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Sutoh Y, Hachiya T, Otsuka-Yamasaki Y, Komaki S, Minabe S, Ohmomo H, Sasaki M, Shimizu A. Healthy lifestyle practice correlates with decreased obesity prevalence in individuals with high polygenic risk: TMM CommCohort study. J Hum Genet 2024:10.1038/s10038-024-01280-3. [PMID: 39174808 DOI: 10.1038/s10038-024-01280-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 06/24/2024] [Accepted: 07/24/2024] [Indexed: 08/24/2024]
Abstract
Obesity and overweight, fundamental components of the metabolic syndrome, predispose individuals to lifestyle-related diseases. The extent to which adopting healthy lifestyles can reduce obesity risk, even in those with a high genetic risk, remains uncertain. Our aim was to assess the extent to which lifestyle modifications can improve outcomes in individuals with a high polygenic score (PGS) for obesity. We quantified the genetic risk of obesity using PGSs. Four datasets from the Tohoku Medical Megabank Community-Based Cohort (TMM CommCohort) were employed in the study. One dataset (n = 9958) was used to select the best model for calculating PGS. The remaining datasets (total n = 69,341) were used in a meta-analysis to validate the model and to evaluate associated risks. The odds ratio (OR) for obesity risk in the intermediate (11th-90th percentiles in the dataset) and high PGS categories (91st-100th) was 2.27 [95% confidence intervals: 2.12-2.44] and 4.83 [4.45-5.25], respectively, compared to that in the low PGS category (1st-10th). Trend analysis showed that an increase in leisure-time physical activity was significantly associated with reduced obesity risk across all genetic risk categories, representing an OR of 0.9 [0.87-0.94] even among individuals in the high PGS category. Similarly, sodium intake displayed a positive association with obesity across all genetic risk categories, yielding an OR of 1.24 [1.17-1.31] in the high PGS category. The risk of obesity was linked to the adoption of healthy lifestyles, even in individuals with high PGS. Our results may provide perspectives for integrating PGSs into preventive medicine.
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Affiliation(s)
- Yoichi Sutoh
- Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, Yahaba, Japan
- Division of Biomedical Information Analysis, Institute for Biomedical Sciences, Iwate Medical University, Yahaba, Japan
| | - Tsuyoshi Hachiya
- Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, Yahaba, Japan
- Division of Biomedical Information Analysis, Institute for Biomedical Sciences, Iwate Medical University, Yahaba, Japan
| | - Yayoi Otsuka-Yamasaki
- Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, Yahaba, Japan
- Division of Biomedical Information Analysis, Institute for Biomedical Sciences, Iwate Medical University, Yahaba, Japan
| | - Shohei Komaki
- Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, Yahaba, Japan
- Division of Biomedical Information Analysis, Institute for Biomedical Sciences, Iwate Medical University, Yahaba, Japan
| | - Shiori Minabe
- Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, Yahaba, Japan
- Division of Biomedical Information Analysis, Institute for Biomedical Sciences, Iwate Medical University, Yahaba, Japan
| | - Hideki Ohmomo
- Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, Yahaba, Japan
- Division of Biomedical Information Analysis, Institute for Biomedical Sciences, Iwate Medical University, Yahaba, Japan
| | - Makoto Sasaki
- Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, Yahaba, Japan
- Division of Ultrahigh Field MRI, Institute for Biomedical Sciences, Iwate Medical University, Yahaba, Japan
| | - Atsushi Shimizu
- Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, Yahaba, Japan.
- Division of Biomedical Information Analysis, Institute for Biomedical Sciences, Iwate Medical University, Yahaba, Japan.
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Kudo H, Ishida N, Nobukuni T, Aoki Y, Saito S, Nishijima I, Terakawa T, Yamamoto M, Minegishi N, Yamashita R, Kumada K. Detection and Correction of Sample Misidentifications in a Biobank Using the MassARRAY System and Genomic Information. Biopreserv Biobank 2024; 22:373-382. [PMID: 38079195 DOI: 10.1089/bio.2022.0211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2024] Open
Abstract
With the number of samples increasing in many biobanks, one of the most pressing tasks is recording the correct relationships between information and the specimens. Genomic information is useful in determining the identity of these specimens. The Tohoku Medical Megabank Organization is running one of the largest biobanks in Japan. Here, we introduce a management system, which includes the development of a new probe set for the MassARRAY system for use during the production of proliferating T cells (T cells) and lymphoblastoid cell lines (LCLs). We selected single nucleotide variants that could be detected by next-generation sequencing and showed high resolution with ∼0.5 minor allele frequencies. After checking the set of probes against 96 samples from 48 people, we obtained no contradictory results in comparison with our genome sequence information. When we applied the set to our 3035 LCLs and 2256 T cells, the result showed 98.93% consistency with the corresponding genomic information. We surveyed the handling records of the 1.07% of samples that showed inconsistencies, and found that most had resulted from human errors (ID swapping between samples) during manual operations. After improving a few error-prone protocols, the error rate dropped to 0.47% for LCLs and 0% for T cells. Overall, the system that we developed shows high accuracy with easy and fast operability, and provides a good opportunity to improve the validation procedure to facilitate high-quality banking, especially in cases involving genomic information.
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Affiliation(s)
- Hisaaki Kudo
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Noriko Ishida
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Takahiro Nobukuni
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Yuichi Aoki
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Sakae Saito
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
| | - Ichiko Nishijima
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Takahiro Terakawa
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Masayuki Yamamoto
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
| | - Naoko Minegishi
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Riu Yamashita
- Division of Translational Informatics, Exploratory Oncology Research & Clinical Trial Center, National Cancer Center Hospital East, Chiba, Japan
- Laboratory of Cancer Medical Informatics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Kazuki Kumada
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
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Yeo NKW, Lim CK, Yaung KN, Khoo NKH, Arkachaisri T, Albani S, Yeo JG. Genetic interrogation for sequence and copy number variants in systemic lupus erythematosus. Front Genet 2024; 15:1341272. [PMID: 38501057 PMCID: PMC10944961 DOI: 10.3389/fgene.2024.1341272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 02/20/2024] [Indexed: 03/20/2024] Open
Abstract
Early-onset systemic lupus erythematosus presents with a more severe disease and is associated with a greater genetic burden, especially in patients from Black, Asian or Hispanic ancestries. Next-generation sequencing techniques, notably whole exome sequencing, have been extensively used in genomic interrogation studies to identify causal disease variants that are increasingly implicated in the development of autoimmunity. This Review discusses the known casual variants of polygenic and monogenic systemic lupus erythematosus and its implications under certain genetic disparities while suggesting an age-based sequencing strategy to aid in clinical diagnostics and patient management for improved patient care.
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Affiliation(s)
- Nicholas Kim-Wah Yeo
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Che Kang Lim
- Duke-NUS Medical School, Singapore, Singapore
- Department of Clinical Translation Research, Singapore General Hospital, Singapore, Singapore
| | - Katherine Nay Yaung
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Nicholas Kim Huat Khoo
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore
| | - Thaschawee Arkachaisri
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
- Rheumatology and Immunology Service, KK Women's and Children's Hospital, Singapore, Singapore
| | - Salvatore Albani
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
- Rheumatology and Immunology Service, KK Women's and Children's Hospital, Singapore, Singapore
| | - Joo Guan Yeo
- Translational Immunology Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
- Rheumatology and Immunology Service, KK Women's and Children's Hospital, Singapore, Singapore
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Saito Y, Sato K, Jinno S, Nakamura Y, Nobukuni T, Ogishima S, Mizuno S, Koshiba S, Kuriyama S, Ohneda K, Morifuji M. Effect of Nicotinamide Mononucleotide Concentration in Human Milk on Neurodevelopmental Outcome: The Tohoku Medical Megabank Project Birth and Three-Generation Cohort Study. Nutrients 2023; 16:145. [PMID: 38201974 PMCID: PMC10780616 DOI: 10.3390/nu16010145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/25/2023] [Accepted: 12/30/2023] [Indexed: 01/12/2024] Open
Abstract
(1) Background: Breast milk is the only source of nutrition for breastfed infants, but few studies have examined the relationship between breast milk micronutrients and infant neurodevelopmental outcome in exclusively breastfed infants. The aim of this study was to characterize the association between nicotinamide adenine dinucleotide (NAD)-related compounds in the breast milk of Japanese subjects and infant neurodevelopmental outcome. (2) Methods: A total of 150 mother-child pairs were randomly selected from the three-generation cohort of the Tohoku Medical Megabank in Japan. Infants were exclusively breastfed for up to 6 months. Breast milk was collected at 1 month postpartum, and the quantity of NAD-related substances in the breast milk was quantified. The mothers also completed developmental questionnaires at 6, 12, and 24 months. The relationship between the concentration of NAD-related substances in breast milk and developmental indicators was evaluated via ordinal logistic regression analysis. (3) Results: Nicotinamide mononucleotide (NMN) was quantified as the major NAD precursor in breast milk. The median amount of NMN in the breast milk was 9.2 μM. The NMN concentration in breast milk was the only NAD-related substance in breast milk that showed a significant positive correlation with neurodevelopmental outcome in infants at 24 months. (4) Conclusions: The results suggest that NMN in human milk may be an important nutrient for early childhood development.
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Affiliation(s)
- Yoshie Saito
- Wellness Science Labs, Meiji Holdings Co., Ltd., Hachioji 192-0919, Japan;
| | - Keigo Sato
- Food Microbiology and Function Research Laboratory, Meiji Co., Ltd., Hachioji 192-0919, Japan; (K.S.); (S.J.); (Y.N.)
| | - Shinji Jinno
- Food Microbiology and Function Research Laboratory, Meiji Co., Ltd., Hachioji 192-0919, Japan; (K.S.); (S.J.); (Y.N.)
| | - Yoshitaka Nakamura
- Food Microbiology and Function Research Laboratory, Meiji Co., Ltd., Hachioji 192-0919, Japan; (K.S.); (S.J.); (Y.N.)
| | - Takahiro Nobukuni
- Tohoku Medical Megabank Organization, Tohoku University, Sendai 980-8573, Japan; (T.N.); (S.O.); (S.M.); (S.K.); (S.K.); (K.O.)
| | - Soichi Ogishima
- Tohoku Medical Megabank Organization, Tohoku University, Sendai 980-8573, Japan; (T.N.); (S.O.); (S.M.); (S.K.); (S.K.); (K.O.)
- Graduate School of Medicine, Tohoku University, Sendai 980-8573, Japan
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai 980-8573, Japan
| | - Satoshi Mizuno
- Tohoku Medical Megabank Organization, Tohoku University, Sendai 980-8573, Japan; (T.N.); (S.O.); (S.M.); (S.K.); (S.K.); (K.O.)
| | - Seizo Koshiba
- Tohoku Medical Megabank Organization, Tohoku University, Sendai 980-8573, Japan; (T.N.); (S.O.); (S.M.); (S.K.); (S.K.); (K.O.)
- Graduate School of Medicine, Tohoku University, Sendai 980-8573, Japan
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai 980-8573, Japan
| | - Shinichi Kuriyama
- Tohoku Medical Megabank Organization, Tohoku University, Sendai 980-8573, Japan; (T.N.); (S.O.); (S.M.); (S.K.); (S.K.); (K.O.)
- Graduate School of Medicine, Tohoku University, Sendai 980-8573, Japan
- International Research Institute of Disaster Science, Tohoku University, Sendai 980-0845, Japan
| | - Kinuko Ohneda
- Tohoku Medical Megabank Organization, Tohoku University, Sendai 980-8573, Japan; (T.N.); (S.O.); (S.M.); (S.K.); (S.K.); (K.O.)
- Graduate School of Medicine, Tohoku University, Sendai 980-8573, Japan
| | - Masashi Morifuji
- Wellness Science Labs, Meiji Holdings Co., Ltd., Hachioji 192-0919, Japan;
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Fukunaga H, Ikeda A. Mitochondrial DNA copy number variation across three generations: a possible biomarker for assessing perinatal outcomes. Hum Genomics 2023; 17:113. [PMID: 38098033 PMCID: PMC10722810 DOI: 10.1186/s40246-023-00567-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 12/11/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND Mitochondria have their own circular multi-copy genome (mtDNA), and abnormalities in the copy number are implicated in mitochondrial dysfunction, which contributes to a variety of aging-related pathologies. However, not much is known about the genetic correlation of mtDNA copy number across multiple generations and its physiological significance. METHODS We measured the mtDNA copy number in cord blood or peripheral blood from 149 three-generation families, specifically the newborns, parents, and grandparents, of 149 families, totaling 1041 individuals. All of the biological specimens and information were provided by the Tohoku Medical Megabank Project in Japan. We also analyzed their maternal factors during pregnancy and neonatal outcomes. RESULTS While the maternal peripheral blood mtDNA copy number was lower than that of other adult family members, it was negatively correlated with cord blood mtDNA copy number in male infants. Also, cord blood mtDNA copy numbers were negatively correlated with perinatal outcomes, such as gestation age, birth weight, and umbilical cord length, for both male and female neonates. Furthermore, the mtDNA copy number in the infants born to mothers who took folic acid supplements during pregnancy would be lower than in the infants born to mothers who did not take them. CONCLUSIONS This data-driven study offers the most comprehensive view to date on the genetic and physiological significance of mtDNA copy number in cord blood or peripheral blood taken from three generations, totaling more than 1000 individuals. Our findings indicate that mtDNA copy number would be one of the transgenerational biomarkers for assessing perinatal outcomes, as well as that appropriate medical interventions could improve the outcomes via quantitative changes in mtDNA.
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Affiliation(s)
- Hisanori Fukunaga
- Center for Environmental and Health Sciences, Hokkaido University, N12 W7 Kita-ku, Sapporo, 060-0812, Japan.
- Faculty of Health Sciences, Hokkaido University, Sapporo, Japan.
| | - Atsuko Ikeda
- Center for Environmental and Health Sciences, Hokkaido University, N12 W7 Kita-ku, Sapporo, 060-0812, Japan
- Faculty of Health Sciences, Hokkaido University, Sapporo, Japan
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Daungsupawong H, Wiwanitkit V. Re: "Validating Tools to Detect and Inactivate Monkeypox Virus in Human Milk" by Clark et al. Breastfeed Med 2023; 18:960. [PMID: 38016148 DOI: 10.1089/bfm.2023.0224] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2023]
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Hishinuma E, Shimada M, Matsukawa N, Shima Y, Li B, Motoike IN, Shibuya Y, Hagihara T, Shigeta S, Tokunaga H, Saigusa D, Kinoshita K, Koshiba S, Yaegashi N. Identification of predictive biomarkers for endometrial cancer diagnosis and treatment response monitoring using plasma metabolome profiling. Cancer Metab 2023; 11:16. [PMID: 37821929 PMCID: PMC10568780 DOI: 10.1186/s40170-023-00317-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 09/27/2023] [Indexed: 10/13/2023] Open
Abstract
BACKGROUND Endometrial cancer (EMC) is the most common female genital tract malignancy with an increasing prevalence in many countries including Japan, a fact that renders early detection and treatment necessary to protect health and fertility. Although early detection and treatment are necessary to further improve the prognosis of women with endometrial cancer, biomarkers that accurately reflect the pathophysiology of EMC patients are still unclear. Therefore, it is clinically critical to identify biomarkers to assess diagnosis and treatment efficacy to facilitate appropriate treatment and development of new therapies for EMC. METHODS In this study, wide-targeted plasma metabolome analysis was performed to identify biomarkers for EMC diagnosis and the prediction of treatment responses. The absolute quantification of 628 metabolites in plasma samples from 142 patients with EMC was performed using ultra-high-performance liquid chromatography with tandem mass spectrometry. RESULTS The concentrations of 111 metabolites increased significantly, while the concentrations of 148 metabolites decreased significantly in patients with EMC compared to healthy controls. Specifically, LysoPC and TGs, including unsaturated fatty acids, were reduced in patients with stage IA EMC compared to healthy controls, indicating that these metabolic profiles could be used as early diagnostic markers of EMC. In contrast, blood levels of amino acids such as histidine and tryptophan decreased as the risk of recurrence increased and the stages of EMC advanced. Furthermore, a marked increase in total TG and a decrease in specific TGs and free fatty acids including polyunsaturated fatty acids levels were observed in patients with EMC. These results suggest that the polyunsaturated fatty acids in patients with EMC are crucial for disease progression. CONCLUSIONS Our data identified specific metabolite profiles that reflect the pathogenesis of EMC and showed that these metabolites correlate with the risk of recurrence and disease stage. Analysis of changes in plasma metabolite profiles could be applied for the early diagnosis and monitoring of the course of treatment of EMC patients.
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Affiliation(s)
- Eiji Hishinuma
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, 980-8573, Japan
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, 980-8573, Japan
| | - Muneaki Shimada
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, 980-8573, Japan.
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, 980-8573, Japan.
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Tohoku University, Sendai, 980-8574, Japan.
| | - Naomi Matsukawa
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, 980-8573, Japan
| | - Yoshiko Shima
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, 980-8573, Japan
| | - Bin Li
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, 980-8573, Japan
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, 980-8573, Japan
| | - Ikuko N Motoike
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, 980-8573, Japan
- Systems Bioinformatics, Graduate School of Information Sciences, Tohoku University, Sendai, 980-8579, Japan
| | - Yusuke Shibuya
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Tohoku University, Sendai, 980-8574, Japan
| | - Tatsuya Hagihara
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Tohoku University, Sendai, 980-8574, Japan
| | - Shogo Shigeta
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Tohoku University, Sendai, 980-8574, Japan
| | - Hideki Tokunaga
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, 980-8573, Japan
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Tohoku University, Sendai, 980-8574, Japan
| | - Daisuke Saigusa
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, 980-8573, Japan
- Laboratory of Biomedical and Analytical Sciences, Faculty of Pharma-Science, Teikyo University, Tokyo, 173-8605, Japan
| | - Kengo Kinoshita
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, 980-8573, Japan
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, 980-8573, Japan
- Systems Bioinformatics, Graduate School of Information Sciences, Tohoku University, Sendai, 980-8579, Japan
| | - Seizo Koshiba
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, 980-8573, Japan
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, 980-8573, Japan
| | - Nobuo Yaegashi
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, 980-8573, Japan
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, 980-8573, Japan
- Department of Gynecology and Obstetrics, Graduate School of Medicine, Tohoku University, Sendai, 980-8574, Japan
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Shiga H, Takahashi T, Shiraki M, Kojima Y, Tsuji T, Takagi S, Hiramoto K, Yokoyama N, Sugimura M, Iwabuchi M, Endo K, Onodera M, Sato Y, Shimodaira Y, Nomura E, Kikuchi T, Chiba H, Oomori S, Kudo H, Kumada K, Nagaie S, Ogishima S, Nagami F, Shimoyama Y, Moroi R, Kuroha M, Kakuta Y, Ishige T, Kinouchi Y, Masamune A. Reduced antiviral seropositivity among patients with inflammatory bowel disease treated with immunosuppressive agents. Scand J Gastroenterol 2023; 58:360-367. [PMID: 36222610 DOI: 10.1080/00365521.2022.2132831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
BACKGROUND Although live-attenuated vaccines are contraindicated under immunosuppression, the immune status of patients with inflammatory bowel disease (IBD) has not been fully assessed prior to immunosuppressive therapy. AIMS To investigate antiviral serostatus against viruses requiring live vaccines for prevention in IBD patients undergoing immunosuppressive therapy. METHODS This multicenter study included IBD patients who were aged <40 years and were treated with thiopurine monotherapy, molecular-targeted monotherapy, or combination therapy. Gender- and age-matched healthy subjects (HS) living in the same areas were included as control group. Antibody titers against measles, rubella, mumps, and varicella were measured by enzyme-linked immunosorbent assays. RESULTS A total of 437 IBD patients (163 ulcerative colitis [UC] and 274 Crohn's disease [CD]) and 225 HS were included in the final analysis. Compared with HS, IBD patients had lower seropositivity rates for measles (IBD vs. HS = 83.91% vs. 85.33%), rubella (77.55% vs. 84.89%), mumps (37.50% vs. 37.78%), and varicella (91.26% vs. 96.44%). Gender- and age-adjusted seropositivity rates were lower in UC patients than in both CD patients and HS for measles (UC, CD, and HS = 81.60%, 85.29%, and 85.33%), rubella (76.40%, 78.23%, and 84.89%), mumps (27.16%, 43.70%, and 37.78%), and varicella (90.80%, 91.54%, and 96.44%); the difference was significant for all viruses except measles. Divided by the degree of immunosuppression, there were no significant differences in seropositivity rates among IBD patients. CONCLUSIONS IBD patients, especially those with UC, exhibit reduced seropositivity rates and may benefit from screening prior to the initiation of immunosuppressive therapy.
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Affiliation(s)
- Hisashi Shiga
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Takahiro Takahashi
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Manabu Shiraki
- Department of Gastroenterology, Tohoku Rosai Hospital, Sendai, Japan
| | - Yasuhiro Kojima
- Department of Gastroenterology, Tohoku Rosai Hospital, Sendai, Japan
| | - Tsuyotoshi Tsuji
- Department of Gastroenterology, Akita City Hospital, Akita, Japan
| | | | - Keiichiro Hiramoto
- Department of Gastroenterology, South Miyagi Medical Center, Ohgawara, Japan
| | - Naonobu Yokoyama
- Department of Gastroenterology, Iwate Prefectural Iwai Hospital, Ichinoseki, Japan
| | - Mikako Sugimura
- Department of Gastroenterology, NHO Sendai Medical Center, Sendai, Japan
| | - Masahiro Iwabuchi
- Department of Gastroenterology, NHO Sendai Medical Center, Sendai, Japan
| | - Katsuya Endo
- Department of Gastroenterology, Tohoku Medical and Pharmaceutical University, Sendai, Japan
| | - Motoyuki Onodera
- Department of Gastroenterology, Osaki Citizen Hospital, Osaki, Japan
| | - Yuichirou Sato
- Department of Gastroenterology, Osaki Citizen Hospital, Osaki, Japan
| | - Yosuke Shimodaira
- Department of Gastroenterology and Neurology, Akita University Graduate School of Medicine, Akita, Japan
| | - Eiki Nomura
- Department of Gastroenterology, Sendai City Hospital, Sendai, Japan
| | - Tatsuya Kikuchi
- Department of Gastroenterology, Sendai City Hospital, Sendai, Japan
| | - Hirofumi Chiba
- Department of Gastroenterology, Iwate Prefectural Isawa Hospital, Oshu, Japan
| | - Shinya Oomori
- Department of Gastroenterology, Japanese Red Cross Sendai Hospital, Sendai, Japan
| | - Hisaaki Kudo
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Kazuki Kumada
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
| | - Satoshi Nagaie
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Soichi Ogishima
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
| | - Fuji Nagami
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
| | - Yusuke Shimoyama
- Department of Gastroenterology, Iwate Prefectural Isawa Hospital, Oshu, Japan
| | - Rintaro Moroi
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Masatake Kuroha
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yoichi Kakuta
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Takashi Ishige
- Department of Pediatrics, Gunma University Graduate School of Medicine, Maebashi, Japan
| | - Yoshitaka Kinouchi
- Student Health Care Center, Institute for Excellence in Higher Education, Tohoku University, Sendai, Japan
| | - Atsushi Masamune
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
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9
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Hishinuma E, Narita Y, Rico EMG, Ueda A, Obuchi K, Tanaka Y, Saito S, Tadaka S, Kinoshita K, Maekawa M, Mano N, Nakayoshi T, Oda A, Hirasawa N, Hiratsuka M. Functional Characterization of 12 Dihydropyrimidinase Allelic Variants in Japanese Individuals for the Prediction of 5-Fluorouracil Treatment-Related Toxicity. Drug Metab Dispos 2023; 51:165-173. [PMID: 36414408 DOI: 10.1124/dmd.122.001045] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 10/11/2022] [Accepted: 10/27/2022] [Indexed: 11/23/2022] Open
Abstract
The drug 5-fluorouracil (5-FU) is the first-choice chemotherapeutic agent against advanced-stage cancers. However, 10% to 30% of treated patients experience grade 3 to 4 toxicity. The deficiency of dihydropyrimidinase (DHPase), which catalyzes the second step of the 5-FU degradation pathway, is correlated with the risk of developing toxicity. Thus, genetic polymorphisms within DPYS, the DHPase-encoding gene, could potentially serve as predictors of severe 5-FU-related toxicity. We identified 12 novel DPYS variants in 3554 Japanese individuals, but the effects of these mutations on function remain unknown. In the current study, we performed in vitro enzymatic analyses of the 12 newly identified DHPase variants. Dihydrouracil or dihydro-5-FU hydrolytic ring-opening kinetic parameters, Km and Vmax , and intrinsic clearance (CLint = Vmax /Km ) of the wild-type DHPase and eight variants were measured. Five of these variants (R118Q, H295R, T418I, Y448H, and T513A) showed significantly reduced CLint compared with that in the wild-type. The parameters for the remaining four variants (V59F, D81H, T136M, and R490H) could not be determined as dihydrouracil and dihydro-5-FU hydrolytic ring-opening activity was undetectable. We also determined DHPase variant protein stability using cycloheximide and bortezomib. The mechanism underlying the observed changes in the kinetic parameters was clarified using blue-native polyacrylamide gel electrophoresis and three-dimensional structural modeling. The results suggested that the decrease or loss of DHPase enzymatic activity was due to reduced stability and oligomerization of DHPase variant proteins. Our findings support the use of DPYS polymorphisms as novel pharmacogenomic markers for predicting severe 5-FU-related toxicity in the Japanese population. SIGNIFICANCE STATEMENT: DHPase contributes to the degradation of 5-fluorouracil, and genetic polymorphisms that cause decreased activity of DHPase can cause severe toxicity. In this study, we performed functional analysis of 12 DHPase variants in the Japanese population and identified 9 genetic polymorphisms that cause reduced DHPase function. In addition, we found that the ability to oligomerize and the conformation of the active site are important for the enzymatic activity of DHPase.
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Affiliation(s)
- Eiji Hishinuma
- Advanced Research Center for Innovations in Next-Generation Medicine (E.H., A.U., Y.T., S.S., K.K., M.M., N.H., M.H.), Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences (Y.N., E.M.G.R., K.O., N.H., M.H.), Tohoku Medical Megabank Organization (E.H., S.S., S.T., K.K., M.H.), Graduate School of Life Sciences (Y.T.), and Graduate School of Information Sciences (K.K.), Tohoku University, Sendai, Japan; Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan (M.M., N.M., N.H., M.H.); Department of Biophysical Chemistry, Faculty of Pharmacy, Meijo University, Nagoya Japan (T.N., A.O.); and Graduate School of Information Sciences, Hiroshima City University, Hiroshima, Japan (T.N.)
| | - Yoko Narita
- Advanced Research Center for Innovations in Next-Generation Medicine (E.H., A.U., Y.T., S.S., K.K., M.M., N.H., M.H.), Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences (Y.N., E.M.G.R., K.O., N.H., M.H.), Tohoku Medical Megabank Organization (E.H., S.S., S.T., K.K., M.H.), Graduate School of Life Sciences (Y.T.), and Graduate School of Information Sciences (K.K.), Tohoku University, Sendai, Japan; Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan (M.M., N.M., N.H., M.H.); Department of Biophysical Chemistry, Faculty of Pharmacy, Meijo University, Nagoya Japan (T.N., A.O.); and Graduate School of Information Sciences, Hiroshima City University, Hiroshima, Japan (T.N.)
| | - Evelyn Marie Gutiérrez Rico
- Advanced Research Center for Innovations in Next-Generation Medicine (E.H., A.U., Y.T., S.S., K.K., M.M., N.H., M.H.), Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences (Y.N., E.M.G.R., K.O., N.H., M.H.), Tohoku Medical Megabank Organization (E.H., S.S., S.T., K.K., M.H.), Graduate School of Life Sciences (Y.T.), and Graduate School of Information Sciences (K.K.), Tohoku University, Sendai, Japan; Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan (M.M., N.M., N.H., M.H.); Department of Biophysical Chemistry, Faculty of Pharmacy, Meijo University, Nagoya Japan (T.N., A.O.); and Graduate School of Information Sciences, Hiroshima City University, Hiroshima, Japan (T.N.)
| | - Akiko Ueda
- Advanced Research Center for Innovations in Next-Generation Medicine (E.H., A.U., Y.T., S.S., K.K., M.M., N.H., M.H.), Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences (Y.N., E.M.G.R., K.O., N.H., M.H.), Tohoku Medical Megabank Organization (E.H., S.S., S.T., K.K., M.H.), Graduate School of Life Sciences (Y.T.), and Graduate School of Information Sciences (K.K.), Tohoku University, Sendai, Japan; Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan (M.M., N.M., N.H., M.H.); Department of Biophysical Chemistry, Faculty of Pharmacy, Meijo University, Nagoya Japan (T.N., A.O.); and Graduate School of Information Sciences, Hiroshima City University, Hiroshima, Japan (T.N.)
| | - Kai Obuchi
- Advanced Research Center for Innovations in Next-Generation Medicine (E.H., A.U., Y.T., S.S., K.K., M.M., N.H., M.H.), Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences (Y.N., E.M.G.R., K.O., N.H., M.H.), Tohoku Medical Megabank Organization (E.H., S.S., S.T., K.K., M.H.), Graduate School of Life Sciences (Y.T.), and Graduate School of Information Sciences (K.K.), Tohoku University, Sendai, Japan; Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan (M.M., N.M., N.H., M.H.); Department of Biophysical Chemistry, Faculty of Pharmacy, Meijo University, Nagoya Japan (T.N., A.O.); and Graduate School of Information Sciences, Hiroshima City University, Hiroshima, Japan (T.N.)
| | - Yoshikazu Tanaka
- Advanced Research Center for Innovations in Next-Generation Medicine (E.H., A.U., Y.T., S.S., K.K., M.M., N.H., M.H.), Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences (Y.N., E.M.G.R., K.O., N.H., M.H.), Tohoku Medical Megabank Organization (E.H., S.S., S.T., K.K., M.H.), Graduate School of Life Sciences (Y.T.), and Graduate School of Information Sciences (K.K.), Tohoku University, Sendai, Japan; Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan (M.M., N.M., N.H., M.H.); Department of Biophysical Chemistry, Faculty of Pharmacy, Meijo University, Nagoya Japan (T.N., A.O.); and Graduate School of Information Sciences, Hiroshima City University, Hiroshima, Japan (T.N.)
| | - Sakae Saito
- Advanced Research Center for Innovations in Next-Generation Medicine (E.H., A.U., Y.T., S.S., K.K., M.M., N.H., M.H.), Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences (Y.N., E.M.G.R., K.O., N.H., M.H.), Tohoku Medical Megabank Organization (E.H., S.S., S.T., K.K., M.H.), Graduate School of Life Sciences (Y.T.), and Graduate School of Information Sciences (K.K.), Tohoku University, Sendai, Japan; Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan (M.M., N.M., N.H., M.H.); Department of Biophysical Chemistry, Faculty of Pharmacy, Meijo University, Nagoya Japan (T.N., A.O.); and Graduate School of Information Sciences, Hiroshima City University, Hiroshima, Japan (T.N.)
| | - Shu Tadaka
- Advanced Research Center for Innovations in Next-Generation Medicine (E.H., A.U., Y.T., S.S., K.K., M.M., N.H., M.H.), Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences (Y.N., E.M.G.R., K.O., N.H., M.H.), Tohoku Medical Megabank Organization (E.H., S.S., S.T., K.K., M.H.), Graduate School of Life Sciences (Y.T.), and Graduate School of Information Sciences (K.K.), Tohoku University, Sendai, Japan; Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan (M.M., N.M., N.H., M.H.); Department of Biophysical Chemistry, Faculty of Pharmacy, Meijo University, Nagoya Japan (T.N., A.O.); and Graduate School of Information Sciences, Hiroshima City University, Hiroshima, Japan (T.N.)
| | - Kengo Kinoshita
- Advanced Research Center for Innovations in Next-Generation Medicine (E.H., A.U., Y.T., S.S., K.K., M.M., N.H., M.H.), Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences (Y.N., E.M.G.R., K.O., N.H., M.H.), Tohoku Medical Megabank Organization (E.H., S.S., S.T., K.K., M.H.), Graduate School of Life Sciences (Y.T.), and Graduate School of Information Sciences (K.K.), Tohoku University, Sendai, Japan; Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan (M.M., N.M., N.H., M.H.); Department of Biophysical Chemistry, Faculty of Pharmacy, Meijo University, Nagoya Japan (T.N., A.O.); and Graduate School of Information Sciences, Hiroshima City University, Hiroshima, Japan (T.N.)
| | - Masamitsu Maekawa
- Advanced Research Center for Innovations in Next-Generation Medicine (E.H., A.U., Y.T., S.S., K.K., M.M., N.H., M.H.), Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences (Y.N., E.M.G.R., K.O., N.H., M.H.), Tohoku Medical Megabank Organization (E.H., S.S., S.T., K.K., M.H.), Graduate School of Life Sciences (Y.T.), and Graduate School of Information Sciences (K.K.), Tohoku University, Sendai, Japan; Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan (M.M., N.M., N.H., M.H.); Department of Biophysical Chemistry, Faculty of Pharmacy, Meijo University, Nagoya Japan (T.N., A.O.); and Graduate School of Information Sciences, Hiroshima City University, Hiroshima, Japan (T.N.)
| | - Nariyasu Mano
- Advanced Research Center for Innovations in Next-Generation Medicine (E.H., A.U., Y.T., S.S., K.K., M.M., N.H., M.H.), Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences (Y.N., E.M.G.R., K.O., N.H., M.H.), Tohoku Medical Megabank Organization (E.H., S.S., S.T., K.K., M.H.), Graduate School of Life Sciences (Y.T.), and Graduate School of Information Sciences (K.K.), Tohoku University, Sendai, Japan; Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan (M.M., N.M., N.H., M.H.); Department of Biophysical Chemistry, Faculty of Pharmacy, Meijo University, Nagoya Japan (T.N., A.O.); and Graduate School of Information Sciences, Hiroshima City University, Hiroshima, Japan (T.N.)
| | - Tomoki Nakayoshi
- Advanced Research Center for Innovations in Next-Generation Medicine (E.H., A.U., Y.T., S.S., K.K., M.M., N.H., M.H.), Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences (Y.N., E.M.G.R., K.O., N.H., M.H.), Tohoku Medical Megabank Organization (E.H., S.S., S.T., K.K., M.H.), Graduate School of Life Sciences (Y.T.), and Graduate School of Information Sciences (K.K.), Tohoku University, Sendai, Japan; Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan (M.M., N.M., N.H., M.H.); Department of Biophysical Chemistry, Faculty of Pharmacy, Meijo University, Nagoya Japan (T.N., A.O.); and Graduate School of Information Sciences, Hiroshima City University, Hiroshima, Japan (T.N.)
| | - Akifumi Oda
- Advanced Research Center for Innovations in Next-Generation Medicine (E.H., A.U., Y.T., S.S., K.K., M.M., N.H., M.H.), Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences (Y.N., E.M.G.R., K.O., N.H., M.H.), Tohoku Medical Megabank Organization (E.H., S.S., S.T., K.K., M.H.), Graduate School of Life Sciences (Y.T.), and Graduate School of Information Sciences (K.K.), Tohoku University, Sendai, Japan; Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan (M.M., N.M., N.H., M.H.); Department of Biophysical Chemistry, Faculty of Pharmacy, Meijo University, Nagoya Japan (T.N., A.O.); and Graduate School of Information Sciences, Hiroshima City University, Hiroshima, Japan (T.N.)
| | - Noriyasu Hirasawa
- Advanced Research Center for Innovations in Next-Generation Medicine (E.H., A.U., Y.T., S.S., K.K., M.M., N.H., M.H.), Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences (Y.N., E.M.G.R., K.O., N.H., M.H.), Tohoku Medical Megabank Organization (E.H., S.S., S.T., K.K., M.H.), Graduate School of Life Sciences (Y.T.), and Graduate School of Information Sciences (K.K.), Tohoku University, Sendai, Japan; Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan (M.M., N.M., N.H., M.H.); Department of Biophysical Chemistry, Faculty of Pharmacy, Meijo University, Nagoya Japan (T.N., A.O.); and Graduate School of Information Sciences, Hiroshima City University, Hiroshima, Japan (T.N.)
| | - Masahiro Hiratsuka
- Advanced Research Center for Innovations in Next-Generation Medicine (E.H., A.U., Y.T., S.S., K.K., M.M., N.H., M.H.), Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences (Y.N., E.M.G.R., K.O., N.H., M.H.), Tohoku Medical Megabank Organization (E.H., S.S., S.T., K.K., M.H.), Graduate School of Life Sciences (Y.T.), and Graduate School of Information Sciences (K.K.), Tohoku University, Sendai, Japan; Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan (M.M., N.M., N.H., M.H.); Department of Biophysical Chemistry, Faculty of Pharmacy, Meijo University, Nagoya Japan (T.N., A.O.); and Graduate School of Information Sciences, Hiroshima City University, Hiroshima, Japan (T.N.)
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10
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Kobayashi T, Kobayashi M, Minegishi N, Kikuya M, Obara T, Ishikuro M, Yamanaka C, Onuma T, Murakami K, Ueno F, Noda A, Uruno A, Sugawara J, Suzuki K, Kodama EN, Hamanaka Y, Tsuchiya N, Kogure M, Nakaya N, Taira M, Sakurai-Yageta M, Tamahara T, Kawashima J, Goto M, Otsuki A, Shimizu R, Ogishima S, Hashizume H, Nagami F, Nakamura T, Hozawa A, Kobayashi T, Fuse N, Kuriyama S, Kure S, Yamamoto M. Design and Progress of Child Health Assessments at Community Support Centers in the Birth and Three-Generation Cohort Study of the Tohoku Medical Megabank Project. TOHOKU J EXP MED 2023; 259:93-105. [PMID: 36450480 DOI: 10.1620/tjem.2022.j103] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
The Tohoku Medical Megabank Project (TMM) has been conducting a birth and three-generation cohort study (the BirThree Cohort Study). We recruited 73,529 pregnant women and their family members for this cohort study, which included 23,143 newborns and 9,459 of their siblings. We designed and are in the process of conducting three-step health assessments for each newborn at approximately ages of 5, 10 and 16. These health assessments are administered at seven community support centers. Trained genome medical research coordinators conduct physical examinations of and collect biological specimens from each participant. The Sendai Children's Health Square has been established as the headquarters for these child health assessments and is utilized to accumulate knowledge that can facilitate the proper practice of child health assessments. We designed all the relevant health assessments facilities to allow parents and their children to participate in the health assessments concomitantly. Our centers serve as places where child participants and their parents can feel at ease as a result of the implementation of safety measures and child hospitality measures. The TMM BirThree Cohort Study is in the process of conducting strategically detailed health assessments and genome analysis, which can facilitate studies concerning the gene-environment interactions relevant to noncommunicable diseases. Through these operations, our study allows for a significant depth of data to be collected in terms of the number of biospecimens under study and the comprehensiveness of both basic and clinical data alongside relevant family information.
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Affiliation(s)
- Tomoko Kobayashi
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Mika Kobayashi
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University
| | | | | | - Taku Obara
- Tohoku Medical Megabank Organization, Tohoku University
| | - Mami Ishikuro
- Tohoku Medical Megabank Organization, Tohoku University
| | | | - Tomomi Onuma
- Tohoku Medical Megabank Organization, Tohoku University
| | | | - Fumihiko Ueno
- Tohoku Medical Megabank Organization, Tohoku University
| | - Aoi Noda
- Tohoku Medical Megabank Organization, Tohoku University
| | - Akira Uruno
- Tohoku Medical Megabank Organization, Tohoku University
| | | | | | - Eiichi N Kodama
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University
| | | | - Naho Tsuchiya
- Tohoku Medical Megabank Organization, Tohoku University
| | - Mana Kogure
- Tohoku Medical Megabank Organization, Tohoku University
| | - Naoki Nakaya
- Tohoku Medical Megabank Organization, Tohoku University
| | - Makiko Taira
- Tohoku Medical Megabank Organization, Tohoku University
| | | | - Toru Tamahara
- Tohoku Medical Megabank Organization, Tohoku University
| | | | - Maki Goto
- Tohoku Medical Megabank Organization, Tohoku University
| | | | | | - Soichi Ogishima
- Tohoku Medical Megabank Organization, Tohoku University.,Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University
| | | | - Fuji Nagami
- Tohoku Medical Megabank Organization, Tohoku University
| | | | | | | | - Nobuo Fuse
- Tohoku Medical Megabank Organization, Tohoku University
| | - Shinichi Kuriyama
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Shigeo Kure
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Masayuki Yamamoto
- Tohoku Medical Megabank Organization, Tohoku University.,Graduate School of Medicine, Tohoku University.,Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University
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11
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Thébault P, Cailhier JF, Lapointe R. Blood Sample Processing and Banking for Functional and Molecular Analyses. Methods Mol Biol 2023; 2614:37-46. [PMID: 36587117 DOI: 10.1007/978-1-0716-2914-7_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Immune monitoring of circulating immune cells in the blood provides insight into a patient's own immune response over the course of a treatment or disease progression. Information such as whether immune cells are functional or non-functional and what specific proteins they express or secrete can be essential to understand if (and how) a treatment is working or a disease is progressing. To do so, it requires careful handling and storage of precious biological samples with the goals of obtaining a large amount of information from limited samples and minimizing future research costs by the use of banked samples. Many factors, including blood sample types, time of collection, containers used, preservatives and other additives, transport means, and length of transit time, all affect the quality of the samples and the stability of biomarkers and must be considered at the initial collection stage. An efficient study design includes provisions for further processing of the original samples, such as cryopreservation of isolated cells, purification of DNA and RNA, and preparation of specimens for genomic, immunological, and biochemical analyses. Development of standard operating procedures and quality control plans is a safeguard of the samples' quality and of the validity of the results. Here, we focus on the collection and processing of blood suitable for plasma and peripheral blood mononuclear cell (PBMC) banking, including collection, processing, and storage of samples, based on our experience.
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Affiliation(s)
- Paméla Thébault
- Axe Cancer, Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC, Canada.,Institut du cancer de Montréal, Montréal, QC, Canada
| | - Jean-François Cailhier
- Axe Cancer, Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC, Canada.,Institut du cancer de Montréal, Montréal, QC, Canada.,Faculté de Médecine, Département de Médecine, Université de Montréal, Montréal, QC, Canada
| | - Réjean Lapointe
- Axe Cancer, Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC, Canada. .,Institut du cancer de Montréal, Montréal, QC, Canada. .,Faculté de Médecine, Département de Médecine, Université de Montréal, Montréal, QC, Canada.
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12
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Ohneda K, Hamanaka Y, Kawame H, Fuse N, Nagami F, Suzuki Y, Yamaguchi-Kabata Y, Shimada M, Masamune A, Aoki Y, Ishida T, Yamamoto M. Returning individual genomic results to population-based cohort study participants with BRCA1/2 pathogenic variants. Breast Cancer 2023; 30:110-120. [PMID: 36161580 DOI: 10.1007/s12282-022-01404-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 09/14/2022] [Indexed: 01/07/2023]
Abstract
BACKGROUND Recent advances in human genome research have provided evidence for genotype-phenotype associations, pathogenicity, and clinical actionability of variants and genomic risk prediction of disease. However, the return of individual genomic results to healthy individuals is fraught with ethical and practical complexity. METHODS Individual genomic results were returned to BRCA1/2 pathogenic variant (PV) carriers of the Tohoku Medical Megabank cohort study participants with an information on hereditary breast and ovarian cancer syndrome (HBOC). One hundred and eighty participants, including 9 BRCA1/2 PV carriers, were asked about their willingness to receive individual genomic results, without revealing the gene name and related disorders, prior to the study. Of the 142 participants who responded, 103 showed willingness to know their genomic information. Each of the six BRCA1/2 PV carriers who consented to participate in the study received information about HBOC in person and underwent validation testing with blood resampling. RESULTS All participants were in their 60s or 70s; of the four females and two males, two had a history of breast cancer and five had a family history of HBOC-related cancers. All participants appreciated the information, without remarkable negative psychological impact of the return, and intended to undergo clinical risk surveillance. Five participants were accompanied by family members while receiving the results, and three first-degree female relatives wished to undergo genomic testing at the hospital. CONCLUSIONS Our results suggest that returning actionable genomic information to participants in a population-based genome cohort study is beneficial for preventing or providing early-stage intervention for associated diseases.
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Affiliation(s)
- Kinuko Ohneda
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan.
| | - Yohei Hamanaka
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan
- Department of Breast and Endocrine Surgical Oncology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Hiroshi Kawame
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan
- Department of Clinical Genetics, Jikei University Hospital, Tokyo, Japan
| | - Nobuo Fuse
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Miyagi, Japan
| | - Fuji Nagami
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Miyagi, Japan
| | - Yoichi Suzuki
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan
- Department of Clinical Genetics, Ageo Central General Hospital, Ageo, Saitama, Japan
| | - Yumi Yamaguchi-Kabata
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan
| | - Muneaki Shimada
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Miyagi, Japan
- Department of Gynecology and Obstetrics, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Atsushi Masamune
- Department of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Yoko Aoki
- Department of Medical Genetics, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Takanori Ishida
- Department of Breast and Endocrine Surgical Oncology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Masayuki Yamamoto
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan.
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Miyagi, Japan.
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13
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Lazareva TE, Barbitoff YA, Changalidis AI, Tkachenko AA, Maksiutenko EM, Nasykhova YA, Glotov AS. Biobanking as a Tool for Genomic Research: From Allele Frequencies to Cross-Ancestry Association Studies. J Pers Med 2022; 12:2040. [PMID: 36556260 PMCID: PMC9783756 DOI: 10.3390/jpm12122040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/19/2022] [Accepted: 11/28/2022] [Indexed: 12/14/2022] Open
Abstract
In recent years, great advances have been made in the field of collection, storage, and analysis of biological samples. Large collections of samples, biobanks, have been established in many countries. Biobanks typically collect large amounts of biological samples and associated clinical information; the largest collections include over a million samples. In this review, we summarize the main directions in which biobanks aid medical genetics and genomic research, from providing reference allele frequency information to allowing large-scale cross-ancestry meta-analyses. The largest biobanks greatly vary in the size of the collection, and the amount of available phenotype and genotype data. Nevertheless, all of them are extensively used in genomics, providing a rich resource for genome-wide association analysis, genetic epidemiology, and statistical research into the structure, function, and evolution of the human genome. Recently, multiple research efforts were based on trans-biobank data integration, which increases sample size and allows for the identification of robust genetic associations. We provide prominent examples of such data integration and discuss important caveats which have to be taken into account in trans-biobank research.
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Affiliation(s)
- Tatyana E. Lazareva
- Departemnt of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, 199034 St. Petersburg, Russia
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Yury A. Barbitoff
- Departemnt of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, 199034 St. Petersburg, Russia
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Anton I. Changalidis
- Departemnt of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, 199034 St. Petersburg, Russia
- Faculty of Software Engineering and Computer Systems, ITMO University, 197101 St. Petersburg, Russia
| | - Alexander A. Tkachenko
- Departemnt of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, 199034 St. Petersburg, Russia
| | - Evgeniia M. Maksiutenko
- Departemnt of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, 199034 St. Petersburg, Russia
| | - Yulia A. Nasykhova
- Departemnt of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, 199034 St. Petersburg, Russia
| | - Andrey S. Glotov
- Departemnt of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, 199034 St. Petersburg, Russia
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14
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Otsuki A, Okamura Y, Ishida N, Tadaka S, Takayama J, Kumada K, Kawashima J, Taguchi K, Minegishi N, Kuriyama S, Tamiya G, Kinoshita K, Katsuoka F, Yamamoto M. Construction of a trio-based structural variation panel utilizing activated T lymphocytes and long-read sequencing technology. Commun Biol 2022; 5:991. [PMID: 36127505 PMCID: PMC9489684 DOI: 10.1038/s42003-022-03953-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 09/06/2022] [Indexed: 11/13/2022] Open
Abstract
Long-read sequencing technology enable better characterization of structural variants (SVs). To adapt the technology to population-scale analyses, one critical issue is to obtain sufficient amount of high-molecular-weight genomic DNA. Here, we propose utilizing activated T lymphocytes, which can be established efficiently in a biobank to stably supply high-grade genomic DNA sufficiently. We conducted nanopore sequencing of 333 individuals constituting 111 trios with high-coverage long-read sequencing data (depth 22.2x, N50 of 25.8 kb) and identified 74,201 SVs. Our trio-based analysis revealed that more than 95% of the SVs were concordant with Mendelian inheritance. We also identified SVs associated with clinical phenotypes, all of which appear to be stably transmitted from parents to offspring. Our data provide a catalog of SVs in the general Japanese population, and the applied approach using the activated T-lymphocyte resource will contribute to biobank-based human genetic studies focusing on SVs at the population scale. Long-read sequencing on activated T-cells from a sample of 333 Japanese individuals (representing 111 parent-offspring trios) provides a useful reference dataset of structural variation in the Japanese population.
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Affiliation(s)
- Akihito Otsuki
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan.,Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8575, Japan
| | - Yasunobu Okamura
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan.,Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan
| | - Noriko Ishida
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan
| | - Shu Tadaka
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan
| | - Jun Takayama
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan.,Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan.,Statistical Genetics Team, RIKEN Center for Advanced Intelligence Project, Nihonbashi 1-chome Mitsui Building 15 F, 1-4-1 Nihonbashi, Chuo-ku, Tokyo, 103-0027, Japan.,Department of AI and Innovative Medicine, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8575, Japan
| | - Kazuki Kumada
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan
| | - Junko Kawashima
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan
| | - Keiko Taguchi
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan.,Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8575, Japan.,Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan
| | - Naoko Minegishi
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan
| | - Shinichi Kuriyama
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan
| | - Gen Tamiya
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan.,Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan.,Statistical Genetics Team, RIKEN Center for Advanced Intelligence Project, Nihonbashi 1-chome Mitsui Building 15 F, 1-4-1 Nihonbashi, Chuo-ku, Tokyo, 103-0027, Japan.,Department of AI and Innovative Medicine, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8575, Japan
| | - Kengo Kinoshita
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan.,Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8575, Japan.,Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan.,Graduate School of Information Sciences, Tohoku University, 6-3-09 Aramaki Aza-Aoba, Aoba-ku, Sendai, Miyagi, 980-8579, Japan
| | - Fumiki Katsuoka
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan.,Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan
| | - Masayuki Yamamoto
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan. .,Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8575, Japan. .,Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan.
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15
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Hishinuma E, Narita Y, Obuchi K, Ueda A, Saito S, Tadaka S, Kinoshita K, Maekawa M, Mano N, Hirasawa N, Hiratsuka M. Importance of Rare DPYD Genetic Polymorphisms for 5-Fluorouracil Therapy in the Japanese Population. Front Pharmacol 2022; 13:930470. [PMID: 35784703 PMCID: PMC9242541 DOI: 10.3389/fphar.2022.930470] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 05/30/2022] [Indexed: 02/02/2023] Open
Abstract
Dihydropyrimidine dehydrogenase (DPD), encoded by the DPYD gene, is the rate-limiting enzyme in 5-fluorouracil (5-FU) degradation. In Caucasians, four DPYD risk variants are recognized to be responsible for interindividual variations in the development of 5-FU toxicity. However, these risk variants have not been identified in Asian populations. Recently, 41 DPYD allelic variants, including 15 novel single nucleotide variants, were identified in 3,554 Japanese individuals by analyzing their whole-genome sequences; however, the effects of these variants on DPD enzymatic activity remain unknown. In the present study, an in vitro analysis was performed on 41 DPD allelic variants and three DPD risk variants to elucidate the changes in enzymatic activity. Wild-type and 44 DPD-variant proteins were heterologously expressed in 293FT cells. DPD expression levels and dimerization of DPD were determined by immunoblotting after SDS-PAGE and blue native PAGE, respectively. The enzymatic activity of DPD was evaluated by quantification of dihydro-5-FU, a metabolite of 5-FU, using high-performance liquid chromatography-tandem mass spectrometry. Moreover, we used 3D simulation modeling to analyze the effect of amino acid substitutions on the conformation of DPD. Among the 41 DPD variants, seven exhibited drastically decreased intrinsic clearance (CLint) compared to the wild-type protein. Moreover, R353C and G926V exhibited no enzymatic activity, and the band patterns observed in the immunoblots after blue native PAGE indicated that DPD dimerization is required for its enzymatic activity. Our data suggest that these variants may contribute to the significant inter-individual variability observed in the pharmacokinetics and pharmacodynamics of 5-FU. In our study, nine DPD variants exhibited drastically decreased or no enzymatic activity due to dimerization inhibition or conformational changes in each domain. Especially, the rare DPYD variants, although at very low frequencies, may serve as important pharmacogenomic markers associated with the severe 5-FU toxicity in Japanese population.
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Affiliation(s)
- Eiji Hishinuma
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Yoko Narita
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Kai Obuchi
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Akiko Ueda
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
| | - Sakae Saito
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Shu Tadaka
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Kengo Kinoshita
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Information Sciences, Tohoku University, Sendai, Japan
| | - Masamitsu Maekawa
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
- Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan
| | - Nariyasu Mano
- Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan
| | - Noriyasu Hirasawa
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
- Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan
| | - Masahiro Hiratsuka
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
- Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai, Japan
- *Correspondence: Masahiro Hiratsuka,
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16
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Sutoh Y, Komaki S, Yamaji T, Suzuki S, Katagiri R, Sawada N, Ono K, Ohmomo H, Hachiya T, Otsuka-Yamasaki Y, Takashima A, Umekage S, Iwasaki M, Shimizu A. Low MICA Gene Expression Confers an Increased Risk of Graves' Disease: A Mendelian Randomization Study. Thyroid 2022; 32:188-195. [PMID: 34861792 DOI: 10.1089/thy.2021.0417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Background: Expression of natural killer group 2 member D (NKG2D) ligand (NKG2DL) plays a major role as a "danger signal" on stressed cells to promote removal of the latter by NKG2D-expressing cytotoxic lymphocytes. NKG2DL expression has been found in peripheral immune cells as well, such as in macrophages; however, the effect of this expression is yet to be determined. Methods: We determined instrumental variables (IVs; R2 <0.01 in linkage disequilibrium), explaining the major variance in major histocompatibility complex class I chain-related protein A (MICA) and B (MICB) gene expression levels from the expression-quantitative trait locus (eQTL) of NKG2DLs based on the RNA-seq analysis of peripheral blood mononuclear cells (PBMCs) from 381 Japanese. Simultaneously, the target outcomes were filtered by PheWAS from 58 health risks, using a community-based cohort study composed of 44,739 Japanese residents. Finally, we estimated the causal effect of gene expression levels on the outcomes using the Mendelian randomization approach. Results: We determined nine and four IVs, explaining 87.6% and 33.0% of MICA and MICB gene expression levels, respectively. In the association test, we identified 10 or 13 significant outcomes associated with the MICA or MICB eQTLs, respectively, as well as the causal effect of MICA expression on Graves' disease (GD) (p = 4.2 × 10-3; odds ratio per 1 S.D. difference in the expression: 0.983 [confidence interval: 0.971-0.995]), using the weighted median estimator, without significant pleiotropy (p > 0.05), and the results were consistent across the sensitivity analyses. Conclusions: Our study provide novel evidence associating NKG2DL expression with GD, an autoimmune thyroiditis; direction of the effect indicated the immunoregulatory role of MICA expression in PBMCs, suggesting the importance of further functional assays in inflammatory diseases.
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Affiliation(s)
- Yoichi Sutoh
- Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, Yahaba, Japan
| | - Shohei Komaki
- Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, Yahaba, Japan
| | - Taiki Yamaji
- Epidemiology and Prevention Group, Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Shiori Suzuki
- Epidemiology and Prevention Group, Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
- Division of Cancer Medicine, Jikei University School of Medicine, Tokyo, Japan
| | - Ryoko Katagiri
- Epidemiology and Prevention Group, Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Norie Sawada
- Epidemiology and Prevention Group, Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Kanako Ono
- Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, Yahaba, Japan
| | - Hideki Ohmomo
- Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, Yahaba, Japan
| | - Tsuyoshi Hachiya
- Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, Yahaba, Japan
| | - Yayoi Otsuka-Yamasaki
- Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, Yahaba, Japan
| | - Akira Takashima
- Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, Yahaba, Japan
| | - So Umekage
- Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, Yahaba, Japan
| | - Motoki Iwasaki
- Epidemiology and Prevention Group, Center for Public Health Sciences, National Cancer Center, Tokyo, Japan
| | - Atsushi Shimizu
- Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, Yahaba, Japan
- Biomedical Laboratory Sciences, Institute of Biomedical Sciences, Iwate Medical University, Yahaba, Japan
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17
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dbTMM: an integrated database of large-scale cohort, genome and clinical data for the Tohoku Medical Megabank Project. Hum Genome Var 2021; 8:44. [PMID: 34887386 PMCID: PMC8660797 DOI: 10.1038/s41439-021-00175-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 09/08/2021] [Accepted: 09/08/2021] [Indexed: 11/08/2022] Open
Abstract
To reveal gene-environment interactions underlying common diseases and estimate the risk for common diseases, the Tohoku Medical Megabank (TMM) project has conducted prospective cohort studies and genomic and multiomics analyses. To establish an integrated biobank, we developed an integrated database called “dbTMM” that incorporates both the individual cohort/clinical data and the genome/multiomics data of 157,191 participants in the Tohoku Medical Megabank project. To our knowledge, dbTMM is the first database to store individual whole-genome data on a variant-by-variant basis as well as cohort/clinical data for over one hundred thousand participants in a prospective cohort study. dbTMM enables us to stratify our cohort by both genome-wide genetic factors and environmental factors, and it provides a research and development platform that enables prospective analysis of large-scale data from genome cohorts. A database integrating 1.3 trillion genome cohort data entries from 157,191 individuals in Japan will facilitate research into the gene-environment interactions underlying common diseases. The Tohoku Medical Megabank integrated database called dbTMM was developed by Soichi Ogishima, Masayuki Yamamoto and colleagues at Tohoku University in Japan. It incorporates the genome, metabolome, proteome, clinical, sociodemographic, lifestyle and environmental data from 84,073 adults, and 73,529 pregnant women and their families, including children. Blood and urine samples were collected from participants and analysed, then obtained genome/multiomics data were stored in dbTMM. Users can stratify the entire population into smaller populations based on multiple data variables, including whole genome variants, to search for statistically significant differences that might warrant further research. The dbTMM is expected to help clarify the genes and gene-environment interactions underlying common diseases and improve disease risk prediction.
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18
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Yamada M, Motoike IN, Kojima K, Fuse N, Hozawa A, Kuriyama S, Katsuoka F, Tadaka S, Shirota M, Sakurai M, Nakamura T, Hamanaka Y, Suzuki K, Sugawara J, Ogishima S, Uruno A, Kodama EN, Fujino N, Numakura T, Ichikawa T, Mitsune A, Ohe T, Kinoshita K, Ichinose M, Sugiura H, Yamamoto M. Genetic loci for lung function in Japanese adults with adjustment for exhaled nitric oxide levels as airway inflammation indicator. Commun Biol 2021; 4:1288. [PMID: 34782693 PMCID: PMC8593164 DOI: 10.1038/s42003-021-02813-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 10/27/2021] [Indexed: 11/08/2022] Open
Abstract
Lung function reflects the ability of the respiratory system and is utilized for the assessment of respiratory diseases. Because type 2 airway inflammation influences lung function, genome wide association studies (GWAS) for lung function would be improved by adjustment with an indicator of the inflammation. Here, we performed a GWAS for lung function with adjustment for exhaled nitric oxide (FeNO) levels in two independent Japanese populations. Our GWAS with genotype imputations revealed that the RNF5/AGER locus including AGER rs2070600 SNP, which introduces a G82S substitution of AGER, was the most significantly associated with FEV1/FVC. Three other rare missense variants of AGER were further identified. We also found genetic loci with three candidate genes (NOS2, SPSB2 and RIPOR2) associated with FeNO levels. Analyses with the BioBank-Japan GWAS resource revealed genetic links of FeNO and asthma-related traits, and existence of common genetic background for allergic diseases and their biomarkers. Our study identified the genetic locus most strongly associated with airway obstruction in the Japanese population and three genetic loci associated with FeNO, an indicator of type 2 airway inflammation in adults.
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Affiliation(s)
- Mitsuhiro Yamada
- Department of Respiratory Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Ikuko N Motoike
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Kaname Kojima
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Nobuo Fuse
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Atsushi Hozawa
- Department of Preventive Medicine and Epidemiology, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Shinichi Kuriyama
- Department of Preventive Medicine and Epidemiology, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Fumiki Katsuoka
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Shu Tadaka
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Matsuyuki Shirota
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Miyuki Sakurai
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Tomohiro Nakamura
- Department of Health Record Informatics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Yohei Hamanaka
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Kichiya Suzuki
- Department of Biobank, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Junichi Sugawara
- Department of Community Medical Supports, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Soichi Ogishima
- Department of Health Record Informatics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
| | - Akira Uruno
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Eiichi N Kodama
- Department of Community Medical Supports, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Naoya Fujino
- Department of Respiratory Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Tadahisa Numakura
- Department of Respiratory Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Tomohiro Ichikawa
- Department of Respiratory Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Ayumi Mitsune
- Department of Respiratory Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Takashi Ohe
- Department of Respiratory Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Kengo Kinoshita
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
- Department of System Bioinformatics, Tohoku University Graduate School of Information Sciences, Sendai, Japan
| | | | - Hisatoshi Sugiura
- Department of Respiratory Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Masayuki Yamamoto
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.
- Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan.
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19
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Tang R, Han C, Yin R, Zhu P, Zhu L, Lu Y, Zheng C. Quality Control of DNA Extracted from All-Cell Pellets After Cryopreservation for More Than 10 Years. Biopreserv Biobank 2021; 20:211-216. [PMID: 34435893 DOI: 10.1089/bio.2021.0052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Background: Cryopreserved whole blood, all-cell pellets (ACPs), and buffy coats in biobanks are widely used to obtain DNA for genetic testing. However, there are few studies concerning the quality control of DNA extracted from them. Our research aimed to perform quality control of DNA extracted from ACPs after cryopreservation for >10 years. Materials and Methods: A total of 1377 ACP samples (separated from 3 mL of whole blood) were retrieved from our biobank, where they had been cryopreserved for 10-15 years. Chemagic STAR was used to extract the DNA. Absorbance at A260, A280, and A230 were measured by spectrophotometry, and integrity was analyzed by agarose gel electrophoresis. The quality thresholds for an Illumina Asian Screening Array (ASA) were yields greater than 0.5 μg, concentration of 25-150 ng/μL, A260/280 ratio of 1.6-2.1, and no degradation fragments in the electrophoresis gel. Results: The median yield of genomic DNA was 54.30 μg (interquartile range [IQR] 35.55-74.64). The median A260/280 and A260/230 ratios were 1.90 (IQR 1.87-1.94) and 1.98 (IQR 1.64-2.41), respectively. In total, 1377 samples (100%) had qualified yields, and 1366 samples (99.20%) had qualified integrity results. Finally, 1328 (96.44%) samples were used for ASA. Of the remaining samples, 34 needed to be repurified, 4 were obtained at an insufficient concentration, and 11 were unqualified for integrity. In addition, we analyzed the influence of hemolysis (90 samples) and clots (102 samples) on the quality of DNA samples. Hemolysis and clotting did not influence yield or integrity, but a significant difference was found in A260/230 compared to normal samples (p < 0.05). Furthermore, the samples (14 samples) with both hemolysis and clots had higher A260/280 (p < 0.05). Conclusion: ACP samples stored for >10 years at -80°C produced DNA with high quality for use in genetic analysis. Hemolysis and clots in the ACPs led to lower purity, but did not significantly affect yield or integrity.
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Affiliation(s)
- Rong Tang
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Cui Han
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Ru Yin
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Ping Zhu
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Ling Zhu
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Yinghui Lu
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Chunxia Zheng
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
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20
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Kawame H, Fukushima A, Fuse N, Nagami F, Suzuki Y, Sakurai-Yageta M, Yasuda J, Yamaguchi-Kabata Y, Kinoshita K, Ogishima S, Takai T, Kuriyama S, Hozawa A, Nakaya N, Nakamura T, Minegishi N, Sugawara J, Suzuki K, Tomita H, Uruno A, Kobayashi T, Aizawa Y, Tokutomi T, Yamamoto K, Ohneda K, Kure S, Aoki Y, Katagiri H, Ishigaki Y, Sawada S, Sasaki M, Yamamoto M. The return of individual genomic results to research participants: design and pilot study of Tohoku Medical Megabank Project. J Hum Genet 2021; 67:9-17. [PMID: 34234266 DOI: 10.1038/s10038-021-00952-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 05/08/2021] [Accepted: 06/14/2021] [Indexed: 12/21/2022]
Abstract
Certain large genome cohort studies attempt to return the individual genomic results to the participants; however, the implementation process and psychosocial impacts remain largely unknown. The Tohoku Medical Megabank Project has conducted large genome cohort studies of general residents. To implement the disclosure of individual genomic results, we extracted the potential challenges and obstacles. Major challenges include the determination of genes/disorders based on the current medical system in Japan, the storage of results, prevention of misunderstanding, and collaboration of medical professionals. To overcome these challenges, we plan to conduct multilayer pilot studies, which deal with different disorders/genes. We finally chose familial hypercholesterolemia (FH) as a target disease for the first pilot study. Of the 665 eligible candidates, 33.5% were interested in the pilot study and provided consent after an educational "genetics workshop" on the basic genetics and medical facts of FH. The genetics professionals disclosed the results to the participants. All positive participants were referred to medical care, and a serial questionnaire revealed no significant psychosocial distress after the disclosure. Return of genomic results to research participants was implemented using a well-prepared protocol. To further elucidate the impact of different disorders, we will perform multilayer pilot studies with different disorders, including actionable pharmacogenomics and hereditary tumor syndromes.
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Affiliation(s)
- Hiroshi Kawame
- Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan.
| | - Akimune Fukushima
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Iwate, Japan
| | - Nobuo Fuse
- Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan
| | - Fuji Nagami
- Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan
| | - Yoichi Suzuki
- Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan
| | | | - Jun Yasuda
- Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan
| | | | - Kengo Kinoshita
- Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan
| | - Soichi Ogishima
- Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan
| | - Takako Takai
- Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan
| | - Shinichi Kuriyama
- Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan
| | - Atsushi Hozawa
- Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan
| | - Naoki Nakaya
- Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan
| | - Tomohiro Nakamura
- Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan
| | - Naoko Minegishi
- Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan
| | - Junichi Sugawara
- Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan
| | - Kichiya Suzuki
- Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan
| | - Hiroaki Tomita
- Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan
| | - Akira Uruno
- Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan
| | - Tomoko Kobayashi
- Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan
| | - Yayoi Aizawa
- Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan
| | - Tomoharu Tokutomi
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Iwate, Japan
| | - Kayono Yamamoto
- Department of Clinical Genetics, Iwate Medical University, Iwate, Japan
| | - Kinuko Ohneda
- Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan.
| | - Shigeo Kure
- Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan
| | - Yoko Aoki
- Department of Medical Genetics, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Hideki Katagiri
- Department of Metabolism and Diabetes, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Yasushi Ishigaki
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Iwate, Japan
| | - Shojiro Sawada
- Department of Metabolism and Diabetes, Tohoku University Graduate School of Medicine, Miyagi, Japan
| | - Makoto Sasaki
- Iwate Tohoku Medical Megabank Organization, Iwate Medical University, Iwate, Japan
| | - Masayuki Yamamoto
- Tohoku Medical Megabank Organization, Tohoku University, Miyagi, Japan.
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21
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Wide-Targeted Metabolome Analysis Identifies Potential Biomarkers for Prognosis Prediction of Epithelial Ovarian Cancer. Toxins (Basel) 2021; 13:toxins13070461. [PMID: 34209281 PMCID: PMC8309959 DOI: 10.3390/toxins13070461] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/21/2021] [Accepted: 06/29/2021] [Indexed: 02/06/2023] Open
Abstract
Epithelial ovarian cancer (EOC) is a fatal gynecologic cancer, and its poor prognosis is mainly due to delayed diagnosis. Therefore, biomarker identification and prognosis prediction are crucial in EOC. Altered cell metabolism is a characteristic feature of cancers, and metabolomics reflects an individual’s current phenotype. In particular, plasma metabolome analyses can be useful for biomarker identification. In this study, we analyzed 624 metabolites, including uremic toxins (UTx) in plasma derived from 80 patients with EOC using ultra-high-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS). Compared with the healthy control, we detected 77 significantly increased metabolites and 114 significantly decreased metabolites in EOC patients. Especially, decreased concentrations of lysophosphatidylcholines and phosphatidylcholines and increased concentrations of triglycerides were observed, indicating a metabolic profile characteristic of EOC patients. After calculating the parameters of each metabolic index, we found that higher ratios of kynurenine to tryptophan correlates with worse prognosis in EOC patients. Kynurenine, one of the UTx, can affect the prognosis of EOC. Our results demonstrated that plasma metabolome analysis is useful not only for the diagnosis of EOC, but also for predicting prognosis with the variation of UTx and evaluating response to chemotherapy.
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22
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Sakurai-Yageta M, Kumada K, Gocho C, Makino S, Uruno A, Tadaka S, Motoike IN, Kimura M, Ito S, Otsuki A, Narita A, Kudo H, Aoki Y, Danjoh I, Yasuda J, Kawame H, Minegishi N, Koshiba S, Fuse N, Tamiya G, Yamamoto M, Kinoshita K. Japonica Array NEO with increased genome-wide coverage and abundant disease risk SNPs. J Biochem 2021; 170:399-410. [PMID: 34131746 PMCID: PMC8510329 DOI: 10.1093/jb/mvab060] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 04/27/2021] [Indexed: 01/12/2023] Open
Abstract
Ethnic-specific SNP arrays are becoming more important to increase the power of genome-wide association studies in diverse population. In the Tohoku Medical Megabank Project, we have been developing a series of Japonica Arrays (JPA) for genotyping participants based on reference panels constructed from whole-genome sequence data of the Japanese population. Here, we designed a novel version of the SNP array for the Japanese population, called Japonica Array NEO (JPA NEO), comprising a total of 666,883 markers. Among them, 654,246 tag SNPs of autosomes and X chromosome were selected from an expanded reference panel of 3,552 Japanese, 3.5KJPNv2, using pairwise r2 of linkage disequilibrium measures. Additionally, 28,298 markers were included for the evaluation of previously identified disease risk markers from the literature and databases, and those present in the Japanese population were extracted using the reference panel. Through genotyping 286 Japanese samples, we found that the imputation quality r2 and INFO score in the minor allele frequency bin >2.5–5% were >0.9 and >0.8, respectively, and >12 million markers were imputed with an INFO score >0.8. From these results, JPA NEO is a promising tool for genotyping the Japanese population with genome-wide coverage, contributing to the development of genetic risk scores.
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Affiliation(s)
- Mika Sakurai-Yageta
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan.,Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Kazuki Kumada
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan.,Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Chinatsu Gocho
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Satoshi Makino
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Akira Uruno
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan.,Graduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan
| | - Shu Tadaka
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Ikuko N Motoike
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan.,Graduate School of Information Sciences, Tohoku University, 6-3-09 Aramaki-Aza-Aoba, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Masae Kimura
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Shin Ito
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Akihito Otsuki
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan.,Graduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan
| | - Akira Narita
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Hisaaki Kudo
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Yuichi Aoki
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan.,Graduate School of Information Sciences, Tohoku University, 6-3-09 Aramaki-Aza-Aoba, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Inaho Danjoh
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Jun Yasuda
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Hiroshi Kawame
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Naoko Minegishi
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan.,Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Seizo Koshiba
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan.,Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Nobuo Fuse
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan.,Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan.,Graduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan
| | - Gen Tamiya
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan.,Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan.,Graduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan
| | - Masayuki Yamamoto
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan.,Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan.,Graduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan
| | - Kengo Kinoshita
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan.,Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan.,Graduate School of Information Sciences, Tohoku University, 6-3-09 Aramaki-Aza-Aoba, Aoba-ku, Sendai, Miyagi 980-8579, Japan
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23
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Saito S, Aoki Y, Tamahara T, Goto M, Matsui H, Kawashima J, Danjoh I, Hozawa A, Kuriyama S, Suzuki Y, Fuse N, Kure S, Yamashita R, Tanabe O, Minegishi N, Kinoshita K, Tsuboi A, Shimizu R, Yamamoto M. Oral Microbiome Analysis in Prospective Genome Cohort Studies of the Tohoku Medical Megabank Project. Front Cell Infect Microbiol 2021; 10:604596. [PMID: 33585276 PMCID: PMC7878372 DOI: 10.3389/fcimb.2020.604596] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 12/07/2020] [Indexed: 12/26/2022] Open
Abstract
A baseline oral microbiome study of the Tohoku Medical Megabank Organization (TMM) was planned to characterize the profile of the oral microbiome in the Japanese population. The study also aimed to clarify risk factors for multifactorial diseases by integrated analysis of the oral microbiome and host genome/omics information. From 2013 to 2016, we collected three types of oral biospecimens, saliva, supragingival plaque, and tongue swab, from a total of 25,101 participants who had a dental examination in TMM. In this study, we used two independent cohorts; the Community-Based Cohort and Birth and Three-Generation Cohort as discovery and validation cohorts, respectively, and we selected participants examined by a single dentist. We found through the 16S ribosomal RNA gene sequencing analysis of 834 participants of the Community-Based Cohort Study that there are differences in the microbial composition and community structure between saliva and plaque. The species diversities in both saliva and plaque were increased in correlation with the severity of periodontal disease. These results were nicely reproduced in the analysis of 455 participants of the Birth and Three-Generation Cohort Study. In addition, strong positive and negative associations of microbial taxa in both plaque and saliva with periodontitis-associated biofilm formation were detected by co-occurrence network analysis. The classes Actinobacteria and Bacilli, including oral health-associated bacterial species, showed a positive correlation in saliva. These results revealed differences in microbial composition and community structure between saliva and plaque and a correlation between microbial species and the severity of periodontal disease. We expect that the large database of the oral microbiome in the TMM biobank will help in the discovery of novel targets for the treatment and prevention of oral diseases, as well as for the discovery of therapeutic and/or preventive targets of systemic diseases.
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Affiliation(s)
- Sakae Saito
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Yuichi Aoki
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Information Sciences, Tohoku University, Sendai, Japan
| | - Toru Tamahara
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Dentistry, Tohoku University, Sendai, Japan
| | - Maki Goto
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Hiroyuki Matsui
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Dentistry, Tohoku University, Sendai, Japan
| | - Junko Kawashima
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Inaho Danjoh
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Atsushi Hozawa
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Shinichi Kuriyama
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
- International Research Institute of Disaster Science, Tohoku University, Sendai, Japan
| | - Yoichi Suzuki
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Department of Clinical Genetics, Ageo Central General Hospital, Ageo, Japan
| | - Nobuo Fuse
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Shigeo Kure
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Riu Yamashita
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Exploratory Oncology Research & Clinical Trial Center, National Cancer Center, Kashiwa, Japan
| | - Osamu Tanabe
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Biosample Research Center, Radiation Effects Research Foundation, Hiroshima, Japan
| | - Naoko Minegishi
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
| | - Kengo Kinoshita
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Information Sciences, Tohoku University, Sendai, Japan
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
| | - Akito Tsuboi
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Dentistry, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Ritsuko Shimizu
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Masayuki Yamamoto
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Japan
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
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24
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Identification of Dominant Transcripts in Oxidative Stress Response by a Full-Length Transcriptome Analysis. Mol Cell Biol 2021; 41:MCB.00472-20. [PMID: 33168698 DOI: 10.1128/mcb.00472-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 11/02/2020] [Indexed: 12/30/2022] Open
Abstract
Our body responds to environmental stress by changing the expression levels of a series of cytoprotective enzymes/proteins through multilayered regulatory mechanisms, including the KEAP1-NRF2 system. While NRF2 upregulates the expression of many cytoprotective genes, there are fundamental limitations in short-read RNA sequencing (RNA-Seq), resulting in confusion regarding interpreting the effectiveness of cytoprotective gene induction at the transcript level. To precisely delineate isoform usage in the stress response, we conducted independent full-length transcriptome profiling (isoform sequencing; Iso-Seq) analyses of lymphoblastoid cells from three volunteers under normal and electrophilic stress-induced conditions. We first determined the first exon usage in KEAP1 and NFE2L2 (encoding NRF2) and found the presence of transcript diversity. We then examined changes in isoform usage of NRF2 target genes under stress conditions and identified a few isoforms dominantly expressed in the majority of NRF2 target genes. The expression levels of isoforms determined by Iso-Seq analyses showed striking differences from those determined by short-read RNA-Seq; the latter could be misleading concerning the abundance of transcripts. These results support that transcript usage is tightly regulated to produce functional proteins under electrophilic stress. Our present study strongly argues that there are important benefits that can be achieved by long-read transcriptome sequencing.
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25
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Novel candidates of pathogenic variants of the BRCA1 and BRCA2 genes from a dataset of 3,552 Japanese whole genomes (3.5KJPNv2). PLoS One 2021; 16:e0236907. [PMID: 33428613 PMCID: PMC7799847 DOI: 10.1371/journal.pone.0236907] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 12/04/2020] [Indexed: 12/17/2022] Open
Abstract
Identification of the population frequencies of definitely pathogenic germline variants in two major hereditary breast and ovarian cancer syndrome (HBOC) genes, BRCA1/2, is essential to estimate the number of HBOC patients. In addition, the identification of moderately penetrant HBOC gene variants that contribute to increasing the risk of breast and ovarian cancers in a population is critical to establish personalized health care. A prospective cohort subjected to genome analysis can provide both sets of information. Computational scoring and prospective cohort studies may help to identify such likely pathogenic variants in the general population. We annotated the variants in the BRCA1 and BRCA2 genes from a dataset of 3,552 whole-genome sequences obtained from members of a prospective cohorts with genome data in the Tohoku Medical Megabank Project (TMM) with InterVar software. Computational impact scores (CADD_phred and Eigen_raw) and minor allele frequencies (MAFs) of pathogenic (P) and likely pathogenic (LP) variants in ClinVar were used for filtration criteria. Familial predispositions to cancers among the 35,000 TMM genome cohort participants were analyzed to verify the identified pathogenicity. Seven potentially pathogenic variants were newly identified. The sisters of carriers of these moderately deleterious variants and definite P and LP variants among members of the TMM prospective cohort showed a statistically significant preponderance for cancer onset, from the self-reported cancer history. Filtering by computational scoring and MAF is useful to identify potentially pathogenic variants in BRCA genes in the Japanese population. These results should help to follow up the carriers of variants of uncertain significance in the HBOC genes in the longitudinal prospective cohort study.
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26
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Hirata M, Masuda M, Noguchi M, Tomita T, Ishibashi-Ueda H. An Efficient Culture Method of CD3-Positive T Cells from Human Cryopreserved Buffy Coat Specimens. Biopreserv Biobank 2020; 19:178-183. [PMID: 33305983 DOI: 10.1089/bio.2020.0031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Context: In the National Cerebral and Cardiovascular Center (NCVC) Biobank, buffy coats have been collected from patients and stored with cryoprotective agents as a possible source for viable blood cells, using cost-efficient methods for storage. However, whether viable cells for in vitro studies can be recovered from these biospecimens has not been verified. Objective: To investigate whether T cells can be collected and expanded as viable cells from cryopreserved human buffy coats. Design: After thawing of cryopreserved buffy coat specimens, CD3-positive cells were isolated from the cell suspension using a leukocyte separation filter coated with an anti-CD3 antibody, and the filter-attached cells were cultured in T cell culture medium. To analyze the characteristics of these cultured cells, histocytological analyses of Giemsa staining, immunocytochemical (ICC) staining for CD3, and flow cytometry for CD3 in live cells were conducted. Results: A few days after starting cell culture, cell clusters were observed, and they gradually grew in size. Using Giemsa staining, the expanded cells were found to be ∼15 μm in diameter, having round nuclei, a high nucleus/cytoplasm ratio, and cytoplasm stained light blue, which is characteristic of lymphocytes. From ICC staining, these cells were CD3 positive, a pan-T cell marker among lymphocytes. Furthermore, CD3 immunoreactivity in live cells was detected in a flow cytometry assay, though that for CD19 was not detected, which is a marker of pan-B cells. Conclusions: These results suggest that T cells can be expanded from buffy coats cryopreserved at -180°C as an adequate method of NCVC Biobank, highlighting these biospecimens as a possible useful source for future in vitro studies.
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Affiliation(s)
- Mitsuhi Hirata
- Biobank, National Cerebral and Cardiovascular Center, Suita, Japan
| | - Michitaka Masuda
- Biobank, National Cerebral and Cardiovascular Center, Suita, Japan
| | - Michio Noguchi
- Biobank, National Cerebral and Cardiovascular Center, Suita, Japan.,Divisions of Diabetes and Lipid Metabolism and National Cerebral and Cardiovascular Center, Suita, Japan
| | - Tsutomu Tomita
- Biobank, National Cerebral and Cardiovascular Center, Suita, Japan.,Divisions of Diabetes and Lipid Metabolism and National Cerebral and Cardiovascular Center, Suita, Japan.,Divisions of Genomic Diagnosis and Health Care, National Cerebral and Cardiovascular Center, Suita, Japan
| | - Hatsue Ishibashi-Ueda
- Biobank, National Cerebral and Cardiovascular Center, Suita, Japan.,Department of Pathology, National Cerebral and Cardiovascular Center, Suita, Japan
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27
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Ishida N, Aoki Y, Katsuoka F, Nishijima I, Nobukuni T, Anzawa H, Bin L, Tsuda M, Kumada K, Kudo H, Terakawa T, Otsuki A, Kinoshita K, Yamashita R, Minegishi N, Yamamoto M. Landscape of electrophilic and inflammatory stress-mediated gene regulation in human lymphoblastoid cell lines. Free Radic Biol Med 2020; 161:71-83. [PMID: 33011271 DOI: 10.1016/j.freeradbiomed.2020.09.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 09/26/2020] [Indexed: 02/08/2023]
Abstract
Human lymphoblastoid cell lines (LCLs) are valuable for the functional analyses of diseases. We have established more than 4200 LCLs as one of the resources of an integrated biobank. While oxidative and inflammatory stresses play critical roles in the onset and progression of various diseases, the responsiveness of LCLs, especially that of biobank-made LCLs, to these stresses has not been established. To address how LCLs respond to these stresses, in this study, we performed RNA sequencing of eleven human LCLs that were treated with an electrophile, diethyl maleate (DEM) and/or an inflammatory mediator, lipopolysaccharide (LPS). We found that over two thousand genes, including those regulated by a master regulator of the electrophilic/oxidative stress response, NRF2, were upregulated in LCLs treated with DEM, while approximately three hundred genes, including inflammation-related genes, were upregulated in LPS-treated LCLs. Of the LPS-induced genes, a subset of proinflammatory genes was repressed by DEM, supporting the notion that DEM suppresses the expression of proinflammatory genes through NRF2 activation. Conversely, a part of DEM-induced gene was repressed by LPS, suggesting reciprocal interference between electrophilic and inflammatory stress-mediated pathways. These data clearly demonstrate that LCLs maintain, by and large, responsive pathways against oxidative and inflammatory stresses and further endorse the usefulness of the LCL supply from the biobank.
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Affiliation(s)
- Noriko Ishida
- Department of Biobank, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan
| | - Yuichi Aoki
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan; Department of System Bioinformatics, Graduate School of Information Sciences, Tohoku University, Sendai, Japan
| | - Fumiki Katsuoka
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan
| | - Ichiko Nishijima
- Department of Biobank, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan
| | - Takahiro Nobukuni
- Department of Biobank, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan
| | - Hayato Anzawa
- Department of System Bioinformatics, Graduate School of Information Sciences, Tohoku University, Sendai, Japan
| | - Li Bin
- Department of Biobank, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan; Advanced Research Center for Innovations in Next Generation Medicine, Tohoku University, Sendai, Miyagi, Japan
| | - Miyuki Tsuda
- Department of Biobank, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan
| | - Kazuki Kumada
- Department of Biobank, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan
| | - Hisaaki Kudo
- Department of Biobank, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan
| | - Takahiro Terakawa
- Department of Biobank, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan
| | - Akihito Otsuki
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan
| | - Kengo Kinoshita
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan; Department of System Bioinformatics, Graduate School of Information Sciences, Tohoku University, Sendai, Japan
| | - Riu Yamashita
- Department of Biobank, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan; Division of Translational Informatics, Exploratory Oncology Research & Clinical Trial Center, National Cancer Center Hospital East, Kashiwa, Chiba, Japan
| | - Naoko Minegishi
- Department of Biobank, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan
| | - Masayuki Yamamoto
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan; Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan.
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28
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Analysis of HLA-G long-read genomic sequences in mother-offspring pairs with preeclampsia. Sci Rep 2020; 10:20027. [PMID: 33208885 PMCID: PMC7675977 DOI: 10.1038/s41598-020-77081-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 11/06/2020] [Indexed: 11/11/2022] Open
Abstract
Preeclampsia is a pregnancy-induced disorder that is characterized by hypertension and is a leading cause of perinatal and maternal–fetal morbidity and mortality. HLA-G is thought to play important roles in maternal–fetal immune tolerance, and the associations between HLA-G gene polymorphisms and the onset of pregnancy-related diseases have been explored extensively. Because contiguous genomic sequencing is difficult, the association between the HLA-G genotype and preeclampsia onset is controversial. In this study, genomic sequences of the HLA-G region (5.2 kb) from 31 pairs of mother–offspring genomic DNA samples (18 pairs from normal pregnancies/births and 13 from preeclampsia births) were obtained by single-molecule real-time sequencing using the PacBio RS II platform. The HLA-G alleles identified in our cohort matched seven known HLA-G alleles, but we also identified two new HLA-G alleles at the fourth-field resolution and compared them with nucleotide sequences from a public database that consisted of coding sequences that cover the 3.1-kb HLA-G gene span. Intriguingly, a potential association between preeclampsia onset and the poly T stretch within the downstream region of the HLA-G*01:01:01:01 allele was found. Our study suggests that long-read sequencing of HLA-G will provide clues for characterizing HLA-G variants that are involved in the pathophysiology of preeclampsia.
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29
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Koshiba S, Motoike IN, Saigusa D, Inoue J, Aoki Y, Tadaka S, Shirota M, Katsuoka F, Tamiya G, Minegishi N, Fuse N, Kinoshita K, Yamamoto M. Identification of critical genetic variants associated with metabolic phenotypes of the Japanese population. Commun Biol 2020; 3:662. [PMID: 33177615 PMCID: PMC7659008 DOI: 10.1038/s42003-020-01383-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 10/18/2020] [Indexed: 02/07/2023] Open
Abstract
We performed a metabolome genome-wide association study for the Japanese population in the prospective cohort study of Tohoku Medical Megabank. By combining whole-genome sequencing and nontarget metabolome analyses, we identified a large number of novel associations between genetic variants and plasma metabolites. Of the identified metabolite-associated genes, approximately half have already been shown to be involved in various diseases. We identified metabolite-associated genes involved in the metabolism of xenobiotics, some of which are from intestinal microorganisms, indicating that the identified genetic variants also markedly influence the interaction between the host and symbiotic bacteria. We also identified five associations that appeared to be female-specific. A number of rare variants that influence metabolite levels were also found, and combinations of common and rare variants influenced the metabolite levels more profoundly. These results support our contention that metabolic phenotyping provides important insights into how genetic and environmental factors provoke human diseases.
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Affiliation(s)
- Seizo Koshiba
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan.
- Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575, Japan.
- The Advanced Research Center for Innovations in Next-Generation Medicine (INGEM), Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan.
| | - Ikuko N Motoike
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan
- Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki Aza-Aoba, Aoba-ku, Sendai, 980-8579, Japan
| | - Daisuke Saigusa
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan
- Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575, Japan
| | - Jin Inoue
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan
- Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575, Japan
| | - Yuichi Aoki
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan
- Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki Aza-Aoba, Aoba-ku, Sendai, 980-8579, Japan
| | - Shu Tadaka
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan
- Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki Aza-Aoba, Aoba-ku, Sendai, 980-8579, Japan
| | - Matsuyuki Shirota
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan
- Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575, Japan
| | - Fumiki Katsuoka
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan
- Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575, Japan
- The Advanced Research Center for Innovations in Next-Generation Medicine (INGEM), Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan
| | - Gen Tamiya
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan
- Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575, Japan
- The Advanced Research Center for Innovations in Next-Generation Medicine (INGEM), Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan
| | - Naoko Minegishi
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan
- Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575, Japan
- The Advanced Research Center for Innovations in Next-Generation Medicine (INGEM), Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan
| | - Nobuo Fuse
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan
- Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575, Japan
- The Advanced Research Center for Innovations in Next-Generation Medicine (INGEM), Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan
| | - Kengo Kinoshita
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan
- The Advanced Research Center for Innovations in Next-Generation Medicine (INGEM), Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan
- Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki Aza-Aoba, Aoba-ku, Sendai, 980-8579, Japan
| | - Masayuki Yamamoto
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan.
- Graduate School of Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8575, Japan.
- The Advanced Research Center for Innovations in Next-Generation Medicine (INGEM), Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, 980-8573, Japan.
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30
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Sutoh Y, Hachiya T, Suzuki Y, Komaki S, Ohmomo H, Kakisaka K, Wang T, Takikawa Y, Shimizu A. ALDH2 genotype modulates the association between alcohol consumption and AST/ALT ratio among middle-aged Japanese men: a genome-wide G × E interaction analysis. Sci Rep 2020; 10:16227. [PMID: 33004991 PMCID: PMC7530747 DOI: 10.1038/s41598-020-73263-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 09/11/2020] [Indexed: 12/19/2022] Open
Abstract
Liver tests (LT), especially to measure AST, ALT and GGT levels, are widely used to evaluate the risk of alcohol-related liver disease (ALD). In this study, we investigated the potential genetic factors that modulate the association between LTs and alcohol consumption. We conducted a genome-wide interaction meta-analysis in 7856 Japanese subjects from Tohoku Medical Megabank Community-Based Cohort (TMM CommCohort) study recruited in 2013, and identified 2 loci (12q24 and 2p16) with genome-wide significance (P > 5 × 10-8). The significant variants in the 12q24 included rs671, a variant associated with alcohol intolerance and located at a coding exon of ALDH2. We found that the amount of alcohol consumption was associated with increased level AST/ALT ratio among the subjects with the rs671 GA genotype. The elevated AST/ALT ratio among subjects with moderate-to-high levels of drinking behavior and the rs671 GA genotype was due to decreased levels of ALT, which was not accompanied with significant differences in AST levels. Although the interaction effect was significant in both men and women, the effect was much larger in men. Our results suggest that the impact of alcohol consumption on LT varies according to the ALDH2 genotype, providing an insight for the accurate screening of ALD in drinkers with the rs671 GA genotype.
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Affiliation(s)
- Yoichi Sutoh
- Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Iwate, 028-3694, Japan
| | - Tsuyoshi Hachiya
- Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Iwate, 028-3694, Japan
| | - Yuji Suzuki
- Division of Hepatology, Department of Internal Medicine, Iwate Medical University, Yahaba, Japan
| | - Shohei Komaki
- Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Iwate, 028-3694, Japan
| | - Hideki Ohmomo
- Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Iwate, 028-3694, Japan
| | - Keisuke Kakisaka
- Division of Hepatology, Department of Internal Medicine, Iwate Medical University, Yahaba, Japan
| | - Ting Wang
- Division of Biomedical Research and Development, Institute of Biomedical Sciences, Iwate Medical University, Morioka, Iwate, Japan
| | - Yasuhiro Takikawa
- Division of Hepatology, Department of Internal Medicine, Iwate Medical University, Yahaba, Japan
| | - Atsushi Shimizu
- Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Iwate, 028-3694, Japan.
- Division of Biomedical Information Analysis, Institute for Biomedical Sciences, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Iwate, 028-3694, Japan.
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31
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Melis E, Gallo E, di Martino S, Gallina FT, Laquintana V, Casini B, Visca P, Ganci F, Alessandrini G, Caterino M, Cecere FL, Mandoj C, Papadantonakis A, De Bello N, Lattanzio R, Palmieri G, Garassino MC, Girard N, Conti L, Blandino G, Fazi F, Facciolo F, Pescarmona E, Ciliberto G, Marino M. Thymic Epithelial Tumors as a Model of Networking: Development of a Synergistic Strategy for Clinical and Translational Research Purposes. Front Oncol 2020; 10:922. [PMID: 32760665 PMCID: PMC7372300 DOI: 10.3389/fonc.2020.00922] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 05/11/2020] [Indexed: 12/23/2022] Open
Abstract
Among the group of thymic epithelial tumors (TET), thymomas often show either uncertain or explicit malignant biological behavior, local invasiveness, and intrathoracic relapse and are often difficult to manage. From the initial stages, thymic carcinomas tend to show aggressive behavior and extrathoracic spread. Moreover, the interplay of epithelial cells and thymocytes in thymomas causes complex immune derangement and related systemic autoimmune diseases. Due to their rare occurrence and to the limited funding opportunities available for rare tumors, it is challenging to make advances in clinical and translational research in TET. The authors of this paper are all members of a multidisciplinary clinical and research thoracic tumor team. Strong input was given to the team by long-standing expertise in TET in the Pathology Department. In addition, thanks to the collaboration between research units at our Institute as well as to national collaborations, over the last 10 years we were able to perform several tissue-based research studies. The most recent studies focused on microRNA and on functional studies on the thymic carcinoma cell line 1889c. The recent implementation of our biobank now provides us with a new tool for networking collaborative research activities. Moreover, the participation in a worldwide community such as ITMIG (International Thymic Malignancy Interest Group) has allowed us to significantly contribute toward fundamental projects/research both in tissue-based studies (The Cancer Genome Atlas) and in clinical studies (TNM staging of TET). Our achievements derive from constant commitment and long-standing experience in diagnosis and research in TET. New perspectives opened up due to the establishment of national [the Italian Collaborative Group for ThYmic MalignanciEs (TYME)] and European reference networks such as EURACAN, for an empowered joint clinical action in adult solid rare tumors. The challenge we face still lies in the advancement of clinical and basic science in thymic epithelial malignancies.
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Affiliation(s)
- Enrico Melis
- Thoracic Surgery Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Enzo Gallo
- Department of Pathology, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Simona di Martino
- Department of Pathology, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | | | - Valentina Laquintana
- Department of Pathology, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Beatrice Casini
- Department of Pathology, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Paolo Visca
- Department of Pathology, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Federica Ganci
- Oncogenomic and Epigenetic Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | | | - Mauro Caterino
- Radiology Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | | | - Chiara Mandoj
- Clinical Pathology, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | | | - Nicoletta De Bello
- Thoracic Surgery Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Rossano Lattanzio
- University “G. d'Annunzio,” Department of Medical, Oral and Biotechnological Sciences, Center for Advanced Studies and Technology (CAST), Chieti, Italy
| | - Giovannella Palmieri
- Scientific Direction, Department of Clinical Medicine and Surgery, Rare Tumors Reference Center, University Federico II, Naples, Italy
| | - Marina Chiara Garassino
- Thoracic Oncology Unit, Division of Medical Oncology, Foundation IRCCS–Italian National Cancer Institute, Milan, Italy
| | - Nicolas Girard
- Institut du Thorax Curie-Montsouris, Institut Curie, Paris, France
| | - Laura Conti
- Clinical Pathology, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Giovanni Blandino
- Oncogenomic and Epigenetic Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Francesco Fazi
- Department of Anatomical, Histological, Forensic & Orthopedic Sciences, Section of Histology & Medical Embryology, Sapienza University of Rome, Laboratory Affiliated to Instituto Pasteur Italia-Fondazione Cenci Bolognetti, Rome, Italy
| | - Francesco Facciolo
- Thoracic Surgery Unit, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Edoardo Pescarmona
- Department of Pathology, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Gennaro Ciliberto
- Scientific Direction, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Mirella Marino
- Department of Pathology, IRCCS Regina Elena National Cancer Institute, Rome, Italy
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32
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Sugawara J, Ishikuro M, Obara T, Onuma T, Murakami K, Kikuya M, Ueno F, Noda A, Mizuno S, Kobayashi T, Hamanaka Y, Suzuki K, Kodama E, Tsuchiya N, Uruno A, Suzuki Y, Tanabe O, Kiyomoto H, Tsuboi A, Shimizu A, Koshiba S, Minegishi N, Ogishima S, Tamiya G, Metoki H, Hozawa A, Fuse N, Kinoshita K, Kure S, Yaegashi N, Kuriyama S, Yamamoto M. Maternal Baseline Characteristics and Perinatal Outcomes: The Tohoku Medical Megabank Project Birth and Three-Generation Cohort Study. J Epidemiol 2020; 32:69-79. [PMID: 33041318 PMCID: PMC8761563 DOI: 10.2188/jea.je20200338] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Background The Tohoku Medical Megabank Project Birth and Three-Generation Cohort Study was launched in 2013 to evaluate the complex interactions of genetic and environmental factors in multifactorial diseases. The present study describes the maternal baseline profile and perinatal data of participating mothers and infants. Methods Expectant mothers living in Miyagi Prefecture were recruited from obstetric facilities or affiliated centers between 2013 and 2017. Three sets of self-administered questionnaires were collected, and the medical records were reviewed to obtain precise information about each antenatal visit and each delivery. Biospecimens, including blood, urine, umbilical cord blood, and breast milk, were collected for the study biobank. The baseline maternal sociodemographic characteristics, results of screening tests, and obstetric outcomes were analyzed according to the maternal age group. Results A total of 23,406 pregnancies involving 23,730 fetuses resulted in 23,143 live births. Younger maternal participants had a tendency toward a higher incidence of threatened abortion and threatened premature labor, while older age groups exhibited a significantly higher rate of low lying placenta, placenta previa, gestational diabetes, and hypertensive disorders of pregnancy. Conclusions The present study clearly shows the distribution of maternal baseline characteristics and the range of perinatal outcomes according to maternal age group. This cohort study can provide strategic information for creating breakthroughs in the pathophysiology of perinatal, developmental, and noncommunicable diseases by collaborative data visiting or sharing.
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Affiliation(s)
- Junichi Sugawara
- Tohoku Medical Megabank Organization, Tohoku University
- Graduate School of Medicine, Tohoku University
- Tohoku University Hospital
| | - Mami Ishikuro
- Tohoku Medical Megabank Organization, Tohoku University
| | - Taku Obara
- Tohoku Medical Megabank Organization, Tohoku University
| | - Tomomi Onuma
- Tohoku Medical Megabank Organization, Tohoku University
| | | | - Masahiro Kikuya
- Tohoku Medical Megabank Organization, Tohoku University
- School of Medicine, Teikyo University
| | - Fumihiko Ueno
- Tohoku Medical Megabank Organization, Tohoku University
| | - Aoi Noda
- Tohoku Medical Megabank Organization, Tohoku University
| | | | | | | | | | - Eiichi Kodama
- Tohoku Medical Megabank Organization, Tohoku University
- Graduate School of Medicine, Tohoku University
- International Research Institute of Disaster Science, Tohoku University
| | - Naho Tsuchiya
- Tohoku Medical Megabank Organization, Tohoku University
| | - Akira Uruno
- Tohoku Medical Megabank Organization, Tohoku University
| | - Yoichi Suzuki
- Tohoku Medical Megabank Organization, Tohoku University
- Ageo Central General Hospital
| | - Osamu Tanabe
- Tohoku Medical Megabank Organization, Tohoku University
- Radiation Effects Research Foundation
| | | | - Akito Tsuboi
- Tohoku Medical Megabank Organization, Tohoku University
- Graduate School of Dentistry, Tohoku University
| | - Atsushi Shimizu
- Tohoku Medical Megabank Organization, Tohoku University
- Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University
| | - Seizo Koshiba
- Tohoku Medical Megabank Organization, Tohoku University
- The Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University
| | | | - Soichi Ogishima
- Tohoku Medical Megabank Organization, Tohoku University
- The Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University
| | - Gen Tamiya
- Tohoku Medical Megabank Organization, Tohoku University
- Center for Advanced Intelligence Project, RIKEN
| | - Hirohito Metoki
- Tohoku Medical Megabank Organization, Tohoku University
- Faculty of Medicine, Tohoku Medical Pharmaceutical University
| | | | - Nobuo Fuse
- Tohoku Medical Megabank Organization, Tohoku University
| | - Kengo Kinoshita
- Tohoku Medical Megabank Organization, Tohoku University
- Graduate School of Information Sciences, Tohoku University
| | - Shigeo Kure
- Tohoku Medical Megabank Organization, Tohoku University
- Graduate School of Medicine, Tohoku University
- Tohoku University Hospital
| | - Nobuo Yaegashi
- Tohoku Medical Megabank Organization, Tohoku University
- Graduate School of Medicine, Tohoku University
- Tohoku University Hospital
| | - Shinichi Kuriyama
- Tohoku Medical Megabank Organization, Tohoku University
- Graduate School of Medicine, Tohoku University
- International Research Institute of Disaster Science, Tohoku University
| | - Masayuki Yamamoto
- Tohoku Medical Megabank Organization, Tohoku University
- Graduate School of Medicine, Tohoku University
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Bardanzellu F, Peila C, Fanos V, Coscia A. Clinical insights gained through metabolomic analysis of human breast milk. Expert Rev Proteomics 2019; 16:909-932. [PMID: 31825672 DOI: 10.1080/14789450.2019.1703679] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Introduction: Among the OMICS technologies, that have emerged in recent years, metabolomics has allowed relevant step forwards in clinical research. Several improvements in disease diagnosis and clinical management have been permitted, even in neonatology. Among potentially evaluable biofluids, breast milk (BM) results are highly interesting, representing a fluid of conjunction between mothers newborns, describing their interaction.Areas covered: in this review, updating a previous review article, we discuss research articles and reviews on BM metabolomics and found in MEDLINE using metabolomics, breast milk, neonatal nutrition, breastfeeding, human milk composition, and preterm neonates as keywords.Expert opinion: Our research group has a profound interest in metabolomics research. In 2012, we published the first metabolomic analysis on BM samples, reporting interesting data on its composition and relevant differences with formula milk (FM), useful to improve FM composition. As confirmed by successive studies, such technology can detect the specific BM composition and its dependence on several variables, including lactation stage, gestational age, maternal or environmental conditions. Moreover, since BM contaminants or drug levels can be detected, metabolomics also results useful to determine BM safety. These are only a few practical applications of BM analysis, which will be reviewed in this paper.
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Affiliation(s)
- Flaminia Bardanzellu
- Neonatal Intensive Care Unit, Department of Surgical Sciences, AOU University of Cagliari, Monserrato, Italy
| | - Chiara Peila
- Neonatology Unit, Department of Public Health and Pediatrics, Università degli Studi di Torino, Turin, Italy
| | - Vassilios Fanos
- Neonatal Intensive Care Unit, Department of Surgical Sciences, AOU University of Cagliari, Monserrato, Italy
| | - Alessandra Coscia
- Neonatology Unit, Department of Public Health and Pediatrics, Università degli Studi di Torino, Turin, Italy
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