Pp 103713- (2022)

2022

Keywords	Science ; Q
Language	English
Publishing date	2022-01-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Impacts of Salt Stress on Locomotor and Transcriptomic Responses in the Intertidal Gastropod

Ho, Phuong-Thao / Rhee, Hwanseok / Kim, Jungmin / Seo, Chaehwa / Park, Joong Ki / Young, Curtis Robert / Won, Yong-Jin

The Biological bulletin

2019 Volume 236, Issue 3, Page(s) 224–241

Abstract: Salinity is one of the most crucial environmental factors that structures biogeographic boundaries of aquatic organisms, affecting distribution, abundance, and behavior. However, the association between behavior and gene regulation underlying acclimation ...

Abstract	Salinity is one of the most crucial environmental factors that structures biogeographic boundaries of aquatic organisms, affecting distribution, abundance, and behavior. However, the association between behavior and gene regulation underlying acclimation to changes in salinity remains poorly understood. In this study, we investigated the effects of salinity stress on behavior (movement distance) and patterns of gene expression (using RNA sequencing) of the intertidal gastropod
MeSH term(s)	Acclimatization/physiology ; Animals ; Behavior, Animal/physiology ; Gastropoda/genetics ; Gastropoda/metabolism ; Gastropoda/physiology ; Gene Expression Profiling ; Gene Expression Regulation ; Locomotion ; Osmotic Pressure ; Salt Stress ; Sequence Analysis, RNA
Language	English
Publishing date	2019-05-13
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1268-3
ISSN	1939-8697 ; 0006-3185 ; 0148-9488
ISSN (online)	1939-8697
ISSN	0006-3185 ; 0148-9488
DOI	10.1086/703186
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Genome-wide association study of metabolic syndrome in Korean populations.

Oh, Seung-Won / Lee, Jong-Eun / Shin, Eunsoon / Kwon, Hyuktae / Choe, Eun Kyung / Choi, Su-Yeon / Rhee, Hwanseok / Choi, Seung Ho

PloS one

2020 Volume 15, Issue 1, Page(s) e0227357

Abstract: Metabolic syndrome (MetS) which is caused by obesity and insulin resistance, is well known for its predictive capability for the risk of type 2 diabetes mellitus and cardiovascular disease. The development of MetS is associated with multiple genetic ... ...

Abstract	Metabolic syndrome (MetS) which is caused by obesity and insulin resistance, is well known for its predictive capability for the risk of type 2 diabetes mellitus and cardiovascular disease. The development of MetS is associated with multiple genetic factors, environmental factors and lifestyle. We performed a genome-wide association study to identify single-nucleotide polymorphism (SNP) related to MetS in large Korean population based samples of 1,362 subjects with MetS and 6,061 controls using the Axiom® Korean Biobank Array 1.0. We replicated the data in another sample including 502 subjects with MetS and 1,751 controls. After adjusting for age and sex, rs662799 located in the APOA5 gene were significantly associated with MetS. 15 SNPs in GCKR, C2orf16, APOA5, ZPR1, and BUD13 were associated with high triglyceride (TG). 14 SNPs in APOA5, ALDH1A2, LIPC, HERPUD1, and CETP, and 2 SNPs in MTNR1B were associated with low high density lipoprotein cholesterol (HDL-C) and high fasting blood glucose respectively. Among these SNPs, 6 TG SNPs: rs1260326, rs1260333, rs1919127, rs964184, rs2075295 and rs1558861 and 11 HDL-C SNPs: rs4775041, rs10468017, rs1800588, rs72786786, rs173539, rs247616, rs247617, rs3764261, rs4783961, rs708272, and rs7499892 were first discovered in Koreans. Additional research is needed to confirm these 17 novel SNPs in Korean population.
MeSH term(s)	Alleles ; Asian Continental Ancestry Group/genetics ; Blood Glucose/genetics ; Cardiovascular Diseases/genetics ; Cardiovascular Diseases/pathology ; Cholesterol, HDL/blood ; Cholesterol, HDL/genetics ; Diabetes Mellitus, Type 2/genetics ; Diabetes Mellitus, Type 2/pathology ; Fasting ; Female ; Genetic Predisposition to Disease ; Genome-Wide Association Study ; Genotype ; Humans ; Insulin Resistance/genetics ; Male ; Metabolic Syndrome/blood ; Metabolic Syndrome/genetics ; Metabolic Syndrome/pathology ; Middle Aged ; Obesity/genetics ; Obesity/pathology ; Polymorphism, Single Nucleotide
Chemical Substances	Blood Glucose ; Cholesterol, HDL
Language	English
Publishing date	2020-01-07
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0227357
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Interleukin-34 Limits the Therapeutic Effects of Immune Checkpoint Blockade.

iScience

2020 Volume 23, Issue 10, Page(s) 101584

Abstract: Interleukin-34 (IL-34) is an alternative ligand to colony-stimulating factor-1 (CSF-1) for the CSF-1 receptor that acts as a key regulator of monocyte/macrophage lineage. In this study, we show that tumor-derived IL-34 mediates resistance to immune ... ...

Abstract	Interleukin-34 (IL-34) is an alternative ligand to colony-stimulating factor-1 (CSF-1) for the CSF-1 receptor that acts as a key regulator of monocyte/macrophage lineage. In this study, we show that tumor-derived IL-34 mediates resistance to immune checkpoint blockade regardless of CSF-1 existence in various murine cancer models. Consistent with its immunosuppressive characteristics, the expression of IL-34 in tumors correlates with decreased frequencies of cellular (such as CD8
Language	English
Publishing date	2020-09-19
Publishing country	United States
Document type	Journal Article
ISSN	2589-0042
ISSN (online)	2589-0042
DOI	10.1016/j.isci.2020.101584
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Interleukin-34 Limits the Therapeutic Effects of Immune Checkpoint Blockade

iScience, Vol 23, Iss 10, Pp 101584- (2020)

2020

Abstract: Summary: Interleukin-34 (IL-34) is an alternative ligand to colony-stimulating factor-1 (CSF-1) for the CSF-1 receptor that acts as a key regulator of monocyte/macrophage lineage. In this study, we show that tumor-derived IL-34 mediates resistance to ... ...

Abstract	Summary: Interleukin-34 (IL-34) is an alternative ligand to colony-stimulating factor-1 (CSF-1) for the CSF-1 receptor that acts as a key regulator of monocyte/macrophage lineage. In this study, we show that tumor-derived IL-34 mediates resistance to immune checkpoint blockade regardless of CSF-1 existence in various murine cancer models. Consistent with its immunosuppressive characteristics, the expression of IL-34 in tumors correlates with decreased frequencies of cellular (such as CD8+ and CD4+ T cells and M1-biased macrophages) and molecular (including various cytokines and chemokines) effectors at the tumor microenvironment. Then, a neutralizing antibody against IL-34 improved the therapeutic effects of the immune checkpoint blockade in combinatorial therapeutic models, including a patient-derived xenograft model. Collectively, we revealed that tumor-derived IL-34 inhibits the efficacy of immune checkpoint blockade and proposed the utility of IL-34 blockade as a new strategy for cancer therapy.
Keywords	Immunology ; Cancer ; Science ; Q
Subject code	616
Language	English
Publishing date	2020-10-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Genome-wide association study of metabolic syndrome in Korean populations.

Seung-Won Oh / Jong-Eun Lee / Eunsoon Shin / Hyuktae Kwon / Eun Kyung Choe / Su-Yeon Choi / Hwanseok Rhee / Seung Ho Choi

PLoS ONE, Vol 15, Iss 1, p e

2020 Volume 0227357

Abstract	Metabolic syndrome (MetS) which is caused by obesity and insulin resistance, is well known for its predictive capability for the risk of type 2 diabetes mellitus and cardiovascular disease. The development of MetS is associated with multiple genetic factors, environmental factors and lifestyle. We performed a genome-wide association study to identify single-nucleotide polymorphism (SNP) related to MetS in large Korean population based samples of 1,362 subjects with MetS and 6,061 controls using the Axiom® Korean Biobank Array 1.0. We replicated the data in another sample including 502 subjects with MetS and 1,751 controls. After adjusting for age and sex, rs662799 located in the APOA5 gene were significantly associated with MetS. 15 SNPs in GCKR, C2orf16, APOA5, ZPR1, and BUD13 were associated with high triglyceride (TG). 14 SNPs in APOA5, ALDH1A2, LIPC, HERPUD1, and CETP, and 2 SNPs in MTNR1B were associated with low high density lipoprotein cholesterol (HDL-C) and high fasting blood glucose respectively. Among these SNPs, 6 TG SNPs: rs1260326, rs1260333, rs1919127, rs964184, rs2075295 and rs1558861 and 11 HDL-C SNPs: rs4775041, rs10468017, rs1800588, rs72786786, rs173539, rs247616, rs247617, rs3764261, rs4783961, rs708272, and rs7499892 were first discovered in Koreans. Additional research is needed to confirm these 17 novel SNPs in Korean population.
Keywords	Medicine ; R ; Science ; Q
Subject code	616
Language	English
Publishing date	2020-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Metabolic Syndrome Prediction Using Machine Learning Models with Genetic and Clinical Information from a Nonobese Healthy Population.

Choe, Eun Kyung / Rhee, Hwanseok / Lee, Seungjae / Shin, Eunsoon / Oh, Seung-Won / Lee, Jong-Eun / Choi, Seung Ho

Genomics & informatics

2018 Volume 16, Issue 4, Page(s) e31

Abstract: The prevalence of metabolic syndrome (MS) in the nonobese population is not low. However, the identification and risk mitigation of MS are not easy in this population. We aimed to develop an MS prediction model using genetic and clinical factors of ... ...

Abstract	The prevalence of metabolic syndrome (MS) in the nonobese population is not low. However, the identification and risk mitigation of MS are not easy in this population. We aimed to develop an MS prediction model using genetic and clinical factors of nonobese Koreans through machine learning methods. A prediction model for MS was designed for a nonobese population using clinical and genetic polymorphism information with five machine learning algorithms, including naïve Bayes classification (NB). The analysis was performed in two stages (training and test sets). Model A was designed with only clinical information (age, sex, body mass index, smoking status, alcohol consumption status, and exercise status), and for model B, genetic information (for 10 polymorphisms) was added to model A. Of the 7,502 nonobese participants, 647 (8.6%) had MS. In the test set analysis, for the maximum sensitivity criterion, NB showed the highest sensitivity: 0.38 for model A and 0.42 for model B. The specificity of NB was 0.79 for model A and 0.80 for model B. In a comparison of the performances of models A and B by NB, model B (area under the receiver operating characteristic curve [AUC] = 0.69, clinical and genetic information input) showed better performance than model A (AUC = 0.65, clinical information only input). We designed a prediction model for MS in a nonobese population using clinical and genetic information. With this model, we might convince nonobese MS individuals to undergo health checks and adopt behaviors associated with a preventive lifestyle.
Language	English
Publishing date	2018-12-28
Publishing country	Korea (South)
Document type	Journal Article
ZDB-ID	2802682-2
ISSN	2234-0742 ; 1598-866X
ISSN (online)	2234-0742
ISSN	1598-866X
DOI	10.5808/GI.2018.16.4.e31
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: MedRefSNP: a database of medically investigated SNPs.

Rhee, Hwanseok / Lee, Jin-Sung

Human mutation

2009 Volume 30, Issue 3, Page(s) E460–6

Abstract: Genetic association studies and linkage analyses using single nucleotide polymorphisms (SNPs) are rapidly increasing in number, and the results are important for evaluating the utility of SNPs in the biomedical sciences. Although many SNP databases have ... ...

Abstract	Genetic association studies and linkage analyses using single nucleotide polymorphisms (SNPs) are rapidly increasing in number, and the results are important for evaluating the utility of SNPs in the biomedical sciences. Although many SNP databases have been established, there is no database focusing on published SNPs, where the research results of scientific investigations are available. To enhance the utilization of such SNP data, we have developed the MedRefSNP database (http://www.medclue.com/medrefsnp) to provide integrated information about SNPs collected from the PubMed and OMIM databases. The RefSNP identifiers are automatically identified and are linked to various information sources such as the dbSNP, the HapMap database, the Entrez Gene database, the UCSC genome browser, the CGAP Pathway Searcher, and genetic association databases. And, each SNP is checked to determine whether the PolyDoms, SNPs3D or PolyPhen databases predicts that the SNP affects the phenotype of the protein encoded by the gene carrying the SNP. Also, neighboring SNPs showing strong linkage disequilibrium (LD) with published SNPs are included, using HapMap data. Currently, 36199 unique SNPs (including 31368 neighboring SNPs) collected from 25906 PubMed abstracts and 590 OMIM records are stored along with 2491 human genes related to 466 molecular pathways. The MedRefSNP database will help researchers to review previously investigated results more efficiently, and will expand knowledge by using the genomic and functional contexts of the SNPs.
MeSH term(s)	Databases, Factual ; Databases, Genetic ; Genetic Predisposition to Disease/genetics ; Humans ; Information Storage and Retrieval ; Internet ; Polymorphism, Single Nucleotide ; PubMed
Language	English
Publishing date	2009-03
Publishing country	United States
Document type	Journal Article
ZDB-ID	1126646-6
ISSN	1098-1004 ; 1059-7794
ISSN (online)	1098-1004
ISSN	1059-7794
DOI	10.1002/humu.20914
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