Publications by authors named "Lara Schneider"

15 Publications

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SUMO pathway inhibition targets an aggressive pancreatic cancer subtype.

Gut 2020 Aug 30;69(8):1472-1482. Epub 2020 Jan 30.

Department of Hematology, Oncology and Tumor Immunology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, Berlin, Germany

Objective: Pancreatic ductal adenocarcinoma (PDAC) still carries a dismal prognosis with an overall 5-year survival rate of 9%. Conventional combination chemotherapies are a clear advance in the treatment of PDAC; however, subtypes of the disease exist, which exhibit extensive resistance to such therapies. Genomic MYC amplifications represent a distinct subset of PDAC with an aggressive tumour biology. It is clear that hyperactivation of MYC generates dependencies that can be exploited therapeutically. The aim of the study was to find and to target MYC-associated dependencies.

Design: We analysed human PDAC gene expression datasets. Results were corroborated by the analysis of the small ubiquitin-like modifier (SUMO) pathway in a large PDAC cohort using immunohistochemistry. A SUMO inhibitor was used and characterised using human and murine two-dimensional, organoid and in vivo models of PDAC.

Results: We observed that MYC is connected to the SUMOylation machinery in PDAC. Components of the SUMO pathway characterise a PDAC subtype with a dismal prognosis and we provide evidence that hyperactivation of MYC is connected to an increased sensitivity to pharmacological SUMO inhibition.

Conclusion: SUMO inhibitor-based therapies should be further developed for an aggressive PDAC subtype.
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http://dx.doi.org/10.1136/gutjnl-2018-317856DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7398468PMC
August 2020

Dietary sodium, potassium, and blood pressure in normotensive pregnant women: the National Health and Nutrition Examination Survey.

Appl Physiol Nutr Metab 2020 Feb 28;45(2):155-160. Epub 2019 Jun 28.

Department of Epidemiology, Arnold School of Public Health, University of South Carolina, Columbia, SC 29201, USA.

Dietary sodium, potassium, and sodium-to-potassium ratio are linearly associated with blood pressure in nonpregnant adults. Earlier investigations suggested null or inverse associations of blood pressure and sodium during normotensive pregnancy; findings have not been confirmed in race/ethnically diverse women or while accounting for potassium. Our purpose was to evaluate associations of blood pressure with sodium and potassium and sodium-to-potassium ratio in race/ethnically diverse normotensive pregnant women. We used cross-sectional blood pressure and dietary data from 984 women in multiple cycles of the National Health and Nutrition Examination Survey (mean age = 27.6 ± 0.2 years). We tested for differences in blood pressure across quartiles of sodium intake using Kruskal-Wallis tests and linear regression to evaluate associations of sodium, potassium, and the sodium-to-potassium ratio with systolic (SBP) and diastolic (DBP) blood pressures. We adjusted for potential confounding variables: age, race/ethnicity, education, marital status, body mass index, smoking, and month of pregnancy. SBP and DBP were similar across quartiles of sodium intake: quartile 1 (lowest sodium intake): 107/59; quartile 2: 106/59; quartile 3: 108/60; quartile 4 (highest sodium intake): 108/58 mm Hg, > 0.60 for all. Sodium (β = 0.16, 95% confidence interval (CI): -0.20 to 0.52) and potassium (β = 0.18, 95% CI: -0.24 to 0.60) and the sodium-to-potassium ratio (β = -0.54, 95% CI: -1.55 to 0.47) were not associated with SBP or DBP. Results were similar in stratified analyses. Blood pressure was similar among quartiles of sodium or potassium intake, even in analyses stratified by race/ethnicity and trimester of pregnancy. There was no association of sodium or potassium with blood pressure. Blood pressure may be insensitive to dietary sodium and potassium during normotensive pregnancy.
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http://dx.doi.org/10.1139/apnm-2019-0186DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7456746PMC
February 2020

ClinOmicsTrailbc: a visual analytics tool for breast cancer treatment stratification.

Bioinformatics 2019 12;35(24):5171-5181

Center for Bioinformatics, Saarbrücken, Germany.

Motivation: Breast cancer is the second leading cause of cancer death among women. Tumors, even of the same histopathological subtype, exhibit a high genotypic diversity that impedes therapy stratification and that hence must be accounted for in the treatment decision-making process.

Results: Here, we present ClinOmicsTrailbc, a comprehensive visual analytics tool for breast cancer decision support that provides a holistic assessment of standard-of-care targeted drugs, candidates for drug repositioning and immunotherapeutic approaches. To this end, our tool analyzes and visualizes clinical markers and (epi-)genomics and transcriptomics datasets to identify and evaluate the tumor's main driver mutations, the tumor mutational burden, activity patterns of core cancer-relevant pathways, drug-specific biomarkers, the status of molecular drug targets and pharmacogenomic influences. In order to demonstrate ClinOmicsTrailbc's rich functionality, we present three case studies highlighting various ways in which ClinOmicsTrailbc can support breast cancer precision medicine. ClinOmicsTrailbc is a powerful integrated visual analytics tool for breast cancer research in general and for therapy stratification in particular, assisting oncologists to find the best possible treatment options for their breast cancer patients based on actionable, evidence-based results.

Availability And Implementation: ClinOmicsTrailbc can be freely accessed at https://clinomicstrail.bioinf.uni-sb.de.

Supplementary Information: Supplementary data are available at Bioinformatics online.
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http://dx.doi.org/10.1093/bioinformatics/btz302DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6954665PMC
December 2019

Dietary patterns based on the Mediterranean diet and DASH diet are inversely associated with high aggressive prostate cancer in PCaP.

Ann Epidemiol 2019 01 5;29:16-22.e1. Epub 2018 Sep 5.

Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, SC. Electronic address:

Background: Several foods and nutrients have been linked to the development of prostate cancer, but the association between healthy dietary patterns and prostate cancer aggressiveness is less studied. The aim of this study was to evaluate the relationship between the Mediterranean diet (MED) and Dietary Approaches to Stop Hypertension (DASH) diet scores and prostate cancer aggressiveness by race.

Methods: Data from the population-based, case-only North Carolina-Louisiana Prostate Cancer Project (PCaP) were used to examine the association between diet quality, measured by MED and DASH scores, and prostate cancer aggressiveness in 1899 African American (AA) and European American (EA) research subjects. Dietary intake was assessed using a modified National Cancer Institute Diet History Questionnaire. Logistic regression was used to estimate adjusted odds ratios (ORs) and 95% confidence intervals (CIs) for high versus low-intermediate aggressive prostate cancer.

Results: Higher MED scores were inversely associated with high aggressive prostate cancer overall (OR: 0.66; 95% CI: 0.46, 0.95 for high versus low scores); results were similar for AA and EA men. A weaker inverse association between DASH scores and prostate cancer aggressiveness was found (OR: 0.76; 95% CI: 0.55, 1.06).

Conclusions: Higher diet quality, as represented by a Mediterranean-style diet or DASH diet, may reduce the odds of high aggressive prostate cancer.
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http://dx.doi.org/10.1016/j.annepidem.2018.08.012DOI Listing
January 2019

The role of TCF3 as potential master regulator in blastemal Wilms tumors.

Int J Cancer 2019 03 13;144(6):1432-1443. Epub 2018 Nov 13.

Center for Bioinformatics, Saarland Informatics Campus, Saarland University, Saarbrücken, Germany.

Wilms tumors are the most common type of pediatric kidney tumors. While the overall prognosis for patients is favorable, especially tumors that exhibit a blastemal subtype after preoperative chemotherapy have a poor prognosis. For an improved risk assessment and therapy stratification, it is essential to identify the driving factors that are distinctive for this aggressive subtype. In our study, we compared gene expression profiles of 33 tumor biopsies (17 blastemal and 16 other tumors) after neoadjuvant chemotherapy. The analysis of this dataset using the Regulator Gene Association Enrichment algorithm successfully identified several biomarkers and associated molecular mechanisms that distinguish between blastemal and nonblastemal Wilms tumors. Specifically, regulators involved in embryonic development and epigenetic processes like chromatin remodeling and histone modification play an essential role in blastemal tumors. In this context, we especially identified TCF3 as the central regulatory element. Furthermore, the comparison of ChIP-Seq data of Wilms tumor cell cultures from a blastemal mouse xenograft and a stromal tumor provided further evidence that the chromatin states of blastemal cells share characteristics with embryonic stem cells that are not present in the stromal tumor cell line. These stem-cell like characteristics could potentially add to the increased malignancy and chemoresistance of the blastemal subtype. Along with TCF3, we detected several additional biomarkers that are distinctive for blastemal Wilms tumors after neoadjuvant chemotherapy and that may provide leads for new therapeutic regimens.
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http://dx.doi.org/10.1002/ijc.31834DOI Listing
March 2019

REGGAE: a novel approach for the identification of key transcriptional regulators.

Bioinformatics 2018 10;34(20):3503-3510

Center for Bioinformatics, Saarland Informatics Campus, Saarland University, Saarbrücken D-66041, Germany.

Motivation: Transcriptional regulators play a major role in most biological processes. Alterations in their activities are associated with a variety of diseases and in particular with tumor development and progression. Hence, it is important to assess the effects of deregulated regulators on pathological processes.

Results: Here, we present REGulator-Gene Association Enrichment (REGGAE), a novel method for the identification of key transcriptional regulators that have a significant effect on the expression of a given set of genes, e.g. genes that are differentially expressed between two sample groups. REGGAE uses a Kolmogorov-Smirnov-like test statistic that implicitly combines associations between regulators and their target genes with an enrichment approach to prioritize the influence of transcriptional regulators. We evaluated our method in two different application scenarios, which demonstrate that REGGAE is well suited for uncovering the influence of transcriptional regulators and is a valuable tool for the elucidation of complex regulatory mechanisms.

Availability And Implementation: REGGAE is freely available at https://regulatortrail.bioinf.uni-sb.de.

Supplementary Information: Supplementary data are available at Bioinformatics online.
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http://dx.doi.org/10.1093/bioinformatics/bty372DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6184769PMC
October 2018

A randomized controlled trial to prevent excessive gestational weight gain and promote postpartum weight loss in overweight and obese women: Health In Pregnancy and Postpartum (HIPP).

Contemp Clin Trials 2018 03 31;66:51-63. Epub 2018 Jan 31.

Prevention Research Center, Arnold School of Public Health, University of South Carolina, Columbia, SC, United States; Department of Health Promotion, Education, and Behavior, Arnold School of Public Health, University of South Carolina, Columbia, SC, United States.

Background: Interventions to prevent excessive gestational weight gain and promote postpartum weight loss have yielded modest results, particularly in overweight and obese women.

Objectives: To examine the impact of a theory-based lifestyle intervention on gestational weight gain, postpartum weight loss, and related maternal and child outcomes and to examine race differences in these outcomes.

Design: A randomized controlled trial (target N=400; 200 intervention, 200 standard care; 200 African American, 200 white).

Methods: Overweight and obese African American and white women ≤16weeks gestation are recruited from obstetrics and gynecology clinics in South Carolina. Intervention participants receive two in-depth counseling sessions (early pregnancy and postpartum), telephone counseling, behavioral podcasts, and social media support that target weight self-monitoring and increasing physical activity and healthy dietary behavior practices, guided by Social Cognitive Theory. Standard care participants receive monthly mailings and a matched number of podcasts on non-weight related topics. All intervention activities last from ≤18weeks gestation to 6months after delivery. Gestational weight gain is the primary outcome. Secondary outcomes are meeting gestational weight gain guidelines (inadequate, adequate, excessive), weekly rate of gestational weight gain, postpartum weight retention, physical activity and dietary behaviors, health-related quality of life, and offspring adiposity. Participants are assessed at baseline (≤16weeks gestation), 32weeks gestation, and 6 and 12months postpartum, and offspring are assessed at 6 and 12months.

Summary: HIPP is an innovative study that addresses significant gaps in the literature. Primary outcome results are expected in 2019.
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http://dx.doi.org/10.1016/j.cct.2018.01.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5841597PMC
March 2018

Evaluation of different adsorbents for acidity reduction in residual oils.

Environ Technol 2019 Apr 18;40(11):1438-1454. Epub 2018 Jan 18.

b Department of Engineering and Exact , Federal University of Parana , Palotina , Brazil.

This work aims to evaluate the adsorption potential of bentonite and sugarcane bagasse clay for the reduction of free fatty acids in cooking oil through batch technique, experimental planning with different operating conditions (temperature, adsorbent mass and agitation). After were carried out kinetic studies and thermodynamic studies. Thus, both adsorbents were characterized by nitrogen dispersion, scanning electron microscopy with coupled energy dispersion spectroscopy. The sugarcane bagasse provided higher reductions compared to the bentonite clay, 58 and 50%, respectively. In the kinetic studies, it was observed that the pseudo-secunda model for both materials. Among the isotherms studied, the Langmuir model was better adjusted for sugarcane bagasse and Freundlich for bentonite clay. Thermodynamic parameters indicated spontaneous and endothermic adsorption at temperatures of 18°C, 20°C and 25°C. Both materials showed an advantageous result with the reduction to the adsorption of free fatty acids in the residual oil, considering that they are low-cost materials, their pre-treatment is simple from the operational point of view and their physical and chemical characteristics are favorable to the adsorption process, sugarcane bagasse contains about 42% hemicellulose, which is a hydroxyl-rich material that attracts the H ions from the medium.
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http://dx.doi.org/10.1080/09593330.2017.1422807DOI Listing
April 2019

Use of rice husk in waste cooking oil pretreatment.

Environ Technol 2019 Feb 10;40(5):594-604. Epub 2017 Nov 10.

b Federal University of Parana , Palotina , Brazil.

Since industrial wastes are increasing, the development of studies to find ways for their use is urgent. Waste cooking oil is an important source for the production of biodiesel, one of the main biofuels in Brazil. However, during cooking, the oil undergoes conditions that change its properties and decrease its quality, such as its acidity value. Current research treats waste cooking oil by the adsorption process using rice husk, an agro-industrial waste, and activated carbon to compare results. The potential of the adsorbents to remove free fatty acids in waste cooking oil has been investigated by the batch technique, evaluating different operating conditions of temperature, adsorbent mass and agitation. Adsorbents were characterized by nitrogen physisorption, scanning electron microscope, energy-dispersive spectroscopy and X-ray diffraction. The maximum result obtained for activated carbon at acidity reduction was 63%, using 22.4°C, 169.64 rpm and 3.39 g of adsorbent mass. Already, using the rice husk the percentage of removal was the same, 63% using 22.4°C, 80.36 rpm and 1.61 g of adsorbent, however in shorter times. The results prove that the application of the rice husk for this purpose is advantageous, for being a low-cost material, available on a large scale and that provide results similar to activated carbon.
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http://dx.doi.org/10.1080/09593330.2017.1397772DOI Listing
February 2019

The Phytochemistry and Pharmacology of Butia sp.: A Systematic Review and an Overview of the Technological Monitoring Process.

Phytother Res 2017 Oct 15;31(10):1495-1503. Epub 2017 Aug 15.

Postgraduate Program in Biochemistry and Bioprospecting, Oral Microbiology Laboratory, Pelotas Dental School, Federal University of Pelotas, Pelotas, RS, Brazil.

The Butia sp. are native South America trees, whose fruits are consumed in natura and have significant biological properties; however, trees of this genus plant are in danger of extinction. A systematic review of the literature and a technological overview were carried out to summarize the available evidence on the therapeutic uses and the phytochemical compounds of Butia sp. The following electronic databases were researched: MedLine (PubMed), Web of Science, Scopus, Scielo, and the gray literature. Furthermore, the online system such as the US Patent and Trademark Office, Espacenet, National Institute of Industrial Property, and Google Patents were accessed to obtain patent data. The inclusion criteria were articles that describe either the therapeutic uses of Butia sp. (antimicrobial activity, antioxidant activity, anti-inflammatory activity, antineoplastic activity) or studies describing phytochemical compounds of Butia sp. A limited amount of manual search was also undertaken. Reference lists were scanned to identify other relevant studies, and requests for unpublished data were conducted to people working in the field. Among 12 papers and 14 patents, 9 complete texts of scientific articles and 1 patent were scrutinised by two reviewers. We concluded that Butia has shown some antioxidant, anti-inflammatory, and antimicrobial activity, and its use could have important implications for future therapeutic uses. Although there is evidence of pharmacological potential from in vitro studies, clinical studies must be conducted to confirm the effectiveness of Butia sp. The evidence of its therapeutic uses has not been extensively studied yet, and the available evidence still needs further confirmation. Copyright © 2017 John Wiley & Sons, Ltd.
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http://dx.doi.org/10.1002/ptr.5883DOI Listing
October 2017

Systematic review and technological overview of the antimicrobial activity of Tagetes minuta and future perspectives.

J Ethnopharmacol 2017 Aug 29;208:8-15. Epub 2017 Jun 29.

Post-graduate Program in Biochemistry and Bioprospection, Federal University of Pelotas, Pelotas, RS, Brazil; Laboratory of Oral Microbiology, Pelotas Dental School, Federal University of Pelotas, Pelotas, RS, Brazil. Electronic address:

Ethnopharmacological Relevance: The antimicrobial potential of Tagetes minuta was correlated with its traditional use as antibacterial, insecticidal, biocide, disinfectant, anthelminthic, antifungal, and antiseptic agent as well as its use in urinary tract infections.

Aim Of The Study: This study aimed to systematically review articles and patents regarding the antimicrobial activity of T. minuta and give rise to perspectives on this plant as a potential antimicrobial agent.

Materials And Methods: A literature search of studies published between 1997 and 2015 was conducted over five databases: MedLine (PubMed), Web of Science, Scopus, Google Scholar, Portal de Periódicos Capes and SciFinder, grey literature was explored using the System for Information on Dissertations database, and theses were searched using the ProQuest Dissertations and Theses Full text database and the Periódicos Capes Theses database. Additionally, the following databases for patents were analysed: United States Patent and Trademark Office (USPTO), Google Patents, National Institute of Industrial Property (INPI) and Espacenet patent search (EPO). The data were tabulated and analysed using Microsoft Office Excel 2010.

Results: After title screening, 51 studies remained and this number decreased to 26 after careful examinations of the abstracts. The full texts of these 26 studies were assessed to check if they were eligible. Among them, 3 were excluded for not having full text access, and 11 were excluded because they did not fit the inclusion criteria, which left 10 articles for this systematic review. The same process was conducted for the patent search, resulting in 4 patents being included in this study.

Conclusion: Recent advances highlighted by this review may shed light on future directions of studies concerning T. minuta as a novel antimicrobial agent, which should be repeatedly proven in future animal and clinical studies. Although more evidence on its specificity and clinical efficacy are necessary to support its clinical use, T. minuta is expected to be a highly effective, safe and affordable treatment for infectious diseases.
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http://dx.doi.org/10.1016/j.jep.2017.06.046DOI Listing
August 2017

RegulatorTrail: a web service for the identification of key transcriptional regulators.

Nucleic Acids Res 2017 07;45(W1):W146-W153

Center for Bioinformatics, Saarland Informatics Campus, Saarland University, 66123 Saarbrücken, Germany.

Transcriptional regulators such as transcription factors and chromatin modifiers play a central role in most biological processes. Alterations in their activities have been observed in many diseases, e.g. cancer. Hence, it is of utmost importance to evaluate and assess the effects of transcriptional regulators on natural and pathogenic processes. Here, we present RegulatorTrail, a web service that provides rich functionality for the identification and prioritization of key transcriptional regulators that have a strong impact on, e.g. pathological processes. RegulatorTrail offers eight methods that use regulator binding information in combination with transcriptomic or epigenomic data to infer the most influential regulators. Our web service not only provides an intuitive web interface, but also a well-documented RESTful API that allows for a straightforward integration into third-party workflows. The presented case studies highlight the capabilities of our web service and demonstrate its potential for the identification of influential regulators: we successfully identified regulators that might explain the increased malignancy in metastatic melanoma compared to primary tumors, as well as important regulators in macrophages. RegulatorTrail is freely accessible at: https://regulatortrail.bioinf.uni-sb.de/.
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http://dx.doi.org/10.1093/nar/gkx350DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5570139PMC
July 2017

miRPathDB: a new dictionary on microRNAs and target pathways.

Nucleic Acids Res 2017 01 13;45(D1):D90-D96. Epub 2016 Oct 13.

Chair for Clinical Bioinformatics, Saarland Informatics Campus, Saarland University, D-66123 Saarbruecken, Germany

In the last decade, miRNAs and their regulatory mechanisms have been intensively studied and many tools for the analysis of miRNAs and their targets have been developed. We previously presented a dictionary on single miRNAs and their putative target pathways. Since then, the number of miRNAs has tripled and the knowledge on miRNAs and targets has grown substantially. This, along with changes in pathway resources such as KEGG, leads to an improved understanding of miRNAs, their target genes and related pathways. Here, we introduce the miRNA Pathway Dictionary Database (miRPathDB), freely accessible at https://mpd.bioinf.uni-sb.de/ With the database we aim to complement available target pathway web-servers by providing researchers easy access to the information which pathways are regulated by a miRNA, which miRNAs target a pathway and how specific these regulations are. The database contains a large number of miRNAs (2595 human miRNAs), different miRNA target sets (14 773 experimentally validated target genes as well as 19 281 predicted targets genes) and a broad selection of functional biochemical categories (KEGG-, WikiPathways-, BioCarta-, SMPDB-, PID-, Reactome pathways, functional categories from gene ontology (GO), protein families from Pfam and chromosomal locations totaling 12 875 categories). In addition to Homo sapiens, also Mus musculus data are stored and can be compared to human target pathways.
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http://dx.doi.org/10.1093/nar/gkw926DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5210630PMC
January 2017

Multi-omics enrichment analysis using the GeneTrail2 web service.

Bioinformatics 2016 05 18;32(10):1502-8. Epub 2016 Jan 18.

Center for Bioinformatics, Saarland University, Saarbrücken D-66041.

Motivation: Gene set analysis has revolutionized the interpretation of high-throughput transcriptomic data. Nowadays, with comprehensive studies that measure multiple -omics from the same sample, powerful tools for the integrative analysis of multi-omics datasets are required.

Results: Here, we present GeneTrail2, a web service allowing the integrated analysis of transcriptomic, miRNomic, genomic and proteomic datasets. It offers multiple statistical tests, a large number of predefined reference sets, as well as a comprehensive collection of biological categories and enables direct comparisons between the computed results. We used GeneTrail2 to explore pathogenic mechanisms of Wilms tumors. We not only succeeded in revealing signaling cascades that may contribute to the malignancy of blastemal subtype tumors but also identified potential biomarkers for nephroblastoma with adverse prognosis. The presented use-case demonstrates that GeneTrail2 is well equipped for the integrative analysis of comprehensive -omics data and may help to shed light on complex pathogenic mechanisms in cancer and other diseases.

Availability And Implementation: GeneTrail2 can be freely accessed under https://genetrail2.bioinf.uni-sb.de

Contact: : dstoeckel@bioinf.uni-sb.de

Supplementary Information: Supplementary data are available at Bioinformatics online.
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http://dx.doi.org/10.1093/bioinformatics/btv770DOI Listing
May 2016

DrugTargetInspector: An assistance tool for patient treatment stratification.

Int J Cancer 2016 Apr;138(7):1765-76

Center for Bioinformatics, Saarland University, Saarbrücken, Germany.

Cancer is a large class of diseases that are characterized by a common set of features, known as the Hallmarks of cancer. One of these hallmarks is the acquisition of genome instability and mutations. This, combined with high proliferation rates and failure of repair mechanisms, leads to clonal evolution as well as a high genotypic and phenotypic diversity within the tumor. As a consequence, treatment and therapy of malignant tumors is still a grand challenge. Moreover, under selective pressure, e.g., caused by chemotherapy, resistant subpopulations can emerge that then may lead to relapse. In order to minimize the risk of developing multidrug-resistant tumor cell populations, optimal (combination) therapies have to be determined on the basis of an in-depth characterization of the tumor's genetic and phenotypic makeup, a process that is an important aspect of stratified medicine and precision medicine. We present DrugTargetInspector (DTI), an interactive assistance tool for treatment stratification. DTI analyzes genomic, transcriptomic, and proteomic datasets and provides information on deregulated drug targets, enriched biological pathways, and deregulated subnetworks, as well as mutations and their potential effects on putative drug targets and genes of interest. To demonstrate DTI's broad scope of applicability, we present case studies on several cancer types and different types of input -omics data. DTI's integrative approach allows users to characterize the tumor under investigation based on various -omics datasets and to elucidate putative treatment options based on clinical decision guidelines, but also proposing additional points of intervention that might be neglected otherwise. DTI can be freely accessed at http://dti.bioinf.uni-sb.de.
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http://dx.doi.org/10.1002/ijc.29897DOI Listing
April 2016