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Kim H, Kim M, Rhee SY, Koyanagi A, Smith L, Kim MS, Fond G, Boyer L, Kim S, Shin JI, Jacob L, Lee J, Rahmati M, Yeo SG, Yon DK. National long-term trends in health-related quality of life using EQ-5D-3L in South Korea, 2008-2021, including the COVID-19 pandemic: a representative serial study of 2.8 million people. Eur Rev Med Pharmacol Sci 2024; 28:242-254. [PMID: 38235875 DOI: 10.26355/eurrev_202401_34909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
OBJECTIVE There is a scarcity of literature investigating the impact of the coronavirus disease 2019 (COVID-19) pandemic on long-term trends in health-related quality of life (HrQoL) using large-scale and representative data. Thus, we aimed to investigate the nationwide and long-term trends in quality of life (QoL) using the European Quality of Life- 5 dimensions, 3-level version (EQ-5D-3L) from a Korean representative serial study of 2.8 million people, 2008-2021. SUBJECTS AND METHODS This Korean study used data on adults between 2008 and 2021 who participated in the Community Health Survey. Timeframes were categorized as COVID-19 mid-pandemic (2021) and pre-pandemic (2008-2019). The mean EQ-5D-3L index for the whole population and subgroups stratified by demographic characters was evaluated for each timeframe, and differences between before and during the COVID-19 pandemic were also analyzed. RESULTS 2,827,240 adults who responded to the survey, 2008-2021, were eligible for this study. Overall EQ-5D index persistently decreased from 2008-2016, then minimally decreased during the pandemic, still being much higher than forecasted before the COVID-19 pandemic. The reduction in the rate of decline in QoL after the COVID-19 outbreak was especially marked in white-collared, young adults, people with 'good' or 'very good' subjective health, and college-educated or above group. On the other hand, the previously increasing trend of QoL in the elderly group has decelerated during the pandemic, and QoL of the 'very bad' subjective health group recorded the lowest in the whole study period. CONCLUSIONS The present study investigated the long-term trend of QoL in Korean adults using serial data over the past 14 years, with a special emphasis on comparing the pre- and mid-COVID-19 pandemic periods.
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Affiliation(s)
- H Kim
- Department of Medicine, Kyung Hee University College of Medicine, Seoul, South Korea.
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Park JJ, Lee M, Kim H, Park JY, Lee H, Kim HJ, Koyanagi A, Smith L, Kim MS, Rahmati M, Rhee SY, Ha Y, Lee K, Yon DK. National trends in the prevalence of hepatitis B and C in South Korea, before and during the COVID-19 pandemic (2007-2021) - a nationwide representative study. Eur Rev Med Pharmacol Sci 2023; 27:12121-12133. [PMID: 38164874 DOI: 10.26355/eurrev_202312_34810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
OBJECTIVE Due to the various changes caused by the COVID-19 pandemic, some infectious diseases showed different epidemiology and prevalence during the pandemic. However, there is a lack of comprehensive studies on trends in the prevalence of hepatitis B and C related to the pandemic. Thus, we compared the prevalence of hepatitis B and C before and during the COVID-19 pandemic in South Korea. SUBJECTS AND METHODS We conducted a comprehensive trend analysis with a nationwide serial cross-sectional survey from 2007 to 2021 (n=86,931) using the Korea National Health and Nutrition Examination Survey (KNHANES). The changes in the prevalence of hepatitis B and C were evaluated using a weighted regression model to assess the impact of the COVID-19 pandemic. RESULTS From 2007 to 2021, 86,931 Korean adults aged 19 or older were included in the KNHANES data. The prevalence of hepatitis B showed a declining trend until the onset of the pandemic (1.80% in 2007-2009; 1.08% in 2016-2019; and 1.01% in 2020), at which point this trend reversed (1.39% in 2021). The prevalence of hepatitis C remained stable (0.14% in 2007-2009 and 0.18% in 2016-2019), with no particular surge related to the COVID-19 pandemic (βdiff, -0.002; 95% CI, -0.761 to 0.756). For hepatitis B, old age was identified as a pandemic-related vulnerable factor (ratio of odds ratio, 1.68; 95% CI, 1.05-2.70). CONCLUSIONS In this study, unlike other infectious diseases, hepatitis B and C did not show a decreasing trend during the pandemic. In particular, hepatitis B showed a rebound trend during the pandemic, which was noticeable in those aged 60 or older. Further studies are needed to support these findings.
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Affiliation(s)
- J-J Park
- Center for Digital Health, Medical Science Research Institute, Kyung Hee University College of Medicine, Seoul, South Korea.
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Yang H, Kim MS, Rhee SY, Lee J, Cho W, Min C, Lee SW, Shin JI, Oh J, Choi Y, Lee JH, Kim H, Rahmati M, Yeo SG, Yon DK. National prevalence and socioeconomic factors associated with the acceptance of COVID-19 vaccines in South Korea: a large-scale representative study in 2021. Eur Rev Med Pharmacol Sci 2023; 27:8943-8951. [PMID: 37782203 DOI: 10.26355/eurrev_202309_33815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
OBJECTIVE Among the global efforts toward preventing the COVID-19 pandemic, vaccines are a pivotal factor in ending the pandemic. Thus, through a large-scale population-based study, we investigated the individual-, social-, and family-associated factors affecting the acceptance of COVID-19 vaccines in South Korea. PATIENTS AND METHODS Data were obtained from a nationwide representative study (Korea Community Health) conducted in 2021. To determine the individual-, social-, and family-associated variables for COVID-19 vaccination acceptance, we investigated data from 225,319 individuals. RESULTS In the total sample (n=225,319), 184,529 COVID-19-vaccinated people and 40,790 non-vaccinated people were evaluated. The factors related to the acceptance of COVID-19 vaccination were significantly associated with the demographic factors, namely, older age group, female sex, and a history of influenza vaccination, as well as medical conditions such as diabetes, hypertension, and depression. Socioeconomic conditions influencing the acceptance of COVID-19 vaccination were significantly associated with low-income families and blue-collar workers. Health-related risk factors were high in the obese group. However, a noteworthy negative association was found between the acceptance of vaccination and smoking habits and alcohol consumption. Conversely, a positive association was observed between academic level and vaccination acceptance. CONCLUSIONS Our findings suggest that old age, female sex, a history of influenza vaccination, medical conditions, such as diabetes, hypertension, and depression, low-income families, blue-collar workers, and health-related risk factors, such as obesity, were associated with the acceptance of COVID-19 vaccination. Additionally, a high academic level, absence of smoking habits, and non-current alcohol use were positively associated with vaccine acceptance.
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Affiliation(s)
- H Yang
- Department of Regulatory Science, Kyung Hee University, Seoul, South Korea.
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Eum S, Son JW, Min C, Cho W, Kim S, Woo HG, Kwon R, Lee KN, Han KD, Yon DK, Rhee SY. Ethnic and sex differences in the distributions of body mass index and waist circumference among adults: a binationally representative study in South Korea and the United States. Eur Rev Med Pharmacol Sci 2023; 27:1889-1903. [PMID: 36930486 DOI: 10.26355/eurrev_202303_31555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
OBJECTIVE The ethnic and sex differences in the distributions of body mass index (BMI) and waist circumference (WC) among adults are largely unknown. Therefore, we aimed to investigate the percentiles of BMI and WC in groups divided according to age, sex, and ethnicity. PATIENTS AND METHODS We conducted a population-based binational study of adults aged ≥20 years based on data from two sources: US National Health and Nutrition Examination Survey (2015 to 2020) and Korea National Health and Nutrition Examination Survey (2016 to 2019). RESULTS Weight, height, and WC were measured in 13,144 American adults and 30,191 Korean adults. Overall, BMI increased at younger ages and decreased at older ages, which indicates a reversed U-shaped relationship, and differed in terms of age, sex, and ethnicity. Women in the other Hispanic, non-Hispanic white, non-Hispanic black, and "other ethnic groups" showed a common BMI peak at ages 50-54 years. The patterns of WC distribution were similar to those of BMI distribution. CONCLUSIONS In this binational representative study, we found varied distributions of ethnic and sex differences in BMI and WC. Considering the differences in these distributions may help improve individual and personalized treatment strategies.
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Affiliation(s)
- S Eum
- Department of Medicine, Kyung Hee University College of Medicine, Seoul, Republic of Korea.
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5
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Kim N, Song JY, Yang H, Kim MJ, Lee K, Shin YH, Rhee SY, Hwang J, Kim MS, Fond G, Boyer L, Kim SY, Shin JI, Lee SW, Yon DK. National trends in suicide-related behaviors among youths between 2005-2020, including COVID-19: a Korean representative survey of one million adolescents. Eur Rev Med Pharmacol Sci 2023; 27:1192-1202. [PMID: 36808368 DOI: 10.26355/eurrev_202302_31226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
OBJECTIVE It is difficult to conclude that COVID-19 is associated with a decrease in the suicide attempts rate by comparing only a short-term period. Therefore, it is necessary to examine attempted suicide rates through a trend analysis over a longer period. This study aimed to investigate an estimated long-term trend regarding the prevalence of suicide-related behaviors among adolescents in South Korea from 2005 to 2020, including COVID-19. SUBJECTS AND METHODS We sourced data from a national representative survey (Korea Youth Risk Behavior Survey) and analyzed one million Korean adolescents aged 13 to 18 years (n=1,057,885) from 2005 to 2020. The 16-year trends regarding the prevalence of sadness or despair and suicidal ideation and attempt and the trend changes before and during COVID-19. RESULTS Data of 1,057,885 Korean adolescents was analyzed (weighted mean age, 15.03 years; males, 52.5%; females, 47.5%). Although the 16-year trend in the prevalence of sadness or despair and suicide ideation and attempt consistently decreased (prevalence of sadness or despair between 2005-2008, 38.0% with 95% confidence interval [CI], 37.7 to 38.4 vs. prevalence in 2020, 25.0% [24.5 to 25.6]; suicide ideation between 2005-2008, 21.9% [21.6 to 22.1] vs. prevalence in 2020, 10.7% [10.3 to 11.1]; and suicide attempt between 2005-2008, 5.0% [4.9 to 5.2] vs. prevalence in 2020, 1.9% [1.8 to 2.0]), the downward slope decreased during COVID-19 (βdiff in sadness, 0.215 with 95% CI 0.206 to 0.224; βdiff in suicidal ideation, 0.245 [0.234 to 0.256]; and βdiff in suicide attempt, 0.219 [0.201 to 0.237]) compared with pre-pandemic period. CONCLUSIONS This study found that the observed risk of suicide-related behaviors during the pandemic was higher than expected through long-term trend analysis of the prevalence of sadness/despair and suicidal ideation and attempts among South Korean adolescents. We need a profound epidemiologic study of the change in mental health due to the pandemic's impact and the establishment of prevention strategies for suicide ideation and attempt.
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Affiliation(s)
- N Kim
- Department of Neuropsychiatry, Seoul National University College of Medicine, Seoul, South Korea.
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Ban CY, Shin H, Eum S, Yon H, Lee SW, Choi YS, Shin YH, Shin JU, Koyanagi A, Jacob L, Smith L, Min C, Yeniova AÖ, Kim SY, Lee J, Yeo SG, Kwon R, Koo MJ, Fond G, Boyer L, Acharya KP, Kim S, Woo HG, Park S, Shin JI, Rhee SY, Yon DK. 17-year trends of body mass index, overweight, and obesity among adolescents from 2005 to 2021, including the COVID-19 pandemic: a Korean national representative study. Eur Rev Med Pharmacol Sci 2023; 27:1565-1575. [PMID: 36876712 DOI: 10.26355/eurrev_202302_31399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
OBJECTIVE There is a lack of pediatric studies that have analyzed trends in mean body mass index (BMI) and the prevalence of obesity and overweight over a period that includes the mid-stage of the COVID-19 pandemic. Thus, we aimed to investigate trends in BMI, overweight, and obesity among Korean adolescents from 2005 to 2021, including the COVID-19 pandemic. SUBJECTS AND METHODS We used data from the Korea Youth Risk Behavior Web-based Survey (KYRBS), which is nationally representative of South Korea. The study included middle- and high-school students between the ages of 12 and 18. We examined trends in mean BMI and prevalence of obesity and/or overweight during the COVID-19 pandemic and compared these to those of pre-pandemic trends in each subgroup by gender, grade, and residential region. RESULTS Data from 1,111,300 adolescents (mean age: 15.04 years) were analyzed. The estimated weighted mean BMI was 20.48 kg/m2 (95% CI, 20.46-20.51) between 2005 and 2007, and this was 21.61 kg/m2 (95% CI, 21.54-21.68) in 2021. The prevalence of overweight and obesity was 13.1% (95% CI, 12.9-13.3%) between 2005 and 2007 and 23.4% (95% CI, 22.8-24.0%) in 2021. The mean BMI and prevalence of obesity and overweight have gradually increased over the past 17 years; however, the extent of change in mean BMI and in the prevalence of obesity and overweight during the pandemic was distinctly less than before. The 17-year trends in the mean BMI, obesity, and overweight exhibited a considerable rise from 2005 to 2021; however, the slope during the COVID-19 pandemic (2020-2021) was significantly less prominent than in the pre-pandemic (2005-2019). CONCLUSIONS These findings enable us to comprehend long-term trends in the mean BMI of Korean adolescents and further emphasize the need for practical prevention measures against youth obesity and overweight.
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Affiliation(s)
- C Y Ban
- Department of Medicine, Kyung Hee University College of Medicine, Seoul, South Korea.
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Kim MJ, Lee KH, Lee JS, Kim N, Song JY, Shin YH, Yang JM, Lee SW, Hwang J, Rhee SY, Yon DK, Shin JI, Choi YJ. Trends in body mass index changes among Korean adolescents between 2005-2020, including the COVID-19 pandemic period: a national representative survey of one million adolescents. Eur Rev Med Pharmacol Sci 2022; 26:4082-4091. [PMID: 35731079 DOI: 10.26355/eurrev_202206_28978] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
OBJECTIVE The impact of the coronavirus disease 2019 (COVID-19) pandemic on weight gain in children and adolescents remains unknown. We aimed to identify an estimated 15-year trend in mean body mass index (BMI) changes and prevalence of obesity and overweight among Korean adolescents from 2005 to 2020, including the period of the COVID-19 pandemic. PATIENTS AND METHODS We analyzed data taken from a nationwide survey (Korea Youth Risk Behavior Survey), between 2005 and 2020. Representative samples of one million Korean adolescents aged 13-18 years (n=1,057,885) were examined. The 15-year trends in mean BMI and proportion of obesity or overweight, and the changes due to the COVID-19 pandemic were analyzed. RESULTS The data of 1,057,885 Korean adolescents were analyzed (mean age: 14.98 years; females, 48.4%). The estimated weighted mean BMI was 20.5 kg/m2 [95% confidence interval (CI), 20.4-20.5] from 2005 to 2008 and 21.5 kg/m2 (95% CI, 21.4-21.6) in 2020 (during the COVID-19 pandemic). Although the 15-year trend of mean BMI gradually increased, the change in mean BMI before and during the pandemic significantly lessened (βdiff, -0.027; 95% CI, -0.028 to -0.026). The 15-year (2005-2020) trend changes in the prevalence of obesity and overweight were similar (obesity prevalence from 2005-2008, 3.2%; 95% CI, 3.1-3.3 vs. obesity prevalence in 2020, 8.6%; 95% CI, 8.2-9.0; βdiff, -0.309; 95% CI, -0.330 to -0.288). CONCLUSIONS The 15-year trend of overall mean BMI and obesity and overweight prevalence demonstrated a significant increase; however, its slope decreased during the pandemic. These landmark results suggest the need for the development of precise strategies to prevent pediatric obesity and overweight during the COVID-19 pandemic.
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Affiliation(s)
- M J Kim
- Department of Pediatrics, Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea.
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8
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Zaiken MC, Flynn R, Paz KG, Rhee SY, Jin S, Mohamed FA, Saha A, Thangavelu G, Park PMC, Hemming ML, Sage PT, Sharpe AH, DuPage M, Bluestone JA, Panoskaltsis-Mortari A, Cutler CS, Koreth J, Antin JH, Soiffer RJ, Ritz J, Luznik L, Maillard I, Hill GR, MacDonald KPA, Munn DH, Serody JS, Murphy WJ, Kean LS, Zhang Y, Bradner JE, Qi J, Blazar BR. BET-bromodomain and EZH2 inhibitor-treated chronic GVHD mice have blunted germinal centers with distinct transcriptomes. Blood 2022; 139:2983-2997. [PMID: 35226736 PMCID: PMC9101246 DOI: 10.1182/blood.2021014557] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 02/09/2022] [Indexed: 01/26/2023] Open
Abstract
Despite advances in the field, chronic graft-versus-host-disease (cGVHD) remains a leading cause of morbidity and mortality following allogenic hematopoietic stem cell transplant. Because treatment options remain limited, we tested efficacy of anticancer, chromatin-modifying enzyme inhibitors in a clinically relevant murine model of cGVHD with bronchiolitis obliterans (BO). We observed that the novel enhancer of zeste homolog 2 (EZH2) inhibitor JQ5 and the BET-bromodomain inhibitor JQ1 each improved pulmonary function; impaired the germinal center (GC) reaction, a prerequisite in cGVHD/BO pathogenesis; and JQ5 reduced EZH2-mediated H3K27me3 in donor T cells. Using conditional EZH2 knockout donor cells, we demonstrated that EZH2 is obligatory for the initiation of cGVHD/BO. In a sclerodermatous cGVHD model, JQ5 reduced the severity of cutaneous lesions. To determine how the 2 drugs could lead to the same physiological improvements while targeting unique epigenetic processes, we analyzed the transcriptomes of splenic GCB cells (GCBs) from transplanted mice treated with either drug. Multiple inflammatory and signaling pathways enriched in cGVHD/BO GCBs were reduced by each drug. GCBs from JQ5- but not JQ1-treated mice were enriched for proproliferative pathways also seen in GCBs from bone marrow-only transplanted mice, likely reflecting their underlying biology in the unperturbed state. In conjunction with in vivo data, these insights led us to conclude that epigenetic targeting of the GC is a viable clinical approach for the treatment of cGVHD, and that the EZH2 inhibitor JQ5 and the BET-bromodomain inhibitor JQ1 demonstrated clinical potential for EZH2i and BETi in patients with cGVHD/BO.
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Affiliation(s)
- Michael C Zaiken
- Division of Blood & Marrow Transplant & Cellular Therapy, Department of Pediatrics, Masonic Cancer Center, University of Minnesota, Minneapolis, MN
| | - Ryan Flynn
- Division of Blood & Marrow Transplant & Cellular Therapy, Department of Pediatrics, Masonic Cancer Center, University of Minnesota, Minneapolis, MN
| | - Katelyn G Paz
- Division of Blood & Marrow Transplant & Cellular Therapy, Department of Pediatrics, Masonic Cancer Center, University of Minnesota, Minneapolis, MN
| | - Stephanie Y Rhee
- Division of Blood & Marrow Transplant & Cellular Therapy, Department of Pediatrics, Masonic Cancer Center, University of Minnesota, Minneapolis, MN
| | - Sujeong Jin
- Division of Blood & Marrow Transplant & Cellular Therapy, Department of Pediatrics, Masonic Cancer Center, University of Minnesota, Minneapolis, MN
| | - Fathima A Mohamed
- Division of Blood & Marrow Transplant & Cellular Therapy, Department of Pediatrics, Masonic Cancer Center, University of Minnesota, Minneapolis, MN
| | - Asim Saha
- Division of Blood & Marrow Transplant & Cellular Therapy, Department of Pediatrics, Masonic Cancer Center, University of Minnesota, Minneapolis, MN
| | - Govindarajan Thangavelu
- Division of Blood & Marrow Transplant & Cellular Therapy, Department of Pediatrics, Masonic Cancer Center, University of Minnesota, Minneapolis, MN
| | - Paul M C Park
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
| | - Matthew L Hemming
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
| | - Peter T Sage
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA
- Evergrande Center for Immunologic Diseases, Harvard Medical School-Brigham and Women's Hospital, Boston, MA
| | - Arlene H Sharpe
- Department of Immunology, Blavatnik Institute, Harvard Medical School, Boston, MA
- Evergrande Center for Immunologic Diseases, Harvard Medical School-Brigham and Women's Hospital, Boston, MA
| | - Michel DuPage
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA
| | | | - Angela Panoskaltsis-Mortari
- Division of Blood & Marrow Transplant & Cellular Therapy, Department of Pediatrics, Masonic Cancer Center, University of Minnesota, Minneapolis, MN
| | | | | | | | - Robert J Soiffer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | | | - Leo Luznik
- Department of Oncology, Sidney Kimmel Cancer Center, Baltimore, MD
| | - Ivan Maillard
- Division of Hematology-Oncology, Department of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Geoffrey R Hill
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
- Division of Medical Oncology, University of Washington, Seattle, WA
| | - Kelli P A MacDonald
- Department of Immunology, Queensland Institute of Medical Research (QIMR), University of Queensland, Brisbane, QLD, Australia
| | - David H Munn
- Georgia Cancer Center, Augusta University, Augusta, GA
| | - Jonathan S Serody
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC
| | - William J Murphy
- Department of Dermatology, School of Medicine, University of California, Davis, Sacramento, CA
| | - Leslie S Kean
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
- Boston Children's Hospital, Dana-Farber Cancer Institute, Boston, MA
| | - Yi Zhang
- Fels Institute for Cancer Research and Molecular Biology, Department of Microbiology and Immunology, Temple University, Philadelphia, PA
| | - James E Bradner
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA; and
| | - Jun Qi
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
| | - Bruce R Blazar
- Division of Blood & Marrow Transplant & Cellular Therapy, Department of Pediatrics, Masonic Cancer Center, University of Minnesota, Minneapolis, MN
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Mohamed FA, Rhee SY, Ly J, Aguilar EG, Sage PT, Schumacher T, Thangavelu G, Zaiken MC, Liu J, Mereddy V, Locasale JW, Blazar BR. Targeting temporal metabolic needs of T follicular helper cells to treat cGVHD utilizing a mitochondrial pyruvate carrier inhibitor. The Journal of Immunology 2022. [DOI: 10.4049/jimmunol.208.supp.175.25] [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] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Abstract
The curative potential of allogeneic hematopoietic stem cell transplantation is limited by development of chronic graft versus host disease (cGVHD) and metabolic regulation of immune cells is a promising therapeutic target. During cGVHD, interactions between T follicular helper (TFH) and germinal center B (GCB) cells result in production of alloreactive class-switched antibodies that attack host tissues, causing multi-organ damage and tissue fibrosis. We show the metabolic dependencies of TFH change throughout cGVHD progression and targeting mitochondrial pyruvate transport is an effective strategy to mitigate disease. Pyruvate, the end product of glycolysis, is transported by the mitochondrial pyruvate carrier (MPC) for use in the tricarboxylic acid cycle and oxidative phosphorylation (OXPHOS). TFH require glycolysis in order to induce a GC reaction, both in an immunization model and in an in vivo systemic cGVHD model with bronchiolitis obliterans (BO). Furthermore, Seahorse data from TFH extracted early in disease development in the BO model demonstrate increased dependency on glycolysis. But Seahorse data also indicates TFH undergo a shift away from glycolysis and toward OXPHOS as cGVHD continues. Based on the central role of MPC in tying pyruvate to multiple metabolic pathways, we examined an inhibitor of MPC (7ACC1) in reducing TFH activity. Administration of 7ACC1 resulted in inhibition of GCB production of class switched antibody in an in vitro assay. These findings were additionally supported in vivo, whereby daily treatment after establishment of cGVHD resulted in a decrease in disease severity. These data provide evidence that inhibiting mitochondrial pyruvate transport is a viable therapeutic strategy for cGVHD.
This work was supported by grants from National Institutes of Health, National Institute of Allergy, and Infectious Diseases R37 AI34495, T32 AI007313; National Heart, Lung, and Blood Institute R01 HL56067, R01 HL11879, R01 HL115114 ; National Cancer Institute P01 CA065493
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Thangavelu G, Zaiken MC, Mohamed FA, Flynn R, Du J, Rhee SY, Riddle MJ, Aguilar EG, Panoskaltsis-Mortari A, Sanders ME, Blazar BR. Targeting the Retinoid X Receptor Pathway Prevents and Ameliorates Murine Chronic Graft-Versus-Host Disease. Front Immunol 2022; 13:765319. [PMID: 35359939 PMCID: PMC8963714 DOI: 10.3389/fimmu.2022.765319] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 01/26/2022] [Indexed: 02/03/2023] Open
Abstract
Most allogeneic hematopoietic stem cell transplant (allo-HSCT) recipients receive peripheral blood stem cell grafts resulting in a 30%-70% incidence of chronic graft-versus-host disease (cGVHD), a major cause of mortality and morbidity in long-term survivors. While systemic steroids remain the standard of care for first-line therapy, patients may require long-term administration, and those with steroid-resistant or refractory cGVHD have a worse prognosis. Although durable and deep responses with second-line therapies can be achieved in some patients, there remains an urgent need for new therapies. In this study, we evaluated the efficacy of IRX4204, a novel agonist that activates RXRs and is in clinical trials for cancer treatment to prevent and treat cGVHD in two complementary murine models. In a major histocompatibility complex mismatched, non-sclerodermatous multiorgan system model with bronchiolitis obliterans, IRX4204 prevented and reversed cGVHD including associated pulmonary dysfunction with restoration of germinal center T-follicular helper: T-follicular regulatory cell balance. In a minor histocompatibility antigen disparate sclerodermatous model, IRX4204 treatment significantly prevented and ameliorated skin cGVHD by reducing Th1 and Th17 differentiation due to anti-inflammatory properties. Together, these results indicate that IRX4204 is a promising therapeutic option to treat cGVHD with bronchiolitis obliterans or sclerodermatous manifestations.
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Affiliation(s)
- Govindarajan Thangavelu
- Department of Pediatrics, Division of Blood & Marrow Transplantation & Cellular Therapy, University of Minnesota, Minneapolis, MN, United States
| | - Michael C. Zaiken
- Department of Pediatrics, Division of Blood & Marrow Transplantation & Cellular Therapy, University of Minnesota, Minneapolis, MN, United States
| | - Fathima A. Mohamed
- Department of Pediatrics, Division of Blood & Marrow Transplantation & Cellular Therapy, University of Minnesota, Minneapolis, MN, United States
| | - Ryan Flynn
- Department of Pediatrics, Division of Blood & Marrow Transplantation & Cellular Therapy, University of Minnesota, Minneapolis, MN, United States
| | - Jing Du
- Department of Pediatrics, Division of Blood & Marrow Transplantation & Cellular Therapy, University of Minnesota, Minneapolis, MN, United States
| | - Stephanie Y. Rhee
- Department of Pediatrics, Division of Blood & Marrow Transplantation & Cellular Therapy, University of Minnesota, Minneapolis, MN, United States
| | - Megan J. Riddle
- Department of Pediatrics, Division of Blood & Marrow Transplantation & Cellular Therapy, University of Minnesota, Minneapolis, MN, United States
| | - Ethan G. Aguilar
- Department of Pediatrics, Division of Blood & Marrow Transplantation & Cellular Therapy, University of Minnesota, Minneapolis, MN, United States
| | - Angela Panoskaltsis-Mortari
- Department of Pediatrics, Division of Blood & Marrow Transplantation & Cellular Therapy, University of Minnesota, Minneapolis, MN, United States
| | | | - Bruce R. Blazar
- Department of Pediatrics, Division of Blood & Marrow Transplantation & Cellular Therapy, University of Minnesota, Minneapolis, MN, United States
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Mohamed FA, Thangavelu G, Rhee SY, Sage PT, O’Connor RS, Rathmell JC, Blazar BR. Recent Metabolic Advances for Preventing and Treating Acute and Chronic Graft Versus Host Disease. Front Immunol 2021; 12:757836. [PMID: 34712243 PMCID: PMC8546182 DOI: 10.3389/fimmu.2021.757836] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 09/13/2021] [Indexed: 01/14/2023] Open
Abstract
The therapeutic efficacy of allogeneic hematopoietic stem cell transplantation (allo-HSCT) is limited by the development of graft-versus-host disease (GVHD). In GVHD, rigorous pre-conditioning regimen resets the immune landscape and inflammatory milieu causing immune dysregulation, characterized by an expansion of alloreactive cells and a reduction in immune regulatory cells. In acute GVHD (aGVHD), the release of damage- and pathogen- associated molecular patterns from damaged tissue caused by the conditioning regimen sets the stage for T cell priming, activation and expansion further exacerbating tissue injury and organ damage, particularly in the gastrointestinal tract. Studies have shown that donor T cells utilize multiple energetic and biosynthetic pathways to mediate GVHD that can be distinct from the pathways used by regulatory T cells for their suppressive function. In chronic GVHD (cGVHD), donor T cells may differentiate into IL-21 producing T follicular helper cells or tissue resident T helper cells that cooperate with germinal center B cells or memory B cells, respectively, to produce allo- and auto-reactive antibodies with subsequent tissue fibrosis. Alternatively, donor T cells can become IFN- γ/IL-17 cytokine expressing T cells that mediate sclerodermatous skin injury. Patients refractory to the first line standard regimens for GVHD treatment have a poor prognosis indicating an urgent need for new therapies to restore the balance between effector and regulatory immune cells while preserving the beneficial graft-versus-tumor effect. Emerging data points toward a role for metabolism in regulating these allo- and auto-immune responses. Here, we will discuss the preclinical and clinical data available on the distinct metabolic demands of acute and chronic GVHD and recent efforts in identifying therapeutic targets using metabolomics. Another dimension of this review will examine the changing microbiome after allo-HSCT and the role of microbial metabolites such as short chain fatty acids and long chain fatty acids on regulating immune responses. Lastly, we will examine the metabolic implications of coinhibitory pathway blockade and cellular therapies in allo-HSCT. In conclusion, greater understanding of metabolic pathways involved in immune cell dysregulation during allo-HSCT may pave the way to provide novel therapies to prevent and treat GVHD.
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Affiliation(s)
- Fathima A. Mohamed
- Department of Pediatrics, Division of Blood & Marrow Transplant & Cellular Therapy, University of Minnesota Cancer Center, Minneapolis, MN, United States
| | - Govindarajan Thangavelu
- Department of Pediatrics, Division of Blood & Marrow Transplant & Cellular Therapy, University of Minnesota Cancer Center, Minneapolis, MN, United States
| | - Stephanie Y. Rhee
- Department of Pediatrics, Division of Blood & Marrow Transplant & Cellular Therapy, University of Minnesota Cancer Center, Minneapolis, MN, United States
| | - Peter T. Sage
- Renal Division, Transplantation Research Center, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Roddy S. O’Connor
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Center for Cellular Immunotherapies, Perelman School of Medicine, Philadelphia, PA, United States
| | - Jeffrey C. Rathmell
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Bruce R. Blazar
- Department of Pediatrics, Division of Blood & Marrow Transplant & Cellular Therapy, University of Minnesota Cancer Center, Minneapolis, MN, United States
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12
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Gregson J, Rhee SY, Datir R, Pillay D, Perno CF, Derache A, Shafer RS, Gupta RK. Human Immunodeficiency Virus-1 Viral Load Is Elevated in Individuals With Reverse-Transcriptase Mutation M184V/I During Virological Failure of First-Line Antiretroviral Therapy and Is Associated With Compensatory Mutation L74I. J Infect Dis 2020; 222:1108-1116. [PMID: 31774913 PMCID: PMC7459140 DOI: 10.1093/infdis/jiz631] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 11/26/2019] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND M184V/I cause high-level lamivudine (3TC) and emtricitabine (FTC) resistance and increased tenofovir disoproxil fumarate (TDF) susceptibility. Nonetheless, 3TC and FTC (collectively referred to as XTC) appear to retain modest activity against human immunodeficiency virus-1 with these mutations possibly as a result of reduced replication capacity. In this study, we determined how M184V/I impacts virus load (VL) in patients failing therapy on a TDF/XTC plus nonnucleoside reverse-transcriptase inhibitor (NNRTI)-containing regimen. METHODS We compared VL in the absence and presence of M184V/I across studies using random effects meta-analysis. The effect of mutations on virus reverse-transcriptase activity and infectiousness was analyzed in vitro. RESULTS M184I/V was present in 817 (56.5%) of 1445 individuals with virologic failure (VF). Virus load was similar in individuals with or without M184I/V (difference in log10 VL, 0.18; 95% confidence interval, .05-.31). CD4 count was lower both at initiation of antiretroviral therapy and at VF in participants who went on to develop M184V/I. L74I was present in 10.2% of persons with M184V/I but absent in persons without M184V/I (P < .0001). In vitro, L74I compensated for defective replication of M184V-mutated virus. CONCLUSIONS Virus loads were similar in persons with and without M184V/I during VF on a TDF/XTC/NNRTI-containing regimen. Therefore, we did not find evidence for a benefit of XTC in the context of first-line failure on this combination.
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Affiliation(s)
- J Gregson
- Department of Biostatistics, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - S Y Rhee
- Department of Medicine, Stanford University, Stanford, California, USA
| | - R Datir
- Division of Infection and Immunity, UCL, London, United Kingdom
| | - D Pillay
- Division of Infection and Immunity, UCL, London, United Kingdom
- Africa Health Research Institute, Durban, South Africa
| | - C F Perno
- Department of Oncology and Haematoncology, University of Milan, Milan, Italy
| | - A Derache
- Africa Health Research Institute, Durban, South Africa
| | - R S Shafer
- Department of Medicine, Stanford University, Stanford, California, USA
| | - R K Gupta
- Africa Health Research Institute, Durban, South Africa
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
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13
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Hippen KL, Aguilar EG, Rhee SY, Bolivar-Wagers S, Blazar BR. Distinct Regulatory and Effector T Cell Metabolic Demands during Graft-Versus-Host Disease. Trends Immunol 2020; 41:77-91. [PMID: 31791718 PMCID: PMC6934920 DOI: 10.1016/j.it.2019.11.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 11/08/2019] [Accepted: 11/08/2019] [Indexed: 02/07/2023]
Abstract
Despite graft-versus-host disease (GVHD) prophylactic agents, the success and wider utilization of allogeneic hematopoietic stem cell transplantation (allo-HSCT) is limited by GVHD. Increasing donor graft regulatory T cell (Treg):effector T cell (Teff) ratios can substantially reduce GVHD in cancer patients, but pre-HSCT conditioning regimens and GVHD create a challenging inflammatory environment for Treg stability, persistence, and function. Metabolism plays a crucial role in T cell and Treg differentiation, and development of effector function. Although glycolysis is a main driver of allogeneic T cell-driven GVHD, oxidative phosphorylation is a main driver of Treg suppressor function. This review focuses on recent advances in our understanding of Treg metabolism in the context of GVHD, and discusses potential therapeutic applications of Tregs in the prevention or treatment of GVHD in cancer patients.
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Affiliation(s)
- Keli L Hippen
- University of Minnesota Cancer Center, Minneapolis, MN 55455, USA; Department of Pediatrics, Division of Blood and Marrow Transplantation, University of Minnesota, Minneapolis, MN 55455, USA.
| | - Ethan G Aguilar
- University of Minnesota Cancer Center, Minneapolis, MN 55455, USA; Department of Pediatrics, Division of Blood and Marrow Transplantation, University of Minnesota, Minneapolis, MN 55455, USA
| | - Stephanie Y Rhee
- University of Minnesota Cancer Center, Minneapolis, MN 55455, USA; Department of Pediatrics, Division of Blood and Marrow Transplantation, University of Minnesota, Minneapolis, MN 55455, USA
| | - Sara Bolivar-Wagers
- University of Minnesota Cancer Center, Minneapolis, MN 55455, USA; Department of Pediatrics, Division of Blood and Marrow Transplantation, University of Minnesota, Minneapolis, MN 55455, USA
| | - Bruce R Blazar
- University of Minnesota Cancer Center, Minneapolis, MN 55455, USA; Department of Pediatrics, Division of Blood and Marrow Transplantation, University of Minnesota, Minneapolis, MN 55455, USA.
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Theys K, Camacho RJ, Gomes P, Vandamme AM, Rhee SY. Predicted residual activity of rilpivirine in HIV-1 infected patients failing therapy including NNRTIs efavirenz or nevirapine. Clin Microbiol Infect 2015; 21:607.e1-8. [PMID: 25704446 DOI: 10.1016/j.cmi.2015.02.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [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: 09/11/2014] [Revised: 01/12/2015] [Accepted: 02/08/2015] [Indexed: 10/24/2022]
Abstract
Rilpivirine is a second-generation nonnucleoside reverse-transcriptase inhibitor (NNRTI) currently indicated for first-line therapy, but its clinical benefit for HIV-1 infected patients failing first-generation NNRTIs is largely undefined. This study quantified the extent of genotypic rilpivirine resistance in viral isolates from 1212 patients upon failure of efavirenz- or nevirapine-containing antiretroviral treatment, of whom more than respectively 80% and 90% showed high-level genotypic resistance to the failing NNRTI. Of all study patients, 47% showed a rilpivirine resistance-associated mutation (RPV-RAM), whereas preserved residual rilpivirine activity was predicted in half of the patients by three genotypic drug resistance interpretation algorithms. An NNRTI-dependent impact on rilpivirine resistance was detected. Compared with the use of nevirapine, the use of efavirenz was associated with a 32% lower risk of having a RPV-RAM and a 50% lower risk of predicted reduced rilpivirine susceptibility. Most prevalent RPV-RAMs after nevirapine experience were Y181C and H221Y, whereas L100I+K103N, Y188L and K101E occurred most in efavirenz-experienced patients. Predicted rilpivirine activity was not affected by HIV-1 subtype, although frequency of individual mutations differed across subtypes. In conclusion, this genotypic resistance analysis strongly suggests that the latest NNRTI, rilpivirine, may retain activity in a large proportion of HIV-1 patients in whom resistance failed while they were on an efavirenz- or nevirapine-containing regimen, and may present an attractive option for second-line treatment given its good safety profile and dosing convenience. However, prospective clinical studies assessing the effectiveness of rilpivirine for NNRTI-experienced patients are warranted to validate knowledge derived from genotypic and phenotypic drug resistance studies.
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Affiliation(s)
- K Theys
- KU Leuven, University of Leuven, Department Microbiology and Immunology, Rega Institute for Medical Research, Leuven, Belgium.
| | - R J Camacho
- KU Leuven, University of Leuven, Department Microbiology and Immunology, Rega Institute for Medical Research, Leuven, Belgium; Centro de Malária e outras Doenças Tropicais, Instituto de Higiene e Medicina Tropical e Unidade de Microbiologia, Universidade Nova de Lisboa, Lisbon, Portugal
| | - P Gomes
- Centro de Malária e outras Doenças Tropicais, Instituto de Higiene e Medicina Tropical e Unidade de Microbiologia, Universidade Nova de Lisboa, Lisbon, Portugal; Centro Hospitalar de Lisboa Ocidental, Lisbon, Portugal; Centro de Investigação Interdisciplinar Egas Moniz (CiiEM), Instituto Superior de Ciências da Saúde Sul, Caparica, Portugal
| | - A M Vandamme
- KU Leuven, University of Leuven, Department Microbiology and Immunology, Rega Institute for Medical Research, Leuven, Belgium; Centro de Malária e outras Doenças Tropicais, Instituto de Higiene e Medicina Tropical e Unidade de Microbiologia, Universidade Nova de Lisboa, Lisbon, Portugal
| | - S Y Rhee
- KU Leuven, University of Leuven, Department Microbiology and Immunology, Rega Institute for Medical Research, Leuven, Belgium; Department of Medicine, Stanford University, Stanford, CA, USA
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Abstract
Methylglyoxal is a reactive dicarbonyl compound produced by glycolytic processing and identified as a precursor of advanced glycation end products. The elevated methylglyoxal levels in patients with diabetes are believed to contribute to diabetic complications, including bone defects. The objective of this study was to evaluate the effect of methylglyoxal on the function of osteoblastic MC3T3-E1 cells. The data indicated that methylglyoxal decreased osteoblast differentiation and induced osteoblast cytotoxicity. Pretreatment of MC3T3-E1 cells with aminoguanidine (a carbonyl scavenger), Trolox (an antioxidant), and cyclosporin A (a blocker of the mitochondrial permeability transition pore) prevented methylglyoxal-induced cytotoxicity in MC3T3-E1 cells. However, BAPTA/AM (an intracellular Ca(2+) chelator) and dantrolene (an inhibitor of endoplasmic reticulum Ca(2+) release) did not reverse the cytotoxic effect of methylglyoxal. Methylglyoxal increased the formation of intracellular reactive oxygen species, mitochondrial superoxide, and cardiolipin peroxidation in osteoblastic MC3T3-E1 cells. Methylglyoxal also decreased the mitochondrial membrane potential and intracellular ATP and nitric oxide levels, suggesting that carbonyl stress-induced loss of mitochondrial integrity contributes to the cytotoxicity of methylglyoxal. Furthermore, the results demonstrated that methylglyoxal induced protein adduct formation, inactivation of glyoxalase I, and activation of glyoxalase II. Aminoguanidine reversed all aforementioned effects of methylglyoxal. Taken together, these data support the notion that high methylglyoxal concentrations have detrimental effects on osteoblasts through a mechanism involving oxidative stress and mitochondrial dysfunction.
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Affiliation(s)
- K S Suh
- Research Institute of Endocrinology, Kyung Hee University Hospital , Seoul , Republic of Korea
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16
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Abstract
AIMS A causal relationship between vitamin D deficiency and the incidence of diabetes mellitus has been suggested, but little research has been conducted on the Korean population. METHODS We analysed the glucose tolerance status and serum 25-hydroxyvitamin D concentrations in 12263 subjects >19 years old who were registered for the Korea National Health and Nutrition Examination Survey, 2008-2009. RESULTS Various demographic variables such as gender, age, season, resident area, physical activity, smoking, alcohol, marital status, education and occupation were associated with serum 25-hydroxyvitamin D concentrations. After adjusting for these variables as confounders, 25-hydroxyvitamin D concentrations in subjects with diabetes were significantly lower than those in subjects with normal glucose tolerance and those with impaired fasting glucose (P=0.005). Compared with the ≥ 75 nmol/l subgroup of serum 25-hydroxyvitamin D concentration, the odds ratios and 95% confidence intervals for diabetes mellitus were 1.206 (95%CI 0.948-1.534) in the 50- to 74-nmol/l subgroup, 1.339 (1.051-1.707) in the 25-to 49-nmol/l subgroup and 1.759 (1.267-2.443) in the <25-nmol/l subgroup. Compared with the serum ≥ 75-nmol/l 25-hydroxyvitamin D subgroup, serum insulin and homeostasis model assessment 2%B, a marker of insulin secretory capacity, were significantly higher, and homeostasis model assessment 2%S, a marker of insulin sensitivity, was significantly lower in the <25- and 25- to 49-nmol/l serum 25-hydroxyvitamin D subgroups than those in the other subgroups (P<0.001). CONCLUSIONS The findings suggest that vitamin D deficiency, possibly involving altered insulin sensitivity, is associated with an increased risk for diabetes mellitus in the Korean population.
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Affiliation(s)
- S Y Rhee
- Department of Endocrinology and Metabolism, Kyung Hee University School of Medicine and Research Institute of Endocrinology, Kyung Hee University, Seoul, Korea
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Harris MA, Clark J, Ireland A, Lomax J, Ashburner M, Foulger R, Eilbeck K, Lewis S, Marshall B, Mungall C, Richter J, Rubin GM, Blake JA, Bult C, Dolan M, Drabkin H, Eppig JT, Hill DP, Ni L, Ringwald M, Balakrishnan R, Cherry JM, Christie KR, Costanzo MC, Dwight SS, Engel S, Fisk DG, Hirschman JE, Hong EL, Nash RS, Sethuraman A, Theesfeld CL, Botstein D, Dolinski K, Feierbach B, Berardini T, Mundodi S, Rhee SY, Apweiler R, Barrell D, Camon E, Dimmer E, Lee V, Chisholm R, Gaudet P, Kibbe W, Kishore R, Schwarz EM, Sternberg P, Gwinn M, Hannick L, Wortman J, Berriman M, Wood V, de la Cruz N, Tonellato P, Jaiswal P, Seigfried T, White R. The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res 2004; 32:D258-61. [PMID: 14681407 PMCID: PMC308770 DOI: 10.1093/nar/gkh036] [Citation(s) in RCA: 2541] [Impact Index Per Article: 127.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The Gene Ontology (GO) project (http://www. geneontology.org/) provides structured, controlled vocabularies and classifications that cover several domains of molecular and cellular biology and are freely available for community use in the annotation of genes, gene products and sequences. Many model organism databases and genome annotation groups use the GO and contribute their annotation sets to the GO resource. The GO database integrates the vocabularies and contributed annotations and provides full access to this information in several formats. Members of the GO Consortium continually work collectively, involving outside experts as needed, to expand and update the GO vocabularies. The GO Web resource also provides access to extensive documentation about the GO project and links to applications that use GO data for functional analyses.
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18
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Huala E, Dickerman AW, Garcia-Hernandez M, Weems D, Reiser L, LaFond F, Hanley D, Kiphart D, Zhuang M, Huang W, Mueller LA, Bhattacharyya D, Bhaya D, Sobral BW, Beavis W, Meinke DW, Town CD, Somerville C, Rhee SY. The Arabidopsis Information Resource (TAIR): a comprehensive database and web-based information retrieval, analysis, and visualization system for a model plant. Nucleic Acids Res 2001; 29:102-5. [PMID: 11125061 PMCID: PMC29827 DOI: 10.1093/nar/29.1.102] [Citation(s) in RCA: 357] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Arabidopsis thaliana, a small annual plant belonging to the mustard family, is the subject of study by an estimated 7000 researchers around the world. In addition to the large body of genetic, physiological and biochemical data gathered for this plant, it will be the first higher plant genome to be completely sequenced, with completion expected at the end of the year 2000. The sequencing effort has been coordinated by an international collaboration, the Arabidopsis Genome Initiative (AGI). The rationale for intensive investigation of Arabidopsis is that it is an excellent model for higher plants. In order to maximize use of the knowledge gained about this plant, there is a need for a comprehensive database and information retrieval and analysis system that will provide user-friendly access to Arabidopsis information. This paper describes the initial steps we have taken toward realizing these goals in a project called The Arabidopsis Information Resource (TAIR) (www.arabidopsis.org).
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Affiliation(s)
- E Huala
- Carnegie Institution, Department of Plant Biology, 260 Panama Street, Stanford, CA 94305, USA.
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Rhee SY. Bioinformatic resources, challenges, and opportunities using Arabidopsis as a model organism in a post-genomic era. Plant Physiol 2000; 124:1460-1464. [PMID: 11115859 PMCID: PMC1539296 DOI: 10.1104/pp.124.4.1460] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Affiliation(s)
- S Y Rhee
- Department of Plant Biology, 260 Panama Street, Carnegie Institution of Washington, Stanford, California 94305, USA.
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20
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Rhee SY, Weng S, Bongard-Pierce DK, García-Hernández M, Malekian A, Flanders DJ, Cherry JM. Unified display of Arabidopsis thaliana physical maps from AtDB, the A.thaliana database. Nucleic Acids Res 1999; 27:79-84. [PMID: 9847147 PMCID: PMC148102 DOI: 10.1093/nar/27.1.79] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In the past several years, there has been a tremendous effort to construct physical maps and to sequence the genome of Arabidopsis thaliana. As a result, four of the five chromosomes are completely covered by overlapping clones except at the centromeric and nucleolus organizer regions (NOR). In addition, over 30% of the genome has been sequenced and completion is anticipated by the end of the year 2000. Despite these accomplishments, the physical maps are provided in many formats on laboratories' Web sites. These data are thus difficult to obtain in a coherent manner for researchers. To alleviate this problem, AtDB (Arabidopsis thaliana DataBase, URL: http://genome-www.stanford.edu/Arabidopsis/) has constructed a unified display of the physical maps where all publicly available physical-map data for all chromosomes are presented through the Web in a clickable, 'on-the-fly' graphic, created by CGI programs that directly consult our relational database.
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Affiliation(s)
- S Y Rhee
- Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA
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21
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Rhee SY, Weng S, Flanders D, Cherry JM, Dean C, Lister C, Anderson M, Koornneef M, Meinke DW, Nickle T, Smith K, Rounsley SD. Genome maps 9. Arabidopsis thaliana. Wall chart. Science 1998; 282:663-7. [PMID: 9841422 DOI: 10.1126/science.282.5389.663] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Rhee SY, Somerville CR. Tetrad pollen formation in quartet mutants of Arabidopsis thaliana is associated with persistence of pectic polysaccharides of the pollen mother cell wall. Plant J 1998; 15:79-88. [PMID: 9744097 DOI: 10.1046/j.1365-313x.1998.00183.x] [Citation(s) in RCA: 76] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The quartet (qrt) mutants of Arabidopsis thaliana produce tetrad pollen in which microspores fail to separate during pollen development. Because the amount of callose deposition between microspores is correlated with tetrad pollen formation in other species, and because pectin is implicated as playing a role in cell adhesion, these cell-wall components in wild-type and mutant anthers were visualized by immunofluorescence microscopy at different stages of microsporogenesis. In wild-type, callose was detected around the pollen mother cell at the onset of meiosis and around the microspores during the tetrad stage. Microspores were released into the anther locule at the stage where callose was no longer detected. Deposition and degradation of callose during tetrad pollen formation in qrt1 and qrt2 mutants were indistinguishable from those in wild-type. Enzymatic removal of callose from wild-type microspores at the tetrad stage did not release the microspores, suggesting that callose removal is not sufficient to disperse the microspores in wild-type. Pectic components were detected in the primary wall of the pollen mother cell. This wall surrounded the callosic wall around the pollen mother cell and the microspores during the tetrad stage. In wild-type, pectic components of this wall were no longer detectable at the time of microspore release. However, in qrt1 and qrt2 mutants, pectic components of this wall persisted after callose degradation. This result suggests that failure of pectin degradation in the pollen mother cell wall is associated with tetrad pollen formation in qrt mutants, and indicates that QRT1 and QRT2 may be required for cell type-specific pectin degradation to separate microspores.
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Affiliation(s)
- S Y Rhee
- Carnegie Institution of Washington, Department of Plant Biology, Stanford, CA 94305, USA
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23
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Abstract
Two Arabidopsis thaliana genes, QRT1 and QRT2, are required for pollen separation during normal development. In qrt mutants, the outer walls of the four meiotic products of the pollen mother cell are fused, and pollen grains are released in tetrads. Pollen is viable and fertile, and the cytoplasmic pollen contents are discrete. Pollination with a single tetrad usually yields four seeds, and genetic analysis confirmed that marker loci segregate in a 2:2 ratio within these tetrads. These mutations allow tetrad analysis to be performed in Arabidopsis and define steps in pollen cell wall development.
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Affiliation(s)
- D Preuss
- Department of Biochemistry, Stanford University, CA 94305-5307
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24
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Ruan ZS, Anantharam V, Crawford IT, Ambudkar SV, Rhee SY, Allison MJ, Maloney PC. Identification, purification, and reconstitution of OxlT, the oxalate: formate antiport protein of Oxalobacter formigenes. J Biol Chem 1992; 267:10537-43. [PMID: 1587834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
We had proposed earlier that the anaerobe Oxalobacter formigenes sustains a proton-motive force by exploiting a secondary carrier rather than a primary proton pump. In this view, a carrier protein would catalyze the exchange of extracellular oxalate, a divalent anion, and intracellular formate, the monovalent product of oxalate decarboxylation. Such an electrogenic exchange develops an internally negative membrane potential, and since the decarboxylation reaction consumes an internal proton, the combined activity of the carrier and the soluble decarboxylase would constitute an "indirect" proton pump with a stoichiometry of 1H+ per turnover. This model is now verified by identification and purification of OxlT, the protein responsible for the anion exchange reaction. Membranes of O. formigenes were solubilized at pH 7 with 1.25% octyl glucoside in 20 mM 3-(N-morpholino)propanesulfonic acid/K, in the presence of 0.4% Escherichia coli phospholipids and with 20% glucerol present as the osmolyte stabilant. Rapid methods for reconstitution were developed to monitor the distribution of OxlT during biochemical fractionation, allowing its purification by sequential anion and cation exchange chromatography. OxlT proved to be a single hydrophobic polypeptide, of 38 kDa mobility during sodium dodecyl sulfate-polyacrylamide gel electrophoresis, with a turnover number estimated as at least 1000/s. The properties of OxlT point to an indirect proton pump as the mechanism by which a proton-motive force arises in O. formigenes, and one may reasonably argue that indirect proton pumps take part in bacterial events such as acetogenesis, malolactate fermentation, and perhaps methanogenesis.
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Affiliation(s)
- Z S Ruan
- Department of Physiology, Johns Hopkins University Medical School, Baltimore, Maryland 21205
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25
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Beyer RE, Burnett BA, Cartwright KJ, Edington DW, Falzon MJ, Kreitman KR, Kuhn TW, Ramp BJ, Rhee SY, Rosenwasser MJ. Tissue coenzyme Q (ubiquinone) and protein concentrations over the life span of the laboratory rat. Mech Ageing Dev 1985; 32:267-81. [PMID: 4087945 DOI: 10.1016/0047-6374(85)90085-5] [Citation(s) in RCA: 91] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The coenzyme Q (ubiquinone) concentrations of a number of tissues have been determined over the life span of the male laboratory rat. Coenzyme Q increased between 2 and 18 months and decreased significantly at 25 months in the heart and kidney, and the gastrocnemius, oblique and deep aspect (red) vastus lateralis muscles. The coenzyme Q concentration of liver increased over the life span, while it remained relatively constant in brain, lung, and the superficial aspect (white) of the vastus lateralis muscle. Data are also included for organ weights and protein contents of tissues over the life span. The various roles of coenzyme Q in cellular electron transfer and its regulation, energy conservation in oxidative phosphorylation, and its clinical efficacy in diseases of energy metabolism are discussed. It is hypothesized that coenzyme Q serves as a free radical quencher in the mitochondrion, a major site of free radical formation, in addition to its other roles in cellular energy metabolism, and that its cellular diminution may contribute to the loss of cellular function accompanying ageing.
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Beyer RE, Morales-Corral PG, Ramp BJ, Kreitman KR, Falzon MJ, Rhee SY, Kuhn TW, Stein M, Rosenwasser MJ, Cartwright KJ. Elevation of tissue coenzyme Q (ubiquinone) and cytochrome c concentrations by endurance exercise in the rat. Arch Biochem Biophys 1984; 234:323-9. [PMID: 6093695 DOI: 10.1016/0003-9861(84)90277-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Six months of enforced and voluntary endurance training of young female Wistar rats resulted in significant decreases of body weight and gastrocnemius muscle wet weight and protein content, and increases in heart weight and protein content, and liver protein content. The coenzyme Q and cytochrome c concentrations of cardiac, gastrocnemius, and deep red region of the vastus lateralis muscles were increased, while small or nonsignificant trends toward increases in cytochrome c and coenzyme Q were seen in kidney, brain, lung, liver, internal + external oblique muscles, and the superficial white region of the vastus lateralis muscle. These results are discussed with regard to several roles for coenzyme Q in cellular function.
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