Facilitates Chromatin Transcription Complex Is an “Accelerator” of Tumor Transformation and Potential Marker and Target of Aggressive Cancers

SummaryThe facilitates chromatin transcription (FACT) complex is involved in chromatin remodeling during transcription, replication, and DNA repair. FACT was previously considered to be ubiquitously expressed and not associated with any disease. However, we discovered that FACT is the target of a class of anticancer compounds and is not expressed in normal cells of adult mammalian tissues, except for undifferentiated and stem-like cells. Here, we show that FACT expression is strongly associated with poorly differentiated aggressive cancers with low overall survival. In addition, FACT was found to be upregulated during in vitro transformation and to be necessary, but not sufficient, for driving transformation. FACT also promoted survival and growth of established tumor cells. Genome-wide mapping of chromatin-bound FACT indicated that FACT’s role in cancer most likely involves selective chromatin remodeling of genes that stimulate proliferation, inhibit cell death and differentiation, and regulate cellular stress responses

Frequency of breast cancer subtypes among African American women in the AMBER consortium

Abstract Background Breast cancer subtype can be classified using standard clinical markers (estrogen receptor (ER), progesterone receptor (PR) and human epidermal growth factor receptor 2 (HER2)), supplemented with additional markers. However, automated biomarker scoring and classification schemes have not been standardized. The aim of this study was to optimize tumor classification using automated methods in order to describe subtype frequency in the African American Breast Cancer Epidemiology and Risk (AMBER) consortium. Methods Using immunohistochemistry (IHC), we quantified the expression of ER, PR, HER2, the proliferation marker Ki67, and two basal-like biomarkers, epidermal growth factor receptor (EGFR) and cytokeratin (CK)5/6, in 1381 invasive breast tumors from African American women. RNA-based (prediction analysis of microarray 50 (PAM50)) subtype, available for 574 (42%) cases, was used to optimize classification. Subtype frequency was calculated, and associations between subtype and tumor characteristics were estimated using logistic regression. Results Relative to ER, PR and HER2 from medical records, central IHC staining and the addition of Ki67 or combined tumor grade improved accuracy for classifying PAM50-based luminal subtypes. Few triple negative cases (< 2%) lacked EGFR and CK5/6 expression, thereby providing little improvement in accuracy for identifying basal-like tumors. Relative to luminal A subtype, all other subtypes had higher combined grade and were larger, and ER-/HER2+ tumors were more often lymph node positive and late stage tumors. The frequency of basal-like tumors was 31%, exceeded only slightly by luminal A tumors (37%). Conclusions Our findings indicate that automated IHC-based classification produces tumor subtype frequencies approximating those from PAM50-based classification and highlight high frequency of basal-like and low frequency of luminal A breast cancer in a large study of African American women

Patterns of Intraspecific DNA Variation in the Daphnia Nuclear Genome

Understanding nucleotide variation in natural populations has been a subject of great interest for decades. However, many taxonomic groups, especially those with atypical life history attributes remain unstudied, and Drosophila is the only arthropod genus for which DNA polymorphism data are presently abundant. As a result of the recent release of the complete genome sequence and a wide variety of new genomic resources, the Daphnia system is quickly becoming a promising new avenue for expanding our knowledge of nucleotide variation in natural populations. Here, we examine nucleotide variation in six protein-coding loci for Daphnia pulex and its congeners with particular emphasis on D. pulicaria, the closest extant relative of D. pulex. Levels of synonymous intraspecific variation, πs, averaged 0.0136 for species in the Daphnia genus, and are slightly lower than most prior estimates in invertebrates. Tests of neutrality indicated that segregating variation conforms to neutral model expectations for the loci that we examined in most species, while Ka/Ks ratios revealed strong purifying selection. Using a full maximum-likelihood coalescent-based method, the ratio of the recombination rate to the mutation rate (c/u), averaged 0.5255 for species of the Daphnia genus. Lastly, a divergence population-genetics approach was used to investigate gene flow and divergence between D. pulex and D. pulicaria

Transcontinental Phylogeography of the <em>Daphnia pulex</em> Species Complex

<div><p><em>Daphnia pulex</em> is quickly becoming an attractive model species in the field of ecological genomics due to the recent release of its complete genome sequence, a wide variety of new genomic resources, and a rich history of ecological data. Sequences of the mitochondrial <em>NADH dehydrogenase</em> subunit 5 and <em>cytochrome</em> c <em>oxidase</em> subunit 1 genes were used to assess the global phylogeography of this species, and to further elucidate its phylogenetic relationship to other members of the <em>Daphnia pulex</em> species complex. Using both newly acquired and previously published data, we analyzed 398 individuals from collections spanning five continents. Eleven strongly supported lineages were found within the <em>D. pulex</em> complex, and one lineage in particular, panarctic <em>D. pulex</em>, has very little phylogeographical structure and a near worldwide distribution. Mismatch distribution, haplotype network, and population genetic analyses are compatible with a North American origin for this lineage and subsequent spatial expansion in the Late Pleistocene. In addition, our analyses suggest that dispersal between North and South America of this and other species in the <em>D. pulex</em> complex has occurred multiple times, and is predominantly from north to south. Our results provide additional support for the evolutionary relationships of the eleven main mitochondrial lineages of the <em>D. pulex</em> complex. We found that the well-studied panarctic <em>D. pulex</em> is present on every continent except Australia and Antarctica. Despite being geographically very widespread, there is a lack of strong regionalism in the mitochondrial genomes of panarctic <em>D. pulex</em> – a pattern that differs from that of most studied cladocerans. Moreover, our analyses suggest recent expansion of the panarctic <em>D. pulex</em> lineage, with some continents sharing haplotypes. The hypothesis that hybrid asexuality has contributed to the recent and unusual geographic success of the panarctic <em>D. pulex</em> lineage warrants further study.</p> </div

Consensus Bayesian phylogeny of the <i>Daphnia species</i> complex based on the mitochondrial COX1 gene.

<p>The alignment contains 52 sequences of length 552 nt with 151 polymorphic positions of which 112 are phylogenetically informative. Nine of the 12 lineages in the <i>Daphnia pulex</i> species complex, including all three South American lineages, are represented. The tree is rooted through the midpoint. Numbers at the nodes are Bayesian posterior probabilities and are not shown if less than 0.80. Branch colors correspond to continents as follows: green = Europe, blue = North America, red = South America. Individual CT-18 was collected from Connecticut, USA.</p

Consensus Bayesian phylogeny of the <i>Daphnia pulex</i> species complex based on the mitochondrial ND5 and COX1 genes.

<p>The alignment contains 95 sequences consisting of 762 nt of ND5 and 1386 nt of COX1 with 321 polymorphic positions of which 204 are phylogenetically informative. The tree is rooted through the midpoint. Posterior probabilities are indicated on the nodes of the tree and are not shown if less than 0.80. Taxon colors represent geographic locations as follows: black = North America, blue = east Asia, red = South America.</p

Median-joining haplotype network (ε = 0) for the panarctic <i>D. pulex</i> lineage.

<p>The network is based on the mitochondrial ND5 gene (496 nt, 173 individuals). Multiple individuals from the same location were removed. Each haplotype is represented by a circle whose area is proportional to the number of times the haplotype was observed. Median vectors, which represent either extant unsampled sequences or extinct ancestral sequences, are indicated by small black circles.</p

Mismatch distribution plot for the panarctic <i>D. pulex</i> lineage.

<p>This plot is based on the mitochondrial ND5 gene (496 nt, 173 individuals). Multiple individuals collected from the same location were removed.</p