Next-generation sequencing of advanced prostate cancer treated with androgen-deprivation therapy

<b>Background:</b> Androgen-deprivation therapy (ADT) is standard treatment for locally advanced or metastatic prostate cancer (PCa). Many patients develop castration resistance (castration-resistant PCa [CRPC]) after approximately 2–3 yr, with a poor prognosis. The molecular mechanisms underlying CRPC progression are unclear.<p></p> <b>Objective:</b> To undertake quantitative tumour transcriptome profiling prior to and following ADT to identify functionally important androgen-regulated pathways or genes that may be reactivated in CRPC.<p></p> <b>Design, setting, and participants:</b> RNA sequencing (RNA-seq) was performed on tumour-rich, targeted prostatic biopsies from seven patients with locally advanced or metastatic PCa before and approximately 22 wk after ADT initiation. Differentially regulated genes were identified in treatment pairs and further investigated by quantitative reverse transcription-polymerase chain reaction (qRT-PCR) on cell lines and immunohistochemistry on a separate CRPC patient cohort. Functional assays were used to determine the effect of pathway modulation on cell phenotypes.<p></p> <b>Outcome measurements and statistical analysis:</b> We searched for gene expression changes affecting key cell signalling pathways that may be targeted as proof of principle in a CRPC in vitro cell line model.<p></p> <b>Results and limitations:</b> We identified ADT-regulated signalling pathways, including the Wnt/β-catenin signalling pathway, and observed overexpression of β-catenin in a subset of CRPC by immunohistochemistry. We validated 6 of 12 (50%) pathway members by qRT-PCR on LNCaP/LNCaP-AI cell RNAs, of which 4 (67%) demonstrated expression changes consistent with RNA-seq data. We show that the tankyrase inhibitor XAV939 (which promotes β-catenin degradation) reduced androgen-independent LNCaP-AI cell line growth compared with androgen-responsive LNCaP cells via an accumulation of cell proportions in the G0/G1 phase and reduction in the S and G2/M phases. Our biopsy protocol did not account for tumour heterogeneity, and pathway inhibition was limited to pharmacologic approaches.<p></p> <b>Conclusions:</b> RNA-seq of paired PCa samples revealed ADT-regulated signalling pathways. Proof-of-principle inhibition of the Wnt/β-catenin signalling pathway specifically delays androgen-independent PCa cell cycle progression and proliferation and warrants further investigation as a potential target for therapy for CRPC.<p></p&gt

A YY1-dependent increase in aerobic metabolism is indispensable for intestinal organogenesis

During late gestation, villi extend into the intestinal lumen to dramatically increase the surface area of the intestinal epithelium, preparing the gut for the neonatal diet. Incomplete development of the intestine is the most common gastrointestinal complication in neonates, but the causes are unclear. We provide evidence in mice that Yin Yang 1 (Yy1) is crucial for intestinal villus development. YY1 loss in the developing endoderm had no apparent consequences until late gestation, after which the intestine differentiated poorly and exhibited severely stunted villi. Transcriptome analysis revealed that YY1 is required for mitochondrial gene expression, and ultrastructural analysis confirmed compromised mitochondrial integrity in the mutant intestine. We found increased oxidative phosphorylation gene expression at the onset of villus elongation, suggesting that aerobic respiration might function as a regulator of villus growth. Mitochondrial inhibitors blocked villus growth in a fashion similar to Yy1 loss, thus further linking oxidative phosphorylation with late-gestation intestinal development. Interestingly, we find that necrotizing enterocolitis patients also exhibit decreased expression of oxidative phosphorylation genes. Our study highlights the still unappreciated role of metabolic regulation during organogenesis, and suggests that it might contribute to neonatal gastrointestinal disorders

Hot Interstellar Gas and Stellar Energy Feedback in the Antennae Galaxies

We have analyzed Chandra archival observations of the Antennae galaxies to study the distribution and physical properties of its hot interstellar gas. Eleven distinct diffuse X-ray emission regions are selected according to their underlying interstellar structures and star formation activity. The X-ray spectra of these regions are used to determine their thermal energy contents and cooling timescales. Young star clusters in these regions are also identified and their photometric measurements are compared to evolutionary stellar population synthesis models to assess their masses and ages. The cluster properties are then used to determine the stellar wind and supernova energies injected into the ISM. Comparisons between the thermal energy in the hot ISM and the expected stellar energy input show that young star clusters are sufficient to power the X-ray-emitting gas in some, but not all, active star formation regions. Super-star clusters, with masses >= 1x10^5 M_sol, heat the ISM, but the yield of hot interstellar gas is not directly proportional to the cluster mass. Finally, there exist diffuse X-ray emission regions which do not show active star formation or massive young star clusters. These regions may be powered by field stars or low-mass clusters formed within the last ~100 Myr.Comment: 36 pages, 6 figures, 8 tables, 2 appendices, to appear in the Astrophysical Journal, April 20 issu

Absorption-Line Probes of Gas and Dust in Galactic Superwinds

We discuss moderate resolution spectra of the NaD absorption-line in a sample of 32 far-IR-bright starburst galaxies. In 18 cases, the line is produced primarily by interstellar gas, and in 12 of these it is blueshifted by over 100 km/s relative to the galaxy systemic velocity. The absorption-line profiles in these outflow sources span the range from near the galaxy systemic velocity to a maximum blueshift of 400 to 600 km/s. The outflows occur in galaxies systematically viewed more nearly face-on than the others. We therefore argue that the absorbing material consists of ambient interstellar gas accelerated along the minor axis of the galaxy by a hot starburst-driven superwind. The NaD lines are optically-thick, but indirect arguments imply total Hydrogen column densities of N_H = few X 10^{21} cm^{-2}. This implies that the superwind is expelling matter at a rate comparable to the star-formation rate. This outflowing material is very dusty: we find a strong correlation between the depth of the NaD profile and the line-of-sight reddening (E(B-V) = 0.3 to 1 over regions several-to-ten kpc in size). The estimated terminal velocities of superwinds inferred from these data and extant X-ray data are typically 400 to 800 km/s, are independent of the galaxy rotation speed, and are comparable to (substantially exceed) the escape velocities for $L_*$ (dwarf) galaxies. The resulting loss of metals can establish the mass-metallicity relation in spheroids, produce the observed metallicity in the ICM, and enrich a general IGM to 10$^{-1}$ solar metallicity. If the outflowing dust grains survive their journey into the IGM, their effect on observations of cosmologically-distant objects is significant.Comment: 65 pages, including 16 figures. ApJ, in pres

Systems biologists seek fuller integration of systems biology approaches in new cancer research programs

Systems biology takes an interdisciplinary approach to the systematic study of complex interactions in biological systems. This approach seeks to decipher the emergent behaviors of complex systems rather than focusing only on their constituent properties. As an increasing number of examples illustrate the value of systems biology approaches to understand the initiation, progression, and treatment of cancer, systems biologists from across Europe and the United States hope for changes in the way their field is currently perceived among cancer researchers. In a recent EU-US workshop, supported by the European Commission, the German Federal Ministry for Education and Research, and the National Cancer Institute of the NIH, the participants discussed the strengths, weaknesses, hurdles, and opportunities in cancer systems biology

Tomb of a sultan: a VR digital heritage approach

This project presents the development of a room-scale Virtual Reality (VR) cultural heritage experience, a transmedia storytelling approach for showing museology VR content in a public setting. "Tomb of a Sultan: A VR Digital Heritage Approach" features the 19 th century tomb of Sultan Hussein Shah as a three dimensional model reproduced using photogrammetry from the actual heritage site in Malacca. Room-scale VR experience has been made possible with the introduction of sensor-based head mount displays (HMD). However, the user experience and criteria for hyper-realistic VR in the cultural heritage context requires further study in terms of method and apparatus. In this paper we describe a prototype system, a user evaluation study and directions for future work