Patterns of structural variation define prostate cancer across disease states

The complex genomic landscape of prostate cancer evolves across disease states under therapeutic pressure directed toward inhibiting androgen receptor (AR) signaling. While significantly altered genes in prostate cancer have been extensively defined, there have been fewer systematic analyses of how structural variation shapes the genomic landscape of this disease across disease states. We uniformly characterized structural alterations across 531 localized and 143 metastatic prostate cancers profiled by whole genome sequencing, 125 metastatic samples of which were also profiled via whole transcriptome sequencing. We observed distinct significantly recurrent breakpoints in localized and metastatic castration-resistant prostate cancers (mCRPC), with pervasive alterations in noncoding regions flanking the AR, MYC, FOXA1, and LSAMP genes enriched in mCRPC and TMPRSS2-ERG rearrangements enriched in localized prostate cancer. We defined 9 subclasses of mCRPC based on signatures of structural variation, each associated with distinct genetic features and clinical outcomes. Our results comprehensively define patterns of structural variation in prostate cancer and identify clinically actionable subgroups based on whole genome profiling.

Machine Learning Prediction of Non-Coding Variant Impact in Human Retinal cis-Regulatory Elements

Purpose

Prior studies have demonstrated the significance of specific cis-regulatory variants in retinal disease; however, determining the functional impact of regulatory variants remains a major challenge. In this study, we utilized a machine learning approach, trained on epigenomic data from the adult human retina, to systematically quantify the predicted impact of cis-regulatory variants.

Methods

We used human retinal DNA accessibility data (ATAC-seq) to determine a set of 18.9k high-confidence, putative cis-regulatory elements. Eighty percent of these elements were used to train a machine learning model utilizing a gapped k-mer support vector machine-based approach. In silico saturation mutagenesis and variant scoring was applied to predict the functional impact of all potential single nucleotide variants within cis-regulatory elements. Impact scores were tested in a 20% hold-out dataset and compared to allele population frequency, phylogenetic conservation, transcription factor (TF) binding motifs, and existing massively parallel reporter assay data.

Results

We generated a model that distinguishes between human retinal regulatory elements and negative test sequences with 95% accuracy. Among a hold-out test set of 3.7k human retinal CREs, all possible single nucleotide variants were scored. Variants with negative impact scores correlated with higher phylogenetic conservation of the reference allele, disruption of predicted TF binding motifs, and massively parallel reporter expression.

Conclusions

We demonstrated the utility of human retinal epigenomic data to train a machine learning model for the purpose of predicting the impact of non-coding regulatory sequence variants. Our model accurately scored sequences and predicted putative transcription factor binding motifs. This approach has the potential to expedite the characterization of pathogenic non-coding sequence variants in the context of unexplained retinal disease.

Translational Relevance

This workflow and resulting dataset serve as a promising genomic tool to facilitate the clinical prioritization of functionally disruptive non-coding mutations in the retina.

Transient expression of a GABA receptor subunit during early development is critical for inhibitory synapse maturation and function

Developing neural circuits, including GABAergic circuits, switch receptor types. But the role of early GABA receptor expression for establishment of functional inhibitory circuits remains unclear. Tracking the development of GABAergic synapses across axon terminals of retinal bipolar cells (BCs), we uncovered a crucial role of early GABA_A receptor expression for the formation and function of presynaptic inhibitory synapses. Specifically, early α3-subunit-containing GABA_A (GABA_Aα3) receptors are a key developmental organizer. Before eye opening, GABA_Aα3 gives way to GABA_Aα1 at individual BC presynaptic inhibitory synapses. The developmental downregulation of GABA_Aα3 is independent of GABA_Aα1 expression. Importantly, lack of early GABA_Aα3 impairs clustering of GABA_Aα1 and formation of functional GABA_A synapses across mature BC terminals. This impacts the sensitivity of visual responses transmitted through the circuit. Lack of early GABA_Aα3 also perturbs aggregation of LRRTM4, the organizing protein at GABAergic synapses of rod BC terminals, and their arrangement of output ribbon synapses.

014.Novel uterine genes in regulation of embryo implantation

Implantation of the embryo into the maternal endometrium is the first and critical step leading to the establishment of a pregnancy. It has been well established that only during the 'window' of implantation, a limited time span when the uterine environment is receptive, can a blastocyst successfully implant into the uterus. The development of uterine receptivity is accompanied by remarkable morphological and physiological changes in the endometrium, and this is primarily driven by the coordinated effects of the ovarian steroid hormones. Uterine tissue remodelling during implantation also contributes significantly to the development of the placenta. Insufficient uterine remodelling causes implantation failure and infertility. To date, the exact molecular events occurring in the uterus during the establishment of receptivity and at the actual site of implantation are still not well understood. We used the mouse as a model and identified a number of previously unrecognised molecules that are uniquely regulated in the early stages of implantation: one of these is proprotein convertase 6 (PC6). The potential importance of these genes and their products in modulating fertility in the primate, including the human, was demonstrated by their unique spatial and temporal expression in the endometrium of human and rhesus monkey during the phase of uterine receptivity and at implantation. The importance of the genes for implantation was ultimately confirmed by functional studies in vivo using morpholino antisense oligonucleotides. These molecules will be discussed in terms of their identity, expression and functions.

Zinc ligand-disrupted recombinant human Endostatin: potent inhibition of tumor growth, safety and pharmacokinetic profile

Endostatin, a potent endogenous inhibitor of angiogenesis, inhibits the growth of primary tumors without induction of acquired drug resistance in mice. We report that a soluble recombinant human (rh) Endostatin produced with characteristics of the native Endostatin, effectively inhibited the growth of primary tumors and pulmonary metastases in a dose-dependent manner. We also show that deletion of two of the four zinc ligands of rhEndostatin did not affect this potent tumor inhibiton. The growth of established Lewis lung primary tumors implanted into mice was inhibited (80-90%) upon systemic treatment with 50 mg/kg/12 h of rhEndostatin. Using the B16-BL6 murine experimental pulmonary metastases model, rhEndostatin administered at 1.5 mg/kg/day or 4.5 mg/kg/day beginning 3- or 11-days post tumor cell injection, respectively, resulted in an approximate 80% inhibition of tumor growth. At effective anti-tumor doses of 1.5 and 50 mg/kg, pharmacokinetic modeling in mice showed (a) the protein was 100% bioavailable, (b) the AUC ranged from 16 to 700 ng ml/h and (c) the Cmax ranged from 161 to 4582 ng/ml. At the highest dose tested (300 mg/kg), delivered as a single bolus, no drug-related toxicity was observed in a Cynomolgus monkey infused with rhEndostatin. No toxicity was observed even at AUC and Cmax values that were 1.3- to 56-fold higher than those observed in mice with tumors that were potently inhibited. Our production system yields a well characterized, soluble and potent rhEndostatin at quantities sufficient for human use. The preclinical studies described herein are an important first step toward the assessment of Endostatin in the clinic.

Metabolic response to radiation therapy in patients with cancer

The effect of radiation therapy on substrate metabolism was evaluated in five patients with head and neck or lung cancer. Stable isotope tracer methodology was used to determine urea, amino acid, glucose, and lipid kinetics during postabsorptive conditions before initiation, near the midpoint (after receiving 2,672 +/- 36 rads), and at completion (after receiving 6,072 +/- 307 rad) of a 6- to 8-week course of radiation therapy. Nutritional status was maintained throughout the treatment period by providing supplemental enteral feedings as needed. Postabsorptive plasma insulin, catecholamine, and amino acid concentrations did not change during the course of treatment. Before radiation therapy was initiated, values for the plasma rate of appearance (Ra) of urea (3.35 +/- 0.33 micromol x kg(-1) x min(-1)), alpha-ketoisocaproate ([alpha-KIC] 2.16 +/- 0.19 micromol x kg(-1) x min(-1)), phenylalanine (0.59 +/- 0.052 micromol x kg(-1) x min(-1)), and glucose (10.56 +/- 1.31 micromol x kg(-1) x min(-1)) were in the normal range. However, glycerol and palmitate Ra values (3.11 +/- 0.30 and 2.01 +/- 0.33 micromol x kg(-1) x min(-1), respectively) were 25% higher than values observed previously in normal subjects. Substrate flux did not change during radiation therapy, and measurements obtained during the midpoint and at completion of treatment were similar to initial values. These results demonstrate that large doses of radiation therapy, administered over 6 to 8 weeks to the upper body, do not cause significant metabolic stress.

Effect of weight loss on whole body and cellular lipid metabolism in severely obese humans

We evaluated the effect of diet-induced weight loss on whole body and cellular lipid metabolism in persons with severe upper body obesity in two study protocols. In protocol 1, palmitate and glycerol rates of appearance (Ra) in plasma were determined during basal conditions in seven subjects [initial body mass index (BMI) = 41.3 +/- 2.2 kg/m2] before and after 20.4 +/- 3.0 kg weight loss. Total glycerol and palmitate Ra decreased from 231.0 +/- 19.4 and 166.2 +/- 16.6 mumol/min, respectively, before weight loss to 162.7 +/- 9.5 and 105.0 +/- 9.7 mumol/min, respectively, after weight loss (P < 0.01). However, glycerol and palmitate Ra expressed per kilogram fat mass were similar both before and after weight loss. In protocol 2, subcutaneous abdominal adipose tissue was obtained before and after 14.4 +/- 2.1 kg weight loss in five subjects (initial BMI = 41.6 +/- 2.6 kg/m2). Weight loss caused a 38 +/- 8% decrease in adipocyte hormone-sensitive lipase concentration (P < 0.05) but was not associated with any consistent changes in the concentrations of GTP-dependent regulatory proteins, Gi1 alpha, Gi2 alpha, and G3 alpha. We conclude that diet-induced weight loss ameliorates the increase in basal lipolytic rates in persons with severe upper body obesity. These alterations are associated with changes in cellular hormone-sensitive lipase but not GTP-dependent regulatory protein concentrations.

The influence of tumor stage and metastasis on the biodistribution of gallium-67 citrate in the murine Lewis lung carcinoma model

The biodistribution of i.v. administered [67Ga]citrate was investigated in the Lewis lung carcinoma/male B6D2F1 mouse model. Tumors were implanted intramuscularly (10(5) cells or 10(6) cells in suspension) into the thigh, or subcutaneously (10(7) cells or 2 mm3 fragments) into the tail of recipient mice. Intramuscular tumors were allowed to grow for 16, 24, or 33 days; tail tumors developed for 2 wk (fragment implants) or 3 wk (10(7) cells in suspension) after which the primary tumor was amputated along with adjacent fragments of the tail tissue. Gamma camera scintigraphy and dissection/radiometric biodistribution studies indicated that: (a) tumors and metastases took up 5-6% of the injected dose/g except when large necrotic areas were present in the primary tumor; (b) blood levels of 67Ga increased in all tumor-bearing animals, with up to tenfold increases in the i.m. tumor model at later stages of the growth; (c) hepatic uptake increased as a function of tumor size/age, and (d) all tissue:blood ratios declined as the neoplastic tissues progressed. The results are discussed with respect to tumor progression and metastatic disease.