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Liu B, Zhu Y, Yang Z, Yan HHN, Leung SY, Shi J. Deep Learning-Based 3D Single-Cell Imaging Analysis Pipeline Enables Quantification of Cell-Cell Interaction Dynamics in the Tumor Microenvironment. Cancer Res 2024; 84:517-526. [PMID: 38085180 DOI: 10.1158/0008-5472.can-23-1100] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 04/29/2023] [Accepted: 12/05/2023] [Indexed: 02/16/2024]
Abstract
The three-dimensional (3D) tumor microenvironment (TME) comprises multiple interacting cell types that critically impact tumor pathology and therapeutic response. Efficient 3D imaging assays and analysis tools could facilitate profiling and quantifying distinctive cell-cell interaction dynamics in the TMEs of a wide spectrum of human cancers. Here, we developed a 3D live-cell imaging assay using confocal microscopy of patient-derived tumor organoids and a software tool, SiQ-3D (single-cell image quantifier for 3D), that optimizes deep learning (DL)-based 3D image segmentation, single-cell phenotype classification, and tracking to automatically acquire multidimensional dynamic data for different interacting cell types in the TME. An organoid model of tumor cells interacting with natural killer cells was used to demonstrate the effectiveness of the 3D imaging assay to reveal immuno-oncology dynamics as well as the accuracy and efficiency of SiQ-3D to extract quantitative data from large 3D image datasets. SiQ-3D is Python-based, publicly available, and customizable to analyze data from both in vitro and in vivo 3D imaging. The DL-based 3D imaging analysis pipeline can be employed to study not only tumor interaction dynamics with diverse cell types in the TME but also various cell-cell interactions involved in other tissue/organ physiology and pathology. SIGNIFICANCE A 3D single-cell imaging pipeline that quantifies cancer cell interaction dynamics with other TME cell types using primary patient-derived samples can elucidate how cell-cell interactions impact tumor behavior and treatment responses.
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Affiliation(s)
- Bodong Liu
- Center for Quantitative Systems Biology, Department of Physics, Hong Kong Baptist University, Hong Kong SAR, P.R. China
| | - Yanting Zhu
- Center for Quantitative Systems Biology, Department of Physics, Hong Kong Baptist University, Hong Kong SAR, P.R. China
- Laboratory for Synthetic Chemistry and Chemical Biology Limited, Hong Kong SAR, P.R. China
| | - Zhenye Yang
- MOE Key Laboratory for Cellular Dynamics, The CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, P.R. China
| | - Helen H N Yan
- Department of Pathology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong SAR, P.R. China
| | - Suet Yi Leung
- Department of Pathology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong SAR, P.R. China
| | - Jue Shi
- Center for Quantitative Systems Biology, Department of Physics, Hong Kong Baptist University, Hong Kong SAR, P.R. China
- Laboratory for Synthetic Chemistry and Chemical Biology Limited, Hong Kong SAR, P.R. China
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2
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Zheng C, Snow BE, Elia AJ, Nechanitzky R, Dominguez-Brauer C, Liu S, Tong Y, Cox MA, Focaccia E, Wakeham AC, Haight J, Tobin C, Hodgson K, Gill KT, Ma W, Berger T, Heikenwälder M, Saunders ME, Fortin J, Leung SY, Mak TW. Tumor-specific cholinergic CD4 + T lymphocytes guide immunosurveillance of hepatocellular carcinoma. Nat Cancer 2023; 4:1437-1454. [PMID: 37640929 PMCID: PMC10597839 DOI: 10.1038/s43018-023-00624-w] [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] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 07/26/2023] [Indexed: 08/31/2023]
Abstract
Cholinergic nerves are involved in tumor progression and dissemination. In contrast to other visceral tissues, cholinergic innervation in the hepatic parenchyma is poorly detected. It remains unclear whether there is any form of cholinergic regulation of liver cancer. Here, we show that cholinergic T cells curtail the development of liver cancer by supporting antitumor immune responses. In a mouse multihit model of hepatocellular carcinoma (HCC), we observed activation of the adaptive immune response and induction of two populations of CD4+ T cells expressing choline acetyltransferase (ChAT), including regulatory T cells and dysfunctional PD-1+ T cells. Tumor antigens drove the clonal expansion of these cholinergic T cells in HCC. Genetic ablation of Chat in T cells led to an increased prevalence of preneoplastic cells and exacerbated liver cancer due to compromised antitumor immunity. Mechanistically, the cholinergic activity intrinsic in T cells constrained Ca2+-NFAT signaling induced by T cell antigen receptor engagement. Without this cholinergic modulation, hyperactivated CD25+ T regulatory cells and dysregulated PD-1+ T cells impaired HCC immunosurveillance. Our results unveil a previously unappreciated role for cholinergic T cells in liver cancer immunobiology.
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Affiliation(s)
- Chunxing Zheng
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Centre for Oncology and Immunology, Hong Kong Science Park, Hong Kong SAR, China
| | - Bryan E Snow
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Andrew J Elia
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Robert Nechanitzky
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | | | - Shaofeng Liu
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Yin Tong
- Centre for Oncology and Immunology, Hong Kong Science Park, Hong Kong SAR, China
- Department of Pathology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong SAR, China
| | - Maureen A Cox
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Enrico Focaccia
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andrew C Wakeham
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Jillian Haight
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Chantal Tobin
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Kelsey Hodgson
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Kyle T Gill
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Wei Ma
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Thorsten Berger
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Mathias Heikenwälder
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
- The M3 Research Center, Medical Faculty Tübingen, Tübingen, Germany
| | - Mary E Saunders
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Jerome Fortin
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Suet Yi Leung
- Centre for Oncology and Immunology, Hong Kong Science Park, Hong Kong SAR, China
- Department of Pathology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong SAR, China
| | - Tak W Mak
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.
- Centre for Oncology and Immunology, Hong Kong Science Park, Hong Kong SAR, China.
- Tumor Immunotherapy Program, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.
- Department of Pathology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong SAR, China.
- Departments of Immunology and Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
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Abstract
Organoids derived from adult stem cells (ASCs) and pluripotent stem cells (PSCs) are important preclinical models for studying cancer and developing therapies. Here, we review primary tissue-derived and PSC-derived cancer organoid models and detail how they have the potential to inform personalized medical approaches in different organ contexts and contribute to the understanding of early carcinogenic steps, cancer genomes, and biology. We also compare the differences between ASC- and PSC-based cancer organoid systems, discuss their limitations, and highlight recent improvements to organoid culture approaches that have helped to make them an even better representation of human tumors.
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Affiliation(s)
- Helen H N Yan
- Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong SAR, China; Centre for Oncology and Immunology, Hong Kong Science Park, Hong Kong SAR, China.
| | - April S Chan
- Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong SAR, China; Centre for Oncology and Immunology, Hong Kong Science Park, Hong Kong SAR, China
| | - Frank Pui-Ling Lai
- Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong SAR, China; Centre for Oncology and Immunology, Hong Kong Science Park, Hong Kong SAR, China
| | - Suet Yi Leung
- Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong SAR, China; Centre for Oncology and Immunology, Hong Kong Science Park, Hong Kong SAR, China; Jockey Club Centre for Clinical Innovation and Discovery, LKS Faculty of Medicine, the University of Hong Kong, Pokfulam, Hong Kong SAR, China; Centre for PanorOmic Sciences, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
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Wong TL, Loh JJ, Lu S, Yan HHN, Siu HC, Xi R, Chan D, Kam MJF, Zhou L, Tong M, Copland JA, Chen L, Yun JP, Leung SY, Ma S. ADAR1-mediated RNA editing of SCD1 drives drug resistance and self-renewal in gastric cancer. Nat Commun 2023; 14:2861. [PMID: 37208334 PMCID: PMC10199093 DOI: 10.1038/s41467-023-38581-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [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: 06/20/2022] [Accepted: 05/05/2023] [Indexed: 05/21/2023] Open
Abstract
Targetable drivers governing 5-fluorouracil and cisplatin (5FU + CDDP) resistance remain elusive due to the paucity of physiologically and therapeutically relevant models. Here, we establish 5FU + CDDP resistant intestinal subtype GC patient-derived organoid lines. JAK/STAT signaling and its downstream, adenosine deaminases acting on RNA 1 (ADAR1), are shown to be concomitantly upregulated in the resistant lines. ADAR1 confers chemoresistance and self-renewal in an RNA editing-dependent manner. WES coupled with RNA-seq identify enrichment of hyper-edited lipid metabolism genes in the resistant lines. Mechanistically, ADAR1-mediated A-to-I editing on 3'UTR of stearoyl-CoA desaturase (SCD1) increases binding of KH domain-containing, RNA-binding, signal transduction-associated 1 (KHDRBS1), thereby augmenting SCD1 mRNA stability. Consequently, SCD1 facilitates lipid droplet formation to alleviate chemotherapy-induced ER stress and enhances self-renewal through increasing β-catenin expression. Pharmacological inhibition of SCD1 abrogates chemoresistance and tumor-initiating cell frequency. Clinically, high proteomic level of ADAR1 and SCD1, or high SCD1 editing/ADAR1 mRNA signature score predicts a worse prognosis. Together, we unveil a potential target to circumvent chemoresistance.
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Affiliation(s)
- Tin-Lok Wong
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- The University of Hong Kong - Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Jia-Jian Loh
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Shixun Lu
- Department of Pathology, Sun Yat-Sen University Cancer Centre, Guangzhou, Guangdong, China
| | - Helen H N Yan
- Department of Pathology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong, China
| | - Hoi Cheong Siu
- Department of Pathology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong, China
| | - Ren Xi
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Dessy Chan
- Department of Pathology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong, China
| | - Max J F Kam
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Lei Zhou
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- The University of Hong Kong - Shenzhen Hospital, Shenzhen, Guangdong, China
| | - Man Tong
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
- The University of Hong Kong - Shenzhen Hospital, Shenzhen, Guangdong, China
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - John A Copland
- Department of Cancer Biology, Mayo Clinic Florida, Jacksonville, FL, USA
| | - Leilei Chen
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Jing-Ping Yun
- Department of Pathology, Sun Yat-Sen University Cancer Centre, Guangzhou, Guangdong, China
| | - Suet Yi Leung
- Department of Pathology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong, China
- The Jockey Club Centre for Clinical Innovation and Discovery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Stephanie Ma
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.
- The University of Hong Kong - Shenzhen Hospital, Shenzhen, Guangdong, China.
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5
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Virwani PD, Qian G, Hsu MSS, Pijarnvanit TKKTS, Cheung CNM, Chow YH, Tang LK, Tse YH, Xian JW, Lam SSW, Lee CPI, Lo CCW, Liu RKC, Ho TL, Chow BY, Leung KS, Tsang HW, Lo EKK, Tung KTS, Chung SK, Yuen MF, Leung SY, Ip P, Hung IFN, Louie JCY, El-Nezami H, Ho JWK, Lau KK. Sex Differences in Association Between Gut Microbiome and Essential Hypertension Based on Ambulatory Blood Pressure Monitoring. Hypertension 2023; 80:1331-1342. [PMID: 37073724 DOI: 10.1161/hypertensionaha.122.20752] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023]
Abstract
BACKGROUND Sex differences in the pathogenesis of hypertension exist. While gut microbiota (GM) has been associated with hypertension, it is unclear whether there are sex-linked differences in the association between GM and hypertension. METHODS We conducted a cross-sectional study to investigate the sex differences in associations between GM characterized by shotgun sequencing, GM-derived short-chain fatty acids, and 24-hour ambulatory blood pressure in 241 Hong Kong Chinese (113 men and 128 women; mean age, 54±6 years). RESULTS The hypertensive group was associated with GM alterations; however, significant differences in β-diversity and GM composition in hypertensive versus normotensive groups were only observed in women and not in men under various statistical models adjusting for the following covariates: age, sex, body mass index, sodium intake estimated by spot urine analysis, blood glucose, triglycerides, low- and high-density lipoprotein cholesterol, smoking, menopause, and fatty liver status. Specifically, Ruminococcus gnavus, Clostridium bolteae, and Bacteroides ovatus were significantly more abundant in the hypertensive women, whereas Dorea formicigenerans was more abundant in the normotensive female group. No bacterial species were found to be significantly associated with hypertension in men. Furthermore, total plasma short-chain fatty acids and propionic acid were independent predictors of systolic and diastolic blood pressure in women but not men. CONCLUSONS GM dysregulation was strongly associated with 24-hour ambulatory blood pressure in women but not men, which may be mediated through propionic acid. Our work suggests that sex differences may be an important consideration while assessing the role of GM in the development and treatment of hypertension.
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Affiliation(s)
- Preeti Dinesh Virwani
- Department of Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China. (P.D.V., M.S.S.H., T.K.K.T.S.P., C.N.-M.C., Y.H.C., L.K.T., Y.-H.T., J.-W.X., S.S.-W.L., C.P.I.L., C.C.W.L., R.K.C.L., T.L.H., B.Y.C., M.-F.Y., I.F.-N.H., K.K.L.)
| | - Gordon Qian
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China. (G.Q., J.W.K.H.)
- Laboratory of Data Discovery for Health Limited (D4H), Hong Kong Science Park, Hong Kong Special Administrative Region, China (G.Q., J.W.K.H.)
| | - Matthew S S Hsu
- Department of Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China. (P.D.V., M.S.S.H., T.K.K.T.S.P., C.N.-M.C., Y.H.C., L.K.T., Y.-H.T., J.-W.X., S.S.-W.L., C.P.I.L., C.C.W.L., R.K.C.L., T.L.H., B.Y.C., M.-F.Y., I.F.-N.H., K.K.L.)
| | - Tommy K K T S Pijarnvanit
- Department of Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China. (P.D.V., M.S.S.H., T.K.K.T.S.P., C.N.-M.C., Y.H.C., L.K.T., Y.-H.T., J.-W.X., S.S.-W.L., C.P.I.L., C.C.W.L., R.K.C.L., T.L.H., B.Y.C., M.-F.Y., I.F.-N.H., K.K.L.)
| | - Carman Nga-Man Cheung
- Department of Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China. (P.D.V., M.S.S.H., T.K.K.T.S.P., C.N.-M.C., Y.H.C., L.K.T., Y.-H.T., J.-W.X., S.S.-W.L., C.P.I.L., C.C.W.L., R.K.C.L., T.L.H., B.Y.C., M.-F.Y., I.F.-N.H., K.K.L.)
| | - Yick Hin Chow
- Department of Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China. (P.D.V., M.S.S.H., T.K.K.T.S.P., C.N.-M.C., Y.H.C., L.K.T., Y.-H.T., J.-W.X., S.S.-W.L., C.P.I.L., C.C.W.L., R.K.C.L., T.L.H., B.Y.C., M.-F.Y., I.F.-N.H., K.K.L.)
| | - Lok Kan Tang
- Department of Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China. (P.D.V., M.S.S.H., T.K.K.T.S.P., C.N.-M.C., Y.H.C., L.K.T., Y.-H.T., J.-W.X., S.S.-W.L., C.P.I.L., C.C.W.L., R.K.C.L., T.L.H., B.Y.C., M.-F.Y., I.F.-N.H., K.K.L.)
| | - Yiu-Hei Tse
- Department of Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China. (P.D.V., M.S.S.H., T.K.K.T.S.P., C.N.-M.C., Y.H.C., L.K.T., Y.-H.T., J.-W.X., S.S.-W.L., C.P.I.L., C.C.W.L., R.K.C.L., T.L.H., B.Y.C., M.-F.Y., I.F.-N.H., K.K.L.)
| | - Jia-Wen Xian
- Department of Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China. (P.D.V., M.S.S.H., T.K.K.T.S.P., C.N.-M.C., Y.H.C., L.K.T., Y.-H.T., J.-W.X., S.S.-W.L., C.P.I.L., C.C.W.L., R.K.C.L., T.L.H., B.Y.C., M.-F.Y., I.F.-N.H., K.K.L.)
| | - Shirley Sau-Wing Lam
- Department of Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China. (P.D.V., M.S.S.H., T.K.K.T.S.P., C.N.-M.C., Y.H.C., L.K.T., Y.-H.T., J.-W.X., S.S.-W.L., C.P.I.L., C.C.W.L., R.K.C.L., T.L.H., B.Y.C., M.-F.Y., I.F.-N.H., K.K.L.)
| | - Crystal P I Lee
- Department of Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China. (P.D.V., M.S.S.H., T.K.K.T.S.P., C.N.-M.C., Y.H.C., L.K.T., Y.-H.T., J.-W.X., S.S.-W.L., C.P.I.L., C.C.W.L., R.K.C.L., T.L.H., B.Y.C., M.-F.Y., I.F.-N.H., K.K.L.)
| | - Chelsea C W Lo
- Department of Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China. (P.D.V., M.S.S.H., T.K.K.T.S.P., C.N.-M.C., Y.H.C., L.K.T., Y.-H.T., J.-W.X., S.S.-W.L., C.P.I.L., C.C.W.L., R.K.C.L., T.L.H., B.Y.C., M.-F.Y., I.F.-N.H., K.K.L.)
| | - Roxanna K C Liu
- Department of Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China. (P.D.V., M.S.S.H., T.K.K.T.S.P., C.N.-M.C., Y.H.C., L.K.T., Y.-H.T., J.-W.X., S.S.-W.L., C.P.I.L., C.C.W.L., R.K.C.L., T.L.H., B.Y.C., M.-F.Y., I.F.-N.H., K.K.L.)
| | - Tsi Lok Ho
- Department of Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China. (P.D.V., M.S.S.H., T.K.K.T.S.P., C.N.-M.C., Y.H.C., L.K.T., Y.-H.T., J.-W.X., S.S.-W.L., C.P.I.L., C.C.W.L., R.K.C.L., T.L.H., B.Y.C., M.-F.Y., I.F.-N.H., K.K.L.)
| | - Bak Yue Chow
- Department of Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China. (P.D.V., M.S.S.H., T.K.K.T.S.P., C.N.-M.C., Y.H.C., L.K.T., Y.-H.T., J.-W.X., S.S.-W.L., C.P.I.L., C.C.W.L., R.K.C.L., T.L.H., B.Y.C., M.-F.Y., I.F.-N.H., K.K.L.)
| | - Kin Sum Leung
- School of Biological Sciences, Faculty of Science, The University of Hong Kong, Hong Kong Special Administrative Region, China. (K.S.L., E.K.K.L., J.C.Y.L., H.E.-N.)
| | - Hing Wai Tsang
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China. (H.W.T., K.T.S.T., P.I.)
| | - Emily K K Lo
- School of Biological Sciences, Faculty of Science, The University of Hong Kong, Hong Kong Special Administrative Region, China. (K.S.L., E.K.K.L., J.C.Y.L., H.E.-N.)
| | - Keith T S Tung
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China. (H.W.T., K.T.S.T., P.I.)
| | - Sookja Kim Chung
- State Key Laboratory of Pharmaceutical Biotechnology, The University of Hong Kong, Hong Kong Special Administrative Region, China. (S.K.C.)
- Faculty of Medicine, Macau University of Science and Technology, Macau Special Administrative Region, China. (S.K.C.)
- Dr Neher's Biophysics Laboratory for Innovative Drug Discovery, Macau University of Science and Technology, Macau Special Administrative Region, China. (S.K.C.)
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau Special Administrative Region, China. (S.K.C.)
| | - Man-Fung Yuen
- Department of Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China. (P.D.V., M.S.S.H., T.K.K.T.S.P., C.N.-M.C., Y.H.C., L.K.T., Y.-H.T., J.-W.X., S.S.-W.L., C.P.I.L., C.C.W.L., R.K.C.L., T.L.H., B.Y.C., M.-F.Y., I.F.-N.H., K.K.L.)
| | - Suet Yi Leung
- Department of Pathology, School of Clinical Medicine, Queen Mary Hospital, The University of Hong Kong, Hong Kong Special Administrative Region, China. (S.Y.L.)
- The Jockey Club Centre for Clinical Innovation and Discovery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China. (S.Y.L., J.W.K.H.)
- Centre for PanorOmic Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China. (S.Y.L., J.W.K.H.)
| | - Patrick Ip
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China. (H.W.T., K.T.S.T., P.I.)
| | - Ivan Fan-Ngai Hung
- Department of Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China. (P.D.V., M.S.S.H., T.K.K.T.S.P., C.N.-M.C., Y.H.C., L.K.T., Y.-H.T., J.-W.X., S.S.-W.L., C.P.I.L., C.C.W.L., R.K.C.L., T.L.H., B.Y.C., M.-F.Y., I.F.-N.H., K.K.L.)
| | - Jimmy Chun Yu Louie
- School of Biological Sciences, Faculty of Science, The University of Hong Kong, Hong Kong Special Administrative Region, China. (K.S.L., E.K.K.L., J.C.Y.L., H.E.-N.)
| | - Hani El-Nezami
- School of Biological Sciences, Faculty of Science, The University of Hong Kong, Hong Kong Special Administrative Region, China. (K.S.L., E.K.K.L., J.C.Y.L., H.E.-N.)
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio (H.E.-N.)
| | - Joshua Wing Kei Ho
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China. (G.Q., J.W.K.H.)
- The Jockey Club Centre for Clinical Innovation and Discovery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China. (S.Y.L., J.W.K.H.)
- Centre for PanorOmic Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China. (S.Y.L., J.W.K.H.)
- Laboratory of Data Discovery for Health Limited (D4H), Hong Kong Science Park, Hong Kong Special Administrative Region, China (G.Q., J.W.K.H.)
| | - Kui Kai Lau
- Department of Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China. (P.D.V., M.S.S.H., T.K.K.T.S.P., C.N.-M.C., Y.H.C., L.K.T., Y.-H.T., J.-W.X., S.S.-W.L., C.P.I.L., C.C.W.L., R.K.C.L., T.L.H., B.Y.C., M.-F.Y., I.F.-N.H., K.K.L.)
- State Key Laboratory of Brain and Cognitive Sciences, The University of Hong Kong, China (K.K.L.)
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6
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Wang L, Yao H, Morgan DC, Lau KS, Leung SY, Ho JWK, Leung WK. Altered human gut virome in patients undergoing antibiotics therapy for Helicobacter pylori. Nat Commun 2023; 14:2196. [PMID: 37069161 PMCID: PMC10110541 DOI: 10.1038/s41467-023-37975-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 04/04/2023] [Indexed: 04/19/2023] Open
Abstract
Transient gut microbiota alterations have been reported after antibiotic therapy for Helicobacter pylori. However, alteration in the gut virome after H. pylori eradication remains uncertain. Here, we apply metagenomic sequencing to fecal samples of 44 H. pylori-infected patients at baseline, 6-week (N = 44), and 6-month (N = 33) after treatment. Following H. pylori eradication, we discover contraction of the gut virome diversity, separation of virome community with increased community difference, and shifting towards a higher proportion of core virus. While the gut microbiota is altered at 6-week and restored at 6-month, the virome community shows contraction till 6-month after the treatment with enhanced phage-bacteria interactions at 6-week. Multiple courses of antibiotic treatments further lead to lower virus community diversity when compared with treatment naive patients. Our results demonstrate that H. pylori eradication therapies not only result in transient alteration in gut microbiota but also significantly alter the previously less known gut virome community.
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Affiliation(s)
- Lingling Wang
- Department of Medicine, School of Clinical Medicine, The University of Hong Kong, Hong Kong, China
| | - Haobin Yao
- School of Biomedical Science, The University of Hong Kong, Hong Kong, China
- Laboratory of Data Discovery for Health, Hong Kong Science Park, Hong Kong, China
| | - Daniel C Morgan
- School of Biomedical Science, The University of Hong Kong, Hong Kong, China
- Laboratory of Data Discovery for Health, Hong Kong Science Park, Hong Kong, China
| | - Kam Shing Lau
- Department of Medicine, School of Clinical Medicine, The University of Hong Kong, Hong Kong, China
| | - Suet Yi Leung
- Centre for PanorOmic Sciences (CPOS), The University of Hong Kong, Pokfulam, Hong Kong, China
- Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong, China
- The Jockey Club Centre for Clinical Innovation and Discovery, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Joshua W K Ho
- School of Biomedical Science, The University of Hong Kong, Hong Kong, China
- Laboratory of Data Discovery for Health, Hong Kong Science Park, Hong Kong, China
- Centre for PanorOmic Sciences (CPOS), The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Wai K Leung
- Department of Medicine, School of Clinical Medicine, The University of Hong Kong, Hong Kong, China.
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7
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Loh JJ, Wong TL, Lu S, Yan HHN, Siu HC, Xi R, Chan D, Kam MJF, Zhou L, Tong M, Copland JA, Chen L, Yun J, Leung SY, Ma S. Abstract 1755: ADAR1-mediated RNA editing of SCD1 links lipid metabolism to gastric cancer drug resistance and self-renewal. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-1755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
Targetable drivers governing to 5-fluorouracil and cisplatin (5FU+CDDP) resistance remain elusive due to the paucity of physiologically and therapeutically relevant models. Accordingly, we established 5FU+CDDP resistant intestinal subtype GC patient-derived organoid lines. JAK/STAT signaling and its downstream, adenosine deaminases acting on RNA 1 (ADAR1), are shown to be concomitantly upregulated in the resistant lines. ADAR1 was demonstrated to confer chemoresistance and self-renewal in an RNA editing-dependent manner. WES-seq coupled with RNA-seq identified enrichment of hyperedited lipid metabolism genes in the resistant lines. Mechanistically, ADAR1-mediated A-to-I editing on 3’UTR of stearoyl-CoA desaturase (SCD1) increased binding of KH domain-containing, RNA-binding, signal transduction-associated 1 (KHDRBS1), thereby augmenting SCD1 mRNA stability. Consequently, SCD1 facilitates lipid droplet formation to alleviate chemotherapy-induced ER stress and enhances self-renewal through increasing β-catenin expression. Pharmacological inhibition of SCD1 abrogated chemoresistance and tumor-initiating cell frequency. Clinically, high proteomic level of ADAR1 and SCD1, or high SCD1 editing/ADAR1 mRNA signature score predicts a worse prognosis. Together, we unveiled a novel actionable target to circumvent chemoresistance.
Citation Format: Jia Jian Loh, Tin Lok Wong, Shixun Lu, Helen HN Yan, Hoi Cheong Siu, Ren Xi, Dessy Chan, Max JF Kam, Lei Zhou, Man Tong, John A. Copland, Leilei Chen, Jingping Yun, Suet Yi Leung, Stephanie Ma. ADAR1-mediated RNA editing of SCD1 links lipid metabolism to gastric cancer drug resistance and self-renewal [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1755.
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Affiliation(s)
- Jia Jian Loh
- 1School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Tin Lok Wong
- 1School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Shixun Lu
- 2Sun Yat-Sen University Cancer Centre, Guangdong, China
| | - Helen HN Yan
- 3School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Pok Fu Lam, Hong Kong
| | - Hoi Cheong Siu
- 3School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Pok Fu Lam, Hong Kong
| | - Ren Xi
- 4Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Dessy Chan
- 3School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Pok Fu Lam, Hong Kong
| | - Max JF Kam
- 1School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Lei Zhou
- 1School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Man Tong
- 1School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | | | - Leilei Chen
- 4Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Jingping Yun
- 2Sun Yat-Sen University Cancer Centre, Guangdong, China
| | - Suet Yi Leung
- 3School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Pok Fu Lam, Hong Kong
| | - Stephanie Ma
- 1School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
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8
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Tong Y, Cheng PSW, Or CS, Yue SSK, Siu HC, Ho SL, Law SYK, Tsui WY, Chan D, Ma S, Lee SP, Chan ASY, Chan AS, Yun SW, Hui HS, Yuen ST, Leung SY, Yan HHN. Escape from cell-cell and cell-matrix adhesion dependence underscores disease progression in gastric cancer organoid models. Gut 2023; 72:242-255. [PMID: 35705367 DOI: 10.1136/gutjnl-2022-327121] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 05/27/2022] [Indexed: 01/27/2023]
Abstract
OBJECTIVE Cell-cell (CC) and cell-matrix (CM) adhesions are essential for epithelial cell survival, yet dissociation-induced apoptosis is frequently circumvented in malignant cells. DESIGN We explored CC and CM dependence in 58 gastric cancer (GC) organoids by withdrawing either ROCK inhibitor, matrix or both to evaluate their tumorigenic potential in terms of apoptosis resistance, correlation with oncogenic driver mutations and clinical behaviour. We performed mechanistic studies to determine the role of diffuse-type GC drivers: ARHGAP fusions, RHOA and CDH1, in modulating CC (CCi) or CM (CMi) adhesion independence. RESULTS 97% of the tumour organoids were CMi, 66% were CCi and 52% were resistant to double withdrawal (CCi/CMi), while normal organoids were neither CMi nor CCi. Clinically, the CCi/CMi phenotype was associated with an infiltrative tumour edge and advanced tumour stage. Moreover, the CCi/CMi transcriptome signature was associated with poor patient survival when applied to three public GC datasets. CCi/CMi and CCi phenotypes were enriched in diffuse-type GC organoids, especially in those with oncogenic driver perturbation of RHO signalling via RHOA mutation or ARHGAP fusions. Inducible knockout of ARHGAP fusions in CCi/CMi tumour organoids led to resensitisation to CC/CM dissociation-induced apoptosis, upregulation of focal adhesion and tight junction genes, partial reversion to a more normal cystic phenotype and inhibited xenograft formation. Normal gastric organoids engineered with CDH1 or RHOA mutations became CMi or CCi, respectively. CONCLUSIONS The CCi/CMi phenotype has a critical role in malignant transformation and tumour progression, offering new mechanistic information on RHO-ROCK pathway inhibition that contributes to GC pathogenicity.
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Affiliation(s)
- Yin Tong
- Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong SAR, China.,Centre for Oncology and Immunology, Hong Kong Science Park, Hong Kong SAR, China
| | - Priscilla S W Cheng
- Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong SAR, China
| | - Chung Sze Or
- Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong SAR, China
| | - Sarah S K Yue
- Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong SAR, China
| | - Hoi Cheong Siu
- Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong SAR, China
| | - Siu Lun Ho
- Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong SAR, China
| | - Simon Y K Law
- Department of Surgery, School of Clinical Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong SAR, China
| | - Wai Yin Tsui
- Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong SAR, China
| | - Dessy Chan
- Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong SAR, China
| | - Stephanie Ma
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Siu Po Lee
- Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong SAR, China
| | - Annie S Y Chan
- Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong SAR, China
| | - April S Chan
- Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong SAR, China
| | - Shui Wa Yun
- Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong SAR, China
| | - Ho Sang Hui
- Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong SAR, China
| | - Siu Tsan Yuen
- Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong SAR, China.,Department of Pathology, St. Paul's Hospital, No. 2, Eastern Hosptial Road, Causeway Bay, Hong Kong SAR, China
| | - Suet Yi Leung
- Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong SAR, China .,Centre for Oncology and Immunology, Hong Kong Science Park, Hong Kong SAR, China.,The Jockey Club Centre for Clinical Innovation and Discovery, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Helen H N Yan
- Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong SAR, China .,Centre for Oncology and Immunology, Hong Kong Science Park, Hong Kong SAR, China
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9
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Fan Y, S Chan A, Zhu J, Yi Leung S, Fan X. A Bayesian model for identifying cancer subtypes from paired methylation profiles. Brief Bioinform 2022; 24:6961790. [PMID: 36575828 PMCID: PMC9851340 DOI: 10.1093/bib/bbac568] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 10/19/2022] [Accepted: 11/22/2022] [Indexed: 12/29/2022] Open
Abstract
Aberrant DNA methylation is the most common molecular lesion that is crucial for the occurrence and development of cancer, but has thus far been underappreciated as a clinical tool for cancer classification, diagnosis or as a guide for therapeutic decisions. Partly, this has been due to a lack of proven algorithms that can use methylation data to stratify patients into clinically relevant risk groups and subtypes that are of prognostic importance. Here, we proposed a novel Bayesian model to capture the methylation signatures of different subtypes from paired normal and tumor methylation array data. Application of our model to synthetic and empirical data showed high clustering accuracy, and was able to identify the possible epigenetic cause of a cancer subtype.
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Affiliation(s)
- Yetian Fan
- School of Mathematics and Statistics, Liaoning University, Shenyang, 110036, China,Department of Statistics, The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong SAR, China
| | - April S Chan
- Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Jun Zhu
- Sema4, Stamford, CT, 06902, USA,Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Suet Yi Leung
- Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Xiaodan Fan
- Corresponding author: Xiaodan Fan, Department of Statistics, The Chinese University of Hong Kong, Sha Tin, New Territories, Hong Kong SAR, China. E-mail:
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10
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Coorens TH, Collord G, Jung H, Wang Y, Zumalave S, Leongamornlert D, Moore L, Mahbubani K, Saeb-Parsy K, Leung SY, Stratton MR. Abstract 226: Recurrent trisomies, variable selection and precancerous evolution in the normal gastric epithelium. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Gastric cancer is the third leading cause of cancer-related mortality globally and is often associated with infectious agents such as the bacterium Helicobacter pylori. However, the background mutational landscape in normal gastric epithelium and the first genomic steps towards the formation of gastric cancer remain poorly understood. Here, we use whole-genome sequencing of microdissected gastric glands (n=271) from 30 patients, 18 of whom had gastric cancer. We show that gastric glands are clonal structures and accrue approximately 27 single base substitutions per year. While the mutational signatures in most normal glands reflect age-related mutagenesis, gastric glands sampled close to a tumor showed exposure to a mutagenic process enriched in tumors (COSMIC reference mutational signature SBS17). Phylogenetic analysis shows that acquisition of SBS17 substitutions is closely linked to overt malignant transformation. We also observe widespread trisomies of specific chromosomes, which are recurrently and independently acquired in many gastric glands of the same patient. Mutations in genes encoding epigenetic modifiers and chromatin remodelers showed evidence of positive selection and were highly enriched in some patients. This was confirmed by targeted sequencing of cancer genes in a further 1008 gastric glands. Strikingly, glands that exhibit driver mutations, a recurrent trisomy or elevated mutation loads only overlap minimally, suggesting a highly variable and patient-specific mutation and selection landscape in the normal gastric epithelium. Taken together, these results give novel insights into the preclinical evolution of gastric malignancies.
Citation Format: Tim H. Coorens, Grace Collord, Hyungchul Jung, Yichen Wang, Sonia Zumalave, Daniel Leongamornlert, Luiza Moore, Krishnaa Mahbubani, Kourosh Saeb-Parsy, Suet Yi Leung, Michael R. Stratton. Recurrent trisomies, variable selection and precancerous evolution in the normal gastric epithelium [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 226.
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Affiliation(s)
| | | | | | - Yichen Wang
- 1Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Sonia Zumalave
- 2University of Santiago de Compostela, Santiago de Compostela, Spain
| | | | - Luiza Moore
- 1Wellcome Sanger Institute, Hinxton, United Kingdom
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11
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Lee BCH, Robinson PS, Coorens THH, Yan HHN, Olafsson S, Lee-Six H, Sanders MA, Siu HC, Hewinson J, Yue SSK, Tsui WY, Chan ASY, Chan AKW, Ho SL, Campbell PJ, Martincorena I, Buczacki SJA, Yuen ST, Leung SY, Stratton MR. Mutational landscape of normal epithelial cells in Lynch Syndrome patients. Nat Commun 2022; 13:2710. [PMID: 35581206 PMCID: PMC9114395 DOI: 10.1038/s41467-022-29920-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 04/07/2022] [Indexed: 01/01/2023] Open
Abstract
Lynch Syndrome (LS) is an autosomal dominant disease conferring a high risk of colorectal cancer due to germline heterozygous mutations in a DNA mismatch repair (MMR) gene. Although cancers in LS patients show elevated somatic mutation burdens, information on mutation rates in normal tissues and understanding of the trajectory from normal to cancer cell is limited. Here we whole genome sequence 152 crypts from normal and neoplastic epithelial tissues from 10 LS patients. In normal tissues the repertoire of mutational processes and mutation rates is similar to that found in wild type individuals. A morphologically normal colonic crypt with an increased mutation burden and MMR deficiency-associated mutational signatures is identified, which may represent a very early stage of LS pathogenesis. Phylogenetic trees of tumour crypts indicate that the most recent ancestor cell of each tumour is already MMR deficient and has experienced multiple cycles of clonal evolution. This study demonstrates the genomic stability of epithelial cells with heterozygous germline MMR gene mutations and highlights important differences in the pathogenesis of LS from other colorectal cancer predisposition syndromes.
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Affiliation(s)
- Bernard C H Lee
- Hereditary Gastrointestinal Cancer Genetic Diagnosis Laboratory, Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Philip S Robinson
- Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
- Department of Paediatrics, University of Cambridge, Cambridge, CB2 0QQ, UK
| | | | - Helen H N Yan
- Hereditary Gastrointestinal Cancer Genetic Diagnosis Laboratory, Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | | | | | | | - Hoi Cheong Siu
- Hereditary Gastrointestinal Cancer Genetic Diagnosis Laboratory, Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | | | - Sarah S K Yue
- Hereditary Gastrointestinal Cancer Genetic Diagnosis Laboratory, Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Wai Yin Tsui
- Hereditary Gastrointestinal Cancer Genetic Diagnosis Laboratory, Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Annie S Y Chan
- Hereditary Gastrointestinal Cancer Genetic Diagnosis Laboratory, Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Anthony K W Chan
- Hereditary Gastrointestinal Cancer Genetic Diagnosis Laboratory, Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Siu Lun Ho
- Hereditary Gastrointestinal Cancer Genetic Diagnosis Laboratory, Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | | | | | - Simon J A Buczacki
- Nuffield Department of Surgical Sciences, University of Oxford, Headington, Oxford, OX3 7DQ, UK
| | - Siu Tsan Yuen
- Hereditary Gastrointestinal Cancer Genetic Diagnosis Laboratory, Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Suet Yi Leung
- Hereditary Gastrointestinal Cancer Genetic Diagnosis Laboratory, Department of Pathology, School of Clinical Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong.
- Centre for PanorOmic Sciences, The University of Hong Kong, Pokfulam, Hong Kong.
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12
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Yu KHO, Fang X, Yao H, Ng B, Leung TK, Wang LL, Lin CH, Chan ASW, Leung WK, Leung SY, Ho JWK. Evaluation of Experimental Protocols for Shotgun Whole-Genome Metagenomic Discovery of Antibiotic Resistance Genes. IEEE/ACM Trans Comput Biol Bioinform 2022; 19:1313-1321. [PMID: 32750872 DOI: 10.1109/tcbb.2020.3004063] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Shotgun metagenomics has enabled the discovery of antibiotic resistance genes (ARGs). Although there have been numerous studies benchmarking the bioinformatics methods for shotgun metagenomic data analysis, there has not yet been a study that systematically evaluates the performance of different experimental protocols on metagenomic species profiling and ARG detection. In this study, we generated 35 whole genome shotgun metagenomic sequencing data sets for five samples (three human stool and two microbial standard) using seven experimental protocols (KAPA or Flex kits at 50ng, 10ng, or 5ng input amounts; XT kit at 1ng input amount). Using this comprehensive resource, we evaluated the seven protocols in terms of robust detection of ARGs and microbial abundance estimation at various sequencing depths. We found that the data generated by the seven protocols are largely similar. The inter-protocol variability is significantly smaller than the variability between samples or sequencing depths. We found that a sequencing depth of more than 30M is suitable for human stool samples. A higher input amount (50ng) is generally favorable for the KAPA and Flex kits. This systematic benchmarking study sheds light on the impact of sequencing depth, experimental protocol, and DNA input amount on ARG detection in human stool samples.
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13
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Wang L, Yao H, Tong T, Lau K, Leung SY, Ho JWK, Leung WK. Dynamic changes in antibiotic resistance genes and gut microbiota after Helicobacter pylori eradication therapies. Helicobacter 2022; 27:e12871. [PMID: 34969161 DOI: 10.1111/hel.12871] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Revised: 12/08/2021] [Accepted: 12/14/2021] [Indexed: 12/19/2022]
Abstract
BACKGROUND Short-term antibiotics exposure is associated with alterations in microbiota and antibiotic resistance genes (ARGs) in the human gut. While antibiotics are critical in the successful eradication of Helicobacter pylori, the short-term and long-term impacts on the composition and quantity of antibiotics resistance genes after H. pylori eradication are unclear. This study used whole-genome shotgun metagenomic of stool samples to characterize the gut microbiota and ARGs, before and after H. pylori eradication therapy. RESULTS Forty-four H. pylori-infected patients were recruited, including 21 treatment naïve patients who received clarithromycin-based triple therapy (CLA group) and 23 patients who failed previous therapies, in which 10 received levofloxacin-based quadruple therapy (LEVO group) and 13 received other combinations (OTHER group). Stool samples were collected at baseline (before current treatment), 6 week and 6 month after eradication therapy. At baseline, there was only a slight difference among the three groups on ARGs and gut microbiota. After eradication therapy, there was a transient but significant increase in gut ARGs 6 week post-therapy, among which the LEVO group had the most significant ARGs alteration compared to other two groups. For treatment naïve patients, those with higher ErmF abundance were prone to fail CLA eradication and gain more ARGs after treatment. For gut microbiota, the bacteria richness decreased at 6 week and there was a significant difference in microbiota community among the three groups at 6 week. CONCLUSIONS Our findings demonstrated the dynamic alterations in gut microbiota and ARGs induced by different eradication therapies, which could influence the choices of antibiotics in eradication therapy.
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Affiliation(s)
- Lingling Wang
- Department of Medicine, The University of Hong Kong, Hong Kong, China
| | - Haobin Yao
- School of Biomedical Science, The University of Hong Kong, Hong Kong, China.,Laboratory of Data Discovery for Health, Hong Kong Science Park, Hong Kong, China
| | - Teresa Tong
- Department of Medicine, The University of Hong Kong, Hong Kong, China
| | - KamShing Lau
- Department of Medicine, The University of Hong Kong, Hong Kong, China
| | - Suet Yi Leung
- Centre for PanorOmic Sciences (CPOS), The University of Hong Kong, Hong Kong, China.,Department of Pathology, Queen Mary Hospital, The University of Hong Kong, Hong Kong, China.,The Jockey Club Centre for Clinical Innovation and Discovery, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Joshua W K Ho
- School of Biomedical Science, The University of Hong Kong, Hong Kong, China.,Laboratory of Data Discovery for Health, Hong Kong Science Park, Hong Kong, China.,Centre for PanorOmic Sciences (CPOS), The University of Hong Kong, Hong Kong, China
| | - Wai K Leung
- Department of Medicine, The University of Hong Kong, Hong Kong, China
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14
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Chong KC, Chan E, Lee TC, Kwok KL, Lau SYF, Wang P, Lam HCY, Goggins W, Mohammad K, Leung SY, Chan PKS. 91Is rainfall associated with paediatric acute gastroenteritis in an affluent setting? A 21-Year Retrospective Investigation. Int J Epidemiol 2021. [DOI: 10.1093/ije/dyab168.131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Background
Although many literatures demonstrated heavy rainfall was associated with an increased risk of acute gastroenteritis via contaminated food and water, we hypothesized there is no association between rainfall and paediatric acute gastroenteritis in a setting with high-standard food and water hygiene.
Methods
Intestinal infection-related hospital admissions data during 1998-2018 for children under 5 years of age in Hong Kong were collected. Meteorological data were collected from the Hong Kong Observatory. A distributed lag nonlinear model was employed to examine the associations between meteorological factors and the risk of hospital admissions due to acute gastroenteritis.
Results
Rainfall did not exhibit a statistically significant association with the risk of paediatric admission due to acute gastroenteritis but low temperature, low and high relative humidity did. The risk was 6.3% higher (95% confidence interval: 0.3% to 12.6%) when temperature was at 15.1oC (i.e. the 5th percentile). The adjusted relative risk was statistically significantly higher when relative humidity was ≤73.0% or ≥ 84.0%.
Conclusions
Text: We suggest rainfall playing a minor role in disease transmission via contaminated food and water in affluent societies like Hong Kong. Instead, we speculate low temperature and humidity extremes have greater impact on transmission through increased stability and infectivity of enteric viruses.
Key messages
Weather plays a minor role in food and water contamination in affluent societies.
Low temperature and humidity extremes might improve survival of enteric viruses.
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Affiliation(s)
- Ka Chun Chong
- School of Public Health and Primary Care, The Chinese University Of Hong Kong, Hong Kong
- Clinical Trials and Biostatistics Laboratory, Shenzhen Research Institute, Shenzhen, China
| | - Emily Chan
- School of Public Health and Primary Care, The Chinese University Of Hong Kong, Hong Kong
| | - TC Lee
- Hong Kong Observatory, Hong Kong
| | - KL Kwok
- Department of Paediatrics, Kwong Wah Hospital, Hong Kong
| | - SYF Lau
- School of Public Health and Primary Care, The Chinese University Of Hong Kong, Hong Kong
| | - P Wang
- School of Public Health and Primary Care, The Chinese University Of Hong Kong, Hong Kong
| | - HCY Lam
- National Heart & Lung Institute, Imperial College London, London, United Kingdom
| | - W Goggins
- School of Public Health and Primary Care, The Chinese University Of Hong Kong, Hong Kong
| | - K Mohammad
- School of Public Health and Primary Care, The Chinese University Of Hong Kong, Hong Kong
| | - SY Leung
- Department of Paediatrics, Kwong Wah Hospital, Hong Kong
| | - PKS Chan
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong
- Stanley Ho Centre for Emerging Infectious Diseases, The Chinese University of Hong Kong, Hong Kong
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15
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Yan HHN, Chan AS, Leung SY. Oncogenic mutations drive intestinal cancer initiation through paracrine remodeling. Cancer Cell 2021; 39:913-915. [PMID: 34256908 DOI: 10.1016/j.ccell.2021.06.013] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Three articles in Nature show that intestinal stem cells with cancer-promoting mutations could shape the surrounding normal tissue in their favor to promote clonal fixation and field expansion, raising the possibility of developing therapeutic strategies that maintain or enhance the health of normal cells to out-compete the mutant cells.
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Affiliation(s)
- Helen H N Yan
- Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong.
| | - April S Chan
- Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Suet Yi Leung
- Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong; Centre for PanorOmic Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong.
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16
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Yan HHN, Siu HC, Ho SL, Yue SSK, Gao Y, Tsui WY, Chan D, Chan AS, Wong JWH, Man AHY, Lee BCH, Chan ASY, Chan AKW, Hui HS, Cheung AKL, Law WL, Lo OSH, Yuen ST, Clevers H, Leung SY. Organoid cultures of early-onset colorectal cancers reveal distinct and rare genetic profiles. Gut 2020; 69:2165-2179. [PMID: 32217638 DOI: 10.1136/gutjnl-2019-320019] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 02/25/2020] [Accepted: 02/27/2020] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Sporadic early-onset colorectal cancer (EOCRC) has bad prognosis, yet is poorly represented by cell line models. We examine the key mutational and transcriptomic alterations in an organoid biobank enriched in EOCRCs. DESIGN We established paired cancer (n=32) and normal organoids (n=18) from 20 patients enriched in microsatellite-stable EOCRC. Exome and transcriptome analysis was performed. RESULTS We observed a striking diversity of molecular phenotypes, including PTPRK-RSPO3 fusions. Transcriptionally, RSPO fusion organoids resembled normal colon organoids and were distinct from APC mutant organoids, with high BMP2 and low PTK7 expression. Single cell transcriptome analysis confirmed the similarity between RSPO fusion organoids and normal organoids, with a propensity for maturation on Wnt withdrawal, whereas the APC mutant organoids were locked in progenitor stages. CRISPR/Cas9 engineered mutation of APC in normal human colon organoids led to upregulation of PTK7 protein and suppression of BMP2, but less so with an engineered RNF43 mutation. The frequent co-occurrence of RSPO fusions with SMAD4 or BMPR1A mutation was confirmed in TCGA database searches. RNF43 mutation was found in organoid from a leukaemia survivor with a novel mutational signature; and organoids with POLE proofreading mutation displayed ultramutation. The cancer organoid genomes were stable over long culture periods, while normal human colon organoids tended to be subject to clonal dominance over time. CONCLUSIONS These organoid models enriched in EOCRCs with linked genomic data fill a gap in existing CRC models and reveal distinct genetic profiles and novel pathway cooperativity.
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Affiliation(s)
- Helen H N Yan
- Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Hoi Cheong Siu
- Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Siu Lun Ho
- Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Sarah S K Yue
- Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Yang Gao
- Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Wai Yin Tsui
- Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Dessy Chan
- Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - April S Chan
- Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Jason W H Wong
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong.,Centre for PanorOmic Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Alice H Y Man
- Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Bernard C H Lee
- Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Annie S Y Chan
- Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Anthony K W Chan
- Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Ho Sang Hui
- Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Arthur K L Cheung
- Centre for PanorOmic Sciences, The University of Hong Kong, Pokfulam, Hong Kong.,The Jockey Club Centre for Clinical Innovation and Discovery, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Wai Lun Law
- Department of Surgery, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Oswens S H Lo
- Department of Surgery, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Siu Tsan Yuen
- Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong.,Department of Pathology, St. Paul's Hospital, No.2, Eastern Hospital Road, Causeway Bay, Hong Kong
| | - Hans Clevers
- Hubrecht Institute for Developmental Biology and Stem Cell Research, University Medical Centre Utrecht, Utrecht, The Netherlands.,Princess Maxima Center for Pediatric Oncology, 3584 CT, Utrecht, The Netherlands
| | - Suet Yi Leung
- Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong .,Centre for PanorOmic Sciences, The University of Hong Kong, Pokfulam, Hong Kong.,The Jockey Club Centre for Clinical Innovation and Discovery, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
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17
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Zhou P, Chan BKC, Wan YK, Yuen CTL, Choi GCG, Li X, Tong CSW, Zhong SSW, Sun J, Bao Y, Mak SYL, Chow MZY, Khaw JV, Leung SY, Zheng Z, Cheung LWT, Tan K, Wong KH, Chan HYE, Wong ASL. A Three-Way Combinatorial CRISPR Screen for Analyzing Interactions among Druggable Targets. Cell Rep 2020; 32:108020. [PMID: 32783942 DOI: 10.1016/j.celrep.2020.108020] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 06/04/2020] [Accepted: 07/20/2020] [Indexed: 12/26/2022] Open
Abstract
We present a CRISPR-based multi-gene knockout screening system and toolkits for extensible assembly of barcoded high-order combinatorial guide RNA libraries en masse. We apply this system for systematically identifying not only pairwise but also three-way synergistic therapeutic target combinations and successfully validate double- and triple-combination regimens for suppression of cancer cell growth and protection against Parkinson's disease-associated toxicity. This system overcomes the practical challenges of experimenting on a large number of high-order genetic and drug combinations and can be applied to uncover the rare synergistic interactions between druggable targets.
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Affiliation(s)
- Peng Zhou
- Laboratory of Combinatorial Genetics and Synthetic Biology, School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Becky K C Chan
- Laboratory of Combinatorial Genetics and Synthetic Biology, School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Yuk Kei Wan
- Laboratory of Combinatorial Genetics and Synthetic Biology, School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Chaya T L Yuen
- Laboratory of Combinatorial Genetics and Synthetic Biology, School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Gigi C G Choi
- Laboratory of Combinatorial Genetics and Synthetic Biology, School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Xinran Li
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Cindy S W Tong
- Laboratory of Combinatorial Genetics and Synthetic Biology, School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Sophia S W Zhong
- Laboratory of Combinatorial Genetics and Synthetic Biology, School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Jieran Sun
- Laboratory of Combinatorial Genetics and Synthetic Biology, School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Yufan Bao
- Ming Wai Lau Centre for Reparative Medicine, Karolinska Institutet, Hong Kong SAR, China; Department of Biomedical Sciences, City University of Hong Kong, Hong Kong SAR, China
| | - Silvia Y L Mak
- Ming Wai Lau Centre for Reparative Medicine, Karolinska Institutet, Hong Kong SAR, China
| | - Maggie Z Y Chow
- Ming Wai Lau Centre for Reparative Medicine, Karolinska Institutet, Hong Kong SAR, China
| | - Jien Vei Khaw
- Laboratory of Combinatorial Genetics and Synthetic Biology, School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Suet Yi Leung
- Department of Pathology, The University of Hong Kong, Pokfulam, Hong Kong SAR, China; Centre for PanorOmic Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China; The Jockey Club Centre for Clinical Innovation and Discovery, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Zongli Zheng
- Ming Wai Lau Centre for Reparative Medicine, Karolinska Institutet, Hong Kong SAR, China; Department of Biomedical Sciences, City University of Hong Kong, Hong Kong SAR, China; Biotechnology and Health Centre, City University of Hong Kong Shenzhen Research Institute, Shenzhen, China
| | - Lydia W T Cheung
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Kaeling Tan
- Faculty of Health Sciences, University of Macau, Macau SAR, China; Genomics, Bioinformatics and Single Cell Analysis Core, Faculty of Health Sciences, University of Macau, Avenida da Universidade, Taipa, Macau SAR, China
| | - Koon Ho Wong
- Faculty of Health Sciences, University of Macau, Macau SAR, China; Institute of Translational Medicine, University of Macau, Avenida da Universidade, Taipa, Macau SAR, China
| | - H Y Edwin Chan
- Laboratory of Drosophila Research, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China; Gerald Choa Neuroscience Centre, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Alan S L Wong
- Laboratory of Combinatorial Genetics and Synthetic Biology, School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong SAR, China; Department of Electrical and Electronic Engineering, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
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18
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Pian C, Mao S, Zhang G, Du J, Li F, Leung SY, Fan X. Discovering Cancer-Related miRNAs from miRNA-Target Interactions by Support Vector Machines. Mol Ther Nucleic Acids 2020; 19:1423-1433. [PMID: 32160711 PMCID: PMC7056629 DOI: 10.1016/j.omtn.2020.01.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 12/20/2019] [Accepted: 01/14/2020] [Indexed: 11/08/2022]
Abstract
MicroRNAs (miRNAs) have been shown to be closely related to cancer progression. Traditional methods for discovering cancer-related miRNAs mostly require significant marginal differential expression, but some cancer-related miRNAs may be non-differentially or only weakly differentially expressed. Such miRNAs are called dark matters miRNAs (DM-miRNAs) and are targeted through the Pearson correlation change on miRNA-target interactions (MTIs), but the efficiency of their method heavily relies on restrictive assumptions. In this paper, a novel method was developed to discover DM-miRNAs using support vector machine (SVM) based on not only the miRNA expression data but also the expression of its regulating target. The application of the new method in breast and kidney cancer datasets found, respectively, 9 and 24 potential DM-miRNAs that cannot be detected by previous methods. Eight and 15 of the newly discovered miRNAs have been found to be associated with breast and kidney cancers, respectively, in existing literature. These results indicate that our new method is more effective in discovering cancer-related miRNAs.
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Affiliation(s)
- Cong Pian
- Department of Statistics, The Chinese University of Hong Kong, Hong Kong SAR, China; Department of Mathematics, College of Science, Nanjing Agricultural University, Nanjing, China
| | - Shanjun Mao
- Department of Statistics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Guangle Zhang
- Binjiang College, Nanjing University of Information Science and Technology, Jiangsu 214105, China
| | - Jin Du
- Department of Statistics, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Fei Li
- Ministry of Agriculture Key Lab of Agricultural Entomology, Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Suet Yi Leung
- Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong SAR, China
| | - Xiaodan Fan
- Department of Statistics, The Chinese University of Hong Kong, Hong Kong SAR, China.
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19
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Chan LH, Zhou L, Ng KY, Wong TL, Lee TK, Sharma R, Loong JH, Ching YP, Yuan YF, Xie D, Lo CM, Man K, Artegiani B, Clevers H, Yan HH, Leung SY, Richard S, Guan XY, Huen MSY, Ma S. PRMT6 Regulates RAS/RAF Binding and MEK/ERK-Mediated Cancer Stemness Activities in Hepatocellular Carcinoma through CRAF Methylation. Cell Rep 2019; 25:690-701.e8. [PMID: 30332648 DOI: 10.1016/j.celrep.2018.09.053] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 07/26/2018] [Accepted: 09/16/2018] [Indexed: 11/18/2022] Open
Abstract
Arginine methylation is a post-translational modification that plays pivotal roles in signal transduction and gene transcription during cell fate determination. We found protein methyltransferase 6 (PRMT6) to be frequently downregulated in hepatocellular carcinoma (HCC) and its expression to negatively correlate with aggressive cancer features in HCC patients. Silencing of PRMT6 promoted the tumor-initiating, metastasis, and therapy resistance potential of HCC cell lines and patient-derived organoids. Consistently, loss of PRMT6 expression aggravated liver tumorigenesis in a chemical-induced HCC PRMT6 knockout (PRMT6-/-) mouse model. Integrated transcriptome and protein-protein interaction studies revealed an enrichment of genes implicated in RAS signaling and showed that PRMT6 interacted with CRAF on arginine 100, which decreased its RAS binding potential and altered its downstream MEK/ERK signaling. Our work describes a critical repressive function for PRMT6 in maintenance of HCC cells by regulating RAS binding and MEK/ERK signaling via methylation of CRAF on arginine 100.
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MESH Headings
- Animals
- Apoptosis
- Carcinoma, Hepatocellular/genetics
- Carcinoma, Hepatocellular/metabolism
- Carcinoma, Hepatocellular/pathology
- Cell Proliferation
- DNA Methylation
- Gene Expression Regulation, Neoplastic
- Humans
- Liver Neoplasms/genetics
- Liver Neoplasms/metabolism
- Liver Neoplasms/pathology
- MAP Kinase Kinase 1/genetics
- MAP Kinase Kinase 1/metabolism
- MAP Kinase Signaling System
- Male
- Mice
- Mice, Inbred BALB C
- Mice, Inbred NOD
- Mice, Knockout
- Mice, Nude
- Mice, SCID
- Neoplastic Stem Cells/metabolism
- Neoplastic Stem Cells/pathology
- Nuclear Proteins/genetics
- Nuclear Proteins/metabolism
- Protein-Arginine N-Methyltransferases/genetics
- Protein-Arginine N-Methyltransferases/metabolism
- Protein-Arginine N-Methyltransferases/physiology
- TNF Receptor-Associated Factor 3/genetics
- Tumor Cells, Cultured
- Xenograft Model Antitumor Assays
- raf Kinases/genetics
- raf Kinases/metabolism
- ras Proteins/genetics
- ras Proteins/metabolism
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Affiliation(s)
- Lok Hei Chan
- School of Biomedical Sciences, University of Hong Kong, Pokfulam, Hong Kong, China
| | - Lei Zhou
- School of Biomedical Sciences, University of Hong Kong, Pokfulam, Hong Kong, China
| | - Kai Yu Ng
- School of Biomedical Sciences, University of Hong Kong, Pokfulam, Hong Kong, China
| | - Tin Lok Wong
- School of Biomedical Sciences, University of Hong Kong, Pokfulam, Hong Kong, China
| | - Terence K Lee
- Department of Applied Biology & Chemical Technology, Hong Kong Polytechnic University, Hong Kong, China
| | - Rakesh Sharma
- Proteomics & Metabolomics Core Facility, Li Ka Shing Faculty of Medicine, University of Hong Kong, Pokfulam, Hong Kong, China
| | - Jane H Loong
- School of Biomedical Sciences, University of Hong Kong, Pokfulam, Hong Kong, China
| | - Yick Pang Ching
- School of Biomedical Sciences, University of Hong Kong, Pokfulam, Hong Kong, China; State Key Laboratory for Liver Research, University of Hong Kong, Pokfulam, Hong Kong, China
| | - Yun-Fei Yuan
- State Key Laboratory of Oncology in Southern China, Sun Yat-Sen University Cancer Centre, Guangzhou, China
| | - Dan Xie
- State Key Laboratory of Oncology in Southern China, Sun Yat-Sen University Cancer Centre, Guangzhou, China
| | - Chung Mau Lo
- State Key Laboratory for Liver Research, University of Hong Kong, Pokfulam, Hong Kong, China; Department of Surgery, University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong, China
| | - Kwan Man
- State Key Laboratory for Liver Research, University of Hong Kong, Pokfulam, Hong Kong, China; Department of Surgery, University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong, China
| | - Benedetta Artegiani
- Hubrecht Institute for Developmental Biology and Stem Cell Research, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Hans Clevers
- Hubrecht Institute for Developmental Biology and Stem Cell Research, University Medical Centre Utrecht, Utrecht, the Netherlands
| | - Helen H Yan
- Department of Pathology, University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong, China
| | - Suet Yi Leung
- Department of Pathology, University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong, China
| | - Stéphane Richard
- Lady Davis Institute, Jewish General Hospital, and Departments of Oncology and Medicine, McGill University, Montreal, QC, Canada
| | - Xin-Yuan Guan
- State Key Laboratory for Liver Research, University of Hong Kong, Pokfulam, Hong Kong, China; Department of Clinical Oncology, University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong, China
| | - Michael S Y Huen
- School of Biomedical Sciences, University of Hong Kong, Pokfulam, Hong Kong, China
| | - Stephanie Ma
- School of Biomedical Sciences, University of Hong Kong, Pokfulam, Hong Kong, China; State Key Laboratory for Liver Research, University of Hong Kong, Pokfulam, Hong Kong, China.
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20
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Tong Y, Sun J, Wong CF, Kang Q, Ru B, Wong CN, Chan AS, Leung SY, Zhang J. MICMIC: identification of DNA methylation of distal regulatory regions with causal effects on tumorigenesis. Genome Biol 2018; 19:73. [PMID: 29871649 PMCID: PMC5989391 DOI: 10.1186/s13059-018-1442-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 05/03/2018] [Indexed: 12/11/2022] Open
Abstract
Aberrant promoter methylation is a common mechanism for tumor suppressor inactivation in cancer. We develop a set of tools to identify genome-wide DNA methylation in distal regions with causal effect on tumorigenesis called MICMIC. Many predictions are directly validated by dCas9-based epigenetic editing to support the accuracy and efficiency of our tool. Oncogenic and lineage-specific transcription factors are shown to aberrantly shape the methylation landscape by modifying tumor-subtype core regulatory circuitry. Notably, the gene regulatory networks orchestrated by enhancer methylation across different cancer types are seen to converge on a common architecture. MICMIC is available on https://github.com/ZhangJlab/MICMIC .
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Affiliation(s)
- Yin Tong
- School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong
| | - Jianlong Sun
- School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong
| | - Chi Fat Wong
- School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong
| | - Qingzheng Kang
- School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong
| | - Beibei Ru
- School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong
| | - Ching Ngar Wong
- School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong
| | - April Sheila Chan
- Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Suet Yi Leung
- Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Jiangwen Zhang
- School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong.
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21
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Kwok TC, Ma CW, Leung SY, Lee J, So WY, Hui E. Chronic disease self-management and cognitive training programme to improve diabetic control in older outpatients with memory complaints: a randomised trial. Hong Kong Med J 2018; 24 Suppl 2:16-20. [PMID: 29938652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023] Open
Affiliation(s)
- T Cy Kwok
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong
| | - C Wr Ma
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong
| | - S Y Leung
- Department of Family Medicine, Prince of Wales Hospital
| | - J Lee
- Medical and Geriatric Unit, Shatin Hospital
| | - W Y So
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong
| | - E Hui
- Medical and Geriatric Unit, Shatin Hospital
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22
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Zhou J, Li C, Zhao G, Chu H, Wang D, Yan HHN, Poon VKM, Wen L, Wong BHY, Zhao X, Chiu MC, Yang D, Wang Y, Au-Yeung RKH, Chan IHY, Sun S, Chan JFW, To KKW, Memish ZA, Corman VM, Drosten C, Hung IFN, Zhou Y, Leung SY, Yuen KY. Human intestinal tract serves as an alternative infection route for Middle East respiratory syndrome coronavirus. Sci Adv 2017; 3:eaao4966. [PMID: 29152574 PMCID: PMC5687858 DOI: 10.1126/sciadv.aao4966] [Citation(s) in RCA: 273] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 10/20/2017] [Indexed: 05/08/2023]
Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) has caused human respiratory infections with a high case fatality rate since 2012. However, the mode of virus transmission is not well understood. The findings of epidemiological and virological studies prompted us to hypothesize that the human gastrointestinal tract could serve as an alternative route to acquire MERS-CoV infection. We demonstrated that human primary intestinal epithelial cells, small intestine explants, and intestinal organoids were highly susceptible to MERS-CoV and can sustain robust viral replication. We also identified the evidence of enteric MERS-CoV infection in the stool specimen of a clinical patient. MERS-CoV was considerably resistant to fed-state gastrointestinal fluids but less tolerant to highly acidic fasted-state gastric fluid. In polarized Caco-2 cells cultured in Transwell inserts, apical MERS-CoV inoculation was more effective in establishing infection than basolateral inoculation. Notably, direct intragastric inoculation of MERS-CoV caused a lethal infection in human DPP4 transgenic mice. Histological examination revealed MERS-CoV enteric infection in all inoculated mice, as shown by the presence of virus-positive cells, progressive inflammation, and epithelial degeneration in small intestines, which were exaggerated in the mice pretreated with the proton pump inhibitor pantoprazole. With the progression of the enteric infection, inflammation, virus-positive cells, and live viruses emerged in the lung tissues, indicating the development of sequential respiratory infection. Taken together, these data suggest that the human intestinal tract may serve as an alternative infection route for MERS-CoV.
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Affiliation(s)
- Jie Zhou
- State Key Laboratory of Emerging Infectious Diseases, University of Hong Kong, Hong Kong, China
- Department of Microbiology, University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong, China
- Research Centre of Infection and Immunology, University of Hong Kong, Hong Kong, China
| | - Cun Li
- Department of Microbiology, University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong, China
| | - Guangyu Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Hin Chu
- State Key Laboratory of Emerging Infectious Diseases, University of Hong Kong, Hong Kong, China
- Department of Microbiology, University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong, China
- Research Centre of Infection and Immunology, University of Hong Kong, Hong Kong, China
| | - Dong Wang
- Department of Microbiology, University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong, China
| | - Helen Hoi-Ning Yan
- Department of Pathology, University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong, China
| | - Vincent Kwok-Man Poon
- Department of Microbiology, University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong, China
| | - Lei Wen
- Department of Microbiology, University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong, China
| | - Bosco Ho-Yin Wong
- Department of Microbiology, University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong, China
| | - Xiaoyu Zhao
- Department of Microbiology, University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong, China
| | - Man Chun Chiu
- Department of Microbiology, University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong, China
| | - Dong Yang
- Department of Microbiology, University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong, China
| | - Yixin Wang
- Department of Microbiology, University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong, China
| | - Rex K. H. Au-Yeung
- Department of Pathology, University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong, China
| | | | - Shihui Sun
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jasper Fuk-Woo Chan
- State Key Laboratory of Emerging Infectious Diseases, University of Hong Kong, Hong Kong, China
- Department of Microbiology, University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong, China
- Research Centre of Infection and Immunology, University of Hong Kong, Hong Kong, China
- Carol Yu Centre for Infection, University of Hong Kong, Hong Kong, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, University of Hong Kong, Hong Kong, China
| | - Kelvin Kai-Wang To
- State Key Laboratory of Emerging Infectious Diseases, University of Hong Kong, Hong Kong, China
- Department of Microbiology, University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong, China
- Research Centre of Infection and Immunology, University of Hong Kong, Hong Kong, China
- Carol Yu Centre for Infection, University of Hong Kong, Hong Kong, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, University of Hong Kong, Hong Kong, China
| | - Ziad A. Memish
- Ministry of Health and College of Medicine, Alfaisal University, Riyadh, Kingdom of Saudi Arabia
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Victor M. Corman
- Institute of Virology, Charité–Universitätsmedizin Berlin, Berlin, Germany
- German Centre for Infection Research (DZIF), Berlin, Germany
| | - Christian Drosten
- Institute of Virology, Charité–Universitätsmedizin Berlin, Berlin, Germany
- German Centre for Infection Research (DZIF), Berlin, Germany
| | - Ivan Fan-Ngai Hung
- Department of Medicine, University of Hong Kong, Queen Mary Hospital, Hong Kong, China
| | - Yusen Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Suet Yi Leung
- Department of Pathology, University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong, China
| | - Kwok-Yung Yuen
- State Key Laboratory of Emerging Infectious Diseases, University of Hong Kong, Hong Kong, China
- Department of Microbiology, University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong, China
- Research Centre of Infection and Immunology, University of Hong Kong, Hong Kong, China
- Carol Yu Centre for Infection, University of Hong Kong, Hong Kong, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, University of Hong Kong, Hong Kong, China
- Corresponding author.
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23
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Zhou J, Li C, Zhao G, Chu H, Wang D, Yan HHN, Poon VKM, Wen L, Wong BHY, Zhao X, Chiu MC, Yang D, Wang Y, Au-Yeung RKH, Chan IHY, Sun S, Chan JFW, To KKW, Memish ZA, Corman VM, Drosten C, Hung IFN, Zhou Y, Leung SY, Yuen KY. Human intestinal tract serves as an alternative infection route for Middle East respiratory syndrome coronavirus. Sci Adv 2017; 3:eaao4966. [PMID: 29152574 DOI: 10.1126/sciadv.aao49660] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 10/20/2017] [Indexed: 05/26/2023]
Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) has caused human respiratory infections with a high case fatality rate since 2012. However, the mode of virus transmission is not well understood. The findings of epidemiological and virological studies prompted us to hypothesize that the human gastrointestinal tract could serve as an alternative route to acquire MERS-CoV infection. We demonstrated that human primary intestinal epithelial cells, small intestine explants, and intestinal organoids were highly susceptible to MERS-CoV and can sustain robust viral replication. We also identified the evidence of enteric MERS-CoV infection in the stool specimen of a clinical patient. MERS-CoV was considerably resistant to fed-state gastrointestinal fluids but less tolerant to highly acidic fasted-state gastric fluid. In polarized Caco-2 cells cultured in Transwell inserts, apical MERS-CoV inoculation was more effective in establishing infection than basolateral inoculation. Notably, direct intragastric inoculation of MERS-CoV caused a lethal infection in human DPP4 transgenic mice. Histological examination revealed MERS-CoV enteric infection in all inoculated mice, as shown by the presence of virus-positive cells, progressive inflammation, and epithelial degeneration in small intestines, which were exaggerated in the mice pretreated with the proton pump inhibitor pantoprazole. With the progression of the enteric infection, inflammation, virus-positive cells, and live viruses emerged in the lung tissues, indicating the development of sequential respiratory infection. Taken together, these data suggest that the human intestinal tract may serve as an alternative infection route for MERS-CoV.
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Affiliation(s)
- Jie Zhou
- State Key Laboratory of Emerging Infectious Diseases, University of Hong Kong, Hong Kong, China
- Department of Microbiology, University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong, China
- Research Centre of Infection and Immunology, University of Hong Kong, Hong Kong, China
| | - Cun Li
- Department of Microbiology, University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong, China
| | - Guangyu Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Hin Chu
- State Key Laboratory of Emerging Infectious Diseases, University of Hong Kong, Hong Kong, China
- Department of Microbiology, University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong, China
- Research Centre of Infection and Immunology, University of Hong Kong, Hong Kong, China
| | - Dong Wang
- Department of Microbiology, University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong, China
| | - Helen Hoi-Ning Yan
- Department of Pathology, University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong, China
| | - Vincent Kwok-Man Poon
- Department of Microbiology, University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong, China
| | - Lei Wen
- Department of Microbiology, University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong, China
| | - Bosco Ho-Yin Wong
- Department of Microbiology, University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong, China
| | - Xiaoyu Zhao
- Department of Microbiology, University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong, China
| | - Man Chun Chiu
- Department of Microbiology, University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong, China
| | - Dong Yang
- Department of Microbiology, University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong, China
| | - Yixin Wang
- Department of Microbiology, University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong, China
| | - Rex K H Au-Yeung
- Department of Pathology, University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong, China
| | | | - Shihui Sun
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jasper Fuk-Woo Chan
- State Key Laboratory of Emerging Infectious Diseases, University of Hong Kong, Hong Kong, China
- Department of Microbiology, University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong, China
- Research Centre of Infection and Immunology, University of Hong Kong, Hong Kong, China
- Carol Yu Centre for Infection, University of Hong Kong, Hong Kong, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, University of Hong Kong, Hong Kong, China
| | - Kelvin Kai-Wang To
- State Key Laboratory of Emerging Infectious Diseases, University of Hong Kong, Hong Kong, China
- Department of Microbiology, University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong, China
- Research Centre of Infection and Immunology, University of Hong Kong, Hong Kong, China
- Carol Yu Centre for Infection, University of Hong Kong, Hong Kong, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, University of Hong Kong, Hong Kong, China
| | - Ziad A Memish
- Ministry of Health and College of Medicine, Alfaisal University, Riyadh, Kingdom of Saudi Arabia
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Victor M Corman
- Institute of Virology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- German Centre for Infection Research (DZIF), Berlin, Germany
| | - Christian Drosten
- Institute of Virology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- German Centre for Infection Research (DZIF), Berlin, Germany
| | - Ivan Fan-Ngai Hung
- Department of Medicine, University of Hong Kong, Queen Mary Hospital, Hong Kong, China
| | - Yusen Zhou
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Suet Yi Leung
- Department of Pathology, University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong, China
| | - Kwok-Yung Yuen
- State Key Laboratory of Emerging Infectious Diseases, University of Hong Kong, Hong Kong, China
- Department of Microbiology, University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong, China
- Research Centre of Infection and Immunology, University of Hong Kong, Hong Kong, China
- Carol Yu Centre for Infection, University of Hong Kong, Hong Kong, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, University of Hong Kong, Hong Kong, China
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Yan HHN, Lai JCW, Ho SL, Leung WK, Law WL, Lee JFY, Chan AKW, Tsui WY, Chan ASY, Lee BCH, Yue SSK, Man AHY, Clevers H, Yuen ST, Leung SY. RNF43 germline and somatic mutation in serrated neoplasia pathway and its association with BRAF mutation. Gut 2017; 66:1645-1656. [PMID: 27329244 DOI: 10.1136/gutjnl-2016-311849] [Citation(s) in RCA: 135] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Revised: 05/10/2016] [Accepted: 05/24/2016] [Indexed: 12/08/2022]
Abstract
OBJECTIVE Serrated polyps (hyperplastic polyps, sessile or traditional serrated adenomas), which can arise in a sporadic or polyposis setting, predispose to colorectal cancer (CRC), especially those with microsatellite instability (MSI) due to MLH1 promoter methylation (MLH1me+). We investigate genetic alterations in the serrated polyposis pathway. DESIGN We used a combination of exome sequencing and target gene Sanger sequencing to study serrated polyposis families, sporadic serrated polyps and CRCs, with validation by analysis of The Cancer Genome Atlas (TCGA) cohort, followed by organoid-based functional studies. RESULTS In one out of four serrated polyposis families, we identified a germline RNF43 mutation that displayed autosomal dominant cosegregation with the serrated polyposis phenotype, along with second-hit inactivation through loss of heterozygosity or somatic mutations in all serrated polyps (16), adenomas (5) and cancer (1) examined, as well as coincidental BRAF mutation in 62.5% of the serrated polyps. Concurrently, somatic RNF43 mutations were identified in 34% of sporadic sessile/traditional serrated adenomas, but 0% of hyperplastic polyps (p=0.013). Lastly, in MSI CRCs, we found significantly more frequent RNF43 mutations in the MLH1me+ (85%) versus MLH1me- (33.3%) group (p<0.001). These findings were validated in the TCGA MSI CRCs (p=0.005), which further delineated a significant differential involvement of three Wnt pathway genes between these two groups (RNF43 in MLH1me+; APC and CTNNB1 in MLH1me-); and identified significant co-occurrence of BRAF and RNF43 mutations in the MSI (p<0.001), microsatellite stable (MSS) (p=0.002) and MLH1me+ MSI CRCs (p=0.042). Functionally, organoid culture of serrated adenoma or mouse colon with CRISPR-induced RNF43 mutations had reduced dependency on R-spondin1. CONCLUSIONS These results illustrate the importance of RNF43, along with BRAF mutation in the serrated neoplasia pathway (both the sporadic and familial forms), inform genetic diagnosis protocol and raise therapeutic opportunities through Wnt inhibition in different stages of evolution of serrated polyps.
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Affiliation(s)
- Helen H N Yan
- Hereditary Gastrointestinal Cancer Genetic Diagnosis Laboratory, Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Jeffrey C W Lai
- Hereditary Gastrointestinal Cancer Genetic Diagnosis Laboratory, Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Siu Lun Ho
- Hereditary Gastrointestinal Cancer Genetic Diagnosis Laboratory, Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Wai Keung Leung
- Department of Medicine, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Wai Lun Law
- Department of Surgery, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Janet F Y Lee
- Department of Surgery, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Anthony K W Chan
- Hereditary Gastrointestinal Cancer Genetic Diagnosis Laboratory, Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Wai Yin Tsui
- Hereditary Gastrointestinal Cancer Genetic Diagnosis Laboratory, Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Annie S Y Chan
- Hereditary Gastrointestinal Cancer Genetic Diagnosis Laboratory, Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Bernard C H Lee
- Hereditary Gastrointestinal Cancer Genetic Diagnosis Laboratory, Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Sarah S K Yue
- Hereditary Gastrointestinal Cancer Genetic Diagnosis Laboratory, Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Alice H Y Man
- Hereditary Gastrointestinal Cancer Genetic Diagnosis Laboratory, Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Hans Clevers
- Hubrecht Institute for Developmental Biology and Stem Cell Research, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Siu Tsan Yuen
- Hereditary Gastrointestinal Cancer Genetic Diagnosis Laboratory, Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Suet Yi Leung
- Hereditary Gastrointestinal Cancer Genetic Diagnosis Laboratory, Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
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25
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Chan LH, Zhou L, Ng KY, Wong TL, Chai S, Lee TK, Guan XY, Ching YP, Lo CM, Man K, Artegiani B, Clevers H, Yan HH, Leung SY, Richard S, Huen MSY, Ma S. Abstract LB-139: PRMT6-dependent CRAF/ERK signaling regulates cancer stem cell plasticity in liver cancer. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-lb-139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Hepatocellular carcinoma (HCC), the major type of liver cancer, remains one of the most prevalent and deadliest cancer types in the world. Contemporary challenge in treating HCC has been the common therapy resistance and recurrence after therapy, all of which have been reported to be associated with stem-like behavior of cancer cells. Our group has previously identified a functional liver cancer stem cell (CSC) subset marked by the CD133 cell surface phenotype. Utilizing a PCR array encompassing diverse human chromatin modifiers, protein arginine methyltransferase 6 (PRMT6) was found to be differentially down-regulated in CD133+ liver CSCs of human HCC cells as well as CD133 enriched chemoresistant hepatospheres as compared to their counterparts. Clinically, reduced PRMT6 expression was detected in HCC specimens and correlated with a higher risk of metastasis. PRMT6 negatively regulated diverse in vitro cancer stem cell properties of HCC cells including self-renewal, therapy resistance, metastasis and expression of CSC and pluripotency markers. In addition, PRMT6 also suppressed in vivo tumor initiation and serial transplantation. Surprising, contrary to its usual localization in the nucleus as a chromatin modification enzyme mediating histone H3R2 methylation, we found PRMT6 to be predominantly expressed in the cytoplasm in normal liver and HCC cells. Through tandem affinity purification and subsequent mass spectrometry profiling, we identified CRAF, a serine/threonine-protein kinase, as a novel cytoplasmic protein partner of PRMT6. Binding of PRMT6 to CRAF inhibited its kinase activity through site-specific arginine methylation, resulting in inhibition of ERK-mediated CSC plasticity in HCC, demonstrated through in vivo / in vitro methylation assays, kinase assay and functional rescue experiments with the ERK inhibitor U0126. The link between PRMT6, ERK and cancer stemness was further substantiated in primary human normal liver and HCC organoids with or without PRMT6 modulated. Taken together, we found PRMT6 to be down-regulated in the liver CSC subset and to be functionally involved in regulating liver CSC plasticity via an unprecedented role in the cytoplasm through suppression of CRAF/ERK cascade.
Citation Format: Lok Hei Chan, Lei Zhou, Kai Yu Ng, Tin Lok Wong, Stella Chai, Terence K Lee, Xin Yuan Guan, Yick Pang Ching, Chung Mau Lo, Kwan Man, Benedetta Artegiani, Hans Clevers, Helen H Yan, Suet Yi Leung, Stèphane Richard, Michael SY Huen, Stephanie Ma. PRMT6-dependent CRAF/ERK signaling regulates cancer stem cell plasticity in liver cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr LB-139. doi:10.1158/1538-7445.AM2017-LB-139
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Affiliation(s)
- Lok Hei Chan
- 1The University of Hong Kong, Hong Kong, Hong Kong
| | - Lei Zhou
- 1The University of Hong Kong, Hong Kong, Hong Kong
| | - Kai Yu Ng
- 1The University of Hong Kong, Hong Kong, Hong Kong
| | - Tin Lok Wong
- 1The University of Hong Kong, Hong Kong, Hong Kong
| | - Stella Chai
- 1The University of Hong Kong, Hong Kong, Hong Kong
| | - Terence K Lee
- 2Hong Kong Polytechnic University, Hong Kong, Hong Kong
| | | | | | - Chung Mau Lo
- 1The University of Hong Kong, Hong Kong, Hong Kong
| | - Kwan Man
- 1The University of Hong Kong, Hong Kong, Hong Kong
| | | | | | - Helen H Yan
- 1The University of Hong Kong, Hong Kong, Hong Kong
| | | | | | | | - Stephanie Ma
- 1The University of Hong Kong, Hong Kong, Hong Kong
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26
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Yan HHN, Lai JCW, Ho SL, Chan AKW, Tsui WY, Chan ASY, Yuen ST, Leung SY. Abstract 1448: Unraveling the oncogenic pathway of serrated polyposis syndrome driven by RNF43 germline mutation. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-1448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Serrated polyps can arise in a sporadic or familial polyposis setting and predispose to colorectal cancer (CRC). Recently, we have identified RNF43 germline mutation in a family with Serrated Polyposis Syndrome (Yan et al, GUT 2016). The presence of second somatic hit in all serrated polyps examined from members of this family further confirmed the pathogenicity of RNF43 germline mutation. In an attempt to further delineate the global genomic alterations in these serrated polyps, so as to understand the RNF43 driven serrated neoplasia pathway for the development of colorectal cancer, we performed whole exome sequencing (WES) on two sessile serrated adenomas (SSAs) resected from an RNF43 germline mutation carrier, together with the paired blood DNA. Consistent with the results from our previous Sanger sequencing study, WES detected complete inactivation of RNF43 through a 2nd hit somatic mutation, c.461 C>T P154L, or loss of heterozygosity (LOH) in the two SSAs, respectively. We also identified 51 and 58 somatic mutations in the two SSAs, respectively. BRAFV600E mutation was the only shared mutation between the two polyps. Interestingly, each of the SSAs carried a truncating mutation in a histone-methyltransferase gene, either PRDM9 or SETD1B, respectively. Other truncating or deleterious mutations included chromatin modifiers (CHD2, CHD4, TSPYL2) or other genes with methyltransferase activity (TRMT2B, METTL12, METTL14, ECE2). In addition, we found few instances of chromosomal aberration or LOH, apart from a region of LOH at chromosome 17 encompassing RNF43 in one of the SSAs.
Overall, we have revealed the genomic landscape of two sessile serrated adenomas resected from a germline RNF43 mutation carrier. The results confirmed somatic RNF43 2nd hit and BRAFV600E mutation as the key events, along with putative roles for histone methyltransferase, as well as other chromatin modifiers. These findings highlight the potentially important role of an altered chromatin in the oncogenic pathway of serrated neoplasia.
Citation Format: Helen Hoi Ning Yan, Jeffrey C W Lai, Siu Lun Ho, Anthony K W Chan, Wai Yin Tsui, Annie S Y Chan, Siu Tsan Yuen, Suet Yi Leung. Unraveling the oncogenic pathway of serrated polyposis syndrome driven by RNF43 germline mutation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1448. doi:10.1158/1538-7445.AM2017-1448
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Affiliation(s)
| | - Jeffrey C W Lai
- Dept. of Pathology, Univ. of Hong Kong, Hong Kong, Hong Kong
| | - Siu Lun Ho
- Dept. of Pathology, Univ. of Hong Kong, Hong Kong, Hong Kong
| | | | - Wai Yin Tsui
- Dept. of Pathology, Univ. of Hong Kong, Hong Kong, Hong Kong
| | - Annie S Y Chan
- Dept. of Pathology, Univ. of Hong Kong, Hong Kong, Hong Kong
| | - Siu Tsan Yuen
- Dept. of Pathology, Univ. of Hong Kong, Hong Kong, Hong Kong
| | - Suet Yi Leung
- Dept. of Pathology, Univ. of Hong Kong, Hong Kong, Hong Kong
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Yue SSK, Yan HHN, Siu HC, Ho SL, Tsui WY, Chan D, Chan ASY, Lee BCH, Chan AKW, Leung SY. Abstract 4378: Gastric cancer organoid culture shows preserved genomic stability in long-term passage. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-4378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
With recent advances in 3D organoid culture techniques, normal epithelial and tumor cells can be directly cultured from clinical specimens in vitro and expanded long-term with a very high success rate. Thus, this constitutes a good platform for various mechanistic functional studies and clinical applications. A previous karyotyping and gene expression profiling study has indicated that organoid culture of normal epithelial cells can be propagated for long periods of time without genomic alterations. However, data on the genomic stability of tumor organoids in long-term culture are not yet available. We have successfully established organoid cultures derived from either primary tumor or lymph node metastasis from 4 gastric cancer patients. For each sample, we performed long-term culture for at least 6 months. DNA was extracted from blood, as well as the early and late passages of these organoids, and submitted for whole-exome sequencing (WES), achieving a mean coverage approaching 50X. Somatic mutations detected in early versus late passage gastric cancer organoids were compared. Furthermore, we examined the organoids for copy number variations based on the coverage and loss of heterozygosity (LOH) information derived from exome sequencing.
We detected between 80 to 228 somatic mutations in the 4 early passage organoids, in which over 84-99% of them were retained during long-term culture. We detected 16, 20, 31 and 98 new mutations in the 4 long-term cultures, respectively. The one case with a substantially large number of new mutations (n=98) appeared to have emerged from a subclone of TP53 wild-type cells in a TP53 mutant tumor. Notably, the C>T mutation was the most dominant mutation spectrum in this case, constituting 48%. Despite the presence of frequent long segment LOH and chromosomal aberrations in early passage organoids, indicating the presence of chromosomal instability, these patterns of aberrations were stably maintained in long-term passage.
Overall, with the current organoid culture protocol, tumor genomes are mostly stably maintained with the accumulation of only a small number of new mutations. Our results indicate that this is a reliable and stable in vitro cell culture model for various cancer-related and clinical studies.
Citation Format: Sarah Siu Kuen Yue, Helen Hoi Ning Yan, Hoi Cheong Siu, Siu Lun Ho, Wai Yin Tsui, Dessy Chan, Annie Shuk Yee Chan, Bernard Chi Hang Lee, Anthony Kin Wang Chan, Suet Yi Leung. Gastric cancer organoid culture shows preserved genomic stability in long-term passage [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4378. doi:10.1158/1538-7445.AM2017-4378
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Affiliation(s)
| | | | - Hoi Cheong Siu
- Department of Pathology, The University of Hong Kong, Hong Kong
| | - Siu Lun Ho
- Department of Pathology, The University of Hong Kong, Hong Kong
| | - Wai Yin Tsui
- Department of Pathology, The University of Hong Kong, Hong Kong
| | - Dessy Chan
- Department of Pathology, The University of Hong Kong, Hong Kong
| | | | | | | | - Suet Yi Leung
- Department of Pathology, The University of Hong Kong, Hong Kong
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28
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Lee VC, Chow JF, Lau EY, Kwong A, Leung SY, Yeung WS, Ho PC, Ng EH. Preimplantation genetic diagnosis for hereditary cancer syndrome: local experience. Hong Kong Med J 2016; 22:289-91. [PMID: 27305697 DOI: 10.12809/hkmj144499] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- V Cy Lee
- Department of Obstetrics and Gynaecology, Queen Mary Hospital, Pokfulam, Hong Kong
| | - J Fc Chow
- Department of Obstetrics and Gynaecology, The University of Hong Kong, Pokfulam, Hong Kong
| | - E Yl Lau
- Department of Obstetrics and Gynaecology, Queen Mary Hospital, Pokfulam, Hong Kong
| | - A Kwong
- Hong Kong Hereditary Breast Cancer Family Registry; Division of Breast Surgery, Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - S Y Leung
- Hereditary Gastrointestinal Cancer Genetic Diagnosis Laboratory, Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - W Sb Yeung
- Department of Obstetrics and Gynaecology, The University of Hong Kong, Pokfulam, Hong Kong
| | - P C Ho
- Department of Obstetrics and Gynaecology, The University of Hong Kong, Pokfulam, Hong Kong
| | - E Hy Ng
- Department of Obstetrics and Gynaecology, The University of Hong Kong, Pokfulam, Hong Kong
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Yoo S, Leung SY, Zhu J. Abstract B22: Integrative analysis of DNA methylation and gene expression data reveals complex regulation of gastric cancer. Cancer Res 2016. [DOI: 10.1158/1538-7445.chromepi15-b22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Gastric cancer is a heterogeneous disease where diverse genetic and epigenetic alternations can accumulate in different molecular and histological subtypes. We applied our recently developed causality test between genome-wide DNA methylation and gene expression profiles to three independent cohorts of gastric tumors (97 in Hong Kong University (HKU), 159 in University of Singapore (Singapore) and 365 samples in TCGA stomach adenocarcinoma (TCGA) ). We focused on methylation variations within CpG islands in promoter regions, where global hypermethylation was observed, and identified 37, 62, and 537 key regulators in HKU, Singapore, and TCGA dataset respectively. There were 5 common key regulators (ADHFE1, CDO1, COX7A1, FSTL1, and TCF21) whose methylation variations had high impact on mRNA level changes of large number of downstream genes in all three dataset where different cohorts were profiled using different platforms. When we compared two dataset, there were 5 common key regulators in HKU and Singapore dataset (Fisher's exact test (FET) p-value = 2.9×e-07), 27 common key regulators in HKU and TCGA dataset (FET p-value = 6.8×e-35), and 30 common key regulators in Singapore and TCGA dataset (FET p-value = 1.0×e-29). By combining these, 52 genes were identified as key regulators within at least two dataset. Several of the key regulators were known for the association between their epigenetic disruption and the disease (for example, BNIP3, CDO1, TCF21, ZSCAN18, and so on) while other genes have not implicated in the gastric cancer previously. More interestingly, the downstream genes of these key regulators were significantly overlapped and the directions of correlation with methylation levels were almost same within the three dataset. Further clustering key regulators based on their downstream genes overlaps revealed that there were two distinct groups of downstream genes commonly regulated by these key regulators and the expression of these two groups were anti-correlated. One group was enriched for cell cycle related genes and the other group was enriched for genes involved in immune responses. This result indicates that cell cycle and immune response functions were inversely regulated by methylation variations of the same set of genes. It is worth to note that methylation patterns of some key regulators were subtype dependent and the subtype specific methylation patterns were only observed in tumor samples, but not in adjacent normal tissues. Based on integrative analysis of genome-wide DNA methylation and gene expression profiles within three independent gastric cancer dataset, we identified a set of key regulators whose methylation changes might play a ‘causal' role in the transcriptional regulation associated with the gastric cancer. Further experiments are needed to validate and dissect these putative candidate genes' roles in tumorigenesis and progression of this complex and heterogeneous disease.
Citation Format: Seungyeul Yoo, Suet Yi Leung, Jun Zhu. Integrative analysis of DNA methylation and gene expression data reveals complex regulation of gastric cancer. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Sep 24-27, 2015; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2016;76(2 Suppl):Abstract nr B22.
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Affiliation(s)
- Seungyeul Yoo
- 1Icahn School of Medicine at Mount Sinai, New York, NY,
| | | | - Jun Zhu
- 1Icahn School of Medicine at Mount Sinai, New York, NY,
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30
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Abstract
Gastric cancer is a heterogeneous disease encompassing diverse morphological (intestinal versus diffuse) and molecular subtypes (MSI, EBV, TP53 mutation). Recent advances in genomic technology have led to an improved understanding of the driver gene mutational profile, gene expression, and epigenetic alterations that underlie each of the subgroups, with therapeutic implications in some of these alterations. There have been attempts to classify gastric cancers based on these genomic features, with an aim to improve prognostication and predict responsiveness to specific drug therapy. The eventual aims of these genomic studies are to develop deep biological insights into the carcinogenic pathway in each of these subtypes. Future large-scale drug screening strategies may then be able to link these genomic features to drug responsiveness, eventually leading to genome-guided personalized medicine with improved cure rates.
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Affiliation(s)
- Siu Tsan Yuen
- Department of Pathology, Queen Mary Hospital, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Suet Yi Leung
- Department of Pathology, Queen Mary Hospital, The University of Hong Kong, Pok Fu Lam, Hong Kong.
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31
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Alexandrov LB, Nik-Zainal S, Siu HC, Leung SY, Stratton MR. A mutational signature in gastric cancer suggests therapeutic strategies. Nat Commun 2015; 6:8683. [PMID: 26511885 PMCID: PMC4918743 DOI: 10.1038/ncomms9683] [Citation(s) in RCA: 133] [Impact Index Per Article: 14.8] [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: 08/06/2015] [Accepted: 09/18/2015] [Indexed: 12/17/2022] Open
Abstract
Targeting defects in the DNA repair machinery of neoplastic cells, for example, those due to inactivating BRCA1 and/or BRCA2 mutations, has been used for developing new therapies in certain types of breast, ovarian and pancreatic cancers. Recently, a mutational signature was associated with failure of double-strand DNA break repair by homologous recombination based on its high mutational burden in samples harbouring BRCA1 or BRCA2 mutations. In pancreatic cancer, all responders to platinum therapy exhibit this mutational signature including a sample that lacked any defects in BRCA1 or BRCA2. Here, we examine 10,250 cancer genomes across 36 types of cancer and demonstrate that, in addition to breast, ovarian and pancreatic cancers, gastric cancer is another cancer type that exhibits this mutational signature. Our results suggest that 7–12% of gastric cancers have defective double-strand DNA break repair by homologous recombination and may benefit from either platinum therapy or PARP inhibitors. Cancer genome analysis has demonstrated that some breast and ovarian tumours show reduced homologous recombination, a feature that can be therapeutically exploited. Here, Alexandrov et al. search for this mutational signature in 36 different cancer types and find that some gastric tumours also harbour this mutational spectrum.
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Affiliation(s)
- Ludmil B Alexandrov
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK.,Theoretical Biology and Biophysics (T-6), Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA.,Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - Serena Nik-Zainal
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK.,Department of Medical Genetics, Addenbrooke's Hospital National Health Service (NHS) Trust, Cambridge CB2 0QQ, UK
| | - Hoi Cheong Siu
- Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Suet Yi Leung
- Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Michael R Stratton
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
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32
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Wang K, Leung SY. Abstract A35: Genomic characterization of immune escape pathways in gastric cancer. Cancer Immunol Res 2015. [DOI: 10.1158/2326-6074.tumimm14-a35] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
This abstract is being presented as a short talk in the scientific program. A full abstract is printed in the Proffered Abstracts section (PR06) of the Conference Proceedings.
Citation Format: Kai Wang, Suet Yi Leung. Genomic characterization of immune escape pathways in gastric cancer. [abstract]. In: Proceedings of the AACR Special Conference: Tumor Immunology and Immunotherapy: A New Chapter; December 1-4, 2014; Orlando, FL. Philadelphia (PA): AACR; Cancer Immunol Res 2015;3(10 Suppl):Abstract nr A35.
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Affiliation(s)
- Kai Wang
- 1Pfizer Oncology, San Diego, CA,
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Yan HHN, Lau JKY, Chan ASY, Tsui WY, Chan TL, Leung SY. Abstract 179: Regulation of stromal miR-125b on normal colonic epithelial cell renewal and its putative role in tumorigenesis. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs which exert their effects by post-transcriptionally silencing target mRNAs. Deregulation of miRNA expression is a frequent event in tumorigenesis. MiR-125b is a highly conserved miRNA among various species and is composed of three homologs: hsa-miR-125a, hsa-miR-125b-1 and hsa-miR-125-2. The tumorigenic roles of miR-125b have been studied in various cancers including prostate, colon, glioma etc, and studies have demonstrated that it can act as a tumor suppressor or an oncogene depending on the cellular context. It was characterized as an oncogene in prostate cancer and glioma through down-regulation of pro-apoptotic regulators BAK1 and Bcl-2 modifying factor (BMF), respectively. In colon cancer, a recent clinico-pathological study showed that high expression of miR-125b was associated with tumor invasion and poor prognosis. However, the localization of miR125b in normal colon and tumors is currently unknown. Therefore, we aimed to address the precise expression and the functional role of miR-125b in normal colon, which may provide insight on its potential oncogenic effects during carcinogenesis.
We performed gene expression analysis of miR-125b in normal colon tissues from 16 pairs of colon top versus basal crypts and 4 pairs of crypts versus stroma by real-time RT-PCR. Colon top and basal crypts were microdissected from frozen sections, whereas pure normal crypts and stromal fractions were isolated from freshly resected human colon specimens. We found that miR-125b was significantly enriched in the basal crypts (p<0.001) and the stromal compartment (p = 0.027). Functionally, knockdown of miR-125b by a specific miRCURY antisense oligonucleotide was able to dose dependently inhibit the growth of a normal colon myofibroblast cell line, CCD18, and significantly increase the mRNA level of several key Hedgehog signaling components, including PTCH (p<0.001), SMO (p<0.001), GLI1 (p<0.001) and its downstream target BMP4 (p = 0.017). Finally, we observed a drastic decrease in both the number and size of normal colon organoids when they were co-cultured with myofibroblasts transfected with miR-125b antisense oligonucleotide, as compared with negative control. Our results suggest that expression of miR-125b in the colonic stromal basal crypt compartment functions to inhibit Hedgehog signaling, leading to paracrine enhancement of colon crypt proliferation and stem cell renewal. Thus, given the well-known importance of hedgehog signaling in colon cancer, our findings suggest that dysregulated miR-125b
expression may contribute to carcinogenesis through disruption of this pathway.
Note: This abstract was not presented at the meeting.
Citation Format: Helen H N Yan, Jackie K Y Lau, Annie S Y Chan, Wai Yin Tsui, Tsun Leung Chan, Suet Yi Leung. Regulation of stromal miR-125b on normal colonic epithelial cell renewal and its putative role in tumorigenesis. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 179. doi:10.1158/1538-7445.AM2015-179
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Affiliation(s)
- Helen H N Yan
- Department of Pathology, Queen Mary Hospital, The University of Hong Kong, Hong Kong, Hong Kong
| | - Jackie K Y Lau
- Department of Pathology, Queen Mary Hospital, The University of Hong Kong, Hong Kong, Hong Kong
| | - Annie S Y Chan
- Department of Pathology, Queen Mary Hospital, The University of Hong Kong, Hong Kong, Hong Kong
| | - Wai Yin Tsui
- Department of Pathology, Queen Mary Hospital, The University of Hong Kong, Hong Kong, Hong Kong
| | - Tsun Leung Chan
- Department of Pathology, Queen Mary Hospital, The University of Hong Kong, Hong Kong, Hong Kong
| | - Suet Yi Leung
- Department of Pathology, Queen Mary Hospital, The University of Hong Kong, Hong Kong, Hong Kong
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Leung WK, Tong DKH, Leung SY, Chan FSY, Tong TSM, Ho RSL, Chu KM, Law SYK. Treatment of Gastric Metaplasia or Dysplasia by Endoscopic Radiofrequency Ablation: A Pilot Study. Hepatogastroenterology 2015; 62:748-751. [PMID: 26897966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
BACKGROUND/AIMS Patients with gastric intestinal metaplasia and dysplasia are at increased risk of gastric cancer development. We tested the feasibility of using endoscopic radiofrequency ablation for the treatment of dysplasia and metaplasia in the stomach. METHODOLOGY Patients who had histologically confirmed low-grade gastric dysplasia or IM were recruited. Endoscopic RFA was performed at 8 week-intervals for a maximum of 3 sessions. All patients were followed up by endoscopy until 12 months post-RFA. The primary outcome was the complete eradication of dysplasia or IM on follow-up. Secondary outcome was adverse events related to RFA. RESULTS A total of 12 patients were recruited. Four patients had low-grade dysplasia and the remaining 8 patients had non-dysplastic IM at baseline. At one year after RFA, complete eradication of dysplasia was noted in four patients with low-grade dysplasia (100%). Gastric IM persisted in all patients with baseline metaplasia but the severity of IM improved in 6 (75%) patients. Endoscopic RFA was safe with minimal complications encountered. CONCLUSIONS RFA successfully eradicated low-grade dysplasia of the stomach. Gastric IM however persisted after RFA but most patients had evidence of histological improvement on follow up.
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Hiyoshi Y, Schetter AJ, Okayama H, Inamura K, Anami K, Nguyen GH, Horikawa I, Hawkes JE, Bowman ED, Leung SY, Harris CC. Increased microRNA-34b and -34c predominantly expressed in stromal tissues is associated with poor prognosis in human colon cancer. PLoS One 2015; 10:e0124899. [PMID: 25894979 PMCID: PMC4404052 DOI: 10.1371/journal.pone.0124899] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 03/08/2015] [Indexed: 12/15/2022] Open
Abstract
The microRNA-34 family (miR-34a, -34b and -34c) have been reported to be tumor suppressor microRNAs (miRNAs) that are regulated by the TP53 and DNA hypermethylation. However, the expression, regulation, and prognostic value of the miR-34 family have not been systematically studied in colon cancer. To elucidate the roles of miR-34 family in colon carcinogenesis, miR-34a/b/c were measured in tumors and adjacent noncancerous tissues from 159 American and 113 Chinese colon cancer patients using quantitative RT-PCR, and we examined associations between miR-34a/b/c expression with TNM staging, cancer-specific mortality, TP53 mutation status and Affymetrix microarray data. All miR-34 family members were significantly increased in colon tumors, counter to the proposed tumor suppressor role for these miRNAs. Increased miR-34b/c were observed in more advanced tumors in two independent cohorts and increased expression of miR-34b/c was associated with poor cancer-specific mortality. While the expression of miR-34 family was not associated with TP53 mutation status, TP53 transcriptional activity was associated with miR-34a/b/c expression that is consistent with the proposed regulation of miR-34a/b/c by TP53. To examine where the miR-34 family is expressed, the expression of miR-34 family was compared between epitheliums and stromal tissues using laser microdissection technique. The expression of miR-34b/c was increased significantly in stromal tissues, especially in cancer stroma, compared with epithelial tissue. In conclusion, increased miR-34b/c predominantly expressed in stromal tissues is associated with poor prognosis in colon cancer. MiR-34 may contribute to cancer-stromal interaction associated with colon cancer progression.
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Affiliation(s)
- Yukiharu Hiyoshi
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Aaron J. Schetter
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Hirokazu Okayama
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Kentaro Inamura
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Katsuhiro Anami
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Giang H. Nguyen
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Izumi Horikawa
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Jason E. Hawkes
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Elise D. Bowman
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Suet Yi Leung
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Curtis C. Harris
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
- * E-mail:
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Kwok CK, Liang Y, Wang H, Dong YH, Leung SY, Wong MH. Bioaccumulation of heavy metals in fish and Ardeid at Pearl River Estuary, China. Ecotoxicol Environ Saf 2014; 106:62-67. [PMID: 24836879 DOI: 10.1016/j.ecoenv.2014.04.016] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 04/11/2014] [Accepted: 04/15/2014] [Indexed: 06/03/2023]
Abstract
Sediment, fish (tilapia, Oreochromis mossambicus and snakehead, Channa asiatica), eggs and eggshells of Little Egrets (Egretta garzetta) and Chinese Pond Herons (Ardeola bacchus) were collected from Mai Po Ramsar site of Hong Kong, as well as from wetlands in the Gu Cheng County, Shang Hu County and Dafeng Milu National Nature Reserve of Jiangsu Province, China between 2004 and 2007 (n=3-9). Concentrations of six heavy metals were analyzed, based on inductively coupled plasma optical emission spectrometry (ICP-OES). Significant bioaccumulations of Cd (BAF: 165-1271 percent) were observed in the muscle and viscera of large tilapia and snakehead, suggesting potential health risks to the two bird species, as the fishes are the main preys of waterbirds. Significant (p<0.01) linear relationships were obtained between concentrations of Cd, Cr, Cu, Mn, Pb and Zn in the eggs and eggshells of various Ardeid species, and these regression models were used to extrapolate the heavy metal concentrations in the Ardeid eggs of Mai Po. Extrapolated concentrations are consistent with data in the available literature, and advocate the potential use of these models as a non-invasive sampling method for predicting heavy metal contamination in Ardeid eggs.
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Affiliation(s)
- C K Kwok
- Croucher Institute for Environmental Sciences, and Department of Biology, Hong Kong Baptist University, Hong Kong, China; Joint Open Laboratory on "Soil and Environment" of Hong Kong Baptist University and Institute of Soil Science of Nanjing, PR China
| | - Y Liang
- Croucher Institute for Environmental Sciences, and Department of Biology, Hong Kong Baptist University, Hong Kong, China; Joint Open Laboratory on "Soil and Environment" of Hong Kong Baptist University and Institute of Soil Science of Nanjing, PR China.
| | - H Wang
- Institute of Soil Science, Chinese Academy of Sciences (ISSAS), Nanjing, Jiangsu, PR China; Joint Open Laboratory on "Soil and Environment" of Hong Kong Baptist University and Institute of Soil Science of Nanjing, PR China
| | - Y H Dong
- Institute of Soil Science, Chinese Academy of Sciences (ISSAS), Nanjing, Jiangsu, PR China; Joint Open Laboratory on "Soil and Environment" of Hong Kong Baptist University and Institute of Soil Science of Nanjing, PR China
| | - S Y Leung
- Croucher Institute for Environmental Sciences, and Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - M H Wong
- Croucher Institute for Environmental Sciences, and Department of Biology, Hong Kong Baptist University, Hong Kong, China; Department of Science and Environmental Studies, Hong Kong Institute of Education, Hong Kong, China; Joint Open Laboratory on "Soil and Environment" of Hong Kong Baptist University and Institute of Soil Science of Nanjing, PR China.
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37
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Wang K, Yuen ST, Xu J, Lee SP, Yan HHN, Shi ST, Siu HC, Deng S, Chu KM, Law S, Chan KH, Chan ASY, Tsui WY, Ho SL, Chan AKW, Man JLK, Foglizzo V, Ng MK, Chan AS, Ching YP, Cheng GHW, Xie T, Fernandez J, Li VSW, Clevers H, Rejto PA, Mao M, Leung SY. Whole-genome sequencing and comprehensive molecular profiling identify new driver mutations in gastric cancer. Nat Genet 2014; 46:573-82. [PMID: 24816253 DOI: 10.1038/ng.2983] [Citation(s) in RCA: 769] [Impact Index Per Article: 76.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Accepted: 04/18/2014] [Indexed: 02/08/2023]
Abstract
Gastric cancer is a heterogeneous disease with diverse molecular and histological subtypes. We performed whole-genome sequencing in 100 tumor-normal pairs, along with DNA copy number, gene expression and methylation profiling, for integrative genomic analysis. We found subtype-specific genetic and epigenetic perturbations and unique mutational signatures. We identified previously known (TP53, ARID1A and CDH1) and new (MUC6, CTNNA2, GLI3, RNF43 and others) significantly mutated driver genes. Specifically, we found RHOA mutations in 14.3% of diffuse-type tumors but not in intestinal-type tumors (P < 0.001). The mutations clustered in recurrent hotspots affecting functional domains and caused defective RHOA signaling, promoting escape from anoikis in organoid cultures. The top perturbed pathways in gastric cancer included adherens junction and focal adhesion, in which RHOA and other mutated genes we identified participate as key players. These findings illustrate a multidimensional and comprehensive genomic landscape that highlights the molecular complexity of gastric cancer and provides a road map to facilitate genome-guided personalized therapy.
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Affiliation(s)
- Kai Wang
- 1] Oncology Research Unit, Pfizer Worldwide Research and Development, San Diego, California, USA. [2]
| | - Siu Tsan Yuen
- 1] Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong. [2]
| | - Jiangchun Xu
- 1] Oncology Research Unit, Pfizer Worldwide Research and Development, San Diego, California, USA. [2] [3]
| | - Siu Po Lee
- 1] Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong. [2]
| | - Helen H N Yan
- 1] Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong. [2]
| | - Stephanie T Shi
- External Research Solutions, Pfizer Worldwide Research and Development, San Diego, California, USA
| | - Hoi Cheong Siu
- Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Shibing Deng
- Oncology Research Unit, Pfizer Worldwide Research and Development, San Diego, California, USA
| | - Kent Man Chu
- Department of Surgery, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Simon Law
- Department of Surgery, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Kok Hoe Chan
- Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Annie S Y Chan
- Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Wai Yin Tsui
- Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Siu Lun Ho
- Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Anthony K W Chan
- Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Jonathan L K Man
- Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Valentina Foglizzo
- Division of Stem Cell Biology and Developmental Genetics, Medical Research Council (MRC) National Institute for Medical Research, London, UK
| | - Man Kin Ng
- Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - April S Chan
- Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Yick Pang Ching
- Department of Anatomy, The University of Hong Kong, Pokfulam, Hong Kong
| | - Grace H W Cheng
- Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Tao Xie
- Oncology Research Unit, Pfizer Worldwide Research and Development, San Diego, California, USA
| | - Julio Fernandez
- Oncology Research Unit, Pfizer Worldwide Research and Development, San Diego, California, USA
| | - Vivian S W Li
- Division of Stem Cell Biology and Developmental Genetics, Medical Research Council (MRC) National Institute for Medical Research, London, UK
| | - Hans Clevers
- Hubrecht Institute for Developmental Biology and Stem Cell Research, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Paul A Rejto
- Oncology Research Unit, Pfizer Worldwide Research and Development, San Diego, California, USA
| | - Mao Mao
- 1] Oncology Research Unit, Pfizer Worldwide Research and Development, San Diego, California, USA. [2]
| | - Suet Yi Leung
- Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
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Thompson BA, Spurdle AB, Plazzer JP, Greenblatt MS, Akagi K, Al-Mulla F, Bapat B, Bernstein I, Capellá G, den Dunnen JT, du Sart D, Fabre A, Farrell MP, Farrington SM, Frayling IM, Frebourg T, Goldgar DE, Heinen CD, Holinski-Feder E, Kohonen-Corish M, Robinson KL, Leung SY, Martins A, Moller P, Morak M, Nystrom M, Peltomaki P, Pineda M, Qi M, Ramesar R, Rasmussen LJ, Royer-Pokora B, Scott RJ, Sijmons R, Tavtigian SV, Tops CM, Weber T, Wijnen J, Woods MO, Macrae F, Genuardi M. Application of a 5-tiered scheme for standardized classification of 2,360 unique mismatch repair gene variants in the InSiGHT locus-specific database. Nat Genet 2013; 46:107-115. [PMID: 24362816 DOI: 10.1038/ng.2854] [Citation(s) in RCA: 342] [Impact Index Per Article: 31.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 11/26/2013] [Indexed: 12/12/2022]
Abstract
The clinical classification of hereditary sequence variants identified in disease-related genes directly affects clinical management of patients and their relatives. The International Society for Gastrointestinal Hereditary Tumours (InSiGHT) undertook a collaborative effort to develop, test and apply a standardized classification scheme to constitutional variants in the Lynch syndrome-associated genes MLH1, MSH2, MSH6 and PMS2. Unpublished data submission was encouraged to assist in variant classification and was recognized through microattribution. The scheme was refined by multidisciplinary expert committee review of the clinical and functional data available for variants, applied to 2,360 sequence alterations, and disseminated online. Assessment using validated criteria altered classifications for 66% of 12,006 database entries. Clinical recommendations based on transparent evaluation are now possible for 1,370 variants that were not obviously protein truncating from nomenclature. This large-scale endeavor will facilitate the consistent management of families suspected to have Lynch syndrome and demonstrates the value of multidisciplinary collaboration in the curation and classification of variants in public locus-specific databases.
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Affiliation(s)
- Bryony A Thompson
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Australia.,School of Medicine, University of Queensland, Brisbane, Australia
| | - Amanda B Spurdle
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - John-Paul Plazzer
- Department of Colorectal Medicine and Genetics, Royal Melbourne Hospital, Australia
| | - Marc S Greenblatt
- Vermont Cancer Center, University of Vermont College of Medicine, Burlington, VT, USA
| | - Kiwamu Akagi
- Division of Molecular Diagnosis and Cancer Prevention, Saitama Cancer Center, Saitama, Japan
| | - Fahd Al-Mulla
- Department of Pathology, Faculty of Medicine, Health Sciences Center, Kuwait University, Safat, Kuwait
| | - Bharati Bapat
- Department of Lab Medicine and Pathobiology, University of Toronto, Canada
| | - Inge Bernstein
- Danish HNPCC Registry, Copenhagen, Denmark.,Surgical Gastroenterology Department, Aalborg University Hospital, Aalborg, Denmark
| | - Gabriel Capellá
- Hereditary Cancer Program, Catalan Institute of Oncology-IDIBELL, Barcelona, Spain
| | - Johan T den Dunnen
- Center of Human and Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Desiree du Sart
- Molecular Genetics Lab, Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, Melbourne, Australia
| | - Aurelie Fabre
- INSERM UMR S910, Department of Medical Genetics and Functional Genomics, Marseille, France
| | - Michael P Farrell
- Department of Cancer Genetics, Mater Private Hospital, Dublin, Ireland
| | - Susan M Farrington
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh, Scotland
| | - Ian M Frayling
- Institute of Medical Genetics, University Hospital of Wales, Cardiff, UK
| | - Thierry Frebourg
- Inserm U1079, Faculty of Medicine, Institute for Biomedical Research, University of Rouen, France
| | - David E Goldgar
- Department of Dermatology, University of Utah Medical School, Salt Lake City, UT, USA.,Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - Christopher D Heinen
- Center for Molecular Medicine, UConn Health Center, Farmington, CT, USA.,Neag Comprehensive Cancer Center, UConn Health Center, Farmington, CT, USA
| | - Elke Holinski-Feder
- MGZ - Medizinisch Genetisches Zentrum, Munich, Germany.,Klinikum der Universität München, Campus Innenstadt, Medizinische Klinik und Poliklinik IV, Munich, Germany
| | - Maija Kohonen-Corish
- School of Medicine, University of Western Sydney, Sydney, Australia.,The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Sydney, Australia.,St Vincent's Clinical School, University of NSW, Sydney, Australia
| | - Kristina Lagerstedt Robinson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Suet Yi Leung
- Hereditary Gastrointestinal Cancer Genetic Diagnosis Laboratory, Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Alexandra Martins
- Inserm U1079, University of Rouen, Institute for Research and Innovation in Biomedicine, Rouen, France
| | - Pal Moller
- Research Group on Inherited Cancer, Department of Medical Genetics, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
| | - Monika Morak
- MGZ - Medizinisch Genetisches Zentrum, Munich, Germany.,Klinikum der Universität München, Campus Innenstadt, Medizinische Klinik und Poliklinik IV, Munich, Germany
| | - Minna Nystrom
- Division of Genetics, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Paivi Peltomaki
- Department of Medical Genetics, Haartman Institute, University of Helsinki, Finland
| | - Marta Pineda
- Hereditary Cancer Program, Catalan Institute of Oncology-IDIBELL, Barcelona, Spain
| | - Ming Qi
- Center for Genetic and Genomic Medicine, The First Affiliated Hospital of Zhejiang University School of Medicine, James Watson Institute of Genomic Sciences, Beijing Genome Institute, China.,University of Rochester Medical Center, NY, USA
| | - Rajkumar Ramesar
- MRC Human Genetics Research Unit, Division of Human Genetics, Institute of Infectious Diseases and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, South Africa
| | | | | | - Rodney J Scott
- Discipline of Medical Genetics, Faculty of Health, University of Newcastle, The Hunter Medical Research Institute, NSW, Australia.,The Division of Molecular Medicine, Hunter Area Pathology Service, John Hunter Hospital, Newcastle, NSW, Australia
| | - Rolf Sijmons
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | | | - Carli M Tops
- Center of Human and Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Thomas Weber
- State University of New York at Downstate, Brooklyn, NY, USA
| | - Juul Wijnen
- Center of Human and Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Michael O Woods
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Finlay Macrae
- Department of Colorectal Medicine and Genetics, Royal Melbourne Hospital, Australia
| | - Maurizio Genuardi
- Department of Biomedical, Experimental and Clinical Sciences, University of Florence, Italy.,Fiorgen Foundation for Pharmacogenomics, Sesto Fiorentino, Italy
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Kwok CK, Liang Y, Leung SY, Wang H, Dong YH, Young L, Giesy JP, Wong MH. Biota-sediment accumulation factor (BSAF), bioaccumulation factor (BAF), and contaminant levels in prey fish to indicate the extent of PAHs and OCPs contamination in eggs of waterbirds. Environ Sci Pollut Res Int 2013; 20:8425-8434. [PMID: 23702571 DOI: 10.1007/s11356-013-1809-4] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Accepted: 05/06/2013] [Indexed: 06/02/2023]
Abstract
Samples of pond sediment, fish, and shrimp were collected from the Ramsar site at Mai Po marshes, Hong Kong (south China), and samples of pond sediment, fish, and shrimp, as well as eggs of water birds (Chinese Pond Herons (Ardeola bacchus) and Little Egrets (Egretta garzetta)), were collected from two smaller wetland sites at Jiangsu Province (mid-China), between 2004 and 2007. Accumulation levels of polycyclic aromatic hydrocarbons (PAHs) and organochlorine pesticides (OCPs) in the biota were used to calculate biota-sediment accumulation factor (BSAF) and bioaccumulation factor (BAF). For fish and shrimp, BSAFs of OCPs (3.8-56) were greater than those of PAHs (0.12-6.3). BSAFs and BAFs of 11-79 and 4-34, respectively, were registered for OCPs in eggs of the birds and were greater than those for PAHs (0.11-1.5 and 0.02-1.3, respectively). Assuming that fish were the main prey of the birds, greater bioaccumulation of OCPs was detected for both bird species (BAFs =4.5-34), while accumulation of PAHs was only detected in Little Egret (BAF=1.3). A significant linear relationship (p<0.01) was observed between concentrations of OCPs in bird eggs and in the prey fish. The present study provides a new possibility of using OCP levels detected in prey fish to predict the extent of OCPs contamination in eggs of waterbirds including the endangered species, as a noninvasive method.
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Affiliation(s)
- C K Kwok
- Croucher Institute for Environmental Sciences, and Department of Biology, Hong Kong Baptist University, Hong Kong SAR, People's Republic of China
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40
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Lintzeris N, Leung SY, Dunlop AJ, Larance B, White N, Rivas GR, Holland RM, Degenhardt L, Muhleisen P, Hurley M, Ali R. A randomised controlled trial of sublingual buprenorphine-naloxone film versus tablets in the management of opioid dependence. Drug Alcohol Depend 2013; 131:119-26. [PMID: 23317685 DOI: 10.1016/j.drugalcdep.2012.12.009] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Revised: 10/28/2012] [Accepted: 12/08/2012] [Indexed: 11/29/2022]
Abstract
BACKGROUND Buprenorphine-naloxone sublingual film was introduced in 2011 in Australia as an alternative to tablets. This study compared the two formulations on subjective dose effects and equivalence, trough plasma levels, adverse events, patient satisfaction, supervised dosing time, and impact upon treatment outcomes (substance use, psychosocial function). METHODS 92 buprenorphine-naloxone tablet patients were recruited to this outpatient multi-site double-blind double-dummy parallel group trial. Patients were randomised to either tablets or film, without dose changes, over a 31 day period. RESULTS No significant group differences were observed for subjective dose effects, trough plasma buprenorphine or norbuprenorphine levels, adverse events and treatment outcomes. Buprenorphine-naloxone film took significantly less time to dissolve than tablets (173±71 versus 242±141s, p=0.007, F=7.67). CONCLUSIONS The study demonstrated dose equivalence and comparable clinical outcomes between the buprenorphine-naloxone film and tablet preparations, whilst showing improved dispensing times and patient ratings of satisfaction with the film.
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Affiliation(s)
- N Lintzeris
- Langton Centre, South Eastern Sydney Local Health District, NSW 2010, Australia.
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41
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Fan B, Dachrut S, Coral H, Yuen ST, Chu KM, Law S, Zhang L, Ji J, Leung SY, Chen X. Integration of DNA copy number alterations and transcriptional expression analysis in human gastric cancer. PLoS One 2012; 7:e29824. [PMID: 22539939 PMCID: PMC3335165 DOI: 10.1371/journal.pone.0029824] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2011] [Accepted: 12/03/2011] [Indexed: 12/16/2022] Open
Abstract
Background Genomic instability with frequent DNA copy number alterations is one of the key hallmarks of carcinogenesis. The chromosomal regions with frequent DNA copy number gain and loss in human gastric cancer are still poorly defined. It remains unknown how the DNA copy number variations contributes to the changes of gene expression profiles, especially on the global level. Principal Findings We analyzed DNA copy number alterations in 64 human gastric cancer samples and 8 gastric cancer cell lines using bacterial artificial chromosome (BAC) arrays based comparative genomic hybridization (aCGH). Statistical analysis was applied to correlate previously published gene expression data obtained from cDNA microarrays with corresponding DNA copy number variation data to identify candidate oncogenes and tumor suppressor genes. We found that gastric cancer samples showed recurrent DNA copy number variations, including gains at 5p, 8q, 20p, 20q, and losses at 4q, 9p, 18q, 21q. The most frequent regions of amplification were 20q12 (7/72), 20q12–20q13.1 (12/72), 20q13.1–20q13.2 (11/72) and 20q13.2–20q13.3 (6/72). The most frequent deleted region was 9p21 (8/72). Correlating gene expression array data with aCGH identified 321 candidate oncogenes, which were overexpressed and showed frequent DNA copy number gains; and 12 candidate tumor suppressor genes which were down-regulated and showed frequent DNA copy number losses in human gastric cancers. Three networks of significantly expressed genes in gastric cancer samples were identified by ingenuity pathway analysis. Conclusions This study provides insight into DNA copy number variations and their contribution to altered gene expression profiles during human gastric cancer development. It provides novel candidate driver oncogenes or tumor suppressor genes for human gastric cancer, useful pathway maps for the future understanding of the molecular pathogenesis of this malignancy, and the construction of new therapeutic targets.
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Affiliation(s)
- Biao Fan
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America
- Department of Surgery, Beijing Cancer Hospital & Institute, Peking University School of Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing, China
| | - Somkid Dachrut
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America
- Liver Fluke and Cholangiocarcinoma Research Center, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Ho Coral
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America
| | - Siu Tsan Yuen
- Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Kent Man Chu
- Department of Surgery; The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Simon Law
- Department of Surgery; The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Lianhai Zhang
- Department of Surgery, Beijing Cancer Hospital & Institute, Peking University School of Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing, China
| | - Jiafu Ji
- Department of Surgery, Beijing Cancer Hospital & Institute, Peking University School of Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing, China
- * E-mail: (XC); (SYL); (JFJ)
| | - Suet Yi Leung
- Department of Pathology, The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
- * E-mail: (XC); (SYL); (JFJ)
| | - Xin Chen
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America
- * E-mail: (XC); (SYL); (JFJ)
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Li G, Fan C, Deng S, Xu J, Shi S, Wang K, Pascual B, Kung PP, Leung SY, Yue ST. Abstract 4535: CENP-E and c-Myc expression identifies a sensitive population of gastric cancer. Cancer Res 2012. [DOI: 10.1158/1538-7445.am2012-4535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Centromere-associated protein E (CENP-E) is expressed during mitosis and plays an essential role in establishing and maintaining stable connections between mitotic chromosomes and the microtubules of the spindle. Previous preclinical studies have shown that inhibition of CENP-E function by small interfering RNA, blocking antibodies or small molecule inhibitors arrested cell cycle before metaphase, and could lead to cell death. In a number of cancers, CENP-E is frequently overexpressed in tumor tissues compared with their normal counterparts. In this study, we showed that CENP-E is overexpressed in about 60% of gastric cancer (intestinal and diffuse-type) tissues. In addition, c-Myc up-regulation was observed in more than 50% of the same samples. Overall, about 40% of all gastric tumor samples harbor both CENP-E and c-Myc upregulation. Using a panel of small molecule inhibitors of CENP-E, we evaluated in vitro anti-proliferation effect in a panel of gastric cancer cell lines. Our data suggested that cells with higher levels of c-Myc transcript were more sensitive to CENP-E inhibition. This preliminary study indicated that c-Myc amplification and/or over-expression could be a potential biomarker for selecting gastric cancer patients more likely to respond to CENP-E inhibition.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4535. doi:1538-7445.AM2012-4535
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Affiliation(s)
- Gang Li
- 1Pfizer, Inc., San Diego, CA
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Wang TN, Lin MC, Wu CC, Huang MS, Leung SY, Huang CC, Ho PS, Ko YC. Role of gender disparity of circulating high-sensitivity C-reactive protein concentrations and obesity on asthma in Taiwan. Clin Exp Allergy 2011; 41:72-7. [PMID: 20701611 DOI: 10.1111/j.1365-2222.2010.03581.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
BACKGROUND Several studies have suggested that the association between obesity and asthma may be stronger in females than in males, but the reason is still unclear. OBJECTIVE The aim of this study was to investigate whether differences in high-sensitivity C-reactive protein (hs-CRP) levels explain why obesity is associated with asthma in females but not in males. METHODS This study prospectively enrolled 754 subjects ≥ 18 years old from hospital-based asthma patients and population-based controls. We measured adiposity factors [body mass index (BMI), waist circumference and waist-hip ratio], hs-CRP and total IgE levels. RESULTS After adjusting for potential confounding factors, we found a significant association between BMI and asthma in females with a significant interaction of gender and BMI on asthma (χ(2) =10.2, P=0.004). If hs-CRP was added to the logistic model, the interaction was attenuated but still significant (χ(2) =7.02, P=0.03). After adjusting for BMI, we did not find that circulating hs-CRP concentrations were significantly associated with asthma in males and females. CONCLUSION We found that BMI was associated with asthma in females, but our results do not support the suggestion that hs-CRP levels contribute significantly to the link between obesity and asthma with respect to gender disparity.
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Affiliation(s)
- T-N Wang
- Department of Public Health, College of Health Science Center of Excellence for Environmental Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
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Leung SY, Lum CM. Use of nutritional health supplements and associated factors among parents with children at kindergartens in Hong Kong. Hong Kong Med J 2011; 17:365-371. [PMID: 21979472] [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: 05/31/2023] Open
Abstract
OBJECTIVES. To estimate the prevalence of so-called nutritional health supplement consumption among kindergarten children; secondarily to explore potential factors associated with such consumption. DESIGN. Cross-sectional, self-administered questionnaire survey. SETTING. One kindergarten each in Hong Kong island, Kowloon, and the New Territories region. SUBJECTS. Parents who had a child studying at the three sampled kindergartens in April 2010. RESULTS. Of 951 sets of parents, 730 (77%) responded. Approximately 52% (95% confidence interval, 47-58%) of the respondents gave regular health supplements to their child. The commonest type of supplement given was cod fish oil (69%). Approximately 36% of the respondents did not know the upper limit dosage of their supplement. Parents of only 66% of regular health supplements consumers, compared to 75% of non-regular users, knew that there was an inherent risk from over-consumption (P=0.018). Parental beliefs that "It is useful/important for normal child development" (adjusted odds ratio=1.93; 95% confidence interval, 1.18-3.16; P=0.009), "It is useful/important for immune function" (1.79; 1.05-3.05; P=0.032) were associated with consumption of health such supplements. CONCLUSION. There is high rate of health supplement consumption among healthy kindergarten children in Hong Kong. There are wrong beliefs from parents that health supplements are important for normal-growing children for their normal growth and body immunity. About one-third of parents has limited knowledge on potential side-effects of overdose and do not know the limit of consumption. Education on "Less (health supplement) is more (health)" is recommended.
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Affiliation(s)
- S Y Leung
- School of Public Health and Primary Care, The Chinese University of Hong Kong, Shatin, Hong Kong
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45
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Kosinski C, Stange DE, Xu C, Chan ASY, Ho C, Yuen ST, Mifflin RC, Powell DW, Clevers H, Leung SY, Chen X. Indian hedgehog regulates intestinal stem cell fate through epithelial-mesenchymal interactions during development. Gastroenterology 2010; 139:893-903. [PMID: 20542037 PMCID: PMC2930094 DOI: 10.1053/j.gastro.2010.06.014] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2009] [Revised: 05/21/2010] [Accepted: 06/01/2010] [Indexed: 12/02/2022]
Abstract
BACKGROUND & AIMS Intestinal stem cells (ISCs) are regulated by the mesenchymal environment via physical interaction and diffusible factors. We examined the role of Indian hedgehog (Ihh) in mesenchymal organization and the mechanisms by which perturbations in epithelial-mesenchymal interactions affect ISC fate. METHODS We generated mice with intestinal epithelial-specific disruption of Ihh. Gross and microscopic anatomical changes were determined using histologic, immunohistochemical, and in situ hybridization analyses. Molecular mechanisms were elucidated by expression profiling and in vitro analyses. RESULTS Deletion of intestinal epithelial Ihh disrupted the intestinal mesenchymal architecture, demonstrated by loss of the muscularis mucosae, deterioration of the extracellular matrix, and reductions in numbers of crypt myofibroblasts. Concurrently, the epithelial compartment had increased Wnt signaling, disturbed crypt polarity and architecture, defective enterocyte differentiation, and increased and ectopic proliferation that was accompanied by increased numbers of ISCs. Mechanistic studies revealed that Hh inhibition deregulates bone morphogenetic protein signaling, increases matrix metalloproteinase levels, and disrupts extracellular matrix proteins, fostering a proliferative environment for ISCs and progenitor cells. CONCLUSIONS Ihh regulates ISC self-renewal and differentiation. Intestinal epithelial Ihh signals to the mesenchymal compartment to regulate formation and proliferation of mesenchymal cells, which in turn affect epithelial proliferation and differentiation. These findings provide a basis for analyses of the role of the muscularis mucosae in ISC regulation.
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Affiliation(s)
- Cynthia Kosinski
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
| | - Daniel E. Stange
- Hubrecht Institute, KNAW & University Medical Center Utrecht, Utrecht, The Netherlands
| | - Chuanrui Xu
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
| | - Annie SY Chan
- Department of Pathology and Center for Cancer Research; The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Coral Ho
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
| | - Siu Tsan Yuen
- Department of Pathology and Center for Cancer Research; The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Randy C. Mifflin
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX, USA
| | - Don W. Powell
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX, USA
| | - Hans Clevers
- Hubrecht Institute, KNAW & University Medical Center Utrecht, Utrecht, The Netherlands
| | - Suet Yi Leung
- Department of Pathology and Center for Cancer Research; The University of Hong Kong, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Xin Chen
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
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Kwok CK, Yang SM, Mak NK, Wong CKC, Liang Y, Leung SY, Young L, Wong MH. Ecotoxicological study on sediments of Mai Po marshes, Hong Kong using organisms and biomarkers. Ecotoxicol Environ Saf 2010; 73:541-549. [PMID: 20153057 DOI: 10.1016/j.ecoenv.2010.01.012] [Citation(s) in RCA: 1] [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] [Received: 11/02/2009] [Revised: 01/14/2010] [Accepted: 01/16/2010] [Indexed: 05/28/2023]
Abstract
Sediments from Mai Po Ramsar site, Hong Kong were in general shown to be highly toxic based on the results of four toxicity tests (Microtox solid-phase test, Daphnia mortality test, algal [Microcystis aeruginosa] growth inhibition test and ryegrass [Lolium perenne] seed germination/root elongation test). Sediment of the mudflat (which is open to Deep Bay, i.e., the pollution source) was the most toxic while sediment of gei wai 24g (an enclosed freshwater pond) was the least toxic. Results of biomarker studies (tilapia hepatic metallothionein; glutathione (GSH) and EROD activity using H4IIE rat hepatoma cell) were also concordant with those in the toxicity tests. Significant liner relationships (p<0.01) were found between GSH contents in the rat hepatoma cells and PAHs, OCPs contents in the sediment extracts. It is recommended that the present suite of bioassays is useful and is biologically relevant for future ecotoxicological studies focusing on similar wetlands.
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Affiliation(s)
- C K Kwok
- Croucher Institute for Environmental Sciences, and Department of Biology, Hong Kong Baptist University, Kowloon Tong, Hong Kong, PR China
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47
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Li C, Yuen ST, Anthony, Chan KW, Tsui WWY, Chan ASY, Leung SY, Chan TL. Abstract 4909: The role of CpG island methylator phenotype 2 (CIMP2) in early onset colorectal cancer patients. Cancer Res 2010. [DOI: 10.1158/1538-7445.am10-4909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
CpG Island Methylator Phenotype (CIMP), characterized by methylation at various promoter sites, has been reported as a subgroup in colorectal cancer. CIMP1 is often associated with microsatellite instability (MSI) as well as BRAF mutation while CIMP negative enriched with P53 mutant. Besides, a CIMP2 classification has also been established and indicated to be associated with KRAS mutation. Most of these experiments related to CIMP were carried out on tumor samples from late onset patients with a mean or median age of at least 60. Thus it was of interest to observe any deviation of such pattern among early onset colorectal cancer population. Bisulfite conversion of the extracted DNA from 73 tumor samples with MSS status were examined via pyrosequence for their methylation status among loci MINT1, MINT2 and MINT27, the most frequently methylated sites reported in CIMP 2 phenomenon. These samples were free from MLH1 methylation and BRAF mutation to exclude conditions of CIMP1. The age group ranged from 29 to 68 years old with a mean age of 50.7 years old. Sequencing of its genomic DNA for KRas mutation was also screened as per se to previous studies. It was found that CIMP2 appeared more frequently in patients over the age of 50 (p=0.04) when compared with patients below 50 years old. Furthermore, methylation of the CIMP 2 loci examined (MINT1, MINT2 and MINT27) were most likely accompanied with the mutation of KRas in patients over 50 years old (p=0.05) while there was no observed correlation of CIMP 2 loci and KRas mutation in patient samples under 50 years of age. Since the CIMP2 phenotype is not seen in early-onset CRC samples, our data suggests that an alternative pathway, but not CIMP, may be responsible for the tumorigenesis of early-onset MSS CRC. Moreover, current studies proposed chromosomal instability may be a distinct mechanism in the pathogenesis of CRC, thus investigation would be carried on this aspect.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 4909.
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Affiliation(s)
- Carmen Li
- 1Hereditary Gastrointestinal Cancer Genetics Diagnosis Laboratory, Department of Pathology, University of Hong Kong, Pokfulam, Hong Kong
| | - Siu Tsan Yuen
- 2Hereditary Gastrointestinal Cancer Registry, Department of Pathology, St. Paul's Hospital, Hong Kong
| | | | - Kin Wang Chan
- 1Hereditary Gastrointestinal Cancer Genetics Diagnosis Laboratory, Department of Pathology, University of Hong Kong, Pokfulam, Hong Kong
| | - Wendy Wai Yin Tsui
- 1Hereditary Gastrointestinal Cancer Genetics Diagnosis Laboratory, Department of Pathology, University of Hong Kong, Pokfulam, Hong Kong
| | - Annie Suk Yee Chan
- 1Hereditary Gastrointestinal Cancer Genetics Diagnosis Laboratory, Department of Pathology, University of Hong Kong, Pokfulam, Hong Kong
| | - Suet Yi Leung
- 1Hereditary Gastrointestinal Cancer Genetics Diagnosis Laboratory, Department of Pathology, University of Hong Kong, Pokfulam, Hong Kong
| | - Tsun Leung Chan
- 1Hereditary Gastrointestinal Cancer Genetics Diagnosis Laboratory, Department of Pathology, University of Hong Kong, Pokfulam, Hong Kong
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Leung SY, Kwok CK, Nie XP, Cheung KC, Wong MH. Risk assessment of residual DDTs in freshwater and marine fish cultivated around the Pearl River Delta, China. Arch Environ Contam Toxicol 2010; 58:415-430. [PMID: 19603131 DOI: 10.1007/s00244-009-9356-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2009] [Accepted: 06/15/2009] [Indexed: 05/28/2023]
Abstract
Six species of freshwater fish collected from 10 fishponds in Shunde and Zhongshan, China, four species of marine fishes collected from different mariculture farms [four in Hong Kong (Tung Lung Chau, Ma Wan, Cheung Chau and Kat O) and two in mainland China (Daya Bay and Shenzhen)] together with feed (both trash fish and commercial pellets) and sediment were analyzed for DDTs. Total DDTs in freshwater fish flesh decreased in the order of: carnivores [1742 microg/kg lipid weight (l.w.)] > herbivores (165 microg/kg, l.w.) > omnivores (42.5 microg/kg, l.w.), with the highest concentration detected in mandarin fish (Siniperca chuatsi) (2641 microg/kg, l.w.). For marine fish, snubnose pompano (Trachinotus blochii) and orange-spotted grouper (Epinephelus coioides) collected in Ma Wan contained elevated levels of total DDTs (2590 and 2034 microg/kg l.w., respectively). Trash fish used in both freshwater and marine fish farms contained significantly higher levels (86.5-641 microg/kg l.w.) (p < 0.05) of DDTs than in commercial pellets, but correlations between DDT levels in fish feed and muscle were not significant. The elevated biota-sediment accumulating factor for tilapia (Tilapia mossambicus) (24.1) indicated that accumulation of DDTs from sediment to the fish was evident. It can be concluded that trash fish should not be used for fish culture in order to lower the level of residual DDTs in fish muscle.
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Affiliation(s)
- S Y Leung
- Croucher Institute for Environmental Sciences and Department of Biology, Hong Kong Baptist University, Hong Kong, People's Republic of China
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Abstract
Groundwater from a xylene-contaminated acquifer was enriched in the laboratory in the presence of toluene, xylenes, ethylbenzene, and benzene. A pure culture that degrades toluene and m-xylene under nitrate-reducing conditions was isolated. Fatty acid analysis, 16S rRNA sequencing, and morphological traits indicate that the isolate was a strain of Azoarcus tolulyticus. The kinetics of toluene degradation under nitrate-reducing conditions by this isolate was determined. Nitrate reduction does not proceed beyond nitrite. Nitrate and toluene are substrate limiting at low concentrations, whereas toluene, nitrate, and nitrite are inhibitory at high concentrations. Several inhibition models were compared to experimental data to represent inhibition by these substrates. A kinetic model for toluene and nitrate degradation as well as for cell growth and nitrite production was developed and compared to experimental data. The results of this work may find important application in the remediation of groundwater aquifers contaminated with aromatic hydrocarbons.
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Affiliation(s)
- J Elmén
- Department of Chemical Engineering, University of California, Berkeley, California 94720-1462, USA
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Schetter AJ, Nguyen GH, Bowman ED, Mathé EA, Yuen ST, Hawkes JE, Croce CM, Leung SY, Harris CC. Association of inflammation-related and microRNA gene expression with cancer-specific mortality of colon adenocarcinoma. Clin Cancer Res 2009; 15:5878-87. [PMID: 19737943 DOI: 10.1158/1078-0432.ccr-09-0627] [Citation(s) in RCA: 154] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
PURPOSE Inflammatory genes and microRNAs have roles in colon carcinogenesis; therefore, they may provide useful biomarkers for colon cancer. This study examines the potential clinical utility of an inflammatory gene expression signature as a prognostic biomarker for colon cancer in addition to previously examined miR-21 expression. EXPERIMENTAL DESIGN Quantitative reverse transcriptase-PCR. was used to measure the expression of 23 inflammatory genes in colon adenocarcinomas and adjacent noncancerous tissues from 196 patients. These data were used to develop models for cancer-specific mortality on a training cohort (n = 57), and this model was tested in both a test (n = 56) and a validation (n = 83) cohort. Expression data for miR-21 were available for these patients and were compared and combined with inflammatory gene expression. RESULTS PRG1, IL-10, CD68, IL-23a, and IL-12a expression in noncancerous tissue, and PRG1, ANXA1, IL-23a, IL-17a, FOXP3, and HLA-DRA expression in tumor tissues were associated with poor prognosis based on Cox regression (/Z-score/ >1.5) and were used to generate the inflammatory risk score (IRS). IRS was associated with cancer-specific mortality in the training, test (P = 0.01), and validation (P = 0.02) cohorts. This association was strong for stage II cases (P = 0.002). Expression of miR-21 was associated with IL-6, IL-8, IL-10, IL-12a, and NOS2a, providing evidence that the function of this microRNA and these inflammatory genes are linked. Both IRS and miR-21 expression were independently associated with cancer-specific mortality, including stage II patients alone. CONCLUSION IRS and miR-21 expression are independent predictors of colon cancer prognosis and may provide a clinically useful tool to identify high-risk patients.
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Affiliation(s)
- Aaron J Schetter
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
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