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Jeon AJ, Anene-Nzelu CG, Teo YY, Chong SL, Sekar K, Wu L, Chew SC, Chen J, Kendarsari RI, Lai H, Ling WH, Kaya NA, Lim JQ, Chung AYF, Cheow PC, Kam JH, Madhavan K, Kow A, Ganpathi IS, Lim TKH, Leow WQ, Loong S, Loh TJ, Wan WK, Soon GST, Pang YH, Yoong BK, Bee-Lan Ong D, Lim J, de Villa VH, dela Cruz RD, Chanwat R, Thammasiri J, Bonney GK, Goh BK, Foo RSY, Chow PKH. A genomic enhancer signature associates with hepatocellular carcinoma prognosis. JHEP Rep 2023; 5:100715. [PMID: 37168287 PMCID: PMC10165154 DOI: 10.1016/j.jhepr.2023.100715] [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] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 01/20/2023] [Accepted: 02/09/2023] [Indexed: 05/13/2023] Open
Abstract
Background & Aims Lifestyle and environmental-related exposures are important risk factors for hepatocellular carcinoma (HCC), suggesting that epigenetic dysregulation significantly underpins HCC. We profiled 30 surgically resected tumours and the matched adjacent normal tissues to understand the aberrant epigenetic events associated with HCC. Methods We identified tumour differential enhancers and the associated genes by analysing H3K27 acetylation (H3K27ac) chromatin immunoprecipitation sequencing (ChIP-seq) and Hi-C/HiChIP data from the resected tumour samples of 30 patients with early-stage HCC. This epigenome dataset was analysed with previously reported genome and transcriptome data of the overlapping group of patients from the same cohort. We performed patient-specific differential expression testing using multiregion sequencing data to identify genes that undergo both enhancer and gene expression changes. Based on the genes selected, we identified two patient groups and performed a recurrence-free survival analysis. Results We observed large-scale changes in the enhancer distribution between HCC tumours and the adjacent normal samples. Many of the gain-in-tumour enhancers showed corresponding upregulation of the associated genes and vice versa, but much of the enhancer and gene expression changes were patient-specific. A subset of the upregulated genes was activated in a subgroup of patients' tumours. Recurrence-free survival analysis revealed that the patients with a more robust upregulation of those genes showed a worse prognosis. Conclusions We report the genomic enhancer signature associated with differential prognosis in HCC. Findings that cohere with oncofoetal reprogramming in HCC were underpinned by genome-wide enhancer rewiring. Our results present the epigenetic changes in HCC that offer the rational selection of epigenetic-driven gene targets for therapeutic intervention or disease prognostication in HCC. Impact and Implications Lifestyle and environmental-related exposures are the important risk factors of hepatocellular carcinoma (HCC), suggesting that tumour-associated epigenetic dysregulations may significantly underpin HCC. We profiled tumour tissues and their matched normal from 30 patients with early-stage HCC to study the dysregulated epigenetic changes associated with HCC. By also analysing the patients' RNA-seq and clinical data, we found the signature genes - with epigenetic and transcriptomic dysregulation - associated with worse prognosis. Our findings suggest that systemic approaches are needed to consider the surrounding cellular environmental and epigenetic changes in HCC tumours.
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Affiliation(s)
- Ah-Jung Jeon
- Program in Clinical and Translational Liver Cancer Research, Division of Medical Science, National Cancer Center Singapore, Singapore
| | - Chukwuemeka George Anene-Nzelu
- Cardiovascular Disease Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Montreal Heart Institute, Montreal, Quebec, Canada
- Department of Medicine, University of Montreal, Quebec, Canada
| | - Yue-Yang Teo
- Program in Clinical and Translational Liver Cancer Research, Division of Medical Science, National Cancer Center Singapore, Singapore
| | - Shay Lee Chong
- Program in Clinical and Translational Liver Cancer Research, Division of Medical Science, National Cancer Center Singapore, Singapore
| | - Karthik Sekar
- Program in Clinical and Translational Liver Cancer Research, Division of Medical Science, National Cancer Center Singapore, Singapore
| | - Lingyan Wu
- Program in Clinical and Translational Liver Cancer Research, Division of Medical Science, National Cancer Center Singapore, Singapore
| | - Sin-Chi Chew
- Program in Clinical and Translational Liver Cancer Research, Division of Medical Science, National Cancer Center Singapore, Singapore
| | - Jianbin Chen
- Genome Institute of Singapore, Agency for Science, Technology and Research (A∗STAR), Singapore
| | - Raden Indah Kendarsari
- Genome Institute of Singapore, Agency for Science, Technology and Research (A∗STAR), Singapore
| | - Hannah Lai
- Genome Institute of Singapore, Agency for Science, Technology and Research (A∗STAR), Singapore
| | - Wen Huan Ling
- Program in Clinical and Translational Liver Cancer Research, Division of Medical Science, National Cancer Center Singapore, Singapore
| | - Neslihan Arife Kaya
- Genome Institute of Singapore, Agency for Science, Technology and Research (A∗STAR), Singapore
| | - Jia Qi Lim
- Genome Institute of Singapore, Agency for Science, Technology and Research (A∗STAR), Singapore
| | - Alexander Yaw Fui Chung
- Department of Hepatopancreatobiliary and Transplant Surgery, National Cancer Centre Singapore and Singapore General Hospital, Singapore
- Academic Clinical Programme for Surgery, Duke-NUS Medical School, Singapore
| | - Peng-Chung Cheow
- Department of Hepatopancreatobiliary and Transplant Surgery, National Cancer Centre Singapore and Singapore General Hospital, Singapore
- Academic Clinical Programme for Surgery, Duke-NUS Medical School, Singapore
| | - Juinn Huar Kam
- Department of Hepatopancreatobiliary and Transplant Surgery, National Cancer Centre Singapore and Singapore General Hospital, Singapore
- Academic Clinical Programme for Surgery, Duke-NUS Medical School, Singapore
| | - Krishnakumar Madhavan
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, University Surgical Cluster, National University Health System, Singapore
| | - Alfred Kow
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, University Surgical Cluster, National University Health System, Singapore
| | - Iyer Shridhar Ganpathi
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, University Surgical Cluster, National University Health System, Singapore
| | - Tony Kiat Hon Lim
- Department of Anatomical Pathology, Singapore General Hospital, Singapore
| | - Wei-Qiang Leow
- Department of Anatomical Pathology, Singapore General Hospital, Singapore
| | - Shihleone Loong
- Department of Anatomical Pathology, Singapore General Hospital, Singapore
| | - Tracy Jiezhen Loh
- Department of Anatomical Pathology, Singapore General Hospital, Singapore
| | - Wei Keat Wan
- Department of Anatomical Pathology, Singapore General Hospital, Singapore
| | | | - Yin Huei Pang
- Department of Pathology, National University Hospital, Singapore
| | - Boon Koon Yoong
- Department of Surgery, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Diana Bee-Lan Ong
- Department of Surgery, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Jasmine Lim
- Department of Surgery, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Vanessa H. de Villa
- Department of Surgery and Center for Liver Health and Transplantation, The Medical City, Pasig City, Philippines
| | - Rouchelle D. dela Cruz
- Department of Laboratory Medicine and Pathology, The Medical City, Pasig City, Philippines
| | - Rawisak Chanwat
- Hepato-Pancreato-Biliary Surgery Unit, Department of Surgery, National Cancer Institute, Bangkok, Thailand
| | | | - Glenn K. Bonney
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, University Surgical Cluster, National University Health System, Singapore
| | - Brian K.P. Goh
- Department of Hepatopancreatobiliary and Transplant Surgery, National Cancer Centre Singapore and Singapore General Hospital, Singapore
- Academic Clinical Programme for Surgery, Duke-NUS Medical School, Singapore
| | - Roger Sik Yin Foo
- Cardiovascular Disease Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Genome Institute of Singapore, Agency for Science, Technology and Research (A∗STAR), Singapore
- Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Pierce Kah-Hoe Chow
- Program in Clinical and Translational Liver Cancer Research, Division of Medical Science, National Cancer Center Singapore, Singapore
- Department of Hepatopancreatobiliary and Transplant Surgery, National Cancer Centre Singapore and Singapore General Hospital, Singapore
- Academic Clinical Programme for Surgery, Duke-NUS Medical School, Singapore
- Corresponding author. Address: National Cancer Centre Singapore, 30 Hospital Boulevard, Singapore 168583, Singapore. Tel.: +65-63065424.
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Girardi F, Matz M, Stiller C, You H, Marcos Gragera R, Valkov MY, Bulliard JL, De P, Morrison D, Wanner M, O'Brian DK, Saint-Jacques N, Coleman MP, Allemani C, Hamdi-Chérif M, Kara L, Meguenni K, Regagba D, Bayo S, Cheick Bougadari T, Manraj SS, Bendahhou K, Ladipo A, Ogunbiyi OJ, Somdyala NIM, Chaplin MA, Moreno F, Calabrano GH, Espinola SB, Carballo Quintero B, Fita R, Laspada WD, Ibañez SG, Lima CA, Da Costa AM, De Souza PCF, Chaves J, Laporte CA, Curado MP, de Oliveira JC, Veneziano CLA, Veneziano DB, Almeida ABM, Latorre MRDO, Rebelo MS, Santos MO, Azevedo e Silva G, Galaz JC, Aparicio Aravena M, Sanhueza Monsalve J, Herrmann DA, Vargas S, Herrera VM, Uribe CJ, Bravo LE, Garcia LS, Arias-Ortiz NE, Morantes D, Jurado DM, Yépez Chamorro MC, Delgado S, Ramirez M, Galán Alvarez YH, Torres P, Martínez-Reyes F, Jaramillo L, Quinto R, Castillo J, Mendoza M, Cueva P, Yépez JG, Bhakkan B, Deloumeaux J, Joachim C, Macni J, Carrillo R, Shalkow Klincovstein J, Rivera Gomez R, Perez P, Poquioma E, Tortolero-Luna G, Zavala D, Alonso R, Barrios E, Eckstrand A, Nikiforuk C, Woods RR, Noonan G, Turner D, Kumar E, Zhang B, Dowden JJ, Doyle GP, Saint-Jacques N, Walsh G, Anam A, De P, McClure CA, Vriends KA, Bertrand C, Ramanakumar AV, Davis L, Kozie S, Freeman T, George JT, Avila RM, O’Brien DK, Holt A, Almon L, Kwong S, Morris C, Rycroft R, Mueller L, Phillips CE, Brown H, Cromartie B, Ruterbusch J, Schwartz AG, Levin GM, Wohler B, Bayakly R, Ward KC, Gomez SL, McKinley M, Cress R, Davis J, Hernandez B, Johnson CJ, Morawski BM, Ruppert LP, Bentler S, Charlton ME, Huang B, Tucker TC, Deapen D, Liu L, Hsieh MC, Wu XC, Schwenn M, Stern K, Gershman ST, Knowlton RC, Alverson G, Weaver T, Desai J, Rogers DB, Jackson-Thompson J, Lemons D, Zimmerman HJ, Hood M, Roberts-Johnson J, Hammond W, Rees JR, Pawlish KS, Stroup A, Key C, Wiggins C, Kahn AR, Schymura MJ, Radhakrishnan S, Rao C, Giljahn LK, Slocumb RM, Dabbs C, Espinoza RE, Aird KG, Beran T, Rubertone JJ, Slack SJ, Oh J, Janes TA, Schwartz SM, Chiodini SC, Hurley DM, Whiteside MA, Rai S, Williams MA, Herget K, Sweeney C, Kachajian J, Keitheri Cheteri MB, Migliore Santiago P, Blankenship SE, Conaway JL, Borchers R, Malicki R, Espinoza J, Grandpre J, Weir HK, Wilson R, Edwards BK, Mariotto A, Rodriguez-Galindo C, Wang N, Yang L, Chen JS, Zhou Y, He YT, Song GH, Gu XP, Mei D, Mu HJ, Ge HM, Wu TH, Li YY, Zhao DL, Jin F, Zhang JH, Zhu FD, Junhua Q, Yang YL, Jiang CX, Biao W, Wang J, Li QL, Yi H, Zhou X, Dong J, Li W, Fu FX, Liu SZ, Chen JG, Zhu J, Li YH, Lu YQ, Fan M, Huang SQ, Guo GP, Zhaolai H, Wei K, Chen WQ, Wei W, Zeng H, Demetriou AV, Mang WK, Ngan KC, Kataki AC, Krishnatreya M, Jayalekshmi PA, Sebastian P, George PS, Mathew A, Nandakumar A, Malekzadeh R, Roshandel G, Keinan-Boker L, Silverman BG, Ito H, Koyanagi Y, Sato M, Tobori F, Nakata I, Teramoto N, Hattori M, Kaizaki Y, Moki F, Sugiyama H, Utada M, Nishimura M, Yoshida K, Kurosawa K, Nemoto Y, Narimatsu H, Sakaguchi M, Kanemura S, Naito M, Narisawa R, Miyashiro I, Nakata K, Mori D, Yoshitake M, Oki I, Fukushima N, Shibata A, Iwasa K, Ono C, Matsuda T, Nimri O, Jung KW, Won YJ, Alawadhi E, Elbasmi A, Ab Manan A, Adam F, Nansalmaa E, Tudev U, Ochir C, Al Khater AM, El Mistiri MM, Lim GH, Teo YY, Chiang CJ, Lee WC, Buasom R, Sangrajrang S, Suwanrungruang K, Vatanasapt P, Daoprasert K, Pongnikorn D, Leklob A, Sangkitipaiboon S, Geater SL, Sriplung H, Ceylan O, Kög I, Dirican O, Köse T, Gurbuz T, Karaşahin FE, Turhan D, Aktaş U, Halat Y, Eser S, Yakut CI, Altinisik M, Cavusoglu Y, Türkköylü A, Üçüncü N, Hackl M, Zborovskaya AA, Aleinikova OV, Henau K, Van Eycken L, Atanasov TY, Valerianova Z, Šekerija M, Dušek L, Zvolský M, Steinrud Mørch L, Storm H, Wessel Skovlund C, Innos K, Mägi M, Malila N, Seppä K, Jégu J, Velten M, Cornet E, Troussard X, Bouvier AM, Guizard AV, Bouvier V, Launoy G, Dabakuyo Yonli S, Poillot ML, Maynadié M, Mounier M, Vaconnet L, Woronoff AS, Daoulas M, Robaszkiewicz M, Clavel J, Poulalhon C, Desandes E, Lacour B, Baldi I, Amadeo B, Coureau G, Monnereau A, Orazio S, Audoin M, D’Almeida TC, Boyer S, Hammas K, Trétarre B, Colonna M, Delafosse P, Plouvier S, Cowppli-Bony A, Molinié F, Bara S, Ganry O, Lapôtre-Ledoux B, Daubisse-Marliac L, Bossard N, Uhry Z, Estève J, Stabenow R, Wilsdorf-Köhler H, Eberle A, Luttmann S, Löhden I, Nennecke AL, Kieschke J, Sirri E, Justenhoven C, Reinwald F, Holleczek B, Eisemann N, Katalinic A, Asquez RA, Kumar V, Petridou E, Ólafsdóttir EJ, Tryggvadóttir L, Murray DE, Walsh PM, Sundseth H, Harney M, Mazzoleni G, Vittadello F, Coviello E, Cuccaro F, Galasso R, Sampietro G, Giacomin A, Magoni M, Ardizzone A, D’Argenzio A, Di Prima AA, Ippolito A, Lavecchia AM, Sutera Sardo A, Gola G, Ballotari P, Giacomazzi E, Ferretti S, Dal Maso L, Serraino D, Celesia MV, Filiberti RA, Pannozzo F, Melcarne A, Quarta F, Andreano A, Russo AG, Carrozzi G, Cirilli C, Cavalieri d’Oro L, Rognoni M, Fusco M, Vitale MF, Usala M, Cusimano R, Mazzucco W, Michiara M, Sgargi P, Boschetti L, Marguati S, Chiaranda G, Seghini P, Maule MM, Merletti F, Spata E, Tumino R, Mancuso P, Cassetti T, Sassatelli R, Falcini F, Giorgetti S, Caiazzo AL, Cavallo R, Piras D, Bella F, Madeddu A, Fanetti AC, Maspero S, Carone S, Mincuzzi A, Candela G, Scuderi T, Gentilini MA, Rizzello R, Rosso S, Caldarella A, Intrieri T, Bianconi F, Contiero P, Tagliabue G, Rugge M, Zorzi M, Beggiato S, Brustolin A, Gatta G, De Angelis R, Vicentini M, Zanetti R, Stracci F, Maurina A, Oniščuka M, Mousavi M, Steponaviciene L, Vincerževskienė I, Azzopardi MJ, Calleja N, Siesling S, Visser O, Johannesen TB, Larønningen S, Trojanowski M, Macek P, Mierzwa T, Rachtan J, Rosińska A, Kępska K, Kościańska B, Barna K, Sulkowska U, Gebauer T, Łapińska JB, Wójcik-Tomaszewska J, Motnyk M, Patro A, Gos A, Sikorska K, Bielska-Lasota M, Didkowska JA, Wojciechowska U, Forjaz de Lacerda G, Rego RA, Carrito B, Pais A, Bento MJ, Rodrigues J, Lourenço A, Mayer-da-Silva A, Coza D, Todescu AI, Valkov MY, Gusenkova L, Lazarevich O, Prudnikova O, Vjushkov DM, Egorova A, Orlov A, Pikalova LV, Zhuikova LD, Adamcik J, Safaei Diba C, Zadnik V, Žagar T, De-La-Cruz M, Lopez-de-Munain A, Aleman A, Rojas D, Chillarón RJ, Navarro AIM, Marcos-Gragera R, Puigdemont M, Rodríguez-Barranco M, Sánchez Perez MJ, Franch Sureda P, Ramos Montserrat M, Chirlaque López MD, Sánchez Gil A, Ardanaz E, Guevara M, Cañete-Nieto A, Peris-Bonet R, Carulla M, Galceran J, Almela F, Sabater C, Khan S, Pettersson D, Dickman P, Staehelin K, Struchen B, Egger Hayoz C, Rapiti E, Schaffar R, Went P, Mousavi SM, Bulliard JL, Maspoli-Conconi M, Kuehni CE, Redmond SM, Bordoni A, Ortelli L, Chiolero A, Konzelmann I, Rohrmann S, Wanner M, Broggio J, Rashbass J, Stiller C, Fitzpatrick D, Gavin A, Morrison DS, Thomson CS, Greene G, Huws DW, Grayson M, Rawcliffe H, Allemani C, Coleman MP, Di Carlo V, Girardi F, Matz M, Minicozzi P, Sanz N, Ssenyonga N, James D, Stephens R, Chalker E, Smith M, Gugusheff J, You H, Qin Li S, Dugdale S, Moore J, Philpot S, Pfeiffer R, Thomas H, Silva Ragaini B, Venn AJ, Evans SM, Te Marvelde L, Savietto V, Trevithick R, Aitken J, Currow D, Fowler C, Lewis C. Global survival trends for brain tumors, by histology: analysis of individual records for 556,237 adults diagnosed in 59 countries during 2000-2014 (CONCORD-3). Neuro Oncol 2023; 25:580-592. [PMID: 36355361 PMCID: PMC10013649 DOI: 10.1093/neuonc/noac217] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Survival is a key metric of the effectiveness of a health system in managing cancer. We set out to provide a comprehensive examination of worldwide variation and trends in survival from brain tumors in adults, by histology. METHODS We analyzed individual data for adults (15-99 years) diagnosed with a brain tumor (ICD-O-3 topography code C71) during 2000-2014, regardless of tumor behavior. Data underwent a 3-phase quality control as part of CONCORD-3. We estimated net survival for 11 histology groups, using the unbiased nonparametric Pohar Perme estimator. RESULTS The study included 556,237 adults. In 2010-2014, the global range in age-standardized 5-year net survival for the most common sub-types was broad: in the range 20%-38% for diffuse and anaplastic astrocytoma, from 4% to 17% for glioblastoma, and between 32% and 69% for oligodendroglioma. For patients with glioblastoma, the largest gains in survival occurred between 2000-2004 and 2005-2009. These improvements were more noticeable among adults diagnosed aged 40-70 years than among younger adults. CONCLUSIONS To the best of our knowledge, this study provides the largest account to date of global trends in population-based survival for brain tumors by histology in adults. We have highlighted remarkable gains in 5-year survival from glioblastoma since 2005, providing large-scale empirical evidence on the uptake of chemoradiation at population level. Worldwide, survival improvements have been extensive, but some countries still lag behind. Our findings may help clinicians involved in national and international tumor pathway boards to promote initiatives aimed at more extensive implementation of clinical guidelines.
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Affiliation(s)
- Fabio Girardi
- Cancer Survival Group, London School of Hygiene and Tropical Medicine, London, UK.,Cancer Division, University College London Hospitals NHS Foundation Trust, London, UK.,Division of Medical Oncology 2, Veneto Institute of Oncology IOV-IRCCS, Padua, Italy
| | - Melissa Matz
- Cancer Survival Group, London School of Hygiene and Tropical Medicine, London, UK
| | - Charles Stiller
- National Cancer Registration and Analysis Service, Public Health England, London, UK
| | - Hui You
- Cancer Information Analysis Unit, Cancer Institute NSW, St Leonards, New South Wales, Australia
| | - Rafael Marcos Gragera
- Epidemiology Unit and Girona Cancer Registry, Catalan Institute of Oncology, Girona, Spain
| | - Mikhail Y Valkov
- Department of Radiology, Radiotherapy and Oncology, Northern State Medical University, Arkhangelsk, Russia
| | - Jean-Luc Bulliard
- Centre for Primary Care and Public Health (Unisanté), University of Lausanne, Lausanne, Switzerland.,Neuchâtel and Jura Tumour Registry, Neuchâtel, Switzerland
| | - Prithwish De
- Surveillance and Cancer Registry, and Research Office, Clinical Institutes and Quality Programs, Ontario Health, Toronto, Ontario, Canada
| | - David Morrison
- Scottish Cancer Registry, Public Health Scotland, Edinburgh, UK
| | - Miriam Wanner
- Cancer Registry Zürich, Zug, Schaffhausen and Schwyz, University Hospital Zürich, Zürich, Switzerland
| | - David K O'Brian
- Alaska Cancer Registry, Alaska Department of Health and Social Services, Anchorage, Alaska, USA
| | - Nathalie Saint-Jacques
- Department of Medicine and Community Health and Epidemiology, Centre for Clinical Research, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Michel P Coleman
- Cancer Survival Group, London School of Hygiene and Tropical Medicine, London, UK.,Cancer Division, University College London Hospitals NHS Foundation Trust, London, UK
| | - Claudia Allemani
- Cancer Survival Group, London School of Hygiene and Tropical Medicine, London, UK
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Jeon AJ, Teo YY, Sekar K, Chong SL, Wu L, Chew SC, Chen J, Kendarsari RI, Lai H, Ling WH, Kaya NA, Lim JQ, Ramasamy A, Oguz G, Chung AYF, Chan CY, Cheow PC, Kam JH, Madhavan K, Kow A, Ganpathi IS, Lim TKH, Leow WQ, Loong S, Loh TJ, Wan WK, Soon GST, Pang YH, Yoong BK, Ong DBL, Lim J, de Villa VH, Cruz RD, Chanwat R, Thammasiri J, Bonney GK, Goh BKP, Tucker-Kellogg G, Foo RSY, Chow PKH. Multi-region sampling with paired sample sequencing analyses reveals sub-groups of patients with novel patient-specific dysregulation in Hepatocellular Carcinoma. BMC Cancer 2023; 23:118. [PMID: 36737737 PMCID: PMC9896715 DOI: 10.1186/s12885-022-10444-3] [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: 06/10/2022] [Accepted: 12/13/2022] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Conventional differential expression (DE) testing compares the grouped mean value of tumour samples to the grouped mean value of the normal samples, and may miss out dysregulated genes in small subgroup of patients. This is especially so for highly heterogeneous cancer like Hepatocellular Carcinoma (HCC). METHODS Using multi-region sampled RNA-seq data of 90 patients, we performed patient-specific differential expression testing, together with the patients' matched adjacent normal samples. RESULTS Comparing the results from conventional DE analysis and patient-specific DE analyses, we show that the conventional DE analysis omits some genes due to high inter-individual variability present in both tumour and normal tissues. Dysregulated genes shared in small subgroup of patients were useful in stratifying patients, and presented differential prognosis. We also showed that the target genes of some of the current targeted agents used in HCC exhibited highly individualistic dysregulation pattern, which may explain the poor response rate. DISCUSSION/CONCLUSION Our results highlight the importance of identifying patient-specific DE genes, with its potential to provide clinically valuable insights into patient subgroups for applications in precision medicine.
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Affiliation(s)
- Ah-Jung Jeon
- grid.410724.40000 0004 0620 9745Department of Hepatopancreatobiliary and Transplant Surgery, Division of Surgery and Surgical Oncology, Singapore General Hospital and National Cancer Centre Singapore, Singapore, Singapore ,grid.410724.40000 0004 0620 9745Program in Clinical and Translational Liver Cancer Research, Division of Medical Science, National Cancer Center Singapore, Singapore, Singapore
| | - Yue-Yang Teo
- grid.410724.40000 0004 0620 9745Department of Hepatopancreatobiliary and Transplant Surgery, Division of Surgery and Surgical Oncology, Singapore General Hospital and National Cancer Centre Singapore, Singapore, Singapore ,grid.410724.40000 0004 0620 9745Program in Clinical and Translational Liver Cancer Research, Division of Medical Science, National Cancer Center Singapore, Singapore, Singapore
| | - Karthik Sekar
- grid.410724.40000 0004 0620 9745Department of Hepatopancreatobiliary and Transplant Surgery, Division of Surgery and Surgical Oncology, Singapore General Hospital and National Cancer Centre Singapore, Singapore, Singapore ,grid.410724.40000 0004 0620 9745Program in Clinical and Translational Liver Cancer Research, Division of Medical Science, National Cancer Center Singapore, Singapore, Singapore
| | - Shay Lee Chong
- grid.410724.40000 0004 0620 9745Department of Hepatopancreatobiliary and Transplant Surgery, Division of Surgery and Surgical Oncology, Singapore General Hospital and National Cancer Centre Singapore, Singapore, Singapore ,grid.410724.40000 0004 0620 9745Program in Clinical and Translational Liver Cancer Research, Division of Medical Science, National Cancer Center Singapore, Singapore, Singapore
| | - Lingyan Wu
- grid.410724.40000 0004 0620 9745Department of Hepatopancreatobiliary and Transplant Surgery, Division of Surgery and Surgical Oncology, Singapore General Hospital and National Cancer Centre Singapore, Singapore, Singapore ,grid.410724.40000 0004 0620 9745Program in Clinical and Translational Liver Cancer Research, Division of Medical Science, National Cancer Center Singapore, Singapore, Singapore
| | - Sin-Chi Chew
- grid.410724.40000 0004 0620 9745Department of Hepatopancreatobiliary and Transplant Surgery, Division of Surgery and Surgical Oncology, Singapore General Hospital and National Cancer Centre Singapore, Singapore, Singapore ,grid.410724.40000 0004 0620 9745Program in Clinical and Translational Liver Cancer Research, Division of Medical Science, National Cancer Center Singapore, Singapore, Singapore
| | - Jianbin Chen
- grid.185448.40000 0004 0637 0221Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Raden Indah Kendarsari
- grid.185448.40000 0004 0637 0221Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Hannah Lai
- grid.185448.40000 0004 0637 0221Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Wen Huan Ling
- grid.410724.40000 0004 0620 9745Department of Hepatopancreatobiliary and Transplant Surgery, Division of Surgery and Surgical Oncology, Singapore General Hospital and National Cancer Centre Singapore, Singapore, Singapore ,grid.410724.40000 0004 0620 9745Program in Clinical and Translational Liver Cancer Research, Division of Medical Science, National Cancer Center Singapore, Singapore, Singapore
| | - Neslihan Arife Kaya
- grid.185448.40000 0004 0637 0221Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Jia Qi Lim
- grid.185448.40000 0004 0637 0221Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Adaikalavan Ramasamy
- grid.185448.40000 0004 0637 0221Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Gokce Oguz
- grid.185448.40000 0004 0637 0221Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Alexander Yaw-Fui Chung
- grid.410724.40000 0004 0620 9745Department of Hepatopancreatobiliary and Transplant Surgery, Division of Surgery and Surgical Oncology, Singapore General Hospital and National Cancer Centre Singapore, Singapore, Singapore ,grid.428397.30000 0004 0385 0924Academic Clinical Programme for Surgery, Duke-NUS Medical School, Singapore, Singapore
| | - Chung Yip Chan
- grid.410724.40000 0004 0620 9745Department of Hepatopancreatobiliary and Transplant Surgery, Division of Surgery and Surgical Oncology, Singapore General Hospital and National Cancer Centre Singapore, Singapore, Singapore ,grid.428397.30000 0004 0385 0924Academic Clinical Programme for Surgery, Duke-NUS Medical School, Singapore, Singapore
| | - Peng-Chung Cheow
- grid.410724.40000 0004 0620 9745Department of Hepatopancreatobiliary and Transplant Surgery, Division of Surgery and Surgical Oncology, Singapore General Hospital and National Cancer Centre Singapore, Singapore, Singapore ,grid.428397.30000 0004 0385 0924Academic Clinical Programme for Surgery, Duke-NUS Medical School, Singapore, Singapore
| | - Juinn Huar Kam
- grid.410724.40000 0004 0620 9745Department of Hepatopancreatobiliary and Transplant Surgery, Division of Surgery and Surgical Oncology, Singapore General Hospital and National Cancer Centre Singapore, Singapore, Singapore ,grid.428397.30000 0004 0385 0924Academic Clinical Programme for Surgery, Duke-NUS Medical School, Singapore, Singapore
| | - Krishnakumar Madhavan
- grid.410759.e0000 0004 0451 6143Division of Hepatobiliary & Pancreatic Surgery, Department of Surgery, University Surgical Cluster, National University Health System, Singapore, Singapore
| | - Alfred Kow
- grid.410759.e0000 0004 0451 6143Division of Hepatobiliary & Pancreatic Surgery, Department of Surgery, University Surgical Cluster, National University Health System, Singapore, Singapore
| | - Iyer Shridhar Ganpathi
- grid.410759.e0000 0004 0451 6143Division of Hepatobiliary & Pancreatic Surgery, Department of Surgery, University Surgical Cluster, National University Health System, Singapore, Singapore
| | - Tony Kiat Hon Lim
- grid.163555.10000 0000 9486 5048Department of Anatomical Pathology, Singapore General Hospital, Singapore, 169608 Singapore
| | - Wei-Qiang Leow
- grid.163555.10000 0000 9486 5048Department of Anatomical Pathology, Singapore General Hospital, Singapore, 169608 Singapore
| | - Shihleone Loong
- grid.163555.10000 0000 9486 5048Department of Anatomical Pathology, Singapore General Hospital, Singapore, 169608 Singapore
| | - Tracy Jiezhen Loh
- grid.163555.10000 0000 9486 5048Department of Anatomical Pathology, Singapore General Hospital, Singapore, 169608 Singapore
| | - Wei Keat Wan
- grid.163555.10000 0000 9486 5048Department of Anatomical Pathology, Singapore General Hospital, Singapore, 169608 Singapore
| | - Gwyneth Shook Ting Soon
- grid.412106.00000 0004 0621 9599Department of Pathology, National University Hospital, Singapore, 119074 Singapore
| | - Yin Huei Pang
- grid.412106.00000 0004 0621 9599Department of Pathology, National University Hospital, Singapore, 119074 Singapore
| | - Boon Koon Yoong
- grid.10347.310000 0001 2308 5949Department of Surgery, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Diana Bee-Lan Ong
- grid.10347.310000 0001 2308 5949Department of Surgery, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Jasmine Lim
- grid.10347.310000 0001 2308 5949Department of Surgery, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Vanessa H. de Villa
- Department of Surgery and Center for Liver Health and Transplantation, The Medical City, Pasig City, Metro Manila Philippines
| | - Rouchelle D.dela Cruz
- Department of Laboratory Medicine and Pathology, The Medical City, Pasig City, Metro Manila Philippines
| | - Rawisak Chanwat
- grid.419173.90000 0000 9607 5779Hepato-Pancreato-Biliary Surgery Unit, Department of Surgery, National Cancer Institute, Bangkok, Thailand
| | - Jidapa Thammasiri
- grid.419173.90000 0000 9607 5779Division of Pathology, National Cancer Institute, Bangkok, Thailand
| | - Glenn K. Bonney
- grid.410759.e0000 0004 0451 6143Division of Hepatobiliary & Pancreatic Surgery, Department of Surgery, University Surgical Cluster, National University Health System, Singapore, Singapore
| | - Brian K. P. Goh
- grid.410724.40000 0004 0620 9745Department of Hepatopancreatobiliary and Transplant Surgery, Division of Surgery and Surgical Oncology, Singapore General Hospital and National Cancer Centre Singapore, Singapore, Singapore ,grid.428397.30000 0004 0385 0924Academic Clinical Programme for Surgery, Duke-NUS Medical School, Singapore, Singapore
| | - Greg Tucker-Kellogg
- grid.4280.e0000 0001 2180 6431Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Roger Sik Yin Foo
- grid.185448.40000 0004 0637 0221Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore ,grid.4280.e0000 0001 2180 6431Cardiovascular Disease Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore ,grid.4280.e0000 0001 2180 6431Cardiovascular Research Institute, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Pierce K. H. Chow
- grid.410724.40000 0004 0620 9745Department of Hepatopancreatobiliary and Transplant Surgery, Division of Surgery and Surgical Oncology, Singapore General Hospital and National Cancer Centre Singapore, Singapore, Singapore ,grid.410724.40000 0004 0620 9745Program in Clinical and Translational Liver Cancer Research, Division of Medical Science, National Cancer Center Singapore, Singapore, Singapore ,grid.428397.30000 0004 0385 0924Academic Clinical Programme for Surgery, Duke-NUS Medical School, Singapore, Singapore
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4
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Abstract
Introduction: Post-implantation rod deformation is anticipated in scoliosis surgery but the difference in rod deformation between titanium and cobalt chrome rod has not been elucidated. This study aims to compare the difference in rod deformation between two groups. Materials and Methods: Twenty-one adolescent idiopathic scoliosis (AIS) patients were recruited from a single center. The over-contoured concave rods were traced prior to insertion. Post-operative sagittal rod shape was determined from lateral radiographs. Rod deformation was determined using maximal rod deflection and angle of the tangents to rod end points. The differences between pre- and post-operative rod contour were analysed statistically. Rod deformation and thoracic kyphosis between two types of implants were analysed. Results: Both rods exhibited significant change of rod angle and deflection post-operatively. Curvature of the titanium rod and cobalt chrome rod decreased from 60.5° to 37°, and 51° to 28° respectively. Deflection of titanium rod and cobalt chrome rod reduced from 28mm to 23.5mm and 30mm to 17mm respectively. There was no significant difference between titanium and cobalt chrome groups with regard to rod angle (p=0.173) and deflection (p=0.654). Thoracic kyphosis was increased from 20° to 26° in titanium group but a reduction from 25° to 23° was noticed in cobalt chrome group, but these findings were not statistically significant. Conclusion: There was no statistical difference in rod deformation between the two groups. Thus, the use of titanium rod in correction of sagittal profile is not inferior in outcome compared with cobalt chrome but with lower cost.
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Affiliation(s)
- U Sia
- Department of Orthopaedics, Kementerian Kesihatan Malaysia, Hospital Umum Sarawak, Kuching, Malaysia.,Department of Orthopaedics, Universiti Malaysia Sarawak, Kota Samarahan, Malaysia
| | - B B Tan
- Department of Orthopaedics, Universiti Malaysia Sarawak, Kota Samarahan, Malaysia
| | - Y Y Teo
- Department of Orthopaedics, Universiti Malaysia Sarawak, Kota Samarahan, Malaysia
| | - C C Wong
- Department of Orthopaedics, Kementerian Kesihatan Malaysia, Hospital Umum Sarawak, Kuching, Malaysia.,Department of Orthopaedics, Universiti Malaysia Sarawak, Kota Samarahan, Malaysia
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5
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Faruk NA, Mohd-Amin MZ, Awang-Ojep DN, Teo YY, Wong CC. Three Level Thoracolumbar Spondylectomy for Recurrent Giant Cell Tumour of the Spine: A Case Report. Malays Orthop J 2018; 12:50-52. [PMID: 30555648 PMCID: PMC6287132 DOI: 10.5704/moj.1811.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Giant cell tumour (GCT) is a benign tumour but can be locally aggressive and with the potential to metastasise especially to the lungs. Successful treatments have been reported for long bone lesions; however, optimal surgical and medical treatment for spinal and sacral lesions are not well established. In treating spinal GCTs, the aim is to achieve complete tumour excision, restore spinal stability and decompress the neural tissues. The ideal surgical procedure is an en bloc spondylectomy or vertebrectomy, where all tumour cells are removed as recurrence is closely related to the extent of initial surgical excision. However, such a surgery has a high complication rate, such as dura tear and massive blood loss. We report a patient with a missed pathological fracture of T12 treated initially with a posterior subtraction osteotomy, who had recurrence three years after the index surgery and subsequently underwent a three level vertebrectomy and posterior spinal fusion.
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Affiliation(s)
- N A Faruk
- Department of Orthopaedics, Sarawak General Hospital, Kuching, Malaysia
| | - M Z Mohd-Amin
- Department of Orthopaedics, Universiti Malaysia Sarawak, Kota Samarahan, Malaysia
| | - D N Awang-Ojep
- *Department of Pathology, Universiti Malaysia Sarawak, Kota Samarahan, Malaysia
| | - Y Y Teo
- Department of Orthopaedics, Universiti Malaysia Sarawak, Kota Samarahan, Malaysia
| | - C C Wong
- Department of Orthopaedics, Sarawak General Hospital, Kuching, Malaysia
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6
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Tan-Koi WC, Lim ESH, Teo YY. Health regulatory communications of well-established safety-related pharmacogenomics associations in six developed countries: an evaluation of alignment. Pharmacogenomics J 2016; 17:121-127. [PMID: 26902540 DOI: 10.1038/tpj.2016.5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 11/25/2015] [Accepted: 01/20/2016] [Indexed: 02/06/2023]
Abstract
Recommendations on genetic testing are typically conveyed by drug regulatory authorities through drug labels, which are legal requirements for market authorization of drugs. We conducted a cross-sectional study of drug labels focusing on three crucial aspects of regulatory pharmacogenomics communications: (i) intent; (ii) interpretation in the local context; and (iii) implications of the genetic information. Labels of drugs associated with well-established safety-related genetic markers for adverse drug reactions across six developed countries of United States, Canada, United Kingdom, Australia, New Zealand and Singapore were reviewed. We found differing medical advice for genotype-positive HLA-B*15:02, HLA-A*31:01, UGT1A1*28 and CYP2D6 ultra-rapid metabolisers in breastfeeding women. This raises questions on implications to clinical practice between these countries. Varying ways of presenting at-risk population and allele frequencies also raises question in incorporating such information in drug labels. An international guidance addressing these crucial aspects of regulatory pharmacogenomic communications in drug labels is long overdue.
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Affiliation(s)
- W C Tan-Koi
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Evelyn S H Lim
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Y Y Teo
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore.,Life Sciences Institute, National University of Singapore, Singapore.,Department of Statistics and Applied Probability, National University of Singapore, Singapore.,NUS Graduate School for Integrative Science and Engineering, National University of Singapore, Singapore.,Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore
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7
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Sureisen M, Tan BB, Teo YY, Wong CC. A Rare Incidence of Breakage of tip of Micropituitary Forceps during Percutaneous Discectomy - How to Remove it: A Case Report. Malays Orthop J 2015; 9:58-60. [PMID: 28611913 PMCID: PMC5393138 DOI: 10.5704/moj.1511.009] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Breakage of the tip of the micropituitary forceps during spine surgery is a rare occurrence. Retrieval of the broken tip could be a challenge in minimally invasive surgeries due to limitation of access and retrieval instruments. We describe our experience in handling such a situation during percutaneous radiofrequency discectomy. The removal was attempted, without converting into open surgery, by utilising percutaneous endoscopic lumbar discectomy working cannula and guided by image intensifier. We were able to remove the fragment without any significant morbidity to the patient. This technique for removal has not been reported previously in the literature.
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Affiliation(s)
- M Sureisen
- Department of Orthopaedic Surgery, Sarawak General Hospital, Kuching, Malaysia
| | - B B Tan
- Department of Orthopaedic Surgery, University Malaysia Sarawak, Kota Samarahan, Malaysia
| | - Y Y Teo
- Department of Orthopaedic Surgery, University Malaysia Sarawak, Kota Samarahan, Malaysia
| | - C C Wong
- Department of Orthopaedic Surgery, Sarawak General Hospital, Kuching, Malaysia
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8
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Thuong NTT, Hawn TR, Chau TTH, Bang ND, Yen NTB, Thwaites GE, Teo YY, Seielstad M, Hibberd M, Lan NTN, Caws M, Farrar JJ, Dunstan SJ. Epiregulin (EREG) variation is associated with susceptibility to tuberculosis. Genes Immun 2011; 13:275-81. [PMID: 22170233 DOI: 10.1038/gene.2011.83] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Although host genetics influences susceptibility to Mycobacterium tuberculosis, the human genes regulating pathogenesis remain largely unknown. We used M. tuberculosis-stimulated macrophage gene expression profiling in conjunction with a case-control genetic association study to discover epiregulin (EREG), as a novel candidate tuberculosis (TB) susceptibility gene. Using a genome-wide association study dataset, we found that among the 21 genes with greater than 50-fold induction, EREG had the most polymorphisms associated with TB. We genotyped haplotype-tagging polymorphisms in discovery (N = 337 cases, N = 380 controls) and validation (N = 332 cases) datasets and an EREG polymorphism (rs7675690) was associated with susceptibility to TB (genotypic comparison; corrected P = 0.00007). rs7675690 was also associated more strongly with infections caused by the Beijing lineage of M. tuberculosis when compared with non-Beijing strains (controls vs Beijing, OR 7.81, P = 8.7 × 10(-5); non-Beijing, OR 3.13, P = 0.074). Furthermore, EREG expression was induced in monocytes and peripheral blood mononuclear cells stimulated with M. tuberculosis as well as TLR4 and TLR2/1/6 ligands. In murine macrophages, EREG expression induced by M. tuberculosis was MYD88- and TLR2-dependent. Together, these data provide the first evidence for an important role for EREG as a susceptibility gene for human TB.
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Affiliation(s)
- N T T Thuong
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
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9
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Tan EK, Lu CS, Peng R, Teo YY, Wu-Chou YH, Chen RS, Weng YH, Chen CM, Fung HC, Tan LC, Zhang ZJ, An XK, Lee-Chen GJ, Lee MC, Fook-Chong S, Burgunder JM, Wu RM, Wu YR. Analysis of the UCHL1 genetic variant in Parkinson's disease among Chinese. Neurobiol Aging 2009; 31:2194-6. [PMID: 19329225 DOI: 10.1016/j.neurobiolaging.2008.11.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2008] [Accepted: 11/29/2008] [Indexed: 10/21/2022]
Abstract
The inverse association of the functional ubiquitin carboxy-terminal hydrolase L1 (UCHL1) S18Y variant with Parkinson's disease (PD) among Caucasian populations has been debated. We conducted a large-scale analysis to investigate the age-of-onset effect of the UCHL1 variant in PD among ethnic Chinese. Individual data sets from 5 centers comprising a total of 4088 study subjects were analyzed. In the univariate analysis, only data from 1 center showed a trend towards a protective effect among young subjects. However, in the combined analysis, no significant association between the UCHL1 variant and PD was detected (A allele frequency 0.531 vs. 0.528, p=0.87, OR 1.01, 95% CI 0.92-1.1). Among subjects less than 60 years old, the OR is 0.99 (95% CI 0.84-1.16, p=0.88). A multivariate logistic regression analysis showed that family history, UCHL1 variant and the interaction of UCHL1 variant and age at onset (p=0.816) were not significantly associated with PD.
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Affiliation(s)
- E K Tan
- Department of Neurology, Singapore General Hospital, National Neuroscience Institute, Singapore.
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10
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Abstract
We introduce a simple and yet scientifically objective criterion for identifying SNPs with genotyping errors due to poor clustering. This yields a metric for assessing the stability of the assigned genotypes by evaluating the extent of discordance between the calls made with the unperturbed and perturbed intensities. The efficacy of the metric is evaluated by: (1) estimating the extent of over-dispersion of the Hardy-Weinberg equilibrium chi-square test statistics; (2) an interim case-control study, where we investigated the efficacy of the introduced metric and standard quality control filters in reducing the number of SNPs with evidence of phenotypic association which are attributed to genotyping errors; (3) investigating the call and concordance rates of SNPs identified by perturbation analysis which have been genotyped on both Affymetrix and Illumina platforms. Removing SNPs identified by the extent of discordance can reduce the degree of over-dispersion of the HWE test statistic. Sensible use of perturbation analysis in an association study can correctly identify SNPs with problematic genotyping, reducing the number required for visual inspection. SNPs identified by perturbation analysis had lower call and concordance rates, and removal of these SNPs significantly improved the performance for the remaining SNPs.
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Affiliation(s)
- Y Y Teo
- Wellcome Trust Centre for Human Genetics, University of Oxford, United Kingdom.
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11
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Tan EK, Lee J, Chen CP, Teo YY, Zhao Y, Lee WL. SORL1 haplotypes modulate risk of Alzheimer's disease in Chinese. Neurobiol Aging 2007; 30:1048-51. [PMID: 18063222 DOI: 10.1016/j.neurobiolaging.2007.10.013] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2007] [Revised: 10/18/2007] [Accepted: 10/25/2007] [Indexed: 11/17/2022]
Abstract
Genetic variants of the neuronal sortilin-related receptor (SORL1) have been demonstrated to modulate the risk of Alzheimer's disease (AD) in different American and European populations [Rogaeva, E., Meng, Y., Lee, J.H., Gu, Y., Kawarai, T., Zou, F., Katayama, T., Baldwin, C.T., Cheng, R., Hasegawa, H., Chen, F., Shibata, N., Lunetta, K.L., Pardossi-Piquard, R., Bohm, C., Wakutani, Y., Cupples, L.A., Cuenco, K.T., Green, R.C., Pinessi, L., Rainero, I., Sorbi, S., Bruni, A., Duara, R., Friedland, R.P., Inzelberg, R., Hampe, W., Bujo, H., Song, Y.Q., Andersen, O.M., Willnow, T.E., Graff-Radford, N., Petersen, R.C., Dickson, D., Der, S.D., Fraser, P.E., Schmitt-Ulms, G., Younkin, S., Mayeux, R., Farrer, L.A., St George-Hyslop, P., 2007. The neuronal sortilin-related receptor SORL1 is genetically associated with Alzheimer disease. Nat. Genet. 39 (2), 168-177]. We conducted haloptype analysis involving two genetic clusters of SORL1 in AD and controls among Han Chinese. rs3824968 (SNP 23) was associated with an increased risk of AD, and there was a trend towards association for rs1699102 (SNP 22) and rs2282649 (SNP 24). More robust associations were found for three-loci haplotypes. In particular, the GCA haplotype at SNPs 19-22-23 was associated with an increased risk (odds ratio 1.4), and CTC haplotype at SNPs 19-22-23 and TCT at SNPs 22-23-24 a decreased risk (odds ratio 0.67) of AD. The complete absence of some at-risk North European haplotypes in our Chinese study subjects was likely due to different ancestral origins, with allelic heterogeneity among races. However, our study suggests that certain SORL1 haplotypes at SNPs 19-24 modulated risk of AD in our Chinese population.
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Affiliation(s)
- E K Tan
- Department of Neurology, Singapore General Hospital, Singapore, Singapore.
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12
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Tan EK, Lu ZY, Fook-Chong SMC, Tan E, Shen H, Chua E, Yih Y, Teo YY, Zhao Y. Exploring an interaction of adenosine A2A receptor variability with coffee and tea intake in Parkinson's disease. Am J Med Genet B Neuropsychiatr Genet 2006; 141B:634-6. [PMID: 16823803 DOI: 10.1002/ajmg.b.30359] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [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: 11/11/2022]
Abstract
Caffeine is an adenosine receptor A1 and A2A receptor antagonist and a putative functional genetic variant of the A2A receptor (2592C > Tins) mediates caffeine-induced anxiety. Here we investigated the potential interaction of this A2A genetic variant with the quantity of coffee and tea intake and their relationship with the risk of PD. A total of 441 subjects consisting of 222 PD and 219 race, gender and age matched controls were included. A multivariate analysis of the variables including the 2592C > Tins A2A genotypes, age of onset, gender, and the quantity of tea and coffee intake, interaction of the A2A genotypes with coffee intake, interaction of A2A genotypes with tea intake demonstrated the quantity of coffee intake to be significantly associated with PD (P < 0.0005, OR = 0.922, 95% CI: 0.881, 0.964). However, there was no significant interaction of the A2A genotypes with the quantity of coffee and tea intake in modulating the risk of PD. The dose dependent protective effect of coffee intake in PD was independent of the 2592C > Tins A2A genotype suggesting that the pharmacogenetic action of caffeine in PD may be mediated differently from other caffeine-induced neurologic syndromes.
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Affiliation(s)
- E K Tan
- Department of Neurology, Singapore General Hospital, Singapore
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13
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Tan EK, Chan DKY, Ng PW, Woo J, Teo YY, Tang K, Wong LP, Chong SS, Tan C, Shen H, Zhao Y, Lee CGL. Effect of MDR1 Haplotype on Risk of Parkinson Disease. ACTA ACUST UNITED AC 2005; 62:460-4. [PMID: 15767512 DOI: 10.1001/archneur.62.3.460] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
BACKGROUND MDR1, a multidrug transporter, encodes a P-glycoprotein that regulates the bioavailability of xenobiotics and is highly expressed at the blood-brain-barrier. Two single nucleotide polymorphisms (SNPs) (e21/2677[G/T/A] and e26/3435[C/T]) in the MDR1 gene can lead to differences in MDR1 expression and function. Specific MDR1 alleles of the 2 SNPs are positively selected among ethnic Chinese but not in the white population. OBJECTIVE To determine whether specific haplotypes formed by SNPs e21/2677 and e26/3435 may protect against Parkinson disease (PD) among ethnic Chinese in Hong Kong. DESIGN Case-control study. SETTING Tertiary referral centers in Hong Kong. SUBJECTS One hundred eighty-five patients with PD and 206 control subjects. INTERVENTIONS The two SNPs were amplified in a single multiplex polymerase chain reaction. Five other SNPs that span 100 kilobases of the gene were also analyzed. MAIN OUTCOME MEASURES Haplotypes frequencies, degree of haplotype association with the disease status, and estimated odds ratio for each haplotype with associated 95% confidence intervals. RESULTS In addition to 2677 G-->T/A (exon 21) and 3435 C-->T (exon 26), the other SNPs that were analyzed were -41 A-->G (intron -1), -145 C-->G (exon 1), -129 T-->C (exon 1), 1236 T-->C (exon 12), and 4036 A-->G (exon 28). Haplotypes containing SNPs e21/2677 and e26/3435 were found to be significantly associated with risk of PD. In particular, the 2677T-3435T haplotype was strongly associated with a reduced risk of PD (P<.001; chi(2) = 14.521; odds ratio, 0.33; 95% confidence interval, 0.19-0.59). CONCLUSIONS An MDR1 haplotype containing SNPs e21/2677T and e26/3435T protects against PD in ethnic Chinese, compatible with the observation of a recent positive selection of the T alleles of these 2 SNPs in this ethnic population.
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Affiliation(s)
- Eng-King Tan
- Department of Neurology, Singapore General Hospital, Singapore.
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Tan EK, Drozdzik M, Bialecka M, Honczarenko K, Klodowska-Duda G, Teo YY, Tang K, Wong LP, Chong SS, Tan C, Yew K, Zhao Y, Lee CG. Analysis of MDR1 haplotypes in Parkinson's disease in a white population. Neurosci Lett 2004; 372:240-4. [PMID: 15542248 DOI: 10.1016/j.neulet.2004.09.046] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2004] [Revised: 09/22/2004] [Accepted: 09/22/2004] [Indexed: 11/20/2022]
Abstract
The MDR1 multidrug transporter is important in regulating environmental xenobiotics and hence may play a causative role in Parkinson's disease (PD). MDR1 haplotype comprising 2677 G > T/A and 3435 C > T may be protective against PD. Using a case control methodology, we investigated the association of MDR1 haplotypes (single nucleotide polymorphisms (SNPs) 2677 G > T/A and 3435 C > T) in a Polish PD population. Seven SNPs, extending from the promoter to exon 28 of the MDR1 gene in 158 PD patients and 139 healthy controls were evaluated. Specifically we examined the association of haplotypes containing SNPs 2677 G > T/A and 3435 C > T and risk of PD. The multivariate logistic regression model was used to evaluate the effects of the covariates on the phenotypes. Haplotypes' frequencies were estimated using the Expectation-Maximization algorithm. The frequency of each individual SNPs; -41 A > G (intron -1), -145 C > G (exon 1), -129 T > C (exon 1), 1236 T > C (exon 12), 2677 G > T/A (exon 21), 3435 C > T (exon 26), and 4036 A > G (exon 28) did not differ between PD and controls. However, there was a trend towards significance in PD patients having the haplotype 2677G-3435C (p < 0.09, chi-square 2.85, odds ratio 0.25, 95% CI 0.06-1.08). Haplotype constructs of the other loci did not differ significantly between the two groups. There was a weak protective effect of the haplotype 2677G-3435C in our white population. However, the MDR1 haplotypes did not generally modulate the risk of PD.
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Affiliation(s)
- Eng-King Tan
- Department of Neurology, Singapore General Hospital, Outram Road, Singapore 169608, Singapore.
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Tan EK, Chai A, Teo YY, Zhao Y, Tan C, Shen H, Chandran VR, Teoh ML, Yih Y, Pavanni R, Wong MC, Puvan K, Lo YL, Yap E. Alpha-synuclein haplotypes implicated in risk of Parkinson's disease. Neurology 2004; 62:128-31. [PMID: 14718715 DOI: 10.1212/01.wnl.0000101721.25345.dc] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The authors examined four- and six-loci haplotype constructs (from five single nucleotide polymorphisms and three microsatellite regions) of the alpha-synuclein gene in patients with Parkinson's disease (PD) and controls in an ethnic Chinese population. Logistic regression analysis demonstrated an association of NACP-Rep1 (p = 0.002) and L478 (p < 0.0001) with risk of PD after correction for the effects of age, sex, and the other polymorphic loci. Specific four-loci and six-loci haplotypes were significantly associated with an increased or decreased risk of PD.
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Affiliation(s)
- E K Tan
- Department of Neurology, Singapore General Hospital, Singapore.
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