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Nevone A, Lattarulo F, Russo M, Panno G, Milani P, Basset M, Avanzini MA, Merlini G, Palladini G, Nuvolone M. A Strategy for the Selection of RT-qPCR Reference Genes Based on Publicly Available Transcriptomic Datasets. Biomedicines 2023; 11:1079. [PMID: 37189697 PMCID: PMC10135859 DOI: 10.3390/biomedicines11041079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/23/2023] [Accepted: 03/27/2023] [Indexed: 04/05/2023] Open
Abstract
In the next-generation sequencing era, RT-qPCR is still widely employed to quantify levels of nucleic acids of interest due to its popularity, versatility, and limited costs. The measurement of transcriptional levels through RT-qPCR critically depends on reference genes used for normalization. Here, we devised a strategy to select appropriate reference genes for a specific clinical/experimental setting based on publicly available transcriptomic datasets and a pipeline for RT-qPCR assay design and validation. As a proof-of-principle, we applied this strategy to identify and validate reference genes for transcriptional studies of bone-marrow plasma cells from patients with AL amyloidosis. We performed a systematic review of published literature to compile a list of 163 candidate reference genes for RT-qPCR experiments employing human samples. Next, we interrogated the Gene Expression Omnibus to assess expression levels of these genes in published transcriptomic studies on bone-marrow plasma cells from patients with different plasma cell dyscrasias and identified the most stably expressed genes as candidate normalizing genes. Experimental validation on bone-marrow plasma cells showed the superiority of candidate reference genes identified through this strategy over commonly employed "housekeeping" genes. The strategy presented here may apply to other clinical and experimental settings for which publicly available transcriptomic datasets are available.
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Affiliation(s)
- Alice Nevone
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Francesca Lattarulo
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Monica Russo
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Giada Panno
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Paolo Milani
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Marco Basset
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Maria Antonietta Avanzini
- Pediatric Hematology Oncology, Cell Factory, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Giampaolo Merlini
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Giovanni Palladini
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Mario Nuvolone
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
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2
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Structural Characterization of Polysaccharide Derived from Gastrodia elata and Its Immunostimulatory Effect on RAW264.7 Cells. Molecules 2022; 27:molecules27228059. [PMID: 36432165 PMCID: PMC9694387 DOI: 10.3390/molecules27228059] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/17/2022] [Accepted: 11/18/2022] [Indexed: 11/22/2022] Open
Abstract
A polysaccharide from Gastrodia elata (named GEP-1) was isolated with a DEAE-52 column and Sephadex G-100 column. The structural characteristics showed that GEP-1 was mainly composed of glucose (92.04%), galactose (4.79%) and arabinose (2.19%) with a molecular weight of 76.444 kDa. The polydispersity (Mw/Mn) of GEP-1 was 1.25, indicating that the distribution of molar mass (Mw) was relatively narrow, which suggested that GEP-1 was a homogeneous polysaccharide. Moreover, the molecular conformation plot of the root mean square (RMS) radius (<rg2> 1/2) versus Mw yielded a line with a slope less than 0.33 (0.15 ± 0.02), displaying that GEP-1 is a compact and curly spherical molecule in NaNO3 aqueous solution. NMR and methylation analyses revealed that the main chain structure of GEP-1 was α-(1→4)-glucans. Furthermore, it was proven that GEP-1 possessed cytoproliferative and enhancing phagocytic activities and induced cytokine (TNF-α, IL1-β) and nitric oxide (NO) release in macrophages by upregulating the related gene expression. In addition, the RNA-seq results suggested that the GEP-1-induced immunomodulatory effect was mainly caused by activation of the NF-κB signaling pathway, which was further verified by NF-κB ELISA and pathway inhibition assays. As a result, GEP-1 exhibits the potential to be developed as a novel cheap immunostimulant without obvious toxicity.
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3
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Lim JM, Tevatia R, Saraf RF. Quantitative PCR of Small Nucleic Acids: Size Matters. ChemistrySelect 2021; 6:2975-2979. [PMID: 36819227 PMCID: PMC9937448 DOI: 10.1002/slct.202100807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 03/19/2021] [Indexed: 11/06/2022]
Abstract
Quantitative dysregulation in small nucleic acids (NA), such as microRNA (miRNA), extracted from minimally invasive biopsies, such as, blood, stool, urine, nose, throat, are promising biomarker for diseases diagnosis and management. We quantify the effect of the extra step of poly(A) ligation for cDNA synthesis and small size of the NA on the limit of quantification (LOQ) of quantitative PCR (qPCR), the gold standard to measure copy number. It was discovered that for small NA, the cycle threshold, Ct that is proportional to -log[c], where [c] is the concentration of the target NA exhibits a sharp transition. The results indicate that although the limit of detection (LOD) of qPCR can be in femtomolar range, the LOQ is significantly reduced by well over three orders of magnitude, in picomolar range. Specifically, the study reveals that the PCR product length is the primary reason the limitation on LOQ and is explicitly shown to be an important consideration for primer design for qPCR in general.
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Affiliation(s)
- Jay Min Lim
- Vajra Instruments Inc., 8300 Cody Drive, Ste C, Lincoln, NE 68512, USA
| | - Rahul Tevatia
- Vajra Instruments Inc., 8300 Cody Drive, Ste C, Lincoln, NE 68512, USA
| | - Ravi F Saraf
- Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln NE 68588, USA
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4
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Rodia MT, Ugolini G, Mattei G, Montroni I, Zattoni D, Ghignone F, Veronese G, Marisi G, Lauriola M, Strippoli P, Solmi R. Systematic large-scale meta-analysis identifies a panel of two mRNAs as blood biomarkers for colorectal cancer detection. Oncotarget 2017; 7:30295-306. [PMID: 26993598 PMCID: PMC5058681 DOI: 10.18632/oncotarget.8108] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 02/28/2016] [Indexed: 12/22/2022] Open
Abstract
Colorectal cancer (CRC) is the third most common cancer in the world. A significant survival rate is achieved if it is detected at an early stage. A whole blood screening test, without any attempt to isolate blood fractions, could be an important tool to improve early detection of colorectal cancer. We searched for candidate markers with a novel approach based on the Transcriptome Mapper (TRAM), aimed at identifying specific RNAs with the highest differential expression ratio between colorectal cancer tissue and normal blood samples. This tool permits a large-scale systematic meta-analysis of all available data obtained by microarray experiments. The targeting of RNA took into consideration that tumour phenotypic variation is associated with changes in the mRNA levels of genes regulating or affecting this variation. A real time quantitative reverse transcription polymerase chain reaction (qRT- PCR) was applied to the validation of candidate markers in the blood of 67 patients and 67 healthy controls. The expression of genes: TSPAN8, LGALS4, COL1A2 and CEACAM6 resulted as being statistically different. In particular ROC curves attested for TSPAN8 an AUC of 0.751 with a sensitivity of 83.6% and a specificity of 58.2% at a cut off of 10.85, while the panel of the two best genes showed an AUC of 0.861 and a sensitivity of 92.5% with a specificity of 67.2%. Our preliminary study on a total of 134 subjects showed promising results for a blood screening test to be validated in a larger cohort with the staging stratification and in patients with other gastrointestinal diseases.
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Affiliation(s)
- Maria Teresa Rodia
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Bologna, Italy.,Centre of Molecular Genetics, "CARISBO Foundation", Bologna, Italy
| | - Giampaolo Ugolini
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
| | - Gabriella Mattei
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Bologna, Italy.,Centre of Molecular Genetics, "CARISBO Foundation", Bologna, Italy
| | - Isacco Montroni
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
| | - Davide Zattoni
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
| | - Federico Ghignone
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
| | - Giacomo Veronese
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy
| | - Giorgia Marisi
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCSS, Meldola, Italy
| | - Mattia Lauriola
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Bologna, Italy.,Centre of Molecular Genetics, "CARISBO Foundation", Bologna, Italy
| | - Pierluigi Strippoli
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Bologna, Italy.,Centre of Molecular Genetics, "CARISBO Foundation", Bologna, Italy.,Interdepartmental Center for Cancer Research "Giorgio Prodi" (CIRC), S. Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy
| | - Rossella Solmi
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Unit of Histology, Embryology and Applied Biology, University of Bologna, Bologna, Italy.,Centre of Molecular Genetics, "CARISBO Foundation", Bologna, Italy
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5
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Lo YT, Shaw PC. Quantification of concentrated Chinese medicine granules by quantitative polymerase chain reaction. J Pharm Biomed Anal 2017; 145:661-665. [PMID: 28800527 DOI: 10.1016/j.jpba.2017.07.047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 07/06/2017] [Accepted: 07/29/2017] [Indexed: 11/19/2022]
Abstract
Determination of the amount of constituent in a multi-herb product is important for quality control. In concentrated Chinese medicine granules (CCMG), no dregs are left after dissolution of the CCMG. This study is the first to examine the feasibility of using quantitative polymerase chain reaction (qPCR) to find the amount of CCMG in solution form. DNA was extracted from Hirudo and Zaocys CCMG mixed at different ratios and amplified in qPCR using species-specific primers. The threshold cycle (CT) obtained was compared with the respective standard curves. Results showed that reproducible quantification results could be obtained (1) for 5-50mg CCMG using a modified DNA extraction protocol, (2) amongst DNA extracted from the same batch of CCMG and (3) amongst different batches of CCMG from the same company. This study demonstrated the constitute amount of CCMG in a mixture could be determined using qPCR. This work has extended the application of DNA techniques for the quantification of herbal products and this approach may be developed for quality assurance in the CCMG industry.
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Affiliation(s)
- Yat-Tung Lo
- Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine, State Key Laboratory of Phytochemistry Plant Resources in West China (CUHK) and School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China.
| | - Pang-Chui Shaw
- Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine, State Key Laboratory of Phytochemistry Plant Resources in West China (CUHK) and School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China.
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Horák D, Hlídková H, Trachtová Š, Šlouf M, Rittich B, Španová A. Evaluation of poly(ethylene glycol)-coated monodispersed magnetic poly(2-hydroxyethyl methacrylate) and poly(glycidyl methacrylate) microspheres by PCR. Eur Polym J 2015. [DOI: 10.1016/j.eurpolymj.2015.03.036] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Gill S, Haince JF, Shi Q, Pavey ES, Beaudry G, Sargent DJ, Fradet Y. Prognostic Value of Molecular Detection of Lymph Node Metastases After Curative Resection of Stage II Colon Cancer: A Systematic Pooled Data Analysis. Clin Colorectal Cancer 2014; 14:99-105. [PMID: 25619805 DOI: 10.1016/j.clcc.2014.12.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Revised: 12/15/2014] [Accepted: 12/16/2014] [Indexed: 02/07/2023]
Abstract
BACKGROUND We aimed to clarify the prognostic value of guanylyl cyclase C (GCC) lymph node ratio (LNR) status as a predictor of recurrence in untreated stage IIA colon cancer on the basis of pooled individual data from previous studies. METHODS Patients were classified according to predefined GCC LNR risk groups (low, LNR ≤ 0.1; intermediate, 0.1 < LNR ≤ 0.2; high, LNR > 0.2). Outcomes included time to recurrence, disease-free survival, and overall survival. Stratified log-rank tests and multivariate Cox models assessed the association between outcomes and GCC lymph node status. RESULTS The final data set contained 553 patients with stage IIA colon cancer with a median of 18 lymph nodes examined after resection; 65 patients (11.8%) had recurrence. Overall, 109 patients (19.7%) were classified high risk on the basis of GCC LNR. In multivariate analysis, high GCC LNR value (> 0.2) was a significant predictor of cancer recurrence (hazard ratio [HR], 3.18; 95% confidence interval [CI], 1.77-5.71; P < .001) and lower disease-free survival (HR, 2.40; 95% CI, 1.60-3.62; P < .001) and overall survival (HR, 2.12; 95% CI, 1.35-3.33; P = .001). CONCLUSION Patients considered at high risk on the basis of their GCC LNR status have significantly inferior outcomes compared to those with low GCC LNR values, particularly among those traditionally considered to be at low risk for recurrence.
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MESH Headings
- Adenocarcinoma/genetics
- Adenocarcinoma/mortality
- Adenocarcinoma/secondary
- Adenocarcinoma/surgery
- Adult
- Aged
- Aged, 80 and over
- Biomarkers, Tumor/genetics
- Colonic Neoplasms/genetics
- Colonic Neoplasms/mortality
- Colonic Neoplasms/pathology
- Colonic Neoplasms/surgery
- Female
- Follow-Up Studies
- Humans
- Lymphatic Metastasis
- Male
- Middle Aged
- Neoplasm Grading
- Neoplasm Invasiveness
- Neoplasm Recurrence, Local/genetics
- Neoplasm Recurrence, Local/mortality
- Neoplasm Recurrence, Local/pathology
- Neoplasm Recurrence, Local/surgery
- Prognosis
- RNA, Messenger/genetics
- Real-Time Polymerase Chain Reaction
- Receptors, Enterotoxin
- Receptors, Guanylate Cyclase-Coupled/genetics
- Receptors, Peptide/genetics
- Reverse Transcriptase Polymerase Chain Reaction
- Survival Rate
- Young Adult
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Affiliation(s)
- Sharlene Gill
- University of British Columbia, BC Cancer Agency, Vancouver, BC, Canada.
| | | | - Qian Shi
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN
| | - Emily S Pavey
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN
| | | | - Daniel J Sargent
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN
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Bujanda L, Sarasqueta C, Cosme A, Hijona E, Enríquez-Navascués JM, Placer C, Villarreal E, Herreros-Villanueva M, Giraldez MD, Gironella M, Balaguer F, Castells A. Evaluation of alpha 1-antitrypsin and the levels of mRNA expression of matrix metalloproteinase 7, urokinase type plasminogen activator receptor and COX-2 for the diagnosis of colorectal cancer. PLoS One 2013; 8:e51810. [PMID: 23300952 PMCID: PMC3534697 DOI: 10.1371/journal.pone.0051810] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Accepted: 11/06/2012] [Indexed: 12/23/2022] Open
Abstract
Background Colorectal cancer (CRC) is the second most common cause of death from cancer in both men and women in the majority of developed countries. Molecular tests of blood could potentially provide this ideal screening tool. Aim Our objective was to assess the usefulness of serum markers and mRNA expression levels in the diagnosis of CRC. Methods In a prospective study, we measured mRNA expression levels of 13 markers (carbonic anhydrase, guanylyl cyclase C, plasminogen activator inhibitor, matrix metalloproteinase 7 (MMP7), urokinase-type plasminogen activator receptor (uPAR), urokinase-type plasminogen activator, survivin, tetranectin, vascular endothelial growth factor (VEGF), cytokeratin 20, thymidylate synthase, cyclooxygenase 2 (COX-2), and CD44) and three proteins in serum (alpha 1 antitrypsin, carcinoembryonic antigen (CEA) and activated C3 in 42 patients with CRC and 33 with normal colonoscopy results. Results Alpha 1-antitrypsin was the serum marker that was most useful for CRC diagnosis (1.79±0.25 in the CRC group vs 1.27±0.25 in the control group, P<0.0005). The area under the ROC curve for alpha 1-antitrypsin was 0.88 (0.79–0.96). The mRNA expression levels of five markers were statistically different between CRC cases and controls: those for which the ROC area was over 75% were MMP7 (0.81) and tetranectin (0.80), COX-2 (0.78), uPAR (0.78) and carbonic anhydrase (0.77). The markers which identified early stage CRC (Stages I and II) were alpha 1-antitrypsin, uPAR, COX-2 and MMP7. Conclusions Serum alpha 1-antitrypsin and the levels of mRNA expression of MMP7, COX-2 and uPAR have good diagnostic accuracy for CRC, even in the early stages.
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Affiliation(s)
- Luis Bujanda
- Department of Gastroenterology, Donostia Hospital-Biodonostia Institute, University of Basque Country, UPV/EHU, Centro de Investigación Biomédica en Enfermedades Hepáticas y Digestivas, San Sebastián, Spain.
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Bustin SA, Murphy J. RNA biomarkers in colorectal cancer. Methods 2013; 59:116-25. [DOI: 10.1016/j.ymeth.2012.10.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Revised: 09/28/2012] [Accepted: 10/04/2012] [Indexed: 02/08/2023] Open
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Modena P, Buttarelli FR, Miceli R, Piccinin E, Baldi C, Antonelli M, Morra I, Lauriola L, Di Rocco C, Garrè ML, Sardi I, Genitori L, Maestro R, Gandola L, Facchinetti F, Collini P, Sozzi G, Giangaspero F, Massimino M. Predictors of outcome in an AIEOP series of childhood ependymomas: a multifactorial analysis. Neuro Oncol 2012; 14:1346-56. [PMID: 23076205 PMCID: PMC3480268 DOI: 10.1093/neuonc/nos245] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Accepted: 08/08/2012] [Indexed: 01/04/2023] Open
Abstract
Several molecular biomarkers have been suggested as predictors of outcome for pediatric ependymomas but deserve further validation in independent case series. We analyzed intracranial ependymomas belonging to a series of 60 patients prospectively treated according to the protocol sponsored by the Italian Association of Pediatric Hematology-Oncology. We used a tissue microarray to analyze nucleolin (NCL), cyclin-dependent kinase inhibitor 2A (CDKN2A), tumor protein 53 (TP53), and epidermal growth factor receptor (EGFR) by immunohistochemistry and by 1q gain by fluorescent in situ hybridization. The mRNA expression levels of EGFR, human telomerase reverse-transcriptase (HTERT), and Prominin 1 (PROM 1)/CD133 were evaluated by quantitative real-time PCR from cases with fresh-frozen tumor material available. Univariate and multivariate analyses of updated clinical data confirmed the prognostic significance of surgery (P < .01) and tumor grading (P < .05) for both relapse-free survival (RFS) and overall survival (OS). Among biomolecular markers, HTERT mRNA expression emerged with the strongest association with OS at multivariate analysis (hazard ratio [HR] = 9.9; P = .011); the 5-year OS was 84% versus 48% in the subgroups with HTERT median value <6 versus ≥ 6, respectively (P = .005). Five-year RFS was 46% versus 20% in the subgroups with low versus high NCL protein expression, respectively (P = .004), while multivariate Cox analyses gave suggestively high HRs for high versus low NCL (HR = 1.9; P = .090). The other genes tested were not significant at multivariate analyses, and genetic alterations of CDKN2A, TP53, EGFR, and HTERT loci were rare. The PROM1/CD133 cancer stem cell marker was strongly expressed at both RNA and protein levels in a substantial fraction of cases and was suggestively associated with a more indolent form of the disease. We conclude that NCL and HTERT represent the strongest prognostic biomarkers of RFS and OS, respectively, in our ependymoma case series.
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Valladares-Ayerbes M, Blanco-Calvo M, Reboredo M, Lorenzo-Patiño MJ, Iglesias-Díaz P, Haz M, Díaz-Prado S, Medina V, Santamarina I, Pértega S, Figueroa A, Antón-Aparicio LM. Evaluation of the adenocarcinoma-associated gene AGR2 and the intestinal stem cell marker LGR5 as biomarkers in colorectal cancer. Int J Mol Sci 2012; 13:4367-4387. [PMID: 22605983 PMCID: PMC3344219 DOI: 10.3390/ijms13044367] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2012] [Revised: 03/20/2012] [Accepted: 03/23/2012] [Indexed: 01/06/2023] Open
Abstract
We aim to estimate the diagnostic performances of anterior gradient homolog-2 (AGR2) and Leucine-rich repeat-containing-G-protein-coupled receptor 5 (LGR5) in peripheral blood (PB) as mRNA biomarkers in colorectal cancer (CRC) and to explore their prognostic significance. Real-time PCR was used to analyze AGR2 and LGR5 in 54 stages I-IV CRC patients and 19 controls. Both mRNAs were significantly increased in PB from CRC patients compared to controls. The area under the receiver-operating characteristic curves were 0.722 (p = 0.006), 0.376 (p = 0.123) and 0.767 (p = 0.001) for AGR2, LGR5 and combined AGR2/LGR5, respectively. The AGR2/LGR5 assay resulted in 67.4% sensitivity and 94.7% specificity. AGR2 correlated with pT3–pT4 and high-grade tumors. LGR5 correlated with metastasis, R2 resections and high-grade. The progression-free survival (PFS) of patients with high AGR2 was reduced (p = 0.037; HR, 2.32), also in the stage I-III subgroup (p = 0.046). LGR5 indicated a poor prognosis regarding both PFS (p = 0.007; HR, 1.013) and overall survival (p = 0.045; HR, 1.01). High AGR2/LGR5 was associated with poor PFS (p = 0.014; HR, 2.8) by multivariate analysis. Our findings indicate that the assessment of AGR2 and LGR5 in PB might reflect the presence of circulating tumor cells (CTC) and stem cell like CTC in CRC. Increased AGR2 and LGR5 are associated with poor outcomes.
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Affiliation(s)
- Manuel Valladares-Ayerbes
- Medical Oncology Department, La Coruña University Hospital, Servicio Galego de Saúde (SERGAS), As Xubias, 84. PC 15006, La Coruña, Spain; E-Mails: (M.R.); (L.M.A.-A.)
- Translational Cancer Research Lab, Biomedical Research Institute (INIBIC), Carretera del Pasaje, s/n. PC 15006, La Coruña, Spain; E-Mails: (M.B.-C.); (M.H.); (V.M.); (I.S.); (A.F.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel. +34-981178000 (ext. 292848); Fax: +34-981178273
| | - Moisés Blanco-Calvo
- Translational Cancer Research Lab, Biomedical Research Institute (INIBIC), Carretera del Pasaje, s/n. PC 15006, La Coruña, Spain; E-Mails: (M.B.-C.); (M.H.); (V.M.); (I.S.); (A.F.)
| | - Margarita Reboredo
- Medical Oncology Department, La Coruña University Hospital, Servicio Galego de Saúde (SERGAS), As Xubias, 84. PC 15006, La Coruña, Spain; E-Mails: (M.R.); (L.M.A.-A.)
| | - María J. Lorenzo-Patiño
- Pathology Department, La Coruña University Hospital, Servicio Galego de Saúde (SERGAS), As Xubias, 84. PC 15006, La Coruña, Spain; E-Mails: (M.J.L.-P.); (P.I.-D.)
| | - Pilar Iglesias-Díaz
- Pathology Department, La Coruña University Hospital, Servicio Galego de Saúde (SERGAS), As Xubias, 84. PC 15006, La Coruña, Spain; E-Mails: (M.J.L.-P.); (P.I.-D.)
| | - Mar Haz
- Translational Cancer Research Lab, Biomedical Research Institute (INIBIC), Carretera del Pasaje, s/n. PC 15006, La Coruña, Spain; E-Mails: (M.B.-C.); (M.H.); (V.M.); (I.S.); (A.F.)
| | - Silvia Díaz-Prado
- Tissue Engineering and Cellular Therapy Lab, INIBIC, Carretera del Pasaje, s/n. PC 15006, La Coruña, Spain; E-Mail:
- Medicine Department, La Coruña University (UDC), Campus de Oza, s/n, PC 15006, La Coruña, Spain
| | - Vanessa Medina
- Translational Cancer Research Lab, Biomedical Research Institute (INIBIC), Carretera del Pasaje, s/n. PC 15006, La Coruña, Spain; E-Mails: (M.B.-C.); (M.H.); (V.M.); (I.S.); (A.F.)
| | - Isabel Santamarina
- Translational Cancer Research Lab, Biomedical Research Institute (INIBIC), Carretera del Pasaje, s/n. PC 15006, La Coruña, Spain; E-Mails: (M.B.-C.); (M.H.); (V.M.); (I.S.); (A.F.)
| | - Sonia Pértega
- Biostatistics and Clinical Epidemiology Unit, La Coruña University Hospital, Servicio Galego de Saúde (SERGAS), As Xubias 84, PC 15006, La Coruña, Spain; E-Mail:
| | - Angélica Figueroa
- Translational Cancer Research Lab, Biomedical Research Institute (INIBIC), Carretera del Pasaje, s/n. PC 15006, La Coruña, Spain; E-Mails: (M.B.-C.); (M.H.); (V.M.); (I.S.); (A.F.)
| | - Luis M. Antón-Aparicio
- Medical Oncology Department, La Coruña University Hospital, Servicio Galego de Saúde (SERGAS), As Xubias, 84. PC 15006, La Coruña, Spain; E-Mails: (M.R.); (L.M.A.-A.)
- Medicine Department, La Coruña University (UDC), Campus de Oza, s/n, PC 15006, La Coruña, Spain
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Raeisossadati R, Farshchian M, Ganji A, Tavassoli A, Velayati A, Dadkhah E, Chavoshi S, Mehrabi Bahar M, Memar B, Rajabi Mashhadi MT, Naseh H, Forghanifard MM, Moghbeli M, Moaven O, Abbaszadegan MR. Quantitative analysis of TEM-8 and CEA tumor markers indicating free tumor cells in the peripheral blood of colorectal cancer patients. Int J Colorectal Dis 2011; 26:1265-70. [PMID: 21573768 DOI: 10.1007/s00384-011-1230-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/19/2011] [Indexed: 02/04/2023]
Abstract
BACKGROUND Colorectal cancer (CRC) remains the third most common cancer in the world. Approximately in 50 percent of patients, metastatic disease is a major cause of death. Therefore, early diagnosis of CRC is crucial for a successful outcome. For the detection of circulating cancer cells, this study applied a sensitive method that employed specific tumor markers for early detection. METHODS A total of 80 blood samples from 40 CRC patients and 40 age-matched healthy controls were collected for the study. The circulating mRNA levels of two CRC tumor markers, tumor endothelial marker 8 (TEM-8) and carcinoembryogenic antigen (CEA) were evaluated using an absolute quantitative real-time PCR assay in a Stratagene Mx-3000P real-time PCR system. GAPDH was used as the endogenous control. RESULTS TEM-8 and CEA were primarily detected more in the CRC patients rather than in the controls: 22/40 vs 9/40, p=0.009 and 30/40 vs 11/40, p=0.00054, respectively. In the CRC patients, the mRNA level of these markers was significantly higher in comparison to the normal controls (p=0.018 and 0.01). The overall sensitivity of this panel was 65% with a specificity of 75%. Statistical analysis for demographic variants did not reach significant values. CONCLUSIONS TEM-8 and CEA markers were detected more frequently and in significantly higher levels in the blood samples of patients compared with samples from age-matched healthy controls. The copy number of CEA and TEM-8 mRNA, as detected by a real-time quantitative PCR, appears to be a promising marker for evaluating the risk of tumor spread.
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Affiliation(s)
- Reza Raeisossadati
- Department of Biology, Faculty of Science, Science and Research Branch, Islamic Azad University, Tehran, Iran
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13
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Sargent DJ, Resnick MB, Meyers MO, Goldar-Najafi A, Clancy T, Gill S, Siemons GO, Shi Q, Bot BM, Wu TT, Beaudry G, Haince JF, Fradet Y. Evaluation of Guanylyl Cyclase C Lymph Node Status for Colon Cancer Staging and Prognosis. Ann Surg Oncol 2011; 18:3261-70. [DOI: 10.1245/s10434-011-1731-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2011] [Indexed: 01/07/2023]
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14
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Chetverina EV, Chetverin AB. Nanocolonies and diagnostics of oncological diseases associated with chromosomal translocations. BIOCHEMISTRY (MOSCOW) 2011; 75:1667-91. [DOI: 10.1134/s0006297910130109] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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15
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Real‐Time Quantitative RT‐PCR for mRNA Profiling. Genomics 2010. [DOI: 10.1002/9780470711675.ch6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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16
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Sørby LA, Andersen SN, Bukholm IRK, Jacobsen MB. Evaluation of suitable reference genes for normalization of real-time reverse transcription PCR analysis in colon cancer. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2010; 29:144. [PMID: 21059236 PMCID: PMC2988724 DOI: 10.1186/1756-9966-29-144] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2010] [Accepted: 11/08/2010] [Indexed: 02/05/2023]
Abstract
Background Real-time reverse transcription PCR (qRT-PCR) is frequently used for gene expression quantification due to its methodological reproducibility and sensitivity. The gene expression is quantified by normalization to one or more reference genes which are presumed stably expressed throughout a given experiment. The aim of this study was to validate a standardized experimental setup to identifying reference genes for normalization of qRT-PCR in the metastatic and non-metastatic colon cancer. Methods In this study, expression of 16 commonly used reference genes was quantified in tumour tissue and individual-matched normal mucosa in 18 non-metastatic colon cancer patients and 20 colon cancer patients with distant metastases using TaqMan Low Density Array (TLDA). The expression stability was determined and compared by means of geNorm and NormFinder. Results Two pairs of genes, HPRT1/PPIA and IPO8/PPIA, were identified to be suitable to normalize gene expression data in metastatic and non-metastatic colon cancer patients, according to geNorm and NormFinder respectively. Conclusion We propose a standardized approach of finding the most suitable reference gene(s) in every qRT-PCR experiment using TLDA.
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Affiliation(s)
- Lise Aa Sørby
- Quality and Research Department, Ostfold Hospital Trust, 1603 Fredrikstad, Norway.
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17
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Bustin SA. Why the need for qPCR publication guidelines?—The case for MIQE. Methods 2010; 50:217-26. [DOI: 10.1016/j.ymeth.2009.12.006] [Citation(s) in RCA: 238] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2009] [Revised: 12/07/2009] [Accepted: 12/11/2009] [Indexed: 12/23/2022] Open
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Murphy J, Bustin SA. Reliability of real-time reverse-transcription PCR in clinical diagnostics: gold standard or substandard? Expert Rev Mol Diagn 2009; 9:187-97. [PMID: 19298142 DOI: 10.1586/14737159.9.2.187] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Molecular diagnostics is one of the major growth areas of modern medicine, with real-time PCR established as a qualitative and quantitative technology that is rapid, accurate and sensitive. The sequencing of the human genome, comprehensive genomic, mRNA and miRNA expression profiling of numerous cancer types, the ongoing identification of disease-associated polymorphisms and the expanding availability of genomic sequence information for human pathogens has opened the door to a wide range of translational applications for this technology. Consequently, novel real-time PCR assays have been developed for diagnosis and prognosis, treatment monitoring, transplant biology and pathogen detection, as well as more controversial uses such as lifestyle genotyping. However, this technology is still troubled by significant technical deficiencies. Hence its often-improper use as a clinical tool has important public health implications, most recently demonstrated through its association with the measles, mumps and rubella vaccine/autism controversy. This serves as a timely reminder of the indispensable requirement for careful experimental design, validation and analysis.
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Affiliation(s)
- Jamie Murphy
- Centre for Academic Surgery, Royal London Hospital, London, UK.
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19
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Bustin SA, Benes V, Garson JA, Hellemans J, Huggett J, Kubista M, Mueller R, Nolan T, Pfaffl MW, Shipley GL, Vandesompele J, Wittwer CT. The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin Chem 2009; 55:611-22. [PMID: 19246619 DOI: 10.1373/clinchem.2008.112797] [Citation(s) in RCA: 10490] [Impact Index Per Article: 699.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Currently, a lack of consensus exists on how best to perform and interpret quantitative real-time PCR (qPCR) experiments. The problem is exacerbated by a lack of sufficient experimental detail in many publications, which impedes a reader's ability to evaluate critically the quality of the results presented or to repeat the experiments. CONTENT The Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines target the reliability of results to help ensure the integrity of the scientific literature, promote consistency between laboratories, and increase experimental transparency. MIQE is a set of guidelines that describe the minimum information necessary for evaluating qPCR experiments. Included is a checklist to accompany the initial submission of a manuscript to the publisher. By providing all relevant experimental conditions and assay characteristics, reviewers can assess the validity of the protocols used. Full disclosure of all reagents, sequences, and analysis methods is necessary to enable other investigators to reproduce results. MIQE details should be published either in abbreviated form or as an online supplement. SUMMARY Following these guidelines will encourage better experimental practice, allowing more reliable and unequivocal interpretation of qPCR results.
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Affiliation(s)
- Stephen A Bustin
- Centre for Academic Surgery, Institute of Cell and Molecular Science, Barts and the London School of Medicine and Dentistry, London, UK.
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Falaleeva MV, Chetverina HV, Kravchenko AV, Chetverin AB. Use of nanocolonies to detect minimal residual disease in patients with leukemia t(8;12). Mol Biol 2009; 43:166-74. [DOI: 10.1134/s0026893309010221] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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22
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Bustin SA. Molecular medicine, gene-expression profiling and molecular diagnostics: putting the cart before the horse. Biomark Med 2008; 2:201-7. [DOI: 10.2217/17520363.2.3.201] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Affiliation(s)
- Stephen A Bustin
- Institute of Cell & Molecular Science, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, UK; 3rd Floor, Alexandra Wing Royal London Hospital, London, E1 1BB, UK
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RNA isolation and quantitative PCR from HOPE- and formalin-fixed bovine lymph node tissues. Pathol Res Pract 2008; 204:105-11. [DOI: 10.1016/j.prp.2007.09.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2007] [Revised: 09/11/2007] [Accepted: 09/13/2007] [Indexed: 11/19/2022]
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Murphy B J, Dorudi S, Bustin SA. Molecular staging of colorectal cancer: new paradigm or waste of time? ACTA ACUST UNITED AC 2007; 1:31-45. [DOI: 10.1517/17530059.1.1.31] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Abstract
The real-time reverse transcription polymerase chain reaction (RT-qPCR) addresses the evident requirement for quantitative data analysis in molecular medicine, biotechnology, microbiology and diagnostics and has become the method of choice for the quantification of mRNA. Although it is often described as a "gold" standard, it is far from being a standard assay. The significant problems caused by variability of RNA templates, assay designs and protocols, as well as inappropriate data normalization and inconsistent data analysis, are widely known but also widely disregarded. As a first step towards standardization, we describe a series of RT-qPCR protocols that illustrate the essential technical steps required to generate quantitative data that are reliable and reproducible. We would like to emphasize, however, that RT-qPCR data constitute only a snapshot of information regarding the quantity of a given transcript in a cell or tissue. Any assessment of the biological consequences of variable mRNA levels must include additional information regarding regulatory RNAs, protein levels and protein activity. The entire protocol described here, encompassing all stages from initial assay design to reliable qPCR data analysis, requires approximately 15 h.
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Affiliation(s)
- Tania Nolan
- Sigma-Aldrich, Homefield Road, Haverhill, UK
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26
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Solmi R, Ugolini G, Rosati G, Zanotti S, Lauriola M, Montroni I, del Governatore M, Caira A, Taffurelli M, Santini D, Coppola D, Guidotti L, Carinci P, Strippoli P. Microarray-based identification and RT-PCR test screening for epithelial-specific mRNAs in peripheral blood of patients with colon cancer. BMC Cancer 2006; 6:250. [PMID: 17054783 PMCID: PMC1629022 DOI: 10.1186/1471-2407-6-250] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2006] [Accepted: 10/20/2006] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND The efficacy of screening for colorectal cancer using a simple blood-based assay for the detection of tumor cells disseminated in the circulation at an early stage of the disease is gaining positive feedback from several lines of research. This method seems able to reduce colorectal cancer mortality and may replace colonoscopy as the most effective means of detecting colonic lesions. METHODS In this work, we present a new microarray-based high-throughput screening method to identifying candidate marker mRNAs for the early detection of epithelial cells diluted in peripheral blood cells. This method includes 1. direct comparison of different samples of colonic mucosa and of blood cells to identify consistent epithelial-specific mRNAs from among 20,000 cDNA assayed by microarray slides; 2. identification of candidate marker mRNAs by data analysis, which allowed selection of only 10 putative differentially expressed genes; 3. Selection of some of the most suitable mRNAs (TMEM69, RANBP3 and PRSS22) that were assayed in blood samples from normal subjects and patients with colon cancer as possible markers for the presence of epithelial cells in the blood, using reverse transcription-polymerase chain reaction (RT-PCR). RESULTS Our present results seem to provide an indication, for the first time obtained by genome-scale screening, that a suitable and consistent colon epithelium mRNA marker may be difficult to identify. CONCLUSION The design of new approaches to identify such markers is warranted.
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Affiliation(s)
- Rossella Solmi
- Department of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, I-40126 Bologna, Italy
| | - Giampaolo Ugolini
- Department of Surgical and Anesthesiological Sciences-General Surgery, University of Bologna, Via Massarenti 9, I-40138 Bologna, Italy
| | - Giancarlo Rosati
- Department of Surgical and Anesthesiological Sciences-General Surgery, University of Bologna, Via Massarenti 9, I-40138 Bologna, Italy
| | - Simone Zanotti
- Department of Surgical and Anesthesiological Sciences-General Surgery, University of Bologna, Via Massarenti 9, I-40138 Bologna, Italy
| | - Mattia Lauriola
- Department of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, I-40126 Bologna, Italy
| | - Isacco Montroni
- Department of Surgical and Anesthesiological Sciences-General Surgery, University of Bologna, Via Massarenti 9, I-40138 Bologna, Italy
| | - Marco del Governatore
- Department of Surgical and Anesthesiological Sciences-General Surgery, University of Bologna, Via Massarenti 9, I-40138 Bologna, Italy
| | - Antonello Caira
- Department of Surgical and Anesthesiological Sciences-General Surgery, University of Bologna, Via Massarenti 9, I-40138 Bologna, Italy
| | - Mario Taffurelli
- Department of Surgical and Anesthesiological Sciences-General Surgery, University of Bologna, Via Massarenti 9, I-40138 Bologna, Italy
| | - Donatella Santini
- Department of Pathology, University of Bologna, Via Massarenti 9, I-40138 Bologna, Italy
| | - Domenico Coppola
- "H.Lee Moffit" Cancer Center and Research Institute, University of South Florida, Tampa, FL, USA
| | - Lia Guidotti
- Department of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, I-40126 Bologna, Italy
| | - Paolo Carinci
- Department of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, I-40126 Bologna, Italy
| | - Pierluigi Strippoli
- Department of Histology, Embryology and Applied Biology, University of Bologna, Via Belmeloro 8, I-40126 Bologna, Italy
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27
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Bustin SA. Nucleic acid quantification and disease outcome prediction in colorectal cancer. Per Med 2006; 3:207-216. [DOI: 10.2217/17410541.3.2.207] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Histopathological stage at diagnosis remains the most important prognostic determinant for colorectal cancer. However, conventional staging is unable to predict disease outcome accurately for each individual patient. This results in considerable prognostic heterogeneity within a given tumor stage and is of particular relevance for a subgroup of patients with stage II disease that would benefit from adjuvant therapy. The recent advances in functional genomics are beginning to have a significant impact on clinical oncology, and there is widespread interest in using molecular techniques for clinical applications. These have focused on two approaches: the use of polymerase chain reaction (PCR)-based methods for the detection of occult disease in lymph nodes, bone marrow and blood and the use of microarrays for the expression profiling of primary tumors. The aim is to develop molecular classifiers that will allow the prediction of disease outcome, thus matching patients with individualized treatment. Despite the obvious attractions of these approaches, there have been significant technical, biological and analytical problems in their translation into clinically relevant practice. This is particularly true for colorectal cancer, the second most common cancer in the western world. Nevertheless, progress is being made and the improved awareness and appreciation of those difficulties is beginning to generate results that should prove useful for clinical oncology.
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Affiliation(s)
- Stephen A Bustin
- University of London, Institute of Cell and Molecular Science, Barts and the London, Queen Mary’s School of Medicine and Dentistry, London, UK
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