Using whole-genome sequencing to implicate the androgen receptor as the predominant driver of DNA breakpoints and fusion events in prostate cancer

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Background: Structural rearrangements in cancers genomes have the potential to disrupt normal gene function and result in a selective growth advantage, either by inactivating tumour suppressors or creating novel gene fusions with oncogenic gain-of-function. Specific fusion genes identified to date are found in particular tumor types rather than being present in all cancers suggesting there are tissue-specific mechanisms underlying these events. The most well-known fusion event in prostate cancer is TMPRSS2-ERG. Recent studies have suggested that androgen receptor may play a role in the formation of TMPRSS2-ERG fusions, bringing the two loci in close proximity in the nucleus and facilitating DNA strand break and repair along with AR associated enzymes. Methods: To explore this mechanism more comprehensively, we performed whole-genome sequencing of 14 prostate cancers from seven patients as well as paired whole blood controls. Results: Across the cancer genomes we identified approximately 4,500 high confidence DNA breakpoints and found that a large proportion of these breakpoints were in close proximity to curated androgen receptor binding sites. Furthermore, when we examined breakpoints in 11 other cancers from the TCGA and ICGC projects, we identified a similar association with androgen (and estrogen) receptor binding sites specifically in hormone-dependent tumour types, suggesting a role for steroid hormone receptors in the formation of cancer driving structural rearrangements. In addition, in at least one patient, the formation of a novel gene fusion contributed directly to the lethal evolution of his tumour. Conclusions: These data suggest that the androgen receptor drives genome wide breakpoints and novel fusion events in prostate cancer.

A preclinical xenograft model identifies castration-tolerant cancer-repopulating cells in localized prostate tumors

A lack of clinically relevant experimental models of human prostate cancer hampers evaluation of potential therapeutic agents. Currently, androgen deprivation therapy is the gold standard treatment for advanced prostate cancer, but inevitably, a subpopulation of cancer cells survives and repopulates the tumor. Tumor cells that survive androgen withdrawal are critical therapeutic targets for more effective treatments, but current model systems cannot determine when they arise in disease progression and are unable to recapitulate variable patient response to treatment. A model system was developed in which stromal-supported xenografts from multiple patients with early-stage localized disease can be tested for response to castration. The histopathology of these xenografts mimicked the original tumors, and short-term host castration resulted in reduced proliferation and increased apoptosis in tumor cells. After 4 weeks of castration, residual populations of quiescent, stem-like tumor cells remained. Without subsequent treatment, these residual cells displayed regenerative potential, because testosterone readministration resulted in emergence of rapidly proliferating tumors. Therefore, this model may be useful for revealing potential cellular targets in prostate cancer, which exist before the onset of aggressive incurable disease. Specific eradication of these regenerative tumor cells that survive castration could then confer survival benefits for patients.

Hedgehog signaling is active in human prostate cancer stroma and regulates proliferation and differentiation of adjacent epithelium

BACKGROUND

Contribution of stromal Hedgehog (Hh) signaling is evident in the prostate gland in mice, but needs translation to human tissues if Hh therapeutics are to be used effectively. Our goal was to determine if primary human prostate fibroblasts contain cilia, and respond to prostate Hh signaling.

METHODS

Primary human prostate cancer-associated (CAFs), and adjacent non-malignant (NPFs) fibroblasts isolated from human tissue specimens were analyzed using immunofluorescence, real-time PCR, and available array data. Cell culture and tissue recombination were used to determine responsiveness of human fibroblasts to Hh pathway manipulation and the paracrine effects of stromal Hh signaling, respectively.

RESULTS

Prostatic fibroblasts were capable of forming primary cilia, with the capacity for active Hh signaling as seen by Smo co-localization to the tip of the primary cilium. Expression of genes known to represent a signature of active Hh signaling in the prostate (especially Fgf5 and Igfbp6) were increased in CAFs compared to NPFs. The level of canonical Hh genes and prostate Hh signature genes were rarely synchronous; with lower doses of Purmorphamine/BMS-833923 regulating canonical transcription factors, and higher doses effecting prostate Hh signature genes. Grafts consisting of NPFs with constitutively active Hh signaling induced increased proliferation and dedifferentiation of adjacent non-malignant BPH-1 epithelial cells.

CONCLUSIONS

These data show that human prostatic fibroblasts have the capacity for Hh signaling and manipulation. Increased expression of a signature of prostatic Hh genes in the prostate tumor microenvironment suggests a role in the epithelial transformations driving prostate cancer (PCa).

Bladder cancer biorepositories in the "-omics" era: integrating quality tissue specimens with comprehensive clinical annotation

Advances in genomic platforms have led to the need for well-characterized, high quality biospecimens for research. Bladder cancer, despite being a major epidemiological concern, has been under-represented in genomic programs due to unique challenges in collection of clinical informatics and tissues. Currently no targeted therapy exists for management of the disease. We report our experiences and lessons learnt in establishing an integrated model of bladder cancer that uses a dedicated bladder cancer team and relational databases. It streamlines both clinical activity and serial harvesting of biospecimens to obtain tissue that is consistently suitable for high-throughput genomic research. Fresh tissue, blood, and urine samples were prospectively collected and stored. RNA and DNA were extracted simultaneously, quality control was performed, and whole transcriptome sequencing also performed using the illumina series of platforms. Over a 15-month period, urine was banked for 209 patients, plasma and whole blood for 185 patients, and tissue for 71 patients. The collections included normal mucosa from patients with and without bladder cancer and cancer tissue across the entire histopathogical spectrum of bladder cancer from low-grade noninvasive cancers to metastatic lymph nodes. We used a relational database to link clinical information to tumor inventory and provide access to richly annotated specimens and matched clinical informatics. We found that tumor tissue was successfully banked more often in patients who had macroscopic papillary disease compared to those without. We also show that the median RNA integrity number (RIN) scores are significantly higher in patients whose tissues were banked using cold-cup biopsies compared to those banked using electrocautery. Transcriptome sequencing of all samples banked using cold-cup biopsies passed bioinformatics quality assessment and had a mean Q30 quality score well over the illumina quality control benchmark. Such an infrastructure will allow genomic profiling of bladder cancer to help us understand the "global picture" in bladder cancer pathogenesis.

Regional treatment margins for prostate brachytherapy

PURPOSE

This study quantified the treatment margin (TM) around the prostate that received 100% of the prescribed dose and analyzed postimplant dosimetry in different regions of the prostate for (125)I seed implants.

METHODS AND MATERIALS

An average target volume (ATV) was created from postoperative MRI scan contours drawn independently by five radiation oncologists in 40 patients. The MRI was fused with the postoperative CT for dosimetry purposes. The TM, defined as the radial distance between the ATV and the 100% isodose line, was measured at 16 points at the base, midgland, and apex. The ATV was divided into four quadrants: anterior-superior, posterior-superior, anterior-inferior, and posterior-inferior quadrants. The values of the dose that covers 90% of the ATV (D90) and the percentage of the ATV receiving the prescribed dose (V100) received by the whole prostate and its four quadrants were documented.

RESULTS

The range of the mean TM, in millimeter, was -8.88 to 3.68, 1.12 to 10.42, and 6.27 to 18.25 at the base, midgland, and apex, respectively. The mean D90 was 135.8, 162.8, 191.0, and 194.6 Gy for the anterior-superior, posterior-superior, anterior-inferior, and posterior-inferior quadrants, respectively.

CONCLUSIONS

Despite having a relatively uniform preoperative planning target volume, this study identified variable TMs postoperatively in different regions of the prostate. In particular, the anterior base is most underdosed, whereas the lateral regions of the midgland and apex have generous TMs. Postimplant dosimetric parameters were lowest in the anterior-inferior quadrant.

Abstract 3575: Integration of estradiol signaling at the translational and transcriptional level in prostate cancer cells

Introduction

The prostate is an organ where the dual actions of estrogen receptors (ERα and ERβ)are just beginning to be understood and appreciated in a physiological context. Steroid receptors can act outside of the nucleus by interacting with cytoplasmic or membrane bound proteins and activating or inhibiting signaling pathways in a ligand dependent or independent manner. However, our understanding of this non-nuclear activity remains partial. Here, we attempt to uncover how estrogens regulate post-transcriptional gene expression programs in prostate cancer. The rationale for studying impacts on post-transcriptional gene expression programs downstream of a transcription factor is that there is often no direct correlation between the level of an mRNA and the corresponding protein product. Additionally, several intracellular signaling pathways affected by estrogen signaling (e.g MAPK and PI3K pathways) directly regulate gene expression post-transcriptionally. One post-transcriptional mechanism that is tightly regulated by various intracellular signaling pathways is mRNA translation initiation - a highly controlled step that is regulated on multiple levels and is commonly deregulated in cancer. Many factors acting on mRNAs in cis and/or in trans, including RNA-binding proteins, RNA secondary structures or modifications of the cap structure by methylation can have strong impact on the efficiency of mRNA translation. Thus, estrogen signaling, by directly and indirectly affecting intracellular signaling can potentially regulate translational activity of its transcriptional targets.

Approach

We used prostate derived cell lines to assess how estrogens regulate proliferation and survival as a function of their ability to modulate transcription and translation. We performed polysome-microarray approach where the cytoplasmic mRNA population is separated based on the number of associated ribosomes followed by quantification of mRNA levels in pools of actively translating mRNAs. Using prostate cell lines, epithelial and stromal in origin, we first characterized the level of transcription and translation in unstimulated conditions to obtain a snapshot of the translational activity of each mRNA in baseline conditions. Secondly, we tested the impact on transcription and translation following stimulation for 2 hours with estradiol or with an ERβ-specific agonist (8β-VE2). We are currently validating ERα/β translational targets and identifying regulatory RNA sequences that enable ER-induced translational control.

Conclusion

We endeavor to determine how the gene expression programs regulated by ERα and ERβ are integrated at the transcriptional and translational level to direct proliferation, growth and survival in prostate tumors.

Citation Format: Luc Furic, Ola Larsson, Ivan Topisirovic, Mark Frydenberg, John Pedersen, Gail Risbridger. Integration of estradiol signaling at the translational and transcriptional level in prostate cancer cells. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3575. doi:10.1158/1538-7445.AM2013-3575

No association between XMRV or related gammaretroviruses in Australian prostate cancer patients

BACKGROUND

Xenotropic murine leukemia virus-related virus (XMRV) is a gammaretrovirus reported to be associated with prostate cancer (PC) and chronic fatigue syndrome (CFS). While the association of XMRV with CFS and PC has recently been discredited, no studies have been performed in Australian patients to investigate the association between PC and XMRV or related murine leukemia virus (MLV) in matched PC and normal tissue.

METHODS

Genomic DNA (gDNA) was purified from matched normal and cancer formalin-fixed paraffin-embedded (FFPE) prostate tissue from 35 Australian PC patients with Gleason scores ranging from 7 - 10. The presence of the ribonuclease L (RNase L) polymorphism R462Q was determined by allele specific PCR. Samples were screened for XMRV and related murine leukemia virus (MLV) variants by qPCR. Contaminating mouse DNA was detected using qPCR targeting mouse intracisternal A particle long terminal repeat DNA.

RESULTS

gDNA was successfully purified from 94% (66/70) of normal and cancer FFPE prostate tissues. RNase L typing revealed 8% were homozygous (QQ), 60% were heterozygous (RQ) and 32% were wild-type (RR) for the RNase L mutation. None of the 66 samples tested were positive for XMRV or related MLV sequences using broad MLV or XMRV specific primers with detection sensitivities of 1 viral copy of MLV/XMRV and XMRV DNA, respectively.

CONCLUSIONS

Using highly sensitive qPCR we found no evidence of XMRV or related gammaretroviruses in prostate tissues from 35 Australian PC patients. Our findings are consistent with other studies demonstrating that XMRV is a laboratory contaminant that has no role in the aetiology of PC.

Glucose metabolism is altered after loss of L cells and α-cells but not influenced by loss of K cells

The enteroendocrine K and L cells are responsible for secretion of glucose-dependent insulinotropic polypeptide (GIP) and glucagon like-peptide 1 (GLP-1), whereas pancreatic α-cells are responsible for secretion of glucagon. In rodents and humans, dysregulation of the secretion of GIP, GLP-1, and glucagon is associated with impaired regulation of metabolism. This study evaluates the consequences of acute removal of Gip- or Gcg-expressing cells on glucose metabolism. Generation of the two diphtheria toxin receptor cellular knockout mice, TgN(GIP.DTR) and TgN(GCG.DTR), allowed us to study effects of acute ablation of K and L cells and α-cells. Diphtheria toxin administration reduced the expression of Gip and content of GIP in the proximal jejunum in TgN(GIP.DTR) and expression of Gcg and content of proglucagon-derived peptides in both proximal jejunum and terminal ileum as well as content of glucagon in pancreas in TgN(GCG.DTR) compared with wild-type mice. GIP response to oral glucose was attenuated following K cell loss, but oral and intraperitoneal glucose tolerances were unaffected. Intraperitoneal glucose tolerance was impaired following combined L cell and α-cell loss and normal following α-cell loss. Oral glucose tolerance was improved following L cell and α-cell loss and supernormal following α-cell loss. We present two mouse models that allow studies of the effects of K cell or L cell and α-cell loss as well as isolated α-cell loss. Our findings show that intraperitoneal glucose tolerance is dependent on an intact L cell mass and underscore the diabetogenic effects of α-cell signaling. Furthermore, the results suggest that K cells are less involved in acute regulation of mouse glucose metabolism than L cells and α-cells.

Human epithelial basal cells are cells of origin of prostate cancer, independent of CD133 status

Normal prostatic epithelium is composed of basal and luminal cells. Prostate cancer can be initiated in both benign basal and luminal stem cells, but because basal cell markers are not expressed in patient tumors, the former result was unexpected. Since the cells of origin of prostate cancer are important therapeutic targets, we sought to provide further proof that basal stem cells have tumorigenic potential. Prostatic basal cells were enriched based on α2β1integrin(hi) expression and further enriched for stem cells using CD133 in nontumorigenic BPH-1 cells. Human embryonic stem cells (hESCs) were also used as a source of normal stem cells. To test their tumorigenicity, we used two alternate stromal-based approaches; (a) recombination with human cancer-associated fibroblasts (CAFs) or (b) recombination with embryonic stroma (urogenital mesenchyme) and treated host mice with testosterone and 17β-estradiol. Enriched α2β1integrin(hi) basal cells from BPH-1 cells resulted in malignant tumor formation using both assays of tumorigenicity. Surprisingly, the tumorigenic potential did not reside in the CD133(+) stem cells but was consistently observed in the CD133(-) population. CAFs also failed to induce prostatic tumors from hESCs. These data confirmed that benign human basal cells include cells of origin of prostate cancer and reinforced their importance as therapeutic targets. In addition, our data suggested that the more proliferative CD133(-) basal cells are more susceptible to tumorigenesis compared to the CD133(+)-enriched stem cells. These findings challenge the current dogma that normal stem cells and cells of origin of cancer are the same cell type(s).

Chemistry and Performance of Blended Cements and Backfills for use in Radioactive Waste Disposal

The ability of NaCl and MgSO4 to impair the performance of Portland cement, blended cements containing slag and fly ash and of a permeable backfill have been measured. Performance is determined by decrease in pH, changes in mineralogy and loss of physical coherence. Experiments have been made at 25°, 55° and 85°C and extensively backed up by chemical models of cement performance. NaCl, up to 1.5M, has a comparatively slight impact on performance but MgSO4 rapidly and almost quantitatively reacts, lowering system pH's to < 10, conditioned by mixtures of Mg(OH)2 and magnesium silicates with gypsum.

A new dimension: robotic reconstruction in plastic surgery

BACKGROUND

Robot-assisted surgery was first approved by the Federal Drug Administration in 1994. The robotic system has the advantages of three-dimensional visualization of the operating field, 7° range of motion, tremor elimination, 360°of freedom at 10-mm distance, and a comfortable, seated operating posture. The purpose of this paper is to present a new surgical tool, the robot, for use in reconstructive surgery.

METHODS

A case is presented in which the robotic system was used to elevate a pedicled, myocutaneous latissimus dorsi flap for shoulder reconstruction.

RESULTS

The robot was used successfully to harvest a pedicled latissimus dorsi flap. Since this case, we have used the robotic system to harvest one other pedicled latissimus flap for breast reconstruction as well as to perform the microvascular anastomoses in a radial forearm and rectus abdominus free flaps to the lower extremity.

CONCLUSION

There is great potential for the use of robot as a surgical tool in the field of plastic surgery. The advantages are numerous, including superior visibility, greater range of motion as a more comfortable position for the operating surgeon. The limitations include the learning curve and the lack of biofeedback.