In cancer research, identifying cell lines with specific mutations is crucial for studying disease mechanisms, developing targeted therapies, and advancing drug discovery. Mutations like KRAS G12C, a common oncogenic driver in cancers such as non-small cell lung cancer (NSCLC) and colorectal cancer, are of particular interest due to their role in tumor growth and resistance to treatment. Researchers often need to find cell lines harboring such mutations to conduct experiments that mimic the genetic landscape of tumors.
Meritudio's Tumor Models Database is an invaluable resource for this purpose, offering a comprehensive collection of genomics data for approximately 2,000 cancer cell lines. Most of these cell lines are annotated with detailed mutation data, enabling researchers to quickly identify models that match their experimental needs. In this tutorial, we will walk you through the process of searching for cell lines with a specific mutation, using KRAS G12C as an example. Screenshots will guide you step-by-step to ensure a seamless experience.
● Open your web browser and navigate to Meritudio Bioinformatics Cloud.
● Enter your credentials (username and password) to log in to the platform.
● Once logged in, locate and click on the Tumor Models Database from the top Menu.
● On the Tumor Models Database homepage, locate the Quick Search box, as shown in the image.
● Type KRAS into the Quick Search box. The database will display relevant results, including gene, pathways, and associated tumor models (cell lines).
● Click on KRAS (KRS1, K-Ras4B) to continue to the KRAS gene page.
● On the KRAS gene page, you will see a graph displaying cell lines. Each dot in the graph represents a cell line.
● Red dots indicate cell lines with KRAS mutations, while blue represents wild-type.
● The graph also provides insights into the frequency of KRAS mutations across different cancer types. For example, you may observe that pancreatic cancer and colorectal cancer have a high frequency of KRAS mutations, which aligns with known oncogenic roles of KRAS in these cancers.
● The graph below also shows that there are 177 cell lines carrying mutations at position 12, of which 25 are G12C mutation.
● On the KRAS gene page, locate the Gene Mutation filter section.
● Click the last bullet point in the filter section to expand the mutation options.
● From the dropdown menu, select p.G12C and click Filter to filter for cell lines with the KRAS G12C mutation.
● The graph and results will update to display only 24 cell lines with the G12C mutation and KRAS expression data, the remaining one cell with G12C mutation has no KRAS expression data so is not in the boxplot, but can be found in the table below the boxplot.
● The table displays detailed information about 25 cell lines that carry the KRAS G12C mutation. We observe that (a) Lung adenocarcinoma and colorectal adenocarcinoma are prominently represented, consistent with the high prevalence of KRAS mutations in these cancers. (b) The mRNA expression and copy number values provide insights into the molecular characteristics of each cell line, which can help researchers select appropriate models for their studies. (c) The mutation frequency and pathogenicity classification (e.g., "likely_pathogenic") underscore the functional significance of the KRAS G12C mutation in driving cancer progression.
By following these steps, you can efficiently identify cell lines with specific mutations like KRAS G12C using Meritudio’s Tumor Models Database. This tool provides detailed genomics data, enabling researchers to explore mutation frequencies, expression levels, and copy number variations across various cancers. It’s an invaluable resource for advancing cancer research and drug development. Happy researching!
