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Gallegos LL, Gilchrist A, Spain L, Stanislaw S, Hill SM, Primus V, Jones C, Agrawal S, Tippu Z, Barhoumi A, Noel-Storr G, Alexander NR, Turajlic S. A protocol for representative sampling of solid tumors to improve the accuracy of sequencing results. STAR Protoc 2021; 2:100624. [PMID: 34223198 PMCID: PMC8243513 DOI: 10.1016/j.xpro.2021.100624] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Owing to spatial segregation of tumor subclones, solid tumor sampling using formalin-fixed, paraffin-embedded blocks is often inadequate to represent the genomic heterogeneity of solid tumors. We present an approach, representative sampling, to dissect and homogenize leftover residual surgical tissue prior to sequencing. We also detail optional tumor cell enrichment and DNA preparation. This method, applicable only to surgically removed tumors with leftover tissue, facilitates robust sampling to avoid missing or over-representing actionable variants. For complete details on the use and execution of this protocol, please refer to Litchfield et al. (2020).
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Affiliation(s)
| | | | - Lavinia Spain
- Royal Marsden NHS Foundation Trust, London, UK
- Francis Crick Institute, London, UK
| | | | | | | | | | | | - Zayd Tippu
- Royal Marsden NHS Foundation Trust, London, UK
- Francis Crick Institute, London, UK
| | | | | | | | - Samra Turajlic
- Royal Marsden NHS Foundation Trust, London, UK
- Francis Crick Institute, London, UK
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2
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Litchfield K, Stanislaw S, Spain L, Gallegos LL, Rowan A, Schnidrig D, Rosenbaum H, Harle A, Au L, Hill SM, Tippu Z, Thomas J, Thompson L, Xu H, Horswell S, Barhoumi A, Jones C, Leith KF, Burgess DL, Watkins TBK, Lim E, Birkbak NJ, Lamy P, Nordentoft I, Dyrskjøt L, Pickering L, Hazell S, Jamal-Hanjani M, Larkin J, Swanton C, Alexander NR, Turajlic S. Representative Sequencing: Unbiased Sampling of Solid Tumor Tissue. Cell Rep 2020; 31:107550. [PMID: 32375028 DOI: 10.1016/j.celrep.2020.107550] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 09/17/2019] [Accepted: 04/01/2020] [Indexed: 01/10/2023] Open
Abstract
Although thousands of solid tumors have been sequenced to date, a fundamental under-sampling bias is inherent in current methodologies. This is caused by a tissue sample input of fixed dimensions (e.g., 6 mm biopsy), which becomes grossly under-powered as tumor volume scales. Here, we demonstrate representative sequencing (Rep-Seq) as a new method to achieve unbiased tumor tissue sampling. Rep-Seq uses fixed residual tumor material, which is homogenized and subjected to next-generation sequencing. Analysis of intratumor tumor mutation burden (TMB) variability shows a high level of misclassification using current single-biopsy methods, with 20% of lung and 52% of bladder tumors having at least one biopsy with high TMB but low clonal TMB overall. Misclassification rates by contrast are reduced to 2% (lung) and 4% (bladder) when a more representative sampling methodology is used. Rep-Seq offers an improved sampling protocol for tumor profiling, with significant potential for improved clinical utility and more accurate deconvolution of clonal structure.
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Affiliation(s)
- Kevin Litchfield
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Stacey Stanislaw
- Roche Tissue Diagnostics, 1910 E. Innovation Park Drive, Tucson, AZ 85755, USA
| | - Lavinia Spain
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Renal and Skin Units, The Royal Marsden Hospital, London SW3 6JJ, UK
| | - Lisa L Gallegos
- Roche Tissue Diagnostics, 1910 E. Innovation Park Drive, Tucson, AZ 85755, USA
| | - Andrew Rowan
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Desiree Schnidrig
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Heidi Rosenbaum
- Roche Sequencing Solutions, Madison, 500 S. Rosa Road, Madison, WI 53719, USA
| | - Alexandre Harle
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Université de Lorraine, CNRS UMR 7039 CRAN, Institut de Cancérologie de Lorraine, Service de Biopathologie, 54000 Nancy, France
| | - Lewis Au
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Renal and Skin Units, The Royal Marsden Hospital, London SW3 6JJ, UK
| | - Samantha M Hill
- Roche Tissue Diagnostics, 1910 E. Innovation Park Drive, Tucson, AZ 85755, USA; Department of Cancer Biology, University of Arizona Cancer Center, Tucson, AZ 85724, USA
| | - Zayd Tippu
- Renal and Skin Units, The Royal Marsden Hospital, London SW3 6JJ, UK
| | - Jennifer Thomas
- Renal and Skin Units, The Royal Marsden Hospital, London SW3 6JJ, UK
| | - Lisa Thompson
- The Centre for Molecular Pathology, The Royal Marsden Hospital, London SW3 6JJ, UK
| | - Hang Xu
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Stuart Horswell
- Department of Bioinformatics and Biostatistics, The Francis Crick Institute, London NW1 1AT, UK
| | - Aoune Barhoumi
- Roche Tissue Diagnostics, 1910 E. Innovation Park Drive, Tucson, AZ 85755, USA
| | - Carol Jones
- Roche Tissue Diagnostics, 1910 E. Innovation Park Drive, Tucson, AZ 85755, USA
| | - Katherine F Leith
- Roche Tissue Diagnostics, 1910 E. Innovation Park Drive, Tucson, AZ 85755, USA
| | - Daniel L Burgess
- Roche Sequencing Solutions, Madison, 500 S. Rosa Road, Madison, WI 53719, USA
| | - Thomas B K Watkins
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Emilia Lim
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Nicolai J Birkbak
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Philippe Lamy
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Iver Nordentoft
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Lars Dyrskjøt
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Lisa Pickering
- Renal and Skin Units, The Royal Marsden Hospital, London SW3 6JJ, UK
| | - Stephen Hazell
- Histopathology Department, Royal Marsden NHS Foundation Trust, London and Sutton, UK
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK; Department of Medical Oncology, University College London Hospitals, London, UK
| | - James Larkin
- Renal and Skin Units, The Royal Marsden Hospital, London SW3 6JJ, UK
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK; Department of Medical Oncology, University College London Hospitals, London, UK.
| | - Nelson R Alexander
- Roche Tissue Diagnostics, 1910 E. Innovation Park Drive, Tucson, AZ 85755, USA.
| | - Samra Turajlic
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Renal and Skin Units, The Royal Marsden Hospital, London SW3 6JJ, UK.
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3
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Spain L, Gallegos L, Tippu Z, Hill S, Litchfield K, Au L, Gilchrist A, Primus V, Barhoumi A, Stanislaw S, Agrawal S, Shaikh N, Patel N, Mendoza MF, Noel-Storr G, Larkin J, Alexander N, Turajlic S. Homogenisation of leftover surgical tissue across multiple cancer types: A feasibility study (HoLST-F). Ann Oncol 2019. [DOI: 10.1093/annonc/mdz268.107] [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: 11/15/2022] Open
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4
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Turajlic S, Xu H, Litchfield K, Rowan A, Chambers T, Lopez JI, Nicol D, O'Brien T, Larkin J, Horswell S, Stares M, Au L, Jamal-Hanjani M, Challacombe B, Chandra A, Hazell S, Eichler-Jonsson C, Soultati A, Chowdhury S, Rudman S, Lynch J, Fernando A, Stamp G, Nye E, Jabbar F, Spain L, Lall S, Guarch R, Falzon M, Proctor I, Pickering L, Gore M, Watkins TBK, Ward S, Stewart A, DiNatale R, Becerra MF, Reznik E, Hsieh JJ, Richmond TA, Mayhew GF, Hill SM, McNally CD, Jones C, Rosenbaum H, Stanislaw S, Burgess DL, Alexander NR, Swanton C. Tracking Cancer Evolution Reveals Constrained Routes to Metastases: TRACERx Renal. Cell 2018; 173:581-594.e12. [PMID: 29656895 PMCID: PMC5938365 DOI: 10.1016/j.cell.2018.03.057] [Citation(s) in RCA: 513] [Impact Index Per Article: 85.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 03/06/2018] [Accepted: 03/20/2018] [Indexed: 01/17/2023]
Abstract
Clear-cell renal cell carcinoma (ccRCC) exhibits a broad range of metastatic phenotypes that have not been systematically studied to date. Here, we analyzed 575 primary and 335 metastatic biopsies across 100 patients with metastatic ccRCC, including two cases sampledat post-mortem. Metastatic competence was afforded by chromosome complexity, and we identify 9p loss as a highly selected event driving metastasis and ccRCC-related mortality (p = 0.0014). Distinct patterns of metastatic dissemination were observed, including rapid progression to multiple tissue sites seeded by primary tumors of monoclonal structure. By contrast, we observed attenuated progression in cases characterized by high primary tumor heterogeneity, with metastatic competence acquired gradually and initial progression to solitary metastasis. Finally, we observed early divergence of primitive ancestral clones and protracted latency of up to two decades as a feature of pancreatic metastases.
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Affiliation(s)
- Samra Turajlic
- Translational Cancer Therapeutics Laboratory, the Francis Crick Institute, London NW1 1AT, UK; Renal and Skin Units, the Royal Marsden Hospital NHS Foundation Trust, London SW3 6JJ, UK
| | - Hang Xu
- Translational Cancer Therapeutics Laboratory, the Francis Crick Institute, London NW1 1AT, UK
| | - Kevin Litchfield
- Translational Cancer Therapeutics Laboratory, the Francis Crick Institute, London NW1 1AT, UK
| | - Andrew Rowan
- Translational Cancer Therapeutics Laboratory, the Francis Crick Institute, London NW1 1AT, UK
| | - Tim Chambers
- Translational Cancer Therapeutics Laboratory, the Francis Crick Institute, London NW1 1AT, UK
| | - Jose I Lopez
- Department of Pathology, Cruces University Hospital, Biocruces Institute, University of the Basque Country, Barakaldo, Spain
| | - David Nicol
- Department of Urology, the Royal Marsden NHS Foundation Trust, London, SW3 6JJ, UK
| | - Tim O'Brien
- Urology Centre, Guy's & St Thomas' NHS Foundation Trust, London, UK
| | - James Larkin
- Renal and Skin Units, the Royal Marsden Hospital NHS Foundation Trust, London SW3 6JJ, UK
| | - Stuart Horswell
- Department of Bioinformatics and Biostatistics, The Francis Crick Institute, London NW1 1AT, UK
| | - Mark Stares
- Translational Cancer Therapeutics Laboratory, the Francis Crick Institute, London NW1 1AT, UK; Renal and Skin Units, the Royal Marsden Hospital NHS Foundation Trust, London SW3 6JJ, UK
| | - Lewis Au
- Renal and Skin Units, the Royal Marsden Hospital NHS Foundation Trust, London SW3 6JJ, UK
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence London, University College London Cancer Institute, London WC1E 6DD, UK
| | - Ben Challacombe
- Urology Centre, Guy's & St Thomas' NHS Foundation Trust, London, UK
| | - Ashish Chandra
- Department of Cellular Pathology, Guy's & St Thomas' NHS Foundation Trust, London SE1 7EH, UK
| | - Steve Hazell
- Department of Pathology, the Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK
| | - Claudia Eichler-Jonsson
- Translational Cancer Therapeutics Laboratory, the Francis Crick Institute, London NW1 1AT, UK
| | - Aspasia Soultati
- Department of Oncology, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Simon Chowdhury
- Department of Oncology, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Sarah Rudman
- Department of Oncology, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Joanna Lynch
- Renal and Skin Units, the Royal Marsden Hospital NHS Foundation Trust, London SW3 6JJ, UK
| | - Archana Fernando
- Urology Centre, Guy's & St Thomas' NHS Foundation Trust, London, UK
| | - Gordon Stamp
- Experimental Histopathology Laboratory, the Francis Crick Institute, London NW1 1AT, UK
| | - Emma Nye
- Experimental Histopathology Laboratory, the Francis Crick Institute, London NW1 1AT, UK
| | - Faiz Jabbar
- Translational Cancer Therapeutics Laboratory, the Francis Crick Institute, London NW1 1AT, UK
| | - Lavinia Spain
- Renal and Skin Units, the Royal Marsden Hospital NHS Foundation Trust, London SW3 6JJ, UK
| | - Sharanpreet Lall
- Department of Oncology, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Rosa Guarch
- Department of Pathology, Complejo Hospitalario de Navarra, 31008 Pamplona, Spain
| | - Mary Falzon
- Department of Pathology, University College London Hospitals, London WC1E 6DE, UK
| | - Ian Proctor
- Department of Pathology, University College London Hospitals, London WC1E 6DE, UK
| | - Lisa Pickering
- Renal and Skin Units, the Royal Marsden Hospital NHS Foundation Trust, London SW3 6JJ, UK
| | - Martin Gore
- Renal and Skin Units, the Royal Marsden Hospital NHS Foundation Trust, London SW3 6JJ, UK
| | - Thomas B K Watkins
- Translational Cancer Therapeutics Laboratory, the Francis Crick Institute, London NW1 1AT, UK
| | - Sophia Ward
- Translational Cancer Therapeutics Laboratory, the Francis Crick Institute, London NW1 1AT, UK; Cancer Research UK Lung Cancer Centre of Excellence London, University College London Cancer Institute, London WC1E 6DD, UK
| | - Aengus Stewart
- Department of Pathology, Cruces University Hospital, Biocruces Institute, University of the Basque Country, Barakaldo, Spain
| | - Renzo DiNatale
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maria F Becerra
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ed Reznik
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - James J Hsieh
- Molecular Oncology, Department of Medicine, Siteman Cancer Center, Washington University, St. Louis, MO, USA
| | - Todd A Richmond
- Roche Sequencing Solutions, Madison, Research & Development, Madison, WI, 53719, USA
| | - George F Mayhew
- Roche Sequencing Solutions, Madison, Research & Development, Madison, WI, 53719, USA
| | | | | | - Carol Jones
- Ventana Medical Systems, Tucson, AZ 85755, USA
| | - Heidi Rosenbaum
- Roche Sequencing Solutions, Madison, Research & Development, Madison, WI, 53719, USA
| | | | - Daniel L Burgess
- Roche Sequencing Solutions, Madison, Research & Development, Madison, WI, 53719, USA
| | | | - Charles Swanton
- Translational Cancer Therapeutics Laboratory, the Francis Crick Institute, London NW1 1AT, UK; Cancer Research UK Lung Cancer Centre of Excellence London, University College London Cancer Institute, London WC1E 6DD, UK; Department of Medical Oncology, University College London Hospitals, London NW1 2BU, UK.
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Aziz D, Etemadmoghadam D, Au-Yeung G, Muranyi A, Gresshoff I, Christie M, Hutchinson R, Ferraro D, Stanislaw S, Henricksen L, Tubbs A, Shanmugam K, Bowtell D, Waring P. 298O The clinical significance of deregulated cyclin E1 in high grade serous ovarian cancer (HGSOC). Ann Oncol 2016. [DOI: 10.1093/annonc/mdw585.002] [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: 11/13/2022] Open
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6
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Aziz D, Etemadmoghadam D, Au-Yeung G, Muranyi A, Gresshoff I, Christie M, Hutchinson R, Ferraro D, Stanislaw S, Henricksen L, Tubbs, Shanmugam K, Bowtell D, Waring P. 298O The clinical significance of deregulated cyclin E1 in high grade serous ovarian cancer (HGSOC). Ann Oncol 2016. [DOI: 10.1016/s0923-7534(21)00456-7] [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: 11/27/2022] Open
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7
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Kendrick SL, Redd L, Muranyi A, Henricksen LA, Stanislaw S, Smith LM, Perry AM, Fu K, Weisenburger DD, Rosenwald A, Ott G, Gascoyne RD, Jaffe ES, Campo E, Delabie J, Braziel RM, Cook JR, Tubbs RR, Staudt LM, Chan WC, Steidl C, Grogan TM, Rimsza LM. BCL2 antibodies targeted at different epitopes detect varying levels of protein expression and correlate with frequent gene amplification in diffuse large B-cell lymphoma. Hum Pathol 2014; 45:2144-53. [PMID: 25090918 DOI: 10.1016/j.humpath.2014.06.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Revised: 05/18/2014] [Accepted: 06/11/2014] [Indexed: 10/25/2022]
Abstract
Patients with aggressive, BCL2 protein-positive (+) diffuse large B-cell lymphoma (DLBCL) often experience rapid disease progression that is refractory to standard therapy. However, there is potential for false-negative staining of BCL2 using the standard monoclonal mouse 124 antibody that hinders the identification of these high-risk DLBCL patients. Herein, we compare 2 alternative rabbit monoclonal antibodies (E17 and SP66) to the 124 clone in staining for BCL2 in formalin-fixed, paraffin-embedded DLBCL tissues. Overall, in 2 independent DLBCL cohorts, E17 and SP66 detected BCL2 expression more frequently than 124. In the context of MYC expression, cases identified as BCL2 (+) with SP66 demonstrated the strongest correlation with worse overall survival. The 124 clone failed to detect BCL2 expression in the majority of translocation (+), amplification (+), and activated B-cell DLBCL cases in which high levels of BCL2 protein are expected. Using dual in situ hybridization as a new tool to detect BCL2 translocation and amplification, we observed similar results as previously reported for fluorescence in situ hybridization for translocation but a higher amplification frequency, indicating that BCL2 amplification may be underreported in DLBCL. Among the discrepant cases, phosphorylation of BCL2 at T69 and/or S70 was more common than in the concordant cases and may contribute to the 124 false negatives, in addition to previously associated mutations within the epitope region. The accurate detection of BCL2 expression is important in the prognosis and treatment of DLBCL particularly with new anti-BCL2 therapies.
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Affiliation(s)
| | - Lucas Redd
- Department of Pathology, University of Arizona, Tucson, AZ 85724
| | | | | | | | - Lynette M Smith
- Department of Biostatistics, University of Nebraska Medical Center, Omaha, NE 68198
| | - Anamarija M Perry
- Department of Pathology, University of Manitoba, Winnipeg, MB, Canada R3A 1R9
| | - Kai Fu
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198
| | | | - Andreas Rosenwald
- Department of Pathology, University of Wuerzburg, Wuerzburg, Germany 97070
| | - German Ott
- Department of Clinical Pathology, Robert-Bosch-Krankenhaus, and Dr. Margarete Fischer-Bosch-Institu fur Klinische Pharmakologie (IKP), 70376 Stuttgart, Germany
| | - Randy D Gascoyne
- Department of Pathology and Laboratory Medicine, British Columbia Cancer Agency, Vancouver, BC, Canada V5Z 4E6
| | - Elaine S Jaffe
- Laboratory of Pathology, National Cancer Institute, Bethesda, MD 20892
| | - Elías Campo
- Department of Pathology, Hospital Clínic, Barcelona, Spain 08028
| | - Jan Delabie
- Department of Pathology, The Norwegian Radium Hospital, University of Oslo, Oslo, Norway 0310
| | - Rita M Braziel
- Department of Clinical Pathology, Oregon Health & Science University, Portland, OR 97239
| | - James R Cook
- Department of Molecular Pathology and Laboratory Medicine, Cleveland Clinic, Cleveland, OH 44195
| | - Raymond R Tubbs
- Department of Molecular Pathology and Laboratory Medicine, Cleveland Clinic, Cleveland, OH 44195
| | - Louis M Staudt
- Metabolism Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892
| | - Wing Chung Chan
- Department of Pathology and Laboratory Medicine, British Columbia Cancer Agency, Vancouver, BC, Canada V5Z 4E6
| | - Christian Steidl
- Department of Pathology and Laboratory Medicine, British Columbia Cancer Agency, Vancouver, BC, Canada V5Z 4E6
| | - Thomas M Grogan
- Department of Pathology, University of Arizona, Tucson, AZ 85724; Ventana Medical Systems, Inc., Tucson, AZ 85755
| | - Lisa M Rimsza
- Department of Pathology, University of Arizona, Tucson, AZ 85724.
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8
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Babic A, Loftin IR, Stanislaw S, Wang M, Miller R, Warren SM, Zhang W, Lau A, Miller M, Wu P, Padilla M, Grogan TM, Pestic-Dragovich L, McElhinny AS. The impact of pre-analytical processing on staining quality for H&E, dual hapten, dual color in situ hybridization and fluorescent in situ hybridization assays. Methods 2010; 52:287-300. [DOI: 10.1016/j.ymeth.2010.08.012] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2010] [Revised: 08/20/2010] [Accepted: 08/22/2010] [Indexed: 11/16/2022] Open
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Darnell DK, Stanislaw S, Kaur S, Antin PB. Whole mount in situ hybridization detection of mRNAs using short LNA containing DNA oligonucleotide probes. RNA 2010; 16:632-637. [PMID: 20086052 PMCID: PMC2822927 DOI: 10.1261/rna.1775610] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2009] [Accepted: 11/19/2009] [Indexed: 05/28/2023]
Abstract
In situ hybridization is widely used to visualize transcribed sequences in embryos, tissues, and cells. For whole mount detection of mRNAs in embryos, hybridization with an antisense RNA probe is followed by visual or fluorescence detection of target mRNAs. A limitation of this approach is that a cDNA template of the target RNA must be obtained in order to generate the antisense RNA probe. Here we investigate the use of short (12-24 nucleotides) locked nucleic acid (LNA) containing DNA probes for whole mount in situ hybridization detection of mRNAs. Following extensive protocol optimization, we show that LNA probes can be used to localize several mRNAs of varying abundances in chicken embryos. LNA probes also detected alternatively spliced exons that are processed in a tissue specific manner. The use of LNA probes for whole mount in situ detection of mRNAs will enable in silico design and chemical synthesis and will expand the general use of in situ hybridization for studies of transcriptional regulation and alternative splicing.
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Affiliation(s)
- Diana K Darnell
- Department of Cell Biology and Anatomy, University of Arizona, Tucson, Arizona 85724, USA
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10
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Darnell DK, Kaur S, Stanislaw S, Davey S, Konieczka JH, Yatskievych TA, Antin PB. GEISHA: an in situ hybridization gene expression resource for the chicken embryo. Cytogenet Genome Res 2007; 117:30-5. [PMID: 17675842 DOI: 10.1159/000103162] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2005] [Accepted: 09/20/2006] [Indexed: 12/19/2022] Open
Abstract
An important and ongoing focus of biomedical and agricultural avian research is to understand gene function, which for a significant fraction of genes remains unknown. A first step is to determine when and where genes are expressed during development and in the adult. Whole mount in situ hybridization gives precise spatial and temporal resolution of gene expression throughout an embryo, and a comprehensive analysis and centralized repository of in situ hybridization information would provide a valuable research tool. The GEISHA project (gallus expression in situ hybridization analysis) was initiated to explore the utility of using high-throughput in situ hybridization as a means for gene discovery and annotation in chicken embryos, and to provide a unified repository for in situ hybridization information. This report describes the design and implementation of a new GEISHA database and user interface (www.geisha.arizona.edu), and illustrates its utility for researchers in the biomedical and poultry science communities. Results obtained from a high throughput screen of microRNA expression in chicken embryos are also presented.
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Affiliation(s)
- D K Darnell
- Department of Cell Biology and Anatomy, University of Arizona, Tucson, AZ 85724, USA
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11
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Antin PB, Kaur S, Stanislaw S, Davey S, Konieczka JH, Yatskievych TA, Darnell DK. Gallus Expression In Situ Hybridization Analysis: A Chicken Embryo Gene Expression Database. Poult Sci 2007; 86:1472-7. [PMID: 17575198 DOI: 10.1093/ps/86.7.1472] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
With sequencing of the chicken genome largely completed, significant effort is focusing on gene annotation, including acquiring information about the patterns of gene expression. The chicken embryo is ideally suited to provide detailed temporal and spatial expression information through in situ hybridization gene expression analysis in vivo. We have developed the Gallus expression in situ hybridization analysis (GEISHA) database and user interface (http://geisha.arizona.edu) to serve as a centralized repository of in situ hybridization photos and metadata from chicken embryos. This report describes the design and implementation the GEISHA database and Web site and illustrates its usefulness for researchers in the biomedical and poultry science communities. Results from a recent comprehensive expression analysis of microRNA expression in chicken embryos are also presented.
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Affiliation(s)
- P B Antin
- Department of Cell Biology and Anatomy, University of Arizona, Tucson 85724, USA.
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12
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Abstract
MicroRNAs (miRNAs) are small, abundant, noncoding RNAs that modulate protein abundance by interfering with target mRNA translation or stability. miRNAs are detected in organisms from all domains and may regulate 30% of transcripts in vertebrates. Understanding miRNA function requires a detailed determination of expression, yet this has not been reported in an amniote species. High-throughput whole mount in situ hybridization was performed on chicken embryos to map expression of 135 miRNA genes including five miRNAs that had not been previously reported in chicken. Eighty-four miRNAs were detected before day 5 of embryogenesis, and 75 miRNAs showed differential expression. Whereas few miRNAs were expressed during formation of the primary germ layers, the number of miRNAs detected increased rapidly during organogenesis. Patterns highlighted cell-type, organ or structure-specific expression, localization within germ layers and their derivatives, and expression in multiple cell and tissue types and within sub-regions of structures and tissues. A novel group of miRNAs was highly expressed in most tissues but much reduced in one or a few organs, including the heart. This study presents the first comprehensive overview of miRNA expression in an amniote organism and provides an important foundation for investigations of miRNA gene regulation and function.
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Affiliation(s)
- Diana K Darnell
- Department of Cell Biology and Anatomy, University of Arizona, Tucson, Arizona, USA
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Darnell DK, Kaur S, Stanislaw S, Konieczka JH, Yatskievych TA, Antin PB. MicroRNA expression during chick embryo development. Dev Dyn 2006. [DOI: 10.1002/dvdy.21017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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