Researchers in China, the US, Germany, and Austria take a look at the immune microenvironment features in hepatocellular carcinoma (HCC) with single-cell sequencing. Using SMART-seq2 and droplet-based single-cell RNA sequencing approaches, the team profiled CD45+ immune cells found within the liver tumor itself, as well as those in adjacent liver cells and cells from the hepatic lymph node, ascites, and blood. Based on transcriptome sequence data for more than 75,000 CD45+ immune cells from 16 untreated HCC patients, the team defined clusters of immune cells at and across sites, before establishing an online tool bringing together the data. "[O]ur comprehensive characterization of immune cells from different tissue sites reveals the dynamic nature of immune cells in the cancer setting," the authors report, adding that the analysis "uncovers differential lineage and migratory relationships of myeloid and lymphoid cells in the [tumor microenvironment], [lymph nodes], and ascites."
An international team, including members of the Clinical Proteomic Tumor Analysis Consortium, presents findings from a proteogenomic analysis of clear cell renal cell carcinoma (ccRCC). Based on genomic, epigenomic, transcriptomic, proteomic, and phosphoproteomic data for more than 100 treatment-naïve ccRCC tumors and 84 matched normal samples, the researchers searched for potential ccRCC drivers and molecular subgroups of the disease. In the process, for example, they uncovered four ccRCC subtypes with distinct immune features revealed by gene expression, proteomic, and phosphoproteomic features in the tumor microenvironment. "[T]his study reveals unique biological insights that are gained only when combining complementary proteomic and genomic analyses that link the functional consequences of genomic aberrations with proteomic outcomes," they write, noting that the approach "identifies underlying molecular mechanisms that are not fully capture at the genomic and transcriptomic levels."
Finally, researchers from the UK, Uganda, Nigeria, and elsewhere describe the Uganda Genome Resource, a collection of array-based SNP profiles for nearly 4,800 individuals from rural Uganda and genome sequences from the Uganda 2000 Genomes project. Using these sequences, the team tracked down 41.5 million SNPs and 4.5 million small insertions and deletions in the Ugandan participant — variants used for a series of population structure, migration, imputation, and cardiometabolic trait, and other analyses. "We find that several functionally important signals are driven by Africa-specific variants," the authors write, "highlighting the value of studying diverse populations across the region." GenomeWeb has more on the study, here.