In Science this week, a team led by Harvard Medical School's George Church report on a new way to localize RNA levels within cells using a novel fluorescent in situ RNA sequencing technique, which they dubbed FISSEQ. In FISSEQ, stably cross-linked cDNA amplicons are sequenced within a biological sample. The scientists used the approach with fibroblasts with a simulated wound-healing assay to identify cell-to-cell differences in gene expression. "If this finding can be generalized, FISSEQ may be used to identify cell types based on gene expression profiles in situ," Church and his colleagues add.
Also in Science, researchers from Rockefeller University, Memorial Sloan-Kettering Cancer Center, and the New York Genome Center report on using whole-transcriptome and whole-genome sequencing to identify a chimeric transcript that is expressed in fibrolamellar hepatocellular carcinomas, a rare liver cancer affecting young adults. The chimeric transcript, they say, appears to be due to an in-frame fusion of one end of the DNAJB1 gene to part of the PRKACA gene. Further, the resulting protein is expressed and appears to keep its kinase activity. "While the role of the DNAJB1-PRKACA chimera in the pathogenesis of FL-HCC has yet to be addressed, our observations raise the possibility that it contributes to the pathogenesis of the tumor and may represent a therapeutic target," the researchers say.
GenomeWeb Daily News has more on this study here.