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Madill-Thomsen K, Halloran P. Precision diagnostics in transplanted organs using microarray-assessed gene expression: concepts and technical methods of the Molecular Microscope® Diagnostic System (MMDx). Clin Sci (Lond) 2024; 138:663-685. [PMID: 38819301 PMCID: PMC11147747 DOI: 10.1042/cs20220530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 04/26/2024] [Accepted: 05/02/2024] [Indexed: 06/01/2024]
Abstract
There is a major unmet need for improved accuracy and precision in the assessment of transplant rejection and tissue injury. Diagnoses relying on histologic and visual assessments demonstrate significant variation between expert observers (as represented by low kappa values) and have limited ability to assess many biological processes that produce little histologic changes, for example, acute injury. Consensus rules and guidelines for histologic diagnosis are useful but may have errors. Risks of over- or under-treatment can be serious: many therapies for transplant rejection or primary diseases are expensive and carry risk for significant adverse effects. Improved diagnostic methods could alleviate healthcare costs by reducing treatment errors, increase treatment efficacy, and serve as useful endpoints for clinical trials of new agents that can improve outcomes. Molecular diagnostic assessments using microarrays combined with machine learning algorithms for interpretation have shown promise for increasing diagnostic precision via probabilistic assessments, recalibrating standard of care diagnostic methods, clarifying ambiguous cases, and identifying potentially missed cases of rejection. This review describes the development and application of the Molecular Microscope® Diagnostic System (MMDx), and discusses the history and reasoning behind many common methods, statistical practices, and computational decisions employed to ensure that MMDx scores are as accurate and precise as possible. MMDx provides insights on disease processes and highly reproducible results from a comparatively small amount of tissue and constitutes a general approach that is useful in many areas of medicine, including kidney, heart, lung, and liver transplants, with the possibility of extrapolating lessons for understanding native organ disease states.
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Affiliation(s)
- Katelynn S. Madill-Thomsen
- Department of Medicine, University of Alberta, Edmonton, AB, Canada
- Alberta Transplant Applied Genomics Center, University of Alberta, Edmonton, AB, Canada
| | - Philip F. Halloran
- Department of Medicine, University of Alberta, Edmonton, AB, Canada
- Alberta Transplant Applied Genomics Center, University of Alberta, Edmonton, AB, Canada
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2
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Wen P, Sun Y, Jiang TX, Qiu XB. PA200-Mediated Proteasomal Protein Degradation and Regulation of Cellular Senescence. Int J Mol Sci 2024; 25:5637. [PMID: 38891826 PMCID: PMC11171664 DOI: 10.3390/ijms25115637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Revised: 04/25/2024] [Accepted: 04/26/2024] [Indexed: 06/21/2024] Open
Abstract
Cellular senescence is closely related to DNA damage, proteasome inactivity, histone loss, epigenetic alterations, and tumorigenesis. The mammalian proteasome activator PA200 (also referred to as PSME4) or its yeast ortholog Blm10 promotes the acetylation-dependent degradation of the core histones during transcription, DNA repair, and spermatogenesis. According to recent studies, PA200 plays an important role in senescence, probably because of its role in promoting the degradation of the core histones. Loss of PA200 or Blm10 is a major cause of the decrease in proteasome activity during senescence. In this paper, recent research progress on the association of PA200 with cellular senescence is summarized, and the potential of PA200 to serve as a therapeutic target in age-related diseases is discussed.
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Affiliation(s)
- Pei Wen
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 211198, China; (P.W.); (Y.S.)
| | - Yan Sun
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 211198, China; (P.W.); (Y.S.)
| | - Tian-Xia Jiang
- Ministry of Education Key Laboratory of Cell Proliferation & Regulation Biology, College of Life Sciences, Beijing Normal University, 19 Xinjiekouwai Avenue, Beijing 100875, China
| | - Xiao-Bo Qiu
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 211198, China; (P.W.); (Y.S.)
- Ministry of Education Key Laboratory of Cell Proliferation & Regulation Biology, College of Life Sciences, Beijing Normal University, 19 Xinjiekouwai Avenue, Beijing 100875, China
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3
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Krause N, Wegner A. N-acetyl-aspartate metabolism at the interface of cancer, immunity, and neurodegeneration. Curr Opin Biotechnol 2024; 85:103051. [PMID: 38103520 DOI: 10.1016/j.copbio.2023.103051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 11/15/2023] [Accepted: 11/27/2023] [Indexed: 12/19/2023]
Abstract
N-acetyl-L-aspartic acid (NAA) is a prominent amino acid derivative primarily associated with vertebrate brain metabolism. This review delineates the critical role of NAA across various cell types and its significance in pathophysiological contexts, including Canavan disease and cancer metabolism. Although traditionally linked with myelination and aspartoacylase-driven carbon donation, its significance as a carbon source for myelination remains debated. Evidence suggests that intact NAA might substantially impact cellular signaling, particularly processes such as histone acetylation. Beyond the brain, NAA metabolism's relevance is evident in diverse tissues, such as adipocytes, immune cells, and notably, cancer cells. In several cancer types, there is an observed upregulation of NAA synthesis accompanied by a simultaneous downregulation of its degradation. This pattern highlights the potential signaling role of intact NAA in disease.
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Affiliation(s)
- Nils Krause
- Department of Bioinformatics and Biochemistry, Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany
| | - Andre Wegner
- Department of Bioinformatics and Biochemistry, Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany.
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4
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Spratt DE, Liu VYT, Michalski J, Davicioni E, Berlin A, Simko JP, Efstathiou JA, Tran PT, Sandler HM, Hall WA, Thompson DJS, Parliament MB, Dayes IS, Correa RJM, Robertson JM, Gore EM, Doncals DE, Vigneault E, Souhami L, Karrison TG, Feng FY. Genomic Classifier Performance in Intermediate-Risk Prostate Cancer: Results From NRG Oncology/RTOG 0126 Randomized Phase 3 Trial. Int J Radiat Oncol Biol Phys 2023; 117:370-377. [PMID: 37137444 PMCID: PMC10949135 DOI: 10.1016/j.ijrobp.2023.04.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 03/15/2023] [Accepted: 04/12/2023] [Indexed: 05/05/2023]
Abstract
PURPOSE Intermediate-risk prostate cancer is a heterogeneous disease state with diverse treatment options. The 22-gene Decipher genomic classifier (GC) retrospectively has shown to improve risk stratification in these patients. We assessed the performance of the GC in men with intermediate-risk disease enrolled in NRG Oncology/RTOG 01-26 with updated follow-up. METHODS AND MATERIALS After National Cancer Institute approval, biopsy slides were collected from NRG Oncology/RTOG 01-26, a randomized phase 3 trial of men with intermediate-risk prostate cancer randomized to 70.2 Gy versus 79.2 Gy of radiation therapy without androgen deprivation therapy. RNA was extracted from the highest-grade tumor foci to generate the locked 22-gene GC model. The primary endpoint for this ancillary project was disease progression (composite of biochemical failure, local failure, distant metastasis, prostate cancer-specific mortality, and use of salvage therapy). Individual endpoints were also assessed. Fine-Gray or cause-specific Cox multivariable models were constructed adjusting for randomization arm and trial stratification factors. RESULTS Two-hundred fifteen patient samples passed quality control for analysis. The median follow-up was 12.8 years (range, 2.4-17.7). On multivariable analysis, the 22-gene GC (per 0.1 unit) was independently prognostic for disease progression (subdistribution hazard ratio [sHR], 1.12; 95% confidence interval [CI], 1.00-1.26; P = .04), biochemical failure (sHR, 1.22; 95% CI, 1.10-1.37; P < .001), distant metastasis (sHR, 1.28; 95% CI, 1.06-1.55; P = .01), and prostate cancer-specific mortality (sHR, 1.45; 95% CI, 1.20-1.76; P < .001). Ten-year distant metastasis in GC low-risk patients was 4% compared with 16% for GC high-risk patients. In patients with lower GC scores, the 10-year difference in metastasis-free survival rate between arms was -7%, compared with 21% for higher GC patients (P-interaction = .04). CONCLUSIONS This study represents the first validation of a biopsy-based gene expression classifier, assessing both its prognostic and predictive value, using data from a randomized phase 3 trial of intermediate-risk prostate cancer. Decipher improves risk stratification and can aid in treatment decision-making in men with intermediate-risk disease.
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Affiliation(s)
- Daniel E Spratt
- Department of Radiation Oncology, University Hospitals Seidman Cancer Center, Cleveland, Ohio.
| | | | - Jeff Michalski
- Department of Radiation Oncology, Washington University, St. Louis, Missouri
| | | | - Alejandro Berlin
- Princess Margaret Cancer Centre, Cancer Clinical Research Unit, Toronto, Ontario, Canada
| | - Jeffry P Simko
- Department of Pathology, UCSF Medical Center-Mount Zion, San Francisco, California
| | - Jason A Efstathiou
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Phuoc T Tran
- Department of Pathology, University of Maryland, Baltimore, Maryland
| | - Howard M Sandler
- Department of Radiation Oncology, Cedars-Sinai Medical Center, Los Angeles, California
| | - William A Hall
- Department of Radiation Oncology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | | | - Matthew B Parliament
- Division of Radiation Oncology, Cross Cancer Institute, Edmonton, Alberta, Canada
| | - Ian S Dayes
- Division of Radiation Oncology, Hamilton Regional Cancer Centre, Ontario, Canada
| | | | - John M Robertson
- Department of Radiation Oncology, Beaumont Health CCOP, Royal Oak, Michigan
| | - Elizabeth M Gore
- Department of Radiation Oncology, Milwaukee VA Medical Center, Milwaukee, Wisconsin
| | | | - Eric Vigneault
- Department of Radiation Oncology, CHU de Quebec Universite Laval, Quebec, Canada
| | - Luis Souhami
- Department of Radiation Oncology, Cedars Cancer Centre, McGill University, Quebec, Canada
| | - Theodore G Karrison
- NRG Oncology Statistics and Data Management Center, Philadelphia, Pennsylvania
| | - Felix Y Feng
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California
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5
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Nguyen PL, Huang HCR, Spratt DE, Davicioni E, Sandler HM, Shipley WU, Efstathiou JA, Simko JP, Pollack A, Dicker AP, Roach M, Rosenthal SA, Zeitzer KL, Mendez LC, Hartford AC, Hall WA, Desai AB, Rabinovitch RA, Peters CA, Rodgers JP, Tran P, Feng FY. Analysis of a Biopsy-Based Genomic Classifier in High-Risk Prostate Cancer: Meta-Analysis of the NRG Oncology/Radiation Therapy Oncology Group 9202, 9413, and 9902 Phase 3 Randomized Trials. Int J Radiat Oncol Biol Phys 2023; 116:521-529. [PMID: 36596347 PMCID: PMC10281690 DOI: 10.1016/j.ijrobp.2022.12.035] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 12/03/2022] [Accepted: 12/19/2022] [Indexed: 01/02/2023]
Abstract
PURPOSE Decipher is a genomic classifier (GC) prospectively validated postprostatectomy. We validated the performance of the GC in pretreatment biopsy samples within the context of 3 randomized phase 3 high-risk definitive radiation therapy trials. METHODS AND MATERIALS A prespecified analysis plan (NRG-GU-TS006) was approved to obtain formalin-fixed paraffin-embedded tissue from biopsy specimens from the NRG biobank from patients enrolled in the NRG/Radiation Therapy Oncology Group (RTOG) 9202, 9413, and 9902 phase 3 randomized trials. After central review, the highest-grade tumors were profiled on clinical-grade whole-transcriptome arrays and GC scores were obtained. The primary objective was to validate the independent prognostic ability for the GC for distant metastases (DM), and secondary for prostate cancer-specific mortality (PCSM) and overall survival (OS) with Cox univariable and multivariable analyses. RESULTS GC scores were obtained on 385 samples, of which 265 passed microarray quality control (69%) and had a median follow-up of 11 years (interquartile range, 9-13). In the pooled cohort, on univariable analysis, the GC was shown to be a prognostic factor for DM (per 0.1 unit; subdistribution hazard ratio [sHR], 1.29; 95% confidence interval [CI], 1.18-1.41; P < .001), PCSM (sHR, 1.28; 95% CI, 1.16-1.41; P < .001), and OS (hazard ratio [HR], 1.16; 95% CI, 1.08-1.22; P < .001). On multivariable analyses, the GC (per 0.1 unit) was independently associated with DM (sHR, 1.22; 95% CI, 1.09-1.36), PCSM (sHR, 1.23; 95% CI, 1.09-1.39), and OS (HR, 1.12; 95% CI, 1.05-1.20) after adjusting for age, Prostate Specific Antigen, Gleason score, cT stage, trial, and randomized treatment arm. GC had similar prognostic ability in patients receiving short-term or long-term androgen-deprivation therapy, but the absolute improvement in outcome varied by GC risk. CONCLUSIONS This is the first validation of a gene expression biomarker on pretreatment prostate cancer biopsy samples from prospective randomized trials and demonstrates an independent association of GC score with DM, PCSM, and OS. High-risk prostate cancer is a heterogeneous disease state, and GC can improve risk stratification to help personalize shared decision making.
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Affiliation(s)
- Paul L Nguyen
- Department of Radiation Oncology, Brigham and Women's Hospital, Boston, Massachusetts; Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts.
| | - Huei-Chung Rebecca Huang
- GenomeDx Inc, Vancouver, British Columbia, Canada; Decipher Biosciences, San Diego, California; Veracyte, South San Francisco CA
| | - Daniel E Spratt
- Department of Radiation Oncology, UH Cleveland Medical Center, Cleveland, Ohio
| | - Elai Davicioni
- Decipher Biosciences, San Diego, California; Veracyte, South San Francisco CA
| | - Howard M Sandler
- Department of Radiation Oncology, Cedars-Sinai Medical Center, Los Angeles, California
| | - William U Shipley
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jason A Efstathiou
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jeffry P Simko
- Department of Pathology, UCSF Medical Center-Mount Zion, San Francisco, California
| | - Alan Pollack
- Department of Radiation Oncology, University of Miami Miller School of Medicine, Miami, Florida
| | - Adam P Dicker
- Department of Radiation Oncology, Thomas Jefferson University Hospital, Philadelphia, Pennsylvania
| | - Mack Roach
- Department of Pathology, UCSF Medical Center-Mount Zion, San Francisco, California
| | - Seth A Rosenthal
- Department of Radiation Oncology, Sutter Cancer Centers Radiation Oncology Services, Roseville, California
| | - Kenneth L Zeitzer
- Department of Radiation Oncology, Einstein Medical Center, Thomas Jefferson University Hospital, Philadelphia, Pennsylvania
| | - Lucas C Mendez
- Department of Radiation Oncology, London Regional Cancer Program, London, Ontario, Canada
| | - Alan C Hartford
- Department of Radiation Oncology, Dartmouth-Hitchcock Medical Center/Norris Cotton Cancer Center, Lebanon, New Hampshire
| | - William A Hall
- Department of Radiation Oncology, Froedtert and the Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Anand B Desai
- Department of Radiation Oncology, Summa Health System, Akron, Ohio
| | - Rachel A Rabinovitch
- Department of Radiation Oncology, University of Colorado Denver, Aurora, Colorado
| | - Christopher A Peters
- Department of Radiation Oncology, Northeast Radiation Oncology Center, Dunmore, Pennsylvania
| | | | - Phuoc Tran
- Department of Radiation Oncology, University of Maryland, Baltimore, Maryland
| | - Felix Y Feng
- Department of Radiation Oncology, UCSF Medical Center-Mission Bay, San Francisco, California
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Yazgili AS, Ebstein F, Meiners S. The Proteasome Activator PA200/PSME4: An Emerging New Player in Health and Disease. Biomolecules 2022; 12:1150. [PMID: 36009043 PMCID: PMC9406137 DOI: 10.3390/biom12081150] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 08/17/2022] [Accepted: 08/18/2022] [Indexed: 11/24/2022] Open
Abstract
Proteasomes comprise a family of proteasomal complexes essential for maintaining protein homeostasis. Accordingly, proteasomes represent promising therapeutic targets in multiple human diseases. Several proteasome inhibitors are approved for treating hematological cancers. However, their side effects impede their efficacy and broader therapeutic applications. Therefore, understanding the biology of the different proteasome complexes present in the cell is crucial for developing tailor-made inhibitors against specific proteasome complexes. Here, we will discuss the structure, biology, and function of the alternative Proteasome Activator 200 (PA200), also known as PSME4, and summarize the current evidence for its dysregulation in different human diseases. We hereby aim to stimulate research on this enigmatic proteasome regulator that has the potential to serve as a therapeutic target in cancer.
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Affiliation(s)
- Ayse Seda Yazgili
- Comprehensive Pneumology Center (CPC), Helmholtz Center Munich, Max-Lebsche Platz 31, 81377 Munich, Germany
| | - Frédéric Ebstein
- Institut für Medizinische Biochemie und Molekularbiologie (IMBM), Universitätsmedizin Greifswald, Ferdinand-Sauerbruch-Straße, Klinikum DZ/7, 17475 Greifswald, Germany
| | - Silke Meiners
- Research Center Borstel/Leibniz Lung Center, Parkallee 1-40, 23845 Borstel, Germany
- Airway Research Center North (ARCN), German Center for Lung Research (DZL), 23845 Sülfeld, Germany
- Institute of Experimental Medicine, Christian-Albrechts University Kiel, 24118 Kiel, Germany
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7
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Lima VR, da Costa Aguiar Alves B, Fonseca FLA, Zveibil DK, Del Giglio A. Pre-analytical processing protocol of breast biopsies affects multigene panel results. Int J Exp Pathol 2022; 103:112-120. [PMID: 35569033 DOI: 10.1111/iep.12444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 04/07/2022] [Accepted: 04/07/2022] [Indexed: 11/28/2022] Open
Abstract
The creation of multigene panels for prognostic and predictive purposes allows a more accurate indication of adjuvant chemotherapy for patients with breast cancer. In a previous study, we reproduced a multigene panel of 21 genes based on the commercial Oncotype-DX method. We submitted 183 embedded specimens obtained from breast surgery on patients with locoregional disease (stages I to III) between 2005 and 2010 performed at the Hospitals of the Medical School of the ABC Foundation. When we analysed the correlations between the score of the multigene panel and the progression-free interval (PFI) in all patients, we did not find a statistically significant association. However, when we selected only the 71 samples that had amplification of at least eight non-housekeeping genes, we observed that those with scores above the 75th percentile had a significantly lower PFI (p = .0054). Samples processed with nonbuffered formaldehyde were associated with a worse quality of extracted RNA (p = .004) and a significantly higher multigene panel score (p = .021). We conclude that variations in the pre-analytical processing of specimens destined for multigene panel amplification can significantly affect the results, with a potential impact on clinical management.
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Affiliation(s)
- Vanessa Reinaldo Lima
- Clinical Analysis Laboratory of the Medical School of the ABC (FMABC) University Center, Santo André, Brazil
| | | | - Fernando Luiz Affonso Fonseca
- Clinical Analysis Laboratory of the Medical School of the ABC (FMABC) University Center, Santo André, Brazil.,Institute of Pharmaceutical Sciences, Federal University of São Paulo (UNIFESP), Diadema, Brazil
| | - Debora Krutman Zveibil
- Department of Pathology, Medical School of the ABC (FMABC) University Center, Santo André, Brazil
| | - Auro Del Giglio
- Discipline of Oncology and Hematology, Medical School of the ABC (FMABC) University Center, Santo André, Brazil
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Wolf J, Hajdu RI, Boneva S, Schlecht A, Lapp T, Wacker K, Agostini H, Reinhard T, Auw-Hädrich C, Schlunck G, Lange C. Characterization of the Cellular Microenvironment and Novel Specific Biomarkers in Pterygia Using RNA Sequencing. Front Med (Lausanne) 2022; 8:714458. [PMID: 35174178 PMCID: PMC8841401 DOI: 10.3389/fmed.2021.714458] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 12/24/2021] [Indexed: 01/04/2023] Open
Abstract
With a worldwide prevalence of ~12%, pterygium is a common degenerative and environmentally triggered ocular surface disorder characterized by wing-shaped growth of conjunctival tissue onto the cornea that can lead to blindness if left untreated. This study characterizes the transcriptional profile and the cellular microenvironment of conjunctival pterygia and identifies novel pterygia-specific biomarkers. Formalin-fixed and paraffin-embedded pterygia as well as healthy conjunctival specimens were analyzed using MACE RNA sequencing (n = 8 each) and immunohistochemistry (pterygia n = 7, control n = 3). According to the bioinformatic cell type enrichment analysis using xCell, the cellular microenvironment of pterygia was characterized by an enrichment of myofibroblasts, T-lymphocytes and various antigen-presenting cells, including dendritic cells and macrophages. Differentially expressed genes that were increased in pterygia compared to control tissue were mainly involved in autophagy (including DCN, TMBIM6), cellular response to stress (including TPT1, DDX5) as well as fibroblast proliferation and epithelial to mesenchymal transition (including CTNNB1, TGFBR1, and FN1). Immunohistochemical analysis confirmed a significantly increased FN1 stromal immunoreactivity in pterygia when compared to control tissue. In addition, a variety of factors involved in apoptosis were significantly downregulated in pterygia, including LCN2, CTSD, and NISCH. Furthermore, 450 pterygia-specific biomarkers were identified by including transcriptional data of different ocular surface pathologies serving as controls (training group), which were then validated using transcriptional data of cultured human pterygium cells. Among the most pterygia-specific factors were transcripts such as AHNAK, RTN4, TPT1, FSTL1, and SPARC. Immunohistochemical validation of SPARC revealed a significantly increased stromal immunoreactivity in pterygia when compared to controls, most notably in vessels and intravascular vessel wall-adherent mononuclear cells. Taken together, the present study provides new insights into the cellular microenvironment and the transcriptional profile of pterygia, identifies new and specific biomarkers and in addition to fibrosis-related genes, uncovers autophagy, stress response and apoptosis modulation as pterygium-associated processes. These findings expand our understanding of the pathophysiology of pterygia, provide new diagnostic tools, and may enable new targeted therapeutic options for this common and sight-threatening ocular surface disease.
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Affiliation(s)
- Julian Wolf
- Eye Center, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg im Breisgau, Germany
| | - Rozina Ida Hajdu
- Eye Center, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg im Breisgau, Germany
- Department of Ophthalmology, Semmelweis University, Budapest, Hungary
| | - Stefaniya Boneva
- Eye Center, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg im Breisgau, Germany
| | - Anja Schlecht
- Eye Center, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg im Breisgau, Germany
- Institute of Anatomy and Cell Biology, Wuerzburg University, Wuerzburg, Germany
| | - Thabo Lapp
- Eye Center, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg im Breisgau, Germany
| | - Katrin Wacker
- Eye Center, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg im Breisgau, Germany
| | - Hansjürgen Agostini
- Eye Center, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg im Breisgau, Germany
| | - Thomas Reinhard
- Eye Center, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg im Breisgau, Germany
| | - Claudia Auw-Hädrich
- Eye Center, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg im Breisgau, Germany
| | - Günther Schlunck
- Eye Center, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg im Breisgau, Germany
| | - Clemens Lange
- Eye Center, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg im Breisgau, Germany
- Ophtha-Lab, Department of Ophthalmology, St. Franziskus Hospital, Münster, Germany
- *Correspondence: Clemens Lange
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9
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Wolf J, Schlecht A, Rosmus DD, Boneva S, Agostini H, Schlunck G, Wieghofer P, Lange C. Comparative transcriptome analysis of human and murine choroidal neovascularization identifies fibroblast growth factor inducible-14 as phylogenetically conserved mediator of neovascular age-related macular degeneration. Biochim Biophys Acta Mol Basis Dis 2022; 1868:166340. [PMID: 35032596 DOI: 10.1016/j.bbadis.2022.166340] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 12/14/2021] [Accepted: 01/03/2022] [Indexed: 12/11/2022]
Abstract
BACKGROUND Visual outcome of patients with neovascular age-related macular degeneration has significantly improved during the last years following the introduction of anti-vascular endothelial growth factor (VEGF) therapy. However, about one third of patients show persistent exudation and decreasing visual acuity despite recurrent anti-VEGF treatment, which implies a role of other, still unknown proangiogenic mediators. METHODS The present study applied transcriptional profiling of human and mouse (C57BL/6J wildtype) choroidal neovascularization (CNV) membranes each with reference to healthy control tissue to identify yet unrecognized mediators of CNV formation. Key factors were further investigated by immunohistochemistry as well as by intravitreal inhibition experiments and multiplex protein assays in the laser-induced CNV mouse model. FINDINGS Transcriptional profiles of CNV membranes were characterized by enhanced activation of blood vessel development, cytoskeletal organization, and cytokine production, with angiogenesis and wound healing processes predominating in humans and activation of immune processes in mice. Besides several species-specific factors, 95 phylogenetically conserved CNV-associated genes were detected, among which fibroblast growth factor inducible-14 (FN14), a member of the tumor necrosis factor (TNF) receptor family, was identified as a key player of CNV formation. Blocking the pathway by intravitreal injection of a FN14 decoy receptor modulated the cytokine profile - most notably IL-6 - and led to a significant reduction of CNV size in vivo. INTERPRETATION This study characterizes the transcriptome of human and mouse CNV membranes in an unprejudiced manner and identifies FN14 as a phylogenetically conserved mediator of CNV formation and a promising new therapeutic target for neovascular AMD. FUNDING This study was funded by the Helmut Ecker Foundation and the Volker Homann Foundation.
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Affiliation(s)
- Julian Wolf
- Eye Center, Medical Center, Faculty of Medicine, University of Freiburg, Germany
| | - Anja Schlecht
- Eye Center, Medical Center, Faculty of Medicine, University of Freiburg, Germany; Institute of Anatomy, Wuerzburg University, Wuerzburg, Germany
| | | | - Stefaniya Boneva
- Eye Center, Medical Center, Faculty of Medicine, University of Freiburg, Germany
| | - Hansjürgen Agostini
- Eye Center, Medical Center, Faculty of Medicine, University of Freiburg, Germany
| | - Günther Schlunck
- Eye Center, Medical Center, Faculty of Medicine, University of Freiburg, Germany
| | - Peter Wieghofer
- Institute of Anatomy, Leipzig University, Leipzig, Germany; Cellular Neuroanatomy, Institute of Theoretical Medicine, Medical Faculty, University of Augsburg, Augsburg, Germany
| | - Clemens Lange
- Eye Center, Medical Center, Faculty of Medicine, University of Freiburg, Germany; Ophtha-Lab, Department of Ophthalmology, St. Franziskus Hospital Muenster, Muenster, Germany.
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10
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Halloran PF, Madill-Thomsen KS, Böhmig GA, Myslak M, Gupta G, Kumar D, Viklicky O, Perkowska-Ptasinska A, Famulski KS. A 2-fold Approach to Polyoma Virus (BK) Nephropathy in Kidney Transplants: Distinguishing Direct Virus Effects From Cognate T Cell-mediated Inflammation. Transplantation 2021; 105:2374-2384. [PMID: 34310102 DOI: 10.1097/tp.0000000000003884] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND BK nephropathy (BKN) in kidney transplants diagnosed by histology is challenging because it involves damage from both virus activity and cognate T cell-mediated inflammation, directed against alloantigens (rejection) or viral antigens. The present study of indication biopsies from the Integrated Diagnostic System in the International Collaborative Microarray Study Extension study measured major capsid viral protein 2 (VP2) mRNA to assess virus activity and a T cell-mediated rejection (TCMR) classifier to assess cognate T cell-mediated inflammation. METHODS Biopsies were assessed by local standard-of-care histology and by genome-wide microarrays and Molecular Microscope Diagnostic System (MMDx) algorithms to detect rejection and injury. In a subset of 102 biopsies (50 BKN and 52 BKN-negative biopsies with various abnormalities), we measured VP2 transcripts by real-time polymerase chain reaction. RESULTS BKN was diagnosed in 55 of 1679 biopsies; 30 had cognate T cell-mediated activity assessed by by MMDx and TCMR lesions, but only 3 of 30 were histologically diagnosed as TCMR. We developed a BKN probability classifier that predicted histologic BKN (area under the curve = 0.82). Virus activity (VP2 expression) was highly selective for BKN (area under the curve = 0.94) and correlated with acute injury, atrophy-fibrosis, macrophage activation, and the BKN classifier, but not with the TCMR classifier. BKN with molecular TCMR had more tubulitis and inflammation than BKN without molecular TCMR. In 5 BKN cases with second biopsies, VP2 mRNA decreased in second biopsies, whereas in 4 of 5 TCMR classifiers, scores increased. Genes and pathways associated with BKN and VP2 mRNA were similar, reflecting injury, inflammation, and macrophage activation but none was selective for BKN. CONCLUSIONS Risk-benefit decisions in BKN may be assisted by quantitative assessment of the 2 major pathologic processes, virus activity and cognate T cell-mediated inflammation.
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Affiliation(s)
- Philip F Halloran
- Alberta Transplant Applied Genomics Centre, Edmonton, AB, Canada
- Department of Medicine, Division of Nephrology and Transplant Immunology, University of Alberta, Edmonton, AB, Canada
| | | | - Georg A Böhmig
- Division of Nephrology and Dialysis, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Marek Myslak
- Department of Nephrology and Kidney Transplantation, SPWSZ Hospital in Szczecin, Pomeranian Medical University, Szczecin, Poland
| | - Gaurav Gupta
- Division of Nephrology, Virginia Commonwealth University, Richmond, VA
| | - Dhiren Kumar
- Division of Nephrology, Virginia Commonwealth University, Richmond, VA
| | - Ondrej Viklicky
- Department of Nephrology and Transplant Center, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
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11
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Guo C, Jiang X, Guo J, Wu Y, Bao G. Integrated bioinformatic analysis identifies COL4A3, COL4A4, and KCNJ1 as key biomarkers in Wilms tumor. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2021; 14:196-208. [PMID: 33564352 PMCID: PMC7868786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 12/06/2020] [Indexed: 06/12/2023]
Abstract
Wilms tumor (WT) is one of the most common pediatric solid tumors, affecting 1 in 10,000 children, worldwide. A subset of WT patients has poor prognosis, which is associated with a high risk of advanced and/or recurrent disease. Therefore, candidate markers are urgently needed for the diagnosis and effective treatment of WT. We evaluated three mRNA microarray datasets to identify the differences between normal kidney tissue and WT tissue. Gene expression profiling revealed 130 differentially expressed genes (DEGs). Enrichment analysis and gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed for the DEGs. Subsequently, we established a protein-protein interaction (PPI) network to reveal the associations among the DEGs and selected 10 hub genes, all of which were downregulated in WT. The expression of COL4A3, COL4A4, KCNJ1, MME, and SLC12A1 in WT tissues was significantly lower than that in normal renal tissues. Survival analyses using the Kaplan-Meier method showed that patients with WT and low expression of COL4A3, COL4A4, and KCNJ1 exhibited remarkably poor overall survival. The correlations among COL4A3, COL4A4, and KCNJ1 in WT were analyzed using cBioPortal; COL4A3, COL4A4, and KCNJ1 were positively correlated with each other. Thus, these genes were considered clinically significant and might therefore play important roles in carcinogenesis and the development of WT.
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Affiliation(s)
- Changgang Guo
- Department of Urology, Affiliated Hospital of Chifeng UniversityChifeng 024000, China
- Urology Research Center, Chifeng UniversityChifeng 024000, China
| | - Xiling Jiang
- Department of Stomatology, Affiliated Hospital of Chifeng UniversityChifeng 024000, China
| | - Junsheng Guo
- Department of Urology, Affiliated Hospital of Chifeng UniversityChifeng 024000, China
- Urology Research Center, Chifeng UniversityChifeng 024000, China
| | - Yanlong Wu
- Department of Urology, Affiliated Hospital of Chifeng UniversityChifeng 024000, China
| | - Guochang Bao
- Department of Urology, Affiliated Hospital of Chifeng UniversityChifeng 024000, China
- Urology Research Center, Chifeng UniversityChifeng 024000, China
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12
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Verma M, Khan MIK, Kadumuri RV, Chakrapani B, Awasthi S, Mahesh A, Govindaraju G, Chavali PL, Rajavelu A, Chavali S, Dhayalan A. PRMT3 interacts with ALDH1A1 and regulates gene-expression by inhibiting retinoic acid signaling. Commun Biol 2021; 4:109. [PMID: 33495566 PMCID: PMC7835222 DOI: 10.1038/s42003-020-01644-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 12/15/2020] [Indexed: 12/23/2022] Open
Abstract
Protein arginine methyltransferase 3 (PRMT3) regulates protein functions by introducing asymmetric dimethylation marks at the arginine residues in proteins. However, very little is known about the interaction partners of PRMT3 and their functional outcomes. Using yeast-two hybrid screening, we identified Retinal dehydrogenase 1 (ALDH1A1) as a potential interaction partner of PRMT3 and confirmed this interaction using different methods. ALDH1A1 regulates variety of cellular processes by catalyzing the conversion of retinaldehyde to retinoic acid. By molecular docking and site-directed mutagenesis, we identified the specific residues in the catalytic domain of PRMT3 that facilitate interaction with the C-terminal region of ALDH1A1. PRMT3 inhibits the enzymatic activity of ALDH1A1 and negatively regulates the expression of retinoic acid responsive genes in a methyltransferase activity independent manner. Our findings show that in addition to regulating protein functions by introducing methylation modifications, PRMT3 could also regulate global gene expression through protein-protein interactions. Here, the authors demonstrate that protein arginine methyltransferase 3 (PRMT3) interacts with and inhibits the retinal dehydrogenase ALDH1A1, negatively regulating the expression of retinoic acid responsive genes. This study shows that PRMT3 affects diverse biological processes not only by globally regulating protein function through methylation but also by regulating gene expression.
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Affiliation(s)
- Mamta Verma
- Department of Biotechnology, Pondicherry University, Puducherry, 605014, India
| | - Mohd Imran K Khan
- Department of Biotechnology, Pondicherry University, Puducherry, 605014, India
| | - Rajashekar Varma Kadumuri
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, Andhra Pradesh, 517507, India
| | - Baskar Chakrapani
- Department of Biotechnology, Pondicherry University, Puducherry, 605014, India
| | - Sharad Awasthi
- Department of Biotechnology, Pondicherry University, Puducherry, 605014, India
| | - Arun Mahesh
- Department of Biotechnology, Pondicherry University, Puducherry, 605014, India
| | - Gayathri Govindaraju
- Interdisciplinary Biology, Rajiv Gandhi Centre for Biotechnology, Trivandrum, Kerala, 695014, India
| | - Pavithra L Chavali
- CSIR-Centre for Cellular & Molecular Biology, Hyderabad, Telangana, 500007, India
| | - Arumugam Rajavelu
- Interdisciplinary Biology, Rajiv Gandhi Centre for Biotechnology, Trivandrum, Kerala, 695014, India
| | - Sreenivas Chavali
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, Andhra Pradesh, 517507, India.
| | - Arunkumar Dhayalan
- Department of Biotechnology, Pondicherry University, Puducherry, 605014, India.
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13
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Large scale, robust, and accurate whole transcriptome profiling from clinical formalin-fixed paraffin-embedded samples. Sci Rep 2020; 10:17597. [PMID: 33077815 PMCID: PMC7572424 DOI: 10.1038/s41598-020-74483-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 09/30/2020] [Indexed: 01/25/2023] Open
Abstract
Transcriptome profiling can provide information of great value in clinical decision-making, yet RNA from readily available formalin-fixed paraffin-embedded (FFPE) tissue is often too degraded for quality sequencing. To assess the clinical utility of FFPE-derived RNA, we performed ribo-deplete RNA extractions on > 3200 FFPE slide samples; 25 of these had direct FFPE vs. fresh frozen (FF) replicates, 57 were sequenced in 2 different labs, 87 underwent multiple library analyses, and 16 had direct microdissected vs. macrodissected replicates. Poly-A versus ribo-depletion RNA extraction methods were compared using transcriptomes of TCGA cohort and 3116 FFPE samples. Compared to FF, FFPE transcripts coding for nuclear/cytoplasmic proteins involved in DNA packaging, replication, and protein synthesis were detected at lower rates and zinc finger family transcripts were of poorer quality. The greatest difference in extraction methods was in histone transcripts which typically lack poly-A tails. Encouragingly, the overall sequencing success rate was 81%. Exome coverage was highly concordant in direct FFPE and FF replicates, with 98% agreement in coding exon coverage and a median correlation of whole transcriptome profiles of 0.95. We provide strong rationale for clinical use of FFPE-derived RNA based on the robustness, reproducibility, and consistency of whole transcriptome profiling.
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14
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Wolf J, Auw-Haedrich C, Schlecht A, Boneva S, Mittelviefhaus H, Lapp T, Agostini H, Reinhard T, Schlunck G, Lange CAK. Transcriptional characterization of conjunctival melanoma identifies the cellular tumor microenvironment and prognostic gene signatures. Sci Rep 2020; 10:17022. [PMID: 33046735 PMCID: PMC7550331 DOI: 10.1038/s41598-020-72864-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 08/28/2020] [Indexed: 02/07/2023] Open
Abstract
This study characterizes the transcriptome and the cellular tumor microenvironment (TME) of conjunctival melanoma (CM) and identifies prognostically relevant biomarkers. 12 formalin-fixed and paraffin-embedded CM were analyzed by MACE RNA sequencing, including six cases each with good or poor clinical outcome, the latter being defined by local recurrence and/or systemic metastases. Eight healthy conjunctival specimens served as controls. The TME of CM, as determined by bioinformatic cell type enrichment analysis, was characterized by the enrichment of melanocytes, pericytes and especially various immune cell types, such as plasmacytoid dendritic cells, natural killer T cells, B cells and mast cells. Differentially expressed genes between CM and control were mainly involved in inhibition of apoptosis, proteolysis and response to growth factors. POU3F3, BIRC5 and 7 were among the top expressed genes associated with inhibition of apoptosis. 20 genes, among them CENPK, INHA, USP33, CASP3, SNORA73B, AAR2, SNRNP48 and GPN1, were identified as prognostically relevant factors reaching high classification accuracy (area under the curve: 1.0). The present study provides new insights into the TME and the transcriptional profile of CM and additionally identifies new prognostic biomarkers. These results add new diagnostic tools and may lead to new options of targeted therapy for CM.
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Affiliation(s)
- Julian Wolf
- Eye Center, Medical Center, Faculty of Medicine, University of Freiburg, Killianstrasse 5, 79106, Freiburg, Germany
| | - Claudia Auw-Haedrich
- Eye Center, Medical Center, Faculty of Medicine, University of Freiburg, Killianstrasse 5, 79106, Freiburg, Germany
| | - Anja Schlecht
- Eye Center, Medical Center, Faculty of Medicine, University of Freiburg, Killianstrasse 5, 79106, Freiburg, Germany
| | - Stefaniya Boneva
- Eye Center, Medical Center, Faculty of Medicine, University of Freiburg, Killianstrasse 5, 79106, Freiburg, Germany
| | - Hans Mittelviefhaus
- Eye Center, Medical Center, Faculty of Medicine, University of Freiburg, Killianstrasse 5, 79106, Freiburg, Germany
| | - Thabo Lapp
- Eye Center, Medical Center, Faculty of Medicine, University of Freiburg, Killianstrasse 5, 79106, Freiburg, Germany
| | - Hansjürgen Agostini
- Eye Center, Medical Center, Faculty of Medicine, University of Freiburg, Killianstrasse 5, 79106, Freiburg, Germany
| | - Thomas Reinhard
- Eye Center, Medical Center, Faculty of Medicine, University of Freiburg, Killianstrasse 5, 79106, Freiburg, Germany
| | - Günther Schlunck
- Eye Center, Medical Center, Faculty of Medicine, University of Freiburg, Killianstrasse 5, 79106, Freiburg, Germany
| | - Clemens A K Lange
- Eye Center, Medical Center, Faculty of Medicine, University of Freiburg, Killianstrasse 5, 79106, Freiburg, Germany.
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15
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Target Enrichment Enables the Discovery of lncRNAs with Somatic Mutations or Altered Expression in Paraffin-Embedded Colorectal Cancer Samples. Cancers (Basel) 2020; 12:cancers12102844. [PMID: 33019720 PMCID: PMC7650602 DOI: 10.3390/cancers12102844] [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: 08/24/2020] [Revised: 09/20/2020] [Accepted: 09/23/2020] [Indexed: 12/25/2022] Open
Abstract
Simple Summary Alterations in long noncoding RNAs and their mutations have been increasingly recognized in tumorogenesis and cancer progression awakening especial interest as potential novel cancer biomarkers and therapeutic targets. The use of adjuvant chemotherapy in stage II colorectal cancer patients is challenging, and new biomarkers are required to identify patients with high probability of relapse. We focused on translational potential of non-coding RNAs in colorectal cancer. In this study, we aim to validate a new tool which couples target enrichment and RNAseq for transcriptomics studies of lncRNAs in formalin-fixed paraffin embedded (FFPE) tissue samples. Our results show that this new approach efficiently detects lncRNAs and differences in their expression between healthy and tumor FFPE tissues, as well as somatic mutations in expressed lncRNAs, identifying novel lncRNAs as potential candidates for colorectal cancer. This new approach could represent a promising avenue that would reduce costs and enable more efficient translational research. Abstract Long non-coding RNAs (lncRNAs) play important roles in cancer and are potential new biomarkers or targets for therapy. However, given the low and tissue-specific expression of lncRNAs, linking these molecules to particular cancer types and processes through transcriptional profiling is challenging. Formalin-fixed, paraffin-embedded (FFPE) tissues are abundant resources for research but are prone to nucleic acid degradation, thereby complicating the study of lncRNAs. Here, we designed and validated a probe-based enrichment strategy to efficiently profile lncRNA expression in FFPE samples, and we applied it for the detection of lncRNAs associated with colorectal cancer (CRC). Our approach efficiently enriched targeted lncRNAs from FFPE samples, while preserving their relative abundance, and enabled the detection of tumor-specific mutations. We identified 379 lncRNAs differentially expressed between CRC tumors and matched healthy tissues and found tumor-specific lncRNA variants. Our results show that numerous lncRNAs are differentially expressed and/or accumulate variants in CRC tumors, thereby suggesting a role in CRC progression. More generally, our approach unlocks the study of lncRNAs in FFPE samples, thus enabling the retrospective use of abundant, well documented material available in hospital biobanks.
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16
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Transcriptomic Characterization of Human Choroidal Neovascular Membranes Identifies Calprotectin as a Novel Biomarker for Patients with Age-Related Macular Degeneration. THE AMERICAN JOURNAL OF PATHOLOGY 2020; 190:1632-1642. [PMID: 32339498 DOI: 10.1016/j.ajpath.2020.04.004] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 03/20/2020] [Accepted: 04/08/2020] [Indexed: 02/08/2023]
Abstract
Recent studies deciphering the transcriptional profile of choroidal neovascularization (CNV) in body donor eyes with neovascular age-related macular degeneration are limited by the time span from death to preservation and the associated 5'-RNA degradation. This study therefore used CNV and control specimens that were formalin-fixed and paraffin-embedded immediately after surgical extraction and analyzed them by a 3'-RNA sequencing approach. Transcriptome profiles were analyzed to estimate content of immune and stromal cells and to define disease-associated gene signatures by using statistical and bioinformatics methods. This study identified 158 differentially expressed genes (DEGs) that were significantly increased in CNV compared with control tissue. Cell type enrichment analysis revealed a diverse cellular landscape with an enrichment of endothelial cells, macrophages, T cells, and natural killer T cells in the CNV. Gene ontology enrichment analysis found that DEGs contributed to blood vessel development, extracellular structure organization, response to wounding, and several immune-related terms. The S100 calcium-binding proteins A8 (S100A8) and A9 (S100A9) emerged among the top DEGs, as confirmed by immunohistochemistry on CNV tissue and protein analysis of vitreous samples. This study provides a high-resolution RNA-sequencing-based transcriptional signature of human CNV, characterizes its compositional pattern of immune and stromal cells, and reveals S100A8/A9 to be a novel biomarker and promising target for therapeutics and diagnostics directed at age-related macular degeneration.
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17
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Brusletto BS, Løberg EM, Hellerud BC, Goverud IL, Berg JP, Olstad OK, Gopinathan U, Brandtzaeg P, Øvstebø R. Extensive Changes in Transcriptomic "Fingerprints" and Immunological Cells in the Large Organs of Patients Dying of Acute Septic Shock and Multiple Organ Failure Caused by Neisseria meningitidis. Front Cell Infect Microbiol 2020; 10:42. [PMID: 32154187 PMCID: PMC7045056 DOI: 10.3389/fcimb.2020.00042] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 01/22/2020] [Indexed: 12/16/2022] Open
Abstract
Background: Patients developing meningococcal septic shock reveal levels of Neisseria meningitidis (106-108/mL) and endotoxin (101-103 EU/mL) in the circulation and organs, leading to acute cardiovascular, pulmonary and renal failure, coagulopathy and a high case fatality rate within 24 h. Objective: To investigate transcriptional profiles in heart, lungs, kidneys, liver, and spleen and immunostain key inflammatory cells and proteins in post mortem formalin-fixed, paraffin-embedded (FFPE) tissue samples from meningococcal septic shock patients. Patients and Methods: Total RNA was isolated from FFPE and fresh frozen (FF) tissue samples from five patients and two controls (acute non-infectious death). Differential expression of genes was detected using Affymetrix microarray analysis. Lung and heart tissue samples were immunostained for T-and B cells, macrophages, neutrophils and the inflammatory markers PAI-1 and MCP-1. Inflammatory mediators were quantified in lysates from FF tissues. Results: The transcriptional profiles showed a complex pattern of protein-coding and non-coding RNAs with significant regulation of pathways associated with organismal death, cell death and survival, leukocyte migration, cellular movement, proliferation of cells, cell-to-cell signaling, immune cell trafficking, and inflammatory responses in an organ-specific clustering manner. The canonical pathways including acute phase response-, EIF2-, TREM1-, IL-6-, HMBG1-, PPAR signaling, and LXR/RXR activation were associated with acute heart, pulmonary, and renal failure. Fewer genes were regulated in the liver and particularly in the spleen. The main upstream regulators were TNF, IL-1β, IL-6, RICTOR, miR-6739-3p, and CD3. Increased numbers of inflammatory cells (CD68+, MPO+, CD3+, and CD20+) were found in lungs and heart. PAI-1 inhibiting fibrinolysis and MCP-1 attracting leukocyte were found significantly present in the septic tissue samples compared to the controls. Conclusions: FFPE tissue samples can be suitable for gene expression studies as well as immunostaining of specific cells or molecules. The most pronounced gene expression patterns were found in the organs with highest levels of Neisseria meningitidis DNA. Thousands of protein-coding and non-coding RNA transcripts were altered in lungs, heart and kidneys. We identified specific biomarker panels both protein-coding and non-coding RNA transcripts, which differed from organ to organ. Involvement of many genes and pathways add up and the combined effect induce organ failure.
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Affiliation(s)
- Berit Sletbakk Brusletto
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Else Marit Løberg
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Department of Pathology, Oslo University Hospital, Oslo, Norway
| | | | - Ingeborg Løstegaard Goverud
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Department of Pathology, Oslo University Hospital, Oslo, Norway
| | - Jens Petter Berg
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | | | - Unni Gopinathan
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Petter Brandtzaeg
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Department of Pediatrics, Oslo University Hospital, Oslo, Norway
| | - Reidun Øvstebø
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway
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18
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Jia G, Wang X, Li Q, Lu W, Tang X, Wistuba I, Xie Y. RCRnorm: An integrated system of random-coefficient hierarchical regression models for normalizing NanoString nCounter data. Ann Appl Stat 2019; 13:1617-1647. [PMID: 33564347 PMCID: PMC7869841 DOI: 10.1214/19-aoas1249] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Formalin-fixed paraffin-embedded (FFPE) samples have great potential for biomarker discovery, retrospective studies, and diagnosis or prognosis of diseases. Their application, however, is hindered by the unsatisfactory performance of traditional gene expression profiling techniques on damaged RNAs. NanoString nCounter platform is well suited for profiling of FFPE samples and measures gene expression with high sensitivity, which may greatly facilitate realization of scientific and clinical values of FFPE samples. However, methodological development for normalization, a critical step when analyzing this type of data, is far behind. Existing methods designed for the platform use information from different types of internal controls separately and rely on an overly-simplified assumption that expression of housekeeping genes is constant across samples for global scaling. Thus, these methods are not optimized for the nCounter system, not mentioning that they were not developed for FFPE samples. We construct an integrated system of random-coefficient hierarchical regression models to capture main patterns and characteristics observed from NanoString data of FFPE samples, and develop a Bayesian approach to estimate parameters and normalize gene expression across samples. Our method, labeled RCRnorm, incorporates information from all aspects of the experimental design and simultaneously removes biases from various sources. It eliminates the unrealistic assumption on housekeeping genes and offers great interpretability. Furthermore, it is applicable to freshly frozen or like samples that can be generally viewed as a reduced case of FFPE samples. Simulation and applications showed the superior performance of RCRnorm.
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Affiliation(s)
- Gaoxiang Jia
- Department of Statistical Science, Southern Methodist University, 3225 Daniel Avenue, P O Box 750332, Dallas, Texas 75275
- Quantitative Biomedical Research Center, Department of Clinical Sciences, The University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Xinlei Wang
- Department of Statistical Science, Southern Methodist University, 3225 Daniel Avenue, P O Box 750332, Dallas, Texas 75275
| | - Qiwei Li
- Quantitative Biomedical Research Center, Department of Clinical Sciences, The University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Wei Lu
- Department of Translational Molecular Pathology, University of Texas, MD Anderson Cancer Center, Houston, Texas 77030
| | - Ximing Tang
- Department of Translational Molecular Pathology, University of Texas, MD Anderson Cancer Center, Houston, Texas 77030
| | - Ignacio Wistuba
- Department of Translational Molecular Pathology, University of Texas, MD Anderson Cancer Center, Houston, Texas 77030
| | - Yang Xie
- Quantitative Biomedical Research Center, Department of Clinical Sciences, The University of Texas Southwestern Medical Center, Dallas, Texas 75390
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Prognostic Role of miR-221 and miR-222 Expression in Cancer Patients: A Systematic Review and Meta-Analysis. Cancers (Basel) 2019; 11:cancers11070970. [PMID: 31336701 PMCID: PMC6678869 DOI: 10.3390/cancers11070970] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 07/08/2019] [Indexed: 12/13/2022] Open
Abstract
Background: A wealth of evidence has shown that microRNAs (miRNAs) can modulate specific genes, increasing our knowledge on the fine-tuning regulation of protein expression. miR-221 and miR-222 have been frequently identified as deregulated across different cancer types; however, their prognostic significance in cancer remains controversial. In view of these considerations, we performed an updated systematic review and meta-analysis of published data investigating the effects of miR-221/222 on overall survival (OS) and other secondary outcomes among cancer patients. A systematic search of PubMed, Web of Knowledge, and Cochrane Library databases was performed. Hazard ratios (HRs) and 95% confidence intervals (95% CIs) were used to assess the strength of association. Results: Fifty studies, analyzing 6086 patients, were included in the systematic review. Twenty-five studies for miR-221 and 17 studies for miR-222 which assessed OS were included in the meta-analysis. High expression of miR-221 and miR-222 significantly predicted poor OS (HR: 1.48, 95% CI: 1.14–1.93, p = 0.003 and HR: 1.90, 95% CI: 1.43–2.54, p < 0.001, respectively). Subgroup analysis revealed that the finding on miR-221 was not as robust as the one on miR-222. Furthermore, high miR-222 expression was also associated with worse progression-free survival and disease-free survival pooled with recurrence-free survival. Conclusions: The meta-analysis demonstrated that high expression of miR-222 is associated with poor prognosis in cancer patients, whereas the significance of miR-221 remains unclear. More work is required to fully elucidate the role of miR-221 and miR-222 in cancer prognosis, particularly in view of the limitations of existing results, including the significant heterogeneity and limited number of studies for some cancers.
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Zhao P, Wu J, Lu F, Peng X, Liu C, Zhou N, Ying M. The imbalance in the complement system and its possible physiological mechanisms in patients with lung cancer. BMC Cancer 2019; 19:201. [PMID: 30841875 PMCID: PMC6404310 DOI: 10.1186/s12885-019-5422-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Accepted: 02/28/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The clinical and experimental evidences for complement-cancer relationships are solid, whereas an epidemiological study reporting the imbalance of complement system in patients is still lacking. METHODS Using publicly available databases, we jointly compared the levels of complement components in plasma and lung cancer tissues. With iTRAQ proteomics, quantitative RT-PCR and western blotting, we analysed the differences in complement levels in lung cancer tissues and normal control tissues. Complement components are mainly synthesized by the liver and secreted into the blood. Using paired co-cultures of human normal QSG-7701 hepatocytes with lung cancer cells (A549, LTEP-α-2 or NCI-H1703) or human normal bronchial epithelial (HBE) cells, we examined the effects of lung cancer cells on complement synthesis and secretion in QSG-7701 hepatocytes. RESULTS An integrated analysis of transcriptome and proteome datasets from 43 previous studies revealed lower mRNA and protein levels of 25 complement and complement-related components in lung cancer tissues than those in normal control tissues; conversely, higher levels of complement proteins were detected in plasma from patients than those in healthy subjects. Our iTRAQ proteome study identified decreased and increased levels of 31 and 2 complement and complement-related proteins, respectively, in lung cancer tissues, of which the reduced levels of 10 components were further confirmed using quantitative RT-PCR and western blotting. Paired co-cultures of QSG-7701 hepatocytes with A549, LTEP-α-2, NCI-H1703 or HBE cells indicated that lung cancer cells increased complement synthesis and secretion in QSG-7701 cells compared to HBE cells. CONCLUSIONS The opposite associations between the levels of complement and complement-related components in lung cancer tissues and plasma from patients that have been repeatedly reported by independent publications may indicate the prevalence of an imbalance in the complement system of lung cancer patients. The possible mechanism of the imbalance may be associated not only with the decreased complement levels in lung cancer tissues but also the concurrent lung cancer tissue-induced increase in hepatocyte complement synthesis and plasma secretion in patients. And the imbalance should be accompanied by a suppression of complement-dependent immunity in lung cancer tissues coupled with a burden of complement immunity in the circulation of patients.
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Affiliation(s)
- Ping Zhao
- Department of Molecular Biology and Biochemistry, Basic Medical College of Nanchang University, Nanchang, People’s Republic of China
| | - Jun Wu
- Department of Molecular Biology and Biochemistry, Basic Medical College of Nanchang University, Nanchang, People’s Republic of China
| | - Feiteng Lu
- Department of Molecular Biology and Biochemistry, Basic Medical College of Nanchang University, Nanchang, People’s Republic of China
| | - Xuan Peng
- Department of Molecular Biology and Biochemistry, Basic Medical College of Nanchang University, Nanchang, People’s Republic of China
| | - Chenlin Liu
- Department of Molecular Biology and Biochemistry, Basic Medical College of Nanchang University, Nanchang, People’s Republic of China
| | - Nanjin Zhou
- Institute of Molecular Medicine, Jiangxi Academy of Medical Sciences, Bayi Road 603, Nanchang, 330006 People’s Republic of China
| | - Muying Ying
- Department of Molecular Biology and Biochemistry, Basic Medical College of Nanchang University, Nanchang, People’s Republic of China
- Institute of Molecular Medicine, Jiangxi Academy of Medical Sciences, Bayi Road 603, Nanchang, 330006 People’s Republic of China
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21
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Factors affecting RNA quantification from tissue long-term stored in formalin. J Pharmacol Toxicol Methods 2019; 96:61-66. [DOI: 10.1016/j.vascn.2019.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 01/29/2019] [Accepted: 02/03/2019] [Indexed: 11/18/2022]
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22
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Xu L, Zhang Y, Tang J, Wang P, Li L, Yan X, Zheng X, Ren S, Zhang M, Xu M. The Prognostic Value and Regulatory Mechanisms of microRNA-145 in Various Tumors: A Systematic Review and Meta-analysis of 50 Studies. Cancer Epidemiol Biomarkers Prev 2019; 28:867-881. [PMID: 30602498 DOI: 10.1158/1055-9965.epi-18-0570] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 08/16/2018] [Accepted: 12/26/2018] [Indexed: 02/05/2023] Open
Abstract
Acting as an important tumor-related miRNA, the clinical significance and underlying mechanisms of miR-145 in various malignant tumors have been investigated by numerous studies. This study aimed to comprehensively estimate the prognostic value and systematically illustrate the regulatory mechanisms of miR-145 based on all eligible literature.Relevant studies were acquired from multiple online databases. Overall survival (OS) and progression-free survival (PFS) were used as primary endpoints. Detailed subgroup analyses were performed to decrease the heterogeneity among studies and recognize the prognostic value of miR-145. All statistical analyses were performed with RevMan software version 5.3 and STATA software version 14.1. A total of 48 articles containing 50 studies were included in the meta-analysis. For OS, the pooled results showed that low miR-145 expression in tumor tissues was significantly associated with worse OS in patients with various tumors [HR = 1.70; 95% confidence interval (CI), 1.46-1.99; P < 0.001). Subgroup analysis based on tumor type showed that the downregulation of miR-145 was associated with unfavorable OS in colorectal cancer (HR = 2.17; 95% CI, 1.52-3.08; P < 0.001), ovarian cancer (HR = 2.15; 95% CI, 1.29-3.59; P = 0.003), gastric cancer (HR = 1.78; 95% CI, 1.35-2.36; P < 0.001), glioma (HR = 1.65; 95% CI, 1.30-2.10; P < 0.001), and osteosarcoma (HR = 2.28; 95% CI, 1.50-3.47; P < 0.001). For PFS, the pooled results also showed that the downregulation of miR-145 was significantly associated with poor PFS in patients with multiple tumors (HR = 1.39; 95% CI, 1.16-1.67; P < 0.001), and the subgroup analyses further identified that the low miR-145 expression was associated with worse PFS in patients with lung cancer (HR = 1.97; 95% CI, 1.25-3.09; P = 0.003) and those of Asian descent (HR = 1.50; 95% CI, 1.23-1.82; P < 0.001). For the regulatory mechanisms, we observed that numerous tumor-related transcripts could be targeted by miR-145-5p or miR-145-3p, as well as the expression and function of miR-145-5p could be regulated by multiple molecules.This meta-analysis indicated that downregulated miR-145 in tumor tissues or peripheral blood predicted unfavorable prognostic outcomes for patients suffering from various malignant tumors. In addition, miR-145 was involved in multiple tumor-related pathways and the functioning of significant biological effects. miR-145 is a well-demonstrated tumor suppressor, and its expression level is significantly correlated with the prognosis of patients with multiple malignant tumors.
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Affiliation(s)
- Liangliang Xu
- Department of Liver Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Yanfang Zhang
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Jianwei Tang
- Department of Liver Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Peng Wang
- Department of Liver Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Lian Li
- Department of Liver Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Xiaokai Yan
- Department of Liver Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Xiaobo Zheng
- Department of Liver Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Shengsheng Ren
- Department of Liver Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Ming Zhang
- Department of Liver Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Mingqing Xu
- Department of Liver Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China.
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Sim J, Kim Y, Kim H, Shin SJ, Kim DH, Paik SS, Jang K. Identification of recurrence-associated microRNAs in stage I lung adenocarcinoma. Medicine (Baltimore) 2018; 97:e10996. [PMID: 29923982 PMCID: PMC6024484 DOI: 10.1097/md.0000000000010996] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Lung cancer is the most common cause of cancer-associated death worldwide. Postoperative relapse and subsequent metastasis result in a high mortality rate, even in early stage lung cancer. MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression at the post-transcriptional level and are frequently dysregulated in various cancers. The aim of this study was to identify recurrence-associated miRNAs in early stage lung cancer. To screen for differentially expressed miRNAs related to postoperative recurrence, miRNA microarray data derived from stage I lung adenocarcinoma formalin-fixed paraffin-embedded (FFPE) tissue samples (n = 6) and publically available the Cancer Genome Atlas (TCGA) data were analyzed. An independent sample (n = 29) was used to validate candidate miRNAs by quantitative real-time polymerase chain reaction (qRT-PCR). In miRNA expression profiling, we identified 60 significantly dysregulated miRNAs in the relapsed group. Additionally, 20 dysregulated miRNAs were found using TCGA data set. Three miRNAs (let-7g-5p, miR-143-3p, and miR-374a-5p) were associated with postoperative recurrence in both microarray and TCGA data sets. All 3 candidate miRNAs were validated in the independent cohort of stage I adenocarcinoma by qRT-PCR. We discovered 3 recurrence-associated miRNAs of stage I lung adenocarcinoma samples using FFPE tissue, which showed possible clinical utility as biomarkers predicting recurrence after curative surgery. Further investigation of the functional properties of these miRNAs is needed.
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Affiliation(s)
- Jongmin Sim
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine
| | - Yeseul Kim
- Department of Pathology, Hanyang University College of Medicine
| | - Hyunsung Kim
- Department of Pathology, Hanyang University College of Medicine
| | - Su-Jin Shin
- Department of Pathology, Hanyang University College of Medicine
| | - Dong-Hoon Kim
- Department of Pathology, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Seung Sam Paik
- Department of Pathology, Hanyang University College of Medicine
| | - Kiseok Jang
- Department of Pathology, Hanyang University College of Medicine
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24
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Haynes HR, Killick-Cole CL, Hares KM, Redondo J, Kemp KC, Moutasim KA, Faulkner C, Wilkins A, Kurian KM. Evaluation of the quality of RNA extracted from archival FFPE glioblastoma and epilepsy surgical samples for gene expression assays. J Clin Pathol 2018; 71:695-701. [DOI: 10.1136/jclinpath-2017-204969] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Revised: 01/29/2018] [Accepted: 01/30/2018] [Indexed: 01/05/2023]
Abstract
AimsHistopathological tissue samples are being increasingly used as sources of nucleic acids in molecular pathology translational research. This study investigated the suitability of glioblastoma and control central nervous system (CNS) formalin-fixed paraffin embedded (FFPE) tissue-derived RNA for gene expression analyses.MethodsTotal RNA was extracted from control (temporal lobe resection tissue) and glioblastoma FFPE tissue samples. RNA purity (260/280 ratios) was determined and RNA integrity number (RIN) analysis was performed. RNA was subsequently used for RT-qPCR for two reference genes,18SandGAPDH.ResultsReference gene expression was equivalent between control and glioblastoma tissue when using RNA extracted from FFPE tissue, which has key implications for biological normalisation for CNS gene expression studies. There was a significant difference between the mean RIN values of control and glioblastoma FFPE tissue. There was no significant correlation between 260/280 or RIN values versus total RNA yield. The age of the tissue blocks did not influence RNA yield, fragmentation or purity. There was no significant correlation between RIN or 260/280 ratios and mean qPCR cycle threshold for either reference gene.ConclusionsThis study showed that routinely available CNS FFPE tissue is suitable for RNA extraction and downstream gene expression studies, even after 60 months of storage. Substantial RNA fragmentation associated with glioblastoma and control FFPE tissue blocks did not preclude downstream RT-qPCR gene expression analyses. Cross validation with both archival and prospectively collated FFPE specimens is required to further demonstrate that CNS tissue blocks can be used in novel translational molecular biomarker studies.
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Abdel-Samad R, Aouad P, Gali-Muhtasib H, Sweidan Z, Hmadi R, Kadara H, D’Andrea EL, Fucci A, Pisano C, Darwiche N. Mechanism of action of the atypical retinoid ST1926 in colorectal cancer: DNA damage and DNA polymerase α. Am J Cancer Res 2018; 8:39-55. [PMID: 29416919 PMCID: PMC5794720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 11/21/2017] [Indexed: 06/08/2023] Open
Abstract
Despite advances in therapeutic strategies, colorectal cancer (CRC) remains the third cause of cancer-related deaths with a relatively low survival rate. Resistance to standard chemotherapy represents a major hurdle in disease management; therefore, developing new therapeutic agents demands a thorough understanding of their mechanisms of action. One of these compounds is ST1926, an adamantyl retinoid that has shown potent antitumor activities in several human cancer models. Here, we show that ST1926 selectively suppressed the proliferation of CRC cells while sparing normal counterparts, and significantly reduced tumor volume in a xenograft cancer mouse model. Next, we investigated the effects of ST1926 in CRC cells and observed early DNA damage, S-phase arrest, dissipation of mitochondrial membrane potential, and apoptosis induction, in a p53 and p21-independent manner. To address the underlying mechanism of resistance to ST1926, we generated ST1926-resistant HCT116 cells and sequenced DNA polymerase α (POLA1), which was reported to be a direct target to the drug's parent molecule, CD437. We identified similar mutations in POLA1 that conferred resistance to ST1926 and CD437. These mutations were absent in 5-fluorouracil-resistant HCT116 cells, clearly validating the specificity of these mutations to the lack of DNA damage and acquired resistance to ST1926. ST1926 also inhibited POLA1 activity and reduced its protein expression levels. Further, in silico analysis of normal and malignant tissue expression data demonstrated that POLA1 levels are elevated in CRC cells and tissues compared to normal counterparts as well as to other cancer types. Our findings highlight previously uncharacterized mechanisms of action of ST1926 in CRC and suggest that elevated POLA1 expression is a pertinent molecular feature and an attractive target in CRC.
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Affiliation(s)
- Rana Abdel-Samad
- Department of Biochemistry and Molecular Genetics, American University of BeirutBeirut, Lebanon
- Faculty of Health Sciences, University of BalamandBeirut, Lebanon
| | - Patrick Aouad
- Department of Biochemistry and Molecular Genetics, American University of BeirutBeirut, Lebanon
| | - Hala Gali-Muhtasib
- Department of Biology and Anatomy, Cell Biology and Physiological Sciences, American University of BeirutBeirut, Lebanon
| | - Zeinab Sweidan
- Department of Biochemistry and Molecular Genetics, American University of BeirutBeirut, Lebanon
| | - Raed Hmadi
- Department of Biochemistry and Molecular Genetics, American University of BeirutBeirut, Lebanon
| | - Humam Kadara
- Department of Biochemistry and Molecular Genetics, American University of BeirutBeirut, Lebanon
| | | | - Alessandra Fucci
- BIOGEM, Medicinal Investigational ResearchAriano Irpino (AV), Italy
| | - Claudio Pisano
- BIOGEM, Medicinal Investigational ResearchAriano Irpino (AV), Italy
| | - Nadine Darwiche
- Department of Biochemistry and Molecular Genetics, American University of BeirutBeirut, Lebanon
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26
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Tsai HK, Lehrer J, Alshalalfa M, Erho N, Davicioni E, Lotan TL. Gene expression signatures of neuroendocrine prostate cancer and primary small cell prostatic carcinoma. BMC Cancer 2017; 17:759. [PMID: 29132337 PMCID: PMC5683385 DOI: 10.1186/s12885-017-3729-z] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 10/30/2017] [Indexed: 12/28/2022] Open
Abstract
Background Neuroendocrine prostate cancer (NEPC) may be rising in prevalence as patients with advanced prostate cancer potentially develop resistance to contemporary anti-androgen treatment through a neuroendocrine phenotype. While prior studies comparing NEPC and prostatic adenocarcinoma have identified important candidates for targeted therapy, most have relied on few NEPC patients due to disease rarity, resulting in thousands of differentially expressed genes collectively and offering an opportunity for meta-analysis. Moreover, past studies have focused on prototypical NEPC samples with classic immunohistochemistry profiles, whereas there is increasing recognition of atypical phenotypes. In the primary setting, small cell prostatic carcinoma (SCPC) is frequently admixed with adenocarcinomas that may be clonally related, and a minority of SCPCs express markers typical of prostatic adenocarcinoma while rare cases do not express neuroendocrine markers. We derived a meta-signature of prototypical high-grade NEPC, then applied it to develop a classifier of primary SCPC incorporating disease heterogeneity. Methods Prototypical NEPC samples from 15 patients across 6 frozen tissue microarray datasets were assessed for genes with consistent outlier expression relative to adenocarcinomas. Resulting genes were used to determine subgroups of primary SCPCs (N=16) and high-grade adenocarcinomas (N=16) profiled by exon arrays using formalin-fixed paraffin-embedded (FFPE) material from our institutional archives. A subgroup classifier was developed using differential expression for feature selection, and applied to radical prostatectomy cohorts. Results Sixty nine and 375 genes demonstrated consistent outlier expression in at least 80% and 60% of NEPC patients, with close resemblance in expression between NEPC and small cell lung cancer. Clustering by these genes generated 3 subgroups among primary samples from our institution. Nearest centroid classification based on the predominant phenotype from each subgroup (9 prototypical SCPCs, 9 prototypical adenocarcinomas, and 4 atypical SCPCs) achieved a 4.5% error rate by leave-one-out cross-validation. The classifier identified SCPC-like expression in 40% (2/5) of mixed adenocarcinomas and 0.3-0.6% of adenocarcinomas from prospective (4/2293) and retrospective (2/355) radical prostatectomy cohorts, where both SCPC-like retrospective cases subsequently developed metastases. Conclusions Meta-analysis generates a robust signature of prototypical high-grade NEPC, and may facilitate development of a primary SCPC classifier based on FFPE material with potential prognostic implications. Electronic supplementary material The online version of this article (10.1186/s12885-017-3729-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Harrison K Tsai
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA. .,Present address: Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA.
| | | | | | - Nicholas Erho
- GenomeDx Biosciences, Vancouver, British Columbia, Canada
| | - Elai Davicioni
- GenomeDx Biosciences, Vancouver, British Columbia, Canada
| | - Tamara L Lotan
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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27
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Reid KM, Maistry S, Ramesar R, Heathfield LJ. A review of the optimisation of the use of formalin fixed paraffin embedded tissue for molecular analysis in a forensic post-mortem setting. Forensic Sci Int 2017; 280:181-187. [PMID: 29078160 DOI: 10.1016/j.forsciint.2017.09.020] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 07/15/2017] [Accepted: 09/26/2017] [Indexed: 11/26/2022]
Abstract
Molecular analyses in a post-mortem setting are becoming increasingly common, particularly in cases of sudden unexplained death, with the aim of identifying genetic mutations which may be responsible for causing death. In retrospective investigations, the access to suitable autopsy biological samples may be limited, and often formalin fixed paraffin embedded (FFPE) tissue is the only sample available. The preservation of tissue in formalin is known to damage DNA through crosslinking activity. This results in the extraction of severely fragmented DNA of variable yields, which subsequently reduces the ability to perform downstream molecular analyses. Numerous studies have investigated possible improvements to various aspects of the DNA extraction and amplification procedures from FFPE tissue and this review aims to collate these optimization steps in a cohesive manner. A systematic review was performed of three major databases, which identified 111 articles meeting the inclusion criteria. Five main areas for optimization and improvements were identified in the workflow: (1) tissue type, (2) fixation process, (3) post-fixation, (4) DNA extraction procedure and (5) amplification. It was found that some factors identified, for example tissue type and fixation process, could not be controlled by the researcher when conducting retrospective analyses. For this reason, optimization should be performed in other areas, within the financial means of the laboratories, and in accordance with the purposes of the investigation. Implementation of one or more of the optimization measures described here is anticipated to assist in the extraction of higher quality DNA. Despite the challenges posed by FFPE tissue, it remains a valuable source of DNA in retrospective molecular forensic investigations.
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Affiliation(s)
- Kate Megan Reid
- Division of Forensic Medicine and Toxicology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory, 7925, South Africa; MRC/UCT Human Genetics Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Diseases and Molecular Medicine, Faculty of Health Science, University of Cape Town, Anzio Road, Observatory, Cape Town, South Africa
| | - Sairita Maistry
- Division of Forensic Medicine and Toxicology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory, 7925, South Africa
| | - Raj Ramesar
- MRC/UCT Human Genetics Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Diseases and Molecular Medicine, Faculty of Health Science, University of Cape Town, Anzio Road, Observatory, Cape Town, South Africa
| | - Laura Jane Heathfield
- Division of Forensic Medicine and Toxicology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Anzio Road, Observatory, 7925, South Africa; MRC/UCT Human Genetics Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Diseases and Molecular Medicine, Faculty of Health Science, University of Cape Town, Anzio Road, Observatory, Cape Town, South Africa.
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28
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Wang J, Heng YJ, Eliassen AH, Tamimi RM, Hazra A, Carey VJ, Ambrosone CB, de Andrade VP, Brufsky A, Couch FJ, King TA, Modugno F, Vachon CM, Hunter DJ, Beck AH, Hankinson SE. Alcohol consumption and breast tumor gene expression. Breast Cancer Res 2017; 19:108. [PMID: 28899409 PMCID: PMC5596493 DOI: 10.1186/s13058-017-0901-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 08/31/2017] [Indexed: 02/07/2023] Open
Abstract
Background Alcohol consumption is an established risk factor for breast cancer and the association generally appears stronger among estrogen receptor (ER)-positive tumors. However, the biological mechanisms underlying this association are not completely understood. Methods We analyzed messenger RNA (mRNA) microarray data from both invasive breast tumors (N = 602) and tumor-adjacent normal tissues (N = 508) from participants diagnosed with breast cancer in the Nurses’ Health Study (NHS) and NHSII. Multivariable linear regression, controlling for other known breast cancer risk factors, was used to identify differentially expressed genes by pre-diagnostic alcohol intake. For pathway analysis, we performed gene set enrichment analysis (GSEA). Differentially expressed genes or enriched pathway-defined gene sets with false discovery rate (FDR) <0.1 identified in tumors were validated in RNA sequencing data of invasive breast tumors (N = 166) from The Cancer Genome Atlas. Results No individual genes were significantly differentially expressed by alcohol consumption in the NHS/NHSII. However, GSEA identified 33 and 68 pathway-defined gene sets at FDR <0.1 among 471 ER+ and 127 ER- tumors, respectively, all of which were validated. Among ER+ tumors, consuming 10+ grams of alcohol per day (vs. 0) was associated with upregulation in RNA metabolism and transport, cell cycle regulation, and DNA repair, and downregulation in lipid metabolism. Among ER- tumors, in addition to upregulation in RNA processing and cell cycle, alcohol intake was linked to overexpression of genes involved in cytokine signaling, including interferon and transforming growth factor (TGF)-β signaling pathways, and translation and post-translational modifications. Lower lipid metabolism was observed in both ER+ tumors and ER+ tumor-adjacent normal samples. Most of the significantly enriched gene sets identified in ER- tumors showed a similar enrichment pattern among ER- tumor-adjacent normal tissues. Conclusions Our data suggest that moderate alcohol consumption (i.e. 10+ grams/day, equivalent to one or more drinks/day) is associated with several specific and reproducible biological processes and pathways, which adds potential new insight into alcohol-related breast carcinogenesis. Electronic supplementary material The online version of this article (doi:10.1186/s13058-017-0901-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jun Wang
- Department of Biostatistics and Epidemiology, School of Public Health and Health Sciences, University of Massachusetts Amherst, 715 N Pleasant Street, Amherst, MA, 01003, USA. .,Present address: Department of Preventive Medicine, University of Southern California, Harlyne J. Norris Research Tower, 1450 Biggy Street, Los Angeles, CA, 90033, USA.
| | - Yujing J Heng
- Department of Pathology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, 02215, USA
| | - A Heather Eliassen
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, 181 Longwood Avenue, Boston, MA, 02115, USA.,Department of Epidemiology, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA, 02115, USA
| | - Rulla M Tamimi
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, 181 Longwood Avenue, Boston, MA, 02115, USA.,Department of Epidemiology, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA, 02115, USA
| | - Aditi Hazra
- Division of Preventive Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, 900 Commonwealth Ave, Boston, MA, 02115, USA
| | - Vincent J Carey
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, 181 Longwood Avenue, Boston, MA, 02115, USA
| | - Christine B Ambrosone
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Elm & Carlton Streets, Buffalo, NY, 14263, USA
| | - Victor P de Andrade
- Departamento de Patologia, A.C. Camargo Cancer Center, São Paulo, SP, 01509-900, Brazil
| | - Adam Brufsky
- Department of Medicine, University of Pittsburgh Medical Center, 300 Halket Street, Pittsburgh, PA, 15213, USA
| | - Fergus J Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Tari A King
- Dana-Farber Cancer Institute and Brigham and Women's Cancer Center, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Francesmary Modugno
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, 300 Halket Street, Pittsburgh, PA, 15213, USA
| | - Celine M Vachon
- Department of Health Sciences Research, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - David J Hunter
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, 181 Longwood Avenue, Boston, MA, 02115, USA.,Department of Epidemiology, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA, 02115, USA.,Department of Nutrition, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA, 02115, USA
| | - Andrew H Beck
- Department of Pathology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, 02215, USA
| | - Susan E Hankinson
- Department of Biostatistics and Epidemiology, School of Public Health and Health Sciences, University of Massachusetts Amherst, 715 N Pleasant Street, Amherst, MA, 01003, USA.,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, 181 Longwood Avenue, Boston, MA, 02115, USA.,Department of Epidemiology, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA, 02115, USA
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29
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Stewart JP, Richman S, Maughan T, Lawler M, Dunne PD, Salto-Tellez M. Standardising RNA profiling based biomarker application in cancer-The need for robust control of technical variables. Biochim Biophys Acta Rev Cancer 2017; 1868:258-272. [PMID: 28549623 DOI: 10.1016/j.bbcan.2017.05.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 05/21/2017] [Accepted: 05/22/2017] [Indexed: 01/10/2023]
Abstract
Histopathology-based staging of colorectal cancer (CRC) has utility in assessing the prognosis of patient subtypes, but as yet cannot accurately predict individual patient's treatment response. Transcriptomics approaches, using array based or next generation sequencing (NGS) platforms, of formalin fixed paraffin embedded tissue can be harnessed to develop multi-gene biomarkers for predicting both prognosis and treatment response, leading to stratification of treatment. While transcriptomics can shape future biomarker development, currently <1% of published biomarkers become clinically validated tests, often due to poor study design or lack of independent validation. In this review of a large number of CRC transcriptional studies, we identify recurrent sources of technical variability that encompass collection, preservation and storage of malignant tissue, nucleic acid extraction, methods to quantitate RNA transcripts and data analysis pipelines. We propose a series of defined steps for removal of these confounding issues, to ultimately aid in the development of more robust clinical biomarkers.
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Affiliation(s)
- James P Stewart
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, UK; Northern Ireland Molecular Pathology Laboratory, Queen's University Belfast, UK
| | - Susan Richman
- Department of Pathology and Tumour Biology, St James University Hospital, Leeds, UK
| | - Tim Maughan
- CRUK/MRC Oxford Institute for Radiation Oncology, University of Oxford, UK
| | - Mark Lawler
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, UK
| | - Philip D Dunne
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, UK
| | - Manuel Salto-Tellez
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, UK; Northern Ireland Molecular Pathology Laboratory, Queen's University Belfast, UK.
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30
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Quiroz-Zárate A, Harshfield BJ, Hu R, Knoblauch N, Beck AH, Hankinson SE, Carey V, Tamimi RM, Hunter DJ, Quackenbush J, Hazra A. Expression Quantitative Trait loci (QTL) in tumor adjacent normal breast tissue and breast tumor tissue. PLoS One 2017; 12:e0170181. [PMID: 28152060 PMCID: PMC5289428 DOI: 10.1371/journal.pone.0170181] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 12/30/2016] [Indexed: 12/31/2022] Open
Abstract
We investigate 71 single nucleotide polymorphisms (SNPs) identified in meta-analytic studies of genome-wide association studies (GWAS) of breast cancer, the majority of which are located in intergenic or intronic regions. To explore regulatory impacts of these variants we conducted expression quantitative loci (eQTL) analyses on tissue samples from 376 invasive postmenopausal breast cancer cases in the Nurses' Health Study (NHS) diagnosed from 1990-2004. Expression analysis was conducted on all formalin-fixed paraffin-embedded (FFPE) tissue samples (and on 264 adjacent normal samples) using the Affymetrix Human Transcriptome Array. Significance and ranking of associations between tumor receptor status and expression variation was preserved between NHS FFPE and TCGA fresh-frozen sample sets (Spearman r = 0.85, p<10^-10 for 17 of the 21 Oncotype DX recurrence signature genes). At an FDR threshold of 10%, we identified 27 trans-eQTLs associated with expression variation in 217 distinct genes. SNP-gene associations can be explored using an open-source interactive browser distributed in a Bioconductor package. Using a new a procedure for testing hypotheses relating SNP content to expression patterns in gene sets, defined as molecular function pathways, we find that loci on 6q14 and 6q25 affect various gene sets and molecular pathways (FDR < 10%). Although the ultimate biological interpretation of the GWAS-identified variants remains to be uncovered, this study validates the utility of expression analysis of this FFPE expression set for more detailed integrative analyses.
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Affiliation(s)
| | - Benjamin J. Harshfield
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Rong Hu
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Nick Knoblauch
- Department of Pathology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Andrew H. Beck
- Department of Pathology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Susan E. Hankinson
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Biostatistics and Epidemiology, School of Public Health and Health Sciences, University of Massachusetts, Amherst, Massachusetts, United States of America
| | - Vincent Carey
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Rulla M. Tamimi
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - David J. Hunter
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - John Quackenbush
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Biostatistics and Computational Biology and Center for Cancer Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Aditi Hazra
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Division of Preventive Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
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The Utilization of Formalin Fixed-Paraffin-Embedded Specimens in High Throughput Genomic Studies. Int J Genomics 2017; 2017:1926304. [PMID: 28246590 PMCID: PMC5299160 DOI: 10.1155/2017/1926304] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 01/09/2017] [Indexed: 01/09/2023] Open
Abstract
High throughput genomic assays empower us to study the entire human genome in short time with reasonable cost. Formalin fixed-paraffin-embedded (FFPE) tissue processing remains the most economical approach for longitudinal tissue specimen storage. Therefore, the ability to apply high throughput genomic applications to FFPE specimens can expand clinical assays and discovery. Many studies have measured the accuracy and repeatability of data generated from FFPE specimens using high throughput genomic assays. Together, these studies demonstrate feasibility and provide crucial guidance for future studies using FFPE specimens. Here, we summarize the findings of these studies and discuss the limitations of high throughput data generated from FFPE specimens across several platforms that include microarray, high throughput sequencing, and NanoString.
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Baehner FL. The analytical validation of the Oncotype DX Recurrence Score assay. Ecancermedicalscience 2016; 10:675. [PMID: 27729940 PMCID: PMC5045300 DOI: 10.3332/ecancer.2016.675] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Indexed: 12/15/2022] Open
Abstract
In vitro diagnostic multivariate index assays are highly complex molecular assays that can provide clinically actionable information regarding the underlying tumour biology and facilitate personalised treatment. These assays are only useful in clinical practice if all of the following are established: analytical validation (i.e., how accurately/reliably the assay measures the molecular characteristics), clinical validation (i.e., how consistently/accurately the test detects/predicts the outcomes of interest), and clinical utility (i.e., how likely the test is to significantly improve patient outcomes). In considering the use of these assays, clinicians often focus primarily on the clinical validity/utility; however, the analytical validity of an assay (e.g., its accuracy, reproducibility, and standardisation) should also be evaluated and carefully considered. This review focuses on the rigorous analytical validation and performance of the Oncotype DX® Breast Cancer Assay, which is performed at the Central Clinical Reference Laboratory of Genomic Health, Inc. The assay process includes tumour tissue enrichment (if needed), RNA extraction, gene expression quantitation (using a gene panel consisting of 16 cancer genes plus 5 reference genes and quantitative real-time RT-PCR), and an automated computer algorithm to produce a Recurrence Score® result (scale: 0–100). This review presents evidence showing that the Recurrence Score result reported for each patient falls within a tight clinically relevant confidence interval. Specifically, the review discusses how the development of the assay was designed to optimise assay performance, presents data supporting its analytical validity, and describes the quality control and assurance programmes that ensure optimal test performance over time.
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Affiliation(s)
- Frederick L Baehner
- Department of Pathology, University of California, San Francisco, CA, USA and Genomic Health, Inc., Redwood City, CA 94063, USA
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33
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Hu S, Parker J, Divaris K, Padilla R, Murrah V, Wright JT. Ameloblastoma Phenotypes Reflected in Distinct Transcriptome Profiles. Sci Rep 2016; 6:30867. [PMID: 27491308 PMCID: PMC4974613 DOI: 10.1038/srep30867] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 07/08/2016] [Indexed: 02/04/2023] Open
Abstract
Ameloblastoma is a locally invasive benign neoplasm derived from odontogenic epithelium and presents with diverse phenotypes yet to be characterized molecularly. High recurrence rates of 50–80% with conservative treatment in some sub-types warrants radical surgical resections resulting in high morbidity. The objective of the study was to characterize the transcriptome of ameloblastoma and identify relevant genes and molecular pathways using normal odontogenic tissue (human “dentome”) for comparison. Laser capture microdissection was used to obtain neoplastic epithelial tissue from 17 tumors which were examined using the Agilent 44 k whole genome microarray. Ameloblastoma separated into 2 distinct molecular clusters that were associated with pre-secretory ameloblast and odontoblast. Within the pre-secretory cluster, 9/10 of samples were of the follicular type while 6/7 of the samples in the odontoblast cluster were of the plexiform type (p < 0.05). Common pathways altered in both clusters included cell-cycle regulation, inflammatory and MAPkinase pathways, specifically known cancer-driving genes such as TP53 and members of the MAPkinase pathways. The pre-secretory ameloblast cluster exhibited higher activation of inflammatory pathways while the odontoblast cluster showed greater disturbances in transcription regulators. Our results are suggestive of underlying inter-tumor molecular heterogeneity of ameloblastoma sub-types and have implications for the use of tailored treatment.
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Affiliation(s)
- Shijia Hu
- Pediatric Dentistry, School of Dentistry, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA.,Faculty of Dentistry, National University of Singapore, Singapore
| | - Joel Parker
- Cancer Genetics, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA
| | - Kimon Divaris
- Pediatric Dentistry, School of Dentistry, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA.,Epidemiology, Gillings School of Global Public Health, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA
| | - Ricardo Padilla
- Diagnostic Sciences, School of Dentistry, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA
| | - Valerie Murrah
- Diagnostic Sciences, School of Dentistry, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA
| | - John Timothy Wright
- Pediatric Dentistry, School of Dentistry, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA
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34
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Characterization of gene expression profiling of mouse tissues obtained during the postmortem interval. Exp Mol Pathol 2016; 100:482-92. [PMID: 27185020 DOI: 10.1016/j.yexmp.2016.05.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 05/13/2016] [Indexed: 12/27/2022]
Abstract
Attempts to establish a tissue bank from autopsy samples have led to uncovering of the secrets of many diseases. Here, we examined the length of time that the RNA from postmortem tissues is available for microarray analysis and reported the gene expression profile for up- and down-regulated genes during the postmortem interval. We extracted RNA from fresh-frozen (FF) and formalin-fixed paraffin-embedded (FFPE) brains and livers of three different groups of mice: 1) mice immediately after death, 2) mice that were stored at room temperature for 3h after death, and 3) mice that were stored at 4°C for 18h after death, as this storage resembles the human autopsy process in Japan. The RNA quality of the brain and the liver was maintained up to 18h during the postmortem interval. Based on the microarray analysis, we selected genes that were altered by >1.3-fold or <0.77-fold and classified these genes using hierarchical cluster analysis following DAVID gene ontology analysis. These studies revealed that cytoskeleton-related genes were enriched in the set of up-regulated genes, while serine protease inhibitors were enriched in the set of down-regulated genes. Interestingly, although the RNA quality was maintained due to high RNA integrity number (RIN) values, up-regulated genes were not validated by quantitative PCR, suggesting that these genes may become fragmented or modified by an unknown mechanism. Taken together, our findings suggest that under typical autopsy conditions, gene expression profiles that reflect disease pathology can be examined by understanding comprehensive recognition of postmortem fluctuation of gene expression.
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Abstract
Although the emergence of proteomics as an independent branch of science is fairly recent, within a short period of time it has contributed substantially in various disciplines. The tool of mass spectrometry has become indispensable in the analysis of complex biological samples. Clinical applications of proteomics include detection of predictive and diagnostic markers, understanding mechanism of action of drugs as well as resistance mechanisms against them and assessment of therapeutic efficacy and toxicity of drugs in patients. Here, we have summarized the major contributions of proteomics towards the study of melanoma, which is a deadly variety of skin cancer with a high mortality rate.
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Affiliation(s)
- Deepanwita Sengupta
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, Arkansas 72205, USA
| | - Alan J Tackett
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, Arkansas 72205, USA; Department of Pathology, University of Arkansas for Medical Sciences, 4301 West Markham Street, Little Rock, Arkansas 72205, USA
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36
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Hu S, Divaris K, Parker J, Padilla R, Murrah V, Wright JT. Transcriptome Variability in Keratocystic Odontogenic Tumor Suggests Distinct Molecular Subtypes. Sci Rep 2016; 6:24236. [PMID: 27066764 PMCID: PMC4828651 DOI: 10.1038/srep24236] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 03/23/2016] [Indexed: 01/02/2023] Open
Abstract
Keratocystic Odontogenic Tumor (KCOT) is a locally aggressive developmental cystic neoplasm thought to arise from the odontogenic epithelium. A high recurrence rate of up to 30% has been found following conservative treatment. Aggressive tumor resection can lead to the need for extensive reconstructive surgery, resulting in significant morbidity and impacting quality of life. Most research has focused on candidate-genes with a handful of studies employing whole transcriptome approaches. There is also the question of which reference tissue is most biologically-relevant. This study characterizes the transcriptome of KCOT using whole genome microarray and compare it with gene expression of different odontogenic tissues (“dentome”). Laser capture microdissection was used to isolate the neoplastic epithelial tissue in 20 cases. KCOT gene expression was compared with the “dentome” and relevant pathways were examined. Cluster analysis revealed 2 distinct molecular subtypes of KCOT. Several inflammatory pathways were activated in both subtypes. The AKT pathway was activated in one subtype while MAP kinase pathway was activated in the other. Additionally, PTCH1 expression was downregulated in both clusters suggesting involvement in KCOT tumorigenesis. In conclusion, this study provides new insights into the transcriptome of KCOT and highlights pathways that could be of diagnostic and prognostic value.
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Affiliation(s)
- Shijia Hu
- Pediatric Dentistry, University of North Carolina, Chapel Hill, NC, USA.,Faculty of Dentistry, National University of Singapore, Singapore
| | - Kimon Divaris
- Pediatric Dentistry, University of North Carolina, Chapel Hill, NC, USA.,Epidemiology, Gillings School of Global Public Health, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA
| | - Joel Parker
- Cancer Genetics, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA
| | - Ricardo Padilla
- Diagnostic Sciences, School of Dentistry, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA
| | - Valerie Murrah
- Diagnostic Sciences, School of Dentistry, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA
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37
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Knudsen BS, Kim HL, Erho N, Shin H, Alshalalfa M, Lam LLC, Tenggara I, Chadwich K, Van Der Kwast T, Fleshner N, Davicioni E, Carroll PR, Cooperberg MR, Chan JM, Simko JP. Application of a Clinical Whole-Transcriptome Assay for Staging and Prognosis of Prostate Cancer Diagnosed in Needle Core Biopsy Specimens. J Mol Diagn 2016; 18:395-406. [PMID: 26945428 DOI: 10.1016/j.jmoldx.2015.12.006] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 12/11/2015] [Accepted: 12/18/2015] [Indexed: 10/22/2022] Open
Abstract
Molecular and genomic analysis of microscopic quantities of tumor from formalin-fixed, paraffin-embedded biopsy specimens has many unique challenges. Herein, we evaluated the feasibility of obtaining transcriptome-wide RNA expression to measure prognostic classifiers in diagnostic prostate needle core biopsy specimens. One-hundred fifty-eight samples from diagnostic needle core biopsy specimens (BX) and radical prostatectomies (RPs) were collected from 33 patients at three hospitals; each patient provided up to six tumor and benign samples. Genome-wide transcriptomic profiles were generated using Affymetrix Human Exon arrays for comparison of gene expression alterations and prognostic signatures between the BX and RP samples. A sufficient amount of RNA (>100 ng) was obtained from all RP specimens (n = 77) and from 72 of 81 of BX specimens. Of transcriptomic features detected in RP, 95% were detectable in BX tissues and demonstrated a high correlation (r = 0.96). Likewise, an expression signature pattern validated on RPs (Decipher prognostic test) showed correlation between BX and RP (r = 0.70). Of matched BX and RP pairs, 25% showed discordant molecular subtypes. Genome-wide exon arrays yielded data of comparable quality from biopsy and RP tissues. The high concordance of tumor-associated gene expression changes between BX and RP samples provides evidence for the adequate performance of the assay platform with samples from prostate needle biopsy specimens with limited tumor volume.
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Affiliation(s)
- Beatrice S Knudsen
- Departments of Biomedical Sciences and Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | - Hyung L Kim
- Division of Urology, Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, California
| | - Nicholas Erho
- Department of Research and Development, GenomeDx Biosciences, Inc., Vancouver, British Columbia, Canada
| | - Heesun Shin
- Department of Research and Development, GenomeDx Biosciences, Inc., Vancouver, British Columbia, Canada
| | - Mohammed Alshalalfa
- Department of Research and Development, GenomeDx Biosciences, Inc., Vancouver, British Columbia, Canada
| | - Lucia L C Lam
- Department of Research and Development, GenomeDx Biosciences, Inc., Vancouver, British Columbia, Canada
| | - Imelda Tenggara
- Department of Urology, University of California San Francisco, San Francisco, California
| | - Karen Chadwich
- Department of Urology, University Health Network, Toronto, Ontario, Canada
| | - Theo Van Der Kwast
- Department of Pathology, Princess Margaret Cancer Center, Toronto, Ontario, Canada
| | - Neil Fleshner
- Department of Urology, University Health Network, Toronto, Ontario, Canada
| | - Elai Davicioni
- Department of Research and Development, GenomeDx Biosciences, Inc., Vancouver, British Columbia, Canada.
| | - Peter R Carroll
- Department of Urology, University of California San Francisco, San Francisco, California
| | - Matthew R Cooperberg
- Department of Urology, University of California San Francisco, San Francisco, California; Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
| | - June M Chan
- Department of Urology, University of California San Francisco, San Francisco, California; Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California
| | - Jeffry P Simko
- Department of Urology, University of California San Francisco, San Francisco, California; Department of Anatomic Pathology, University of California San Francisco, San Francisco, California
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38
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Dal Pra A, Locke JA, Borst G, Supiot S, Bristow RG. Mechanistic Insights into Molecular Targeting and Combined Modality Therapy for Aggressive, Localized Prostate Cancer. Front Oncol 2016; 6:24. [PMID: 26909338 PMCID: PMC4754414 DOI: 10.3389/fonc.2016.00024] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2015] [Accepted: 01/22/2016] [Indexed: 12/12/2022] Open
Abstract
Radiation therapy (RT) is one of the mainstay treatments for prostate cancer (PCa). The potentially curative approaches can provide satisfactory results for many patients with non-metastatic PCa; however, a considerable number of individuals may present disease recurrence and die from the disease. Exploiting the rich molecular biology of PCa will provide insights into how the most resistant tumor cells can be eradicated to improve treatment outcomes. Important for this biology-driven individualized treatment is a robust selection procedure. The development of predictive biomarkers for RT efficacy is therefore of utmost importance for a clinically exploitable strategy to achieve tumor-specific radiosensitization. This review highlights the current status and possible opportunities in the modulation of four key processes to enhance radiation response in PCa by targeting the: (1) androgen signaling pathway; (2) hypoxic tumor cells and regions; (3) DNA damage response (DDR) pathway; and (4) abnormal extra-/intracell signaling pathways. In addition, we discuss how and which patients should be selected for biomarker-based clinical trials exploiting and validating these targeted treatment strategies with precision RT to improve cure rates in non-indolent, localized PCa.
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Affiliation(s)
- Alan Dal Pra
- Radiation Medicine Program, Ontario Cancer Institute, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada
| | - Jennifer A Locke
- Radiation Medicine Program, Ontario Cancer Institute, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada
| | - Gerben Borst
- Radiation Medicine Program, Ontario Cancer Institute, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada
| | - Stephane Supiot
- Integrated Center of Oncology (ICO) René Gauducheau , Nantes , France
| | - Robert G Bristow
- Radiation Medicine Program, Ontario Cancer Institute, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada
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Belder N, Coskun Ö, Doganay Erdogan B, Ilk O, Savas B, Ensari A, Özdağ H. From RNA isolation to microarray analysis: Comparison of methods in FFPE tissues. Pathol Res Pract 2016; 212:678-85. [PMID: 27161306 DOI: 10.1016/j.prp.2015.11.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 10/15/2015] [Accepted: 11/09/2015] [Indexed: 01/06/2023]
Abstract
BACKGROUND Genome-wide gene expression profiling analysis of FFPE tissue samples is indispensable for cancer research and provides the opportunity to evaluate links between molecular and clinical information, however, working with FFPE samples is challenging due to extensive cross-linking, fragmentation and limited quantities of nucleic acid. Thus, processing of FFPE tissue samples from RNA extraction to microarray analysis still needs optimization. MATERIALS AND METHODS In this study, a modified deparaffinization protocol was conducted prior to RNA isolation. Trizol, Qiagen RNeasy FFPE and Arcturus PicoPure RNA Isolation kits were used in parallel to compare their impact on RNA isolation. We also evaluated the effect of two different cRNA/cDNA preparation and labeling protocols with two different array platforms (Affymetrix Human Genome U133 Plus 2.0 and U133_X3P) on the percentage of present calls. RESULTS Our optimization study shows that the Qiagen RNeasy FFPE kit with modified deparaffinization step gives better results (RNA quantity and quality) than the other two isolation kits. The Ribo-SPIA protocol gave a significantly higher percentage of present calls than the 3' IVT cDNA amplification and labeling system. However, no significant differences were found between the two array platforms. CONCLUSION Our study paves the way for future high-throughput transcriptional analysis by optimizing FFPE tissue sample processing from RNA isolation to microarray analysis.
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Affiliation(s)
- Nevin Belder
- Ankara University, Biotechnology Institute, Ankara, Turkey
| | - Öznur Coskun
- Ankara University, School of Medicine, Department of Pathology, Ankara, Turkey
| | | | - Ozlem Ilk
- Middle East Technical University, Department of Statistics, Ankara, Turkey
| | - Berna Savas
- Ankara University, School of Medicine, Department of Pathology, Ankara, Turkey
| | - Arzu Ensari
- Ankara University, School of Medicine, Department of Pathology, Ankara, Turkey
| | - Hilal Özdağ
- Ankara University, Biotechnology Institute, Ankara, Turkey.
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40
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Mustafa DAM, Sieuwerts AM, Smid M, de Weerd V, van der Weiden M, Meijer - van Gelder ME, Martens JWM, Foekens JA, Kros JM. A Method to Correlate mRNA Expression Datasets Obtained from Fresh Frozen and Formalin-Fixed, Paraffin-Embedded Tissue Samples: A Matter of Thresholds. PLoS One 2015; 10:e0144097. [PMID: 26716838 PMCID: PMC4696787 DOI: 10.1371/journal.pone.0144097] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 11/12/2015] [Indexed: 11/19/2022] Open
Abstract
Background Gene expression profiling of tumors is a successful tool for the discovery of new cancer biomarkers and potential targets for the development of new therapeutic strategies. Reliable profiling is preferably performed on fresh frozen (FF) tissues in which the quality of nucleic acids is better preserved than in formalin-fixed paraffin-embedded (FFPE) material. However, since snap-freezing of biopsy materials is often not part of daily routine in pathology laboratories, one may have to rely on archival FFPE material. Procedures to retrieve the RNAs from FFPE materials have been developed and therefore, datasets obtained from FFPE and FF materials need to be made compatible to ensure reliable comparisons are possible. Aim To develop an efficient method to compare gene expression profiles obtained from FFPE and FF samples using the same platform. Methods Twenty-six FFPE-FF sample pairs of the same tumors representing various cancer types, and two FFPE-FF sample pairs of breast cancer cell lines, were included. Total RNA was extracted and gene expression profiling was carried out using Illumina’s Whole-Genome cDNA-mediated Annealing, Selection, extension and Ligation (WG-DASL) V3 arrays, enabling the simultaneous detection of 24,526 mRNA transcripts. A sample exclusion criterion was created based on the expression of 11 stably expressed reference genes. Pearson correlation at the probe level was calculated for paired FFPE-FF, and three cut-off values were chosen. Spearman correlation coefficients between the matched FFPE and FF samples were calculated for three probe lists with varying levels of significance and compared to the correlation based on all measured probes. Unsupervised hierarchical cluster analysis was performed to verify performance of the included probe lists to compare matched FPPE-FF samples. Results Twenty-seven FFPE-FF pairs passed the sample exclusion criterion. From the profiles of 27 FFPE and FF matched samples, the best correlating probes were identified for various levels of significance (Pearson P<0.01, n = 1,432; P<0.05, n = 2,530; and P<0.10, n = 3,351 probes). Unsupervised hierarchical clustering of the 27 pairs using the resulting probes yielded 25, 21, and 19 correctly clustered pairs, respectively, compared to 1 pair when all probes were used. Conclusion The proposed method enables comparison of gene expression profiles of FFPE and/or FF origin measured on the same platform.
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Affiliation(s)
- Dana A. M. Mustafa
- Dept. of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
- * E-mail:
| | - Anieta M. Sieuwerts
- Dept. of Medical Oncology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Marcel Smid
- Dept. of Medical Oncology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Vania de Weerd
- Dept. of Medical Oncology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | | | - John W. M. Martens
- Dept. of Medical Oncology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - John A. Foekens
- Dept. of Medical Oncology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Johan M. Kros
- Dept. of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
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41
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Marrone M, Potosky AL, Penson D, Freedman AN. A 22 Gene-expression Assay, Decipher® (GenomeDx Biosciences) to Predict Five-year Risk of Metastatic Prostate Cancer in Men Treated with Radical Prostatectomy. PLOS CURRENTS 2015; 7. [PMID: 26664778 PMCID: PMC4659515 DOI: 10.1371/currents.eogt.761b81608129ed61b0b48d42c04f92a4] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Among the estimated 230,000 men diagnosed with prostate cancer in the US each year there has been a rise in the number of radical prostatectomies (RP). There is some debate over the value of immediate adjuvant therapy following RP in men with high-risk pathological features versus delayed salvage radiation therapy when signs of disease progression are observed. Thus, it would be potentially useful to inform post-RP management strategies by more clearly identifying those patients at higher risk of progression and death from prostate cancer. A 22 gene-expression assay, Decipher® (GenomeDx Biosciences), has been developed in men treated with radical prostatectomy to predict the five-year risk of metastatic prostate cancer. Published and unpublished literature was evaluated to determine the analytic validity, clinical validity and clinical utility of Decipher. Limited information is available on the analytic validity of Decipher. In both discovery and validation studies, Decipher was shown to have good performance in discriminating men with metastasis from men without metastasis five years after surgery (AUC 0.75 to 0.90). In terms of clinical utility, no evidence was found reporting improved outcomes (lower prostate cancer specific mortality and treatment related adverse effects) from using this test to guide post-operative treatment. Four studies provided weak indirect evidence of clinical utility in which 31% to 43% of post-operative treatment recommendations were changed in men with high-risk prostate cancer based on test results, with 27% to 52% of treatment recommendations changing from any treatment to no treatment.
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Affiliation(s)
- Michael Marrone
- Epidemiology and Genomics Research Program, Division of Cancer Control and Population Sciences, National Cancer Institute, NIH, Rockville, Maryland, USA
| | - Arnold L Potosky
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington DC, USA
| | - David Penson
- Department of Urology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Andrew N Freedman
- Epidemiology and Genomics Research Program, Division of Cancer Control and Population Sciences, National Cancer Institute, NIH, Rockville, Maryland, USA
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Tomlins SA, Alshalalfa M, Davicioni E, Erho N, Yousefi K, Zhao S, Haddad Z, Den RB, Dicker AP, Trock BJ, DeMarzo AM, Ross AE, Schaeffer EM, Klein EA, Magi-Galluzzi C, Karnes RJ, Jenkins RB, Feng FY. Characterization of 1577 primary prostate cancers reveals novel biological and clinicopathologic insights into molecular subtypes. Eur Urol 2015; 68:555-67. [PMID: 25964175 PMCID: PMC4562381 DOI: 10.1016/j.eururo.2015.04.033] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 04/21/2015] [Indexed: 01/09/2023]
Abstract
BACKGROUND Prostate cancer (PCa) molecular subtypes have been defined by essentially mutually exclusive events, including ETS gene fusions (most commonly involving ERG) and SPINK1 overexpression. Clinical assessment may aid in disease stratification, complementing available prognostic tests. OBJECTIVE To determine the analytical validity and clinicopatholgic associations of microarray-based molecular subtyping. DESIGN, SETTING, AND PARTICIPANTS We analyzed Affymetrix GeneChip expression profiles for 1577 patients from eight radical prostatectomy cohorts, including 1351 cases assessed using the Decipher prognostic assay (GenomeDx Biosciences, San Diego, CA, USA) performed in a laboratory with Clinical Laboratory Improvements Amendment certification. A microarray-based (m-) random forest ERG classification model was trained and validated. Outlier expression analysis was used to predict other mutually exclusive non-ERG ETS gene rearrangements (ETS(+)) or SPINK1 overexpression (SPINK1(+)). OUTCOME MEASUREMENTS Associations with clinical features and outcomes by multivariate logistic regression analysis and receiver operating curves. RESULTS AND LIMITATIONS The m-ERG classifier showed 95% accuracy in an independent validation subset (155 samples). Across cohorts, 45% of PCas were classified as m-ERG(+), 9% as m-ETS(+), 8% as m-SPINK1(+), and 38% as triple negative (m-ERG(-)/m-ETS(-)/m-SPINK1(-)). Gene expression profiling supports three underlying molecularly defined groups: m-ERG(+), m-ETS(+), and m-SPINK1(+)/triple negative. On multivariate analysis, m-ERG(+) tumors were associated with lower preoperative serum prostate-specific antigen and Gleason scores, but greater extraprostatic extension (p<0.001). m-ETS(+) tumors were associated with seminal vesicle invasion (p=0.01), while m-SPINK1(+)/triple negative tumors had higher Gleason scores and were more frequent in Black/African American patients (p<0.001). Clinical outcomes were not significantly different among subtypes. CONCLUSIONS A clinically available prognostic test (Decipher) can also assess PCa molecular subtypes, obviating the need for additional testing. Clinicopathologic differences were found among subtypes based on global expression patterns. PATIENT SUMMARY Molecular subtyping of prostate cancer can be achieved using extra data generated from a clinical-grade, genome-wide expression-profiling prognostic assay (Decipher). Transcriptomic and clinical analysis support three distinct molecular subtypes: (1) m-ERG(+), (2) m-ETS(+), and (3) m-SPINK1(+)/triple negative (m-ERG(-)/m-ETS(-)/m-SPINK1(-)). Incorporation of subtyping into a clinically available assay may facilitate additional applications beyond routine prognosis.
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Affiliation(s)
- Scott A Tomlins
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Urology, University of Michigan Medical School, Ann Arbor, MI, USA; Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA.
| | | | - Elai Davicioni
- GenomeDx Bioscience Inc., Vancouver, British Columbia, Canada
| | - Nicholas Erho
- GenomeDx Bioscience Inc., Vancouver, British Columbia, Canada
| | - Kasra Yousefi
- GenomeDx Bioscience Inc., Vancouver, British Columbia, Canada
| | - Shuang Zhao
- Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Zaid Haddad
- GenomeDx Bioscience Inc., Vancouver, British Columbia, Canada
| | - Robert B Den
- Kimmel Cancer Center, Jefferson Medical College of Thomas Jefferson University, Philadelphia, PA, USA
| | - Adam P Dicker
- Kimmel Cancer Center, Jefferson Medical College of Thomas Jefferson University, Philadelphia, PA, USA
| | - Bruce J Trock
- James Buchanan Brady Urological Institute, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Angelo M DeMarzo
- James Buchanan Brady Urological Institute, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Ashley E Ross
- James Buchanan Brady Urological Institute, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Edward M Schaeffer
- James Buchanan Brady Urological Institute, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Eric A Klein
- Glickman Urological & Kidney Institute, Cleveland Clinic, Cleveland, OH, USA
| | | | | | - Robert B Jenkins
- Department of Pathology and Laboratory Medicine, Mayo Clinic, Rochester, MN, USA
| | - Felix Y Feng
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI, USA; Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, MI, USA.
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Insulin-like Growth Factor 2 Gene Expression Molecularly Differentiates Pleuropulmonary Blastoma and Embryonal Rhabdomyosarcoma. J Pediatr Hematol Oncol 2015; 37:e356-60. [PMID: 26056800 PMCID: PMC4506202 DOI: 10.1097/mph.0000000000000382] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The sarcomatous element in pleuropulmonary blastoma (PPB) is often histologically indistinguishable from embryonal rhabdomyosarcoma (ERMS). A diagnosis of PPB is often made after definitive surgical resection based on pathologic features, most notably the presence of hamartomatous pulmonary elements. Samples from seven PPB patients were obtained from the rhabdomyosarcomatous portion of the tumor by macrodissection. Representative ERMS tumor tissue was selected from 21 ERMS patient samples. Formalin-fixed paraffin-embedded tissue scrolls from each sample were analyzed using the Affymetrix Human Exon arrays. All PPB patients and 7 of 21 ERMS patients were 3 years old and younger. Twenty transcripts (10 annotated, 10 noncoding RNAs) were significantly differentially expressed in ERMS when compared with PPB samples. Insulin-like growth factor 2 (IGF2) was uniformly overexpressed in ERMS (19/21>400) but was expressed at low levels in PPB (P<0.001). Two ERMS cases that had low level IGF2 expression were 3 years and younger of age. No other differences between the 2 approached this degree of significance, despite a common rhabdomyogenic phenotype in the sarcomatous areas of PPB. PPB, unlike most ERMS, appears not to be driven by autocrine IGF2 signaling.
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Worley MJ, Liu S, Hua Y, Kwok JSL, Samuel A, Hou L, Shoni M, Lu S, Sandberg EM, Keryan A, Wu D, Ng SK, Kuo WP, Parra-Herran CE, Tsui SKW, Welch W, Crum C, Berkowitz RS, Ng SW. Molecular changes in endometriosis-associated ovarian clear cell carcinoma. Eur J Cancer 2015; 51:1831-42. [PMID: 26059197 DOI: 10.1016/j.ejca.2015.05.011] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Revised: 05/12/2015] [Accepted: 05/14/2015] [Indexed: 01/16/2023]
Abstract
BACKGROUND Endometriosis is frequently associated with and thought of having propensity to develop into ovarian clear cell carcinoma (OCCC), although the molecular transformation mechanism is not completely understood. METHODS We employed immunohistochemical (IHC) staining for marker expression along the potential progression continuum. Expression profiling of microdissected endometriotic and OCCC cells from patient-matched formalin-fixed, paraffin-embedded samples was performed to explore the carcinogenic pathways. Function of novel biomarkers was confirmed by knockdown experiments. RESULTS PTEN was significantly lost in both endometriosis and invasive tumour tissues, while oestrogen receptor (ER) expression was lost in OCCC relative to endometriosis. XRCC5, PTCH2, eEF1A2 and PPP1R14B were significantly overexpressed in OCCC and associated endometriosis, but not in benign endometriosis (p ⩽ 0.004). Knockdown experiments with XRCC5 and PTCH2 in a clear cell cancer cell line resulted in significant growth inhibition. There was also significant silencing of a panel of target genes with histone H3 lysine 27 trimethylation, a signature of polycomb chromatin-remodelling complex in OCCC. IHC confirmed the loss of expression of one such polycomb target gene, the serous ovarian cancer lineage marker Wilms' tumour protein 1 (WT1) in OCCC, while endometriotic tissues showed significant co-expression of WT1 and ER. CONCLUSIONS Loss of PTEN expression is proposed as an early and permissive event in endometriosis development, while the loss of ER and polycomb-mediated transcriptional reprogramming for pluripotency may play an important role in the ultimate transformation process. Our study provides new evidence to redefine the pathogenic programme for lineage-specific transformation of endometriosis to OCCC.
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Affiliation(s)
- Michael J Worley
- Division of Gynecologic Oncology, Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Shubai Liu
- Division of Gynecologic Oncology, Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Yuanyuan Hua
- Department of Obstetrics & Gynecology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, PR China; Division of Gynecologic Oncology, Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jamie Sui-Lam Kwok
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong
| | - Anicka Samuel
- Division of Gynecologic Oncology, Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Lei Hou
- Division of Gynecologic Oncology, Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Melina Shoni
- Division of Gynecologic Oncology, Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Shi Lu
- Division of Gynecologic Oncology, Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Evelien M Sandberg
- Division of Gynecologic Oncology, Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Anna Keryan
- Division of Gynecologic Oncology, Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Di Wu
- Statistics Department, Harvard University, Boston, MA, USA
| | - Shu-Kay Ng
- School of Medicine, Griffith University, Meadowbrook, Australia
| | - Winston P Kuo
- Harvard Catalyst Laboratory for Innovative Translational Technologies, Harvard Medical School, Boston, MA, USA
| | - Carlos E Parra-Herran
- Division of Women's and Perinatal Pathology, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Stephen K W Tsui
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong
| | - William Welch
- Division of Women's and Perinatal Pathology, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Christopher Crum
- Division of Women's and Perinatal Pathology, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Ross S Berkowitz
- Division of Gynecologic Oncology, Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Shu-Wing Ng
- Division of Gynecologic Oncology, Department of Obstetrics, Gynecology, and Reproductive Biology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
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Tyekucheva S, Martin NE, Stack EC, Wei W, Vathipadiekal V, Waldron L, Fiorentino M, Lis RT, Stampfer MJ, Loda M, Parmigiani G, Mucci LA, Birrer M. Comparing Platforms for Messenger RNA Expression Profiling of Archival Formalin-Fixed, Paraffin-Embedded Tissues. J Mol Diagn 2015; 17:374-81. [PMID: 25937617 DOI: 10.1016/j.jmoldx.2015.02.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 01/29/2015] [Accepted: 02/24/2015] [Indexed: 12/19/2022] Open
Abstract
Archival formalin-fixed, paraffin-embedded (FFPE) tissue specimens represent a readily available but largely untapped resource for gene expression profiling-based biomarker discovery. Several technologies have been proposed to cope with the bias from RNA cross-linking and degradation associated with archival specimens to generate data comparable with RNA from fresh-frozen materials. Direct comparison studies of these RNA expression platforms remain rare. We compared two commercially available platforms for RNA expression profiling of archival FFPE specimens from clinical studies of prostate and ovarian cancer: the Affymetrix Human Gene 1.0ST Array following whole-transcriptome amplification using the NuGen WT-Ovation FFPE System V2, and the NanoString nCounter without amplification. For each assay, we profiled 7 prostate and 11 ovarian cancer specimens, with a block age of 4 to 21 years. Both platforms produced gene expression profiles with high sensitivity and reproducibility through technical repeats from FFPE materials. Sensitivity and reproducibility remained high across block age within each cohort. A strong concordance was shown for the transcript expression values for genes detected by both platforms. We showed the biological validity of specific gene signatures generated by both platforms for both cohorts. Our study supports the feasibility of gene expression profiling and large-scale signature validation on archival prostate and ovarian tumor specimens using commercial platforms. These approaches have the potential to aid precision medicine with biomarker discovery and validation.
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Affiliation(s)
- Svitlana Tyekucheva
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts; Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts.
| | - Neil E Martin
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Edward C Stack
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts; Center for Molecular Oncologic Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Wei Wei
- Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts
| | - Vinod Vathipadiekal
- Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts
| | - Levi Waldron
- City University of New York School of Public Health, Hunter College, New York, New York
| | | | - Rosina T Lis
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts; Center for Molecular Oncologic Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Meir J Stampfer
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts; Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts; Department of Nutrition, Harvard School of Public Health, Boston, Massachusetts
| | - Massimo Loda
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts; Center for Molecular Oncologic Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts; Broad Institute, Cambridge, Massachusetts; Division of Cancer Studies, King's College London, London, United Kingdom
| | - Giovanni Parmigiani
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts; Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts
| | - Lorelei A Mucci
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts; Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts
| | - Michael Birrer
- Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts
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Musella V, Callari M, Di Buduo E, Scuro M, Dugo M, Miodini P, Bianchini G, Paolini B, Gianni L, Daidone MG, Cappelletti V. Use of formalin-fixed paraffin-embedded samples for gene expression studies in breast cancer patients. PLoS One 2015; 10:e0123194. [PMID: 25844937 PMCID: PMC4386823 DOI: 10.1371/journal.pone.0123194] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 02/18/2015] [Indexed: 01/16/2023] Open
Abstract
To obtain gene expression profiles from samples collected in clinical trials, we conducted a pilot study to assess feasibility and estimate sample attrition rates when profiling formalin-fixed, paraffin-embedded specimens. Ten matched fresh-frozen and fixed breast cancer samples were profiled using the Illumina HT-12 and Ref-8 chips, respectively. The profiles obtained with Ref 8, were neither technically nor biologically reliable since they failed to yield the expected separation between estrogen receptor positive and negative samples. With the use of Affymetrix HG-U133 2.0 Plus chips on fixed samples and a quantitative polymerase chain reaction -based sample pre-assessment step, results were satisfactory in terms of biological reliability, despite the low number of present calls (M = 21%±5). Compared with the Illumina DASL WG platform, Affymetrix data showed a wider interquartile range (1.32 vs 0.57, P<2.2 E-16,) and larger fold changes. The Affymetrix chips were used to run a pilot study on 60 fixed breast cancers. By including in the workflow the sample pre-assessment steps, 96% of the samples predicted to give good results (44/46), were in fact rated as satisfactory from the point of view of technical and biological meaningfulness. Our gene expression profiles showed strong agreement with immunohistochemistry data, were able to reproduce breast cancer molecular subtypes, and allowed the validation of an estrogen receptor status classifier derived in frozen samples. The approach is therefore suitable to profile formalin-fixed paraffin-embedded samples collected in clinical trials, provided that quality controls are run both before (sample pre-assessment) and after hybridization on the array.
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Affiliation(s)
- Valeria Musella
- Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Maurizio Callari
- Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Eleonora Di Buduo
- Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Manuela Scuro
- Department of Pathology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Matteo Dugo
- Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Patrizia Miodini
- Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | | | - Biagio Paolini
- Department of Pathology, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Luca Gianni
- Department of Medical Oncology, Ospedale San Raffaele, Milan, Italy
| | - Maria Grazia Daidone
- Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
- * E-mail:
| | - Vera Cappelletti
- Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
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Greytak SR, Engel KB, Bass BP, Moore HM. Accuracy of Molecular Data Generated with FFPE Biospecimens: Lessons from the Literature. Cancer Res 2015; 75:1541-7. [PMID: 25836717 DOI: 10.1158/0008-5472.can-14-2378] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 12/22/2014] [Indexed: 12/15/2022]
Abstract
Formalin-fixed and paraffin-embedded (FFPE) tissue biospecimens are a valuable resource for molecular cancer research. Although much can be gained from their use, it remains unclear whether the genomic and expression profiles obtained from FFPE biospecimens accurately reflect the physiologic condition of the patient from which they were procured, or if such profiles are confounded by biologic effects from formalin fixation and processing. To assess the physiologic accuracy of genomic and expression data generated with FFPE specimens, we surveyed the literature for articles investigating genomic and expression endpoints in case-matched FFPE and fresh or frozen human biospecimens using the National Cancer Institute's Biospecimen Research Database (http://biospecimens.cancer.gov/brd). Results of the survey revealed that the level of concordance between differentially preserved biospecimens varied among analytical parameters and platforms but also among reports, genes/transcripts of interest, and tumor status. The identified analytical techniques and parameters that resulted in strong correlations between FFPE and frozen biospecimens may provide guidance when optimizing molecular protocols for FFPE use; however, discrepancies reported for similar assays also illustrate the importance of validating protocols optimized for use with FFPE specimens with a case-matched fresh or frozen cohort for each platform, gene or transcript, and FFPE processing regime. On the basis of evidence published to date, validation of analytical parameters with a properly handled frozen cohort is necessary to ensure a high degree of concordance and confidence in the results obtained with FFPE biospecimens.
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Affiliation(s)
| | | | | | - Helen M Moore
- Biorepositories and Biospecimen Research Branch, Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, Maryland.
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Gene expression in hepatocellular carcinoma: pilot study of potential transarterial chemoembolization response biomarkers. J Vasc Interv Radiol 2015; 26:723-32. [PMID: 25724086 DOI: 10.1016/j.jvir.2014.12.610] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Revised: 12/16/2014] [Accepted: 12/20/2014] [Indexed: 02/06/2023] Open
Abstract
PURPOSE To perform a feasibility study to explore the relationship between hepatocellular carcinoma genetics and transarterial chemoembolization treatment response to identify potential biomarkers associated with enhanced treatment efficacy. MATERIALS AND METHODS In this single-institution study, pretreatment hepatocellular carcinoma biopsy specimens for tumors in 19 patients (14 men, five women; mean age, 59 y) treated with chemoembolization between 2007 and 2013 were analyzed for a panel of 60 chemotherapy-sensitivity, hypoxia, mitosis, and inflammatory genes with the QuantiGene Plex 2.0 mRNA detection assay. Demographic, disease, and procedure data and tumor response outcomes were collected. Quantitative mRNA levels were compared based on radiologic response between tumors exhibiting complete response (CR) versus partial response (PR). RESULTS The study sample included 19 biopsy specimens from tumors (mean size, 3.0 cm; grade 1, n = 6; grade 2, n = 9; grade 3, n = 4) in patients treated with a mean of two conventional chemoembolization sessions. Thirteen and six tumors exhibited CR and PR, respectively, at a mean of 116 days after treatment. Tumors with CR showed a significant increase in (P < .05) or trend toward (P < .1) greater (range, 1.49-3.50 fold) pretreatment chemotherapy-sensitivity and mitosis (ATF4, BAX, CCNE1, KIF11, NFX1, PPP3CA, SNX1, TOP2A, and TOP2B) gene mRNA expression compared with tumors with PR, in addition to lower CXCL10 levels (0.48-fold), and had significantly (P < .05) higher (1.65-fold) baseline VEGFA levels. CONCLUSIONS Genetic signatures may allow prechemoembolization stratification of tumor response probability, and gene analysis may therefore offer an opportunity to personalize locoregional therapy by enhancing treatment modality allocation. Further corroboration of identified markers and exploration of their respective predictive capacity thresholds is necessary.
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Bass BP, Engel KB, Greytak SR, Moore HM. A review of preanalytical factors affecting molecular, protein, and morphological analysis of formalin-fixed, paraffin-embedded (FFPE) tissue: how well do you know your FFPE specimen? Arch Pathol Lab Med 2015; 138:1520-30. [PMID: 25357115 DOI: 10.5858/arpa.2013-0691-ra] [Citation(s) in RCA: 191] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT Formalin fixation and paraffin embedding is a timeless, cost-efficient, and widely adopted method of preserving human tissue biospecimens that has resulted in a substantial reservoir of formalin-fixed, paraffin-embedded blocks that represent both the pathology and preanalytical handling of the biospecimen. This reservoir of specimens is increasingly being used for DNA, RNA, and proteomic analyses. OBJECTIVE To evaluate the impact of preanalytical factors associated with the formalin fixation and paraffin embedding process on downstream morphological and molecular endpoints. DATA SOURCES We surveyed the existing literature using the National Cancer Institute's Biospecimen Research Database for published reports investigating the potential influence of preanalytical factors associated with the formalin fixation and paraffin embedding process on DNA, RNA, protein, and morphological endpoints. CONCLUSIONS Based on the literature evidence, the molecular, proteomic, and morphological endpoints can be altered in formalin-fixed, paraffin-embedded specimens by suboptimal processing conditions. While the direction and magnitude of effects associated with a given preanalytical factor were dependent on the analyte (DNA, RNA, protein, and morphology) and analytical platform, acceptable conditions are highlighted, and a summary of conditions that could preclude analysis is provided.
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Affiliation(s)
- B Paige Bass
- From the Kelly Government Solutions Program, Kelly Services, Rockville (Drs Bass and Greytak), and the Biorepositories and Biospecimen Research Branch, Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda (Dr Moore), Maryland; and the Preferred Solutions Group, Arlington, Virginia (Dr Engel)
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Molecular and ultrastuctural changes of rat pre-implantation embryos during two-cell developmental arrest. J Assist Reprod Genet 2015; 31:767-80. [PMID: 24658924 DOI: 10.1007/s10815-014-0213-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Accepted: 03/04/2014] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Rat pre-implantation embryos often suffer 2-cell stage developmental arrest and fail to progress further under in-vitro conditions. OBJECTIVE In order to understand underlying mechanism leading to 2-cell arrest, we investigated the molecular changes, culture conditions and subcellular changes. METHODS Gene expression in in-vivo developed 2-cell embryos (in-vivo), in- vitro developed 2-cell embryos (in-vitro), and in-vitro 2-cell arrested embryos (arrested) were investigated using microarrays and real-time PCR. Ultra-structural changes were determined using electron microscopy. RESULTS Gene expression was similar between in-vivo and in-vitro embryos. Over 2400 genes changed in arrested embryos compared to in-vivo and in-vitro embryos. The mRNAs encoding proteins involved in translation were elevated in arrested embryos. In-vivo and in-vitro embryos highly expressed genes that were involved in cell cycle, and protein catabolic process compared to arrested embryos. Gene expression data suggested subcellular changes associated with 2-cell block. Transmission electron microscopy showed that in-vivo embryos had healthy subcellular structure, whereas arrested embryos did not have a nuclear membrane, contained small mitochondria and autophagic vacuoles. Furthermore, gene expression data was used for the optimization of culture media conditions to obtain better in-vitro embryonic development. Comparison of five and 20 % oxygen in culture resulted in two times more blastocyst formation with 5 % oxygen. CONCLUSIONS These results showed that although all experimental groups appeared morphologically similar, arrested embryos had ultra-structural and molecular changes associated with oxidative stress and apoptosis. In-vitro culture under low oxygen and media additives reduced 2-cell block in rat embryos.
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