Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1-3. Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter4; identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation5,6; analyses timings and patterns of tumour evolution7; describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity8,9; and evaluates a range of more-specialized features of cancer genomes8,10-18.

The behavior of dairy cattle in late gestation: Effects of parity and dystocia

The aim of this study was to objectively assess, using an automated behavioral monitoring system, any behavioral differences between primiparous and multiparous cows before calving, and to quantify any behavioral differences between assisted (dystocic) and unassisted (eutocic) calvings. Data were collected from 32 multiparous and 12 primiparous Holstein dairy cattle to describe normal calving behavior and parity differences. To quantify behavior related to calving difficulty, the data from 14 animals that had dystocia at calving were matched to cows that had an eutocic calving based on parity, locomotion score, calf breed, calf sex, month, and year of calving. An IceQube (IceRobotics Ltd., South Queensferry, United Kingdom) was fitted to the right hind leg of cows 4 wk before their expected calving date. Data for lying time, standing time, number of steps, motion index (total motion), and the total number of standing and lying bouts (postural transitions) were automatically collected and summed into 15-min blocks. Behavioral variables were summarized into 2-h periods and 24-h periods before analyses. Mixed-effect models were used to analyze cow behavior in the last 4 d before calving (d -4 to -1), and on the day of calving. In the 4 d before calving, compared with multiparous cows, primiparous cows lay down an average 2.8 h/d less, had 9.1 more postural transitions/d (37.7 ± 1.2 vs. 27.6 ± 0.7), walked 172 more steps/d, and had a higher motion index (2,673.2 vs. 1,981.5 units/d). There was an effect of 2-h period on all behavioral variables on the day of calving. No indicator of calving difficulty was found on the day of calving, nor the days leading up to calving. These findings suggest that parity should be considered when predicting the day of calving, and changes in cow behavior on the day of calving could be used to identify calving cows, and to predict the time of calving.

Abstract 295: CASC-578, a novel Chk1 inhibitor, is active as a single agent in solid tumors and displays synergistic anti-tumor activity in combination with Wee1 inhibition

Background: Checkpoint kinase 1 (Chk1) is a serine/threonine protein kinase that regulates cell division in response to genotoxic stress by arresting cell cycle progression in the S & G2 phases. Pharmacological inhibition of Chk1 is proposed to target tumor cells with increased DNA replication stress, resulting in the uncoupling of DNA replication checkpoint function and the induction of DNA damage and cell death. These properties make Chk1 inhibition a novel therapeutic approach as a single agent in cancers with high replication stress that is driven by oncogenic signaling and loss of parallel DNA damage response pathway function.

Methods and Results: This report highlights the activity of the orally bioavailable, selective small molecule Chk1 inhibitor, CASC-578, in solid tumor derived cell lines. CASC-578 is a sub-nanomolar enzymatic inhibitor of Chk1 with limited off-target activity against a panel of protein kinases. When evaluated in a large cell line panel in vitro, CASC-578 demonstrated a broad potency range as a single agent in solid tumor derived cells lines, with IC50s ranging from 30 nM to greater than 50 μM. Several solid tumor types demonstrated enriched sensitivity to CASC-578 in vitro, including gastric, non-small cell lung and ovarian cancers. Treatment of sensitive cell lines with CASC-578 resulted in the induction of DNA damage, as measured by phosphorylated histone H2AX, and the induction of cell death. CASC-578 was active as a single agent in SK-MES-1 and NCI-H727 NSCLC tumor xenograft models in vivo with minimal effects on body weight in treated mice. In addition to the potent single agent activity of CASC-578, combination with the Wee1 inhibitor AZD-1775 was highly synergistic in vitro in multiple solid tumor cell lines and the combination was more efficacious than either agent alone in NSCLC tumor xenograft models. These data support the advancement of CASC-578 into clinical development as a potential therapeutic agent for the treatment of solid tumor diseases. Experiments are ongoing to identify biomarkers associated with sensitivity to CASC-578 as a single agent in solid tumor cell lines to prospectively identify tumor genotypes that are more responsive to the drug.

Citation Format: Alex Vo, Janelle Taylor, Robert Rosler, Julia Piasecki, Dina Leviten, Teresa Sierra, Ashley Dozier, Kevin Klucher, Bob Boyle, Rich Boyce, Scott Peterson. CASC-578, a novel Chk1 inhibitor, is active as a single agent in solid tumors and displays synergistic anti-tumor activity in combination with Wee1 inhibition [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 295. doi:10.1158/1538-7445.AM2017-295

Abstract 297: The novel orally available sub-nanomolar potent and selective checkpoint kinase 1 inhibitor CASC-578 is highly active in mantle cell lymphoma as a single agent and in combination with Wee1 inhibition

Background: Checkpoint kinase 1 (Chk1) is a serine/threonine protein kinase that regulates cell division by arresting progression in the S & G2 phases of the cell cycle in response to genotoxic stress. Pharmacological inhibition of Chk1 uncouples the completion of DNA replication from G2/M phase transition in tumor cells that have impaired DNA damage response networks, resulting in DNA damage induction, mitotic catastrophe and cell death. These properties make Chk1 inhibition an attractive therapeutic approach as a single agent, or to enhance the efficacy of other cancer drugs that target DNA damage response pathways.

Methods and Results: This report highlights the activity of the orally bioavailable, selective, small molecule Chk1 inhibitor, CASC-578, in multiple mantle cell lymphoma (MCL) models in vitro and in tumor mouse xenograft studies. MCL have the common genetic biomarker t(11;14)(q13;q32), a chromosomal translocation leading to the constitutive expression of the oncogene CCND1 which encodes cyclin D1, a cell cycle-regulating protein. This genotypic characteristic has been observed in the clear majority of patients with MCL in the clinic and may provide a rationale for sensitivity to Chk1 inhibition. Consistent with this idea, CASC-578 demonstrated remarkable potency as a single agent in blocking the proliferation of MCL cell lines in vitro, with an average IC50 of 61 nM. Treatment with CASC-575 as a single agent resulted in the induction of DNA damage, as measured by phosphorylated histone H2AX and activation of apoptosis, as measured by cleaved caspase. In a JEKO-1 xenograft tumor study, CASC-578 as a single agent completely regressed subcutaneously implanted tumors in the majority of mice after oral drug administration using 20 mg/kg daily or when dosed on an intermittent schedule at 25 mg/kg, with minimal effects on body weight. In addition to the observed single agent activity of CASC-578, the combination of CASC-578, and the Wee1 inhibitor AZD-1775, was highly synergistic in MCL cell lines including JEKO-1, REC-1, Z-138 and MAVER-1 in vitro. CASC-578 was also highly potent as a single agent, and in combination with AZD-1775, in blocking the proliferation of a variety of leukemia derived cell lines in vitro. Taken together, these data support the advancement of CASC-578 into clinical development as a potential therapeutic agent for the treatment of MCL, as well as other hematological malignancies.

Citation Format: Robert Rosler, Janelle Taylor, Dina Leviten, Teresa Sierra, Ashley Dozier, Kevin Klucher, Rich Boyce, Bob Boyle, Alex Vo, Scott Peterson. The novel orally available sub-nanomolar potent and selective checkpoint kinase 1 inhibitor CASC-578 is highly active in mantle cell lymphoma as a single agent and in combination with Wee1 inhibition [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 297. doi:10.1158/1538-7445.AM2017-297

Hypothermic machine perfusion of liver grafts for transplantation: technical development in human discard and miniature swine models

INTRODUCTION

Cold storage (CS) is the standard preservation technique for liver transplantation (LTx). Hypothermic machine perfusion (HMP) is an alternative preservation technique that provides a continuous supply of substrates and removes waste products. HMP improves early graft function in kidney transplantation, especially for marginal organs: To our knowledge there have been no reports HMP in human LTx. The aim of this study was to develop a reproducible technique for liver HMP prior to initiating a clinical trial.

METHODS

For the discard protocol, between May 2001 and March 2002, 10 nontransplantable human livers were obtained. We designed a model of atraumatic, centrifugal HMP of the portal vein (PV) and hepatic artery (HA) via donor vascular conduit. Livers were perfused at 3 degrees C to 5 degrees C with Vasosol solution for 5 to 10 hours using a modified Medtronic Portable Bypass System. Perfusion variables (temp, flow, pressure) where recorded every 30 minutes. During the study, we also validated our techniques in an animal model. For the animal protocol; six swine were used as liver donors and randomized to 12 hours of CS in UW (n = 3) or 12 hours of HMP using Vasosol solution (n = 3). LTx was performed in six swine. Animals survived until postoperative day 5.

RESULTS

For the discard protocol, mean HMP time was 6.7 +/- 1.8 hours. Target flow was 0.7 mL/g liver/min. PV and HA pressure ranged from 3 to 5 and 12 to 18 mm Hg, respectively. All grafts were maintained at 3 degrees C to 5 degrees C during HMP. For the animal protocol, all recipients had good liver function and survived to postoperative day 5. AST and TBili were similar between CS and HMP.

CONCLUSIONS

Our method of liver HMP appears to be a safe and reliable method to preserve livers. A clinical trial is now underway to evaluate this technique in human LTx.

In vivo myocardial protection from ischemia/reperfusion injury by the peroxisome proliferator-activated receptor-gamma agonist rosiglitazone

BACKGROUND

Diabetes is associated with increased risk of mortality as a consequence of acute myocardial infarction. This study determined whether rosiglitazone (ROSI) could reduce myocardial infarction after ischemia/reperfusion injury.

METHODS AND RESULTS

Male Lewis rats were anesthetized, and the left anterior descending coronary artery was ligated for 30 minutes. After reperfusion for 24 hours, the ischemic and infarct sizes were determined. ROSI at 1 and 3 mg/kg IV reduced infarct size by 30% and 37%, respectively (P<0.01 versus vehicle). Pretreatment with ROSI (3 mg. kg(-1). d(-1) PO) for 7 days also reduced infarct size by 24% (P<0.01). ROSI also improved ischemia/reperfusion-induced myocardial contractile dysfunction. Left ventricular systolic pressure and positive and negative maximal values of the first derivative of left ventricular pressure (dP/dt) were significantly improved in ROSI-treated rats. ROSI reduced the accumulation of neutrophils and macrophages in the ischemic heart by 40% and 43%, respectively (P<0.01). Ischemia/reperfusion induced upregulation of CD11b/CD18 and downregulation of L-selectin on neutrophils and monocytes; these effects were significantly attenuated in ROSI-treated animals. Likewise, intercellular adhesion molecule-1 expression in ischemic hearts was markedly diminished by ROSI, as was the ischemia/reperfusion-stimulated upregulation of monocyte chemoattractant protein-1.

CONCLUSIONS

ROSI reduced myocardial infarction and improved contractile dysfunction caused by ischemia/reperfusion injury. The cardioprotective effect of ROSI was most likely due to inhibition of the inflammatory response.

Cloning, expression, and pharmacological characterization of a novel human histamine receptor

Using a genomics-based reverse pharmacological approach for screening orphan G-protein coupled receptors, we have identified and cloned a novel high-affinity histamine receptor. This receptor, termed AXOR35, is most closely related to the H3 histamine receptor, sharing 37% protein sequence identity. A multiple responsive element/cyclic AMP-responsive element-luciferase reporter assay was used to identify histamine as a ligand for AXOR35. When transfected into human embryonic kidney 293 cells, the AXOR35 receptor showed a strong, dose-dependent calcium mobilization response to histamine and H3 receptor agonists including imetit and immepip. Radioligand binding confirmed that the AXOR35 receptor was a high-affinity histamine receptor. The pharmacology of the AXOR35 receptor was found to closely resemble that of the H3 receptor; the major difference was that (R)-alpha-methylhistamine was a low potency agonist of the AXOR35 receptor. Thioperamide is an antagonist at AXOR 35. Expression of AXOR35 mRNA in human tissues is highest in peripheral blood mononuclear cells and in tissues likely to contain high concentrations of blood cells, such as bone marrow and lung. In situ hybridization analysis of a wide survey of mouse tissues showed that mouse AXOR35 mRNA is selectively expressed in hippocampus. The identification and localization of this new histamine receptor will expand our understanding of the physiological and pathological roles of histamine and may provide additional opportunities for pharmacological modification of these actions.

Systemic administration of acidic fibroblast growth factor (FGF-1) prevents bone loss and increases new bone formation in ovariectomized rats

There are no universally accepted agents that will substantially increase bone mass in osteoporotic patients. A number of peptides important in normal bone formation, such as members of the transforming growth factor-beta superfamily, are not satisfactory for this purpose either because their beneficial effects are predominantly local or there is systemic toxicity associated with their administration. We have examined the effects of exogenous fibroblast growth factor-1 and -2 (FGF-1 and FGF-2) on bone in vivo, since FGFs have been shown recently to be essential for normal skeletal development. FGF-1 was injected daily (0.2 mg/kg intravenously) for 28 days into the tail vein of adult female rats immediately following and 6 months after sham operation or ovariectomy (OVX). In rats treated immediately post-OVX, OVX produced more than a 30% decrease in tibial bone density, which was prevented by FGF-1 and estrogen. However, FGF-1 also had an anabolic effect. In sham-operated rats, FGF-1 increased bone density to 2-fold, whereas estrogen had no effect. In rats 6 months post-OVX, severe bone loss and disruption of trabecular microarchitecture occurred similar to that seen in patients with severe osteoporosis. In these rats, administration of FGF-1 induced extensive new woven bone formation with new trabecular-like structures filling much of the marrow spaces, and bone density in the tibial metaphysis increased 3-fold. FGF-1 and FGF-2 were also administered subcutaneously over the calvaria of mice in doses of 2-2000 microg/day for 3 days and shown to produce substantial increases in bone formation when examined morphologically. Thus, we conclude that both local and systemic FGF-1 increases new bone formation and bone density, and systemic FGF-1 also appears to restore bone microarchitecture and prevent bone loss associated with estrogen-withdrawal.

Bisphosphonate risedronate reduces metastatic human breast cancer burden in bone in nude mice

Human breast cancer frequently metastasizes to the skeleton to cause osteolysis and subsequent pain, pathological fracture, and hypercalcemia. Because bone continuously releases growth factors stored in bone matrix by bone resorption during physiological remodeling and, thus, possibly provides a favorable microenvironment for metastatic breast cancer cells to proliferate, inhibitors of bone resorption used either prophylactically or in patients with established disease, therefore, would seem likely to be useful adjuvant therapy in patients with breast cancer. However, the parameters for monitoring progressive osteolytic bone disease in humans are imprecise. We examined the effects of the third generation bisphosphonate, risedronate, which is a specific inhibitor of osteoclastic bone resorption, in a bone metastasis model in nude mice in which intracardiac injection of the human breast cancer cell line MDA-231 leads to osteolytic bone metastases. Risedronate (4 micrograms/animal/day) was given s.c. to animals (a) after radiologically small but defined osteolytic metastases were observed; (b) simultaneously with MDA-231 cell inoculation through the entire experimental period; or (c) by short-term prophylactic administration before inoculation of MDA-231 cells. In all experiments, risedronate either slowed progression or inhibited the development of bone metastases assessed radiographically. Furthermore, mice treated continuously with risedronate showed significantly longer survival than did control mice. Histomorphometrical analysis revealed that osteoclast numbers were diminished at metastatic tumor sites. Unexpectedly, there was also a marked decrease in tumor burden in bone in risedronate-treated animals. In contrast, the growth of metastatic breast cancer in soft tissues surrounding bones was not affected by risedronate. Moreover, risedronate had no effects on the local growth of s.c. implanted MDA-231 breast cancers in nude mice or on MDA-231 cell proliferation in culture. These data demonstrate that risedronate decreases metastatic MDA-231 breast cancer burden selectively in bone, as well as suppresses progression of established osteolytic lesions and prevents the development of new osteolytic lesions; thus, the data suggest that inhibition of osteoclastic bone resorption may be a useful adjunctive therapy for the treatment of cancers that have colonized in bone.

Validation of wall thickness estimates obtained with polarized light microscopy using multiple fluorochrome labels: correlation with erosion depth estimates obtained by lamellar counting

Numerous methods are currently being employed to estimate completed wall thickness and final erosion depth. Conflicting estimates of calculated bone balance have been obtained from the estimates of wall thickness and erosion depth using these various methods. To assess the utility of two specific methods to estimate wall thickness (polarized microscopy) and erosion depth (lamellar counts), we conducted a study in normal young adult beagle dogs, a model where bone balance should approximate 0. Dogs were administered multiple fluorochrome labels in vivo to label activity forming bone pockets. These labels were used to confirm the position of the cement line of the bone structural unit (BSU) in fluorescent light. Parallel measurements of wall thickness were then collected in polarized light. These estimates were compared to estimates of erosion depth obtained by lamellar counting and bone balance was calculated. Estimates of wall thickness correlated well with estimates of erosion depth with bone balance not differing significantly from 0. These data suggest that the combination of these two methods is a reasonable approach to obtaining estimates of bone balance at the level of the remodeling unit.

Finding time for counseling

To implement patient counseling, pharmacists must integrate new services into a significantly restructured prescription dispensing process to prevent marked reductions in efficiencies. Trying to add on counseling services--without changing existing systems--will reduce efficiency and increase unnecessary frustrations. Most pharmacy restructuring will require little or no additional expense--just changes in work flow, procedures, and functions, and/or small changes in physical layout. In a few situations, increasing efficiency may require major physical and design changes.

Why aren't more pharmacists counseling?

Clearly, the answers to the question "Why aren't more pharmacists counseling patients?" are complex. Factors affecting counseling vary by practice site, geographical region, and pharmacists' attitudes. Advocates of patient counseling may label many factors mentioned by workshop participants as "just excuses not to change" or may question their validity. However, our experiences have shown that these are real problems with logical explanations and relatively simple solutions. By focusing this column on the steps for overcoming these common barriers to counseling, we hope to help pharmacists expand their role in patient care.

Inhibition of IL-1 release from human monocytes and suppression of streptococcal cell wall and adjuvant-induced arthritis in rats by an extract of Tripterygium wilfordii Hook

1. It was investigated whether an extract of Tripterygium wilfordii Hook f (TW) inhibits IL-1 production by monocytes and suppresses the development of IL-1-dependent arthritis induced in rats with streptococcal cell wall and adjuvant. 2. TW preferentially inhibited IL-1 alpha and IL-1 beta production by bacterial lipopolysaccharide (LPS)-stimulated human monocytes with IC50 of approximately 1 microgram/ml. 3. Oral administration of TW dose-dependently suppressed joint swelling and structural damage in streptococcal cell wall-induced arthritis (ED50 = 20 mg/kg/day) and in adjuvant-induced arthritis (ED50 = 46 mg/kg/day for developing and 8 mg/kg/day for established arthritis).

Altered actin and immunoglobulin C mu expression in nitrogen mustard-resistant human Burkitt lymphoma cells

Raji-HN2 is a B cell lymphoma (Burkitt lymphoma) line that was made resistant to nitrogen mustard. The drug-resistant phenotype was accompanied by changes in gene expression. The expression of four unrelated genes was examined by Northern blot analysis. Raji-HN2 cells were found to contain about twice the number of actin mRNA found in Raji cells. Both cell lines were found to contain equivalent amounts of beta 2-microglobulin, c-myc oncogene, and immunoglobulin C mu mRNAs. The C mu mRNA was, however, larger in size in Raji-HN2 cells. Alterations in actin and C mu mRNAs in Raji-HN2 cells were not due to gene amplification or rearrangement because Southern blot analysis revealed no changes in the genomic organization of these genes. The increased actin mRNA content was correlated with an increased actin content of Raji-HN2 cells. The F-actin (stained with 7-nitrobenz-2-oxa-1,3-diazolylphallacidin) content of single cells was quantitated in a meridian interactive laser cytometer. Raji-HN2 cells contained about twice the amount of F-actin present in the parental Raji cells. Similar results were obtained when large populations, 10(6) cells each, were examined in a flow cytometer.

Resorption is not essential for the stimulation of bone growth by hPTH-(1-34) in rats in vivo

Chronic low doses of hPTH-(1-34) stimulate bone growth in rats in vivo. The objective of these studies was to determine if the anabolic effect of hPTH-(1-34) on rat bone in vivo is dependent on an initial stimulation of resorption by blocking resorption with either salmon calcitonin (CT) or dichloromethylene diphosphonate (Cl2MDP). Male Sprague-Dawley rats, 70-100 g, were treated with daily subcutaneous (SC) injections of vehicle (V) or hPTH-(1-34), 8 micrograms per 100 g (PTH), for 12 days. In experiment 1, rats were given CT for 3 (CT3) or 12 (CT12) days, either alone or in combination with hPTH-(1-34) (CT3-PTH and CT12-PTH) or vehicle for 12 days. In experiment 2, rats were pretreated for 4 days with Cl2MDP or its vehicle before starting the daily PTH or vehicle injections. Rats were then killed. Sera, femora, tibiae, and kidneys were removed for chemical and histomorphometric analyses. PTH, PTH-CT3, and PTH-CT12 rats showed significant increases in total bone calcium (18-23%), dry weight (DW, 13-25%), and bone-forming surfaces compared with their respective controls. Eroded (resorption) surfaces were comparable between the groups. Although weight gain and serum calcium were normal in rats treated for 3 days with CT, rats treated for 12 days with CT gained 14% less weight than controls and were hypophosphatemic, with reduced serum calcium and urea nitrogen. Total bone mass increased both in Cl2MDP rats (Ca 21%, DW 2%), where resorption was presumably blocked, and in PTH rats (Ca 31%, DW 19%). The increase in bone mass was greater in PTH-Cl2MDP rats (Ca 48%, DW 29%) than in rats treated with Cl2MDP alone, suggesting that although Cl2MDP blocked resorption, the anabolic response to PTH was not altered. As neither short-term treatment with CT nor Cl2MDP blocked the anabolic response of bone to hPTH-(1-34), this response does not appear to depend on the early stimulation of resorption.

Transitional cell carcinoma of the urethra metastatic to the eyes in a dog

Hyphema and secondary glaucoma were ocular manifestations of disseminated neoplasia in a 4-year-old dog. The dog was euthanatized following enucleation after disseminated intravascular coagulopathy had developed. The histopathologic diagnosis was transitional cell carcinoma of the urethra, with metastasis to the lungs, heart, adrenal gland, and eyes.