The Challenges of Glioblastoma
As exciting advances in cancer immunotherapies help revolutionize treatment of lung, colon, urothelial and more types of cancer, other kinds of cancer remain extremely challenging to detect early and treat. Glioblastoma is one such cancer, as the most common, most aggressive and most heterogenous form of adult brain cancer. Sadly, even with surgical intervention and radiation, the median survival time is just over a year. New diagnostic tools and avenues for therapeutic intervention are desperately needed for this deadly disease.
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Improving Whole Blood Transcriptomic Analysis
High-throughput single cell RNA sequencing-based analyses have already yielded some promising targets for further investigation in glioblastoma, including a potential immunotherapy target and a protein involved in epigenetic regulation of tumor recurrence. However, for an aggressive cancer type like glioblastoma, early detection may be especially critical for treatments to be as effective as possible, and thus new biomarkers to detect the cancer are also needed.
In a recent paper in npj Genomic Medicine, Qi et. al. describe an innovative method to create a more sensitive and robust whole blood RNA-seq protocol to search for glioblastoma biomarkers. Whole blood is considered to contain a more complete picture of physiological states than serum or plasma alone, but the extremely high hemoglobin content (the protein that carries oxygen in the blood) make transcriptomic analysis challenging, as an overwhelming majority of sequenced transcripts are hemoglobin mRNAs.
RNA-Seq-Based Analysis Uncovers Potential New Biomarker Profile
By depleting the amount of hemoglobin in the sample, the authors hoped to decrease background noise, thus enriching the signals of any transcriptomic biomarkers present. After refining an initial panel of transcriptomic traits identified as unique to glioblastoma, further analysis yielded a 10-gene panel including mRNA, long noncoding RNA and microRNA that together creates a profile that could serve as a diagnostic and clinical management tool for glioblastoma.
Liquid biopsies (using blood or other bodily fluids to detect disease) have significant advantages over traditional tissue biopsies, reducing pain and invasiveness for the patient and allowing easier analysis of difficult-to-access tissues like the brain. The innovation of globin reduction in whole blood analysis for biomarkers helped the authors determine a biomarker profile for glioblastoma and may be useful for profiling other challenging heterogeneous diseases in the future.
Outsourcing Bioinformatics Analysis: How Bridge Informatics Can Help
Many of our clients at Bridge Informatics are pursuing these kinds of research questions with sophisticated bioinformatics approaches. From pipeline development and software engineering to deploying existing bioinformatics tools, Bridge Informatics can help you on every step of your research journey.
As experts across data types from cutting-edge sequencing platforms, we can help you tackle the challenging computational tasks of storing, analyzing and interpreting genomic and transcriptomic data. Bridge Informatics’ bioinformaticians are trained bench biologists, so they understand the biological questions driving your computational analysis. Click here to schedule a free introductory call with a member of our team.
Jane Cook, Biochemist & Content Writer, Bridge Informatics
Jane Cook, leading Content Writer for Bridge Informatics, has written over 100 articles on the latest topics and trends for the bioinformatics community. Jane’s broad and deep interdisciplinary molecular biology experience spans developing biochemistry assays to genomics. Prior to joining Bridge, Jane held research assistant roles in biochemistry research labs across a variety of therapeutic areas. While obtaining her B.A. in Biochemistry from Trinity College in Dublin, Ireland, Jane also studied journalism at New York University’s Arthur L. Carter Journalism Institute. As a native Texan, she embraces any challenge that comes her way. Jane hails from Dallas but returns to Ireland any and every chance she gets. If you’re interested in reaching out, please email jennifer.martinez@old.bridgeinformatics.com or dan.ryder@old.bridgeinformatics.com.
