Evolution under Spatially Heterogeneous Selection in Solid Tumors.

Spatial genetic and phenotypic diversity within solid tumors has been well documented. Nevertheless, how this heterogeneity affects temporal dynamics of tumorigenesis has not been rigorously examined because solid tumors do not evolve as the standard population genetic model due to the spatial constraint. We therefore, propose a neutral spatial (NS) model whereby the mutation accumulation increases toward the periphery; the genealogical relationship is spatially determined and the selection efficacy is blunted (due to kin competition). In this model, neutral mutations are accrued and spatially distributed in manners different from those of advantageous mutations. Importantly, the distinctions could be blurred in the conventional model. To test the NS model, we performed a three-dimensional multiple microsampling of two hepatocellular carcinomas. Whole-genome sequencing (WGS) revealed a 2-fold increase in mutations going from the center to the periphery. The operation of natural selection can then be tested by examining the spatially determined clonal relationships and the clonal sizes. Due to limited migration, only the expansion of highly advantageous clones can sweep through a large part of the tumor to reveal the selective advantages. Hence, even multiregional sampling can only reveal a fraction of fitness differences in solid tumors. Our results suggest that the NS patterns are crucial for testing the influence of natural selection during tumorigenesis, especially for small solid tumors.

The dynamics of DNA methylation fidelity during mouse embryonic stem cell self-renewal and differentiation.

The faithful transmission of DNA methylation patterns through cell divisions is essential for the daughter cells to retain a proper cell identity. To achieve a comprehensive assessment of methylation fidelity, we implemented a genome-scale hairpin bisulfite sequencing approach to generate methylation data for DNA double strands simultaneously. We show here that methylation fidelity increases globally during differentiation of mouse embryonic stem cells (mESCs), and is particularly high in the promoter regions of actively expressed genes and positively correlated with active histone modification marks and binding of transcription factors. The majority of intermediately (40%-60%) methylated CpG dinucleotides are hemi-methylated and have low methylation fidelity, particularly in the differentiating mESCs. While 5-hmC and 5-mC tend to coexist, there is no significant correlation between 5-hmC levels and methylation fidelity. Our findings may shed new light on our understanding of the origins of methylation variations and the mechanisms underlying DNA methylation transmission.

DMEAS: DNA methylation entropy analysis software.

SUMMARY: DMEAS is the first user-friendly tool dedicated to analyze the distribution of DNA methylation patterns for the quantification of epigenetic heterogeneity. It supports the analysis of both locus-specific and genome-wide bisulfite sequencing data. DMEAS progressively scans the mapping results of bisulfite sequencing reads to extract DNA methylation patterns for contiguous CpG dinucleotides. It determines the DNA methylation level and calculates methylation entropy for genomic segments to enable the quantitative assessment of DNA methylation variations observed in cell populations. AVAILABILITY AND IMPLEMENTATION: DMEAS program, user guide and all the testing data are freely available from http://sourceforge.net/projects/dmeas/files/

[Variant fusion transcripts and genomic DNA breakpoint of sil-tal1 in T-ALL cells].

The aim of this study was to investigate the nucleotide sequence of one distinct fusion transcript of sil-tal1 in childhood T-ALL. The PCR product was cloned into plasmid vector and then sequenced. Genomic DNA was analyzed with PCR using the designed primer pairs representing distinct sequences. The product was sequenced and analyzed with database. The results indicated that 4 different fusion transcripts were detected at cDNA level, in which a part of exons or introns of sil are reserved respectively, and some additions and deletions existed. After analyzing genomic DNA sequence of leukemic cells, the breakpoint in gene sil of this case was proved to be different at DNA level from references. Hence, the sil-tal1 rearrangement was defined to be a new type. It is concluded tal1 rearrangement of leukemic cells in this case is a new type, which expresses classical and at least 3 variant fusion transcripts, presumably caused by extraordinary mechanisms of splicing and transcription in leukemic stem cells.