A paper published last week in Cancer Cell describes a new method for cancer detection from a simple blood sample. So far, one limitation of this type of non-invasive “liquid biopsy” for early detection of cancer has been the inability to identify the nature of the primary tumor. This new method, based on sequencing mRNA from platelets, overcomes this limitation in spectacular fashion—providing accurate identification of the primary tumor location in 71% of the samples tested.
Human blood platelets contain small amounts of mRNA. The RNA profile of “tumor-educated” platelets changes in response to tumor growth as the platelets take up mRNA from tumor cells. In this study, the authors sequenced the platelet mRNA of various cancer patients and healthy donors, and then searched for cancer-associated expression profiles. Continue reading “Big Data. Bigger Hope.”
Riboprobes are RNA probes that can be produced by in vitro transcription of cloned DNA inserted in a suitable plasmid downstream of a viral promoter.
Viruses code for their own RNA polymerases, which are highly specific for the viral promoters. Using these enzymes, labeled NTPs, and inserts in both forward and reverse orientations, both sense and antisense riboprobes can be generated from a cloned gene.
Transcription of RNA is performed with the appropriate RNA polymerase (T3, T7 or SP6), depending on the RNA polymerase promoter sites present in the chosen vector. Because these polymerases are extremely promoter-specific (i.e., there is almost no transcriptional cross talk), virtually homogeneous RNA can be obtained using plasmid DNA as the template in a transcription reaction. When it is desirable to copy only insert DNA sequences, the plasmid is linearized at an appropriate restriction site before the transcription reaction and only discrete “run-off” transcripts are obtained, virtually free of vector sequences. RNA transcripts may be used to generate radioactive probes for hybridization to Northern and Southern blots, plaque and colony lifts as well as non-radioactive probes (i.e, labeled with digoxgenin)for in situ hybridization.
Recent references using riboprobes include: Continue reading “Riboprobes: RNA Probes Are Still Valuable Research Tools”