1
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Funnell T, O’Flanagan CH, Williams MJ, McPherson A, McKinney S, Kabeer F, Lee H, Salehi S, Vázquez-García I, Shi H, Leventhal E, Masud T, Eirew P, Yap D, Zhang AW, Lim JLP, Wang B, Brimhall J, Biele J, Ting J, Au V, Van Vliet M, Liu YF, Beatty S, Lai D, Pham J, Grewal D, Abrams D, Havasov E, Leung S, Bojilova V, Moore RA, Rusk N, Uhlitz F, Ceglia N, Weiner AC, Zaikova E, Douglas JM, Zamarin D, Weigelt B, Kim SH, Da Cruz Paula A, Reis-Filho JS, Martin SD, Li Y, Xu H, de Algara TR, Lee SR, Llanos VC, Huntsman DG, McAlpine JN, Shah SP, Aparicio S, Cannell IG, Casbolt H, Jauset C, Kovačević T, Mulvey CM, Nugent F, Ribes MP, Pearson I, Qosaj F, Sawicka K, Wild SA, Williams E, Laks E, Smith A, Lai D, Roth A, Balasubramanian S, Lee M, Bodenmiller B, Burger M, Kuett L, Tietscher S, Windhager J, Boyden ES, Alon S, Cui Y, Emenari A, Goodwin DR, Karagiannis ED, Sinha A, Wassie AT, Caldas C, Bruna A, Callari M, Greenwood W, Lerda G, Eyal-Lubling Y, Rueda OM, Shea A, Harris O, Becker R, Grimaldo F, Harris S, Vogl SL, Joyce JA, Watson SS, Tavare S, Dinh KN, Fisher E, Kunes R, Walton NA, Al Sa’d M, Chornay N, Dariush A, González-Solares EA, González-Fernández C, Yoldaş AK, Miller N, Zhuang X, Fan J, Lee H, Sepúlveda LA, Xia C, Zheng P, Shah SP, Aparicio S. Single-cell genomic variation induced by mutational processes in cancer. Nature 2022; 612:106-115. [PMID: 36289342 PMCID: PMC9712114 DOI: 10.1038/s41586-022-05249-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [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: 06/03/2021] [Accepted: 08/17/2022] [Indexed: 12/15/2022]
Abstract
How cell-to-cell copy number alterations that underpin genomic instability1 in human cancers drive genomic and phenotypic variation, and consequently the evolution of cancer2, remains understudied. Here, by applying scaled single-cell whole-genome sequencing3 to wild-type, TP53-deficient and TP53-deficient;BRCA1-deficient or TP53-deficient;BRCA2-deficient mammary epithelial cells (13,818 genomes), and to primary triple-negative breast cancer (TNBC) and high-grade serous ovarian cancer (HGSC) cells (22,057 genomes), we identify three distinct 'foreground' mutational patterns that are defined by cell-to-cell structural variation. Cell- and clone-specific high-level amplifications, parallel haplotype-specific copy number alterations and copy number segment length variation (serrate structural variations) had measurable phenotypic and evolutionary consequences. In TNBC and HGSC, clone-specific high-level amplifications in known oncogenes were highly prevalent in tumours bearing fold-back inversions, relative to tumours with homologous recombination deficiency, and were associated with increased clone-to-clone phenotypic variation. Parallel haplotype-specific alterations were also commonly observed, leading to phylogenetic evolutionary diversity and clone-specific mono-allelic expression. Serrate variants were increased in tumours with fold-back inversions and were highly correlated with increased genomic diversity of cellular populations. Together, our findings show that cell-to-cell structural variation contributes to the origins of phenotypic and evolutionary diversity in TNBC and HGSC, and provide insight into the genomic and mutational states of individual cancer cells.
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Affiliation(s)
- Tyler Funnell
- grid.5386.8000000041936877XTri-Institutional PhD Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, NY USA ,grid.51462.340000 0001 2171 9952Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Ciara H. O’Flanagan
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada
| | - Marc J. Williams
- grid.51462.340000 0001 2171 9952Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Andrew McPherson
- grid.51462.340000 0001 2171 9952Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Steven McKinney
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada
| | - Farhia Kabeer
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada ,grid.17091.3e0000 0001 2288 9830Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia Canada
| | - Hakwoo Lee
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada ,grid.17091.3e0000 0001 2288 9830Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia Canada
| | - Sohrab Salehi
- grid.51462.340000 0001 2171 9952Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Ignacio Vázquez-García
- grid.51462.340000 0001 2171 9952Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Hongyu Shi
- grid.51462.340000 0001 2171 9952Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Emily Leventhal
- grid.51462.340000 0001 2171 9952Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Tehmina Masud
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada
| | - Peter Eirew
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada
| | - Damian Yap
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada
| | - Allen W. Zhang
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada
| | - Jamie L. P. Lim
- grid.51462.340000 0001 2171 9952Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Beixi Wang
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada
| | - Jazmine Brimhall
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada
| | - Justina Biele
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada
| | - Jerome Ting
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada
| | - Vinci Au
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada
| | - Michael Van Vliet
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada
| | - Yi Fei Liu
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada
| | - Sean Beatty
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada
| | - Daniel Lai
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada ,grid.17091.3e0000 0001 2288 9830Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia Canada
| | - Jenifer Pham
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada
| | - Diljot Grewal
- grid.51462.340000 0001 2171 9952Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Douglas Abrams
- grid.51462.340000 0001 2171 9952Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Eliyahu Havasov
- grid.51462.340000 0001 2171 9952Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Samantha Leung
- grid.51462.340000 0001 2171 9952Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Viktoria Bojilova
- grid.51462.340000 0001 2171 9952Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Richard A. Moore
- grid.434706.20000 0004 0410 5424Michael Smith Genome Sciences Centre, Vancouver, British Columbia Canada
| | - Nicole Rusk
- grid.51462.340000 0001 2171 9952Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Florian Uhlitz
- grid.51462.340000 0001 2171 9952Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Nicholas Ceglia
- grid.51462.340000 0001 2171 9952Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Adam C. Weiner
- grid.5386.8000000041936877XTri-Institutional PhD Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, NY USA ,grid.51462.340000 0001 2171 9952Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Elena Zaikova
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada
| | - J. Maxwell Douglas
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada
| | - Dmitriy Zamarin
- grid.51462.340000 0001 2171 9952GYN Medical Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Britta Weigelt
- grid.51462.340000 0001 2171 9952Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Sarah H. Kim
- grid.51462.340000 0001 2171 9952Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Arnaud Da Cruz Paula
- grid.51462.340000 0001 2171 9952Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Jorge S. Reis-Filho
- grid.51462.340000 0001 2171 9952Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Spencer D. Martin
- grid.17091.3e0000 0001 2288 9830Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia Canada
| | - Yangguang Li
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada
| | - Hong Xu
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada
| | - Teresa Ruiz de Algara
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada
| | - So Ra Lee
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada
| | - Viviana Cerda Llanos
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada
| | - David G. Huntsman
- grid.248762.d0000 0001 0702 3000Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia Canada ,grid.17091.3e0000 0001 2288 9830Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia Canada
| | - Jessica N. McAlpine
- grid.17091.3e0000 0001 2288 9830Department of Gynecology and Obstetrics, University of British Columbia, Vancouver, British Columbia Canada
| | | | - Sohrab P. Shah
- grid.51462.340000 0001 2171 9952Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY USA
| | - Samuel Aparicio
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada. .,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.
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2
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Salehi S, Kabeer F, Ceglia N, Andronescu M, Williams MJ, Campbell KR, Masud T, Wang B, Biele J, Brimhall J, Gee D, Lee H, Ting J, Zhang AW, Tran H, O'Flanagan C, Dorri F, Rusk N, de Algara TR, Lee SR, Cheng BYC, Eirew P, Kono T, Pham J, Grewal D, Lai D, Moore R, Mungall AJ, Marra MA, McPherson A, Bouchard-Côté A, Aparicio S, Shah SP. Clonal fitness inferred from time-series modelling of single-cell cancer genomes. Nature 2021; 595:585-590. [PMID: 34163070 PMCID: PMC8396073 DOI: 10.1038/s41586-021-03648-3] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 05/17/2021] [Indexed: 02/02/2023]
Abstract
Progress in defining genomic fitness landscapes in cancer, especially those defined by copy number alterations (CNAs), has been impeded by lack of time-series single-cell sampling of polyclonal populations and temporal statistical models1-7. Here we generated 42,000 genomes from multi-year time-series single-cell whole-genome sequencing of breast epithelium and primary triple-negative breast cancer (TNBC) patient-derived xenografts (PDXs), revealing the nature of CNA-defined clonal fitness dynamics induced by TP53 mutation and cisplatin chemotherapy. Using a new Wright-Fisher population genetics model8,9 to infer clonal fitness, we found that TP53 mutation alters the fitness landscape, reproducibly distributing fitness over a larger number of clones associated with distinct CNAs. Furthermore, in TNBC PDX models with mutated TP53, inferred fitness coefficients from CNA-based genotypes accurately forecast experimentally enforced clonal competition dynamics. Drug treatment in three long-term serially passaged TNBC PDXs resulted in cisplatin-resistant clones emerging from low-fitness phylogenetic lineages in the untreated setting. Conversely, high-fitness clones from treatment-naive controls were eradicated, signalling an inversion of the fitness landscape. Finally, upon release of drug, selection pressure dynamics were reversed, indicating a fitness cost of treatment resistance. Together, our findings define clonal fitness linked to both CNA and therapeutic resistance in polyclonal tumours.
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Affiliation(s)
- Sohrab Salehi
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Farhia Kabeer
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Nicholas Ceglia
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mirela Andronescu
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Marc J Williams
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kieran R Campbell
- Lunenfeld-Tanenbaum Research Institute Mount Sinai Hospital Joseph & Wolf Lebovic Health Complex, Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Tehmina Masud
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Beixi Wang
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Justina Biele
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Jazmine Brimhall
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - David Gee
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Hakwoo Lee
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Jerome Ting
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Allen W Zhang
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Hoa Tran
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Ciara O'Flanagan
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Fatemeh Dorri
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada
- Department of Computer Science, University of British Columbia, Vancouver, British Columbia, Canada
| | - Nicole Rusk
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - So Ra Lee
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Brian Yu Chieh Cheng
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Peter Eirew
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Takako Kono
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Jenifer Pham
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Diljot Grewal
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daniel Lai
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Richard Moore
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Andrew McPherson
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexandre Bouchard-Côté
- Department of Statistics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Samuel Aparicio
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada.
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.
| | - Sohrab P Shah
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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3
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Laks E, McPherson A, Zahn H, Lai D, Steif A, Brimhall J, Biele J, Wang B, Masud T, Ting J, Grewal D, Nielsen C, Leung S, Bojilova V, Smith M, Golovko O, Poon S, Eirew P, Kabeer F, Ruiz de Algara T, Lee SR, Taghiyar MJ, Huebner C, Ngo J, Chan T, Vatrt-Watts S, Walters P, Abrar N, Chan S, Wiens M, Martin L, Scott RW, Underhill TM, Chavez E, Steidl C, Da Costa D, Ma Y, Coope RJN, Corbett R, Pleasance S, Moore R, Mungall AJ, Mar C, Cafferty F, Gelmon K, Chia S, Marra MA, Hansen C, Shah SP, Aparicio S. Clonal Decomposition and DNA Replication States Defined by Scaled Single-Cell Genome Sequencing. Cell 2019; 179:1207-1221.e22. [PMID: 31730858 PMCID: PMC6912164 DOI: 10.1016/j.cell.2019.10.026] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 06/14/2019] [Accepted: 10/22/2019] [Indexed: 01/21/2023]
Abstract
Accurate measurement of clonal genotypes, mutational processes, and replication states from individual tumor-cell genomes will facilitate improved understanding of tumor evolution. We have developed DLP+, a scalable single-cell whole-genome sequencing platform implemented using commodity instruments, image-based object recognition, and open source computational methods. Using DLP+, we have generated a resource of 51,926 single-cell genomes and matched cell images from diverse cell types including cell lines, xenografts, and diagnostic samples with limited material. From this resource we have defined variation in mitotic mis-segregation rates across tissue types and genotypes. Analysis of matched genomic and image measurements revealed correlations between cellular morphology and genome ploidy states. Aggregation of cells sharing copy number profiles allowed for calculation of single-nucleotide resolution clonal genotypes and inference of clonal phylogenies and avoided the limitations of bulk deconvolution. Finally, joint analysis over the above features defined clone-specific chromosomal aneuploidy in polyclonal populations.
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Affiliation(s)
- Emma Laks
- Department of Molecular Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada; Genome Science and Technology Graduate Program, University of British Columbia, Vancouver, BC, Canada
| | - Andrew McPherson
- Department of Molecular Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada; Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, 417 East 68th St., New York, NY 10065, USA
| | - Hans Zahn
- Department of Molecular Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Genome Science and Technology Graduate Program, University of British Columbia, Vancouver, BC, Canada; Centre for High Throughput Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Daniel Lai
- Department of Molecular Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Adi Steif
- Department of Molecular Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada; Genome Science and Technology Graduate Program, University of British Columbia, Vancouver, BC, Canada
| | - Jazmine Brimhall
- Department of Molecular Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Justina Biele
- Department of Molecular Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Beixi Wang
- Department of Molecular Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Tehmina Masud
- Department of Molecular Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Jerome Ting
- Department of Molecular Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Diljot Grewal
- Department of Molecular Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada; Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, 417 East 68th St., New York, NY 10065, USA
| | - Cydney Nielsen
- Department of Molecular Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Samantha Leung
- Department of Molecular Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada; Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, 417 East 68th St., New York, NY 10065, USA
| | - Viktoria Bojilova
- Department of Molecular Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada; Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, 417 East 68th St., New York, NY 10065, USA
| | - Maia Smith
- Department of Molecular Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Oleg Golovko
- Department of Molecular Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Steven Poon
- Department of Molecular Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada
| | - Peter Eirew
- Department of Molecular Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Farhia Kabeer
- Department of Molecular Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Teresa Ruiz de Algara
- Department of Molecular Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - So Ra Lee
- Department of Molecular Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - M Jafar Taghiyar
- Department of Molecular Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Curtis Huebner
- Department of Molecular Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Jessica Ngo
- Department of Molecular Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Tim Chan
- Department of Molecular Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Spencer Vatrt-Watts
- Department of Molecular Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada; Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, 417 East 68th St., New York, NY 10065, USA
| | - Pascale Walters
- Department of Molecular Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Nafis Abrar
- Department of Molecular Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Sophia Chan
- Department of Molecular Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Matt Wiens
- Department of Molecular Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Lauren Martin
- Department of Molecular Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - R Wilder Scott
- Department of Molecular Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - T Michael Underhill
- Centre for High Throughput Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Elizabeth Chavez
- Centre for Lymphoid Cancer, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada
| | - Christian Steidl
- Centre for Lymphoid Cancer, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada
| | - Daniel Da Costa
- Department of Molecular Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Centre for High Throughput Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Yussanne Ma
- Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 1L3, Canada
| | - Robin J N Coope
- Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 1L3, Canada
| | - Richard Corbett
- Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 1L3, Canada
| | - Stephen Pleasance
- Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 1L3, Canada
| | - Richard Moore
- Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 1L3, Canada
| | - Andrew J Mungall
- Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 1L3, Canada
| | - Colin Mar
- Department of Radiology, BC Cancer, 600 West 10th Avenue, Vancouver, BC V5Z 4E6, Canada
| | - Fergus Cafferty
- Department of Radiology, BC Cancer, 600 West 10th Avenue, Vancouver, BC V5Z 4E6, Canada
| | - Karen Gelmon
- Department of Medical Oncology, BC Cancer, 600 West 10th Avenue, Vancouver, BC V5Z 4E6, Canada
| | - Stephen Chia
- Department of Medical Oncology, BC Cancer, 600 West 10th Avenue, Vancouver, BC V5Z 4E6, Canada
| | - Marco A Marra
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Carl Hansen
- Centre for High Throughput Biology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 2B5, Canada
| | - Sohrab P Shah
- Department of Molecular Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada; Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, 417 East 68th St., New York, NY 10065, USA.
| | - Samuel Aparicio
- Department of Molecular Oncology, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 2B5, Canada.
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4
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Yap DB, Walker DC, Prentice LM, McKinney S, Turashvili G, Mooslehner-Allen K, de Algara TR, Fee J, de Tassigny XD, Colledge WH, Aparicio S. Mll5 is required for normal spermatogenesis. PLoS One 2011; 6:e27127. [PMID: 22069496 PMCID: PMC3206077 DOI: 10.1371/journal.pone.0027127] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2010] [Accepted: 10/11/2011] [Indexed: 12/02/2022] Open
Abstract
Background Mll5 is currently a member of the Mll family of SET domain histone methyltransferase proteins but studies have also showed that it could be part of the SET3 branch of proteins. Recently, constitutive knock out animal studies have shown that Mll5 is required for proper haematopoietic stem cell differentiation, and loss of Mll5 results in synthetic lethality for genome de-methylation. Mll5 deficient male mice are infertile and here we analyse the consequences of Mll5 deficiency for spermatogenesis. Methodology/Principal Findings Mll5 deficient male mice, but not female mice, are infertile. Here we show using RNA in-situ hybridization that Mll5 is expressed in the germ cells of the testes of wild type mice. Consistent with the expression of Mll5, we demonstrate by electron microscopy, video microscopy and in vitro fertilisation techniques that Mll5 deficient mice have defects in terminal maturation and packaging of sperm. The defects seen include detachment of the acrosomal cap and impaired excess cytoplasm removal. Functional tests of sperm motility show a lack of progressive motility of spermatozoa from Mll5 deficient animals. None of these defects could be rescued by in vitro fertilization. Using microarray analysis we show that transcripts implicated in spermatogenesis are dysregulated. Conclusions/Significance Our data demonstrate a clear role of Mll5 in mammalian spermatogenesis at the level of terminal differentiation providing further support for its classification in the SET3 branch of proteins. Moreover, this study identifies Tlk2, Utx, Gpr64, Sult4a1, Rap2ip, Vstm2 and HoxA10 as possible Mll5 targets that together may account for the observed spermatozoa maturation defects.
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Affiliation(s)
- Damian B. Yap
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - David C. Walker
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Leah M. Prentice
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Steven McKinney
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Gulisa Turashvili
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | | | - Teresa Ruiz de Algara
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - John Fee
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Xavier d'Anglemont de Tassigny
- Physiological Laboratory, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - William H. Colledge
- Physiological Laboratory, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Samuel Aparicio
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- * E-mail:
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5
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Hoffman BG, Zavaglia B, Witzsche J, Ruiz de Algara T, Beach M, Hoodless PA, Jones SJM, Marra MA, Helgason CD. Identification of transcripts with enriched expression in the developing and adult pancreas. Genome Biol 2008; 9:R99. [PMID: 18554416 PMCID: PMC2481431 DOI: 10.1186/gb-2008-9-6-r99] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2008] [Revised: 05/13/2008] [Accepted: 06/14/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Despite recent advances, the transcriptional hierarchy driving pancreas organogenesis remains largely unknown, in part due to the paucity of comprehensive analyses. To address this deficit we generated ten SAGE libraries from the developing murine pancreas spanning Theiler stages 17-26, making use of available Pdx1 enhanced green fluorescent protein (EGFP) and Neurog3 EGFP reporter strains, as well as tissue from adult islets and ducts. RESULTS We used a specificity metric to identify 2,536 tags with pancreas-enriched expression compared to 195 other mouse SAGE libraries. We subsequently grouped co-expressed transcripts with differential expression during pancreas development using K-means clustering. We validated the clusters first using quantitative real time PCR and then by analyzing the Theiler stage 22 pancreas in situ hybridization staining patterns of over 600 of the identified genes using the GenePaint database. These were then categorized into one of the five expression domains within the developing pancreas. Based on these results we identified a cascade of transcriptional regulators expressed in the endocrine pancreas lineage and, from this, we developed a predictive regulatory network describing beta-cell development. CONCLUSION Taken together, this work provides evidence that the SAGE libraries generated here are a valuable resource for continuing to elucidate the molecular mechanisms regulating pancreas development. Furthermore, our studies provide a comprehensive analysis of pancreas development, and insights into the regulatory networks driving this process are revealed.
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Affiliation(s)
- Brad G Hoffman
- Department of Cancer Endocrinology, BC Cancer Research Center, West 10th Ave, Vancouver, BC V5Z 1L3, Canada.
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6
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Aiga C, Helgason C, Wederell E, Wu M, Vrljicak P, Ruiz de Algara T, Hoodless. WITHDRAWN: Study of epithelial-mesenchymal interactions during organogenesis by Serial Analysis of Gene Expression (SAGE). Dev Biol 2007. [DOI: 10.1016/j.ydbio.2007.03.327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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7
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Noorali S, Kurita T, Woolcock B, de Algara TR, Lo M, Paralkar V, Hoodless P, Vielkind J. Dynamics of expression of growth differentiation factor 15 in normal and PIN development in the mouse. Differentiation 2007; 75:325-36. [PMID: 17286605 DOI: 10.1111/j.1432-0436.2006.00142.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [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: 12/12/2022]
Abstract
Growth differentiation factor (GDF15) is a distant member of the transforming growth factor-beta superfamily, a diverse group of structurally related proteins that exert multiple effects on cell fate such as on cell growth and differentiation but little is known about GDF15 in these processes. Previously we observed the mature GDF15 to be associated with human prostate carcinogenesis hence prompting us to study GDF15 further. Here we report gdf15 expression both at the RNA and protein levels, in normal prostatic tissues of wild type (wt) and prostatic intraepithelial neoplasia (PIN) of transgenic (Tg) 12T-7s model mice during embryonic, postnatal, and adult prostate formation up to 15 weeks after birth. Dynamic changes in expression, at both the mRNA and protein level, correlated with cell proliferation and differentiation during distinct phases of normal mouse prostate development and alterations in the dynamics of gdf15 expression correlated with the changes in development resulting in PIN formation. Most notably mature gdf15 protein was significantly elevated during hyperplasia and PIN development. Changes in the protein levels did not always correlate well with the mRNA levels. This was more prominent during PIN than during normal prostate development suggesting that this may also be an indicator of disturbed regulation of gdf15 in PIN. We propose that gdf15 is a growth factor with dual function either promoting proliferation or growth arrest and differentiation due most likely to differences in cellular differentiation. Because of the differentiation defect in PIN its epithelium no longer responds to gdf15 by cellular growth arrest as does the normal epithelium and gdf may even stimulate proliferation. The data supports our hypothesis that GDF15 plays a role in the early stages of human prostate cancer.
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Affiliation(s)
- Samina Noorali
- Department of Cancer Endocrinology, BC Cancer Research Centre/BC Cancer Agency, Vancouver, BC, Canada
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Zhang TJ, Hoffman BG, Ruiz de Algara T, Helgason CD. SAGE reveals expression of Wnt signalling pathway members during mouse prostate development. Gene Expr Patterns 2005; 6:310-24. [PMID: 16378759 DOI: 10.1016/j.modgep.2005.07.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2005] [Revised: 07/05/2005] [Accepted: 07/15/2005] [Indexed: 12/29/2022]
Abstract
To identify genes and pathways not previously implicated in the mesenchymal-epithelial (M/E) interactions that are critical for normal mouse prostate development, we constructed six serial analysis of gene expression (SAGE) libraries. Bioinformatic analyses revealed expression of various members of numerous signalling pathways and the differential expression of several members of the wingless-related MMTV integration site (Wnt) signalling pathway. This pathway has not been previously implicated in prostate development thus expression of selected Wnt pathway members in the developing prostate was confirmed by RT-qPCR. Of particular interest, an antagonist of the Wnt pathway, secreted frizzled related protein 2 (Sfrp2), was highly expressed in the early prostate libraries and down regulated at later developmental stages. The expression levels of four Wnt ligands reported to interact with Sfrp2 were, therefore, examined by RT-qPCR. We found that only Wnt4 transcripts were detectable in the developing prostate. Expression of Sfrp2 was validated using RT-qPCR and localization of Sfrp2 transcripts and protein was carried out using in situ hybridization and immunofluorescence, respectively. These studies provide the first evidence that Wnt pathway members are expressed in the developing prostate. Functional analyses are now required to establish the biological significance of this observation.
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Affiliation(s)
- Tian-Jiao Zhang
- Department of Cancer Endocrinology, British Columbia Cancer Agency, 675 West 10th Avenue, Vancouver, BC, Canada V5Z 1L3
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Siddiqui AS, Khattra J, Delaney AD, Zhao Y, Astell C, Asano J, Babakaiff R, Barber S, Beland J, Bohacec S, Brown-John M, Chand S, Charest D, Charters AM, Cullum R, Dhalla N, Featherstone R, Gerhard DS, Hoffman B, Holt RA, Hou J, Kuo BYL, Lee LLC, Lee S, Leung D, Ma K, Matsuo C, Mayo M, McDonald H, Prabhu AL, Pandoh P, Riggins GJ, de Algara TR, Rupert JL, Smailus D, Stott J, Tsai M, Varhol R, Vrljicak P, Wong D, Wu MK, Xie YY, Yang G, Zhang I, Hirst M, Jones SJM, Helgason CD, Simpson EM, Hoodless PA, Marra MA. A mouse atlas of gene expression: large-scale digital gene-expression profiles from precisely defined developing C57BL/6J mouse tissues and cells. Proc Natl Acad Sci U S A 2005; 102:18485-90. [PMID: 16352711 PMCID: PMC1311911 DOI: 10.1073/pnas.0509455102] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We analyzed 8.55 million LongSAGE tags generated from 72 libraries. Each LongSAGE library was prepared from a different mouse tissue. Analysis of the data revealed extensive overlap with existing gene data sets and evidence for the existence of approximately 24,000 previously undescribed genomic loci. The visual cortex, pancreas, mammary gland, preimplantation embryo, and placenta contain the largest number of differentially expressed transcripts, 25% of which are previously undescribed loci.
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Affiliation(s)
- Asim S Siddiqui
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Research Centre, British Columbia Cancer Agency, Vancouver, BC, Canada V5Z 4S6
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