دورية أكاديمية
أعرض في EDS

Radiogenomic Analysis of F-18-Fluorodeoxyglucose Positron Emission Tomography and Gene Expression Data Elucidates the Epidemiological Complexity of Colorectal Cancer Landscape.

التفاصيل البيبلوغرافية
العنوان: Radiogenomic Analysis of F-18-Fluorodeoxyglucose Positron Emission Tomography and Gene Expression Data Elucidates the Epidemiological Complexity of Colorectal Cancer Landscape.
المؤلفون: Vlachavas EI; Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece.; Department of Molecular Biology and Genetics, Democritus University of Thrace, 68100 Dragana, Greece.; Enios Applications Private Limited Company, A17671 Athens, Greece., Pilalis E; Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece.; Enios Applications Private Limited Company, A17671 Athens, Greece., Papadodima O; Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece., Koczan D; Core Facility Micro-Array-Technology, Center of Medical Research, University of Rostock, Germany., Willis S; Surgical Clinic A, Klinikum Ludwigshafen, Germany., Klippel S; Surgical Clinic A, Klinikum Ludwigshafen, Germany., Cheng C; Clinical Cooperation Unit Nuclear Medicine, German Cancer Research Center, Heidelberg, Germany., Pan L; Clinical Cooperation Unit Nuclear Medicine, German Cancer Research Center, Heidelberg, Germany., Sachpekidis C; Clinical Cooperation Unit Nuclear Medicine, German Cancer Research Center, Heidelberg, Germany., Pintzas A; Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece., Gregoriou V; Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece., Dimitrakopoulou-Strauss A; Clinical Cooperation Unit Nuclear Medicine, German Cancer Research Center, Heidelberg, Germany., Chatziioannou A; Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece.; Enios Applications Private Limited Company, A17671 Athens, Greece.
المصدر: Computational and structural biotechnology journal [Comput Struct Biotechnol J] 2019 Jan 25; Vol. 17, pp. 177-185. Date of Electronic Publication: 2019 Jan 25 (Print Publication: 2019).
نوع المنشور: Journal Article
اللغة: English
بيانات الدورية: Publisher: Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology Country of Publication: Netherlands NLM ID: 101585369 Publication Model: eCollection Cited Medium: Print ISSN: 2001-0370 (Print) Linking ISSN: 20010370 NLM ISO Abbreviation: Comput Struct Biotechnol J Subsets: PubMed not MEDLINE
أسماء مطبوعة: Publication: Amsterdam : Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology
Original Publication: Gothenburg, Sweden : Research Network of Computational and Structural Biotechnology
مستخلص: Purpose: Transcriptomic profiling has enabled the neater genomic characterization of several cancers, among them colorectal cancer (CRC), through the derivation of genes with enhanced causal role and informative gene sets. However, the identification of small-sized gene signatures, which can serve as potential biomarkers in CRC, remains challenging, mainly due to the great genetic heterogeneity of the disease.
Methods: We developed and exploited an analytical framework for the integrative analysis of CRC datasets, encompassing transcriptomic data and positron emission tomography (PET) measurements. Profiling data comprised two microarray datasets, pertaining biopsy specimen from 30 untreated patients with primary CRC, coupled by their F-18-Fluorodeoxyglucose (FDG) PET values, using tracer kinetic analysis measurements. The computational framework incorporates algorithms for semantic processing, multivariate analysis, data mining and dimensionality reduction.
Results: Transcriptomic and PET data feature sets, were evaluated for their discrimination performance between primary colorectal adenocarcinomas and adjacent normal mucosa. A composite signature was derived, pertaining 12 features: 7 genes and 5 PET variables. This compact signature manifests superior performance in classification accuracy, through the integration of gene expression and PET data.
Conclusions: This work represents an effort for the integrative, multilayered, signature-oriented analysis of CRC, in the context of radio-genomics, inferring a composite signature with promising results for patient stratification.
References: Nucleic Acids Res. 2005 Nov 10;33(20):e175. (PMID: 16284200)
Eur J Nucl Med Mol Imaging. 2007 Jun;34(6):868-77. (PMID: 17219134)
J Nucl Med. 2008 Aug;49(8):1238-44. (PMID: 18632818)
Clin Cancer Res. 2008 Nov 1;14(21):6751-60. (PMID: 18980968)
J Stat Softw. 2010;33(1):1-22. (PMID: 20808728)
Mol Imaging Biol. 2011 Dec;13(6):1290-300. (PMID: 21153447)
Cell. 2011 Mar 4;144(5):646-74. (PMID: 21376230)
DNA Cell Biol. 2012 Jan;31(1):74-9. (PMID: 21711092)
Cancer Cell. 2012 Mar 20;21(3):297-308. (PMID: 22439925)
Nature. 2012 Jul 18;487(7407):330-7. (PMID: 22810696)
Nat Rev Cancer. 2013 Apr;13(4):227-32. (PMID: 23446547)
Cancer Res. 2013 Sep 15;73(18):5754-63. (PMID: 24008320)
Am J Nucl Med Mol Imaging. 2013 Sep 19;3(5):417-24. (PMID: 24116350)
Front Physiol. 2014 Apr 16;5:130. (PMID: 24795638)
Dis Markers. 2014;2014:634123. (PMID: 24959000)
Am J Nucl Med Mol Imaging. 2014 Aug 15;4(5):471-82. (PMID: 25143865)
AJR Am J Roentgenol. 2014 Nov;203(5):1109-19. (PMID: 25341152)
PLoS One. 2014 Nov 25;9(11):e113071. (PMID: 25423035)
Nucleic Acids Res. 2015 Apr 20;43(7):e47. (PMID: 25605792)
Nat Methods. 2015 Feb;12(2):115-21. (PMID: 25633503)
Front Oncol. 2015 Feb 02;5:13. (PMID: 25699236)
Nat Med. 2015 Nov;21(11):1350-6. (PMID: 26457759)
Nucleic Acids Res. 2016 May 5;44(8):e71. (PMID: 26704973)
Sci Rep. 2016 May 16;6:25795. (PMID: 27180817)
Bioinformatics. 2016 Sep 15;32(18):2847-9. (PMID: 27207943)
Nat Rev Cancer. 2017 Feb;17(2):79-92. (PMID: 28050011)
Sci Rep. 2017 Jan 04;7:39999. (PMID: 28051182)
Science. 2017 Aug 18;357(6352):. (PMID: 28818916)
Proc Natl Acad Sci U S A. 2017 Sep 12;114(37):E7697-E7706. (PMID: 28847964)
Oncotarget. 2017 May 15;8(37):61107-61117. (PMID: 28977850)
EMBO Mol Med. 2018 Mar;10(3):. (PMID: 29311133)
Cell Metab. 2018 Apr 3;27(4):828-842.e7. (PMID: 29551590)
فهرسة مساهمة: Keywords: 18F-FDG PET; ACADM, Acyl-Coenzyme A Dehydrogenase; AUC, Area Under the Curve; CCT7, Chaperonin Containing TCP1 Subunit 7; CD44, CD44 Molecule (Indian Blood Group); CRC, Colorectal cancer; Colorectal cancer; DE, Differentially Expressed; FD, Fractal Dimension; FDG, F-18-Fluorodeoxyglucose; GDC, Genomics Data Commons; GEO, Gene Expression Omnibus; GSTP1, Glutathione S-Transferase Pi 1; KIT, Proto-Oncogene Receptor Tyrosine Kinase; Lasso, least absolute shrinkage and selection operator; MFA, Multiple Factor Analysis; Microarray analysis; PCs, Principal Components; PET, Positron Emission Tomography; ROC, Receiver-operator Characteristic curve; Radiogenomics; SUV, Standardized Uptake Value; TCGA; TCGA-COAD, The Cancer Genome Atlas-Colon Adenocarcinoma; Translational bioinformatics
تواريخ الأحداث: Date Created: 20190228 Latest Revision: 20220408
رمز التحديث: 20240628
مُعرف محوري في PubMed: PMC6374701
DOI: 10.1016/j.csbj.2019.01.007
PMID: 30809322
قاعدة البيانات: MEDLINE
الوصف
تدمد:2001-0370
DOI:10.1016/j.csbj.2019.01.007