Frequent somatic transfer of mitochondrial DNA into the nuclear genome of human cancer cells

Mitochondrial genomes are separated from the nuclear genome for most of the cell cycle by the nuclear double membrane, intervening cytoplasm, and the mitochondrial double membrane. Despite these physical barriers, we show that somatically acquired mitochondrial-nuclear genome fusion sequences are present in cancer cells. Most occur in conjunction with intranuclear genomic rearrangements, and the features of the fusion fragments indicate that nonhomologous end joining and/or replication-dependent DNA double-strand break repair are the dominant mechanisms involved. Remarkably, mitochondrial-nuclear genome fusions occur at a similar rate per base pair of DNA as interchromosomal nuclear rearrangements, indicating the presence of a high frequency of contact between mitochondrial and nuclear DNA in some somatic cells. Transmission of mitochondrial DNA to the nuclear genome occurs in neoplastically transformed cells, but we do not exclude the possibility that some mitochondrial-nuclear DNA fusions observed in cancer occurred years earlier in normal somatic cells.This work was supported by the Wellcome Trust. Y.S.J is supported by a European Molecular Biology Organization long-term fellowship (LTF 1203_2012). J.M.C.T. is supported by Marie Curie Fellowship FP7 PEOPLE-2012-IEF (project number 328264). P.J.C. is a Wellcome Trust Senior Clinical Fellow. Support was provided to A.M.F. by the National Institute for Health Research (NIHR) UCLH Biomedical Research Centre. The ICGC Breast Cancer Consortium was supported by a grant from the European Union (BASIS) and the Wellcome Trust. The ICGC Prostate Cancer Consortium was funded by Cancer Research UK with a grant from the Dallaglio Foundation (grant number C5047/A14835). R.E. is supported by National Institute for Health Research support to the Biomedical Research Centre at The Institute of Cancer Research and Royal Marsden NHS Foundation Trust. We also thank the National Cancer Research Prostate Cancer Mechanisms of Progression and Treatment (PROMPT) collaborative (grant code G0500966/75466) which has funded tissue and urine collections in Cambridge. The authors also acknowledge financial support from the Department of Health via the National Institute for Health Research comprehensive Biomedical Research Centre award to Guy’s and St. Thomas’ NHS Foundation Trust and Breakthrough Breast Cancer Research (ICGC 08/09 and KCL) (A.T.)

Direct Transcriptional Consequences of Somatic Mutation in Breast Cancer.

Disordered transcriptomes of cancer encompass direct effects of somatic mutation on transcription, coordinated secondary pathway alterations, and increased transcriptional noise. To catalog the rules governing how somatic mutation exerts direct transcriptional effects, we developed an exhaustive pipeline for analyzing RNA sequencing data, which we integrated with whole genomes from 23 breast cancers. Using X-inactivation analyses, we found that cancer cells are more transcriptionally active than intermixed stromal cells. This is especially true in estrogen receptor (ER)-negative tumors. Overall, 59% of substitutions were expressed. Nonsense mutations showed lower expression levels than expected, with patterns characteristic of nonsense-mediated decay. 14% of 4,234 rearrangements caused transcriptional abnormalities, including exon skips, exon reusage, fusions, and premature polyadenylation. We found productive, stable transcription from sense-to-antisense gene fusions and gene-to-intergenic rearrangements, suggesting that these mutation classes drive more transcriptional disruption than previously suspected. Systematic integration of transcriptome with genome data reveals the rules by which transcriptional machinery interprets somatic mutation

Genetic Diversity in Wheat: Analysis using Diversity Arrays Technology (DArT) in bread and durum wheats

With increasing demands on the quality and quantity of food required now and in the future, improvements to current agriculture practices are required. Increased food production requires utilisation of more agricultural land, pushing crops into non- traditional areas. The need for advances in agricultural technologies are not only required for current crop varieties, but for new varieties with increased tolerance to environmental stresses. Technological improvement means better crop yields and reduced land, water, fertilizer and pesticide use. Diversity Arrays Technology (DArT) was used to study wheat diversity, specifically to identify polymorphic markers between various wheat cultivars for use in marker- assisted breeding programs. The hybridisation based technology was used to analyse various bread and durum wheat cultivars for increased understanding of genomic diversity. Analysis shows that DArT is able to discriminate between tissue samples from wheat cultivars grown under various environmental stresses with polymorphic markers identified between samples treated with differing salt, light and temperature conditions. Epigenetic diversity was analysed through methylation detection using DArT to identify a list of candidate polymorphic markers. Markers were identified using the methylation sensitive restriction enzyme McrBC to generate control and treated targets. Diversity through cultivar exploration, looking at breeding experiments between cultivars with phenotypic extremes to examine salt tolerance versus in-tolerance using DArT produced a recombinant inbred line genetic linkage map. Bulk segregant analysis was also used to group phenotypic samples. Candidate markers were identified between cultivars that can be used to genotyping tetraploid and hexaploid wheat cultivars for germplasm identification. In addition, the identification of trait-linked molecular markers, such as salt resistance, plant breeders can genotype individual plants and populations of cultivars to determine the most suitable cultivar to plant that best complements to its local environment. This eliminates the need for multiple planting cycles to optimize crop selections, and gives the plant breeder the highest possible chance for crop success (yield, quality, performance and cost)

Processed pseudogenes acquired somatically during cancer development.

Cancer evolves by mutation, with somatic reactivation of retrotransposons being one such mutational process. Germline retrotransposition can cause processed pseudogenes, but whether this occurs somatically has not been evaluated. Here we screen sequencing data from 660 cancer samples for somatically acquired pseudogenes. We find 42 events in 17 samples, especially non-small cell lung cancer (5/27) and colorectal cancer (2/11). Genomic features mirror those of germline LINE element retrotranspositions, with frequent target-site duplications (67%), consensus TTTTAA sites at insertion points, inverted rearrangements (21%), 5' truncation (74%) and polyA tails (88%). Transcriptional consequences include expression of pseudogenes from UTRs or introns of target genes. In addition, a somatic pseudogene that integrated into the promoter and first exon of the tumour suppressor gene, MGA, abrogated expression from that allele. Thus, formation of processed pseudogenes represents a new class of mutation occurring during cancer development, with potentially diverse functional consequences depending on genomic context

Direct transcriptional consequences of somatic mutation in breast cancer.

The disordered transcriptomes of cancer encompass direct effects of somatic mutation on transcription; co-ordinated secondary alterations in transcriptional pathways; and increased transcriptional noise. To catalogue the rules governing how somatic mutation exerts direct transcriptional effects, we developed an exhaustive bioinformatics pipeline for analyzing RNA-sequencing data, which we integrated with whole genome sequencing from 23 breast cancers. Using X-inactivation analyses, we find cancer cells are more transcriptionally active than intermixed stromal cells. This is especially true in ER-negative tumours. Overall, 59% of 6980 exonic substitutions were expressed. Compared to other classes, nonsense mutations showed lower expression levels than expected with patterns characteristic of nonsense-mediated decay. 14% of 4234 genomic rearrangements caused transcriptional abnormalities, including exon skips, exon reusage, fusion transcripts and premature poly-adenylation. We found productive, stable transcription from sense-to-antisense gene fusions and gene-to-intergenic rearrangements, suggesting that these mutation classes may drive more transcriptional disruption than previously suspected. Systematic integration of transcriptome with genome data therefore reveals the rules by which transcriptional machinery interprets somatic mutation

Corrigendum: Frequent somatic transfer of mitochondrial DNA into the nuclear genome of human cancer cells.

info:eu-repo/semantics/publishe

Mobile DNA in cancer. Extensive transduction of nonrepetitive DNA mediated by L1 retrotransposition in cancer genomes.

Long interspersed nuclear element-1 (L1) retrotransposons are mobile repetitive elements that are abundant in the human genome. L1 elements propagate through RNA intermediates. In the germ line, neighboring, nonrepetitive sequences are occasionally mobilized by the L1 machinery, a process called 3' transduction. Because 3' transductions are potentially mutagenic, we explored the extent to which they occur somatically during tumorigenesis. Studying cancer genomes from 244 patients, we found that tumors from 53% of the patients had somatic retrotranspositions, of which 24% were 3' transductions. Fingerprinting of donor L1s revealed that a handful of source L1 elements in a tumor can spawn from tens to hundreds of 3' transductions, which can themselves seed further retrotranspositions. The activity of individual L1 elements fluctuated during tumor evolution and correlated with L1 promoter hypomethylation. The 3' transductions disseminated genes, exons, and regulatory elements to new locations, most often to heterochromatic regions of the genome.SCOPUS: re.jinfo:eu-repo/semantics/publishe

Mobile DNA in cancer. Extensive transduction of nonrepetitive DNA mediated by L1 retrotransposition in cancer genomes

Long interspersed nuclear element-1 (L1) retrotransposons are mobile repetitive elements that are abundant in the human genome. L1 elements propagate through RNA intermediates. In the germ line, neighboring, nonrepetitive sequences are occasionally mobilized by the L1 machinery, a process called 3' transduction. Because 3' transductions are potentially mutagenic, we explored the extent to which they occur somatically during tumorigenesis. Studying cancer genomes from 244 patients, we found that tumors from 53% of the patients had somatic retrotranspositions, of which 24% were 3' transductions. Fingerprinting of donor L1s revealed that a handful of source L1 elements in a tumor can spawn from tens to hundreds of 3' transductions, which can themselves seed further retrotranspositions. The activity of individual L1 elements fluctuated during tumor evolution and correlated with L1 promoter hypomethylation. The 3' transductions disseminated genes, exons, and regulatory elements to new locations, most often to heterochromatic regions of the genome