26 results on '"Huei San Leong"'
Search Results
2. Retrovirus Mediated Malignant Transformation of Mouse Embryonic Fibroblasts
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Huei San Leong and Marnie Blewitt
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Biology (General) ,QH301-705.5 - Abstract
Cellular transformation is a widely used method to artificially induce cells to form tumours in vivo. Here, we describe the methodology for malignant transformation of mouse embryonic fibroblasts (MEFs) for transplantation into immunodeficient nude mice, as used in Leong et al. (2013). The two-step process involves: 1) down-regulation of Trp53 expression using a short hairpin RNA (shRNA); and 2) overexpression of the oncogenic HRasV12 protein. Reduction of Trp53 expression leads to cell immortalisation, and the subsequent overexpression of oncogenic HRasV12 results in malignant transformation of a cell.
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- 2013
- Full Text
- View/download PDF
3. Optimising clinical care through CDH1-specific germline variant curation: improvement of clinical assertions and updated curation guidelines
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Xi Luo, Jamie L Maciaszek, Bryony A Thompson, Huei San Leong, Katherine Dixon, Sónia Sousa, Michael Anderson, Maegan E Roberts, Kristy Lee, Amanda B Spurdle, Arjen R Mensenkamp, Terra Brannan, Carolina Pardo, Liying Zhang, Tina Pesaran, Sainan Wei, Grace-Ann Fasaye, Chimene Kesserwan, Brian H Shirts, Jeremy L Davis, Carla Oliveira, Sharon E Plon, Kasmintan A Schrader, and Rachid Karam
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All institutes and research themes of the Radboud University Medical Center ,Women's cancers Radboud Institute for Molecular Life Sciences [Radboudumc 17] ,Genetics ,Genetics (clinical) - Abstract
BackgroundGermline pathogenic variants inCDH1are associated with increased risk of diffuse gastric cancer and lobular breast cancer. Risk reduction strategies include consideration of prophylactic surgery, thereby making accurate interpretation of germlineCDH1variants critical for physicians deciding on these procedures. The Clinical Genome Resource (ClinGen)CDH1Variant Curation Expert Panel (VCEP) developed specifications forCDH1variant curation with a goal to resolve variants of uncertain significance (VUS) and with ClinVar conflicting interpretations and continues to update these specifications.MethodsCDH1variant classification specifications were modified based on updated genetic testing clinical criteria, new recommendations from ClinGen and expert knowledge from ongoingCDH1variant curations. TheCDH1VCEP reviewed 273 variants using updatedCDH1specifications and incorporated published and unpublished data provided by diagnostic laboratories.ResultsUpdatedCDH1-specific interpretation guidelines include 11 major modifications since the initial specifications from 2018. Using the refined guidelines, 97% (36 of 37) of variants with ClinVar conflicting interpretations were resolved to benign, likely benign, likely pathogenic or pathogenic, and 35% (15 of 43) of VUS were resolved to benign or likely benign. Overall, 88% (239 of 273) of curated variants had non-VUS classifications. To date, variants classified as pathogenic are either nonsense, frameshift, splicing, or affecting the translation initiation codon, and the only missense variants classified as pathogenic or likely pathogenic have been shown to affect splicing.ConclusionsThe development and evolution ofCDH1-specific criteria by the expert panel resulted in decreased uncertain and conflicting interpretations of variants in this clinically actionable gene, which can ultimately lead to more effective clinical management recommendations.
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- 2023
4. Supplementary Material from Epigenetic Regulator Smchd1 Functions as a Tumor Suppressor
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Marnie E. Blewitt, Douglas J. Hilton, Warren S. Alexander, Gordon K. Smyth, Ian J. Majewski, James M. Murphy, Miha Pakusch, Jason Corbin, Stanley Lee, Yifang Hu, Kelan Chen, and Huei San Leong
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Supplementary Material PDF file - 709K, Supplementary Tables 1 and 2, supplementary methods, supplementary figure legends and supplementary figures
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- 2023
5. Supplementary Tables S3-S4 from Epigenetic Regulator Smchd1 Functions as a Tumor Suppressor
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Marnie E. Blewitt, Douglas J. Hilton, Warren S. Alexander, Gordon K. Smyth, Ian J. Majewski, James M. Murphy, Miha Pakusch, Jason Corbin, Stanley Lee, Yifang Hu, Kelan Chen, and Huei San Leong
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Supplementary Tables S3-S4 XLSX file - 576K, Gene set analysis (Camera) and differentially expressed genes
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- 2023
6. Optimising clinical care through
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Xi, Luo, Jamie L, Maciaszek, Bryony A, Thompson, Huei San, Leong, Katherine, Dixon, Sónia, Sousa, Michael, Anderson, Maegan E, Roberts, Kristy, Lee, Amanda B, Spurdle, Arjen R, Mensenkamp, Terra, Brannan, Carolina, Pardo, Liying, Zhang, Tina, Pesaran, Sainan, Wei, Grace-Ann, Fasaye, Chimene, Kesserwan, Brian H, Shirts, Jeremy L, Davis, Carla, Oliveira, Sharon E, Plon, Kasmintan A, Schrader, and Rachid, Karam
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Article - Abstract
BACKGROUND: Germline pathogenic variants in CDH1 are associated with increased risk for diffuse gastric cancer and lobular breast cancer. Risk-reduction strategies include consideration of prophylactic surgery, thereby making accurate interpretation of germline CDH1 variants critical for physicians deciding upon these procedures. The Clinical Genome Resource (ClinGen) CDH1 Variant Curation Expert Panel (VCEP) developed specifications for CDH1 variant curation with a goal to resolve variants of uncertain significance (VUS) and with ClinVar conflicting interpretations and continues to update these specifications. METHODS: CDH1 variant classification specifications were modified based on updated genetic testing clinical criteria, new recommendations from ClinGen, and expert knowledge from ongoing CDH1 variant curations. The CDH1 VCEP reviewed 273 variants using updated CDH1 specifications and incorporated published and unpublished data provided by diagnostic laboratories. RESULTS: Updated CDH1-specific interpretation guidelines include eleven major modifications since the initial specifications from 2018. Using the refined guidelines, 97% (36/37) of variants with ClinVar conflicting interpretations were resolved into benign, likely benign, likely pathogenic, or pathogenic, and 35% (15/43) of VUS were resolved into benign or likely benign. Overall, 88% (239/273) of curated variants had non-VUS classifications. To date, the only missense variants classified as pathogenic or likely pathogenic are known to affect splicing and therefore, functional studies are not validated for use in the interpretation of CDH1 variants. CONCLUSIONS: The development and evolution of CDH1-specific criteria by the expert panel results in decreased uncertain and conflicting interpretations of variants in this clinically actionable gene which ultimately leads to more effective clinical management recommendations.
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- 2022
7. Shariant platform: Enabling evidence sharing across Australian clinical genetic-testing laboratories to support variant interpretation
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Emma Tudini, James Andrews, David M. Lawrence, Sarah L. King-Smith, Naomi Baker, Leanne Baxter, John Beilby, Bruce Bennetts, Victoria Beshay, Michael Black, Tiffany F. Boughtwood, Kristian Brion, Pak Leng Cheong, Michael Christie, John Christodoulou, Belinda Chong, Kathy Cox, Mark R. Davis, Lucas Dejong, Marcel E. Dinger, Kenneth D. Doig, Evelyn Douglas, Andrew Dubowsky, Melissa Ellul, Andrew Fellowes, Katrina Fisk, Cristina Fortuno, Kathryn Friend, Renee L. Gallagher, Song Gao, Emma Hackett, Johanna Hadler, Michael Hipwell, Gladys Ho, Georgina Hollway, Amanda J. Hooper, Karin S. Kassahn, Rahul Krishnaraj, Chiyan Lau, Huong Le, Huei San Leong, Ben Lundie, Sebastian Lunke, Anthony Marty, Mary McPhillips, Lan T. Nguyen, Katia Nones, Kristen Palmer, John V. Pearson, Michael C.J. Quinn, Lesley H. Rawlings, Simon Sadedin, Louisa Sanchez, Andreas W. Schreiber, Emanouil Sigalas, Aygul Simsek, Julien Soubrier, Zornitza Stark, Bryony A. Thompson, James U, Cassandra G. Vakulin, Amanda V. Wells, Cheryl A. Wise, Rick Woods, Andrew Ziolkowski, Marie-Jo Brion, Hamish S. Scott, Natalie P. Thorne, Amanda B. Spurdle, Lauren Akesson, Richard Allcock, Katie Ashton, Damon A. Bell, Anna Brown, Michael Buckley, John R. Burnett, Linda Burrows, Alicia Byrne, Eva Chan, Corrina Cliffe, Roderick Clifton-Bligh, Susan Dooley, Miriam Fanjul Fernandez, Elizabeth Farnsworth, Thuong Ha, Denae Henry, Duncan Holds, Katherine Holman, Matilda Jackson, Sinlay Kang, Catherine Luxford, Sam McManus, Rachael Mehrtens, Cliff Meldrum, David Mossman, Sarah-Jane Pantaleo, Dean Phelan, Electra Pontikinas, Anja Ravine, Tony Roscioli, Rodney Scott, Keryn Simons, Oliver Vanwageningen, Tudini, Emma, Andrews, James, Lawrence, David M., King-Smith, Sarah L., Schreiber, Andreas W, James, U, and Shariant Consortium
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genomic variant ,variant interpretations ,Databases, Genetic ,Technology Review ,Genetics ,Australia ,Humans ,Genetic Variation ,Genetic Testing ,Laboratories ,Genetics (clinical) ,Australian laboratories - Abstract
Sharing genomic variant interpretations across laboratories promotes consistency in variant assertions. A landscape analysis of Australian clinical genetic-testing laboratories in 2017 identified that, despite the national-accreditation-body recommendations encouraging laboratories to submit genotypic data to clinical databases, fewer than 300 variants had been shared to the ClinVar public database. Consultations with Australian laboratories identified resource constraints limiting routine application of manual processes, consent issues, and differences in interpretation systems as barriers to sharing. This information was used to define key needs and solutions required to enable national sharing of variant interpretations. The Shariant platform, using both the GRCh37 and GRCh38 genome builds, was developed to enable ongoing sharing of variant interpretations and associated evidence between Australian clinical genetic-testing laboratories. Where possible, two-way automated sharing was implemented so that disruption to laboratory workflows would be minimized. Terms of use were developed through consultation and currently restrict access to Australian clinical genetic-testing laboratories. Shariant was designed to store and compare structured evidence, to promote and record resolution of inter-laboratory classification discrepancies, and to streamline the submission of variant assertions to ClinVar. As of December 2021, more than 14,000 largely prospectively curated variant records from 11 participating laboratories have been shared. Discrepant classifications have been identified for 11% (28/260) of variants submitted by more than one laboratory. We have demonstrated that co-design with clinical laboratories is vital to developing and implementing a national variant-interpretation sharing effort. This approach has improved inter-laboratory concordance and enabled opportunities to standardize interpretation practices.
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- 2022
8. Development and Validation of the Gene Expression Predictor of High-grade Serous Ovarian Carcinoma Molecular SubTYPE (PrOTYPE)
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Sven Mahner, Robertson Mackenzie, Aline Talhouk, Linda E. Kelemen, Gottfried E. Konecny, Jennifer Alsop, Rosalind Glasspool, Chiu-Chen Tseng, Joy Hendley, Dennis J. Slamon, Jennifer A. Doherty, Andrew Berchuck, Anna H. Wu, Anna M. Piskorz, Chen Wang, Cristina Rodríguez-Antona, D.G.H. de Silva, Valerie Rhenius, Peter A. Fasching, Stacey J. Winham, Gary L. Keeney, Teodora Goranova, Joshy George, Jan Lubinski, Michelle J. Henderson, Rex C. Bentley, Jenny Lester, Sabine Behrens, Joellen M. Schildkraut, Michael E. Carney, Timothy Budden, David G. Huntsman, Oleg Oszurek, Michael S. Anglesio, Jacek Gronwald, Ruby Yun-Ju Huang, Martin Köbel, Javier Benitez, Martin Widschwendter, Melissa C. Larson, Raghwa Sharma, Clara Bodelon, Usha Menon, Janusz Menkiszak, Blake Gilks, María Josefa Mosteiro García, Jesús García-Donas, Wafaa Elatre, Scott H. Kaufmann, Paul Haluska, Pamela J. Thompson, Boris Winterhoff, Susan J. Ramus, Louise A. Brinton, Simon A. Gayther, Mary Anne Rossing, Georgia Chenevix-Trench, Hugh Luk, Jolanta Lissowska, Marc T. Goodman, Billy Chen, Beth Y. Karlan, Naveena Singh, Sian Fereday, Mark E. Sherman, Ana Osorio, Lynne R. Wilkens, Maria P. Intermaggio, Brenda Y. Hernandez, Britton Trabert, Esther Herpel, Mercedes Jimenez-Linan, Janine Senz, Geyi Liu, Celeste Leigh Pearce, Samuel C Y Leong, Iain A. McNeish, Isabelle Ray-Coquard, Susana Banerjee, Malcolm C. Pike, Liz-Anne Lewsley, Helen Steed, Honglin Song, Samantha Hinsley, David D.L. Bowtell, James D. Brenton, Holly R. Harris, Tuan Zea Tan, Cezary Cybulski, Alicia Beeghly-Fadiel, A. Toloczko, Nikilyn Nevins, Robert S. Brown, Darren Ennis, Stephanie Chen, Euan A. Stronach, José Palacios, Sandra Orsulic, Anna deFazio, Geoff Macintyre, Kara L. Cushing-Haugen, Mila Volchek, Aleksandra Gentry-Maharaj, Jenny Chang-Claude, Ellen L. Goode, Paul D.P. Pharoah, Hanwei Sudderuddin, Stefan Kommoss, Derek S. Chiu, Huei San Leong, Peter Sinn, Catherine J. Kennedy, Chloe Karpinskyj, Alison Brand, Amy Lum, Veronica Chow, Nicolas Wentzensen, Tayyebeh M. Nazeran, Nadia Traficante, Dustin Johnson, Yoke-Eng Chiew, Casey S. Greene, Jennifer M Koziak, Renée T. Fortner, Imperial College Healthcare NHS Trust- BRC Funding, Cancer Research UK, Ovarian Cancer Action, Talhouk, Aline [0000-0001-7760-410X], George, Joshy [0000-0001-8510-8229], Wang, Chen [0000-0003-2638-3081], Tan, Tuan Zea [0000-0001-6624-1593], Behrens, Sabine [0000-0002-9714-104X], Bodelon, Clara [0000-0002-6578-2678], Brinton, Louise [0000-0003-3853-8562], Fortner, Renée T [0000-0002-1426-8505], García-Donas, Jesús [0000-0001-7731-3601], Gentry-Maharaj, Aleksandra [0000-0001-7270-9762], Glasspool, Rosalind [0000-0002-5000-1680], Greene, Casey S [0000-0001-8713-9213], Harris, Holly R [0000-0002-2572-6727], Kaufmann, Scott H [0000-0002-4900-7145], Kennedy, Catherine J [0000-0002-4465-5784], Köbel, Martin [0000-0002-6615-2037], Koziak, Jennifer M [0000-0001-5830-0397], Lissowska, Jolanta [0000-0003-2695-5799], McNeish, Iain A [0000-0002-9387-7586], Menkiszak, Janusz [0000-0001-8279-7196], Hinsley, Samantha [0000-0001-6903-4688], Pike, Malcolm C [0000-0003-4891-1199], Rodriguez-Antona, Cristina [0000-0001-8750-7338], Sinn, Peter [0000-0003-2836-6699], Trabert, Britton [0000-0002-1539-6090], Widschwendter, Martin [0000-0002-7778-8380], Winham, Stacey J [0000-0002-8492-9102], Brenton, James D [0000-0002-5738-6683], Brown, Robert [0000-0001-7960-5755], Chang-Claude, Jenny [0000-0001-8919-1971], deFazio, Anna [0000-0003-0057-4744], Fasching, Peter A [0000-0003-4885-8471], Kelemen, Linda E [0000-0003-4362-9784], Menon, Usha [0000-0003-3708-1732], Pharoah, Paul DP [0000-0001-8494-732X], Ramus, Susan J [0000-0003-0005-7798], Doherty, Jennifer A [0000-0002-1454-8187], Anglesio, Michael S [0000-0003-1639-5003], and Apollo - University of Cambridge Repository
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0301 basic medicine ,Oncology ,Cancer Research ,medicine.medical_specialty ,Neoplasm, Residual ,Bevacizumab ,03 medical and health sciences ,Ovarian tumor ,Lymphocytes, Tumor-Infiltrating ,0302 clinical medicine ,Ovarian carcinoma ,Internal medicine ,medicine ,Humans ,1112 Oncology and Carcinogenesis ,Oncology & Carcinogenesis ,Stage (cooking) ,Aged ,Ovarian Neoplasms ,business.industry ,Cystadenoma, Serous ,Cancer ,Middle Aged ,Precision medicine ,Omics ,medicine.disease ,Neoplasm Proteins ,Gene Expression Regulation, Neoplastic ,Serous fluid ,030104 developmental biology ,030220 oncology & carcinogenesis ,Female ,Neoplasm Grading ,Transcriptome ,business ,Algorithms ,medicine.drug - Abstract
Purpose: Gene expression–based molecular subtypes of high-grade serous tubo-ovarian cancer (HGSOC), demonstrated across multiple studies, may provide improved stratification for molecularly targeted trials. However, evaluation of clinical utility has been hindered by nonstandardized methods, which are not applicable in a clinical setting. We sought to generate a clinical grade minimal gene set assay for classification of individual tumor specimens into HGSOC subtypes and confirm previously reported subtype-associated features. Experimental Design: Adopting two independent approaches, we derived and internally validated algorithms for subtype prediction using published gene expression data from 1,650 tumors. We applied resulting models to NanoString data on 3,829 HGSOCs from the Ovarian Tumor Tissue Analysis consortium. We further developed, confirmed, and validated a reduced, minimal gene set predictor, with methods suitable for a single-patient setting. Results: Gene expression data were used to derive the predictor of high-grade serous ovarian carcinoma molecular subtype (PrOTYPE) assay. We established a de facto standard as a consensus of two parallel approaches. PrOTYPE subtypes are significantly associated with age, stage, residual disease, tumor-infiltrating lymphocytes, and outcome. The locked-down clinical grade PrOTYPE test includes a model with 55 genes that predicted gene expression subtype with >95% accuracy that was maintained in all analytic and biological validations. Conclusions: We validated the PrOTYPE assay following the Institute of Medicine guidelines for the development of omics-based tests. This fully defined and locked-down clinical grade assay will enable trial design with molecular subtype stratification and allow for objective assessment of the predictive value of HGSOC molecular subtypes in precision medicine applications. See related commentary by McMullen et al., p. 5271
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- 2020
9. Suspected clonal hematopoiesis as a natural functional assay of TP53 germline variant pathogenicity
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Paul A. James, Amanda B. Spurdle, Victoria Beshay, Jill S. Dolinsky, Jeffrey N. Weitzel, Kelly McGoldrick, Tina Pesaran, Huei San Leong, Lily Hoang, and Cristina Fortuno
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Genetics ,Functional assay ,Clonal hematopoiesis ,Variant allele ,Biology ,Pathogenicity ,Germline ,Humans ,Genetic Predisposition to Disease ,Clonal Hematopoiesis ,Tumor Suppressor Protein p53 ,Gene ,Genetics (clinical) ,Germ-Line Mutation - Abstract
Some variants identified by multigene panel testing of DNA from blood present with low variant allele fraction (VAF), often a manifestation of clonal hematopoiesis. Research has shown that the proportion of variants with low VAF is especially high in TP53, the Li-Fraumeni syndrome gene. Based on the hypothesis that variants with low VAF are positively selected as drivers of clonal hematopoiesis, we investigated the use of VAF as a predictor of TP53 germline variant pathogenicity.We used data from 260,681 TP53 variants identified at 2 laboratories to compare the distribution of pathogenic and benign variants at different VAF intervals.Likelihood ratios toward pathogenicity associated with a VAF26% equated to the American College of Medical Genetics/Association of Molecular Pathology strong strength level and were applicable for 1 in 5 variants of unknown significance.In conclusion, detection of variants with low VAF in blood can be considered an in vivo functional assay to aid assessment of TP53 variant pathogenicity.
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- 2021
10. Publisher Correction: CNspector: a web-based tool for visualisation and clinical diagnosis of copy number variation from next generation sequencing
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Richard Lupat, Jason Li, Jason Ellul, Satwica Yerneni, Anthony T. Papenfuss, Georgina L Ryland, Andrew Fellowes, Piers Blombery, Stephen B. Fox, Ella R. Thompson, Huei San Leong, Michael Dickinson, Amit Kumar, John F. Markham, and Wasanthi De Silva
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Multidisciplinary ,Information retrieval ,business.industry ,Computer science ,Published Erratum ,lcsh:R ,MEDLINE ,lcsh:Medicine ,DNA sequencing ,Visualization ,Clinical diagnosis ,Web application ,lcsh:Q ,Copy-number variation ,lcsh:Science ,business - Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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- 2020
11. SDH-deficient renal cell carcinoma associated with biallelic mutation in succinate dehydrogenase A: comprehensive genetic profiling and its relation to therapy response
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Lisa Koe, Stephen B. Fox, Deme Karikios, Jeffrey D Plew, Huei San Leong, Andrew Fellowes, David Y.H. Choong, Huiling Xu, Christopher R McEvoy, and Owen W.J. Prall
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0301 basic medicine ,Biallelic Mutation ,Cancer Research ,Somatic cell ,SDHA ,Context (language use) ,Case Report ,macromolecular substances ,Biology ,medicine.disease_cause ,urologic and male genital diseases ,lcsh:RC254-282 ,Germline ,03 medical and health sciences ,0302 clinical medicine ,medicine ,Genetic testing ,medicine.diagnostic_test ,Cancer ,medicine.disease ,lcsh:Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,030104 developmental biology ,Oncology ,030220 oncology & carcinogenesis ,Cancer research ,Carcinogenesis - Abstract
Succinate dehydrogenase (SDH)-deficient renal cell carcinoma (RCC) is a rare RCC subtype that is caused by biallelic mutation of one of the four subunits of the SDH complex (SDHA, B, C, and D) and results in inactivation of the SDH enzyme. Here we describe a case of genetically characterized SDH-deficient RCC caused by biallelic (germline plus somatic) SDHA mutations. SDHA pathogenic variants were detected using comprehensive genomic profiling and SDH absence was subsequently confirmed by immunohistochemistry. Very little is known regarding the genomic context of SDH-deficient RCC. Interestingly we found genomic amplifications commonly observed in RCC but there was an absence of additional variants in common cancer driver genes. Prior to genetic testing a PD-1 inhibitor treatment was administered. However, following the genetic results a succession of tyrosine kinase inhibitors were administered as targeted treatment options and we highlight how the genetic results provide a rationale for their effectiveness. We also describe how the genetic results benefited the patient by empowering him to adopt dietary and lifestyle changes in accordance with knowledge of the mechanisms of SDH-related tumorigenesis.
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- 2018
12. CNspector: a web-based tool for visualisation and clinical diagnosis of copy number variation from next generation sequencing
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Jason Li, Georgina L Ryland, Richard Lupat, Jason Ellul, Satwica Yerneni, Andrew Fellowes, Anthony T. Papenfuss, Stephen B. Fox, Ella R. Thompson, Michael Dickinson, Huei San Leong, Amit Kumar, Wasanthi De Silva, John F. Markham, and Piers Blombery
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0301 basic medicine ,Source code ,Computer science ,Somatic cell ,lcsh:Medicine ,Web Browser ,medicine.disease_cause ,Genome ,Germline ,Exon ,chemistry.chemical_compound ,0302 clinical medicine ,Chromosome Duplication ,Gene duplication ,Copy-number variation ,lcsh:Science ,media_common ,Mutation ,Multidisciplinary ,medicine.diagnostic_test ,High-Throughput Nucleotide Sequencing ,Basal Cell Nevus Syndrome ,Exons ,Publisher Correction ,Chromosome Arm ,Chromosome Deletion ,DNA Copy Number Variations ,Sequence analysis ,media_common.quotation_subject ,Context (language use) ,Computational biology ,DNA sequencing ,03 medical and health sciences ,Chromosome (genetic algorithm) ,medicine ,Humans ,Web application ,Genetic testing ,Internet ,Genome, Human ,business.industry ,lcsh:R ,Chromosome ,Sequence Analysis, DNA ,030104 developmental biology ,chemistry ,Carcinoma, Basal Cell ,lcsh:Q ,Human genome ,business ,030217 neurology & neurosurgery ,DNA - Abstract
Next Generation Sequencing is now routinely used in the practice of diagnostic pathology to detect clinically relevant somatic and germline sequence variations in patient samples. However, clinical assessment of copy number variations (CNVs) and large-scale structural variations (SVs) is still challenging. While tools exist to estimate both, their results are typically presented separately in tables or static plots which can be difficult to read and are unable to show the context needed for clinical interpretation and reporting. We have addressed this problem with CNspector, a multi-scale interactive browser that shows CNVs in the context of other relevant genomic features to enable fast and effective clinical reporting. We illustrate the utility of CNspector at different genomic scales across a variety of sample types in a range of case studies. We show how CNspector can be used for diagnosis and reporting of exon-level deletions, focal gene-level amplifications, chromosome and chromosome arm level amplifications/deletions and in complex genomic rearrangements. CNspector is a web-based clinical variant browser tailored to the clinical application of next generation sequencing for CNV assessment. We have demonstrated the utility of this interactive software in typical applications across a range of tissue types and disease contexts encountered in the context of diagnostic pathology. CNspector is written in R and the source code is available for download under the GPL3 Licence from https://github.com/PapenfussLab/CNspector.
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- 2019
13. Profound MEK inhibitor response in a cutaneous melanoma harboring a GOLGA4-RAF1 fusion
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Judy Browning, Jayesh Desai, Stephen B. Fox, Dariush Etemadmoghadam, David Y.H. Choong, Chloe Khoo, Huiling Xu, Andrew Fellowes, Sophie Beck, Anthony Bell, Huei San Leong, Christopher R McEvoy, Richard W. Tothill, Owen W.J. Prall, Linda Mileshkin, David D.L. Bowtell, Kortnye Smith, Amir Iravani, Bindi M. Bates, David J Byrne, and Violeta Nastevski
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0301 basic medicine ,MAPK/ERK pathway ,Male ,Skin Neoplasms ,Oncogene Proteins, Fusion ,medicine.medical_treatment ,MAP Kinase Kinase 1 ,Autoantigens ,Targeted therapy ,03 medical and health sciences ,0302 clinical medicine ,CDKN2A ,Fluorodeoxyglucose F18 ,Medicine ,Humans ,Neoplasm Metastasis ,Extracellular Signal-Regulated MAP Kinases ,Melanoma ,Protein Kinase Inhibitors ,Alleles ,Cyclin-Dependent Kinase Inhibitor p16 ,beta Catenin ,Aged ,business.industry ,MEK inhibitor ,Concise Communication ,Cancer ,General Medicine ,medicine.disease ,Gene Expression Regulation, Neoplastic ,Proto-Oncogene Proteins c-raf ,030104 developmental biology ,Tumor progression ,030220 oncology & carcinogenesis ,Positron-Emission Tomography ,Cutaneous melanoma ,Cancer research ,business - Abstract
The serine/threonine kinases BRAF and CRAF are critical components of the MAPK signaling pathway that is activated in many cancer types. In approximately 1% of melanomas, BRAF or CRAF is activated through structural arrangements. We describe a metastatic melanoma with a GOLGA4-RAF1 fusion and pathogenic variants in catenin β 1 (CTNNB1) and cyclin-dependent kinase inhibitor 2A (CDKN2A). Anti–cytotoxic T-lymphocyte–associated protein 4/anti–programmed cell death 1 (anti-CTLA4/anti–PD-1) combination immunotherapy failed to control tumor progression. In the absence of other actionable variants, the patient was administered MEK inhibitor therapy on the basis of its potential action against RAF1 fusions. This resulted in a profound and clinically significant response. We demonstrated that GOLGA4-RAF1 expression was associated with ERK activation, elevated expression of the RAS/RAF downstream coeffector ETV5, and a high Ki67 index. These findings provide a rationale for the dramatic response to targeted therapy. This study shows that molecular characterization of treatment-resistant cancers can identify therapeutic targets and personalize therapy management, leading to improved patient outcomes.
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- 2019
14. Efficient molecular subtype classification of high-grade serous ovarian cancer
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Laura Galletta, Dariush Etemadmoghadam, Martin Köbel, Huei San Leong, Joshy George, David D.L. Bowtell, and Susan J. Ramus
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Gene expression profiling ,Serous fluid ,Microarray ,Sequence analysis ,Microarray analysis techniques ,Gene expression ,TaqMan ,Cancer research ,Biology ,Molecular biology ,Gene ,Pathology and Forensic Medicine - Abstract
High-grade serous carcinomas (HGSCs) account for approximately 70% of all epithelial ovarian cancers diagnosed. Using microarray gene expression profiling, we previously identified four molecular subtypes of HGSC: C1 (mesenchymal), C2 (immunoreactive), C4 (differentiated), and C5 (proliferative), which correlate with patient survival and have distinct biological features. Here, we describe molecular classification of HGSC based on a limited number of genes to allow cost-effective and high-throughput subtype analysis. We determined a minimal signature for accurate classification, including 39 differentially expressed and nine control genes from microarray experiments. Taqman-based (low-density arrays and Fluidigm), fluorescent oligonucleotides (Nanostring), and targeted RNA sequencing (Illumina) assays were then compared for their ability to correctly classify fresh and formalin-fixed, paraffin-embedded samples. All platforms achieved > 90% classification accuracy with RNA from fresh frozen samples. The Illumina and Nanostring assays were superior with fixed material. We found that the C1, C2, and C4 molecular subtypes were largely consistent across multiple surgical deposits from individual chemo-naive patients. In contrast, we observed substantial subtype heterogeneity in patients whose primary ovarian sample was classified as C5. The development of an efficient molecular classifier of HGSC should enable further biological characterization of molecular subtypes and the development of targeted clinical trials.
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- 2015
15. Immune response to RB1-regulated senescence limits radiation-induced osteosarcoma formation
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Marieke L. Kuijjer, Jason Ellul, Dale W. Garsed, Maya Kansara, Huei San Leong, Sophie Popkiss, Carl R. Walkley, Rod Hicks, Puiyi Pang, Mark J. Smyth, Philip W. Hinds, Carleen Cullinane, Anne-Marie Cleton-Jansen, Nicole M. Haynes, Dan Mei Lin, and David Thomas
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Senescence ,Neoplasms, Radiation-Induced ,Tumor suppressor gene ,Bone Neoplasms ,Retinoblastoma Protein ,Mice ,medicine ,Animals ,Humans ,Genes, Retinoblastoma ,Immunologic Surveillance ,Cellular Senescence ,Osteosarcoma ,Osteoblasts ,biology ,Interleukin-6 ,Retinoblastoma ,Calcium Radioisotopes ,Retinoblastoma protein ,General Medicine ,Prognosis ,medicine.disease ,Pediatric cancer ,eye diseases ,Neoplasm Proteins ,Mice, Inbred C57BL ,Immunosurveillance ,Phenotype ,Immunology ,Cancer research ,biology.protein ,Cytokines ,Intercellular Signaling Peptides and Proteins ,Natural Killer T-Cells ,RNA Interference ,Cell aging ,Neoplasm Transplantation ,Research Article - Abstract
Ionizing radiation (IR) and germline mutations in the retinoblastoma tumor suppressor gene (RB1) are the strongest risk factors for developing osteosarcoma. Recapitulating the human predisposition, we found that Rb1+/- mice exhibited accelerated development of IR-induced osteosarcoma, with a latency of 39 weeks. Initial exposure of osteoblasts to carcinogenic doses of IR in vitro and in vivo induced RB1-dependent senescence and the expression of a panel of proteins known as senescence-associated secretory phenotype (SASP), dominated by IL-6. RB1 expression closely correlated with that of the SASP cassette in human osteosarcomas, and low expression of both RB1 and the SASP genes was associated with poor prognosis. In vivo, IL-6 was required for IR-induced senescence, which elicited NKT cell infiltration and a host inflammatory response. Mice lacking IL-6 or NKT cells had accelerated development of IR-induced osteosarcomas. These data elucidate an important link between senescence, which is a cell-autonomous tumor suppressor response, and the activation of host-dependent cancer immunosurveillance. Our findings indicate that overcoming the immune response to senescence is a rate-limiting step in the formation of IR-induced osteosarcoma.
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- 2013
16. Polycomb repressive complex 2 (PRC2) suppresses Eμ-myc lymphoma
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Stanley Chun-Wei Lee, Craig D. Hyland, Stephen L. Nutt, Warren S. Alexander, Huei San Leong, Ian J. Majewski, Aaron T. L. Lun, Gordon K. Smyth, Marnie E. Blewitt, Belinda Phipson, Douglas J. Hilton, and Rhys S. Allan
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Lymphoma, B-Cell ,Myeloid ,Immunology ,Mice, Transgenic ,macromolecular substances ,Precursor T-Cell Lymphoblastic Leukemia-Lymphoma ,Biochemistry ,Proto-Oncogene Proteins c-myc ,Loss of heterozygosity ,Mice ,SUZ12 ,medicine ,Animals ,Enhancer of Zeste Homolog 2 Protein ,Lymphopoiesis ,Cells, Cultured ,B cell ,Polycomb Repressive Complex 1 ,B-Lymphocytes ,Gene knockdown ,biology ,business.industry ,EZH2 ,Polycomb Repressive Complex 2 ,Cell Biology ,Hematology ,Gene Expression Regulation, Neoplastic ,Mice, Inbred C57BL ,medicine.anatomical_structure ,Cancer research ,biology.protein ,business ,PRC2 - Abstract
Deregulation of polycomb group complexes polycomb repressive complex 1 (PRC1) and 2 (PRC2) is associated with human cancers. Although inactivating mutations in PRC2-encoding genes EZH2, EED, and SUZ12 are present in T-cell acute lymphoblastic leukemia and in myeloid malignancies, gain-of-function mutations in EZH2 are frequently observed in B-cell lymphoma, implying disease-dependent effects of individual mutations. We show that, in contrast to PRC1, PRC2 is a tumor suppressor in Eµ-myc lymphomagenesis, because disease onset was accelerated by heterozygosity for Suz12 or by short hairpin RNA-mediated knockdown of Suz12 or Ezh2. Accelerated lymphomagenesis was associated with increased accumulation of B-lymphoid cells in the absence of effects on apoptosis or cell cycling. However, Suz12-deficient B-lymphoid progenitors exhibit enhanced serial clonogenicity. Thus, PRC2 normally restricts the self-renewal of B-lymphoid progenitors, the disruption of which contributes to lymphomagenesis. This finding provides new insight regarding the functional contribution of mutations in PRC2 in a range of leukemias.
- Published
- 2013
17. Epigenetic Regulator Smchd1 Functions as a Tumor Suppressor
- Author
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Marnie E. Blewitt, Jason Corbin, Huei San Leong, Ian J. Majewski, Yifang Hu, Stanley Chun-Wei Lee, Kelan Chen, James M. Murphy, Warren S. Alexander, Gordon K. Smyth, Miha Pakusch, and Douglas J. Hilton
- Subjects
Male ,Genetically modified mouse ,Cancer Research ,Lymphoma, B-Cell ,Chromosomal Proteins, Non-Histone ,Transgene ,Down-Regulation ,Mice, Nude ,Mice, Transgenic ,Biology ,medicine.disease_cause ,Epigenesis, Genetic ,Gene Knockout Techniques ,Mice ,medicine ,Animals ,Humans ,Genes, Tumor Suppressor ,Fibroblasts ,medicine.disease ,Molecular biology ,Candidate Tumor Suppressor Gene ,Fusion protein ,Gene expression profiling ,Transplantation ,Leukemia ,Cell Transformation, Neoplastic ,Oncology ,Cancer research ,Carcinogenesis - Abstract
SMCHD1 is an epigenetic modifier of gene expression that is critical to maintain X chromosome inactivation. Here, we show in mouse that genetic inactivation of Smchd1 accelerates tumorigenesis in male mice. Loss of Smchd1 in transformed mouse embryonic fibroblasts increased tumor growth upon transplantation into immunodeficient nude mice. In addition, loss of Smchd1 in Eμ-Myc transgenic mice that undergo lymphomagenesis reduced disease latency by 50% relative to control animals. In premalignant Eμ-Myc transgenic mice deficient in Smchd1, there was an increase in the number of pre-B cells in the periphery, likely accounting for the accelerated disease in these animals. Global gene expression profiling suggested that Smchd1 normally represses genes activated by MLL chimeric fusion proteins in leukemia, implying that Smchd1 loss may work through the same pathways as overexpressed MLL fusion proteins do in leukemia and lymphoma. Notably, we found that SMCHD1 is underexpressed in many types of human hematopoietic malignancy. Together, our observations collectively highlight a hitherto uncharacterized role for SMCHD1 as a candidate tumor suppressor gene in hematopoietic cancers. Cancer Res; 73(5); 1591–9. ©2012 AACR.
- Published
- 2013
18. Genome-wide binding and mechanistic analyses of Smchd1-mediated epigenetic regulation
- Author
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Matthew E. Ritchie, Andrew Keniry, Jiang Hu, Richard J.L.F. Lemmers, Clare L. Parish, Silvère M. van der Maarel, Sarah A. Kessans, Peter E. Czabotar, Marnie E. Blewitt, Renwick C. J. Dobson, Darcy Moore, Ruijie Liu, Kelsey Breslin, Isabelle S Lucet, Huei San Leong, Douglas J. Hilton, Graham F. Kay, James M. Murphy, and Kelan Chen
- Subjects
Male ,CCCTC-Binding Factor ,Chromosomal Proteins, Non-Histone ,Blotting, Western ,Biology ,Methylation ,Ctcf ,Epigenesis, Genetic ,Histones ,Genomic Imprinting ,Mice, Congenic ,Neural Stem Cells ,Transcriptional regulation ,Animals ,Epigenetics ,Smchd1 ,Cells, Cultured ,Genetics ,Regulation of gene expression ,Mice, Knockout ,clustered protocadherins ,Multidisciplinary ,Binding Sites ,Genome ,Reverse Transcriptase Polymerase Chain Reaction ,Brain ,Gene Expression Regulation, Developmental ,epigenetic control ,Chromatin ,Cell biology ,Mice, Inbred C57BL ,Repressor Proteins ,Histone ,PNAS Plus ,CTCF ,DNA methylation ,biology.protein ,Female ,Genomic imprinting ,Transcriptome ,Protein Binding - Abstract
Structural maintenance of chromosomes flexible hinge domain containing 1 (Smchd1) is an epigenetic repressor with described roles in X inactivation and genomic imprinting, but Smchd1 is also critically involved in the pathogenesis of facioscapulohumeral dystrophy. The underlying molecular mechanism by which Smchd1 functions in these instances remains unknown. Our genome-wide transcriptional and epigenetic analyses show that Smchd1 binds cis-regulatory elements, many of which coincide with CCCTC-binding factor (Ctcf) binding sites, for example, the clustered protocadherin (Pcdh) genes, where we show Smchd1 and Ctcf act in opposing ways. We provide biochemical and biophysical evidence that Smchd1–chromatin interactions are established through the homodimeric hinge domain of Smchd1 and, intriguingly, that the hinge domain also has the capacity to bind DNA and RNA. Our results suggest Smchd1 imparts epigenetic regulation via physical association with chromatin, which may antagonize Ctcf-facilitated chromatin interactions, resulting in coordinated transcriptional control.
- Published
- 2015
19. Efficient molecular subtype classification of high-grade serous ovarian cancer
- Author
-
Huei San, Leong, Laura, Galletta, Dariush, Etemadmoghadam, Joshy, George, Martin, Köbel, Susan J, Ramus, and David, Bowtell
- Subjects
Ovarian Neoplasms ,Paraffin Embedding ,Sequence Analysis, RNA ,Gene Expression Profiling ,High-Throughput Nucleotide Sequencing ,Reproducibility of Results ,Carcinoma, Ovarian Epithelial ,Cystadenocarcinoma, Serous ,Gene Expression Regulation, Neoplastic ,Frozen Sections ,Humans ,Female ,Neoplasms, Glandular and Epithelial ,Oligonucleotide Array Sequence Analysis - Abstract
High-grade serous carcinomas (HGSCs) account for approximately 70% of all epithelial ovarian cancers diagnosed. Using microarray gene expression profiling, we previously identified four molecular subtypes of HGSC: C1 (mesenchymal), C2 (immunoreactive), C4 (differentiated), and C5 (proliferative), which correlate with patient survival and have distinct biological features. Here, we describe molecular classification of HGSC based on a limited number of genes to allow cost-effective and high-throughput subtype analysis. We determined a minimal signature for accurate classification, including 39 differentially expressed and nine control genes from microarray experiments. Taqman-based (low-density arrays and Fluidigm), fluorescent oligonucleotides (Nanostring), and targeted RNA sequencing (Illumina) assays were then compared for their ability to correctly classify fresh and formalin-fixed, paraffin-embedded samples. All platforms achieved90% classification accuracy with RNA from fresh frozen samples. The Illumina and Nanostring assays were superior with fixed material. We found that the C1, C2, and C4 molecular subtypes were largely consistent across multiple surgical deposits from individual chemo-naive patients. In contrast, we observed substantial subtype heterogeneity in patients whose primary ovarian sample was classified as C5. The development of an efficient molecular classifier of HGSC should enable further biological characterization of molecular subtypes and the development of targeted clinical trials.
- Published
- 2015
20. Whole-genome characterization of chemoresistant ovarian cancer
- Author
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Catherine Kennedy, Peter Bailey, Michael Friedlander, Conrad Leonard, Euan A. Stronach, Jodie Leditschke, Prue A. Cowin, Darrin Taylor, David D.L. Bowtell, Chris Mitchell, Felicity Newell, Senel Idrisoglu, Ravikiran Vedururu, Kathryn Alsop, Ehsan Nourbakhsh, Patricia C. M. O’Brien, Nathan E. Hall, Collin Stewart, Ann-Marie Patch, Linda Mileshkin, Gisela Mir Arnau, Charlotte Wilhelm-Benartzi, Shivashankar H. Nagaraj, Nadia Traficante, Angelika N. Christ, Edward Curry, Qinying Xu, Stephen H. Kazakoff, Emma Markham, Kate Strachan, Timothy J. C. Bruxner, David Miller, Nick Waddell, Yoke Eng Chiew, Karin S. Kassahn, A. Jewell, Barsha Poudel, Ronny Drapkin, Ernst Lengyel, Oliver Holmes, George Au-Yeung, Joshy George, Kelly Quek, Richard W. Tothill, Orla McNally, John V. Pearson, J. Lynn Fink, Greg Young, Nicola Waddell, Elizabeth L. Christie, Jillian Hung, Michael C. J. Quinn, Ivon Harliwong, Jan Pyman, Jason Ellul, Walid J Azar, Katia Nones, Andrew Lonie, Sian Fereday, Craig Nourse, Stephen Cordner, Dariush Etemadmoghadam, Anna deFazio, Paul R. Harnett, Scott Wood, Maria A. Doyle, Michael C.J. Quinn, Robert S. Brown, Hani Gabra, Peter Wilson, Joy Hendley, Timothy P. Holloway, Sean M. Grimmond, Heather Thorne, Matthew J. Anderson, Mark Shackleton, Suzanne Manning, Anne Hamilton, Dale W. Garsed, Huei San Leong, Timothy Semple, and Paul Waring
- Subjects
DNA Mutational Analysis ,Genes, BRCA2 ,Genes, BRCA1 ,Drug resistance ,Biology ,Retinoblastoma Protein ,Germline ,Cohort Studies ,Germline mutation ,Cyclin E ,Genes, Neurofibromatosis 1 ,medicine ,PTEN ,Humans ,ATP Binding Cassette Transporter, Subfamily B, Member 1 ,Promoter Regions, Genetic ,Germ-Line Mutation ,Genetics ,Oncogene Proteins ,Ovarian Neoplasms ,Multidisciplinary ,Genome, Human ,PTEN Phosphohydrolase ,Combination chemotherapy ,DNA Methylation ,medicine.disease ,Cystadenocarcinoma, Serous ,DNA-Binding Proteins ,Serous fluid ,Drug Resistance, Neoplasm ,Mutagenesis ,DNA methylation ,Cancer research ,biology.protein ,Female ,Ovarian cancer - Abstract
Patients with high-grade serous ovarian cancer (HGSC) have experienced little improvement in overall survival, and standard treatment has not advanced beyond platinum-based combination chemotherapy, during the past 30 years. To understand the drivers of clinical phenotypes better, here we use whole-genome sequencing of tumour and germline DNA samples from 92 patients with primary refractory, resistant, sensitive and matched acquired resistant disease. We show that gene breakage commonly inactivates the tumour suppressors RB1, NF1, RAD51B and PTEN in HGSC, and contributes to acquired chemotherapy resistance. CCNE1 amplification was common in primary resistant and refractory disease. We observed several molecular events associated with acquired resistance, including multiple independent reversions of germline BRCA1 or BRCA2 mutations in individual patients, loss of BRCA1 promoter methylation, an alteration in molecular subtype, and recurrent promoter fusion associated with overexpression of the drug efflux pump MDR1.
- Published
- 2014
21. Why weight? Modelling sample and observational level variability improves power in RNA-seq analyses
- Author
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Shian Su, Huei San Leong, Marnie E. Blewitt, Kelan Chen, Gordon K. Smyth, Matthew E. Ritchie, Marie Liesse Asselin-Labat, Ruijie Liu, Aliaksei Holik, and Natasha Jansz
- Subjects
Genetics ,Normalization (statistics) ,Differential expression analysis ,Chromosomal Proteins, Non-Histone ,Sequence Analysis, RNA ,Gene Expression Profiling ,Linear model ,Reproducibility of Results ,RNA-Seq ,Biology ,Bioconductor ,Mice ,Cell Line, Tumor ,Statistics ,Linear Models ,Methods Online ,Animals ,Humans ,Sample variance ,Observational study ,Noise level - Abstract
Variations in sample quality are frequently encountered in small RNA-sequencing experiments, and pose a major challenge in a differential expression analysis. Removal of high variation samples reduces noise, but at a cost of reducing power, thus limiting our ability to detect biologically meaningful changes. Similarly, retaining these samples in the analysis may not reveal any statistically significant changes due to the higher noise level. A compromise is to use all available data, but to down-weight the observations from more variable samples. We describe a statistical approach that facilitates this by modelling heterogeneity at both the sample and observational levels as part of the differential expression analysis. At the sample level this is achieved by fitting a log-linear variance model that includes common sample-specific or group-specific parameters that are shared between genes. The estimated sample variance factors are then converted to weights and combined with observational level weights obtained from the mean–variance relationship of the log-counts-per-million using ‘voom’. A comprehensive analysis involving both simulations and experimental RNA-sequencing data demonstrates that this strategy leads to a universally more powerful analysis and fewer false discoveries when compared to conventional approaches. This methodology has wide application and is implemented in the open-source ‘limma’ package.
- Published
- 2015
22. Why weight? Modelling sample and observational level variability improves power in RNA-seq analyses.
- Author
-
Ruijie Liu, Holik, Aliaksei Z., Shian Su, Jansz, Natasha, Kelan Chen, Huei San Leong, Blewitt, Marnie E., Asselin-Labat, Marie-Liesse, Smyth, Gordon K., and Ritchie, Matthew E.
- Published
- 2015
- Full Text
- View/download PDF
23. Immune response to RB1-regulated senescence limits radiation-induced osteosarcoma formation.
- Author
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Kansara, Maya, Huei San Leong, Dan Mei Lin, Popkiss, Sophie, Puiyi Pang, Garsed, Dale W., Walkley, Carl R., Cullinane, Carleen, Ellul, Jason, Haynes, Nicole M., Hicks, Rod, Kuijjer, Marieke L., Cleton-Jansen, Anne-Marie, Hinds, Philip W., Smyth, Mark J., and Thomas, David M.
- Subjects
- *
IONIZING radiation , *GERM cell tumors , *RETINOBLASTOMA , *CARCINOGENS research , *OSTEOSARCOMA - Abstract
Ionizing radiation (IR) and germline mutations in the retinoblastoma tumor suppressor gene (RB1) are the strongest risk factors for developing osteosarcoma. Recapitulating the human predisposition, we found that Rb1+/- mice exhibited accelerated development of IR-induced osteosarcoma, with a latency of 39 weeks. Initial exposure of osteoblasts to carcinogenic doses of IR in vitro and in vivo induced RB1-dependent senescence and the expression of a panel of proteins known as senescence-associated secretory phenotype (SASP), dominated by IL-6. RB1 expression closely correlated with that of the SASP cassette in human osteosarcomas, and low expression of both RB1 and the SASP genes was associated with poor prognosis. In vivo, IL-6 was required for IR-induced senescence, which elicited NKT cell infiltration and a host inflammatory response. Mice lacking IL-6 or NKT cells had accelerated development of IR-induced osteosarcomas. These data elucidate an important link between senescence, which is a cell-autonomous tumor suppressor response, and the activation of host-dependent cancer immunosurveillance. Our findings indicate that overcoming the immune response to senescence is a rate-limiting step in the formation of IR-induced osteosarcoma. [ABSTRACT FROM AUTHOR]
- Published
- 2013
- Full Text
- View/download PDF
24. Epigenetic Regulator Smchd1 Functions as a Tumor Suppressor.
- Author
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Huei San Leong, Kelan Chen, Yifang Hu, Lee, Stanley, Corbin, Jason, Pakusch, Miha, Murphy, James M., Majewski, Ian J., Smyth, Gordon K., Alexander, Warren S., Hilton, Douglas J., and Blewitt, Marnie E.
- Subjects
- *
EPIGENESIS , *EPIGENETICS , *GENE expression , *X chromosome , *NEOPLASTIC cell transformation , *LEUKEMIA - Abstract
SMCHD1 is an epigenetic modifier of gene expression that is critical to maintain X chromosome inactivation. Here, we show in mouse that genetic inactivation of Smchd1 accelerates tumorigenesis in male mice. Loss of Smchd1 in transformed mouse embryonic fibroblasts increased tumor growth upon transplantation into immunodeficient nude mice. In addition, loss of Smchd1 in Em-Myc transgenic mice that undergo lymphomagenesis reduced disease latency by 50% relative to control animals. In premalignant Em-Myc transgenic mice deficient in Smchd1, there was an increase in the number of pre-B cells in the periphery, likely accounting for the accelerated disease in these animals. Global gene expression profiling suggested that Smchd1 normally represses genes activated by MLL chimeric fusion proteins in leukemia, implying that Smchd1 loss may work through the same pathways as overexpressed MLL fusion proteins do in leukemia and lymphoma. Notably, we found that SMCHD1 is underexpressed in many types of human hematopoietic malignancy. Together, our observations collectively highlight a hitherto uncharacterized role for SMCHD1 as a candidate tumor suppressor gene in hematopoietic cancers. [ABSTRACT FROM AUTHOR]
- Published
- 2013
- Full Text
- View/download PDF
25. Profound MEK inhibitor response in a cutaneous melanoma harboring a GOLGA4-RAF1 fusion.
- Author
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McEvoy, Christopher R., Huiling Xu, Smith, Kortnye, Etemadmoghadam, Dariush, Huei San Leong, Choong, David Y., Byrne, David J., Iravani, Amir, Beck, Sophie, Mileshkin, Linda, Tothill, Richard W., Bowtell, David D., Bates, Bindi M., Nastevski, Violeta, Browning, Judy, Bell, Anthony H., Chloe Khoo, Desai, Jayesh, Fellowes, Andrew P., and Fox, Stephen B.
- Subjects
- *
SERINE/THREONINE kinases , *CYCLIN-dependent kinase inhibitors , *MELANOMA , *CANCER invasiveness , *CELL death , *PROTEIN metabolism , *RESEARCH , *PROTEIN kinase inhibitors , *RESEARCH methodology , *CYTOSKELETAL proteins , *ALLELES , *METASTASIS , *EVALUATION research , *MEDICAL cooperation , *SKIN tumors , *COMPARATIVE studies , *TRANSFERASES , *POSITRON emission tomography , *RADIOPHARMACEUTICALS , *GENES , *DEOXY sugars , *ANTIGENS , *PHARMACODYNAMICS - Abstract
BRAF and CRAF are critical components of the MAPK signaling pathway which is activated in many cancer types. In approximately 1% of melanomas, BRAF or CRAF are activated through structural arrangements. We describe here a metastatic melanoma with a GOLGA4-RAF1 fusion and pathogenic variants in CTNNB1 and CDKN2A. Anti-CTLA4/anti-PD1 combination immunotherapy failed to control tumor progression. In the absence of other actionable variants the patient was administered MEK inhibitor therapy on the basis of its potential action against RAF1 fusions. This resulted in a profound and clinically significant response. We demonstrated that GOLGA4-RAF1 expression was associated with ERK activation, elevated expression of the RAS/RAF downstream co-effector ETV5, and a high Ki67 index. These findings provide a rationale for the dramatic response to targeted therapy. This study shows that thorough molecular characterization of treatment-resistant cancers can identify therapeutic targets and personalize management, leading to improved patient outcomes. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
- View/download PDF
26. Polycomb repressive complex 2 (PRC2) suppresses Eμ-myc lymphoma.
- Author
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Lee, Stanley C. W., Phipson, Belinda, Hyland, Craig D., Huei San Leong, Allan, Rhys S., Lun, Aaron, Hilton, Douglas J., Nutt, Stephen L., Blewitt, Marnie E., Smyth, Gordon K., Alexander, Warren S., and Majewski, Ian J.
- Subjects
- *
POLYCOMB group proteins , *CANCER risk factors , *B cell lymphoma , *T cells , *TUMOR suppressor proteins , *HETEROZYGOSITY , *TUMORS - Abstract
Deregulation of polycomb group complexes polycomb repressive complex 1 (PRC1) and 2 (PRC2) is associated with human cancers. Although inactivating mutations in PRC2-encoding genes EZH2, EED, and SUZ12 are present in T-cell acute lymphoblastic leukemia and in myeloid malignancies, gain-of-function mutations in EZH2 are frequently observed in B-cell lymphoma, implying disease-dependent effects of individual mutations. We show that, in contrast to PRC1, PRC2 is a tumor suppressor in Eμ-myc lymphomagenesis, because disease onset was accelerated by heterozygosity for Suz12 or by short hairpin RNA-mediated knockdown of Suz12 or Ezh2. Accelerated lymphomagenesis was associated with increased accumulation of B-lymphoid cells in the absence of effects on apoptosis or cell cycling. However, Suz12-deficient B-lymphoid progenitors exhibit enhanced serial clonogenicity. Thus, PRC2 normally restricts the self-renewal of B-lymphoid progenitors, the disruption of which contributes to lymphomagenesis. This finding provides new insight regarding the functional contribution of mutations in PRC2 in a range of leukemias. [ABSTRACT FROM AUTHOR]
- Published
- 2013
- Full Text
- View/download PDF
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