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Xu C, Xia P, Li J, Lewis KB, Ciombor KK, Wang L, Smith JJ, Beauchamp RD, Chen XS. Discovery and validation of a 10-gene predictive signature for response to adjuvant chemotherapy in stage II and III colon cancer. Cell Rep Med 2024; 5:101661. [PMID: 39059386 PMCID: PMC11384724 DOI: 10.1016/j.xcrm.2024.101661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 12/30/2023] [Accepted: 07/02/2024] [Indexed: 07/28/2024]
Abstract
Identifying patients with stage II and III colon cancer who will benefit from 5-fluorouracil (5-FU)-based adjuvant chemotherapy is crucial for the advancement of personalized cancer therapy. We employ a semi-supervised machine learning approach to analyze a large dataset with 933 stage II and III colon cancer samples. Our analysis leverages gene regulatory networks to discover an 18-gene prognostic signature and to explore a 10-gene signature that potentially predicts chemotherapy benefits. The 10-gene signature demonstrates strong prognostic power and shows promising potential to predict chemotherapy benefits. We establish a robust clinical assay on the NanoString nCounter platform, validated in a retrospective formalin-fixed paraffin-embedded (FFPE) cohort, which represents an important step toward clinical application. Our study lays the groundwork for improving adjuvant chemotherapy and potentially expanding into immunotherapy decision-making in colon cancer. Future prospective studies are needed to validate and establish the clinical utility of the 10-gene signature in clinical settings.
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Affiliation(s)
- Chaohan Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China; Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Peng Xia
- School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Jie Li
- Academy of Biomedical Engineering, Kunming Medical University, Kunming 650500, China
| | - Keeli B Lewis
- Section of Surgical Sciences, Department of Surgery, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Kristen K Ciombor
- Division of Hematology and Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Lily Wang
- Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - J Joshua Smith
- Colorectal Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| | - R Daniel Beauchamp
- Section of Surgical Sciences, Department of Surgery, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - X Steven Chen
- Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA.
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2
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Moellmer SA, Hagen OL, Farhang PA, Duke VR, Fallon ME, Hinds MT, McCarty OJT, Lo JO, Nakayama KH. Effects of in utero delta-9-tetrahydrocannabinol (THC) exposure on fetal and infant musculoskeletal development in a preclinical nonhuman primate model. PLoS One 2024; 19:e0306868. [PMID: 39083456 PMCID: PMC11290632 DOI: 10.1371/journal.pone.0306868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 06/17/2024] [Indexed: 08/02/2024] Open
Abstract
The endocannabinoid system (ECS) plays a major role in the maintenance of bodily homeostasis and adaptive response to external insults. It has been shown to regulate crucial physiological processes and behaviors, spanning nervous functions, anxiety, cognition, and pain sensation. Due to this broad activity, the ECS has been explored as a potential therapeutic target in the treatment of select diseases. However, until there is a more comprehensive understanding of how ECS activation by exogenous and endogenous ligands manifests across disparate tissues and cells, discretion should be exercised. Previous work has investigated how endogenous cannabinoid signaling impacts skeletal muscle development and differentiation. However, the effects of activation of the ECS by delta-9-tetrahydrocannabinol (THC, the most psychoactive component of cannabis) on skeletal muscle development, particularly in utero, remain unclear. To address this research gap, we used a highly translational non-human primate model to examine the potential impact of chronic prenatal THC exposure on fetal and infant musculoskeletal development. RNA was isolated from the skeletal muscle and analyzed for differential gene expression using a Nanostring nCounter neuroinflammatory panel comprised of 770 genes. Histomorphological evaluation of muscle morphology and composition was also performed. Our findings suggest that while prenatal THC exposure had narrow overall effects on fetal and infant muscle development, the greatest impacts were observed within pathways related to inflammation and cytokine signaling, which suggest the potential for tissue damage and atrophy. This pilot study establishes feasibility to evaluate neuroinflammation due to prenatal THC exposure and provides rationale for follow-on studies that explore the longer-term implications and functional consequences encountered by offspring as they continue to mature.
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Affiliation(s)
- Samantha A. Moellmer
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, United States of America
| | - Olivia L. Hagen
- Division of Reproduction and Developmental Sciences, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, United States of America
| | - Parsa A. Farhang
- Department of Molecular Microbiology and Immunology, Johns Hopkins University, Baltimore, MD, United States of America
| | - Victoria R. Duke
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, United States of America
| | - Meghan E. Fallon
- Yale Cardiovascular Research Center, Section of Cardiovascular Medicine, Department of Internal Medicine Yale School of Medicine, New Haven, CT, United States of America
| | - Monica T. Hinds
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, United States of America
| | - Owen J. T. McCarty
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, United States of America
| | - Jamie O. Lo
- Division of Reproduction and Developmental Sciences, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, United States of America
- Department of Obstetrics and Gynecology, Division of Maternal Fetal Medicine, Oregon Health & Science University, Portland, OR, United States of America
| | - Karina H. Nakayama
- Department of Biomedical Engineering, Oregon Health & Science University, Portland, OR, United States of America
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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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Barth J, Yang Y, Xiao G, Wang X. MetaNorm: incorporating meta-analytic priors into normalization of NanoString nCounter data. Bioinformatics 2024; 40:btae024. [PMID: 38237909 PMCID: PMC10826904 DOI: 10.1093/bioinformatics/btae024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 12/28/2023] [Accepted: 01/12/2024] [Indexed: 02/01/2024] Open
Abstract
MOTIVATION Non-informative or diffuse prior distributions are widely employed in Bayesian data analysis to maintain objectivity. However, when meaningful prior information exists and can be identified, using an informative prior distribution to accurately reflect current knowledge may lead to superior outcomes and great efficiency. RESULTS We propose MetaNorm, a Bayesian algorithm for normalizing NanoString nCounter gene expression data. MetaNorm is based on RCRnorm, a powerful method designed under an integrated series of hierarchical models that allow various sources of error to be explained by different types of probes in the nCounter system. However, a lack of accurate prior information, weak computational efficiency, and instability of estimates that sometimes occur weakens the approach despite its impressive performance. MetaNorm employs priors carefully constructed from a rigorous meta-analysis to leverage information from large public data. Combined with additional algorithmic enhancements, MetaNorm improves RCRnorm by yielding more stable estimation of normalized values, better convergence diagnostics and superior computational efficiency. AVAILABILITY AND IMPLEMENTATION R Code for replicating the meta-analysis and the normalization function can be found at github.com/jbarth216/MetaNorm.
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Affiliation(s)
- Jackson Barth
- Department of Statistics and Data Science, Southern Methodist University, Dallas, TX 75275, United States
- Department of Statistical Science, Baylor University, Waco, TX 76798, United States
| | - Yuqiu Yang
- Department of Statistics and Data Science, Southern Methodist University, Dallas, TX 75275, United States
| | - Guanghua Xiao
- Quantitative Biomedical Research Center, The University of Texas Southwestern Medical Center, Dallas, TX 75390, United States
| | - Xinlei Wang
- Department of Statistics and Data Science, Southern Methodist University, Dallas, TX 75275, United States
- Department of Mathematics, University of Texas at Arlington, Arlington, TX 76019 United States
- Division of Data Science, College of Science, University of Texas at Arlington, Arlington, TX 76019, United States
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Unal U, Gov E. Drug Repurposing Analysis for Colorectal Cancer through Network Medicine Framework: Novel Candidate Drugs and Small Molecules. Cancer Invest 2023; 41:713-733. [PMID: 37682113 DOI: 10.1080/07357907.2023.2255672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 02/04/2023] [Accepted: 09/01/2023] [Indexed: 09/09/2023]
Abstract
This study aimed to reveal the drug-repurposing candidates for colorectal cancer (CRC) via drug-repurposing methods and network biology approaches. A novel, differentially co-expressed, highly interconnected, and co-regulated prognostic gene module was identified for CRC. Based on the gene module, polyethylene glycol (PEG), gallic acid, pyrazole, cordycepin, phenothiazine, pantoprazole, cysteamine, indisulam, valinomycin, trametinib, BRD-K81473043, AZD8055, dovitinib, BRD-A17065207, and tyrphostin AG1478 presented as drugs and small molecule candidates previously studied in the CRC. Lornoxicam, suxamethonium, oprelvekin, sirukumab, levetiracetam, sulpiride, NVP-TAE684, AS605240, 480743.cdx, HDAC6 inhibitor ISOX, BRD-K03829970, and L-6307 are proposed as novel drugs and small molecule candidates for CRC.
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Affiliation(s)
- Ulku Unal
- Department of Bioengineering, Adana Alparslan Türkeş Science and Technology University, Adana, Turkey
| | - Esra Gov
- Department of Bioengineering, Adana Alparslan Türkeş Science and Technology University, Adana, Turkey
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Teerapakpinyo C, Areeruk W, Tantbirojn P, Phupong V, Shuangshoti S, Lertkhachonsuk R. MicroRNA Expression Profiling in Hydatidiform Mole for the Prediction of Postmolar GTN : MicroRNA Profile in Postmolar GTN. Technol Cancer Res Treat 2022; 21:15330338211067309. [PMID: 35023789 PMCID: PMC8785350 DOI: 10.1177/15330338211067309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Objectives: The primary aim of the study was to identify miRNAs that were differentially expressed between complete hydatidiform moles (CHMs) that turned out to be gestational trophoblastic neoplasia (GTN) [GTN moles] and CHMs that regressed spontaneously after evacuation [remission moles]. The secondary aim was to study the profiles of miRNA expressions in CHMs. Methods: A case-control study was conducted on GTN moles and remission moles. We quantitatively assessed the expression of 800 human miRNAs from molar tissues using Nanostring nCounter. Results: From a pilot study, 21 miRNAs were significantly downregulated in GTN moles compared to the remission moles. Five of them (miR-566, miR-608, miR-1226-3p, miR-548ar-3p and miR-514a-3p) were downregulated for >4 folds. MiR-608 was selected as a candidate for further analysis on 18 CHMs (9 remission moles and 9 GTN moles) due to its striking association with malignant formation. MiR-608 expression was slightly lower in GTN moles compared to the remission moles, that is, 2.22 folds change [p = 0.063]. Conclusion: We identified 21 miRNAs that were differentially expressed between GTN moles and remission moles suggesting that miRNA profiles can distinguish between the two groups. Although not reaching statistically significant, miR-608 expression was slightly lower in GTN moles compared to remission moles.
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Affiliation(s)
| | - Wilasinee Areeruk
- Department of Obstetrics and Gynecology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Patou Tantbirojn
- Department of Obstetrics and Gynecology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Vorapong Phupong
- Department of Obstetrics and Gynecology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Shanop Shuangshoti
- Department of Pathology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Ruangsak Lertkhachonsuk
- Department of Obstetrics and Gynecology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
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A Germinal Center-Associated Microenvironmental Signature Reflects Malignant Phenotype and Outcome of DLBCL. Blood Adv 2021; 6:2388-2402. [PMID: 34638128 PMCID: PMC9006269 DOI: 10.1182/bloodadvances.2021004618] [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: 03/01/2021] [Accepted: 08/29/2021] [Indexed: 12/03/2022] Open
Abstract
The DLBCL microenvironment signature scoring system was established using nCounter-based profiling of GC-related microenvironmental genes. DMS scores stratified DLBCL patients with different prognosis independently of existing prognostic models.
Diffuse large B-cell lymphoma (DLBCL) is the most common B-cell malignancy, with varying prognosis after the gold standard rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP). Several prognostic models have been established by focusing primarily on characteristics of lymphoma cells themselves, including cell-of-origin (COO), genomic alterations, and gene/protein expressions. However, the prognostic impact of the lymphoma microenvironment and its association with characteristics of lymphoma cells are not fully understood. Using the nCounter-based gene expression profiling of untreated DLBCL tissues, we assess the clinical impact of lymphoma microenvironment on the clinical outcomes and pathophysiological, molecular signatures in DLBCL. The presence of normal germinal center (GC)-microenvironmental cells, including follicular T cells, macrophage/dendritic cells, and stromal cells in lymphoma tissue indicates a positive therapeutic response. Our prognostic model, based on quantitation of transcripts from distinct GC-microenvironmental cell markers, clearly identified patients with graded prognosis independently of existing prognostic models. We observed increased incidences of genomic alterations and aberrant gene expression associated with poor prognosis in DLBCL tissues lacking GC-microenvironmental cells relative to those containing these cells. These data suggest that the loss of GC-associated microenvironmental signature dictates clinical outcomes of DLBCL patients reflecting the accumulation of “unfavorable” molecular signatures.
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8
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Lambracht-Washington D, Fu M, Hynan LS, Rosenberg RN. Changes in the brain transcriptome after DNA Aβ42 trimer immunization in a 3xTg-AD mouse model. Neurobiol Dis 2021; 148:105221. [PMID: 33316368 PMCID: PMC7845550 DOI: 10.1016/j.nbd.2020.105221] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 11/23/2020] [Accepted: 12/07/2020] [Indexed: 12/23/2022] Open
Abstract
Alzheimer's disease (AD) has been associated with accumulation of amyloid beta (Aβ) peptides in brain, and immunotherapy targeting Aβ provides potential for AD prevention. We have used a DNA Aβ42 trimer construct for immunization of 3xTg-AD mice and found previously significant reduction of amyloid and tau pathology due to the immunotherapy. We show here that DNA Aβ42 immunized 3xTg-AD mice showed better performance in nest building activities and had a higher 24 months survival rate compared to the non-treated AD controls. The analysis of differently expressed genes in brains from 24 months old mice showed significant increases transcript levels between non-immunized AD mice and wild-type controls for genes involved in microglia and astrocyte function, cytokine and inflammatory signaling, apoptosis, the innate and adaptive immune response and are consistent with an inflammatory phenotype in AD. Most of these upregulated genes were downregulated in the DNA Aβ42 immunized 3xTg-AD mice due to the vaccine. Transcript numbers for the immediate early genes, Arc, Bdnf, Homer1, Egr1 and cfos, involved in neuronal and neurotransmission pathways which were much lower in the non-immunized 3xTg-AD mice, were restored to wild-type mouse brain levels in DNA Aβ42 immunized 3xTg-AD mice indicating positive effects of DNA Aβ42 immunotherapy on synapse stability and plasticity. The immune response after immunization is complex, but the multitude of changes after DNA Aβ42 immunization shows that this response moves beyond the amyloid hypothesis and into direction of disease prevention.
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Affiliation(s)
- Doris Lambracht-Washington
- Department of Neurology, UT Southwestern Medical Center Dallas, USA; Doris Lambracht Washington, UT Southwestern Medical Center Dallas, Department of Neurology , 5323 Harry Hines Blvd, Dallas, TX 75390-8813, USA.
| | - Min Fu
- Department of Neurology, UT Southwestern Medical Center Dallas, USA.
| | - Linda S Hynan
- Departments of Population and Data Sciences (Biostatistics) & Psychiatry, UT Southwestern Medical Center Dallas, USA.
| | - Roger N Rosenberg
- Department of Neurology, UT Southwestern Medical Center Dallas, USA.
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Acharjee A, Larkman J, Xu Y, Cardoso VR, Gkoutos GV. A random forest based biomarker discovery and power analysis framework for diagnostics research. BMC Med Genomics 2020; 13:178. [PMID: 33228632 PMCID: PMC7685541 DOI: 10.1186/s12920-020-00826-6] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 11/15/2020] [Indexed: 11/25/2022] Open
Abstract
Background Biomarker identification is one of the major and important goal of functional genomics and translational medicine studies. Large scale –omics data are increasingly being accumulated and can provide vital means for the identification of biomarkers for the early diagnosis of complex disease and/or for advanced patient/diseases stratification. These tasks are clearly interlinked, and it is essential that an unbiased and stable methodology is applied in order to address them. Although, recently, many, primarily machine learning based, biomarker identification approaches have been developed, the exploration of potential associations between biomarker identification and the design of future experiments remains a challenge. Methods In this study, using both simulated and published experimentally derived datasets, we assessed the performance of several state-of-the-art Random Forest (RF) based decision approaches, namely the Boruta method, the permutation based feature selection without correction method, the permutation based feature selection with correction method, and the backward elimination based feature selection method. Moreover, we conducted a power analysis to estimate the number of samples required for potential future studies. Results We present a number of different RF based stable feature selection methods and compare their performances using simulated, as well as published, experimentally derived, datasets. Across all of the scenarios considered, we found the Boruta method to be the most stable methodology, whilst the Permutation (Raw) approach offered the largest number of relevant features, when allowed to stabilise over a number of iterations. Finally, we developed and made available a web interface (https://joelarkman.shinyapps.io/PowerTools/) to streamline power calculations thereby aiding the design of potential future studies within a translational medicine context. Conclusions We developed a RF-based biomarker discovery framework and provide a web interface for our framework, termed PowerTools, that caters the design of appropriate and cost-effective subsequent future omics study.
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Affiliation(s)
- Animesh Acharjee
- College of Medical and Dental Sciences, Institute of Cancer and Genomic Sciences, Centre for Computational Biology, University of Birmingham, Birmingham, B15 2TT, UK. .,Institute of Translational Medicine, University Hospitals Birmingham NHS, Foundation Trust, Birmingham, B15 2TT, UK. .,NIHR Surgical Reconstruction and Microbiology Research Centre, University Hospital Birmingham, Birmingham, B15 2WB, UK.
| | - Joseph Larkman
- College of Medical and Dental Sciences, Institute of Cancer and Genomic Sciences, Centre for Computational Biology, University of Birmingham, Birmingham, B15 2TT, UK.,Institute of Translational Medicine, University Hospitals Birmingham NHS, Foundation Trust, Birmingham, B15 2TT, UK
| | - Yuanwei Xu
- College of Medical and Dental Sciences, Institute of Cancer and Genomic Sciences, Centre for Computational Biology, University of Birmingham, Birmingham, B15 2TT, UK.,Institute of Translational Medicine, University Hospitals Birmingham NHS, Foundation Trust, Birmingham, B15 2TT, UK
| | - Victor Roth Cardoso
- College of Medical and Dental Sciences, Institute of Cancer and Genomic Sciences, Centre for Computational Biology, University of Birmingham, Birmingham, B15 2TT, UK.,Institute of Translational Medicine, University Hospitals Birmingham NHS, Foundation Trust, Birmingham, B15 2TT, UK.,MRC Health Data Research UK (HDR UK), London, UK
| | - Georgios V Gkoutos
- College of Medical and Dental Sciences, Institute of Cancer and Genomic Sciences, Centre for Computational Biology, University of Birmingham, Birmingham, B15 2TT, UK.,Institute of Translational Medicine, University Hospitals Birmingham NHS, Foundation Trust, Birmingham, B15 2TT, UK.,NIHR Surgical Reconstruction and Microbiology Research Centre, University Hospital Birmingham, Birmingham, B15 2WB, UK.,MRC Health Data Research UK (HDR UK), London, UK.,NIHR Experimental Cancer Medicine Centre, Birmingham, B15 2TT, UK.,NIHR Biomedical Research Centre, University Hospital Birmingham, Birmingham, B15 2TT, UK
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10
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Identification of Monotonically Differentially Expressed Genes across Pathologic Stages for Cancers. JOURNAL OF ONCOLOGY 2020; 2020:8458190. [PMID: 33273919 PMCID: PMC7676961 DOI: 10.1155/2020/8458190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 10/17/2020] [Accepted: 10/28/2020] [Indexed: 12/09/2022]
Abstract
Given the fact that cancer is a multistage progression process resulting from genetic sequence mutations, the genes whose expression values increase or decrease monotonically across pathologic stages are potentially involved in tumor progression. This may provide insightful clues about how human cancers advance, thereby facilitating more personalized treatments. By replacing the expression values of genes with their GeneRanks, we propose a procedure capable of identifying monotonically differentially expressed genes (MEGs) as the disease advances. Using three real-world gene expression data that cover three distinct cancer types-colon, esophageal, and lung cancers-the proposed procedure has demonstrated excellent performance in detecting the potential MEGs. To conclude, the proposed procedure can detect MEGs across pathologic stages of cancers very efficiently and is thus highly recommended.
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11
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Jordan SE, Saad H, Covarrubias AS, Siemon J, Pearson JM, Slomovitz BM, Huang M, Pinto A, Schlumbrecht M, George SH. mRNA expression in low grade serous ovarian cancer: Results of a nanoString assay in a diverse population. Gynecol Oncol 2020; 159:554-562. [PMID: 32951896 PMCID: PMC8054444 DOI: 10.1016/j.ygyno.2020.08.030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 08/24/2020] [Indexed: 01/31/2023]
Abstract
OBJECTIVE Mutations in the MAP kinase pathway (KRAS, NRAS, BRAF) are common in low grade serous ovarian carcinoma (LGSOC). The effect of these and other mutations on RNA transcription in this disease is poorly understood. Our objective was to describe patterns of somatic mutations and gene transcription in a racially diverse population with LGSOC. METHODS Utilizing an institutional tumor registry, patients with LGSOC were identified and charts were reviewed. RNA was extracted from available tumor tissue. Commercial tumor profiling results were analyzed with PanCancer pathway nanoString mRNA expression data. Along with nanoString n-Solver software, Chi-squared, Fishers Exact, and Cox proportional hazards models were used for statistical analysis, with significance set at p < 0.05. RESULTS 39 patients were identified-20% Black, 43% Hispanic, and 36% non-Hispanic White. 18 patients had commercial somatic DNA test results, and 23 had available tumor tissue for RNA extraction and nanoString analysis. The most common somatic alterations identified was KRAS (11 patients, 61%), followed by ERCC1 and TUBB3 (9 each, 50%). KRAS mutations were less common in smokers (14.3% vs 90.9%, p = 0.002). RNA expression analysis demonstrated a greater than two-fold decrease in expression of HRAS in tumors from older patients (p = 0.04), and a greater than two-fold decrease in the expression of HRAS in recurrent tumors (p = 0.007). No significant differences were seen in somatic testing results, RNA expression analysis, or progression free survival between different racial and ethnic cohorts. CONCLUSIONS Somatic deficiencies in ERCC1, TUBB3, and KRAS are common in LGSOC in a population of minority patients. HRAS demonstrates decreased expression in tumors from older patients and recurrent tumors.
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Affiliation(s)
- Scott E Jordan
- Sylvester Comprehensive Cancer Center, University of Miami, Division of Gynecologic Oncology, USA
| | - Heba Saad
- University of Miami Miller School of Medicine, Department of Pathology, USA
| | - Alex Sanchez Covarrubias
- Sylvester Comprehensive Cancer Center, University of Miami, Division of Gynecologic Oncology, USA
| | - John Siemon
- Sylvester Comprehensive Cancer Center, University of Miami, Division of Gynecologic Oncology, USA
| | - J Matt Pearson
- Sylvester Comprehensive Cancer Center, University of Miami, Division of Gynecologic Oncology, USA
| | - Brian M Slomovitz
- Sylvester Comprehensive Cancer Center, University of Miami, Division of Gynecologic Oncology, USA; Dr. Slomovitz present affiliation: Broward Health, Florida International University Wertheim College Of Medicine, USA
| | - Marilyn Huang
- Sylvester Comprehensive Cancer Center, University of Miami, Division of Gynecologic Oncology, USA
| | - Andre Pinto
- University of Miami Miller School of Medicine, Department of Pathology, USA
| | - Matthew Schlumbrecht
- Sylvester Comprehensive Cancer Center, University of Miami, Division of Gynecologic Oncology, USA
| | - Sophia Hl George
- Sylvester Comprehensive Cancer Center, University of Miami, Division of Gynecologic Oncology, USA.
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Wang M, Lessard SG, Singh P, Pannellini T, Chen T, Rourke BJ, Chowdhury L, Craveiro V, Sculco PK, Meulen MCH, Otero M. Knee fibrosis is associated with the development of osteoarthritis in a murine model of tibial compression. J Orthop Res 2020. [DOI: 10.1002/jor.24815] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Affiliation(s)
- Mengying Wang
- HSS Research Institute Hospital for Special Surgery New York New York
- School of Public Health, Xi'an Jiaotong University Health Science Center Xi'an China
| | | | - Purva Singh
- HSS Research Institute Hospital for Special Surgery New York New York
| | - Tania Pannellini
- HSS Research Institute Hospital for Special Surgery New York New York
| | - Tony Chen
- HSS Research Institute Hospital for Special Surgery New York New York
| | - Brennan J. Rourke
- HSS Research Institute Hospital for Special Surgery New York New York
| | - Luvana Chowdhury
- HSS Research Institute Hospital for Special Surgery New York New York
| | - Vinicius Craveiro
- HSS Research Institute Hospital for Special Surgery New York New York
| | - Peter K. Sculco
- The Stavros Niarchos Foundation Complex Joint Reconstruction Center Hospital for Special Surgery New York New York
| | - Marjolein C. H. Meulen
- HSS Research Institute Hospital for Special Surgery New York New York
- Sibley School of Mechanical and Aerospace Engineering Cornell University Ithaca New York
- Meinig School of Biomedical Engineering Cornell University Ithaca New York
| | - Miguel Otero
- HSS Research Institute Hospital for Special Surgery New York New York
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13
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Comparison of GeneChip, nCounter, and Real-Time PCR-Based Gene Expressions Predicting Locoregional Tumor Control after Primary and Postoperative Radiochemotherapy in Head and Neck Squamous Cell Carcinoma. J Mol Diagn 2020; 22:801-810. [PMID: 32247864 DOI: 10.1016/j.jmoldx.2020.03.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 02/21/2020] [Accepted: 03/10/2020] [Indexed: 02/07/2023] Open
Abstract
This article compares the expression and applicability of biomarkers, from single genes and gene signatures, identified in patients with locally advanced head and neck squamous cell carcinoma using the GeneChip Human Transcriptome Array 2.0, nCounter, and real-time PCR analyses. Two multicenter, retrospective cohorts of patients with head and neck squamous cell carcinoma from the German Cancer Consortium Radiation Oncology Group who received postoperative radiochemotherapy or primary radiochemotherapy were considered. Real-time PCR was performed for a limited number of 38 genes of the cohort who received postoperative radiochemotherapy only. Correlations between the methods were evaluated by the Spearman rank correlation coefficient. Patients were stratified based on the expression of putative cancer stem cell markers, hypoxia-associated gene signatures, and a previously developed seven-gene signature. Locoregional tumor control was compared between these patient subgroups using log-rank tests. Gene expressions obtained from nCounter analyses were moderately correlated to GeneChip analyses (median ρ = approximately 0.68). A higher correlation was obtained between nCounter analyses and real-time PCR (median ρ = 0.84). Significant associations with locoregional tumor control were observed for most of the considered biomarkers evaluated by GeneChip and nCounter analyses. In general, all applied biomarkers (single genes and gene signatures) classified approximately 70% to 85% of the patients similarly. Overall, gene signatures seem to be more robust and had a better transferability among different measurement methods.
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14
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Wang KYX, Menzies AM, Silva IP, Wilmott JS, Yan Y, Wongchenko M, Kefford RF, Scolyer RA, Long GV, Tarr G, Mueller S, Yang JYH. bcGST-an interactive bias-correction method to identify over-represented gene-sets in boutique arrays. Bioinformatics 2020; 35:1350-1357. [PMID: 30215668 DOI: 10.1093/bioinformatics/bty783] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 07/31/2018] [Accepted: 09/11/2018] [Indexed: 02/01/2023] Open
Abstract
MOTIVATION Gene annotation and pathway databases such as Gene Ontology and Kyoto Encyclopaedia of Genes and Genomes are important tools in Gene-Set Test (GST) that describe gene biological functions and associated pathways. GST aims to establish an association relationship between a gene-set of interest and an annotation. Importantly, GST tests for over-representation of genes in an annotation term. One implicit assumption of GST is that the gene expression platform captures the complete or a very large proportion of the genome. However, this assumption is neither satisfied for the increasingly popular boutique array nor the custom designed gene expression profiling platform. Specifically, conventional GST is no longer appropriate due to the gene-set selection bias induced during the construction of these platforms. RESULTS We propose bcGST, a bias-corrected GST by introducing bias-correction terms in the contingency table needed for calculating the Fisher's Exact Test. The adjustment method works by estimating the proportion of genes captured on the array with respect to the genome in order to assist filtration of annotation terms that would otherwise be falsely included or excluded. We illustrate the practicality of bcGST and its stability through multiple differential gene expression analyses in melanoma and the Cancer Genome Atlas cancer studies. AVAILABILITY AND IMPLEMENTATION The bcGST method is made available as a Shiny web application at http://shiny.maths.usyd.edu.au/bcGST/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Kevin Y X Wang
- School of Mathematics and Statistics, The University of Sydney, Sydney, NSW, Australia
| | - Alexander M Menzies
- Melanoma Institute of Australia, Wollstonecraft, NSW, Australia.,Sydney Medical School, The University of Sydney, Sydney, NSW, Australia.,Royal North Shore Hospital, Sydney, NSW, Australia
| | - Ines P Silva
- Melanoma Institute of Australia, Wollstonecraft, NSW, Australia
| | - James S Wilmott
- Melanoma Institute of Australia, Wollstonecraft, NSW, Australia
| | - Yibing Yan
- Genentech Inc, South San Francisco, CA, USA
| | | | - Richard F Kefford
- Melanoma Institute of Australia, Wollstonecraft, NSW, Australia.,Department of Clinical Medicine, Macquarie University, Sydney, NSW, Australia
| | - Richard A Scolyer
- Melanoma Institute of Australia, Wollstonecraft, NSW, Australia.,Sydney Medical School, The University of Sydney, Sydney, NSW, Australia.,Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Georgina V Long
- Melanoma Institute of Australia, Wollstonecraft, NSW, Australia.,Sydney Medical School, The University of Sydney, Sydney, NSW, Australia.,Royal North Shore Hospital, Sydney, NSW, Australia
| | - Garth Tarr
- School of Mathematics and Statistics, The University of Sydney, Sydney, NSW, Australia
| | - Samuel Mueller
- School of Mathematics and Statistics, The University of Sydney, Sydney, NSW, Australia
| | - Jean Y H Yang
- School of Mathematics and Statistics, The University of Sydney, Sydney, NSW, Australia.,The Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
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15
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Multi-gene technical assessment of qPCR and NanoString n-Counter analysis platforms in cynomolgus monkey cardiac allograft recipients. Cell Immunol 2019; 347:104019. [PMID: 31744596 DOI: 10.1016/j.cellimm.2019.104019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 11/06/2019] [Accepted: 11/07/2019] [Indexed: 12/17/2022]
Abstract
Quantitative gene expression profiling of cardiac allografts characterizes the phenotype of the alloimmune response, yields information regarding differential effects that may be associated with various anti-rejection drug regimens, and generates testable hypotheses regarding the pathogenesis of the chronic rejection lesions typically observed in non-human primate heart transplant models. The goal of this study was to assess interplatform performance and variability between the relatively novel NanoString nCounter Analysis System, ΔΔCT (relative) RT-qPCR, and standard curve (absolute) RT-qPCR utilizing cynomolgus monkey cardiac allografts. Methods for RNA isolation and preamplification were also systematically evaluated and effective methods are proposed. In this study, we demonstrate strong correlation between the two RT-qPCR methods, but variable and, at times, weak correlation between RT-qPCR and NanoString. NanoString fold change results demonstrate less sensitivity to small changes in gene expression than RT-qPCR. These findings appear to be driven by technical aspects of each platform that influence the conditions under which each technique is ideal. Collectively, our data contribute to the general effort to optimally utilize gene expression profiling techniques, not only for transplanted tissues, but for many other applications where accurate rank-order of gene expression versus precise quantification of absolute gene transcript number may be relatively valuable.
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16
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Ito T, Matoba R, Maekawa H, Sakurada M, Kushida T, Orita H, Wada R, Sato K. Detection of gene mutations in gastric cancer tissues using a commercial sequencing panel. Mol Clin Oncol 2019; 11:455-460. [PMID: 31620276 PMCID: PMC6787944 DOI: 10.3892/mco.2019.1926] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 08/26/2019] [Indexed: 12/24/2022] Open
Abstract
Predicting malignancy is important for adequate adjuvant therapy in patients with cancer. Due to cancer being a genetic disease, the detection of gene mutations could be helpful in predicting the prognosis and efficacy of drugs. Gastric cancer is the fifth most common cancer and is the third leading cause of cancer associated mortality worldwide. Mutations in genes may correlate with clinical information in patients with gastric cancer after surgery and, therefore, may be useful for predicting the prognosis of this disease. In the present study, to assess the usefulness of a commercial sequencing panel, TruSeq® Amplicon-Cancer Panel (Illumina), using a next-generation sequencer (Illumina MiSeq), mutation analysis of fresh as well as formalin-fixed paraffin-embedded (FFPE) gastric cancer tissues was performed retrospectively. The study group comprised of 4 patients who underwent gastrectomy for gastric cancer. Cancer and normal stomach tissues were collected immediately following surgical removal. Thereafter, the specimens were fixed in 10% neutral formalin for 24–72 h. Normal and FFPE cancer tissues were histologically examined and confirmed. A total of 3 mutations were identified in the driver genes (KRAS, TP53 and APC) in cancer tissues from 2 of the 4 patients, using fresh samples. In addition, FFPE samples were analysed for the same tissues and the same results were obtained by setting the threshold for the percentage of the mutation rate to avoid detection of pseudo-positive mutations. In conclusion, the sequencing analysis using FFPE-derived DNA samples was successfully performed.
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Affiliation(s)
- Tomoaki Ito
- Department of Surgery, Juntendo University Shizuoka Hospital, Juntendo University School of Medicine, Shizuoka 410-2295, Japan
| | - Ryo Matoba
- DNA Chip Research Inc., Tokyo 105-0022, Japan
| | - Hiroshi Maekawa
- Department of Surgery, Juntendo University Shizuoka Hospital, Juntendo University School of Medicine, Shizuoka 410-2295, Japan
| | - Mutsumi Sakurada
- Department of Surgery, Juntendo University Shizuoka Hospital, Juntendo University School of Medicine, Shizuoka 410-2295, Japan
| | - Tomoyuki Kushida
- Department of Surgery, Juntendo University Shizuoka Hospital, Juntendo University School of Medicine, Shizuoka 410-2295, Japan
| | - Hajime Orita
- Department of Surgery, Juntendo University Shizuoka Hospital, Juntendo University School of Medicine, Shizuoka 410-2295, Japan
| | - Ryo Wada
- Department of Pathology, Juntendo University Shizuoka Hospital, Juntendo University School of Medicine, Shizuoka 410-2295, Japan
| | - Koichi Sato
- Department of Surgery, Juntendo University Shizuoka Hospital, Juntendo University School of Medicine, Shizuoka 410-2295, Japan
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17
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Microenvironmental immune cell signatures dictate clinical outcomes for PTCL-NOS. Blood Adv 2019; 2:2242-2252. [PMID: 30194138 DOI: 10.1182/bloodadvances.2018018754] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 07/23/2018] [Indexed: 12/23/2022] Open
Abstract
Peripheral T-cell lymphoma (PTCL), not otherwise specified (PTCL-NOS) is among the most common disease subtypes of PTCL, one that exhibits heterogeneous clinicopathological features. Although multiple disease-stratification models, including the cell-of-origin or gene-expression profiling methods, have been proposed for this condition, their clinical significance remains unclear. To establish a clinically meaningful stratification model, we analyzed gene-expression signatures of tumors and tumor-infiltrating immune cells using the nCounter system, which enables accurate quantification of low abundance and/or highly fragmented transcripts. To do so, we assessed transcripts of 120 genes related to cancer or immune cells using tumor samples from 68 newly diagnosed PTCL-NOS patients and validated findings by immunofluorescence in tumor sections. We show that gene-expression signatures representing tumor-infiltrating immune cells, but not those of cancerous T cells, dictate patient clinical outcomes. Cases exhibiting both B-cell and dendritic cell (DC) signatures (BD subgroup) showed favorable clinical outcomes, whereas those exhibiting neither B-cell nor DC signatures (non-BD subgroup) showed extremely poor prognosis. Notably, half of the non-BD cases exhibited a macrophage signature, and macrophage infiltration was evident in those cases, as revealed by immunofluorescence. Importantly, tumor-infiltrating macrophages expressed the immune-checkpoint molecules programmed death ligand 1/2 and indoleamine 2, 3-dioxygenase 1 at high levels, suggesting that checkpoint inhibitors could serve as therapeutic options for patients in this subgroup. Our study identifies clinically distinct subgroups of PTCL-NOS and suggests a novel therapeutic strategy for 1 subgroup associated with a poor prognosis. Our data also suggest functional interactions between cancerous T cells and tumor-infiltrating immune cells potentially relevant to PTCL-NOS pathogenesis.
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18
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Picornell AC, Echavarria I, Alvarez E, López-Tarruella S, Jerez Y, Hoadley K, Parker JS, del Monte-Millán M, Ramos-Medina R, Gayarre J, Ocaña I, Cebollero M, Massarrah T, Moreno F, García Saenz JA, Gómez Moreno H, Ballesteros A, Ruiz Borrego M, Perou CM, Martin M. Breast cancer PAM50 signature: correlation and concordance between RNA-Seq and digital multiplexed gene expression technologies in a triple negative breast cancer series. BMC Genomics 2019; 20:452. [PMID: 31159741 PMCID: PMC6547580 DOI: 10.1186/s12864-019-5849-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 05/27/2019] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Full RNA-Seq is a fundamental research tool for whole transcriptome analysis. However, it is too costly and time consuming to be used in routine clinical practice. We evaluated the transcript quantification agreement between RNA-Seq and a digital multiplexed gene expression platform, and the subtype call after running the PAM50 assay in a series of breast cancer patients classified as triple negative by IHC/FISH. The goal of this study is to analyze the concordance between both expression platforms overall, and for calling PAM50 triple negative breast cancer intrinsic subtypes in particular. RESULTS The analyses were performed in paraffin-embedded tissues from 96 patients recruited in a multicenter, prospective, non-randomized neoadjuvant triple negative breast cancer trial (NCT01560663). Pre-treatment core biopsies were obtained following clinical practice guidelines and conserved as FFPE for further RNA extraction. PAM50 was performed on both digital multiplexed gene expression and RNA-Seq platforms. Subtype assignment was based on the nearest centroid classification following this procedure for both platforms and it was concordant on 96% of the cases (N = 96). In four cases, digital multiplexed gene expression analysis and RNA-Seq were discordant. The Spearman correlation to each of the centroids and the risk of recurrence were above 0.89 in both platforms while the agreement on Proliferation Score reached up to 0.97. In addition, 82% of the individual PAM50 genes showed a correlation coefficient > 0.80. CONCLUSIONS In our analysis, the subtype calling in most of the samples was concordant in both platforms and the potential discordances had reduced clinical implications in terms of prognosis. If speed and cost are the main driving forces then the preferred technique is the digital multiplexed platform, while if whole genome patterns and subtype are the driving forces, then RNA-Seq is the preferred method.
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Affiliation(s)
- A. C. Picornell
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Doctor Esquerdo 46, 28007 Madrid, Spain
| | - I. Echavarria
- Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - E. Alvarez
- Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Doctor Esquerdo 46, 28007 Madrid, Spain
| | - S. López-Tarruella
- Medical Oncology Service, Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM). CiberOnc, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Y. Jerez
- Medical Oncology Service, Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM). CiberOnc, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - K. Hoadley
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - J. S. Parker
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC USA
| | - M. del Monte-Millán
- Medical Oncology Service, Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM). CiberOnc, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - R. Ramos-Medina
- Medical Oncology Service, Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM). CiberOnc, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - J. Gayarre
- Medical Oncology Service, Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM). CiberOnc, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - I. Ocaña
- Medical Oncology Service, Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM). CiberOnc, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - M. Cebollero
- Anatomical Pathology Service, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - T. Massarrah
- Medical Oncology Service, Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM). CiberOnc, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - F. Moreno
- Medical Oncology Service, Hospital Universitario Clínico San Carlos, Madrid, Spain
| | - J. A. García Saenz
- Medical Oncology Service, Hospital Universitario Clínico San Carlos, Madrid, Spain
| | - H. Gómez Moreno
- Medicina Oncológic, Instituto Nacional de Enfermedades Neoplásicas (INEN), Lima, Peru
| | - A. Ballesteros
- Medical Oncology Service, Hospital Universitario de La Princesa, Madrid, Spain
| | | | - C. M. Perou
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC USA
| | - M. Martin
- Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón (IiSGM), Universidad Complutense, CiberOnc, GEICAM, Madrid, Spain
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19
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Expression Concordance of 325 Novel RNA Biomarkers between Data Generated by NanoString nCounter and Affymetrix GeneChip. DISEASE MARKERS 2019; 2019:1940347. [PMID: 31217830 PMCID: PMC6536986 DOI: 10.1155/2019/1940347] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 02/09/2019] [Accepted: 02/15/2019] [Indexed: 02/06/2023]
Abstract
Background With the development of new drug combinations and targeted treatments for multiple types of cancer, the ability to stratify categories of patient populations and to develop companion diagnostics has become increasingly important. A panel of 325 RNA biomarkers was selected based on cancer-related biological processes of healthy cells and gene expression changes over time during nonmalignant epithelial cell organization. This "cancer in reverse" approach resulted in a panel of biomarkers relevant for at least 7 cancer types, providing gene expression profiles representing key cellular signaling pathways beyond mutations in "driver genes." Objective. To further investigate this biomarker panel, the objective of the current study is to (1) validate the assay reproducibility for the 325 RNA biomarkers and (2) compare gene expression profiles side by side using two technology platforms. Methods and Results We have mapped the 325 RNA transcripts and in a custom NanoString nCounter expression panel to be compared to all potential probe sets in the Affymetrix Human Genome U133 Plus 2.0. The experiments were conducted with 10 unique biological formalin-fixed paraffin-embedded (FFPE) breast tumor samples. Each site extracted RNA from four sections of 10-micron thick FFPE tissue over three different days by two different operators using an optimized standard operating procedure and quality control criteria. Samples were analyzed using mas5 in BioConductor and NanoStringNorm in R. Pearson correlation showed reproducibility between sites for all 60 samples with r = 0.995 for Affymetrix and r = 0.999 for NanoString. Correlation in multiple days and multiple users was for Affymetrix r = (0.962 - 0.999) and for NanoString r = (0.982 - 0.991). Conclusion The 325 RNA biomarkers showed reproducibility in two technology platforms with moderate to high concordance. Future directions include performing clinical validation studies and generating rationale for patient selection in clinical trials using the technically validated assay.
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20
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Piskol R, Huw L, Sergin I, Kljin C, Modrusan Z, Kim D, Kljavin N, Tam R, Patel R, Burton J, Penuel E, Qu X, Koeppen H, Sumiyoshi T, de Sauvage F, Lackner MR, de Sousa e Melo F, Kabbarah O. A Clinically Applicable Gene-Expression Classifier Reveals Intrinsic and Extrinsic Contributions to Consensus Molecular Subtypes in Primary and Metastatic Colon Cancer. Clin Cancer Res 2019; 25:4431-4442. [DOI: 10.1158/1078-0432.ccr-18-3032] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 01/29/2019] [Accepted: 04/15/2019] [Indexed: 01/10/2023]
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21
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Fontana E, Eason K, Cervantes A, Salazar R, Sadanandam A. Context matters-consensus molecular subtypes of colorectal cancer as biomarkers for clinical trials. Ann Oncol 2019; 30:520-527. [PMID: 30796810 PMCID: PMC6503627 DOI: 10.1093/annonc/mdz052] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The Colorectal Cancer Subtyping Consortium identified four gene expression consensus molecular subtypes, CMS1 (immune), CMS2 (canonical), CMS3 (metabolic), and CMS4 (mesenchymal), using multiple microarray or RNA-sequencing datasets of primary tumor samples mainly from early stage colon cancer patients. Consequently, rectal tumors and stage IV tumors (possibly reflective of more aggressive disease) were underrepresented, and no chemo- and/or radiotherapy pretreated samples or metastatic lesions were included. In view of their possible effect on gene expression and consequently subtype classification, sample source and treatments received by the patients before collection must be carefully considered when applying the classifier to new datasets. Recently, several correlative analyses of clinical trials demonstrated the applicability of this classification to the metastatic setting, confirmed the prognostic value of CMS subtypes after relapse and hinted at differential sensitivity to treatments. Here, we discuss why contexts and equivocal factors need to be taken into account when analyzing clinical trial data, including potential selection biases, type of platform, and type of algorithm used for subtype prediction. This perspective article facilitates both our clinical and research understanding of the application of this classifier to expedite subtype-based clinical trials.
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Affiliation(s)
- E Fontana
- Division of Molecular Pathology, The Institute of Cancer Research, London; Centre for Molecular Pathology, The Royal Marsden NHS Foundation Trust, London, UK
| | - K Eason
- Division of Molecular Pathology, The Institute of Cancer Research, London
| | - A Cervantes
- CIBERONC, Department of Medical Oncology, Biomedical Research Institute INCLIVA, University of Valencia, Valencia
| | - R Salazar
- Institut Catala d'Oncologia, L'Institut d'Investigació Biomèdica de Bellvitge, Barcelona, Spain
| | - A Sadanandam
- Division of Molecular Pathology, The Institute of Cancer Research, London; Centre for Molecular Pathology, The Royal Marsden NHS Foundation Trust, London, UK.
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22
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Narrandes S, Xu W. Gene Expression Detection Assay for Cancer Clinical Use. J Cancer 2018; 9:2249-2265. [PMID: 30026820 PMCID: PMC6036716 DOI: 10.7150/jca.24744] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 05/15/2018] [Indexed: 12/23/2022] Open
Abstract
Cancer is a genetic disease where genetic variations cause abnormally functioning genes that appear to alter expression. Proteins, the final products of gene expression, determine the phenotypes and biological processes. Therefore, detecting gene expression levels can be used for cancer diagnosis, prognosis, and treatment prediction in a clinical setting. In this review, we investigated six gene expression assay systems (qRT-PCR, DNA microarray, nCounter, RNA-Seq, FISH, and tissue microarray) that are currently being used in clinical cancer studies. Some of these methods are also commonly used in a modified way; for example, detection of DNA content or protein expression. Herein, we discuss their principles, sample preparation, design, quantification and sensitivity, data analysis, time for sample preparation and processing, and cost. We also compared these methods according to their sample selection, particularly for the feasibility of using formalin-fixed paraffin-embedded (FFPE) samples, which are routinely archived for clinical cancer studies. We intend to provide a guideline for choosing an assay method with respect to its oncological applications in a clinical setting.
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Affiliation(s)
- Shavira Narrandes
- Departments of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Canada.,Research Institute of Oncology and Hematology, CancerCare Manitoba, Winnipeg, Canada
| | - Wayne Xu
- Departments of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Canada.,Research Institute of Oncology and Hematology, CancerCare Manitoba, Winnipeg, Canada.,College of Pharmacy, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Canada
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23
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Yu T, Zhang H, Qi H. Transcriptome profiling analysis reveals biomarkers in colon cancer samples of various differentiation. Oncol Lett 2018; 16:48-54. [PMID: 29928385 PMCID: PMC6006489 DOI: 10.3892/ol.2018.8668] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Accepted: 10/13/2018] [Indexed: 12/17/2022] Open
Abstract
The aim of the present study was to investigate more colon cancer-related genes in different stages. Gene expression profile E-GEOD-62932 was extracted for differentially expressed gene (DEG) screening. Series test of cluster analysis was used to obtain significant trending models. Based on the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes databases, functional and pathway enrichment analysis were processed and a pathway relation network was constructed. Gene co-expression network and gene signal network were constructed for common DEGs. The DEGs with the same trend were clustered and in total, 16 clusters with statistical significance were obtained. The screened DEGs were enriched into small molecule metabolic process and metabolic pathways. The pathway relation network was constructed with 57 nodes. A total of 328 common DEGs were obtained. Gene signal network was constructed with 71 nodes. Gene co-expression network was constructed with 161 nodes and 211 edges. ABCD3, CPT2, AGL and JAM2 are potential biomarkers for the diagnosis of colon cancer.
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Affiliation(s)
- Tonghu Yu
- Department of Gastrointestinal Surgery, The Affiliated Yantai Yuhuangding Hospital of Qingdao University Medical College, Yantai, Shandong 264000, P.R. China
| | - Huaping Zhang
- Department of Gastrointestinal Surgery, The Affiliated Yantai Yuhuangding Hospital of Qingdao University Medical College, Yantai, Shandong 264000, P.R. China
| | - Hong Qi
- Department of General Surgery, Qingdao Municipal Hospital, Qingdao, Shandong 266071, P.R. China
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24
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Chen R, Guan Q, Cheng J, He J, Liu H, Cai H, Hong G, Zhang J, Li N, Ao L, Guo Z. Robust transcriptional tumor signatures applicable to both formalin-fixed paraffin-embedded and fresh-frozen samples. Oncotarget 2018; 8:6652-6662. [PMID: 28036264 PMCID: PMC5351660 DOI: 10.18632/oncotarget.14257] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 12/02/2016] [Indexed: 12/19/2022] Open
Abstract
Formalin-fixed paraffin-embedded (FFPE) samples represent a valuable resource for clinical researches. However, FFPE samples are usually considered an unreliable source for gene expression analysis due to the partial RNA degradation. In this study, through comparing gene expression profiles between FFPE samples and paired fresh-frozen (FF) samples for three cancer types, we firstly showed that expression measurements of thousands of genes had at least two-fold change in FFPE samples compared with paired FF samples. Therefore, for a transcriptional signature based on risk scores summarized from the expression levels of the signature genes, the risk score thresholds trained from FFPE (or FF) samples could not be applied to FF (or FFPE) samples. On the other hand, we found that more than 90% of the relative expression orderings (REOs) of gene pairs in the FF samples were maintained in their paired FFPE samples and largely unaffected by the storage time. The result suggested that the REOs of gene pairs were highly robust against partial RNA degradation in FFPE samples. Finally, as a case study, we developed a REOs-based signature to distinguish liver cirrhosis from hepatocellular carcinoma (HCC) using FFPE samples. The signature was validated in four datasets of FFPE samples and eight datasets of FF samples. In conclusion, the valuable FFPE samples can be fully exploited to identify REOs-based diagnostic and prognostic signatures which could be robustly applicable to both FF samples and FFPE samples with degraded RNA.
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Affiliation(s)
- Rou Chen
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, Fujian Medical University, Fuzhou 350001, China
| | - Qingzhou Guan
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, Fujian Medical University, Fuzhou 350001, China
| | - Jun Cheng
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, Fujian Medical University, Fuzhou 350001, China
| | - Jun He
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, Fujian Medical University, Fuzhou 350001, China
| | - Huaping Liu
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, Fujian Medical University, Fuzhou 350001, China
| | - Hao Cai
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, Fujian Medical University, Fuzhou 350001, China
| | - Guini Hong
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, Fujian Medical University, Fuzhou 350001, China
| | - Jiahui Zhang
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, Fujian Medical University, Fuzhou 350001, China
| | - Na Li
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, Fujian Medical University, Fuzhou 350001, China
| | - Lu Ao
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, Fujian Medical University, Fuzhou 350001, China
| | - Zheng Guo
- Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, Fujian Medical University, Fuzhou 350001, China
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Targeted Transcriptional Profiling of Kidney Transplant Biopsies. Kidney Int Rep 2018; 3:722-731. [PMID: 29854981 PMCID: PMC5976814 DOI: 10.1016/j.ekir.2018.01.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 01/30/2018] [Indexed: 02/06/2023] Open
Abstract
Introduction Studies are needed to assess the quality of transcriptome analysis in paired human tissue samples preserved by different methods and different gene amplification platforms to enable data comparisons across experimenters. Methods RNA was extracted from kidney biopsies, either submerged in RNA-stabilizing solution (RSS) or stored in formalin-fixed, paraffin-embedded (FFPE) blocks. RNA quality and integrity were compared. Gene expression of the common rejection module and other immune cell genes were quantified for both tissue preservation methods in the same sample using conventional quantitative polymerase chain reaction (QPCR) by 2 different commercial platforms, (fluidigm [FD]) or barcoded-oligos (nanostring [NS]). Results RNA quality was inferior in FFPE tissues. Despite this, gene expression for 19 measured genes on the same sample, stored in FFPE or RSS, were strongly correlated on the FD (r = 0.81) or NS platforms (r = 0.82). For the same samples, interplatform gene expression correlations were excellent (r = 0.80) for RSS and moderate (r = 0.66) for FFPE. Significant differences in gene expression were confirmed on both platforms (FD: P = 1.1E-03; NS: P = 2.5E-04) for biopsy-confirmed acute rejection. Conclusion Our study provided supportive evidence that despite a low RNA quality of archival FFPE kidney transplantation tissue, small quantities of this tissue can be obtained from existing paraffin blocks to provide a viable and rich biospecimen source for focused gene expression assays. In addition, reliable and reproducible gene expression evaluation can be performed on these FFPE tissues using either a QPCR-based or a barcoded-oligo approach, which provides opportunities for collaborative analytics.
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Abstract
Anaplastic Large Cell Lymphoma (ALCL) is a clinical and biological heterogeneous disease including systemic ALK positive and ALK negative entities. Whereas ALK positive ALCLs are molecularly characterized and readily diagnosed, specific immunophenotypic or genetic features to define ALK negative ALCL are missing, and their distinction from other T-cell non-Hodgkin lymphomas (T-NHLs) can be controversial. In recent years, great advances have been made in dissecting the heterogeneity of ALK negative ALCLs and in providing new diagnostic and treatment options for these patients. A new revision of the World Health Organization (WHO) classification promoted ALK negative ALCL to a definite entity that includes cytogenetic subsets with prognostic implications. However, a further understanding of the genetic landscape of ALK negative ALCL is required to dictate more effective therapeutic strategies specifically tailored for each subgroup of patients.
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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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Tsang HF, Xue VW, Koh SP, Chiu YM, Ng LPW, Wong SCC. NanoString, a novel digital color-coded barcode technology: current and future applications in molecular diagnostics. Expert Rev Mol Diagn 2016; 17:95-103. [DOI: 10.1080/14737159.2017.1268533] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Hin-Fung Tsang
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Vivian Weiwen Xue
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Su-Pin Koh
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Ya-Ming Chiu
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Lawrence Po-Wah Ng
- Department of Pathology, Queen Elizabeth Hospital, Hospital Authority, Hong Kong Special Administrative Region, China
| | - Sze-Chuen Cesar Wong
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
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Evaluation of frozen tissue-derived prognostic gene expression signatures in FFPE colorectal cancer samples. Sci Rep 2016; 6:33273. [PMID: 27623752 PMCID: PMC5021945 DOI: 10.1038/srep33273] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 08/24/2016] [Indexed: 12/31/2022] Open
Abstract
Defining molecular features that can predict the recurrence of colorectal cancer (CRC) for stage II-III patients remains challenging in cancer research. Most available clinical samples are Formalin-Fixed, Paraffin-Embedded (FFPE). NanoString nCounter® and Affymetrix GeneChip® Human Transcriptome Array 2.0 (HTA) are the two platforms marketed for high-throughput gene expression profiling for FFPE samples. In this study, to evaluate the gene expression of frozen tissue-derived prognostic signatures in FFPE CRC samples, we evaluated the expression of 516 genes from published frozen tissue-derived prognostic signatures in 42 FFPE CRC samples measured by both platforms. Based on HTA platform-derived data, we identified both gene (99 individual genes, FDR < 0.05) and gene set (four of the six reported multi-gene signatures with sufficient information for evaluation, P < 0.05) expression differences associated with survival outcomes. Using nCounter platform-derived data, one of the six multi-gene signatures (P < 0.05) but no individual gene was associated with survival outcomes. Our study indicated that sufficiently high quality RNA could be obtained from FFPE tumor tissues to detect frozen tissue-derived prognostic gene expression signatures for CRC patients.
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