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Paper Review #1
"The genomic complexity of primary human prostate cancer"
Berger, et al., 2011
| Overview | Conclusions |
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Figures:
Table 1: Landscape of somatic alterations in primary human prostate cancers
Berger, et al., 2011
http://www.nature.com/nature/journal/v470/n7333/fig_tab/nature09744_T1.html
This table depicts the sequencing details of all seven genomes. Confidence levels in parentheses indicate quality control measures. The median number of apparent somatic base mutations was 3,866. The mean mutation frequency was estimated at 0.9 per megabase, a value similar to those found in previous studies of acute myeloid leukaemia and breast cancer but 7-15-fold lower than those found in previous studies of small cell lung cancer and melanoma. CpG (cytosine-phosphate-guanine) dinucleotides demonstrated mutation rates over 10-fold higher than at any other genomic position. The median number of non-synonymous base mutations per sample within protein-coding genes was 20. These coding mutations may be able to aid in possible future therapy development.
More specifically, in multiple tumors mutations were identified in the PTEN gene (phosphatase and tensin homologue); SPTA1 (gene encoding a scaffold protein that plays a role in specification of erythroid cell shape); SPOP (gene encoding a modulator of Daxx-mediated ubiquitination and transcriptional regulation); CHD1, CHD5, and HDAC9 (chromatin modifiers regulating embryonic stem cell pluripotency, gene regulation, and tumor suppression); and members of the HSP-1 stress response complex (HSPA2, HSPA5, and HSP90AB1) whose corresponding proteins make up a chaperone complex that several anticancer drugs are being developed to target. The median number of chromosomal rearrangements per genome was 90, a value similar to that of the previous study of breast cancer. Further analyses indicated that prostate and breast cancers differ in terms of the mechanisms of generating rearrangements.
Figure 1: Graphical representation of seven prostate cancer genomes.
Berger, et al., 2011
http://www.nature.com/nature/journal/v470/n7333/fig_tab/nature09744_F1.html
This figure displays the seven prostate cancer genomes that were sequenced: the top three with the TMPRSS2 (trans-membrane protease, serine 2)-ERG (v-ets erythroblastosis virus E26 oncogene homologue (avian)) gene fusion, and the bottom four without it. Each outer ring shows the genomic location while each inner ring shows chromosomal copy number: red meaning copy increase and blue meaning copy decrease. Within the rings, purple lines indicate interchromosomal translocations while green lines indicate intrachromosomal translocations. It is clear that chromosomal rearrangements are complex and not uniform among the seven samples.
Figure 2: Complex structural rearrangements in prostate cancer.
Berger, et al., 2011
http://www.nature.com/nature/journal/v470/n7333/fig_tab/nature09744_F2.html
a) This figure outlines the general ‘closed chain’ mechanism of chromosomal rearrangements, consisting of balanced (copy-neutral) breaking and rejoining, in the samples that was not detected previously in solid tumors. As shown by the four loci, such translocations do not result in loss of chromosomal material. b) While all three TMPRSS2-ERG fusion-positive tumors demonstrated this pattern, this figure specifically outlines the pattern in tumor )PR-1701: a closed quartet of balanced rearrangements of four loci on chromosomes 1 and 21. In the top half, thin bars (presumably the thin grey bars) indicate sequence reads and directionality indicates the reference genome’s mapping orientation; however, it is difficult to determine what is meant by ‘thin bars’ and ‘directionality.’ Each of the four loci is zoomed in to show disagreeing read pairs in the tumor genome (colored bars joined by purple lines) and agreeing read pairs in the normal genome, specifically illustrating the complex rearrangements in the tumors. The bottom half depicts a representation similar to part (a), of the specific breaking and rejoining pattern of the four loci on chromosomes 1 and 21, leading to two interchromosomal balanced translocations and two intrachromosomal balanced translocations (right). Hatch-marks represent sequences that are duplicated at the final fusion junctions (right). It is noteworthy that one of the four loci is an intergenic region, demonstrating the importance of complete genome sequencing. The nearest genes for this region are not shown, however. c) This figure, similar to the bottom half of part (b), displays the complex chromosomal rearrangement in the PR-2832 tumor, which is also TMPRSS2-ERG fusion-positive. Rearrangements are indicated for nine loci on chromosomes 12, 17, 5, and 9. Hatch-marks here represent sequences that are either duplicated or deleted at the final fusion junctions (right). The nearest genes for each intergenic region are shown here. Of note are the high number of regions rearranged, illustrating the complexity of the pattern, as well as the number of breakpoints near or in genes associated with cancer (i.e. TBK1, MAP2K4, TP53, and ABLi). This implies that formation of prostate cancer tumors may be caused by complex interchromosomal/intrachromosomal rearrangements that affect multiple genes in parallel.
Figure 2 as a whole implies that genomic regions could become co-localized spatially before rearrangement occurs. Such co-localization could imply a trend toward ‘transcription factories,’ or ‘preassembled nuclear subcompartments that contain RNA polymerase II holoenzyme.’ Researchers used previously published data on ChIP-seq (chromatin immunoprecipitation and massively parallel sequencing) data from VCaP (an androgen-sensitive prostate cancer cell line that harbors the TMPRSS2-ERG gene fusion) to analyze whether the genomic regions with rearrangements share any transcriptional patterns or chromatin marks.
Figure 3: Association between rearrangement breakpoints and genome-wide transcriptional/histone marks in prostate cancer.
*Significant associations passing a false discovery rate cut-off of 5%.
Berger, et al., 2011
http://www.nature.com/nature/journal/v470/n7333/fig_tab/nature09744_F3.html
This figure displays the results of the ChIP-seq data analysis previously described, comparing genomic regions in terms of transcriptional patterns or chromatin marks. On the left side are the seven ChIP-seq binding peaks for the TMPRSS2-ERG positive prostate cancer cell line VCaP, while the graph itself shows each prostate tumor sample genome’s enrichment (positive values) or depletion (negative values) of breakpoints within 50 kb of each binding peak. These values represent the ratios of the observed breakpoint rates to the previously published background rates. Black bars represent TMPRSS2-ERG-positive prostate tumors and white bars represent ETS fusion-negative prostate tumors. The display of the seven prostate tumors is a bit difficult to read, as one must constantly refer to the order shown on the right side. It is noteworthy that for ETS fusion-negative tumors, breakpoint depletion tends to occur close to peaks of active transcription (AR, ERG, H3K4me3, H3K36me3, Pol II, and H3ace) while breakpoint enrichment tends to occur close to peaks of closed chromatin (H3K27me3). Thus, somatic rearrangements may occur in closed chromatin in some tumor cells, an assumption further supported by PR-2832’s results. It is noteworthy that tumor PR-2832 demonstrates significant spatial co-localization with peaks of open chromatin in VCaP cells. Further analysis of previously obtained data on other cancer types compared with this prostate cancer study showed similar patterns among 16 of 18 breast cancer tumors and prostate tumor PR-2832. This implies possible shared rearrangement patterns in some hormone-driven cancer cells.
Figure 4: Disruption of CADM2 and the PTEN pathway by rearrangements.
Berger, et al., 2011
http://www.nature.com/nature/journal/v470/n7333/fig_tab/nature09744_F4.html
a) This figure shows the somatic rearrangements in the CADM2 (cell adhesion molecule 2) gene, apparent in three out of the seven prostate tumors. The intragenic breakpoints are shown for all three tumors, with the complexity and varying lengths of the rearrangements implying that a validation approach using FISH might not be able to accurately and fully detect the complex rearrangements for this gene. b) Researchers performed a ‘break-apart’ FISH assay on CADM2 anyway, but on 90 independent prostate tumors. Six out of ninety showed evidence of disruption, 5 being rearrangements and 1 being a copy gain. This figure displays one of the break-apart rearrangements. c) The top half of this figure depicts the intragenic rearrangements in the PTEN tumor suppressor gene, observed in two of the seven prostate tumors. The bottom half shows those disrupting the MAGI2 (membrane associated guanylate kinase, WW and PDZ domain containing 2) gene, also observed in two of the seven prostate tumors. It is noteworthy that these four tumors include all three tumors with TMPRSS2-ERG rearrangements. Researchers concluded that rearrangements disrupting PTEN might directly or indirectly (by disrupting MAGI2) disrupt the PI3 kinase pathway in prostate cancer. d) Researchers used FISH inversion probes to screen 88 independent prostate tumors for the MAGI2 locus, with 3 out of 88 showing inversions similar to the prostate tumors in the study. This figure displays one of those inversions. All samples showing MAGI2 inversions are wild type for PTEN.
Because these FISH probes were specific to this study, results represent a lower bound for the actual incidence of rearrangements for these genes.
References
Berger MF, Lawrence MS, Demichelis F, Drier Y, Cibulskis K, Sivachenko AY, Sboner A, Esgueva R, Pflueger D, Sougnez C, et al. The genomic complexity of primary human prostate cancer. Nature [Internet]. 2011 Feb 10 [cited 2011 Feb 21];470(7333): 214-220. Available from: http://www.nature.com/nature/journal/v470/n7333/full/nature09744.html
*Note: All citable information was taken from this original paper.
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