A pair of researchers from Johns Hopkins Bloomberg School of Public Health and Duke University School of Medicine has developed a new tool to visualize cells and samples from within single-cell genomic data. The approach, dubbed SCUBI, addresses two main biases the researchers uncovered within scatterplots: the masking of cells by other cells and an unbalanced number of cell types in the sample. As they write in Cell Reports Methods, the researchers developed SCUBI to instead visualize cell data in non-overlapping squares and to visualize the difference in cell proportions across samples. "We show that our method, SCUBI, can address these biases and provide an unbiased view of the data, which will benefit the study design and follow-up data analysis and, ultimately, the soundness and reproducibility of the scientific conclusions," the researchers add.
Beijing Forestry University's Harry Wu and colleagues have generated a chromosome-level assembly of the Chinese pine genome. As they report in Cell, the researchers' 25.4-Gb chromosome-level assembly revealed that the tree genome's large size was due to large stretches of intergenic regions and introns with a number of transposable elements. By folding in methylome data, the researchers found that the transposable elements are targeted by an epigenetic silencing system that may then reduce the need for the elements to be removed from the Chinese pine genome. "Overall, the nearly complete P. tabuliformis genome and gene space annotation provided us with insights into conifer evolution and will facilitate various evolutionary studies on conifer-specific traits of interest, comparative and functional genomics, GWAS, and genomics-assisted breeding," Wu and colleagues say.
Lastly, researchers from Fudan University and elsewhere conducted a proteogenomic analysis of intrahepatic cholangiocarcinoma (iCCA) by comparing affected and matched normal liver tissue samples from 262 people. As they report in Cancer Cell, the researchers linked an aflatoxin signature with tumor initiation and proliferation as well as with immune suppression. At the same time, they noted a role for the integrin-FAK-SRC pathway in iCCA metastasis and suggested that FGFR2 fusions could represent a source of neoantigens. Their analysis further uncovered four iCCA subtypes marked by differences in genetic alterations and the tumor microenvironment but also in prognostic outlook and therapeutic opportunities.