Computational drug discovery for castration-resistant prostate cancers through in vitro drug response modeling.

Prostate cancer (PC) is the most frequently diagnosed malignancy and a leading cause of cancer deaths in US men. Many PC cases metastasize and develop resistance to systemic hormonal therapy, a stage known as castration-resistant prostate cancer (CRPC). Therefore, there is an urgent need to develop effective therapeutic strategies for CRPC. Traditional drug discovery pipelines require significant time and capital input, which highlights a need for novel methods to evaluate the repositioning potential of existing drugs. Here, we present a computational framework to predict drug sensitivities of clinical CRPC tumors to various existing compounds and identify treatment options with high potential for clinical impact. We applied this method to a CRPC patient cohort and nominated drugs to combat resistance to hormonal therapies including abiraterone and enzalutamide. The utility of this method was demonstrated by nomination of multiple drugs that are currently undergoing clinical trials for CRPC. Additionally, this method identified the tetracycline derivative COL-3, for which we validated higher efficacy in an isogenic cell line model of enzalutamide-resistant vs. enzalutamide-sensitive CRPC. In enzalutamide-resistant CRPC cells, COL-3 displayed higher activity for inhibiting cell growth and migration, and for inducing G1-phase cell cycle arrest and apoptosis. Collectively, these findings demonstrate the utility of a computational framework for independent validation of drugs being tested in CRPC clinical trials, and for nominating drugs with enhanced biological activity in models of enzalutamide-resistant CRPC. The efficiency of this method relative to traditional drug development approaches indicates a high potential for accelerating drug development for CRPC.

PyQMC: An all-Python real-space quantum Monte Carlo module in PySCF.

We describe a new open-source Python-based package for high accuracy correlated electron calculations using quantum Monte Carlo (QMC) in real space: PyQMC. PyQMC implements modern versions of QMC algorithms in an accessible format, enabling algorithmic development and easy implementation of complex workflows. Tight integration with the PySCF environment allows for a simple comparison between QMC calculations and other many-body wave function techniques, as well as access to high accuracy trial wave functions.

Zebrafish rbm8a and magoh mutants reveal EJC developmental functions and new 3'UTR intron-containing NMD targets.

Many post-transcriptional mechanisms operate via mRNA 3'UTRs to regulate protein expression, and such controls are crucial for development. We show that homozygous mutations in two zebrafish exon junction complex (EJC) core genes rbm8a and magoh leads to muscle disorganization, neural cell death, and motor neuron outgrowth defects, as well as dysregulation of mRNAs subjected to nonsense-mediated mRNA decay (NMD) due to translation termination ≥ 50 nts upstream of the last exon-exon junction. Intriguingly, we find that EJC-dependent NMD also regulates a subset of transcripts that contain 3'UTR introns (3'UI) < 50 nts downstream of a stop codon. Some transcripts containing such stop codon-proximal 3'UI are also NMD-sensitive in cultured human cells and mouse embryonic stem cells. We identify 167 genes that contain a conserved proximal 3'UI in zebrafish, mouse and humans. foxo3b is one such proximal 3'UI-containing gene that is upregulated in zebrafish EJC mutant embryos, at both mRNA and protein levels, and loss of foxo3b function in EJC mutant embryos significantly rescues motor axon growth defects. These data are consistent with EJC-dependent NMD regulating foxo3b mRNA to control protein expression during zebrafish development. Our work shows that the EJC is critical for normal zebrafish development and suggests that proximal 3'UIs may serve gene regulatory function in vertebrates.

Androgen receptor variants: RNA-based mechanisms and therapeutic targets.

Prostate cancer is the second leading cause of male cancer death in the United States. The androgen receptor (AR) transcription factor is a master regulator of normal glandular homeostasis in the prostate, as well as growth and survival of prostate cancer cells. Therefore, AR-targeted therapies are effective for improving overall survival of patients with advanced prostate cancer that is incurable by surgery or radiation. However, prostate cancer will inevitably progress on AR-targeted therapies to a castration-resistant prostate cancer (CRPC) phenotype that accounts for virtually all prostate cancer-specific death. mRNA transcript variants of the AR gene are expressed in CRPC cells and can be translated to produce AR variant (AR-V) proteins that function as ligand-independent, constitutively active transcription factors. AR-Vs are able to support growth of CRPC cells by promoting expression of AR target genes that are normally suppressed by AR-targeted therapies. Knowledge of mechanisms that govern expression of AR-Vs is incomplete. Studies have shown genomic rearrangements of the AR gene underlie expression of diverse AR-Vs in certain CRPC tumors, but post-transcriptional processes represent a broader regulatory mechanism for expression of AR-Vs in CRPC. This review focuses on alternative splicing, 3' end processing, miRNA-mediated mRNA repression, of AR and AR-V expression and the potential these mechanisms hold as therapeutic targets for CRPC.

Pumilio response and AU-rich elements drive rapid decay of Pnrc2-regulated cyclic gene transcripts.

Vertebrate segmentation is regulated by the segmentation clock, a biological oscillator that controls periodic formation of somites, or embryonic segments, which give rise to many mesodermal tissue types. This molecular oscillator generates cyclic gene expression with the same periodicity as somite formation in the presomitic mesoderm (PSM), an area of mesenchymal cells that give rise to mature somites. Molecular components of the clock include the Hes/her family of genes that encode transcriptional repressors, but additional genes cycle. Cyclic gene transcripts are cleared rapidly, and clearance depends upon the pnrc2 (proline-rich nuclear receptor co-activator 2) gene that encodes an mRNA decay adaptor. Previously, we showed that the her1 3'UTR confers instability to otherwise stable transcripts in a Pnrc2-dependent manner, however, the molecular mechanism(s) by which cyclic gene transcripts are cleared remained largely unknown. To identify features of the her1 3'UTR that are critical for Pnrc2-mediated decay, we developed an array of transgenic inducible reporter lines carrying different regions of the 3'UTR. We find that the terminal 179 nucleotides (nts) of the her1 3'UTR are necessary and sufficient to confer rapid instability. Additionally, we show that the 3'UTR of another cyclic gene, deltaC (dlc), also confers Pnrc2-dependent instability. Motif analysis reveals that both her1 and dlc 3'UTRs contain terminally-located Pumilio response elements (PREs) and AU-rich elements (AREs), and we show that the PRE and ARE in the last 179 â€‹nts of the her1 3'UTR drive rapid turnover of reporter mRNA. Finally, we show that mutation of Pnrc2 residues and domains that are known to facilitate interaction of human PNRC2 with decay factors DCP1A and UPF1 reduce the ability of Pnrc2 to restore normal cyclic gene expression in pnrc2 mutant embryos. Our findings suggest that Pnrc2 interacts with decay machinery components and cooperates with Pumilio (Pum) proteins and ARE-binding proteins to promote rapid turnover of cyclic gene transcripts during somitogenesis.

Constitutive expression of microRNA-150 in mammary epithelium suppresses secretory activation and impairs de novo lipogenesis.

Profiling of RNA from mouse mammary epithelial cells (MECs) isolated on pregnancy day (P)14 and lactation day (L)2 revealed that the majority of differentially expressed microRNA declined precipitously between late pregnancy and lactation. The decline in miR-150, which exhibited the greatest fold-decrease, was verified quantitatively and qualitatively. To test the hypothesis that the decline in miR-150 is crucial for lactation, MEC-specific constitutive miR-150 was achieved by crossing ROSA26-lox-STOP-lox-miR-150 mice with WAP-driven Cre recombinase mice. Both biological and foster pups nursed by bitransgenic dams exhibited a dramatic decrease in survival compared with offspring nursed by littermate control dams. Protein products of predicted miR-150 targets Fasn, Olah, Acaca, and Stat5B were significantly suppressed in MECs of bitransgenic mice with constitutive miR-150 expression as compared with control mice at L2. Lipid profiling revealed a significant reduction in fatty acids synthesized by the de novo pathway in L2 MECs of bitransgenic versus control mice. Collectively, these data support the hypothesis that a synchronized decrease in miRNAs, such as miR-150, at late pregnancy serves to allow translation of targets crucial for lactation.

Pnrc2 regulates 3'UTR-mediated decay of segmentation clock-associated transcripts during zebrafish segmentation.

Vertebrate segmentation is controlled by the segmentation clock, a molecular oscillator that regulates gene expression and cycles rapidly. The expression of many genes oscillates during segmentation, including hairy/Enhancer of split-related (her or Hes) genes, which encode transcriptional repressors that auto-inhibit their own expression, and deltaC (dlc), which encodes a Notch ligand. We previously identified the tortuga (tor) locus in a zebrafish forward genetic screen for genes involved in cyclic transcript regulation and showed that cyclic transcripts accumulate post-splicing in tor mutants. Here we show that cyclic mRNA accumulation in tor mutants is due to loss of pnrc2, which encodes a proline-rich nuclear receptor co-activator implicated in mRNA decay. Using an inducible in vivo reporter system to analyze transcript stability, we find that the her1 3'UTR confers Pnrc2-dependent instability to a heterologous transcript. her1 mRNA decay is Dicer-independent and likely employs a Pnrc2-Upf1-containing mRNA decay complex. Surprisingly, despite accumulation of cyclic transcripts in pnrc2-deficient embryos, we find that cyclic protein is expressed normally. Overall, we show that Pnrc2 promotes 3'UTR-mediated decay of developmentally-regulated segmentation clock transcripts and we uncover an additional post-transcriptional regulatory layer that ensures oscillatory protein expression in the absence of cyclic mRNA decay.

Generation of an Induced Pluripotent Stem Cell Line with the Constitutive EGFP Reporter.

The discovery of induced pluripotent stem cell (iPSC) technology has provided a versatile platform for basic science research and regenerative medicine. With the rise of clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) systems and the ease at which they can be utilized for gene editing, creating genetically modified iPSCs has never been more advantageous for studying both organism development and potential clinical applications. However, to better understand the behavior and true therapeutic potential of iPSCs and iPSC-derived cells, a tool for labeling and monitoring these cells in vitro and in vivo is needed. Here, we describe a protocol that provides a straightforward method for introducing a stable, highly expressed fluorescent protein into iPSCs using the CRISPR/Cas9 system and a standardized donor vector. The approach involves the integration of the EGFP transgene into the transcriptionally active adeno-associated virus integration site 1 (AAVS1) locus through homology directed repair. The knockin of this transgene results in the generation of iPSC lines with constitutive expression of the EGFP protein that also persists in differentiated iPSCs. These EGFP-labeled iPSC lines are ideal for assessing iPSC differentiation in vitro and evaluating the distribution of iPSC-derived cells in vivo after transplantation into model animals.

Community-based preferences for stool cards versus colonoscopy in colorectal cancer screening.

BACKGROUND: In the United States, compliance with colorectal cancer (CRC) screening recommendations remains suboptimal. Professional organizations advocate use of shared decision making in screening test discussions, but strategies to facilitate informed choice in CRC screening have not been well elucidated. OBJECTIVE: The objectives of the study were to determine screening test preference among colonoscopy-naïve adults after considering a detailed, written presentation of fecal occult blood testing (FOBT) and colonoscopy and to assess whether their preferences are associated with demographic characteristics, attitudes, and knowledge. DESIGN: The design of the study was a cross-sectional survey. PARTICIPANTS: Colonoscopy-naïve supermarket shoppers age 40-79 in low- and middle-income, multiethnic neighborhoods in Denver, CO, reviewed a detailed, side-by-side description of FOBT and colonoscopy and answered questions about test preference, strength of preference, influence of physician recommendation, basic knowledge of CRC, and demographic characteristics. MEASUREMENTS AND MAIN RESULTS: Descriptive statistics characterized the sample, and bivariate and multivariable logistic regression analyses identified correlates of screening test preference. In a diverse sample of 323 colonoscopy-naïve adults, 53% preferred FOBT, and 47% preferred colonoscopy for CRC screening. Individuals of Latino ethnicity and those with lower educational attainment were more likely to prefer FOBT than non-Latino whites and those with at least some college. Almost half of the respondents felt "very strongly" about their preferences, and one third said they would adhere to their choice regardless of physician recommendation. CONCLUSION: After considering a detailed, side-by-side comparison of the FOBT and colonoscopy, a large proportion of community-dwelling, colonoscopy-naïve adults prefer FOBT over colonoscopy for CRC screening. In light of professional guidelines and time-limited primary care visits, it is important to develop improved ways of facilitating informed patient decision making for CRC screening.

MMTV-PyMT and Derived Met-1 Mouse Mammary Tumor Cells as Models for Studying the Role of the Androgen Receptor in Triple-Negative Breast Cancer Progression.

Triple-negative breast cancer (TNBC) has a faster rate of metastasis compared to other breast cancer subtypes, and no effective targeted therapies are currently FDA-approved. Recent data indicate that the androgen receptor (AR) promotes tumor survival and may serve as a potential therapeutic target in TNBC. Studies of AR in disease progression and the systemic effects of anti-androgens have been hindered by the lack of an AR-positive (AR+) immunocompetent preclinical model. In this study, we identified the transgenic MMTV-PyMT (mouse mammary tumor virus-polyoma middle tumor-antigen) mouse mammary gland carcinoma model of breast cancer and Met-1 cells derived from this model as tools to study the role of AR in breast cancer progression. AR protein expression was examined in late-stage primary tumors and lung metastases from MMTV-PyMT mice as well as in Met-1 cells by immunohistochemistry (IHC). Sensitivity of Met-1 cells to the AR agonist dihydrotestosterone (DHT) and anti-androgen therapy was examined using cell viability, migration/invasion, and anchorage-independent growth assays. Late-stage primary tumors and lung metastases from MMTV-PyMT mice and Met-1 cells expressed abundant nuclear AR protein, while negative for estrogen and progesterone receptors. Met-1 sensitivity to DHT and AR antagonists demonstrated a reliance on AR for survival, and AR antagonists inhibited invasion and anchorage-independent growth. These data suggest that the MMTV-PyMT model and Met-1 cells may serve as valuable tools for mechanistic studies of the role of AR in disease progression and how anti-androgens affect the tumor microenvironment.

Using local operator fluctuations to identify wave function improvements.

A method is developed that allows analysis of quantum Monte Carlo simulations to identify errors in trial wave functions. The purpose of this method is to allow for the systematic improvement of variational wave functions by identifying degrees of freedom that are not well described by an initial trial state. We provide proof of concept implementations of this method by identifying the need for a Jastrow correlation factor and implementing a selected multideterminant wave function algorithm for small dimers that systematically decreases the variational energy. Selection of the two-particle excitations is done using the quantum Monte Carlo method within the presence of a Jastrow correlation factor and without the need to explicitly construct the determinants. We also show how this technique can be used to design compact wave functions for transition metal systems. This method may provide a route to analyze and systematically improve descriptions of complex quantum systems in a scalable way.

Cooperative Dynamics of AR and ER Activity in Breast Cancer.

Androgen receptor (AR) is expressed in 90% of estrogen receptor alpha-positive (ER+) breast tumors, but its role in tumor growth and progression remains controversial. Use of two anti-androgens that inhibit AR nuclear localization, enzalutamide and MJC13, revealed that AR is required for maximum ER genomic binding. Here, a novel global examination of AR chromatin binding found that estradiol induced AR binding at unique sites compared with dihydrotestosterone (DHT). Estradiol-induced AR-binding sites were enriched for estrogen response elements and had significant overlap with ER-binding sites. Furthermore, AR inhibition reduced baseline and estradiol-mediated proliferation in multiple ER+/AR+ breast cancer cell lines, and synergized with tamoxifen and fulvestrant. In vivo, enzalutamide significantly reduced viability of tamoxifen-resistant MCF7 xenograft tumors and an ER+/AR+ patient-derived model. Enzalutamide also reduced metastatic burden following cardiac injection. Finally, in a comparison of ER+/AR+ primary tumors versus patient-matched local recurrences or distant metastases, AR expression was often maintained even when ER was reduced or absent. These data provide preclinical evidence that anti-androgens that inhibit AR nuclear localization affect both AR and ER, and are effective in combination with current breast cancer therapies. In addition, single-agent efficacy may be possible in tumors resistant to traditional endocrine therapy, as clinical specimens of recurrent disease demonstrate AR expression in tumors with absent or refractory ER. IMPLICATIONS: This study suggests that AR plays a previously unrecognized role in supporting E2-mediated ER activity in ER+/AR+ breast cancer cells, and that enzalutamide may be an effective therapeutic in ER+/AR+ breast cancers. Mol Cancer Res; 14(11); 1054-67. ©2016 AACR.

The use of thoracoscopy in the treatment of iatrogenic esophageal perforations.

Treatment options for patients with iatrogenic esophageal perforations are multiple and remain a source of controversy. Therapeutic options range from conservative, non-operative treatment to esophageal exclusion or esophagectomy. We present herein what we believe to be the first described repair of an esophageal perforation using thoracoscopic surgical techniques. We believe this approach offers several advantages over open thoracic surgery and has a role in minimizing postoperative morbidity in an already potentially life-threatening condition.

Laminopathy-inducing mutations reduce nuclear import of expressed prelamin A.

Lamins are structural components of the nuclear lamina and integral parts of the nucleoplasm. The tripartite domain structure partitions the molecule into an amino-terminal head, central rod and a carboxy-terminal tail domain. The tail domain contains a nuclear localization sequence and in most lamins an additional CaaX motif, which is necessary to post-translationally process prelamin to mature lamin. As players of nuclear and cellular integrity, lamins must possess unrestrained access to the nucleus. To study whether nuclear trafficking of lamins is compromised in laminopathies, we determined relative nuclear import activities between expressed prelamin A and selected laminopathy-inducing mutants thereof. Furthermore, the impact of inhibition of maturation on nuclear import of expressed prelamin A was examined. To perform quantitative transport measurements, import competent but lamina incorporation-deficient GFP- or DsRed-tagged prelamin A deletion mutants were used, which lacked the head and rod domain (ΔHR-prelamin A). Nuclear accumulation of ΔHR-prelamin A carrying the lipodystrophy and metabolic syndrome-inducing mutations R419C and L421P or progeria-causing deletions was significantly reduced, but that of the maturation-deficient mutant ΔHR-prelamin A SSIM was significantly increased. In the case of the full length prelamin A mutants R419C and L421P altered subcellular localization and reduced lamina incorporation were detected, with the prelamin A-binding protein Narf being redistributed into R419-containing aggregates. The results suggest that impaired nuclear transport of certain prelamin A mutants may represent a contributing factor in the pathogenesis of certain laminopathies.

Endogenous enzymes (NOX and ECSOD) regulate smoke-induced oxidative stress.

Chronic obstructive pulmonary disease (COPD) is the fourth leading cause of death in the United States and the incidence is increasing as the population ages. Cigarette smoking is the primary risk factor; however, only a minority of smokers develop the disease. Inhalation of cigarette smoke introduces an abundance of free radicals into the lungs, causing oxidative stress and inflammation. We hypothesized that after the initial burst of oxidative stress associated with cigarette smoke exposure, a sustained source of endogenous free radical production is modulated by the antioxidant enzyme extracellular superoxide dismutase (ECSOD) and the superoxide-generating complex NADPH oxidase (NOX). Primary mouse macrophages exposed to cigarette smoke extract exhibited increased oxidative stress as indicated by fluorogenic dyes and isoprostane concentration, which was suppressed in the presence of both a superoxide dismutase mimetic and a NOX inhibitor. Similarly, primary macrophages isolated from ECSOD-overexpressing mice or NOX-deficient mice showed reduced oxidative stress in response to cigarette smoke treatment. In addition, both reduced glutathione and cytokines (MIP2 and IFNγ) were increased in bronchoalveolar lavage fluid of wild-type mice exposed to cigarette smoke but not in ECSOD-overexpressing or NOX-deficient mice. These data suggest that the mechanisms underlying the host defense against cigarette smoke-induced oxidative damage and subsequent development of COPD may include endogenous oxidases and antioxidant enzymes.

Evolving techniques in endoscopic extraperitoneal herniorrhaphy.

Endoscopic extraperitoneal herniorrhaphy (EEPH) was utilized to repair 326 groin hernias in 249 patients over a 32-month period. Nearly one in ten of the repairs was for a recurrent hernia. Several patients had contralateral hernias diagnosed only at the time of endoscopic examination. A recurrence rate of 1.6% and an overall complication rate of 5.2% are cited. After a plateau was reached on the surgeon's learning curve, various modifications in technique were implemented. Through these modifications, EEPH has become a safe, efficient, and standardized operation that can be performed with decreasing costs to the hospital and with increasing advantages to the patient.

Laparoscopic resection of a large hepatic tumor.

Increasing experience among surgeons and a proliferation of endoscopic instrumentation have allowed a greater number of intraabdominal organs to be approached laparoscopically. Procedures once delegated to standard open technique are now attempted laparoscopically with increasing success. The following case report describes the laparoscopic removal of a large segment IV liver tumor. A review of the literature shows this to be one of the most complex hepatic lesions to be removed laparoscopically to date.

The role of the endoscopic extraperitoneal approach in large inguinal scrotal hernias.

The role of endoscopic extraperitoneal herniorrhaphy (EEPH) in the management of giant scrotal hernias has not been well defined, and the technical details relating to operations on such hernias have not been described. We present our experience with 17 patients undergoing repair of giant scrotal hernias. Foley catheter bladder decompression was routinely employed. The Retzius space was developed early in the procedure and hernia sac contents were reduced in all cases. The inferior epigastric vessels were likewise divided in all patients. The average operative time was 76 min and all patients were discharged home the same day. There have been no recurrences on follow-up. There was no mortality, and morbidity was limited to seroma formation in two patients. We conclude that with certain technical modifications, EEPH can be safely employed for the treatment of giant scrotal hernias.

Combined use of laparoscopy and endoscopy in diagnosing and treating Dieulafoy's vascular malformations of the stomach.

We present the case of a 70-year-old female successfully treated for a bleeding Dieulafoy's gastric lesion with a combined laparoscopic/endoscopic approach. An increasing percentage of surgery is now being performed laparoscopically and the authors feel that combined laparoscopic/endoscopic surgery offers advantages to the patient over either of these methods individually and over open surgery. This report demonstrates that a bleeding point anywhere on the gastric wall is amenable to laparoscopic intervention if the localization techniques we describe are utilized.

Changing experiences with 1848 cholecystectomies at a single institution.

A retrospective review of all cholecystectomies performed at a single institution since the advent of laparoscopic cholecystectomy at that institution was undertaken. Of the 1848 cases analyzed, 1372 were completed laparoscopically. There was an increase in utilization of ERCP prior to cholecystectomy, and an increase in the number of cases being done laparoscopically for acute and gangrenous cholecystitis over the 48 months of the study. Of the 1442 cases started laparoscopically, eight technical complications were recognized, and conversion was required in five of these. Only two bile duct injuries were identified in the laparoscopic group. Data analyzed over the past 2 years of the study, when the number of surgeons performing laparoscopy remained stable, showed a decrease in both complication and conversion rates. There are no strong data to support the practice of routine intraoperative cholangiography.