Cancer genomics identifies determinants of tumor biology

Abstract

Unbiased sequencing and analysis of human tumors is revealing unsuspected somatic changes that, upon further study, are elucidating aspects of tumor biology and identifying new biomarkers.

Figure 1

General schema for targeted exome capture, whole genome sequencing, and transcriptome sequencing. (a) In exome capture, a random library of genomic fragments, each containing platform-specific adapters on each end, is combined with a set of probes that define the human exome. Following hybridization, the probe:genomic library fragment hybrids are captured using magnetic beads and isolated from solution by the application of a magnet, or by solid phase capture. Denaturing conditions are used to elute the captured genomic library fragment population from the hybrids, and prepared for sequencing. (b) In whole genome sequencing, the same random fragment library is constructed as in (a), but the resulting fragments are sequenced directly without a capture step. (c) In transcriptome sequencing, the RNA is converted to cDNA, the resulting cDNAs are fragmented, and the library adapters are ligated to the resulting fragments, followed by sequencing. Panel (a) reproduced with permission from [27].

Figure 2

Impact of IDH1/2 mutations on tumor cell biology. (a) In normal cells, the role of IDH1 and IDH2 enzymes is to convert isocitrate to α-ketoglutarate (α-KG), converting NADP+ to NADPH. The presence of α-KG regulates prolylhydroxylases (PHD) that, in turn, promote the degradation of hypoxia-inducible factor 1α (HIF-1α). HIF-1α is a transcription factor that regulates the expression of genes related to glucose metabolism, angiogenesis, and other signaling pathways by sensing low cellular oxygen levels. The mutant IDH enzymes convert α-KG to 2-hydroxyglutarate (2-HG), leading to the build up of this oncometabolite. (b) Comparison of metabolomic profiling of IDH wild-type (upper panel) and mutant (lower panel) cells, indicating the increased levels of 2-HG associated with the mutation. 2-HG is absent in IDH wild-type cells. Panel (b) reproduced with permission from [15].

Figure 3

Two overlapping CTNNA1 deletions on chromosome 5 in three tumors. A graph of sequence depths, read pairs and genes in a 638,468-bp region containing two overlapping deletions. The top four panels display the read depths at each base, and the reads within the region whose mates mapped at an abnormal distance are displayed as bars, with matched pairs connected by arcs. Two different shades of blue indicate the two separate allelic deletion events (538,467 bp and 515,465 bp in length). The bottom panel displays genes annotated in this genomic region. Reproduced with permission from [17].