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Aisner DL, Gocke CD, Jones D, Limson M, Morrissette J, Segal JP. The Genomics Organization for Academic Laboratories (GOAL): A vision for a genomics future for academic pathology. Acad Pathol 2023; 10:100090. [PMID: 37583476 PMCID: PMC10424130 DOI: 10.1016/j.acpath.2023.100090] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 05/26/2023] [Accepted: 06/18/2023] [Indexed: 08/17/2023] Open
Abstract
Innovative and self-sustaining clinical genomics laboratories specializing in cutting-edge oncology testing are critical to the success of academic pathology departments and resident and fellow education in molecular pathology. However, the pressures and challenges facing these laboratories are numerous, including the complexities of validating comprehensive cancer next-generation sequencing (NGS) panels, competition from commercial laboratories, and the reimbursement and regulatory hurdles inherent in high-complexity testing. Cross-institutional collaborations, including shared assay content and interpretative frameworks, are a valuable element to academic laboratory success. To address these and other needs, the Genomics Organization for Academic Laboratories (GOAL) was conceived in 2018, incorporated in 2020 and has grown to include 29 participating institutions in 2022. Here, we describe the mission of GOAL, its structure, and the outcomes and projects undertaken in its first years.
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Affiliation(s)
- Dara L. Aisner
- Department of Pathology, University of Colorado, Denver, CO, USA
| | | | - Daniel Jones
- Department of Pathology, The Ohio State University, Columbus, OH, USA
| | - Melvin Limson
- Genomics Organization for Academic Laboratories and the Association of Pathology Chairs, Wilmington, DE, USA
| | - Jennifer Morrissette
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jeremy P. Segal
- Department of Pathology, University of Chicago, Chicago, IL, USA
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2
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Malapelle U, Pepe F, Pisapia P, Sgariglia R, Nacchio M, Barberis M, Bilh M, Bubendorf L, Büttner R, Cabibi D, Castiglia M, De Andrea CE, de Biase D, Dumur CI, Fontanini G, Freire J, Gristina V, Hofman P, Ilie M, Lozano MD, Merkelbach-Bruse S, Pappesch R, Pelusi N, Roma G, Russo A, Savic S, Siemanowski J, Tallini G, Tischler V, Vander Borght S, Weynand B, Xu T, Troncone G. TargetPlex FFPE-Direct DNA Library Preparation Kit for SiRe NGS panel: an international performance evaluation study. J Clin Pathol 2022; 75:416-421. [PMID: 33766954 DOI: 10.1136/jclinpath-2021-207450] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/01/2021] [Accepted: 03/01/2021] [Indexed: 02/05/2023]
Abstract
AIM Next generation sequencing (NGS) represents a key diagnostic tool to identify clinically relevant gene alterations for treatment-decision making in cancer care. However, the complex manual workflow required for NGS has limited its implementation in routine clinical practice. In this worldwide study, we validated the clinical performance of the TargetPlex FFPE-Direct DNA Library Preparation Kit for NGS analysis. Impressively, this new assay obviates the need for separate, labour intensive and time-consuming pre-analytical steps of DNA extraction, purification and isolation from formalin-fixed paraffin embedded (FFPE) specimens in the NGS workflow. METHODS The TargetPlex FFPE-Direct DNA Library Preparation Kit, which enables NGS analysis directly from FFPE, was specifically developed for this study by TargetPlex Genomics Pleasanton, California. Eleven institutions agreed to take part in the study coordinated by the Molecular Cytopathology Meeting Group (University of Naples Federico II, Naples, Italy). All participating institutions received a specific Library Preparation Kit to test eight FFPE samples previously assessed with standard protocols. The analytical parameters and mutations detected in each sample were then compared with those previously obtained with standard protocols. RESULTS Overall, 92.8% of the samples were successfully analysed with the TargetPlex FFPE-Direct DNA Library Preparation Kit on Thermo Fisher Scientific and Illumina platforms. Altogether, in comparison with the standard workflow, the TargetPlex FFPE-Direct DNA Library Preparation Kit was able to detect 90.5% of the variants. CONCLUSION The TargetPlex FFPE-Direct DNA Library Preparation Kit combined with the SiRe panel constitutes a convenient, practical and robust cost-saving solution for FFPE NGS analysis in routine practice.
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Affiliation(s)
| | - Francesco Pepe
- Public Health, University of Naples Federico II, Naples, Italy
| | | | | | | | - Massimo Barberis
- Clinic Unit of Histopathology and Molecular Diagnostics, Istituto Europeo di Oncologia, Milano, Italy
| | - Michel Bilh
- Department of Pathology, University Hospital Basel, Basel, Switzerland
| | - Lukas Bubendorf
- Department of Pathology, University Hospital Basel, Basel, Switzerland
| | - Reinhard Büttner
- Department of Pathology, University of Cologne, Cologne, Germany
| | - Daniela Cabibi
- Health Promotion Sciences, Maternal and Infantile Care, Internal Medicine and Medical Specialties, University of Palermo, Palermo, Italy
| | - Marta Castiglia
- Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | | | - Dario de Biase
- Medicine (DIMES)a Hospital, Anatomic Pathology Unit, University of Bologna, Bologna, Italy
| | - Catherine I Dumur
- Molecular Diagnostic Department, Aurora Diagnostics, Jacksonville, Florida, USA
| | - Gabriella Fontanini
- Surgical, Medical, Molecular Pathology and Critical Area, University of Pisa, Pisa, Italy
| | - Javier Freire
- Pathology, Hospital Universitario Marques de Valdecilla, Santander, Spain
| | - Valerio Gristina
- Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | | | - Marius Ilie
- Laboratory of Clinical and Experimental Pathology, Université Côte d'Azur, Nice, France
| | - Maria Dolores Lozano
- Pathology, Universidad de Navarra-Clínica Universidad de Navarra, Pamplona, Spain
| | | | - Roberto Pappesch
- Department of Pathology, University of Cologne, Cologne, Germany
| | | | - Gianluca Roma
- R&D Department, TargetPlex Genomics, Belmont, California, USA
| | - Antonio Russo
- Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Spasenija Savic
- Department of Pathology, University Hospital Basel, Basel, Switzerland
| | | | | | | | - Sara Vander Borght
- Department of Pathology, Katholieke Universiteit Leuven UZ Leuven, Leuven, Belgium
| | - Birgit Weynand
- Department of Pathology, Katholieke Universiteit Leuven UZ Leuven, Leuven, Belgium
| | - Tom Xu
- R&D Department, SenseCare Medicals, Inc, Pleasanton, California, USA
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Malapelle U, Pepe F, Pisapia P, Sgariglia R, Nacchio M, De Luca C, Lacalamita R, Tommasi S, Pinto R, Palomba G, Palmieri G, Vacirca D, Barberis M, Bottillo I, Grammatico P, Grillo LR, Costa V, Smeraglio R, Bruzzese D, Troncone G. Harmonization of Next-Generation Sequencing Procedure in Italian Laboratories: A Multi-Institutional Evaluation of the SiRe® Panel. Front Oncol 2020; 10:236. [PMID: 32219061 PMCID: PMC7078327 DOI: 10.3389/fonc.2020.00236] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 02/12/2020] [Indexed: 01/08/2023] Open
Abstract
Background: Next-generation sequencing (NGS) needs to be validated and standardized to ensure that cancer patients are reliably selected for target treatments. In Italy, NGS is performed in several institutions and harmonization of wet and dry procedures is needed. To this end, a consortium of five different laboratories, covering the most part of the Italian peninsula, was constituted. A narrow gene panel (SiRe®) covering 568 clinically relevant mutations in six different genes (EGFR, KRAS, NRAS, BRAF, cKIT, and PDGFRα) with a predictive role for therapy selection in non-small cell lung cancer (NSCLC), gastrointestinal stromal tumor, colorectal carcinoma (CRC), and melanoma was evaluated in each participating laboratory. Methods: To assess the NGS inter-laboratory concordance, the SiRe® panel, with a related kit and protocol for library preparation, was used in each center to analyze a common set of 20 NSCLC and CRC routine samples. Concordance rate, in terms of mutation detected and relative allelic frequencies, was assessed. Then, each institution prospectively analyzed an additional set of 40 routine samples (for a total of 160 specimens) to assess the reproducibility of the NGS run parameters in each institution. Results: An inter-laboratory agreement of 100% was reached in analyzing the data obtained from the 20 common sample sets; the concordance rate of allelic frequencies distribution was 0.989. The prospective analysis of the run metric parameters obtained by each center locally showed that the analytical performance of the SiRe® panel in the different institutions was highly reproducible. Conclusions: The SiRe® panel represents a robust diagnostic tool to harmonize the NGS procedure in different Italian laboratories.
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Affiliation(s)
- Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Francesco Pepe
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Pasquale Pisapia
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Roberta Sgariglia
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Mariantonia Nacchio
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Caterina De Luca
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Rosanna Lacalamita
- Molecular Diagnostics and Pharmacogenetics Unit, IRCCS Istituto Tumori "Giovanni Paolo II,", Bari, Italy
| | - Stefania Tommasi
- Molecular Diagnostics and Pharmacogenetics Unit, IRCCS Istituto Tumori "Giovanni Paolo II,", Bari, Italy
| | - Rosamaria Pinto
- Molecular Diagnostics and Pharmacogenetics Unit, IRCCS Istituto Tumori "Giovanni Paolo II,", Bari, Italy
| | - Grazia Palomba
- Unit of Cancer Genetics, Institute of Biomolecular Chemistry (ICB), National Research Council (CNR), Sassari, Italy
| | - Giuseppe Palmieri
- Unit of Cancer Genetics, Institute of Biomolecular Chemistry (ICB), National Research Council (CNR), Sassari, Italy
| | - Davide Vacirca
- Pathology Unit, European Institute of Oncology, Milan, Italy
| | | | - Irene Bottillo
- Laboratory of Medical Genetics, Department of Molecular Medicine, San Camillo-Forlanini Hospital, Sapienza University, Rome, Italy
| | - Paola Grammatico
- Laboratory of Medical Genetics, Department of Molecular Medicine, San Camillo-Forlanini Hospital, Sapienza University, Rome, Italy
| | - Lucia Rosalba Grillo
- Department of Pathology, San Camillo-Forlanini Hospital, Sapienza University, Rome, Italy
| | - Valerio Costa
- Institute of Genetics and Biophysics (CNR), Naples, Italy
| | - Riccardo Smeraglio
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Dario Bruzzese
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Giancarlo Troncone
- Department of Public Health, University of Naples Federico II, Naples, Italy
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Yu KH, Berry GJ, Rubin DL, Ré C, Altman RB, Snyder M. Association of Omics Features with Histopathology Patterns in Lung Adenocarcinoma. Cell Syst 2017; 5:620-627.e3. [PMID: 29153840 PMCID: PMC5746468 DOI: 10.1016/j.cels.2017.10.014] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 07/30/2017] [Accepted: 10/19/2017] [Indexed: 12/16/2022]
Abstract
Adenocarcinoma accounts for more than 40% of lung malignancy, and microscopic pathology evaluation is indispensable for its diagnosis. However, how histopathology findings relate to molecular abnormalities remains largely unknown. Here, we obtained H&E-stained whole-slide histopathology images, pathology reports, RNA sequencing, and proteomics data of 538 lung adenocarcinoma patients from The Cancer Genome Atlas and used these to identify molecular pathways associated with histopathology patterns. We report cell-cycle regulation and nucleotide binding pathways underpinning tumor cell dedifferentiation, and we predicted histology grade using transcriptomics and proteomics signatures (area under curve >0.80). We built an integrative histopathology-transcriptomics model to generate better prognostic predictions for stage I patients (p = 0.0182 ± 0.0021) compared with gene expression or histopathology studies alone, and the results were replicated in an independent cohort (p = 0.0220 ± 0.0070). These results motivate the integration of histopathology and omics data to investigate molecular mechanisms of pathology findings and enhance clinical prognostic prediction.
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Affiliation(s)
- Kun-Hsing Yu
- Biomedical Informatics Program, Stanford University, Stanford, CA 94305-5479, USA; Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Gerald J Berry
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Daniel L Rubin
- Biomedical Informatics Program, Stanford University, Stanford, CA 94305-5479, USA; Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA; Department of Radiology, Stanford University, Stanford, CA 94305-5105, USA; Department of Medicine (Biomedical Informatics Research), Stanford University, Stanford, CA 94305-5479, USA
| | - Christopher Ré
- Department of Computer Science, Stanford University, Stanford, CA 94305-9025, USA
| | - Russ B Altman
- Biomedical Informatics Program, Stanford University, Stanford, CA 94305-5479, USA; Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA; Department of Computer Science, Stanford University, Stanford, CA 94305-9025, USA; Department of Bioengineering, Stanford University, Stanford, CA 94305-4125, USA
| | - Michael Snyder
- Department of Genetics, Stanford University, Stanford, CA 94305-5120, USA.
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Scoazec JY. [Not Available]. Bull Cancer 2016; 103:S55-62. [PMID: 27494975 DOI: 10.1016/s0007-4551(16)30146-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
MOLECULAR EVALUATION OF METASTATIC DISEASE WHY PATHOLOGY REMAINS (AND WILL REMAIN) MANDATORY?: Numerous techniques are now available for the molecular evaluation of a tissular or cellular sample in the context of metastatic disease. They include in situ molecular techniques, such as immunohistochemistry for the study of proteins and peptides, in situ hybridization for the study of nucleic acids and in situ cytogenetics (FISH and its variants) for the demonstration of chromosome alterations. They also include all the techniques of molecular biology, which can now be applied to frozen as well as fixed tissue samples. The combination of all these techniques makes it possible an integrated and coherent approach, not limited to the description of DNA abnormalities, but able to correlate genomic alterations with functional, and even structural changes. A second major interest of the analysis of tissue samples is that they make it possible to analyzing not only tumor cells, but also their environment, formed by the stroma and its populations. The study of stroma and of stromal cells, in particular of immune cells, is now of paramount importance for providing new prognostic and predictive biomarkers, especially for anti-angiogenic strategies and for cancer immunotherapy. Tissue analysis is therefore the only way to perform a « total », « phenogenomic » characterization of the tumor as an organ : this is particularly important in the moment in which descriptive genomics is substituted by functional genomics and integrated biology.
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Affiliation(s)
- Jean-Yves Scoazec
- Services de pathologie morphologique et moléculaire, Département de biologie et pathologie médicales; AMMICa, Inserm US23/CNRS UMS3655, Gustave Roussy Cancer Campus, 114, rue Edouard Vaillant, 94805 Villejuif cedex, France..
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Yu KH, Snyder M. Omics Profiling in Precision Oncology. Mol Cell Proteomics 2016; 15:2525-36. [PMID: 27099341 PMCID: PMC4974334 DOI: 10.1074/mcp.o116.059253] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 04/15/2016] [Indexed: 12/11/2022] Open
Abstract
Cancer causes significant morbidity and mortality worldwide, and is the area most targeted in precision medicine. Recent development of high-throughput methods enables detailed omics analysis of the molecular mechanisms underpinning tumor biology. These studies have identified clinically actionable mutations, gene and protein expression patterns associated with prognosis, and provided further insights into the molecular mechanisms indicative of cancer biology and new therapeutics strategies such as immunotherapy. In this review, we summarize the techniques used for tumor omics analysis, recapitulate the key findings in cancer omics studies, and point to areas requiring further research on precision oncology.
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Affiliation(s)
- Kun-Hsing Yu
- From the ‡Department of Genetics, Stanford University School of Medicine, Stanford, California; §Biomedical Informatics Program, Stanford University School of Medicine, Stanford, California
| | - Michael Snyder
- From the ‡Department of Genetics, Stanford University School of Medicine, Stanford, California;
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7
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Klassisk fag i rask endring. TIDSSKRIFT FOR DEN NORSKE LEGEFORENING 2015. [DOI: 10.4045/tidsskr.15.0612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
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LaChance A, Murphy MJ. Keeping up with the times: revising the dermatology residency curriculum in the era of molecular diagnostics and personalized medicine. Int J Dermatol 2014; 53:1377-82. [DOI: 10.1111/ijd.12621] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Avery LaChance
- Division of Dermatopathology; Department of Dermatology; University of Connecticut Health Center; Farmington CT USA
| | - Michael J. Murphy
- Division of Dermatopathology; Department of Dermatology; University of Connecticut Health Center; Farmington CT USA
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van der Nest MA, Bihon W, De Vos L, Naidoo K, Roodt D, Rubagotti E, Slippers B, Steenkamp ET, Wilken PM, Wilson A, Wingfield MJ, Wingfield BD. IMA Genome-F 2: Ceratocystis manginecans, Ceratocystis moniliformis, Diplodia sapinea: Draft genome sequences of Diplodia sapinea, Ceratocystis manginecans, and Ceratocystis moniliformis. IMA Fungus 2014; 5:135-40. [PMID: 25083413 PMCID: PMC4107891 DOI: 10.5598/imafungus.2014.05.01.13] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 06/06/2014] [Indexed: 01/15/2023] Open
Abstract
The draft nuclear genomes of Diplodia sapinea, Ceratocystis moniliformis s. str., and C. manginecans are presented. Diplodia sapinea is an important shoot-blight and canker pathogen of Pinus spp., C. moniliformis is a saprobe associated with wounds on a wide range of woody angiosperms and C. manginecans is a serious wilt pathogen of mango and Acacia mangium. The genome size of D. sapinea is estimated at 36.97 Mb and contains 13 020 predicted genes. Ceratocystis moniliformis includes 25.43 Mb and is predicted to encode at least 6 832 genes. This is smaller than that reported for the mango wilt pathogen C. manginecans which is 31.71 Mb and is predicted to encode at least 7 494 genes. The latter is thus more similar to C. fimbriata s.str., the type species of the genus. The genome sequences presented here provide an important resource to resolve issues pertaining to the taxonomy, biology and evolution of these fungi.
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Affiliation(s)
- Magriet A. van der Nest
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P. Bag X20, Pretoria 0028, South Africa
| | - Wubetu Bihon
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P. Bag X20, Pretoria 0028, South Africa
- Agricultural Research Council, Vegetable and Ornamental Plant Institute, P. Bag X293, Pretoria 0001, South Africa
| | - Lieschen De Vos
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P. Bag X20, Pretoria 0028, South Africa
| | - Kershney Naidoo
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P. Bag X20, Pretoria 0028, South Africa
| | - Danielle Roodt
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P. Bag X20, Pretoria 0028, South Africa
| | - Enrico Rubagotti
- Genomic Research Institute, University of Pretoria, Pretoria, 0002, South Africa
| | - Bernard Slippers
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P. Bag X20, Pretoria 0028, South Africa
| | - Emma T. Steenkamp
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag x20, Pretoria 0028, South Africa
| | - P. Markus Wilken
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P. Bag X20, Pretoria 0028, South Africa
| | - Andrea Wilson
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P. Bag X20, Pretoria 0028, South Africa
| | - Michael J. Wingfield
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P. Bag X20, Pretoria 0028, South Africa
| | - Brenda D. Wingfield
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, P. Bag X20, Pretoria 0028, South Africa
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Jacob HJ, Abrams K, Bick DP, Brodie K, Dimmock DP, Farrell M, Geurts J, Harris J, Helbling D, Joers BJ, Kliegman R, Kowalski G, Lazar J, Margolis DA, North P, Northup J, Roquemore-Goins A, Scharer G, Shimoyama M, Strong K, Taylor B, Tsaih SW, Tschannen MR, Veith RL, Wendt-Andrae J, Wilk B, Worthey EA. Genomics in clinical practice: lessons from the front lines. Sci Transl Med 2014; 5:194cm5. [PMID: 23863829 DOI: 10.1126/scitranslmed.3006468] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The price of whole-genome and -exome sequencing has fallen to the point where these methods can be applied to clinical medicine. Here, we outline the lessons we have learned in converting a sequencing laboratory designed for research into a fully functional clinical program.
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Affiliation(s)
- Howard J Jacob
- Human and Molecular Genetic Center, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA.
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Flynn C, James J, Maxwell P, McQuaid S, Ervine A, Catherwood M, Loughrey MB, McGibben D, Somerville J, McManus DT, Gray M, Herron B, Salto-Tellez M. Integrating molecular diagnostics into histopathology training: the Belfast model. J Clin Pathol 2014; 67:632-6. [PMID: 24493649 DOI: 10.1136/jclinpath-2014-202176] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Molecular medicine is transforming modern clinical practice, from diagnostics to therapeutics. Discoveries in research are being incorporated into the clinical setting with increasing rapidity. This transformation is also deeply changing the way we practise pathology. The great advances in cell and molecular biology which have accelerated our understanding of the pathogenesis of solid tumours have been embraced with variable degrees of enthusiasm by diverse medical professional specialties. While histopathologists have not been prompt to adopt molecular diagnostics to date, the need to incorporate molecular pathology into the training of future histopathologists is imperative. Our goal is to create, within an existing 5-year histopathology training curriculum, the structure for formal substantial teaching of molecular diagnostics. This specialist training has two main goals: (1) to equip future practising histopathologists with basic knowledge of molecular diagnostics and (2) to create the option for those interested in a subspecialty experience in tissue molecular diagnostics to pursue this training. It is our belief that this training will help to maintain in future the role of the pathologist at the centre of patient care as the integrator of clinical, morphological and molecular information.
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Affiliation(s)
- C Flynn
- Tissue Pathology, Belfast Health and Social Care Trust, Belfast, Northern Ireland
| | - J James
- Tissue Pathology, Belfast Health and Social Care Trust, Belfast, Northern Ireland Northern Ireland Molecular Pathology Laboratory, Centre for Cancer Research and Cell Biology, Queen's University, Belfast, Northern Ireland
| | - P Maxwell
- Tissue Pathology, Belfast Health and Social Care Trust, Belfast, Northern Ireland Northern Ireland Molecular Pathology Laboratory, Centre for Cancer Research and Cell Biology, Queen's University, Belfast, Northern Ireland
| | - S McQuaid
- Tissue Pathology, Belfast Health and Social Care Trust, Belfast, Northern Ireland Northern Ireland Molecular Pathology Laboratory, Centre for Cancer Research and Cell Biology, Queen's University, Belfast, Northern Ireland
| | - A Ervine
- Tissue Pathology, Belfast Health and Social Care Trust, Belfast, Northern Ireland
| | - M Catherwood
- Haemato-Oncology Laboratory, Belfast Health and Social Care Trust, Belfast, Northern Ireland
| | - M B Loughrey
- Tissue Pathology, Belfast Health and Social Care Trust, Belfast, Northern Ireland
| | - D McGibben
- Tissue Pathology, Belfast Health and Social Care Trust, Belfast, Northern Ireland
| | - J Somerville
- Tissue Pathology, Belfast Health and Social Care Trust, Belfast, Northern Ireland
| | - D T McManus
- Tissue Pathology, Belfast Health and Social Care Trust, Belfast, Northern Ireland
| | - M Gray
- Tissue Pathology, Belfast Health and Social Care Trust, Belfast, Northern Ireland
| | - B Herron
- Tissue Pathology, Belfast Health and Social Care Trust, Belfast, Northern Ireland
| | - M Salto-Tellez
- Tissue Pathology, Belfast Health and Social Care Trust, Belfast, Northern Ireland Northern Ireland Molecular Pathology Laboratory, Centre for Cancer Research and Cell Biology, Queen's University, Belfast, Northern Ireland
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Yang YT, Lin CY, Jeng J, Ong CW. Impact of pyrrolidine-bispyrrole DNA minor groove binding agents and chirality on global proteomic profile in Escherichia Coli. Proteome Sci 2013; 11:23. [PMID: 23702249 PMCID: PMC3669006 DOI: 10.1186/1477-5956-11-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 05/13/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND There is great interest in the design of small molecules that selectively target minor grooves of duplex DNA for controlling specific gene expression implicated in a disease. The design of chiral small molecules for rational drug design has attracted increasing attention due to the chirality of DNA. Yet, there is limited research on the chirality effect of minor groove binders on DNA interaction, especially at the protein expression level. This paper is an attempt to illustrate that DNA binding affinity might not provide a full picture on the biological activities. Drug interacting at the genomic level can be translated to the proteomic level. Here we have illustrated that although the chiral bispyrrole-pyrrolidine-oligoamides, PySSPy and PyRSPy, showed low binding affinity to DNA, their influence at the proteomic level is significant. More importantly, the chirality also plays a role. Two-dimensional proteomic profile to identify the differentially expressed protein in Escherichia coli DH5α (E coli DH5α) were investigated. RESULTS E coli DH5α incubated with the chiral PySSPy and PyRSPy, diastereomeric at the pyrrolidine ring, showed differential expression of eighteen proteins as observed through two dimensional proteomic profiling. These eighteen proteins identified by MALDI_TOF/TOF MS include antioxidant defense, DNA protection, protein synthesis, chaperone, and stress response proteins. No statistically significant toxicity was observed at the tested drug concentrations as measured via MTT assay. CONCLUSION The current results showed that the chiral PySSPy and PyRSPy impact on the proteomic profiling of E coli DH5α, implicating the importance of drug chirality on biological activities at the molecular level.
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Affiliation(s)
- Ya-Ting Yang
- Department of Chemistry, National Sun Yat-sen University, No, 70, Lienhai Rd,, Kaohsiung, 80424, Taiwan.
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Roth KA. The American Journal of Pathology Centennial Project. THE AMERICAN JOURNAL OF PATHOLOGY 2013; 182:1050-1. [DOI: 10.1016/j.ajpath.2013.02.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Accepted: 02/12/2013] [Indexed: 10/27/2022]
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