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Lo YC, Chan TF, Jeon S, Maskarinec G, Taparra K, Nakatsuka N, Yu M, Chen CY, Lin YF, Wilkens LR, Le Marchand L, Haiman CA, Chiang CWK. The accuracy of polygenic score models for anthropometric traits and Type II Diabetes in the Native Hawaiian Population. medRxiv 2023:2023.12.25.23300499. [PMID: 38234828 PMCID: PMC10793530 DOI: 10.1101/2023.12.25.23300499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Polygenic scores (PGS) are promising in stratifying individuals based on the genetic susceptibility to complex diseases or traits. However, the accuracy of PGS models, typically trained in European- or East Asian-ancestry populations, tend to perform poorly in other ethnic minority populations, and their accuracies have not been evaluated for Native Hawaiians. Using body mass index, height, and type-2 diabetes as examples of highly polygenic traits, we evaluated the prediction accuracies of PGS models in a large Native Hawaiian sample from the Multiethnic Cohort with up to 5,300 individuals. We evaluated both publicly available PGS models or genome-wide PGS models trained in this study using the largest available GWAS. We found evidence of lowered prediction accuracies for the PGS models in some cases, particularly for height. We also found that using the Native Hawaiian samples as an optimization cohort during training did not consistently improve PGS performance. Moreover, even the best performing PGS models among Native Hawaiians would have lowered prediction accuracy among the subset of individuals most enriched with Polynesian ancestry. Our findings indicate that factors such as admixture histories, sample size and diversity in GWAS can influence PGS performance for complex traits among Native Hawaiian samples. This study provides an initial survey of PGS performance among Native Hawaiians and exposes the current gaps and challenges associated with improving polygenic prediction models for underrepresented minority populations.
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Affiliation(s)
- Ying-Chu Lo
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Tsz Fung Chan
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Soyoung Jeon
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Gertraud Maskarinec
- Epidemiology Program, University of Hawai'i Cancer Center, University of Hawai'i, Manoa, Honolulu, HI, USA
| | - Kekoa Taparra
- Standard Health Care, Department of Radiation Oncology, Palo Alto, CA, USA
| | | | - Mingrui Yu
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Neuropsychiatric Research, National Health Research Institutes, Miaoli, Taiwan
| | - Chia-Yen Chen
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Center for Neuropsychiatric Research, National Health Research Institutes, Miaoli, Taiwan
- Biogen, Cambridge, MA, USA
- Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Yen-Feng Lin
- Center for Neuropsychiatric Research, National Health Research Institutes, Miaoli, Taiwan
- Department of Public Health & Medical Humanities, School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Institute of Behavioral Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Lynne R Wilkens
- Epidemiology Program, University of Hawai'i Cancer Center, University of Hawai'i, Manoa, Honolulu, HI, USA
| | - Loic Le Marchand
- Epidemiology Program, University of Hawai'i Cancer Center, University of Hawai'i, Manoa, Honolulu, HI, USA
| | - Christopher A Haiman
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Cancer Epidemiology Program, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Charleston W K Chiang
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Cancer Epidemiology Program, Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
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Chan TF, Rui X, Conti DV, Fornage M, Graff M, Haessler J, Haiman C, Highland HM, Jung SY, Kenny EE, Kooperberg C, Le Marchand L, North KE, Tao R, Wojcik G, Gignoux CR, Chiang CWK, Mancuso N. Estimating heritability explained by local ancestry and evaluating stratification bias in admixture mapping from summary statistics. Am J Hum Genet 2023; 110:1853-1862. [PMID: 37875120 PMCID: PMC10645552 DOI: 10.1016/j.ajhg.2023.09.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 09/20/2023] [Accepted: 09/21/2023] [Indexed: 10/26/2023] Open
Abstract
The heritability explained by local ancestry markers in an admixed population (hγ2) provides crucial insight into the genetic architecture of a complex disease or trait. Estimation of hγ2 can be susceptible to biases due to population structure in ancestral populations. Here, we present heritability estimation from admixture mapping summary statistics (HAMSTA), an approach that uses summary statistics from admixture mapping to infer heritability explained by local ancestry while adjusting for biases due to ancestral stratification. Through extensive simulations, we demonstrate that HAMSTA hγ2 estimates are approximately unbiased and are robust to ancestral stratification compared to existing approaches. In the presence of ancestral stratification, we show a HAMSTA-derived sampling scheme provides a calibrated family-wise error rate (FWER) of ∼5% for admixture mapping, unlike existing FWER estimation approaches. We apply HAMSTA to 20 quantitative phenotypes of up to 15,988 self-reported African American individuals in the Population Architecture using Genomics and Epidemiology (PAGE) study. We observe hˆγ2 in the 20 phenotypes range from 0.0025 to 0.033 (mean hˆγ2 = 0.012 ± 9.2 × 10-4), which translates to hˆ2 ranging from 0.062 to 0.85 (mean hˆ2 = 0.30 ± 0.023). Across these phenotypes we find little evidence of inflation due to ancestral population stratification in current admixture mapping studies (mean inflation factor of 0.99 ± 0.001). Overall, HAMSTA provides a fast and powerful approach to estimate genome-wide heritability and evaluate biases in test statistics of admixture mapping studies.
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Affiliation(s)
- Tsz Fung Chan
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Xinyue Rui
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - David V Conti
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Myriam Fornage
- Brown Foundation Institute for Molecular Medicine, The University of Texas Health Science Center, Houston, TX, USA
| | - Mariaelisa Graff
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Jeffrey Haessler
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Christopher Haiman
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Heather M Highland
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Su Yon Jung
- Translational Sciences Section, School of Nursing, Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, USA
| | - Eimear E Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Kari E North
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Ran Tao
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Genevieve Wojcik
- Department of Epidemiology, Bloomberg School of Public Health, John Hopkins University, Baltimore, MD, USA
| | - Christopher R Gignoux
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Charleston W K Chiang
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Nicholas Mancuso
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA.
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3
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Chan TF, Rui X, Conti DV, Fornage M, Graff M, Haessler J, Haiman C, Highland HM, Jung SY, Kenny E, Kooperberg C, Marchland LL, North KE, Tao R, Wojcik G, Gignoux CR, Chiang CWK, Mancuso N. Estimating heritability explained by local ancestry and evaluating stratification bias in admixture mapping from summary statistics. bioRxiv 2023:2023.04.10.536252. [PMID: 37131817 PMCID: PMC10153181 DOI: 10.1101/2023.04.10.536252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The heritability explained by local ancestry markers in an admixed population h γ 2 provides crucial insight into the genetic architecture of a complex disease or trait. Estimation of h γ 2 can be susceptible to biases due to population structure in ancestral populations. Here, we present a novel approach, Heritability estimation from Admixture Mapping Summary STAtistics (HAMSTA), which uses summary statistics from admixture mapping to infer heritability explained by local ancestry while adjusting for biases due to ancestral stratification. Through extensive simulations, we demonstrate that HAMSTA h γ 2 estimates are approximately unbiased and are robust to ancestral stratification compared to existing approaches. In the presence of ancestral stratification, we show a HAMSTA-derived sampling scheme provides a calibrated family-wise error rate (FWER) of ~5% for admixture mapping, unlike existing FWER estimation approaches. We apply HAMSTA to 20 quantitative phenotypes of up to 15,988 self-reported African American individuals in the Population Architecture using Genomics and Epidemiology (PAGE) study. We observe h ˆ γ 2 in the 20 phenotypes range from 0.0025 to 0.033 (mean h ˆ γ 2 = 0.012 + / - 9.2 × 10 - 4 ), which translates to h ˆ 2 ranging from 0.062 to 0.85 (mean h ˆ 2 = 0.30 + / - 0.023 ). Across these phenotypes we find little evidence of inflation due to ancestral population stratification in current admixture mapping studies (mean inflation factor of 0.99 +/- 0.001). Overall, HAMSTA provides a fast and powerful approach to estimate genome-wide heritability and evaluate biases in test statistics of admixture mapping studies.
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Affiliation(s)
- Tsz Fung Chan
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California
| | - Xinyue Rui
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California
| | - David V Conti
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California
| | - Myriam Fornage
- Brown Foundation Institute for Molecular Medicine, The University of Texas Health Science Center, Houston, TX, USA
| | - Mariaelisa Graff
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Jeffrey Haessler
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Christopher Haiman
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California
| | - Heather M Highland
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Su Yon Jung
- Translational Sciences Section, School of Nursing, Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, United States
| | - Eimear Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Loic Le Marchland
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, USA
| | - Kari E North
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Ran Tao
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Genevieve Wojcik
- Department of Epidemiology, Bloomberg School of Public Health, John Hopkins University, Baltimore, MD, USA
| | - Christopher R Gignoux
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Charleston W K Chiang
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California
- Department of Quantitative and Computational Biology, University of Southern California
| | - Nicholas Mancuso
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California
- Department of Quantitative and Computational Biology, University of Southern California
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Li S, Chiang CWK, Myint SS, Arroyo K, Chan TF, Morimoto L, Metayer C, de Smith AJ, Walsh KM, Wiemels JL. Localized variation in ancestral admixture identifies pilocytic astrocytoma risk loci among Latino children. PLoS Genet 2022; 18:e1010388. [PMID: 36070312 PMCID: PMC9484652 DOI: 10.1371/journal.pgen.1010388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 09/19/2022] [Accepted: 08/21/2022] [Indexed: 11/18/2022] Open
Abstract
Background Pilocytic astrocytoma (PA) is the most common pediatric brain tumor. PA has at least a 50% higher incidence in populations of European ancestry compared to other ancestral groups, which may be due in part to genetic differences. Methods We first compared the global proportions of European, African, and Amerindian ancestries in 301 PA cases and 1185 controls of self-identified Latino ethnicity from the California Biobank. We then conducted admixture mapping analysis to assess PA risk with local ancestry. Results We found PA cases had a significantly higher proportion of global European ancestry than controls (case median = 0.55, control median = 0.51, P value = 3.5x10-3). Admixture mapping identified 13 SNPs in the 6q14.3 region (SNX14) contributing to risk, as well as three other peaks approaching significance on chromosomes 7, 10 and 13. Downstream fine mapping in these regions revealed several SNPs potentially contributing to childhood PA risk. Conclusions There is a significant difference in genomic ancestry associated with Latino PA risk and several genomic loci potentially mediating this risk. Childhood brain tumors are among the most prevalent and lethal childhood cancers. Despite this, the epidemiology as well as genetic risks are not well defined. For example, children of European ancestry have a higher risk of contracting pilocytic astrocytoma (PA) compared to other ancestries, but the genetic or environmental basis for this is unknown. Latino children are a mixture of multiple ancestries including European, African, and Native American. Using a group of Californian Latino children, we show that the risk of PA increases when a Latino child has a higher proportion of European ancestry. This global ancestry difference shows that germline genetic risk alleles contribute to a higher PA risk in children of European descendent. Moreover, this ancestral risk is localized to specific regions of the genome, especially in Chromosome 6 near the SNX14 gene, which is associated with cancer-related growth signaling pathway described by MAPK/ERK. This result brings us one step closer to understanding the etiology of this common childhood brain tumor.
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Affiliation(s)
- Shaobo Li
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California, Los Angeles, California, United States of America
| | - Charleston W. K. Chiang
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California, Los Angeles, California, United States of America
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California, United States of America
| | - Swe Swe Myint
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California, Los Angeles, California, United States of America
| | - Katti Arroyo
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California, Los Angeles, California, United States of America
| | - Tsz Fung Chan
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California, Los Angeles, California, United States of America
| | - Libby Morimoto
- School of Public Health, University of California Berkeley, Berkeley, California, United States of America
| | - Catherine Metayer
- School of Public Health, University of California Berkeley, Berkeley, California, United States of America
| | - Adam J. de Smith
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California, Los Angeles, California, United States of America
| | - Kyle M. Walsh
- Division of Neuro-Epidemiology, Department of Neurosurgery, Duke University, Durham, North Carolina, United States of America
- * E-mail: (KMW); (JLW)
| | - Joseph L. Wiemels
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California, Los Angeles, California, United States of America
- * E-mail: (KMW); (JLW)
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5
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Jeon S, de Smith AJ, Li S, Chen M, Chan TF, Muskens IS, Morimoto LM, DeWan AT, Mancuso N, Metayer C, Ma X, Wiemels JL, Chiang CWK. Genome-wide trans-ethnic meta-analysis identifies novel susceptibility loci for childhood acute lymphoblastic leukemia. Leukemia 2022; 36:865-868. [PMID: 34750507 PMCID: PMC9075725 DOI: 10.1038/s41375-021-01465-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 10/12/2021] [Accepted: 10/21/2021] [Indexed: 02/08/2023]
Affiliation(s)
- Soyoung Jeon
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Cancer Biology and Genomics Graduate Program, Program in Biological and Biomedical Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Adam J de Smith
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Shaobo Li
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Cancer Biology and Genomics Graduate Program, Program in Biological and Biomedical Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Minhui Chen
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Tsz Fung Chan
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Ivo S Muskens
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Libby M Morimoto
- Division of Epidemiology & Biostatistics, School of Public Health, University of California, Berkeley, CA, USA
| | - Andrew T DeWan
- Center for Perinatal, Pediatric and Environmental Epidemiology, Yale School of Public Health, New Haven, CT, USA
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT, USA
| | - Nicholas Mancuso
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Catherine Metayer
- Division of Epidemiology & Biostatistics, School of Public Health, University of California, Berkeley, CA, USA
| | - Xiaomei Ma
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT, USA
| | - Joseph L Wiemels
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
| | - Charleston W K Chiang
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA.
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Zhu P, Wong MKS, Lin X, Chan TF, Wong CKC, Lai KP, Tse WKF. Changes of the intestinal microbiota along the gut of Japanese Eel (Anguilla japonica). Lett Appl Microbiol 2021; 73:529-541. [PMID: 34265084 DOI: 10.1111/lam.13539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 06/21/2021] [Accepted: 07/13/2021] [Indexed: 10/20/2022]
Abstract
Fish intestine contains different types of microbiomes, and bacteria are the dominant microbiota in fishes. Studies have identified various core gut bacteria in fishes. However, little is known about the composition and their relative functions of gut microbial community along the intestine. To explore this, the current study investigated the microbial community distribution along the gut in Anguilla japonica. By 16S rRNA gene sequencing, we profiled the gut microbiota in eel along the three regions (anterior intestine (AI), the middle intestine (MI) and the posterior intestine (PI)). Results suggested that the three regions did not have significant differences on the observed species and diversities. The cluster tree analysis showed that the bacteria community in MI was closer to PI than the AI. The dominant bacteria in AI were the Proteobacteria, in which the majority was graduated replaced by Bacteroidetes along the gut to PI region. Through PICRUSt analysis, shifts in the bacterial community along the gut were found to affect the genetic information processing pathways. Higher levels of translation and transcriptional pathway activities were found in MI and PI than in AI. The dominant bacterial species were different among the regions and contributed to various biological functions along the gut.
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Affiliation(s)
- P Zhu
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf University, Qinzhou, Guangxi, PR China
| | - M K-S Wong
- Laboratory of Physiology, Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
| | - X Lin
- School of Life Sciences, Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - T F Chan
- School of Life Sciences, Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - C K C Wong
- Department of Biology, Croucher Institute for Environmental Sciences, Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guanzhou), The Hong Kong Baptist University, Kowloon, Hong Kong
| | - K P Lai
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf University, Qinzhou, Guangxi, PR China.,Department of Biology, Croucher Institute for Environmental Sciences, Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guanzhou), The Hong Kong Baptist University, Kowloon, Hong Kong.,Guangxi Key Laboratory of Tumor Immunology and Microenvironmental Regulation, Guilin Medical University, Guilin, PR China
| | - W K F Tse
- Center for Promotion of International Education and Research, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
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7
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Sun H, Lin M, Russell EM, Minster RL, Chan TF, Dinh BL, Naseri T, Reupena MS, Lum-Jones A, Cheng I, Wilkens LR, Le Marchand L, Haiman CA, Chiang CWK. The impact of global and local Polynesian genetic ancestry on complex traits in Native Hawaiians. PLoS Genet 2021; 17:e1009273. [PMID: 33571193 PMCID: PMC7877570 DOI: 10.1371/journal.pgen.1009273] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 11/18/2020] [Indexed: 12/17/2022] Open
Abstract
Epidemiological studies of obesity, Type-2 diabetes (T2D), cardiovascular diseases and several common cancers have revealed an increased risk in Native Hawaiians compared to European- or Asian-Americans living in the Hawaiian islands. However, there remains a gap in our understanding of the genetic factors that affect the health of Native Hawaiians. To fill this gap, we studied the genetic risk factors at both the chromosomal and sub-chromosomal scales using genome-wide SNP array data on ~4,000 Native Hawaiians from the Multiethnic Cohort. We estimated the genomic proportion of Native Hawaiian ancestry ("global ancestry," which we presumed to be Polynesian in origin), as well as this ancestral component along each chromosome ("local ancestry") and tested their respective association with binary and quantitative cardiometabolic traits. After attempting to adjust for non-genetic covariates evaluated through questionnaires, we found that per 10% increase in global Polynesian genetic ancestry, there is a respective 8.6%, and 11.0% increase in the odds of being diabetic (P = 1.65×10-4) and having heart failure (P = 2.18×10-4), as well as a 0.059 s.d. increase in BMI (P = 1.04×10-10). When testing the association of local Polynesian ancestry with risk of disease or biomarkers, we identified a chr6 region associated with T2D. This association was driven by an uniquely prevalent variant in Polynesian ancestry individuals. However, we could not replicate this finding in an independent Polynesian cohort from Samoa due to the small sample size of the replication cohort. In conclusion, we showed that Polynesian ancestry, which likely capture both genetic and lifestyle risk factors, is associated with an increased risk of obesity, Type-2 diabetes, and heart failure, and that larger cohorts of Polynesian ancestry individuals will be needed to replicate the putative association on chr6 with T2D.
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Affiliation(s)
- Hanxiao Sun
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Meng Lin
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Emily M. Russell
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Ryan L. Minster
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Tsz Fung Chan
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Bryan L. Dinh
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California, United States of America
| | - Take Naseri
- Ministry of Health, Government of Samoa, Apia, Samoa
| | | | - Annette Lum-Jones
- Epidemiology Program, University of Hawai‘i Cancer Center, University of Hawai‘i, Manoa, Honolulu, Hawaii, United States of America
| | | | - Iona Cheng
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, United States of America
| | - Lynne R. Wilkens
- Epidemiology Program, University of Hawai‘i Cancer Center, University of Hawai‘i, Manoa, Honolulu, Hawaii, United States of America
| | - Loïc Le Marchand
- Epidemiology Program, University of Hawai‘i Cancer Center, University of Hawai‘i, Manoa, Honolulu, Hawaii, United States of America
| | - Christopher A. Haiman
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Charleston W. K. Chiang
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, California, United States of America
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8
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Chim SSC, Chan TF, Leung TY. Whole-transcriptome analysis of maternal blood for identification of RNA markers for predicting spontaneous preterm birth among preterm labour women: abridged secondary publication. Hong Kong Med J 2020; 26 Suppl 6:20-23. [PMID: 33229598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023] Open
Affiliation(s)
- S S C Chim
- Department of Obstetrics & Gynaecology, Faculty of Medicine, The Chinese University of Hong Kong
| | - T F Chan
- School of Life Sciences, The Chinese University of Hong Kong
| | - T Y Leung
- Department of Obstetrics & Gynaecology, Faculty of Medicine, The Chinese University of Hong Kong
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9
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Kwok SLJ, Hau WLE, Chan TF, Lo FMI, Fung LWE, Tsui SKW. Whole exome sequencing for developmental delay and learning difficulties: abridged secondary publication. Hong Kong Med J 2020; 26 Suppl 7:4-6. [PMID: 33229608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023] Open
Affiliation(s)
- S L J Kwok
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong
| | - W L E Hau
- Clinical Genetic Service, Department of Health, Hong Kong
| | - T F Chan
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong
- Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong
| | - F M I Lo
- Clinical Genetic Service, Department of Health, Hong Kong
| | - L W E Fung
- Department of Paediatrics, The Chinese University of Hong Kong, Hong Kong
| | - S K W Tsui
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong
- Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong
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10
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Ng RMK, Chan TF, Herrman H, Dowrick C. What do psychiatrists think about primary mental health competencies among family doctors? A WPA-WONCA global survey. BJPsych Int 2020; 18:18-22. [PMID: 34287405 PMCID: PMC8274417 DOI: 10.1192/bji.2020.32] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 02/17/2020] [Accepted: 04/22/2020] [Indexed: 11/23/2022] Open
Abstract
People with common mental disorders often seek medical attention from their family doctors. Thus, it is essential for family doctors to possess primary mental health knowledge. The aim of this study was to understand whether psychiatrists endorse the primary mental health competencies identified by the World Organization of Family Doctors and whether they agree that family doctors are demonstrating these competencies. A questionnaire was constructed based on 32 core competencies. Presidents of all World Psychiatric Association member societies were invited to complete the questionnaire or to forward it to local experts. According to the respondents, these competencies are considered relevant yet not sufficiently possessed by typical primary care doctors. Proposals are made to bridge this assumed competency gap.
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Affiliation(s)
- R M K Ng
- Secretary for Education, World Psychiatric Association, Geneva, Switzerland.
| | - T F Chan
- Resident Trainee, Department of Psychiatry, Kowloon Hospital, Hong Kong, China
| | - H Herrman
- President, World Psychiatric Association, Geneva, Switzerland
| | - C Dowrick
- Chair, Working Party on Mental Health, World Organization of Family Doctors (WONCA)
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11
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Hui KF, Chan TF, Yang W, Shen JJ, Lam KP, Kwok H, Sham PC, Tsao SW, Kwong DL, Lung ML, Chiang AKS. High risk Epstein-Barr virus variants characterized by distinct polymorphisms in the EBER locus are strongly associated with nasopharyngeal carcinoma. Int J Cancer 2019; 144:3031-3042. [PMID: 30536939 DOI: 10.1002/ijc.32049] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 11/19/2018] [Accepted: 11/30/2018] [Indexed: 01/05/2023]
Abstract
Whether certain variants of Epstein-Barr virus (EBV) are linked to the pathogenesis of nasopharyngeal carcinoma (NPC), which shows a marked geographic restriction, remains an unresolved issue. We performed a case-control study comparing genomic sequences of EBV isolated from saliva samples of 142 population carriers with those from primary tumour biopsies derived from 62 patients with NPC of Hong Kong. Cluster analysis discovered five EBV subgroups 1A-C and 2A-B amongst the population carriers in contrast to the predominance of 1A and -B in the majority of NPC. Genome-wide association study (GWAS) identified a panel of NPC-associated single nucleotide polymorphisms (SNPs) and indels in the EBER locus. The most significant polymorphism, which can be found in 96.8% NPC cases and 40.1% population carriers of Hong Kong, is a four-base-deletion polymorphism downstream of EBER2 (EBER-del) from coordinates 7188-7191 (p = 1.91 × 10-7 ). In addition, the predicted secondary structure of EBER2 is altered with likely functional consequence in nearly all NPC cases. Using the SNPs and indels associated with NPC, genetic risk score is assigned for each EBV variant. EBV variants with high genetic risk score are found to be much more prevalent in Hong Kong Chinese than individuals of other geographic regions and in NPC than other EBV-associated cancers. We conclude that high risk EBV variants with polymorphisms in the EBER locus, designated as HKNPC-EBERvar, are strongly associated with NPC. Further investigation of the biological function and potential clinical application of these newly identified polymorphisms in NPC and other EBV-associated cancers is warranted.
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Affiliation(s)
- Kwai Fung Hui
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong SAR, China
| | - Tsz Fung Chan
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong SAR, China
| | - Wanling Yang
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong SAR, China.,Center for Nasopharyngeal Carcinoma Research, The University of Hong Kong, Hong Kong SAR, China
| | - Jiangshan Jane Shen
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong SAR, China
| | - Ki Pui Lam
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong SAR, China
| | - Hin Kwok
- Centre for Genomic Sciences, The Hong Kong Jockey Club Building for Interdisciplinary Research, The University of Hong Kong, Hong Kong, China
| | - Pak C Sham
- Center for Nasopharyngeal Carcinoma Research, The University of Hong Kong, Hong Kong SAR, China.,Centre for Genomic Sciences, The Hong Kong Jockey Club Building for Interdisciplinary Research, The University of Hong Kong, Hong Kong, China
| | - Sai Wah Tsao
- Center for Nasopharyngeal Carcinoma Research, The University of Hong Kong, Hong Kong SAR, China.,School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Dora L Kwong
- Center for Nasopharyngeal Carcinoma Research, The University of Hong Kong, Hong Kong SAR, China.,Department of Clinical Oncology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Maria Li Lung
- Center for Nasopharyngeal Carcinoma Research, The University of Hong Kong, Hong Kong SAR, China.,Department of Clinical Oncology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Alan Kwok Shing Chiang
- Department of Paediatrics and Adolescent Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong SAR, China.,Center for Nasopharyngeal Carcinoma Research, The University of Hong Kong, Hong Kong SAR, China
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12
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Shen J, Tsoi H, Liang Q, Chu ESH, Liu D, Yu ACS, Chan TF, Li X, Sung JJY, Wong VWS, Yu J. Oncogenic mutations and dysregulated pathways in obesity-associated hepatocellular carcinoma. Oncogene 2016; 35:6271-6280. [PMID: 27132506 PMCID: PMC5153568 DOI: 10.1038/onc.2016.162] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 04/01/2016] [Accepted: 04/03/2016] [Indexed: 02/07/2023]
Abstract
Epidemiological studies showed that obesity and its related non-alcoholic fatty liver disease (NAFLD) promote hepatocellular carcinoma (HCC) development. We aimed to uncover the genetic alterations of NAFLD-HCC using whole-exome sequencing. We compared HCC development in genetically obese mice and dietary obese mice with wild-type lean mice fed a normal chow after treatment with diethylnitrosamine. HCC tumor and adjacent normal samples from obese and lean mice were then subjected to whole-exome sequencing. Functional and mechanistic importance of the identified mutations in Carboxyl ester lipase (Cel) gene and Harvey rat sarcoma virus oncogene 1 (Hras) was further elucidated. We demonstrated significantly higher incidences of HCC in both genetic and dietary obese mice with NAFLD development as compared with lean mice without NAFLD. The mutational signatures of NAFLD-HCC and lean HCC were distinct, with <3% overlapped. Eight metabolic or oncogenic pathways were found to be significantly enriched by mutated genes in NAFLD-HCC, but only two of these pathways were dysregulated by mutations in lean HCC. In particular, Cel was mutated significantly more frequently in NAFLD-HCC than in lean HCC. The multiple-site mutations in Cel are loss-of-function mutations, with effects similar to Cel knock-down. Mutant Cel caused accumulation of cholesteryl ester in liver cells, which led to induction of endoplasmic reticulum stress and consequently activated the IRE1α/c-Jun N-terminal kinase (JNK)/c-Jun/activating protein-1 (AP-1) signaling cascade to promote liver cell growth. In addition, single-site mutations in Hras at codon 61 were found in NAFLD-HCC but none in lean HCC. The gain-of-function mutations in Hras (Q61R and Q61K) significantly promoted liver cell growth through activating the mitogen-activated protein kinase (MAPK) and phosphatidylinositol-4,5-bisphosphate 3-kinase (PI3K)/3-phosphoinositide-dependent protein kinase-1 (PDK1)/Akt pathways. In conclusion, we have identified mutation signature and pathways in NAFLD-associated HCC. Mutations in Cel and Hras have important roles in NAFLD-associated hepatocellular carcinogenesis.
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Affiliation(s)
- J Shen
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - H Tsoi
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - Q Liang
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - E S H Chu
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - D Liu
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - A C-S Yu
- School of Life Sciences, and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - T F Chan
- School of Life Sciences, and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - X Li
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - J J Y Sung
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - V W S Wong
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
| | - J Yu
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, China
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13
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Kenny NJ, Chan KW, Nong W, Qu Z, Maeso I, Yip HY, Chan TF, Kwan HS, Holland PWH, Chu KH, Hui JHL. Ancestral whole-genome duplication in the marine chelicerate horseshoe crabs. Heredity (Edinb) 2016; 116:190-9. [PMID: 26419336 PMCID: PMC4806888 DOI: 10.1038/hdy.2015.89] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2015] [Revised: 08/17/2015] [Accepted: 08/18/2015] [Indexed: 01/03/2023] Open
Abstract
Whole-genome duplication (WGD) results in new genomic resources that can be exploited by evolution for rewiring genetic regulatory networks in organisms. In metazoans, WGD occurred before the last common ancestor of vertebrates, and has been postulated as a major evolutionary force that contributed to their speciation and diversification of morphological structures. Here, we have sequenced genomes from three of the four extant species of horseshoe crabs-Carcinoscorpius rotundicauda, Limulus polyphemus and Tachypleus tridentatus. Phylogenetic and sequence analyses of their Hox and other homeobox genes, which encode crucial transcription factors and have been used as indicators of WGD in animals, strongly suggests that WGD happened before the last common ancestor of these marine chelicerates >135 million years ago. Signatures of subfunctionalisation of paralogues of Hox genes are revealed in the appendages of two species of horseshoe crabs. Further, residual homeobox pseudogenes are observed in the three lineages. The existence of WGD in the horseshoe crabs, noted for relative morphological stasis over geological time, suggests that genomic diversity need not always be reflected phenotypically, in contrast to the suggested situation in vertebrates. This study provides evidence of ancient WGD in the ecdysozoan lineage, and reveals new opportunities for studying genomic and regulatory evolution after WGD in the Metazoa.
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Affiliation(s)
- N J Kenny
- Simon F.S. Li Marine Science Laboratory,
School of Life Sciences, Center of Soybean Research, State Key Laboratory of
Agrobiotechnology, The Chinese University of Hong Kong, Shatin,
Hong Kong
| | - K W Chan
- Simon F.S. Li Marine Science Laboratory,
School of Life Sciences, Center of Soybean Research, State Key Laboratory of
Agrobiotechnology, The Chinese University of Hong Kong, Shatin,
Hong Kong
| | - W Nong
- Simon F.S. Li Marine Science Laboratory,
School of Life Sciences, Center of Soybean Research, State Key Laboratory of
Agrobiotechnology, The Chinese University of Hong Kong, Shatin,
Hong Kong
| | - Z Qu
- Simon F.S. Li Marine Science Laboratory,
School of Life Sciences, Center of Soybean Research, State Key Laboratory of
Agrobiotechnology, The Chinese University of Hong Kong, Shatin,
Hong Kong
| | - I Maeso
- Centro Andaluz de Biología del
Desarrollo (CABD), Consejo Superior de Investigaciones
Científicas/Universidad Pablo de Olavide, Sevilla,
Spain
| | - H Y Yip
- Simon F.S. Li Marine Science Laboratory,
School of Life Sciences, Center of Soybean Research, State Key Laboratory of
Agrobiotechnology, The Chinese University of Hong Kong, Shatin,
Hong Kong
| | - T F Chan
- School of Life Sciences, Center of
Soybean Research, State Key Laboratory of Agrobiotechnology, The Chinese
University of Hong Kong, Shatin, Hong Kong
| | - H S Kwan
- School of Life Sciences, The Chinese
University of Hong Kong, Shatin, Hong Kong
| | - P W H Holland
- Department of Zoology, University of
Oxford, Oxford, UK
| | - K H Chu
- Simon F.S. Li Marine Science Laboratory,
School of Life Sciences, The Chinese University of Hong Kong,
Shatin, Hong Kong
| | - J H L Hui
- Simon F.S. Li Marine Science Laboratory,
School of Life Sciences, Center of Soybean Research, State Key Laboratory of
Agrobiotechnology, The Chinese University of Hong Kong, Shatin,
Hong Kong
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14
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Yuan SS, Hou MF, Chang HL, Chan TF, Wu YH, Wu YC, Su JH. Arsenite-induced nitric oxide generation is cell cycle-dependent and aberrant in NBS cells. Toxicol In Vitro 2003; 17:139-43. [PMID: 12650666 DOI: 10.1016/s0887-2333(02)00129-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Exposure to arsenic has been reported to cause DNA damage and eventually the occurrence of bladder, lung and skin cancers. A previous report has demonstrated that arsenite-induced phosphorylation of Mre11, a protein involved in the repair of DNA double strand breaks (DSBs), is M phase-dependent and requires the Nijmegen breakage syndrome (NBS) protein, NBS1 [DNA Repair 1 (2002) 137]. Furthermore, arsenite treatment arrests cells at the M phase and the cells eventually go through apoptosis [Biochemical Pharmacology 60 (2000) 771]. Here we demonstrate that arsenite treatment enhances the generation of nitric oxide (NO), and that the enhanced NO generation is dominant at the G2/M phase. Arsenite-induced NO generation is impaired in DSB repair-defective NBS cells, but not in NBS1-reconstituted NBS cells, suggesting NBS1 is required for effective NO generation. In summary, our study showed, for the first time, that arsenite-induced NO generation is cell-cycle- and NBS1-dependent.
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Affiliation(s)
- S S Yuan
- Department of Obstetrics and Gynecology, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan 807, Republic of China
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15
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Lau L, Jan G, Chan TF. Preparation of patients for anaesthesia - achieving quality care. Hong Kong Med J 2002; 8:99-105. [PMID: 11937664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023] Open
Abstract
Implementation of anaesthesia begins with a preoperative assessment of the surgical patient and development of an anaesthetic plan. Preparation of the patient includes the preoperative assessment, review of preoperative tests, optimisation of medical conditions, adequate preoperative fasting, appropriate premedication, and the explanation of anaesthetic risk to patients. The goals of preoperative preparation are to reduce the morbidity of surgery, to increase the quality while decreasing the cost of perioperative care, and to return the patient to desirable functioning as quickly as possible. A knowledgeable anaesthesiologist is the 'final clinical gatekeeper', who coordinates perioperative management and ensures that the patient is in the optimal state for anaesthesia and surgery.
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Affiliation(s)
- L Lau
- Department of Anaesthesia and Intensive Care, Tuen Mun Hospital, Tsing Chung Koon Road, Hong Kong
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16
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Abstract
Gln3p is a nitrogen catabolite repression-sensitive GATA-type transcription factor. Its nuclear accumulation was recently shown to be under the control of TOR signaling. Gln3p normally resides in the cytoplasm. When cells are starved from nitrogen nutrients or treated with rapamycin, however, Gln3p becomes translocated into the nucleus, thereby activating the expression of genes involved in nitrogen utilization and transport. To identify other genes under the control of Gln3p, we searched for the Gln3p-binding GATAA motifs within 500 base pairs of the promoter sequences upstream of the yeast open reading frames in the Saccharomyces Genome Database. APG14, a gene essential for autophagy, was found to have the most GATAA motifs. We show that nitrogen starvation or rapamycin treatment rapidly causes a more than 20-fold induction of APG14. The expression of APG14 is dependent on Gln3p; deletion of Gln3p severely reduced its induction by rapamycin, whereas depletion of Ure2p caused its constitutive expression. However, overexpression of APG14 led to only a slight increase in autophagy in nitrogen-rich medium. Therefore, these results define a signaling cascade leading to the expression of APG14 in response to the availability of nitrogen nutrients and suggest that the regulated expression of APG14 contributes to but is not sufficient for the control of autophagy.
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Affiliation(s)
- T F Chan
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
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17
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Abstract
Motivated by the classical TV (total variation) restoration model, we propose a new nonlinear filter-the digital TV filter for denoising and enhancing digital images, or more generally, data living on graphs. The digital TV filter is a data dependent lowpass filter, capable of denoising data without blurring jumps or edges. In iterations, it solves a global total variational (or L(1)) optimization problem, which differs from most statistical filters. Applications are given in the denoising of one dimensional (1-D) signals, two-dimensional (2-D) data with irregular structures, gray scale and color images, and nonflat image features such as chromaticity.
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Affiliation(s)
- T F Chan
- Department of Mathematics, University of California, Los Angeles, CA 90095-1555, USA.
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18
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Abstract
We propose a new model for active contours to detect objects in a given image, based on techniques of curve evolution, Mumford-Shah (1989) functional for segmentation and level sets. Our model can detect objects whose boundaries are not necessarily defined by the gradient. We minimize an energy which can be seen as a particular case of the minimal partition problem. In the level set formulation, the problem becomes a "mean-curvature flow"-like evolving the active contour, which will stop on the desired boundary. However, the stopping term does not depend on the gradient of the image, as in the classical active contour models, but is instead related to a particular segmentation of the image. We give a numerical algorithm using finite differences. Finally, we present various experimental results and in particular some examples for which the classical snakes methods based on the gradient are not applicable. Also, the initial curve can be anywhere in the image, and interior contours are automatically detected.
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Affiliation(s)
- T F Chan
- Mathematics Department, University of California, Los Angeles, CA 90095-1555, USA.
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19
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Chan TF, Carvalho J, Riles L, Zheng XF. A chemical genomics approach toward understanding the global functions of the target of rapamycin protein (TOR). Proc Natl Acad Sci U S A 2000; 97:13227-32. [PMID: 11078525 PMCID: PMC27207 DOI: 10.1073/pnas.240444197] [Citation(s) in RCA: 140] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The target of rapamycin protein (TOR) is a highly conserved ataxia telangiectasia-related protein kinase essential for cell growth. Emerging evidence indicates that TOR signaling is highly complex and is involved in a variety of cellular processes. To understand its general functions, we took a chemical genomics approach to explore the genetic interaction between TOR and other yeast genes on a genomic scale. In this study, the rapamycin sensitivity of individual deletion mutants generated by the Saccharomyces Genome Deletion Project was systematically measured. Our results provide a global view of the rapamycin-sensitive functions of TOR. In contrast to conventional genetic analysis, this approach offers a simple and thorough analysis of genetic interaction on a genomic scale and measures genetic interaction at different possible levels. It can be used to study the functions of other drug targets and to identify novel protein components of a conserved core biological process such as DNA damage checkpoint/repair that is interfered with by a cell-permeable chemical compound.
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Affiliation(s)
- T F Chan
- Departments of Pathology and Immunology and Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
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20
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Abstract
Gln3p is a GATA-type transcription factor responsive to different nitrogen nutrients and starvation in yeast Saccharomyces cerevisiae. Recent evidence has linked TOR signaling to Gln3p. Rapamycin causes dephosphorylation and nuclear translocation of Gln3p, thereby activating nitrogen catabolite repressible-sensitive genes. However, a detailed mechanistic understanding of this process is lacking. In this study, we show that Tor1p physically interacts with Gln3p. An intact TOR kinase domain is essential for the phosphorylation of Gln3p, inhibition of Gln3p nuclear entry and repression of Gln3p-dependent transcription. In contrast, at least two distinct protein phosphatases, Pph3p and the Tap42p-dependent phosphatases, are involved in the activation of Gln3p. The yeast pro-prion protein Ure2p binds to both hyper- and hypo-phosphorylated Gln3p. In contrast to the free Gln3p, the Ure2p-bound Gln3p is signifcantly resistant to dephosphorylation. Taken together, these results reveal a tripartite regulatory mechanism by which the phosphorylation of Gln3p is regulated.
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Affiliation(s)
- P G Bertram
- Department of Pathology and Immunology and the Molecular Genetics and Molecular Cell Biology Programs, Washington University School of Medicine, St. Louis, Missouri 63110, USA
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21
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Abstract
The functional diversity and structural heterogeneity of microtubules are largely determined by microtubule-associated proteins (MAPs) [1] [2]. Bik1p (bilateral karyogamy defect protein) is one of the MAPs required for microtubule assembly, stability and function in cell processes such as karyogamy and nuclear migration and positioning in the yeast Saccharomyces cerevisiae [3]. The macrocyclic immunosuppressive antibiotic rapamycin, complexed with its binding protein FKBP12, binds to and inhibits the target of rapamycin protein (TOR) in yeast [4] [5]. We report here that TOR physically interacts with Bik1p, the yeast homolog of human CLIP-170/Restin [6] [7]. Inhibition of TOR by rapamycin significantly affects microtubule assembly, elongation and stability. This function of TOR is independent of new protein synthesis. Rapamycin also causes defects in spindle orientation, nuclear movement and positioning, karyogamy and chromosomal stability, defects also found in the bikDelta mutant. Our data suggest a role for TOR signaling in regulating microtubule stability and function, possibly through Bik1p.
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Affiliation(s)
- J H Choi
- Departments of Pathology, Washington University School of Medicine, St Louis, MO 63110, USA
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22
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Chan RH, Chan TF, Wong CK. Cosine transform based preconditioners for total variation deblurring. IEEE Trans Image Process 1999; 8:1472-1478. [PMID: 18267422 DOI: 10.1109/83.791976] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
In PDE image restoration problems, one has to invert operators which is a sum of a blurring operator and an elliptic operator with highly varying coefficient. We present a preconditioner for such operators, which can be used with the conjugate gradient (CG) method, and compare it with Vogel and Oman's product preconditioner.
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23
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Abstract
We propose a new definition of the total variation (TV) norm for vector-valued functions that can be applied to restore color and other vector-valued images. The new TV norm has the desirable properties of 1) not penalizing discontinuities (edges) in the image, 2) being rotationally invariant in the image space, and 3) reducing to the usual TV norm in the scalar case. Some numerical experiments on denoising simple color images in red-green-blue (RGB) color space are presented.
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Affiliation(s)
- P Blomgren
- Dept. of Math., California Univ., Los Angeles, CA 90095-1555, USA.
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24
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Abstract
In this paper, we present a blind deconvolution algorithm based on the total variational (TV) minimization method proposed. The motivation for regularizing with the TV norm is that it is extremely effective for recovering edges of images as well as some blurring functions, e.g., motion blur and out-of-focus blur. An alternating minimization (AM)implicit iterative scheme is devised to recover the image and simultaneously identify the point spread function (psf). Numerical results indicate that the iterative scheme is quite robust, converges very fast (especially for discontinuous blur), and both the image and the psf can be recovered under the presence of high noise level. Finally, we remark that psf's without sharp edges, e.g., Gaussian blur, can also be identified through the TV approach.
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Affiliation(s)
- T F Chan
- Dept. of Math., California Univ., Los Angeles, CA 90095-1555, USA.
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Yip AS, Chow WH, Yung TC, Chau EM, Chan TF. Radiofrequency catheter ablation of left-sided accessory pathways using a transeptal technique and specialized long intravascular sheaths. Efficacy, recurrence rate and complications. Jpn Heart J 1997; 38:643-50. [PMID: 9462413 DOI: 10.1536/ihj.38.643] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
49 patients with 51 left-sided accessory pathways underwent radiofrequency catheter ablation for symptomatic supraventricular tachycardia via the transeptal route using specialised long vascular sheaths with compound curves. The procedure was successful in 45 patients (92%). The mean fluroscopic time was 22.5 +/- 15.2 mins and the mean procedure time was 1.7 +/- 0.5 hours. Pericardial tamponade occurred in 2 patients (4%) and 2 patients (4%) required switching to the retrograde transaortic route for successful ablation of the pathways. During the period of follow-up of 16.8 +/- 6.9 months, clinical recurrence occurred in 2 patients (4%). In conclusion, the transeptal route of radiofrequency catheter ablation is a useful alternative strategy to the transaortic approach with good long term results. The use of specialised sheaths may help in stabilisation of the catheter during the procedure which can generate more adequate lesions and consequently a lower recurrence rate.
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Affiliation(s)
- A S Yip
- Department of Cardiology, Grantham Hospital, Aberdeen, Hong Kong
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Abstract
An excess of schizophrenia has been observed in the biological relatives of adoptees with schizophrenia. The present analysis examined the possibility that illness observed among 90 half-siblings may have been influenced by assortative mating resulting in excess illness in the biological parents of the half-siblings not biologically related to the adoptees (the coparents). We found no difference in the prevalence of mental illness between 44 index and 26 control coparents.
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Affiliation(s)
- L J Ingraham
- Laboratory of Psychology and Psychopathology, NIMH, Bethesda, Maryland 20892-1366, USA
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Abstract
Standardized activated charcoal canisters (according to the U.S. EPA) have been used to collect radon exhaled from concrete surfaces covered with thin plaster (categorically different from thick plaster) of 32 buildings of different ages (0.5-31 y) in Hong Kong. Concrete surfaces covered with thin plaster is the commonest wall configuration in Hong Kong. The canisters are analyzed using gamma spectroscopy to obtain the radon exhalation rates. The results show that the radon exhalation rate decreases with the building age.
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Affiliation(s)
- K N Yu
- Department of Physics and Materials Science, City Polytechnic of Hong Kong, Kowloon
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