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Chu C, Chang C, Lin C, Ko T. ISQUA18-2405Sharing Decision Making (SDM) Approach Applicable to Whole Hospital - A Medical Center in Northern Taiwan. Int J Qual Health Care 2018. [DOI: 10.1093/intqhc/mzy167.31] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Wang Y, Hu JW, Wang KK, Yan Y, Chu C, Zheng WL, Lv YB, Ma Q, Gao K, Yuan Y, Yuan ZY, Mu JJ. P5722Association between salt intake and uric acid, and its interaction on the incidence of prehypertension among Chinese young adults. Eur Heart J 2018. [DOI: 10.1093/eurheartj/ehy566.p5722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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53
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Papatla K, Halpern M, Hernandez E, Brown J, Benrubi I, Houck K, Chu C, Rubin S. Patients with a history of cervical cancer are at an increased risk of developing primary anal or oropharyngeal cancer. Gynecol Oncol 2018. [DOI: 10.1016/j.ygyno.2018.04.475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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54
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Roberts M, Hall M, Woodman S, Glass D, Brown J, Benrubi I, Jain A, Martin L, Chu C, Rubin S, Mantia-Smaldone G. Opportunities for improved Lynch syndrome tumor screening in endometrial cancer patients surgically treated at an NCI-designated comprehensive cancer center. Gynecol Oncol 2018. [DOI: 10.1016/j.ygyno.2018.04.473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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55
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Chu C, Syu Y, Sheen Y, Chu C. 147 Novel RNA targets regulated by insulin-like growth factor 2 mRNA-binding protein 3 (IMP-3) in human melanoma. J Invest Dermatol 2018. [DOI: 10.1016/j.jid.2018.03.152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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56
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Liu C, Chu C, Zhang J, Wu D, Xu D, Li P, Chen Y, Liu B, Pei L, Zhang L, Liu S, Qi T, Lou XY, Li L. IRX3 is a genetic modifier for birth weight, adolescent obesity and transaminase metabolism. Pediatr Obes 2018; 13:141-148. [PMID: 28316138 DOI: 10.1111/ijpo.12214] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 01/20/2017] [Indexed: 01/29/2023]
Abstract
OBJECTIVE IRX3 expression has been functionally associated in obesity-associated long-distance susceptibility loci, but the effect of the IRX3 genetic variants on human obesity and obesity-related metabolism remains uncertain. METHODS To determine the genetic role of IRX3, we conducted a molecular epidemiological analysis using three haplotype tagging single nucleotide polymorphisms (SNPs; rs8053360, rs3751723 and rs12445085) and one nonsynonymous SNP (rs1126960) at the IRX3 locus in 333 junior and senior high school students from a northeast Chinese population. RESULTS We identified significant associations between IRX3 SNPs and birth weight, body mass index (BMI), aspartate aminotransferase (AST), alanine aminotransferase (ALT) and AST/ALT ratio. The rs8053360 CC and rs1126960 GG genotypes were associated with increased birth weight and BMI, especially in females. Individuals with the rs12445085 TT genotype had significantly higher levels of AST and ALT, whereas individuals with the rs1126960 GG genotype had a significantly lower AST/ALT ratio than did individuals with other genotypes. However, no significant relationships were found between any of the IRX3 SNPs and metabolic syndrome or diabetes. CONCLUSIONS IRX3 genetic variants associate with birth weight, BMI and AST/ALT-related transaminase metabolism, supporting the role of IRX3 as an obesity-associated susceptibility gene.
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Li L, Leung AKY, Kwok TP, Lai YYY, Pang IK, Chung GTY, Mak ACY, Poon A, Chu C, Li M, Wu JJK, Lam ET, Cao H, Lin C, Sibert J, Yiu SM, Xiao M, Lo KW, Kwok PY, Chan TF, Yip KY. OMSV enables accurate and comprehensive identification of large structural variations from nanochannel-based single-molecule optical maps. Genome Biol 2017; 18:230. [PMID: 29195502 PMCID: PMC5709945 DOI: 10.1186/s13059-017-1356-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 11/03/2017] [Indexed: 12/20/2022] Open
Abstract
We present a new method, OMSV, for accurately and comprehensively identifying structural variations (SVs) from optical maps. OMSV detects both homozygous and heterozygous SVs, SVs of various types and sizes, and SVs with or without creating or destroying restriction sites. We show that OMSV has high sensitivity and specificity, with clear performance gains over the latest method. Applying OMSV to a human cell line, we identified hundreds of SVs >2 kbp, with 68 % of them missed by sequencing-based callers. Independent experimental validation confirmed the high accuracy of these SVs. The OMSV software is available at http://yiplab.cse.cuhk.edu.hk/omsv/ .
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Luo X, Liao R, Hanley KL, Zhu HH, Malo KN, Hernandez C, Wei X, Varki NM, Alderson N, Chu C, Li S, Fan J, Loomba R, Qiu SJ, Feng GS. Dual Shp2 and Pten Deficiencies Promote Non-alcoholic Steatohepatitis and Genesis of Liver Tumor-Initiating Cells. Cell Rep 2017; 17:2979-2993. [PMID: 27974211 DOI: 10.1016/j.celrep.2016.11.048] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 10/20/2016] [Accepted: 11/15/2016] [Indexed: 01/14/2023] Open
Abstract
The complexity of liver tumorigenesis is underscored by the recently observed anti-oncogenic effects of oncoproteins, although the mechanisms are unclear. Shp2/Ptpn11 is a proto-oncogene in hematopoietic cells and antagonizes the effect of tumor suppressor Pten in leukemogenesis. In contrast, we show here cooperative functions of Shp2 and Pten in suppressing hepatocarcinogenesis. Ablating both Shp2 and Pten in hepatocytes induced early-onset non-alcoholic steatohepatitis (NASH) and promoted genesis of liver tumor-initiating cells likely due to augmented cJun expression/activation and elevated ROS and inflammation in the hepatic microenvironment. Inhibiting cJun partially suppressed NASH-driven liver tumorigenesis without improving NASH. SHP2 and PTEN deficiencies were detected in liver cancer patients with poor prognosis. These data depict a mechanism of hepato-oncogenesis and suggest a potential therapeutic strategy.
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Yen Y, Chu C, Wei Y, Cheng Y, Tseng Y, Su W, Lin C. MA 16.02 Different Pattern and Prognostic Role of PD-L1, IDO, and Foxp3 Treg Expression in Thymoma and Thymic Carcinoma. J Thorac Oncol 2017. [DOI: 10.1016/j.jtho.2017.09.597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Rousseau J, Chu C, Guitard P. HOME ASSESSMENT OF PERSON-ENVIRONMENT INTERACTION (HOPE): A CROSS-CULTURAL VALIDATION STUDY. Innov Aging 2017. [DOI: 10.1093/geroni/igx004.1237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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61
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Chu C, Yang C, Lin L, Hughes M, Tsai Y. 271 The role of local and systemic leptin in androgenetic alopecia. J Invest Dermatol 2017. [DOI: 10.1016/j.jid.2017.02.287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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62
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Dwipayanti N, Rutherford S, Phung D, Chu C. How Important is Culture to Sanitation Uptake? The Influence of Local Values in Rural Bali. ACTA ACUST UNITED AC 2017. [DOI: 10.1166/asl.2017.9160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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63
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Gill TA, Chu C, Pelz-Stelinski KS. Comparative proteomic analysis of hemolymph from uninfected and Candidatus Liberibacter asiaticus-infected Diaphorina citri. Amino Acids 2016; 49:389-406. [DOI: 10.1007/s00726-016-2373-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 11/25/2016] [Indexed: 01/13/2023]
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64
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Wong JY, Chu C, Chong VC, Dhillon SK, Loh KH. Automated otolith image classification with multiple views: an evaluation on Sciaenidae. JOURNAL OF FISH BIOLOGY 2016; 89:1324-1344. [PMID: 27364089 DOI: 10.1111/jfb.13039] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 04/13/2016] [Indexed: 06/06/2023]
Abstract
Combined multiple 2D views (proximal, anterior and ventral aspects) of the sagittal otolith are proposed here as a method to capture shape information for fish classification. Classification performance of single view compared with combined 2D views show improved classification accuracy of the latter, for nine species of Sciaenidae. The effects of shape description methods (shape indices, Procrustes analysis and elliptical Fourier analysis) on classification performance were evaluated. Procrustes analysis and elliptical Fourier analysis perform better than shape indices when single view is considered, but all perform equally well with combined views. A generic content-based image retrieval (CBIR) system that ranks dissimilarity (Procrustes distance) of otolith images was built to search query images without the need for detailed information of side (left or right), aspect (proximal or distal) and direction (positive or negative) of the otolith. Methods for the development of this automated classification system are discussed.
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Xiu J, Reddy S, Chu C. Multiplatform tumor-profiling of 43 malignant Sertoli-Leydig cell tumors of the ovary reveals therapeutic opportunities. Gynecol Oncol 2016. [DOI: 10.1016/j.ygyno.2016.04.299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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66
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Shaikh T, Churilla T, Mantia-Smaldone G, Chu C, Rubin S, Anderson P. The role of adjuvant radiation in lymph node-positive endometrial adenocarcinoma. Gynecol Oncol 2016. [DOI: 10.1016/j.ygyno.2016.04.132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Mostovoy Y, Levy-Sakin M, Lam J, Lam ET, Hastie AR, Marks P, Lee J, Chu C, Lin C, Džakula Ž, Cao H, Schlebusch SA, Giorda K, Schnall-Levin M, Wall JD, Kwok PY. A hybrid approach for de novo human genome sequence assembly and phasing. Nat Methods 2016; 13:587-90. [PMID: 27159086 PMCID: PMC4927370 DOI: 10.1038/nmeth.3865] [Citation(s) in RCA: 151] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 04/08/2016] [Indexed: 12/11/2022]
Abstract
Despite tremendous progress in genome sequencing, the basic goal of producing phased (haplotype-resolved) genome sequence with end-to-end contiguity for each chromosome at reasonable cost and effort is still unrealized. In this study, we describe a new approach to perform de novo genome assembly and experimental phasing by integrating the data from Illumina short-read sequencing, 10X Genomics Linked-Read sequencing, and BioNano Genomics genome mapping to yield a high-quality, phased, de novo assembled human genome.
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69
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Levy-Sakin M, Chu C, Lin C. Single Molecule Analysis of Chromatin Structure. Biophys J 2016. [DOI: 10.1016/j.bpj.2015.11.2174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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70
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Chu C, Noël-Hudson M, Bénard J, Ha-Duong T, Allaoui F, Farinotti R, Bonhomme-Faivre L. Cetuximab directly inhibits P-glycoprotein function in vitro independently of EGFR binding. Eur J Pharm Sci 2015; 76:18-26. [DOI: 10.1016/j.ejps.2015.04.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 04/17/2015] [Accepted: 04/19/2015] [Indexed: 12/17/2022]
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71
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Cory L, Haggerty A, Hwang W, Chu C. Factors influencing acceptability of the HPV vaccine among urban women. Gynecol Oncol 2015. [DOI: 10.1016/j.ygyno.2015.01.168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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72
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Haggerty A, Raggio G, Spitzer J, Boyer J, Sarwer D, Chu C, Allison K. Longitudinal analysis of cancer-associated biomarkers within weight loss intervention for endometrial cancer survivors with obesity. Gynecol Oncol 2015. [DOI: 10.1016/j.ygyno.2015.01.219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Mak ACY, Pullinger CR, Tang LF, Wong JS, Deo RC, Schwarz JM, Gugliucci A, Movsesyan I, Ishida BY, Chu C, Poon A, Kim P, Stock EO, Schaefer EJ, Asztalos BF, Castellano JM, Wyss-Coray T, Duncan JL, Miller BL, Kane JP, Kwok PY, Malloy MJ. Effects of the absence of apolipoprotein e on lipoproteins, neurocognitive function, and retinal function. JAMA Neurol 2015; 71:1228-36. [PMID: 25111166 DOI: 10.1001/jamaneurol.2014.2011] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
IMPORTANCE The identification of a patient with a rare form of severe dysbetalipoproteinemia allowed the study of the consequences of total absence of apolipoprotein E (apoE). OBJECTIVES To discover the molecular basis of this rare disorder and to determine the effects of complete absence of apoE on neurocognitive and visual function and on lipoprotein metabolism. DESIGN, SETTING, AND PARTICIPANTS Whole-exome sequencing was performed on the patient's DNA. He underwent detailed neurological and visual function testing and lipoprotein analysis. Lipoprotein analysis was also performed in the Cardiovascular Research Institute, University of California, San Francisco, on blood samples from the proband's mother, wife, 2 daughters, and normolipidemic control participants. MAIN OUTCOME MEASURES Whole-exome sequencing, lipoprotein analysis, and neurocognitive function. RESULTS The patient was homozygous for an ablative APOE frameshift mutation (c.291del, p.E97fs). No other mutations likely to contribute to the phenotype were discovered, with the possible exception of two, in ABCC2 (p.I670T) and LIPC (p.G137R). Despite complete absence of apoE, he had normal vision, exhibited normal cognitive, neurological, and retinal function, had normal findings on brain magnetic resonance imaging, and had normal cerebrospinal fluid levels of β-amyloid and tau proteins. He had no significant symptoms of cardiovascular disease except a suggestion of myocardial ischemia on treadmill testing and mild atherosclerosis noted on carotid ultrasonography. He had exceptionally high cholesterol content (760 mg/dL; to convert to millimoles per liter, multiply by 0.0259) and a high cholesterol to triglycerides ratio (1.52) in very low-density lipoproteins with elevated levels of small-diameter high-density lipoproteins, including high levels of prebeta-1 high-density lipoprotein. Intermediate-density lipoproteins, low-density lipoproteins, and very low-density lipoproteins contained elevated apoA-I and apoA-IV levels. The patient's apoC-III and apoC-IV levels were decreased in very low-density lipoproteins. Electron microscopy revealed large lamellar particles having electron-opaque cores attached to electron-lucent zones in intermediate-density and low-density lipoproteins. Low-density lipoprotein particle diameters were distributed bimodally. CONCLUSIONS AND RELEVANCE Despite a profound effect on lipoprotein metabolism, detailed neurocognitive and retinal studies failed to demonstrate any defects. This suggests that functions of apoE in the brain and eye are not essential or that redundant mechanisms exist whereby its role can be fulfilled. Targeted knockdown of apoE in the central nervous system might be a therapeutic modality in neurodegenerative disorders.
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Yuan Q, Rubic M, Seah J, Rae C, Wright IMR, Kaltenbach K, Feller JM, Abdel-Latif ME, Chu C, Oei JL. Do maternal opioids reduce neonatal regional brain volumes? A pilot study. J Perinatol 2014; 34:909-13. [PMID: 24945162 DOI: 10.1038/jp.2014.111] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 04/18/2014] [Accepted: 04/21/2014] [Indexed: 01/17/2023]
Abstract
OBJECTIVE A substantial number of children exposed to gestational opioids have neurodevelopmental, behavioral and cognitive problems. Opioids are not neuroteratogens but whether they affect the developing brain in more subtle ways (for example, volume loss) is unclear. We aimed to determine the feasibility of using magnetic resonance imaging (MRI) to assess volumetric changes in healthy opioid-exposed infants. STUDY DESIGN Observational pilot cohort study conducted in two maternity hospitals in New South Wales, Australia. Maternal history and neonatal urine and meconium screens were obtained to confirm drug exposure. Volumetric analysis of MRI scans was performed with the ITK-snap program. RESULT Scans for 16 infants (mean (s.d.) gestational age: 40.9 (1.5) weeks, birth weight: 3022.5 (476.6) g, head circumference (HC): 33.7 (1.5 cm)) were analyzed. Six (37.5%) infants had HC <25th percentile. Fourteen mothers used methadone, four used buprenorphine and 11 used more than one opioid (including heroin, seven). All scans were structurally normal whole brain volumes (357.4 (63.8)) and basal ganglia (14.5 (3.5)) ml were significantly smaller than population means (425.4 (4.8), 17.1 (4.4) ml, respectively) but lateral ventricular volumes (3.5 (1.8) ml) were larger than population values (2.1(1.5)) ml. CONCLUSION Our pilot study suggests that brain volumes of opioid-exposed babies may be smaller than population means and that specific regions, for example, basal ganglia, that are involved in neurotransmission, may be particularly affected. Larger studies including correlation with neurodevelopmental outcomes are warranted to substantiate this finding.
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