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A perceptually optimised bivariate visualisation scheme for high-dimensional fold-change data. ADV DATA ANAL CLASSI 2020. [DOI: 10.1007/s11634-020-00416-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
AbstractVisualising data as diagrams using visual attributes such as colour, shape, size, and orientation is challenging. In particular, large data sets demand graphical display as an essential step in the analysis. In order to achieve comprehension often different attributes need to be displayed simultaneously. In this work a comprehensible bivariate, perceptually optimised visualisation scheme for high-dimensional data is proposed and evaluated. It can be used to show fold changes together with confidence values within a single diagram. The visualisation scheme consists of two parts: a uniform, symmetric, two-sided colour scale and a patch grid representation. Evaluation of uniformity and symmetry of the two-sided colour scale was performed in comparison to a standard RGB scale by twenty-five observers. Furthermore, the readability of the generated map was validated and compared to a bivariate heat map scheme.
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Fan Z, Zhou Y, Ressom HW. MOTA: Multi-omic integrative analysis for biomarker discovery. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2020; 2019:243-247. [PMID: 31945887 DOI: 10.1109/embc.2019.8857049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Recent advancement of omic technologies provides researchers with opportunities to search for disease biomarkers at the systems level. However, selection of biomarker candidates from a large number of molecules involved at various layers of the biological system is challenging. In this paper, we propose multi-omic integrative analysis (MOTA), a network-based method that uses information from multi-omic data to identify candidate disease biomarkers. We evaluated the performance of MOTA in selecting disease-associated molecules from four sets of multi-omic data representing three cohorts of hepatocellular carcinoma (HCC) cases and patients with liver cirrhosis. The results demonstrate that MOTA leads to selection of more biomarker candidates that shared by two different cohorts compared to traditional statistical methods. Also, the networks constructed by MOTA allow users to investigate biological significance of the selected biomarker candidates.
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Best LMJ, Rawji V, Pereira SP, Davidson BR, Gurusamy KS. Imaging modalities for characterising focal pancreatic lesions. Cochrane Database Syst Rev 2017; 4:CD010213. [PMID: 28415140 PMCID: PMC6478242 DOI: 10.1002/14651858.cd010213.pub2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
BACKGROUND Increasing numbers of incidental pancreatic lesions are being detected each year. Accurate characterisation of pancreatic lesions into benign, precancerous, and cancer masses is crucial in deciding whether to use treatment or surveillance. Distinguishing benign lesions from precancerous and cancerous lesions can prevent patients from undergoing unnecessary major surgery. Despite the importance of accurately classifying pancreatic lesions, there is no clear algorithm for management of focal pancreatic lesions. OBJECTIVES To determine and compare the diagnostic accuracy of various imaging modalities in detecting cancerous and precancerous lesions in people with focal pancreatic lesions. SEARCH METHODS We searched the CENTRAL, MEDLINE, Embase, and Science Citation Index until 19 July 2016. We searched the references of included studies to identify further studies. We did not restrict studies based on language or publication status, or whether data were collected prospectively or retrospectively. SELECTION CRITERIA We planned to include studies reporting cross-sectional information on the index test (CT (computed tomography), MRI (magnetic resonance imaging), PET (positron emission tomography), EUS (endoscopic ultrasound), EUS elastography, and EUS-guided biopsy or FNA (fine-needle aspiration)) and reference standard (confirmation of the nature of the lesion was obtained by histopathological examination of the entire lesion by surgical excision, or histopathological examination for confirmation of precancer or cancer by biopsy and clinical follow-up of at least six months in people with negative index tests) in people with pancreatic lesions irrespective of language or publication status or whether the data were collected prospectively or retrospectively. DATA COLLECTION AND ANALYSIS Two review authors independently searched the references to identify relevant studies and extracted the data. We planned to use the bivariate analysis to calculate the summary sensitivity and specificity with their 95% confidence intervals and the hierarchical summary receiver operating characteristic (HSROC) to compare the tests and assess heterogeneity, but used simpler models (such as univariate random-effects model and univariate fixed-effect model) for combining studies when appropriate because of the sparse data. We were unable to compare the diagnostic performance of the tests using formal statistical methods because of sparse data. MAIN RESULTS We included 54 studies involving a total of 3,196 participants evaluating the diagnostic accuracy of various index tests. In these 54 studies, eight different target conditions were identified with different final diagnoses constituting benign, precancerous, and cancerous lesions. None of the studies was of high methodological quality. None of the comparisons in which single studies were included was of sufficiently high methodological quality to warrant highlighting of the results. For differentiation of cancerous lesions from benign or precancerous lesions, we identified only one study per index test. The second analysis, of studies differentiating cancerous versus benign lesions, provided three tests in which meta-analysis could be performed. The sensitivities and specificities for diagnosing cancer were: EUS-FNA: sensitivity 0.79 (95% confidence interval (CI) 0.07 to 1.00), specificity 1.00 (95% CI 0.91 to 1.00); EUS: sensitivity 0.95 (95% CI 0.84 to 0.99), specificity 0.53 (95% CI 0.31 to 0.74); PET: sensitivity 0.92 (95% CI 0.80 to 0.97), specificity 0.65 (95% CI 0.39 to 0.84). The third analysis, of studies differentiating precancerous or cancerous lesions from benign lesions, only provided one test (EUS-FNA) in which meta-analysis was performed. EUS-FNA had moderate sensitivity for diagnosing precancerous or cancerous lesions (sensitivity 0.73 (95% CI 0.01 to 1.00) and high specificity 0.94 (95% CI 0.15 to 1.00), the extremely wide confidence intervals reflecting the heterogeneity between the studies). The fourth analysis, of studies differentiating cancerous (invasive carcinoma) from precancerous (dysplasia) provided three tests in which meta-analysis was performed. The sensitivities and specificities for diagnosing invasive carcinoma were: CT: sensitivity 0.72 (95% CI 0.50 to 0.87), specificity 0.92 (95% CI 0.81 to 0.97); EUS: sensitivity 0.78 (95% CI 0.44 to 0.94), specificity 0.91 (95% CI 0.61 to 0.98); EUS-FNA: sensitivity 0.66 (95% CI 0.03 to 0.99), specificity 0.92 (95% CI 0.73 to 0.98). The fifth analysis, of studies differentiating cancerous (high-grade dysplasia or invasive carcinoma) versus precancerous (low- or intermediate-grade dysplasia) provided six tests in which meta-analysis was performed. The sensitivities and specificities for diagnosing cancer (high-grade dysplasia or invasive carcinoma) were: CT: sensitivity 0.87 (95% CI 0.00 to 1.00), specificity 0.96 (95% CI 0.00 to 1.00); EUS: sensitivity 0.86 (95% CI 0.74 to 0.92), specificity 0.91 (95% CI 0.83 to 0.96); EUS-FNA: sensitivity 0.47 (95% CI 0.24 to 0.70), specificity 0.91 (95% CI 0.32 to 1.00); EUS-FNA carcinoembryonic antigen 200 ng/mL: sensitivity 0.58 (95% CI 0.28 to 0.83), specificity 0.51 (95% CI 0.19 to 0.81); MRI: sensitivity 0.69 (95% CI 0.44 to 0.86), specificity 0.93 (95% CI 0.43 to 1.00); PET: sensitivity 0.90 (95% CI 0.79 to 0.96), specificity 0.94 (95% CI 0.81 to 0.99). The sixth analysis, of studies differentiating cancerous (invasive carcinoma) from precancerous (low-grade dysplasia) provided no tests in which meta-analysis was performed. The seventh analysis, of studies differentiating precancerous or cancerous (intermediate- or high-grade dysplasia or invasive carcinoma) from precancerous (low-grade dysplasia) provided two tests in which meta-analysis was performed. The sensitivity and specificity for diagnosing cancer were: CT: sensitivity 0.83 (95% CI 0.68 to 0.92), specificity 0.83 (95% CI 0.64 to 0.93) and MRI: sensitivity 0.80 (95% CI 0.58 to 0.92), specificity 0.81 (95% CI 0.53 to 0.95), respectively. The eighth analysis, of studies differentiating precancerous or cancerous (intermediate- or high-grade dysplasia or invasive carcinoma) from precancerous (low-grade dysplasia) or benign lesions provided no test in which meta-analysis was performed.There were no major alterations in the subgroup analysis of cystic pancreatic focal lesions (42 studies; 2086 participants). None of the included studies evaluated EUS elastography or sequential testing. AUTHORS' CONCLUSIONS We were unable to arrive at any firm conclusions because of the differences in the way that study authors classified focal pancreatic lesions into cancerous, precancerous, and benign lesions; the inclusion of few studies with wide confidence intervals for each comparison; poor methodological quality in the studies; and heterogeneity in the estimates within comparisons.
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Affiliation(s)
- Lawrence MJ Best
- Royal Free Campus, UCL Medical SchoolDepartment of SurgeryRowland Hill StreetLondonUKNW32PF
| | - Vishal Rawji
- University College London Medical SchoolLondonUK
| | - Stephen P Pereira
- Royal Free Hospital CampusUCL Institute for Liver and Digestive HealthUpper 3rd FloorLondonUKNW3 2PF
| | - Brian R Davidson
- Royal Free Campus, UCL Medical SchoolDepartment of SurgeryRowland Hill StreetLondonUKNW32PF
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Duconseil P, Gilabert M, Gayet O, Loncle C, Moutardier V, Turrini O, Calvo E, Ewald J, Giovannini M, Gasmi M, Bories E, Barthet M, Ouaissi M, Goncalves A, Poizat F, Raoul JL, Secq V, Garcia S, Viens P, Iovanna J, Dusetti N. Transcriptomic analysis predicts survival and sensitivity to anticancer drugs of patients with a pancreatic adenocarcinoma. THE AMERICAN JOURNAL OF PATHOLOGY 2015; 185:1022-32. [PMID: 25765988 DOI: 10.1016/j.ajpath.2014.11.029] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 11/03/2014] [Accepted: 11/25/2014] [Indexed: 12/15/2022]
Abstract
A major impediment to the effective treatment of patients with pancreatic ductal adenocarcinoma (PDAC) is the molecular heterogeneity of this disease, which is reflected in an equally diverse pattern of clinical outcome and in responses to therapies. We developed an efficient strategy in which PDAC samples from 17 consecutive patients were collected by endoscopic ultrasound-guided fine-needle aspiration or surgery and were preserved as breathing tumors by xenografting and as a primary culture of epithelial cells. Transcriptomic analysis was performed from breathing tumors by an Affymetrix approach. We observed significant heterogeneity in the RNA expression profile of tumors. However, the bioinformatic analysis of these data was able to discriminate between patients with long- and short-term survival corresponding to patients with moderately or poorly differentiated PDAC tumors, respectively. Primary culture of cells allowed us to analyze their relative sensitivity to anticancer drugs in vitro using a chemogram, similar to the antibiogram for microorganisms, establishing an individual profile of drug sensitivity. As expected, the response was patient dependent. We also found that transcriptomic analysis predicts the sensitivity of cells to the five anticancer drugs most frequently used to treat patients with PDAC. In conclusion, using this approach, we found that transcriptomic analysis could predict the sensitivity to anticancer drugs and the clinical outcome of patients with PDAC.
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Affiliation(s)
- Pauline Duconseil
- Cancer Research Center of Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Aix-Marseille University and Paoli-Calmettes Institute, Scientific and Technological Park of Luminy, Marseille, France
| | - Marine Gilabert
- Cancer Research Center of Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Aix-Marseille University and Paoli-Calmettes Institute, Scientific and Technological Park of Luminy, Marseille, France
| | - Odile Gayet
- Cancer Research Center of Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Aix-Marseille University and Paoli-Calmettes Institute, Scientific and Technological Park of Luminy, Marseille, France
| | - Celine Loncle
- Cancer Research Center of Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Aix-Marseille University and Paoli-Calmettes Institute, Scientific and Technological Park of Luminy, Marseille, France
| | - Vincent Moutardier
- Cancer Research Center of Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Aix-Marseille University and Paoli-Calmettes Institute, Scientific and Technological Park of Luminy, Marseille, France; Department of Surgery, Hôpital Nord, Marseille, France
| | - Olivier Turrini
- Cancer Research Center of Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Aix-Marseille University and Paoli-Calmettes Institute, Scientific and Technological Park of Luminy, Marseille, France; Paoli-Calmettes Institute, Marseille, France
| | - Ezequiel Calvo
- Genomic Center, CHUL Research Centre, Quebec City, Quebec, Canada
| | | | | | - Mohamed Gasmi
- Department of Gastroenterology, Hôpital Nord, Marseille, France
| | | | - Marc Barthet
- Department of Gastroenterology, Hôpital Nord, Marseille, France
| | - Mehdi Ouaissi
- Department of Surgery, La Timone Hospital, Marseille, France
| | | | | | | | - Veronique Secq
- Cancer Research Center of Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Aix-Marseille University and Paoli-Calmettes Institute, Scientific and Technological Park of Luminy, Marseille, France; Department of Surgery, Hôpital Nord, Marseille, France
| | - Stephane Garcia
- Cancer Research Center of Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Aix-Marseille University and Paoli-Calmettes Institute, Scientific and Technological Park of Luminy, Marseille, France; Department of Surgery, Hôpital Nord, Marseille, France
| | | | - Juan Iovanna
- Cancer Research Center of Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Aix-Marseille University and Paoli-Calmettes Institute, Scientific and Technological Park of Luminy, Marseille, France.
| | - Nelson Dusetti
- Cancer Research Center of Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Aix-Marseille University and Paoli-Calmettes Institute, Scientific and Technological Park of Luminy, Marseille, France.
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Lausser L, Schmid F, Schmid M, Kestler HA. Unlabeling data can improve classification accuracy. Pattern Recognit Lett 2014. [DOI: 10.1016/j.patrec.2013.03.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Shivapurkar N, Weiner LM, Marshall JL, Madhavan S, Deslattes Mays A, Juhl H, Wellstein A. Recurrence of early stage colon cancer predicted by expression pattern of circulating microRNAs. PLoS One 2014; 9:e84686. [PMID: 24400111 PMCID: PMC3882238 DOI: 10.1371/journal.pone.0084686] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Accepted: 11/18/2013] [Indexed: 02/06/2023] Open
Abstract
Systemic treatment of patients with early-stage cancers attempts to eradicate occult metastatic disease to prevent recurrence and increased morbidity. However, prediction of recurrence from an analysis of the primary tumor is limited because disseminated cancer cells only represent a small subset of the primary lesion. Here we analyze the expression of circulating microRNAs (miRs) in serum obtained pre-surgically from patients with early stage colorectal cancers. Groups of five patients with and without disease recurrence were used to identify an informative panel of circulating miRs using quantitative PCR of genome-wide miR expression as well as a set of published candidate miRs. A panel of six informative miRs (miR-15a, mir-103, miR-148a, miR-320a, miR-451, miR-596) was derived from this analysis and evaluated in a separate validation set of thirty patients. Hierarchical clustering of the expression levels of these six circulating miRs and Kaplan-Meier analysis showed that the risk of disease recurrence of early stage colon cancer can be predicted by this panel of miRs that are measurable in the circulation at the time of diagnosis (P = 0.0026; Hazard Ratio 5.4; 95% CI of 1.9 to 15).
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Affiliation(s)
- Narayan Shivapurkar
- Lombardi Cancer Center, Georgetown University, Washington, District of Columbia, United States of America
- * E-mail: (NS); (AW)
| | - Louis M. Weiner
- Lombardi Cancer Center, Georgetown University, Washington, District of Columbia, United States of America
| | - John L. Marshall
- Lombardi Cancer Center, Georgetown University, Washington, District of Columbia, United States of America
| | - Subha Madhavan
- Lombardi Cancer Center, Georgetown University, Washington, District of Columbia, United States of America
| | - Anne Deslattes Mays
- Lombardi Cancer Center, Georgetown University, Washington, District of Columbia, United States of America
| | - Hartmut Juhl
- Lombardi Cancer Center, Georgetown University, Washington, District of Columbia, United States of America
- Indivumed GmbH, Hamburg, Germany
| | - Anton Wellstein
- Lombardi Cancer Center, Georgetown University, Washington, District of Columbia, United States of America
- * E-mail: (NS); (AW)
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Three Transductive Set Covering Machines. STUDIES IN CLASSIFICATION, DATA ANALYSIS, AND KNOWLEDGE ORGANIZATION 2014. [DOI: 10.1007/978-3-319-01595-8_33] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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Human equilibrative nucleoside transporter 1 and Notch3 can predict gemcitabine effects in patients with unresectable pancreatic cancer. Br J Cancer 2013; 108:1488-94. [PMID: 23492684 PMCID: PMC3629422 DOI: 10.1038/bjc.2013.108] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Background: Pancreatic ductal carcinoma (PDC) is one of the most lethal human carcinomas. Expression patterns of some genes may predict gemcitabine (GEM) treatment efficacy. We examined predictive indicators of survival in GEM-treated patients by quantifying the expression of several genes in pre-treatment endoscopic ultrasound-guided fine-needle aspiration (EUS-FNA) samples from patients with PDC. Methods: The expressions of human equilibrative nucleoside transporter 1 (hENT1), deoxycitidine kinase, ribonucleoside reductase 1, ribonucleoside reductase 2 and Notch3 in EUS-FNA tissue samples from 71 patients with unresectable PDC were quantified using real-time reverse transcription–polymerase chain reactions and examined for correlations with GEM sensitivity. Results: The log-rank test detected no significant differences in overall survival between GEM-treated patients with low and high mRNA levels of all genes examined. However, low Notch3 mRNA expression was significantly associated with longer overall survival in a multivariate analysis for survival (P=0.0094). High hENT1 expression level was significantly associated with a longer time to progression (P=0.039). Interaction tests for GEM administration and hENT1 or Notch3 mRNA expression were statistically significant (P=0.0054 and 0.0047, respectively). Conclusion: hENT1 and Notch3 mRNA expressions in EUS-FNA specimens were the key predictive biomarkers of GEM effect and GEM sensitivity in patients with unresectable PDC.
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Ferlinz A, Miller C, Formosa R, Lee KY. Gene expression analysis of both mRNA and miRNA on the same TaqMan® Array Card. Methods 2013; 59:S11-5. [DOI: 10.1016/j.ymeth.2012.09.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Alhamdani MSS, Youns M, Buchholz M, Gress TM, Beckers MC, Maréchal D, Bauer A, Schröder C, Hoheisel JD. Immunoassay-based proteome profiling of 24 pancreatic cancer cell lines. J Proteomics 2012; 75:3747-59. [PMID: 22579748 DOI: 10.1016/j.jprot.2012.04.042] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2012] [Revised: 04/24/2012] [Accepted: 04/27/2012] [Indexed: 01/29/2023]
Abstract
Pancreatic ductal adenocarcinoma is one of the most deadly forms of cancers, with a mortality that is almost identical to incidence. The inability to predict, detect or diagnose the disease early and its resistance to all current treatment modalities but surgery are the prime challenges to changing the devastating prognosis. Also, relatively little is known about pancreatic carcinogenesis. In order to better understand relevant aspects of pathophysiology, differentiation, and transformation, we analysed the cellular proteomes of 24 pancreatic cancer cell lines and two controls using an antibody microarray that targets 741 cancer-related proteins. In this analysis, 72 distinct disease marker proteins were identified that had not been described before. Additionally, categorizing cancer cells in accordance to their original location (primary tumour, liver metastases, or ascites) was made possible. A comparison of the cells' degree of differentiation (well, moderately, or poorly differentiated) resulted in unique marker sets of high relevance. Last, 187 proteins were differentially expressed in primary versus metastatic cancer cells, of which the majority is functionally related to cellular movement.
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Affiliation(s)
- Mohamed Saiel Saeed Alhamdani
- Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum (DKFZ), Im Neuenheimer Feld 580, Heidelberg, Germany.
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Bauer AS, Keller A, Costello E, Greenhalf W, Bier M, Borries A, Beier M, Neoptolemos J, Büchler M, Werner J, Giese N, Hoheisel JD. Diagnosis of pancreatic ductal adenocarcinoma and chronic pancreatitis by measurement of microRNA abundance in blood and tissue. PLoS One 2012; 7:e34151. [PMID: 22511932 PMCID: PMC3325244 DOI: 10.1371/journal.pone.0034151] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Accepted: 02/22/2012] [Indexed: 01/03/2023] Open
Abstract
A solid process for diagnosis could have a substantial impact on the successful treatment of pancreatic cancer, for which currently mortality is nearly identical to incidence. Variations in the abundance of all microRNA molecules from peripheral blood cells and pancreas tissues were analyzed on microarrays and in part validated by real-time PCR assays. In total, 245 samples from two clinical centers were studied that were obtained from patients with pancreatic ductal adenocarcinoma or chronic pancreatitis and from healthy donors. Utilizing the minimally invasive blood test, receiver operating characteristic (ROC) curves and the corresponding area under the curve (AUC) analysis demonstrated very high sensitivity and specificity of a distinction between healthy people and patients with either cancer or chronic pancreatitis; respective AUC values of 0.973 and 0.950 were obtained. Confirmative and partly even more discriminative diagnosis could be performed on tissue samples with AUC values of 1.0 and 0.937, respectively. In addition, discrimination between cancer and chronic pancreatitis was achieved (AUC = 0.875). Also, several miRNAs were identified that exhibited abundance variations in both tissue and blood samples. The results could have an immediate diagnostic value for the evaluation of tumor reoccurrence in patients, who have undergone curative surgical resection, and for people with a familial risk of pancreatic cancer.
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Affiliation(s)
- Andrea S Bauer
- Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum, Heidelberg, Germany
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Road to early detection of pancreatic cancer: Attempts to utilize epigenetic biomarkers. Cancer Lett 2012; 342:231-7. [PMID: 22450751 DOI: 10.1016/j.canlet.2012.03.022] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2012] [Revised: 03/20/2012] [Accepted: 03/20/2012] [Indexed: 12/14/2022]
Abstract
The prognosis of pancreatic cancer is extremely poor, mainly because of its aggressive biological behavior and late onset of symptoms for clinical diagnosis; these impose limitations on therapeutic intervention. Deeper genomic sequencing analyses of pancreatic cancers revealed 12 core pathways and a long duration, nearly 20 years from initiation to distant metastases. This evidence will offer a broader aspect and time window of opportunity for early detection, thus preventing deaths from this cruel cancer. Epigenetic biomarkers can be utilized for assessing cancer risk, early detection, and predicting prognosis and therapeutic responses. In this review, we briefly summarize relevant issues associated with pancreatic cancer progression and recent advances in epigenetic biomarkers such as DNA methylation, miRNAs, satellite repeats, and histone modifications for early diagnosis.
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Gress TM, Kestler HA, Lausser L, Fiedler L, Sipos B, Michalski CW, Werner J, Giese N, Scarpa A, Buchholz M. Differentiation of multiple types of pancreatico-biliary tumors by molecular analysis of clinical specimens. J Mol Med (Berl) 2011; 90:457-64. [PMID: 22119958 DOI: 10.1007/s00109-011-0832-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2011] [Revised: 10/11/2011] [Accepted: 10/28/2011] [Indexed: 12/30/2022]
Abstract
Timely and accurate diagnosis of pancreatic ductal adenocarcinoma (PDAC) is critical in order to provide adequate treatment to patients. However, the clinical signs and symptoms of PDAC are shared by several types of malignant or benign tumors which may be difficult to differentiate from PDAC with conventional diagnostic procedures. Among others, these include ampullary cancers, solid pseudopapillary tumors, and adenocarcinomas of the distant bile duct, as well as inflammatory masses developing in chronic pancreatitis. Here, we report an approach to accurately differentiate between these different types of pancreatic masses based on molecular analysis of biopsy material. A total of 156 bulk tissue and fine needle aspiration biopsy samples were analyzed using a dedicated diagnostic cDNA array and a composite classification algorithm developed based on linear support vector machines. All five histological subtypes of pancreatic masses were clearly separable with 100% accuracy when using all 156 individual samples for classification. Generalized performance of the classification system was tested by 10 × 10-fold cross validation (100 test runs). Correct classification into the five diagnostic groups was demonstrated for 81.5% of 1,560 test set predictions. Performance increased to 85.3% accuracy when PDAC and distant bile duct carcinomas were combined in a single diagnostic class. Importantly, overall sensitivity of detection of malignant disease was 92.2%. The molecular diagnostic approach presented here is suitable to significantly aid in the differential diagnosis of undetermined pancreatic masses. To our knowledge, this is the first study reporting accurate differentiation between several types of pancreatico-biliary tumors in a single molecular analytical procedure.
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Affiliation(s)
- Thomas M Gress
- Division of Gastroenterology, University Hospital, Philipps-Universitaet Marburg, Marburg, Germany.
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Tissue and serum microRNAs in the Kras(G12D) transgenic animal model and in patients with pancreatic cancer. PLoS One 2011; 6:e20687. [PMID: 21738581 PMCID: PMC3124473 DOI: 10.1371/journal.pone.0020687] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2011] [Accepted: 05/06/2011] [Indexed: 12/30/2022] Open
Abstract
microRNAs (miRs) modulate the expression levels of mRNAs and proteins and can thus contribute to cancer initiation and progression. In addition to their intracelluar function, miRs are released from cells and shed into the circulation. We postulated that circulating miRs could provide insight into pathways altered during cancer progression and may indicate responses to treatment. Here we focus on pancreatic cancer malignant progression. We report that changes in miR expression patterns during progression of normal tissues to invasive pancreatic adenocarcinoma in the p48-Cre/LSL-KrasG12D mouse model mirrors the miR changes observed in human pancreatic cancer tissues. miR-148a/b and miR-375 expression were found decreased whereas miR-10, miR-21, miR-100 and miR-155 were increased when comparing normal tissues, premalignant lesions and invasive carcinoma in the mouse model. Predicted target mRNAs FGFR1 (miR-10) and MLH1 (miR-155) were found downregulated. Quantitation of nine microRNAs in plasma samples from patients distinguished pancreatic cancers from other cancers as well as non-cancerous pancreatic disease. Finally, gemcitabine treatment of control animals and p48-Cre/LSL-KrasG12D animals with pancreatic cancer caused distinct and up to 60-fold changes in circulating miRs that indicate differential drug effects on normal and cancer tissues. These findings support the significance of detecting miRs in the circulation and suggests that circulating miRs could serve as indicators of drug response.
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Schröder C, Jacob A, Tonack S, Radon TP, Sill M, Zucknick M, Rüffer S, Costello E, Neoptolemos JP, Crnogorac-Jurcevic T, Bauer A, Fellenberg K, Hoheisel JD. Dual-color proteomic profiling of complex samples with a microarray of 810 cancer-related antibodies. Mol Cell Proteomics 2010; 9:1271-80. [PMID: 20164060 PMCID: PMC2877986 DOI: 10.1074/mcp.m900419-mcp200] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Antibody microarrays have the potential to enable comprehensive proteomic analysis of small amounts of sample material. Here, protocols are presented for the production, quality assessment, and reproducible application of antibody microarrays in a two-color mode with an array of 1,800 features, representing 810 antibodies that were directed at 741 cancer-related proteins. In addition to measures of array quality, we implemented indicators for the accuracy and significance of dual-color detection. Dual-color measurements outperform a single-color approach concerning assay reproducibility and discriminative power. In the analysis of serum samples, depletion of high-abundance proteins did not improve technical assay quality. On the contrary, depletion introduced a strong bias in protein representation. In an initial study, we demonstrated the applicability of the protocols to proteins derived from urine samples. We identified differences between urine samples from pancreatic cancer patients and healthy subjects and between sexes. This study demonstrates that biomedically relevant data can be produced. As demonstrated by the thorough quality analysis, the dual-color antibody array approach proved to be competitive with other proteomic techniques and comparable in performance to transcriptional microarray analyses.
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Affiliation(s)
- Christoph Schröder
- Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum, 69120 Heidelberg, Germany.
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Ashida R, Nakata B, Shigekawa M, Mizuno N, Sawaki A, Hirakawa K, Arakawa T, Yamao K. Gemcitabine sensitivity-related mRNA expression in endoscopic ultrasound-guided fine-needle aspiration biopsy of unresectable pancreatic cancer. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2009; 28:83. [PMID: 19531250 PMCID: PMC2705349 DOI: 10.1186/1756-9966-28-83] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2009] [Accepted: 06/16/2009] [Indexed: 12/15/2022]
Abstract
Background The aim of this study was to determine a predictive indicator of gemcitabine (GEM) efficacy in unresectable pancreatic cancer using tissue obtained by endoscopic ultrasound-guided fine-needle aspiration biopsy (EUS-FNA). Methods mRNAs extracted from 35 pancreatic tubular adenocarcinoma tissues obtained by EUS-FNA before GEM-treatment were studied. mRNAs were amplified and applied to a Focused DNA Array, which was restricted to well-known genes, including GEM sensitivity-related genes, deoxycytidine kinase (dCK), human equilibrative nucleoside transporter 1 (hENT1), hENT2, dCMP deaminase, cytidine deaminase, 5'-nucleotidase, ribonucleotide reductase 1 (RRM1) and RRM2. mRNA levels were classified into high and low expression based on a cut-off value defined as the average expression of 35 samples. These 35 patients were divided into the following two groups. Patients with partial response and those with stable disease whose tumor markers decreased by 50% or more were classified as the effective group. The rest of patients were classified as the non-effective group. The relationship between GEM efficacy and mRNA expression was then examined by chi-squared test. Results Among these GEM sensitivity-related genes, dCK alone showed a significant correlation with GEM efficacy. Eight of 12 patients in the effective group had high dCK expression, whereas 16 of 23 patients in non-effective group had low dCK expressions (P = 0.0398). Conclusion dCK mRNA expression is a candidate indicator for GEM efficacy in unresectable pancreatic cancer. Quantitative mRNA measurements of dCK using EUS-FNA samples are necessary for definitive conclusions.
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Affiliation(s)
- Reiko Ashida
- Department of Gastroenterology, Osaka City University Graduate School of Medicine, Osaka, Japan.
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Voidonikolas G, Kreml SS, Chen C, Fisher WE, Brunicardi FC, Gibbs RA, Gingras MC. Basic principles and technologies for deciphering the genetic map of cancer. World J Surg 2009; 33:615-29. [PMID: 19115029 PMCID: PMC2924149 DOI: 10.1007/s00268-008-9851-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The progress achieved in the field of genomics in recent years is leading medicine to adopt a personalized model in which the knowledge of individual DNA alterations will allow a targeted approach to cancer. Using pancreatic cancer as a model, we discuss herein the fundamentals that need to be considered for the high throughput and global identification of mutations. These include patient-related issues, sample collection, DNA isolation, gene selection, primer design, and sequencing techniques. We also describe the possible applications of the discovery of DNA changes to the approach of this disease and cite preliminary efforts where the knowledge has been translated into the clinical or preclinical setting.
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Affiliation(s)
- Georgios Voidonikolas
- Michael E. DeBakey Department of Surgery, Baylor College of Medicine, Houston, Texas, USA
| | - Stephanie S. Kreml
- Michael E. DeBakey Department of Surgery, Baylor College of Medicine, Houston, Texas, USA
| | - Changyi Chen
- Michael E. DeBakey Department of Surgery, Baylor College of Medicine, Houston, Texas, USA
| | - William E. Fisher
- Michael E. DeBakey Department of Surgery, Baylor College of Medicine, Houston, Texas, USA
- The Elkins Pancreas Center, Baylor College of Medicine, Houston, Texas, USA
| | - F. Charles Brunicardi
- Michael E. DeBakey Department of Surgery, Baylor College of Medicine, Houston, Texas, USA
| | - Richard A. Gibbs
- Human Genome Sequencing Center; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Marie-Claude Gingras
- Michael E. DeBakey Department of Surgery, Baylor College of Medicine, Houston, Texas, USA
- Human Genome Sequencing Center; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
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Bauer A, Kleeff J, Bier M, Wirtz M, Kayed H, Esposito I, Korc M, Hafner M, Hoheisel JD, Friess H. Identification of malignancy factors by analyzing cystic tumors of the pancreas. Pancreatology 2008; 9:34-44. [PMID: 19077453 DOI: 10.1159/000178873] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
AIM The diversity in the aggressiveness of cystic tumors of the pancreas - ranging from the usually benign serous cystadenoma to lesions of variable degrees of malignancy - was utilized for the identification of molecular factors that are involved in the occurrence of malignancy. METHODS We analyzed the transcript profiles of different cystic tumor types. The results were confirmed at the protein level by immunohistochemistry. Also, functional studies with siRNA silencing were performed. RESULTS Expression variations at the RNA and protein level were identified that are closely correlated with the degree of malignancy. Besides, all tumors could be classified effectively by this means. Many of the identified factors had not previously been known to be associated with malignant cystic lesions. siRNA silencing of the gene with the most prominent variation - the anti-apoptotic factor FASTK (Fas-activated serine/threonine kinase) - revealed a regulative effect on several genes known to be relevant to the development of tumors. CONCLUSION By a molecular analysis of rare types of pancreatic cancer, which are less frequent in terms of disease, variations could be identified that could be critical for the regulation of malignancy and thus relevant to the treatment of also the majority of pancreatic tumors.
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Affiliation(s)
- Andrea Bauer
- Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum, Heidelberg, Germany.
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König A, König U, Gress T. [Diagnostics and therapy of chronic pancreatitis]. Internist (Berl) 2008; 49:695-707; quiz 708-9. [PMID: 18437329 DOI: 10.1007/s00108-008-2131-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Chronic pancreatitis (CP) is characterized by progressive, chronic inflammation of the pancreas, resulting in loss of exocrine and endocrine function and chronic abdominal pain. In most cases, CP is induced by long-term alcoholism. The second most frequent diagnosis is idiopathic CP, in the absence of known causes of CP. However, the identification of genetic and immunological causes continuously reduces the number of cases classified as idiopathic pancreatitis. Common symptoms of CP comprise abdominal pain radiating to the back, diarrhea, steatorrhea and the development of diabetes. The diagnosis is mainly based on clinical features, typical morphological findings such as pancreatic calcifications, duct stenoses and dilatations, as well as pathologic pancreatic function tests. Treatment of CP includes watch and wait strategies in asymptomatic patients, symptomatic treatment of the clinical features such as pain, exocrine and endocrine insufficiency, as well as interventional or surgical therapy of complications such as pseudocysts, pancreatic duct stenosis, stones or biliary obstruction.
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Affiliation(s)
- A König
- Klinik für Gastroenterologie, Endokrinologie und Stoffwechsel, Universitätsklinikum Giessen und Marburg GmbH, Standort Marburg, Baldingerstrasse, 35043, Marburg, Germany
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Buchholz M, Kestler H, Gress TM. Differential diagnosis of pancreatic tumors by molecular analysis of clinical specimens. Pancreatology 2008; 8:551-7. [PMID: 18818507 DOI: 10.1159/000159213] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
OBJECTIVE To describe the capabilities and limitations of the current state of the art in pancreatic cancer diagnostics and to discuss recent progress in the development of novel, highly accurate molecular diagnostic approaches. RESULTS Molecular analyses currently under evaluation as novel diagnostic tests include detection of point mutations, genomic imbalances, aberrant methylation patterns and gene expression changes on the mRNA and protein levels in pancreatic juice, fine needle aspiration biopsies and brush cytologies. CONCLUSIONS In exploratory studies, several candidate molecular markers show great potential to serve as general indicators of malignancy, but need to be validated in large, controlled, prospective studies. Multiplexing of diagnostic tests, e.g. in the form of specialized DNA microarrays, may provide more differentiated diagnoses such as the distinction of various tumor types or prognostic information for individual patients. The MolDiag-Paca consortium is strongly engaged in advancing these developments on a European level.
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Affiliation(s)
- Malte Buchholz
- Division of Gastroenterology, University Hospital, Philipps-Universität Marburg, Marburg, Germany
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Pitman MB, Deshpande V. Endoscopic ultrasound-guided fine needle aspiration cytology of the pancreas: a morphological and multimodal approach to the diagnosis of solid and cystic mass lesions. Cytopathology 2007; 18:331-47. [PMID: 17559566 DOI: 10.1111/j.1365-2303.2007.00457.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cytological evaluation of pancreatic masses and cysts is the preferred pre-operative diagnostic modality and is increasingly being performed by endoscopic ultrasound. This review focuses on the multimodal approach at the Massachusetts General Hospital that utilizes clinical, cytological, radiological and ancillary studies in rendering a final cytological diagnosis.
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Affiliation(s)
- M B Pitman
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA.
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Chen R, Brentnall TA, Pan S, Cooke K, Moyes KW, Lane Z, Crispin DA, Goodlett DR, Aebersold R, Bronner MP. Quantitative proteomics analysis reveals that proteins differentially expressed in chronic pancreatitis are also frequently involved in pancreatic cancer. Mol Cell Proteomics 2007; 6:1331-42. [PMID: 17496331 DOI: 10.1074/mcp.m700072-mcp200] [Citation(s) in RCA: 124] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The effective treatment of pancreatic cancer relies on the diagnosis of the disease at an early stage, a difficult challenge. One major obstacle in the development of diagnostic biomarkers of early pancreatic cancer has been the dual expression of potential biomarkers in both chronic pancreatitis and cancer. To better understand the limitations of potential protein biomarkers, we used ICAT technology and tandem mass spectrometry-based proteomics to systematically study protein expression in chronic pancreatitis. Among the 116 differentially expressed proteins identified in chronic pancreatitis, most biological processes were responses to wounding and inflammation, a finding consistent with the underlining inflammation and tissue repair associated with chronic pancreatitis. Furthermore 40% of the differentially expressed proteins identified in chronic pancreatitis have been implicated previously in pancreatic cancer, suggesting some commonality in protein expression between these two diseases. Biological network analysis further identified c-MYC as a common prominent regulatory protein in pancreatic cancer and chronic pancreatitis. Lastly five proteins were selected for validation by Western blot and immunohistochemistry. Annexin A2 and insulin-like growth factor-binding protein 2 were overexpressed in cancer but not in chronic pancreatitis, making them promising biomarker candidates for pancreatic cancer. In addition, our study validated that cathepsin D, integrin beta1, and plasminogen were overexpressed in both pancreatic cancer and chronic pancreatitis. The positive involvement of these proteins in chronic pancreatitis and pancreatic cancer will potentially lower the specificity of these proteins as biomarker candidates for pancreatic cancer. Altogether our study provides some insights into the molecular events in chronic pancreatitis that may lead to diverse strategies for diagnosis and treatment of these diseases.
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Affiliation(s)
- Ru Chen
- Division of Gastroenterology, Department of Medicine, University of Washington, Seattle, Washington 98195, USA.
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Kestler HA, Kraus JM, Palm G, Schwenker F. On the Effects of Constraints in Semi-supervised Hierarchical Clustering. ARTIFICIAL NEURAL NETWORKS IN PATTERN RECOGNITION 2006. [DOI: 10.1007/11829898_6] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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