Comprehensive analysis of the chromatin landscape in Drosophila melanogaster.

Chromatin is composed of DNA and a variety of modified histones and non-histone proteins, which have an impact on cell differentiation, gene regulation and other key cellular processes. Here we present a genome-wide chromatin landscape for Drosophila melanogaster based on eighteen histone modifications, summarized by nine prevalent combinatorial patterns. Integrative analysis with other data (non-histone chromatin proteins, DNase I hypersensitivity, GRO-Seq reads produced by engaged polymerase, short/long RNA products) reveals discrete characteristics of chromosomes, genes, regulatory elements and other functional domains. We find that active genes display distinct chromatin signatures that are correlated with disparate gene lengths, exon patterns, regulatory functions and genomic contexts. We also demonstrate a diversity of signatures among Polycomb targets that include a subset with paused polymerase. This systematic profiling and integrative analysis of chromatin signatures provides insights into how genomic elements are regulated, and will serve as a resource for future experimental investigations of genome structure and function.

Functional genomic analysis of chromosomal aberrations in a compendium of 8000 cancer genomes.

A large database of copy number profiles from cancer genomes can facilitate the identification of recurrent chromosomal alterations that often contain key cancer-related genes. It can also be used to explore low-prevalence genomic events such as chromothripsis. In this study, we report an analysis of 8227 human cancer copy number profiles obtained from 107 array comparative genomic hybridization (CGH) studies. Our analysis reveals similarity of chromosomal arm-level alterations among developmentally related tumor types as well as a number of co-occurring pairs of arm-level alterations. Recurrent ("pan-lineage") focal alterations identified across diverse tumor types show an enrichment of known cancer-related genes and genes with relevant functions in cancer-associated phenotypes (e.g., kinase and cell cycle). Tumor type-specific ("lineage-restricted") alterations and their enriched functional categories were also identified. Furthermore, we developed an algorithm for detecting regions in which the copy number oscillates rapidly between fixed levels, indicative of chromothripsis. We observed these massive genomic rearrangements in 1%-2% of the samples with variable tumor type-specific incidence rates. Taken together, our comprehensive view of copy number alterations provides a framework for understanding the functional significance of various genomic alterations in cancer genomes.

Identification of rare germline copy number variations over-represented in five human cancer types.

BACKGROUND: Copy number variations (CNVs) are increasingly recognized as significant disease susceptibility markers in many complex disorders including cancer. The availability of a large number of chromosomal copy number profiles in both malignant and normal tissues in cancer patients presents an opportunity to characterize not only somatic alterations but also germline CNVs, which may confer increased risk for cancer. RESULTS: We explored the germline CNVs in five cancer cohorts from the Cancer Genome Atlas (TCGA) consisting of 351 brain, 336 breast, 342 colorectal, 370 renal, and 314 ovarian cancers, genotyped on Affymetrix SNP6.0 arrays. Comparing these to ~3000 normal controls from another study, our case-control association study revealed 39 genomic loci (9 brain, 3 breast, 4 colorectal, 11 renal, and 12 ovarian cancers) as potential candidates of tumor susceptibility loci. Many of these loci are new and in some cases are associated with a substantial increase in disease risk. The majority of the observed loci do not overlap with coding sequences; however, several observed genomic loci overlap with known cancer genes including RET in brain cancers, ERBB2 in renal cell carcinomas, and DCC in ovarian cancers, all of which have not been previously associated with germline changes in cancer. CONCLUSIONS: This large-scale genome-wide association study for CNVs across multiple cancer types identified several novel rare germline CNVs as cancer predisposing genomic loci. These loci can potentially serve as clinically useful markers conferring increased cancer risk.

High-Resolution Optical Imaging of Benign and Malignant Mucosa in the Upper Aerodigestive Tract: An Atlas for Image-Guided Surgery.

BACKGROUND: High-resolution optical imaging provides real-time visualization of mucosa in the upper aerodigestive tract (UADT) which allows non-invasive discrimination of benign and neoplastic epithelium. The high-resolution microendoscope (HRME) utilizes a fiberoptic probe in conjunction with a tissue contrast agent to display nuclei and cellular architecture. This technology has broad potential applications to intraoperative margin detection and early cancer detection. METHODS: Our group has created an extensive image collection of both neoplastic and normal epithelium of the UADT. Here, we present and describe imaging characteristics of benign, dysplastic, and malignant mucosa in the oral cavity, oropharynx, larynx, and esophagus. RESULTS: There are differences in the nuclear organization and overall tissue architecture of benign and malignant mucosa which correlate with histopathologic diagnosis. Different anatomic subsites also display unique imaging characteristics. CONCLUSION: HRME allows discrimination between benign and neoplastic mucosa, and familiarity with the characteristics of each subsite facilitates correct diagnosis.

Estrogen coordinates translation and transcription, revealing a role for NRSF in human breast cancer cells.

Posttranscriptional regulation may enhance or inhibit estrogen transcriptional control to promote proliferation of breast cancer cells. To understand how transcriptome and translational responses coordinate to drive proliferation, we determined estrogen's global and specific effects on translation regulation by comparing the genome-wide profiles of total mRNA, polysome-associated mRNA, and monosome-associated mRNAs in MCF-7 cells after stimulation by 1 h of 10 nm 17beta-estradiol (E2). We observe three significant, novel findings. 1) E2 regulates several transcripts and pathways at the translation level. 2) We find that polysome analysis has higher sensitivity than total RNA in detecting E2-regulated transcripts as exemplified by observing stronger E2-induced enrichment of E2 expression signatures in polysomes more than in total RNA. This increased sensitivity allowed the identification of the repression of neural restrictive silencing factor targets in polysome-associated RNA but not total RNA. NRSF activity was required for E2 stimulation of the cell cycle. 3) We observe that the initial translation state is already high for E2 up-regulated transcripts before E2 treatment and vice versa for E2 down-regulated transcripts. This suggests that the translation state anticipates potential E2-induced transcriptome levels. Together, these data suggest that E2 stimulates breast cancer cells by regulating translation using multiple mechanisms. In sum, we show that polysome profiling of E2 regulation of breast cancer cells provides novel insights into hormone action and can identify novel factors critical for breast cancer cell growth.