Comparison of actionable events detected in cancer genomes by whole-genome sequencing, in silico whole-exome and mutation panels.

BACKGROUND: Next-generation sequencing is used in cancer research to identify somatic and germline mutations, which can predict sensitivity or resistance to therapies, and may be a useful tool to reveal drug repurposing opportunities between tumour types. Multigene panels are used in clinical practice for detecting targetable mutations. However, the value of clinical whole-exome sequencing (WES) and whole-genome sequencing (WGS) for cancer care is less defined, specifically as the majority of variants found using these technologies are of uncertain significance. PATIENTS AND METHODS: We used the Cancer Genome Interpreter and WGS in 726 tumours spanning 10 cancer types to identify drug repurposing opportunities. We compare the ability of WGS to detect actionable variants, tumour mutation burden (TMB) and microsatellite instability (MSI) by using in silico down-sampled data to mimic WES, a comprehensive sequencing panel and a hotspot mutation panel. RESULTS: We reveal drug repurposing opportunities as numerous biomarkers are shared across many solid tumour types. Comprehensive panels identify the majority of approved actionable mutations, with WGS detecting more candidate actionable mutations for biomarkers currently in clinical trials. Moreover, estimated values for TMB and MSI vary when calculated from WGS, WES and panel data, and are dependent on whether all mutations or only non-synonymous mutations were used. Our results suggest that TMB and MSI thresholds should not only be tumour-dependent, but also be sequencing platform-dependent. CONCLUSIONS: There is a large opportunity to repurpose cancer drugs, and these data suggest that comprehensive sequencing is an invaluable source of information to guide clinical decisions by facilitating precision medicine and may provide a wealth of information for future studies. Furthermore, the sequencing and analysis approach used to estimate TMB may have clinical implications if a hard threshold is used to indicate which patients may respond to immunotherapy.

Anticancer activity of the liposome-encapsulated cyclic dipeptides, cyclo(His-Gly) and cyclo(His-Ala).

Cyclic dipeptides have been well characterized for their biological activity, including antimicrobial and anticancer activities. Cyclo(His-Gly) and cyclo(His-Ala) have also recently demonstrated significant anticancer activity against a range of cell lines, however, as a result of their physicochemistry, namely high solubility and low lipophilicity, it can be predicted that cellular permeability would be low, making them ideal candidates for liposome drug delivery. Liposomes were composed of phosphatidylcholine, hydrogenated soy phosphatidylcholine (HSPC), stearylamine, alpha-tocopherol and 1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-[amino(polyethylene glycol)-2000] (PEG-DSPE) or folate-polyethylene glycol-cholesteryl hemisuccinate (F-PEG-CHEMS) using the thin-film hydration method and characterized for size and encapsulation. The cytotoxic activity of the encapsulated cyclic dipeptides was tested against HeLa, low folate HeLa and MCF-7 cells and found to have limited improvement in activity. However, modification of the polyethylene glycol with folic acid to target folate receptors significantly decreased the IC50 values recorded in all cells lines tested, particularly HeLa cells cultured in media containing physiological concentrations of folic acid with the lowest IC50 being recorded as 0.0962 mM for folate-targeted cyclo(His-Ala). Therefore, hydrophilic cyclic dipeptides are ideal candidates for inclusion into targeted drug delivery systems such as liposomes.

Antimicrobial activity of liposome encapsulated cyclo(L-tyrosyl-L-prolyl).

Various studies have shown the potentially beneficial biological activities of cyclic dipeptides and in particular, cyclo(L-tyrosyl-L-prolyl) (cyclo(Tyr-Pro)) has shown fair antibacterial activity in vitro. This study aimed to determine if liposome encapsulation would have any significant effects on the antibacterial activity of this compound. The thin-film hydration method with extrusion was used to produce small unilamellar vesicles containing cyclo(Tyr-Pro) that were shown to have an average encapsulation of 9.4% with a mean particle size of 160.4 nm. Minimum inhibitory concentrations tested against Staphylococcus aureus, Escherichia coli, Klebsiella pneumoniae and Bacillus subtillis were shown to be lower in liposome encapsulated cyclo(Tyr-Pro) than for the free form, while no antimicrobial activity was noted for either encapsulated nor non-encapsulated drug against the fungus Candida albicans or two methicillin-resistant strains of Staphylococcus aureus (MRSA). A positive control of liposome encapsulated amoxicillin was shown to be extremely active against both MRSA strains. The results confirm that liposome encapsulation has the potential to enhance activity as well as to overcome bacterial resistance towards current antibacterial agents.

Is it safe to prescribe clomiphene citrate without ultrasound monitoring facilities?

The majority of triplet and higher order multiple pregnancies now result from ovulation induction/superovulation rather than in vitro fertilisation. However, clomiphene citrate is still widely prescribed by gynaecologists and general practitioners who do not have access to ultrasound monitoring. The objective of our study was to determine the prevalence of multifollicular development with different doses of clomiphene citrate. A retrospective review of transvaginal ultrasound monitoring of 425 cycles in 182 women receiving clomiphene citrate from January 2002 to December 2003, was studied. Three or more follicles of >or= 14 mm were identified in 58 cycles (14%). Patients received 50 mg of clomiphene citrate in 52 of these 58 cycles and 25 mg in the remaining six. One patient was noted to have developed five follicles and 10 patients developed four follicles. One patient developed six follicles, despite receiving only 25 mg clomiphene citrate daily. It was concluded that a significant number of women (14%) developed three or more follicles, despite receiving low doses of clomiphene citrate.

Reducing twin pregnancy rates after IVF--elective single embryo transfer (eSET).

Multiple pregnancy is a major complication of IVF and is associated with increased maternal, fetal and neonatal morbidity. Elective single embryo transfer (eSET) during IVF, rather than the more standard transfer of two embryos (double embryo transfer or DET), has been shown to significantly reduce the multiple pregnancy rate associated with IVF, while maintaining acceptable pregnancy rates. Couples undergoing IVF in 2008 who met good prognostic criteria had eSET performed. Pregnancy and twinning rates were compared with those for similar couples in 2007 who had DET. Couples unsuccessful with a fresh cycle of treatment had subsequent frozen embryo transfer cycles with DET. The cumulative pregnancy rate was similar for each group. However there were no multiple pregnancies in the eSET group, compared to 4 twins of 5 pregnancies in the DET group. 96% of eligible couples agreed to eSET. ESET is successful in and acceptable to good prognosis Irish couples undergoing IVF.

A relativistic type Ibc supernova without a detected gamma-ray burst.

Long duration gamma-ray bursts (GRBs) mark the explosive death of some massive stars and are a rare sub-class of type Ibc supernovae. They are distinguished by the production of an energetic and collimated relativistic outflow powered by a central engine (an accreting black hole or neutron star). Observationally, this outflow is manifested in the pulse of gamma-rays and a long-lived radio afterglow. Until now, central-engine-driven supernovae have been discovered exclusively through their gamma-ray emission, yet it is expected that a larger population goes undetected because of limited satellite sensitivity or beaming of the collimated emission away from our line of sight. In this framework, the recovery of undetected GRBs may be possible through radio searches for type Ibc supernovae with relativistic outflows. Here we report the discovery of luminous radio emission from the seemingly ordinary type Ibc SN 2009bb, which requires a substantial relativistic outflow powered by a central engine. A comparison with our radio survey of type Ibc supernovae reveals that the fraction harbouring central engines is low, about one per cent, measured independently from, but consistent with, the inferred rate of nearby GRBs. Independently, a second mildly relativistic supernova has been reported.

In vitro anti-HIV activity of five selected South African medicinal plant extracts.

AIM OF THE STUDY: Five South African medicinal plants, Bulbine alooides (L.) Willd. (Asphodelaceae), Crinummacowani Baker (Amaryllidaceae), Hypoxis sobolifera var. sobolifera (Jacq.) Nel (Hypoxidaceae), Leonotisleonurus (L.) R.Br. (Lamiaceae) and Tulbaghiaviolacea Harv (Liliaceae) used for the treatment of various ailments, including infectious diseases, were screened for activity against human immunodeficiency virus (HIV). MATERIALS AND METHODS: Aqueous and ethanol extracts were tested for inhibitory activity in HIV-1 infected CEM.NK(R)-CCR5 cells, and against HIV-1 reverse transcriptase (RT) and HIV-1 protease (PR). RESULTS: In CEM.NK(R)-CCR5 cells, ethanol extracts of Leonotisleonurus inhibited HIV-1 significantly (33% reduction in HIV-1 p24, P<0.05). HIV-1 RT inhibition (> or =50%) was shown for extracts of Bulbine alooides (aqueous and ethanol), Hypoxis sobolifera (aqueous and ethanol) and Leonotisleonurus (aqueous), but inhibitory activity was lost upon dereplication for removal of non-specific tannins/polysaccharides. HIV-1 PR inhibition was observed for extracts of Hypoxis sobolifera (aqueous), Bulbine alooides (aqueous and ethanol) and Leonotisleonurus (ethanol). Only ethanolic extracts of Bulbine alooides and Leonotisleonurus retained HIV-1 PR inhibition after dereplication with IC50 of 94 microg/ml and 120 microg/ml, respectively. CONCLUSION: The dereplicated ethanolic extracts of Leonotisleonurus and Bulbine alooides showed the greatest anti-HIV potential in this study through inhibition of HIV-1 PR.

An extremely luminous X-ray outburst at the birth of a supernova.

Massive stars end their short lives in spectacular explosions--supernovae--that synthesize new elements and drive galaxy evolution. Historically, supernovae were discovered mainly through their 'delayed' optical light (some days after the burst of neutrinos that marks the actual event), preventing observations in the first moments following the explosion. As a result, the progenitors of some supernovae and the events leading up to their violent demise remain intensely debated. Here we report the serendipitous discovery of a supernova at the time of the explosion, marked by an extremely luminous X-ray outburst. We attribute the outburst to the 'break-out' of the supernova shock wave from the progenitor star, and show that the inferred rate of such events agrees with that of all core-collapse supernovae. We predict that future wide-field X-ray surveys will catch each year hundreds of supernovae in the act of exploding.

The synthesis and anticancer activity of selected diketopiperazines.

Six selected diketopiperazines, cyclo(Gly-Val), cyclo(Gly-D-Val), cyclo(Gly-Leu), cyclo(Gly-Ile), cyclo(Phe-Cys) and cyclo(Tyr-Cys), were synthesized via various synthetic routes. Their potential to inhibit cancer cell growth in HT-29, HeLa and MCF-7 cells was determined. Cyclo(Tyr-Cys) caused the greatest inhibition in cervical carcinoma cells with near equivalent activity against HT-29 and MCF-7 cells. The other cyclic dipeptides tested were effective in the inhibition of colon, cervical and breast carcinoma cells, respectively, but the percentage inhibition was lower than for cyclo(Tyr-Cys).

The biological activity of the histidine-containing diketopiperazines cyclo(His-Ala) and cyclo(His-Gly).

Two cyclic dipeptides, cyclo(His-Ala) and cyclo(His-Gly,) were synthesized from their linear counterparts and their structures elucidated using standard elucidation techniques. Molecular modeling and predictive NMR results indicated that the majority of energetically favourable conformers adopted a boat conformation with respect to the diketopiperazine ring. Cyclo(His-Ala), at concentrations of 100 microM inhibited the growth, in vitro, of various cancer cell lines, including HT-29, MCF-7 and HeLa carcinoma cells while cyclo(His-Gly) inhibited the growth of MCF-7 cells. While the antibacterial potential of these two compounds was limited, both cyclic dipeptides significantly inhibited the growth of C. albicans. Both compounds at a concentration of 100 microM resulted in a decrease in heart rate, coronary flow rate and left ventricular systolic pressure in the isolated rat heart. Inhibition of thrombin, amounting to a 63.3% and 36.7% reduction in the rate of fibrin formation, was noted for cyclo(His-Ala) and cyclo(His-Gly), respectively. While cyclo(His-Ala) showed no notable effects on platelet aggregation, cyclo(His-Gly) significantly inhibited both pathways tested with greatest effects on thrombin-induced platelet aggregation, yielding an IC(50) of 0.0662 mM (R(2)=0.989). The results of the anticancer and hematological studies indicate that histidine-containing diketopiperazines have potential as a novel group of cytotoxic agents with antithrombotic effects.

Biological activity of selected tyrosine-containing 2,5-diketopiperazines.

The study investigates two cyclic dipeptides, cyclo(Tyr-Tyr) (cTT) and cyclo(Phe-Tyr) (cPT) with respect to their biological activity. Investigations using the whole-cell patch-clamp technique testing the effects of 100 microM cyclic dipeptide on ion channels, revealed reversible voltage-dependant blockade for cTT, while cPT exhibited irreversible time-dependant blockade of L-type calcium channels. The isolated retrogradely-perfused rat heart was used to determine the effects of 100 microM of either cTT or cPT on heart rate (HR), coronary flow rate (CFR), left ventricular systolic pressure (LVSP) and cardiac conduction speed. Results indicated opposing effects for the two compounds, where cTT increased HR and CF while cPT decreased HR, CF, LVSP as well as conduction speed. Other biological investigations included opioid binding and anti-neoplastic assays. Competitive binding curves, using tritiated DAMGO, revealed significant binding to micro-opioid receptors with IC50 values for cTT and cPT being 0.82 microM and 69.7 microM respectively. Anti-neoplastic activity was tested using three cultured cell lines: HT-29, MCF-7 and HeLa which were exposed to 2.5 mM cyclic dipeptide or 0.1 mM melphalan as a positive control. While cTT showed little activity against these lines, cPT resulted in as much as a 75.6% growth inhibition of MCF-7 cells, while also being active against HeLa (73.4% inhibition) and HT-29 (60.6%). The results indicate potential biological activity, showing a need for more investigation into tyrosine containing cyclic dipeptides and their analogues as potential bioactive compounds.

Employment characteristics and job loss in patients awaiting surgery on the hip or knee.

AIMS: To investigate the factors, including size of organisation, associated with job loss in patients awaiting surgery to the hip or knee joint. METHODS: A questionnaire was mailed to 498 consecutive patients of working age listed at a district general hospital for major joint replacement, knee arthroscopy, or periacetabular osteotomy. Questions were asked about level of physical disability, duration of symptoms, employment circumstances at the time the joint problem began, and job changes since the onset of symptoms with their reasons. Analysis focused on those in work when their health problem began. Cox regression was used to examine risk factors for job loss related and unrelated to the joint problem, and results were summarised as adjusted hazard ratios (HRs) with 95% confidence intervals (95% CI). RESULTS: Responses came from 370 (74%) of those mailed, including 278 who were in work when their joint problem began. Of these, 82 (30%) had left their original job mainly or partly because of their joint disorder. Such job loss was more common in those employed in small businesses (HR for <10 v > or =10 employees: 1.9, 95% CI 1.2-3.0) and those whose work involved standing for >2 hours per day (HR 2.7, 95% CI 1.2-6.1) No similar associations were found when jobs were left for other reasons. After adjustment for non-sedentary work the association with small business employment remained but was weaker (HR 1.5, 95% CI 0.9-2.5). Modifications to work and access to occupational health advice were not associated with better job retention. CONCLUSIONS: In subjects with disabling hip or knee disease, job retention is poorer in those from small companies-a matter of concern given the rising prevalence of serious joint disease in the British workforce and the tendency of businesses to downsize and subcontract services to smaller enterprises.

An investigation into the biological activity of the selected histidine-containing diketopiperazines cyclo(His-Phe) and cyclo(His-Tyr).

Although cyclic diketopiperazines have been known since the beginning of the century, only now have they attracted considerable interest with respect to their biological activity. The aim of this study was to determine if the diketopiperazines cyclo(L-histidyl-L-phenylalanyl) (cyclo(His-Phe)) and cyclo(L-histidyl-L-tyrosyl) (cyclo(His-Tyr)) have significant biological activity relevant to the treatment of cardiovascular-related disease states, cancer and infectious diseases. Haematological studies were performed, including thrombin substrate binding, blood clotting time, platelet adhesion, platelet aggregation and fibrinolysis assays. A cytotoxicity screening utilizing a tetrazolium-based assay on the cell lines HeLa, WHCO3, and MCF-7 was performed. The whole-cell patch-clamp technique was used to investigate ion-channel activity in ventricular myocytes of rats, and isolated rat heart studies were performed to investigate the cardiac effects involving heart rate and coronary flow rate. Cyclo(His-Tyr) produced a significant prolongation of blood clotting time, slowing of clot lysis and inhibition of ADP-induced platelet adhesion and aggregation (P < 0.05). Cyclo(His-Phe) showed significant (P < 0.05) anti-tumour activity, causing greatest reduction of cell viability in cervical carcinoma cells. Preliminary results from patch-clamp studies indicate that both diketopiperazines caused blocking of sodium and calcium ion channels, but opening of inward rectifying potassium ion channels. In the rat isolated heart studies, cyclo(His-Phe) caused a gradual reduction in heart rate (P = 0.0027) and a decrease in coronary flow rate (P = 0.0017). Cyclo(His-Tyr) significantly increased the heart rate (P = 0.0016) but did not cause any significant change of coronary flow rate (P > 0.05). Cyclo(His-Tyr) showed notable (P < 0.05) antibacterial activity and both diketopiperazines showed excellent antifungal activity (P < 0.05). These observations reveal diketopiperazines to be ideal lead compounds for the rational design of an agent capable of preventing metastasis, inhibiting tumour growth, and as potential chemotherapeutic, antiarrhythmic and antihypertensive agents, as well as potential antibacterial and antifungal agents.

Hepatotoxicity of the isomers of cyclo(Trp-Pro).

The hepatotoxicity of the novel cyclic dipeptide cyclo(Trp-Pro), which has shown potential usage in various pharmacological fields, had not been assessed. Further studies on the isomers of this cyclic dipeptide (cyclo(L-Trp-L-Pro), cyclo-(L-Trp-D-Pro), cyclo(D-Trp-L-Pro) and cyclo(D-Trp-D-Pro)) revealed further biological activities. The assessment of hepatotoxicity of these isomers was thus warranted. In vitro screens were performed on primary isolated rat hepatocytes, the Chang liver and N-2-alpha cell lines. In vivo screening involved the assessment of serum levels of lactate dehydrogenase, aspartate transaminase, ATP, Ca2+ and albumin after intraperitoneal injection over a 1 and 5 day period in the rat model. Liver samples were also obtained for the assessment of lipid peroxidation. It was found that only cyclo(D-Trp-L-Pro) was hepato-specific in its action, while the other isomers were not. The greatest effect on any biochemical or physiological parameter was noted after 5 days. LDH secretion was greatly increased in the presence of cyclo(L-Trp-L-Pro) and cyclo-(L-Trp-D-Pro) (p < 0.05). Significantly increased levels of lipid peroxidation were observed in all the isomer-treated samples (p < 0.05), while Ca2+ concentrations were decreased at day 5. Decreased protein synthesis was noted in the presence of all the isomers at day 1. These results indicate the potential harm involved in the administration of the isomers, which may limit their potential usage in the treatment of various diseases.

The effects of creatine on the retrogradely perfused isolated rat heart.

Although the role of creatine in muscle metabolism is well understood, there is still uncertainty as to its effects at supplemented levels. With this in mind, this study was designed to investigate the direct effects of commercially available creatine on the isolated rat heart, retrogradely perfused and infused with varying concentrations of creatine (1.25, 2.5, 5 and 10 mM) to determine its effects on heart rate, coronary flow and ventricular pressure. Furthermore, tissue from these hearts was used to investigate the cardiotoxic potential of supplemented levels of creatine. Results indicate that creatine directly improves the functioning of the heart under normal conditions with respect to heart rate and ventricular pressure, but may be detrimental to the functioning of energy-deprived hearts. It also showed no cardiotoxic properties since it increased the baseline levels of adenosine triphosphate (ATP) and decreased the levels of isocitrate dehydrogenase (lCD), indicating a decrease in cellular death compared with non-supplemented control hearts.

Tandem lesions of the carotid circulation: combined extracranial endarterectomy and intracranial transluminal angioplasty.

A case series is presented demonstrating a unique approach to the treatment of tandem atherosclerotic lesions of the internal carotid artery. Between 1994 and 1999 eight patients with tandem lesions of the internal carotid artery were treated by combined carotid endarterectomy for the proximal lesion and intraoperative angioplasty of the distal intracranial lesion via the carotid arteriotomy. The success and complication rates were evaluated. A 100% technical success rate was achieved with one post procedural complication by ipsilateral stroke within 24 h. The advantages of this technique include the treatment of tandem lesions by the one procedure, improved transluminal access to the intracranial lesion and the ability to reduce the risk of embolism by flow control during balloon inflation.

The influence of acetoacetate and butyrate on calcium influx and ATP concentrations in HT-29 cells.

The effects of acetoacetate and butyrate on Ca(2+)-influx in HT-29 cells were unknown. Extracellular signals can be transferred to the intracellular environment of the cell via changes in the Ca(2+)-concentration. Extracellular Ca2+ may enter the cell via Ca(2+)-channels in the plasma membrane. Physiological processes occurring within the cell are dependent on Ca(2+)-concentration, including enzyme activity. Intracellular Ca(2+)-concentrations were measured using Fura-2/AM, a fluorescent intracellular Ca(2+)-probe. Ca(2+)-concentrations were measured immediately on application of the inducers to the cells, as well as after a 9 day incubation period. The effect of these inducers on the L-type voltage-operated Ca(2+)-channels were determined using the whole-cell patch-clamp technique. To validate these results for the intestinal epithelial model, membrane current studies were performed on HT-29 cells grown on a polycarbonate membrane. ATP concentrations were measured, and the theoretical effect of the inducers on PDE 4 activity was determined. It was found that both acetoacetate and butyrate blocked Ca(2+)-influx through the L-type voltage-operated Ca(2+)-channels, resulting in the initial low Ca(2+)-concentration (p < 0.05). The blockage effect is short-lived as after a 9 day incubation period in the presence of the inducers, Ca(2+)-concentrations were higher than that of the HT-29 control sample (p < 0.05). ATP concentrations of the cells were decreased in the presence of the inducers (p < 0.05), whilst it was suggested that no interaction between the catalytic site of PDE 4 and the inducers existed.

Cyclic dipeptides in the induction of maturation for cancer therapy.

Studies have suggested a possible form of therapy based on the use of maturation-inducing compounds to induce differentiation of neoplastic cells and stimulate faster recovery of the normal cell population. The study of the effects of nine cyclic dipeptides on biochemical markers of differentiation implicated their potential to induce differentiation. Studies were undertaken to determine the specificity of these agents for HT-29 cell cultures as well as the identification of the signal transduction pathways affected by these agents inducing the differential gene expression observed in the cells. The cyclic dipeptides studied showed a high degree of specificity, having no significant effect on Caco-2 cells (P > 0.05), representing the normal gastrointestinal mucosa. All inducers administered were shown to affect the total energy state of HT-29 cells, an effect which increased the probability of HT-29 cell differentiation. Results indicated that those agents which induced differential gene expression acted at different steps in the isolated signal transduction pathway. Cyclo(Trp-Trp) and cyclo(Phe-Pro) induced a high degree of acetylation of histones (P < 0.05), while the remaining cyclic dipeptides induced a high degree of phosphorylation of histones (P < 0.05) (cyclo(Trp-Trp) induced a moderate degree of histone phosphorylation). The results from histone phosphorylation and acetylation and cyclic AMP responsive element binding protein phosphorylation studies suggest that the cyclic dipeptides activate a chromatin switch, which leads to the increase in accessibility of lineage-specific genes for transcription.