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field--label-hidden field__items"> <div class="field__item">Biomarker Discovery </div> </div> </div> </div> </div> </div> </div> </div> </section> <div id="main-content"> <div id="block-proquinase-breadcrumbs" class="color-scheme-turquoise block block-system block-system-breadcrumb-block"> <div class="container"> <nav class="breadcrumb" role="navigation" aria-labelledby="system-breadcrumb"> <ol> <li><a href="https://www.reactionbiology.com">Home</a></li> <li>Resources</li><li>Tools</li> <li>Biomarker Analysis</li> </ol> </nav> </div> </div> <div class="view-container view-simple-page-conent"> <div class="container"> <article id="post-2356" class="post-2356 page type-page status-publish hentry" itemtype="https://schema.org/CreativeWork" itemscope=""> <div class="entry-content entry-content-servises "> <h1>Biomarker Analysis Tool</h1> <div class="text-mit-bild-text"> <div class="clearfix text-formatted field field--name-field-text field--type-text-long field--label-hidden field__items"> <p>The Biomarker Analysis Tool enables the identification of genetic signatures of tumor cell lines responsive to a customer’s drug including the gene expression signature and the mutational signature of the drug. The goal of the genetic signature analysis is to reveal prognostic biomarkers in the early discovery phase to predict response to drug treatment.</p> <h2>How Does the Biomarker Analysis Tool Work?</h2> <p>The Biomarker Analysis Tool exploits the IC50 raw data set obtained by profiling customers compounds such as the <a href="https://www.reactionbiology.com/services/cell-based-assays/prolifiler-cell-line-panel-screening">ProLiFiler<sup>TM</sup> </a>– Reaction Biology’s Cell Line Panel Screening service.<br /> The biomarker identification includes gene expression levels, somatic gene copy numbers, or genetic mutations. These biomarkers are indicative for the efficacy of a drug and may serve as predictive biomarkers in disease models and patient cohorts to stratify responders from non-responders.</p> </div> <div class="contact-buttons"> <div class="color-scheme-turquoise block block-block-content block-block-content9594f627-1f8b-4f13-b65e-979c19e399c0"> <a href="https://www.reactionbiology.com/contact/contact-us"> <div class="field field--name-field-icon field--type-image field--label-hidden field__items"> <img decoding="async" src="https://www.reactionbiology.com/wp-content/themes/Divi-child/images/icons-email.svg" alt="E-Mail" title="E-Mail" typeof="foaf:Image"> </div> <div class="field field--name-field-text field--type-string field--label-hidden field__items"> Contact an expert </div> </a> </div> <div class="color-scheme-turquoise block block-block-content block-block-contentc2ce2ae7-66e6-4f1b-87fb-ded5e6bcfb90"> <a class="newsletter-icon-box" href="#"> <div class="field field--name-field-icon field--type-image field--label-hidden field__items"> <img decoding="async" src="https://www.reactionbiology.com/wp-content/themes/Divi-child/images/icons-newsletter.svg" alt="Subscribe to Newsletter" title="Subscribe to Newsletter" typeof="foaf:Image"> </div> <div class="field field--name-field-text field--type-string field--label-hidden field__items"> Subscribe to our newsletter </div> </a> </div> <div class="color-scheme-turquoise block block-block-content block-block-content427638f8-6c52-46af-9064-2fe39ae6579d"> <a href="/#conferences"> <div class="field field--name-field-icon field--type-image field--label-hidden field__items"> <img decoding="async" src="https://www.reactionbiology.com/wp-content/themes/Divi-child/images/icons-meeting.svg" alt="Meet us at your next conference" title="Meet us at your next conference" typeof="foaf:Image"> </div> <div class="field field--name-field-text field--type-string field--label-hidden field__items"> Meet us at your next conference </div> </a> </div> <div class="color-scheme-turquoise block block-block-content block-block-contentff27f1d7-2f17-4dd2-ad72-3ef66b6982de"> <a href="/cdn-cgi/l/email-protection#ffc08c8a9d959a9c8bc2b6df889e918bdf8b90df8c979e8d9adf8b97968cdfad9a9e9c8b969091dfbd969093909886df93969194df88968b97df86908ad99e928fc49d909b86c2978b8b8f8cc5d0d0888888d18d9a9e9c8b9690919d969093909886d19c9092d08c9a8d89969c9a8cd09d9690929e8d949a8dd29b968c9c90899a8d86d0989a919a8b969cd29d9690929e8d949a8d8cd09d9690929e8d949a8dd29e919e93868c968cd0"> <div class="field field--name-field-icon field--type-image field--label-hidden field__items"> <img decoding="async" src="https://www.reactionbiology.com/wp-content/themes/Divi-child/images/icons-share.svg" alt="Share" title="Share" typeof="foaf:Image"> </div> <div class="field field--name-field-text field--type-string field--label-hidden field__items"> Share </div> </a> </div> </div> </div> </div> </article> </div> </div> <div id="_anchor" class="paragraph weiss black paragraph--type--paragraph-container paragraph--view-mode--default"><div id="ba-id" class="paragraph text-right headline-left paragraph--type--text-with-video paragraph--view-mode--default"><div class="container center"><div class="text-wrapper"><h3>Bioinformatic biomarker analysis in a nutshell</h3> <div class="text-mit-bild-text"> <div class="clearfix text-formatted field field--name-field-text field--type-text-long field--label-hidden field__items"> <p>Watch to learn how Reaction Biology uses bioinformatics to identify the genetic signature of tumor cells that are responsive to the treatment of your drug and how this can help your drug discovery project. Watch to learn how Reaction Biology uses bioinformatics to identify the genetic signature of tumor cells that are responsive to the treatment of your drug and how this can help your drug discovery project.</p> </div> </div> <div class="text-mit-bild-bild field field--name-field-images field--type-image field--label-hidden field__items field--name-field-video"> <div class="text-mit-bild-bild-rahmen"> <div class="field__item"> <p><iframe loading="lazy" src="https://www.youtube.com/embed/Ko8W5ecBxF4?autoplay=0&start=0&rel=0" width="854" height="480" frameborder="0" allowfullscreen="allowfullscreen"></iframe></p> <div class="caption">undefined</div> </div> </div> </div> </div></div></div><div id="ba-id2" class="paragraph paragraph--type--tab-container paragraph--view-mode--default"><div class="container center"><h2>Additional Information about the Biomarker Analysis Tool</h2> <div class="tab-container"><ul class="tab-navigation"><li class="tab-active" data-id="#tab-ba-id221">Case Study Nutlin-3a - sensitivity data</li><li data-id="#tab-ba-id222">Case Study Nutlin-3a - Gene Expression</li><li data-id="#tab-ba-id223">Case Study Nutlin-3a - Mutation Analysis</li><li data-id="#tab-ba-id224">Biomarker Analysis Details</li></ul><div class="field field--name-field-paragraph field--type-entity-reference-revisions field--label-hidden field__items"><div id="tab-ba-id221" class="tab-content-active paragraph paragraph--type--tab-text-with-image paragraph--view-mode--default"><div class="field field--name-field-title field--type-string field--label-hidden field__items">Case Study Nutlin-3a - sensitivity data</div><div class="tab-content"><div class="tab-content-wrapper"><div class="clearfix text-formatted field field--name-field-text field--type-text-long field--label-hidden field__items"><h2>Case Study Nutlin-3a – sensitivity data</h2> <p>This case study investigates nutlin-3a which is a small molecule that occupies the p53 binding pocket of MDM2 and effectively disrupts the p53–MDM2 interaction that leads to activation of the p53 pathway.</p> <p><img loading="lazy" decoding="async" class="alignnone size-full wp-image-2364" src="https://www.reactionbiology.com/wp-content/uploads/2023/07/Biomarker-Example-IC50-ranking-Nutlin_white-frame.png" alt="" width="1351" height="835" srcset="https://www.reactionbiology.com/wp-content/uploads/2023/07/Biomarker-Example-IC50-ranking-Nutlin_white-frame.png 1351w, https://www.reactionbiology.com/wp-content/uploads/2023/07/Biomarker-Example-IC50-ranking-Nutlin_white-frame-300x185.png 300w, https://www.reactionbiology.com/wp-content/uploads/2023/07/Biomarker-Example-IC50-ranking-Nutlin_white-frame-1024x633.png 1024w, https://www.reactionbiology.com/wp-content/uploads/2023/07/Biomarker-Example-IC50-ranking-Nutlin_white-frame-768x475.png 768w, https://www.reactionbiology.com/wp-content/uploads/2023/07/Biomarker-Example-IC50-ranking-Nutlin_white-frame-1080x668.png 1080w" sizes="(max-width: 1351px) 100vw, 1351px" /></p> <p>The IC50 values of nutlin-3a were determined on 274 tumor cell lines and ranked. The tumor cell lines could be grouped as resistant, intermediated sensitive, and highly sensitive. The highest testing concentration was 30 µM with semi-log increments.</p> <p> </p> <p><img loading="lazy" decoding="async" class="alignnone size-full wp-image-2365" src="https://www.reactionbiology.com/wp-content/uploads/2023/07/Biomarker-Example-responder-Nutlin.png" alt="" width="1300" height="651" srcset="https://www.reactionbiology.com/wp-content/uploads/2023/07/Biomarker-Example-responder-Nutlin.png 1300w, https://www.reactionbiology.com/wp-content/uploads/2023/07/Biomarker-Example-responder-Nutlin-300x150.png 300w, https://www.reactionbiology.com/wp-content/uploads/2023/07/Biomarker-Example-responder-Nutlin-1024x513.png 1024w, https://www.reactionbiology.com/wp-content/uploads/2023/07/Biomarker-Example-responder-Nutlin-768x385.png 768w, https://www.reactionbiology.com/wp-content/uploads/2023/07/Biomarker-Example-responder-Nutlin-1080x541.png 1080w" sizes="(max-width: 1300px) 100vw, 1300px" /></p> <p>The IC50 values of nutlin-3a are shown in a scatter plot for each cell line. The tumor types were ranked for the highest median IC50. The median IC50 for all tumor types (red line) coincides at 30 µM testing concentration because of the high number of resistant tumor cell lines.</p> <p>The most susceptible tumor types are leukemia AML, melanoma, leukemia ALL, Hodgkin’s lymphoma.</p> </div></div></div></div><div id="tab-ba-id222" class=" paragraph paragraph--type--tab-text-with-image paragraph--view-mode--default"><div class="field field--name-field-title field--type-string field--label-hidden field__items">Case Study Nutlin-3a - Gene Expression</div><div class="tab-content"><div class="tab-content-wrapper"><div class="clearfix text-formatted field field--name-field-text field--type-text-long field--label-hidden field__items"><h2>Case Study Nutlin-3a – Gene Expression</h2> <p>This case study investigates nutlin-3a which is a small molecule that occupies the p53 binding pocket of MDM2 and effectively disrupts the p53–MDM2 interaction that leads to activation of the p53 pathway.</p> <p><img loading="lazy" decoding="async" class="alignnone size-full wp-image-2366" src="https://www.reactionbiology.com/wp-content/uploads/2023/07/Biomarker-Gene-Nutlin.png" alt="" width="1186" height="476" srcset="https://www.reactionbiology.com/wp-content/uploads/2023/07/Biomarker-Gene-Nutlin.png 1186w, https://www.reactionbiology.com/wp-content/uploads/2023/07/Biomarker-Gene-Nutlin-300x120.png 300w, https://www.reactionbiology.com/wp-content/uploads/2023/07/Biomarker-Gene-Nutlin-1024x411.png 1024w, https://www.reactionbiology.com/wp-content/uploads/2023/07/Biomarker-Gene-Nutlin-768x308.png 768w, https://www.reactionbiology.com/wp-content/uploads/2023/07/Biomarker-Gene-Nutlin-1080x433.png 1080w" sizes="(max-width: 1186px) 100vw, 1186px" /></p> <p><strong>Example</strong> <strong>of</strong><strong> nutlin-3a </strong><strong>gene</strong> <strong>expression</strong> <strong>analysis</strong><strong>. </strong>Graphical presentation of Limma test results show which genes are highly expressed in drug-resistant and drug-sensitive cell lines. MDM2 and other p53 pathway-related genes were highly expressed in tumor cell lines, which were sensitive to nutlin-3 treatment.</p> <p><img loading="lazy" decoding="async" class="alignnone size-full wp-image-2367" src="https://www.reactionbiology.com/wp-content/uploads/2023/07/Biomarker-Example-Gene-expression-Nutlin.png" alt="" width="1392" height="409" srcset="https://www.reactionbiology.com/wp-content/uploads/2023/07/Biomarker-Example-Gene-expression-Nutlin.png 1392w, https://www.reactionbiology.com/wp-content/uploads/2023/07/Biomarker-Example-Gene-expression-Nutlin-300x88.png 300w, https://www.reactionbiology.com/wp-content/uploads/2023/07/Biomarker-Example-Gene-expression-Nutlin-1024x301.png 1024w, https://www.reactionbiology.com/wp-content/uploads/2023/07/Biomarker-Example-Gene-expression-Nutlin-768x226.png 768w, https://www.reactionbiology.com/wp-content/uploads/2023/07/Biomarker-Example-Gene-expression-Nutlin-1080x317.png 1080w" sizes="(max-width: 1392px) 100vw, 1392px" /></p> <p>In the table are 10 genes listed which show high expression in tumor cell lines sensitive to nutlin-3a treatment. The results show that MDM2 expression is a predictor of sensitivity to nutlin-3a treatment.</p> </div></div></div></div><div id="tab-ba-id223" class=" paragraph paragraph--type--tab-text-with-image paragraph--view-mode--default"><div class="field field--name-field-title field--type-string field--label-hidden field__items">Case Study Nutlin-3a - Mutation Analysis</div><div class="tab-content"><div class="tab-content-wrapper"><div class="clearfix text-formatted field field--name-field-text field--type-text-long field--label-hidden field__items"><h2>Case Study Nutlin-3a – Mutation Analysis</h2> <p>This case study investigates nutlin-3a which is a small molecule that occupies the p53 binding pocket of MDM2 and effectively disrupts the p53–MDM2 interaction that leads to activation of the p53 pathway.</p> <p><img loading="lazy" decoding="async" class="alignnone size-full wp-image-2368" src="https://www.reactionbiology.com/wp-content/uploads/2023/07/Biomarker-Mutation-Nutlin.png" alt="" width="1070" height="521" srcset="https://www.reactionbiology.com/wp-content/uploads/2023/07/Biomarker-Mutation-Nutlin.png 1070w, https://www.reactionbiology.com/wp-content/uploads/2023/07/Biomarker-Mutation-Nutlin-300x146.png 300w, https://www.reactionbiology.com/wp-content/uploads/2023/07/Biomarker-Mutation-Nutlin-1024x499.png 1024w, https://www.reactionbiology.com/wp-content/uploads/2023/07/Biomarker-Mutation-Nutlin-768x374.png 768w" sizes="(max-width: 1070px) 100vw, 1070px" /></p> <p><strong>Example of nutlin-3a mutation analysis. </strong>Nutlin-3 was tested for dose-response in a panel of tumor cell lines. These cell lines contain a total of 16,998 mutated genes. The volcano plot shows for each gene (one dot) the Wilcoxon test p-value for the correlation of the drug response in proportion to the existence of mutants. For example, p53 mutations were found mostly in tumor cell lines that did not respond to nutlin-3a. KIAA1522, on the other hand, was found the most probable mutation that exists in cell lines responding to nutlin-3a treatment.</p> <p><img loading="lazy" decoding="async" class="alignnone size-full wp-image-2369" src="https://www.reactionbiology.com/wp-content/uploads/2023/07/Biomarker-Example-mutation-Nutlin.png" alt="" width="1000" height="236" srcset="https://www.reactionbiology.com/wp-content/uploads/2023/07/Biomarker-Example-mutation-Nutlin.png 1000w, https://www.reactionbiology.com/wp-content/uploads/2023/07/Biomarker-Example-mutation-Nutlin-300x71.png 300w, https://www.reactionbiology.com/wp-content/uploads/2023/07/Biomarker-Example-mutation-Nutlin-768x181.png 768w" sizes="(max-width: 1000px) 100vw, 1000px" /></p> <p><strong>The top three mutated genes correlated with nutlin-3a efficacy. </strong>P53 was found mutated in 10 cell lines, which responded to nutlin-3a treatment, and in 152 cell lines, which did not respond to nutlin-3a treatment. The mean IC50 value of nutlin-3a in tumor cell lines with p53 wild type was about 11.6 µM compared to 27.5 µM in cell lines with p53 mutation resulting in a difference of 16 µM between mutated and non-mutated cell lines which was used as a measure for resistance.</p> <p>In a mutation position analysis, amino acid Arg 273 in TP53 was shown to be the strongest marker of resistance.</p> </div></div></div></div><div id="tab-ba-id224" class=" paragraph paragraph--type--tab-text-with-image paragraph--view-mode--default"><div class="field field--name-field-title field--type-string field--label-hidden field__items">Biomarker Analysis Details</div><div class="tab-content"><div class="tab-content-wrapper"><div class="clearfix text-formatted field field--name-field-text field--type-text-long field--label-hidden field__items"><h2>Biomarker Analysis Details</h2> <p>Biomarker analysis at Reaction Biology is performed using a computational tool, the Cancer Data Miner, developed by our collaborator 4HF Biotec, a bioinformatics firm specializing in cancer data mining to discover new anti-cancer drugs.</p> <p><strong>Primary data set:</strong> We will perform the <a href="https://www.reactionbiology.com/services/cell-based-assays/prolifiler-cell-line-panel-screening">ProLiFiler<sup>TM</sup> assay</a> for testing the anti-proliferative effects of your drug on a set of 140 human tumor cell lines for IC50 determination, also called the ‘sensitivity profile’ of your compound.</p> <p><strong>Database</strong>: Our collaborator 4HF Biotec has built a comprehensive database, including data from more than 1,800 preclinical samples comprising multiple cancer datasets that are integrated into a single platform for visualization and statistical analysis.<br /> The data relevant for the Biomarker Analysis Tool are mutations (whole-exome sequencing), gene copy numbers, and gene expression data (Affymetrix).</p> <p><strong>Approach</strong>: The ProLiFiler<sup>TM</sup> results are correlated with the gene expression, mutation, and somatic copy number alteration data of the tumor cell lines that were used in the ProLiFiler<sup>TM</sup> study. A correlation analysis is performed for each cell line to determine the correlation of the drug sensitivity to each gene in regards to the expression level, mutation status, and/or somatic copy number. Watch the above video for more information.</p> <p><strong>Analysis: </strong>The Biomarker Analysis is performed with two statistical tests for each correlation; one uses the IC50 value of the test drug; and the other compares the gene data of responding and non-responding cell lines.</p> <p><strong>Deliverables</strong>:</p> <p><u>Mutation analysis</u></p> <ul> <li>Excel tables with raw data</li> <li>Graphical presentation of the correlation of mutation status for each gene and the drug sensitivity for each cell line</li> <li>Graphical presentation of the correlation of the position of each mutation and the drug sensitivity for each cell line</li> <li>Optional: Presentation of the amino acid position of relevant mutations</li> </ul> <p><u>Gene copy analysis</u></p> <ul> <li>Excel tables with raw data</li> <li>Graphical presentation of the correlation of gene copy gain and the drug sensitivity for each cell line</li> <li>Graphical presentation of correlation of gene copy loss and the drug sensitivity for each cell line</li> <li>For selected genes, additional plots can be generated</li> </ul> <p><u>Gene expression analysis</u></p> <ul> <li>Excel table with raw data</li> <li>Graphical presentation of the correlation of the expression of each gene and drug sensitivity for every cell line</li> <li>Graphical presentation of the cluster analysis to identify differential gene expression signatures and different response rates to the test drug</li> <li>Optional: Literature search of gene function for most relevant genes</li> </ul> <p>Additional analyses can be performed upon requests such as target gene analysis, pathway analysis, subtype analysis, hypothesis-driven analysis, predictive model development, and more.</p> </div></div></div></div></div></div></div></div><div id="ba-id3" class="paragraph paragraph--type--related-resources-container paragraph--view-mode--default"><div class="container center"><h2>Related Resources</h2><div class="field--name-field-paragraph related-resources-reference-wrapper"><div class="paragraph--type--related-resource node--type-related-resource"><div class="related-resource-wrapper"><div class="field--name-field-image"><div class="field field--name-field-image field--type-image field--label-hidden field__items"><img src="https://www.reactionbiology.com/wp-content/uploads/2023/07/ProLiFiler-and-Data-Mining-Infosheet-1.png" alt="ProLiFiler™ and Data Mining " title="ProLiFiler™ and Data Mining " typeof="foaf:Image" class="image-style-large"></div></div><div class="related-resource-text"> <div class="field--name-field-resource-category"> Info sheet </div> <div class="field--name-field-title"> <span class="field field--name-title field--type-string field--label-hidden"> ProLiFiler™ and Data Mining </span> </div> <div class="field--name-field-download"> <span class="pdfpreview-image-wrapper"> <a href="https://www.reactionbiology.com/wp-content/uploads/2023/07/ReactionBiology_ProLiFiler-plus-bioinformatics_InfoSheet-1.pdf" target="_blank">Download PDF</a> </span> </div> </div></div></div><div class="paragraph--type--related-resource node--type-related-resource"><div class="related-resource-wrapper"><div class="field--name-field-image"><div class="field field--name-field-image field--type-image field--label-hidden field__items"><img src="https://www.reactionbiology.com/wp-content/uploads/2023/07/Vincent-paper-thumbnail-2.png" alt="Pharmacogenomics characterization of the MDM2 inhibitor MI-773 reveals candidate tumours and predictive biomarkers. NPJ Precision Oncology, 2021 " title="Pharmacogenomics characterization of the MDM2 inhibitor MI-773 reveals candidate tumours and predictive biomarkers. NPJ Precision Oncology, 2021 " typeof="foaf:Image" class="image-style-large"></div></div><div class="related-resource-text"> <div class="field--name-field-resource-category"> Publication </div> <div class="field--name-field-title"> <span class="field field--name-title field--type-string field--label-hidden"> Pharmacogenomics characterization of the MDM2 inhibitor MI-773 reveals candidate tumours and predictive biomarkers. NPJ Precision Oncology, 2021 </span> </div> <div class="field--name-field-download"> <span class="pdfpreview-image-wrapper"> <a href="https://www.reactionbiology.com/wp-content/uploads/2023/07/211027_4HF_computational-analysis-of-MI-773-2.pdf" target="_blank">Download PDF</a> </span> </div> </div></div></div><div class="paragraph--type--related-resource node--type-related-resource"><div class="related-resource-wrapper"><div class="field--name-field-image"><div class="field field--name-field-image field--type-image field--label-hidden field__items"><img src="https://www.reactionbiology.com/wp-content/uploads/2023/07/ReactionBiology_ProLiFiler_Poster-1.png" alt="A systems biology approach combining ProLiFiler™ and Cancer Data Miner for an enhanced preclinical characterization of the Wee1 inhibitor adavosertib " title="A systems biology approach combining ProLiFiler™ and Cancer Data Miner for an enhanced preclinical characterization of the Wee1 inhibitor adavosertib " typeof="foaf:Image" 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