Antibiotic use among hospitalised patients in Sierra Leone: a national point prevalence survey using the WHO survey methodology

OBJECTIVE

Inappropriate use of antibiotics is a major driver of antibiotic resistance. A few studies conducted in Africa have documented that about half of hospitalised patients who receive antibiotics should not have received them. A few hospital-based studies that have been conducted in Sierra Leone have documented a high usage of antibiotics in hospitals. Therefore, we conducted a nationwide point prevalence survey on antibiotic use among hospitalised patients in Sierra Leone.

DESIGN

We conducted a hospital-based, cross-sectional survey on the use of antibiotics using the WHO point prevalence survey methodology.

SETTING

The study was conducted in 26 public and private hospitals that are providing inpatient healthcare services.

PARTICIPANTS

All patients admitted to paediatric and adult inpatient wards before or at 08:00 on the survey date were enrolled.

OUTCOME MEASURES

Prevalence of antibiotic use, antibiotics Access, Watch and Reserve (AWaRe) categorisation, indication for antibiotic use prevalence and proportion of bacteria culture done.

RESULTS

Of the 1198 patient records reviewed, 883 (73.7%, 95% CI 71.1% to 76.2%) were on antibiotics. Antibiotic use was highest in the paediatric wards (306, 85.7%), followed by medical wards (158, 71.2%), surgical wards (146, 69.5%), mixed wards (97, 68.8%) and lowest in the obstetrics and gynaecology wards (176, 65.7%). The most widely prescribed antibiotics were metronidazole (404, 22.2%), ceftriaxone (373, 20.5%), ampicillin (337, 18.5%), gentamicin (221, 12.1%) and amoxicillin (90, 5.0%). Blood culture was only done for one patient and antibiotic treatments were given empirically. The most common indication for antibiotic use was community-acquired infection (484, 51.9%) followed by surgical prophylaxis (222, 23.8%).

CONCLUSION

There was high usage of antibiotics in hospitals in Sierra Leone as the majority of patients admitted received an antibiotic. This has the potential to increase the burden of antibiotic resistance in the country. We, therefore, recommend the establishment of hospital antimicrobial stewardship programmes according to the WHO core components.

Analysis of dog bite surveillance data, Volta Region, Ghana, 2020

Introduction

Dog bite is the second most common injury sustained by humans after snake bites, and it is amongst the top 12 causes of non-fatal injuries worldwide. Globally, 59,000 human deaths occur annually due to rabies, and 95% of these deaths occur in Asia and Africa. Dog bites remained a public health concern in Ghana, with three out of every 1000 incidence resulting in human rabies. Analysis of the surveillance data is key in understanding the burden of dog bites in the Volta region. This study describes the epidemiology of dog bites in the Volta Region, Ghana, to inform policy on prevention and control.

Methods

We conducted a descriptive analysis of secondary data on dog bites. We obtained aggregate data from 2015 to 2019 from the District Health Management Information System (DHMIS). Variables extracted were gender, age, and location. Data were entered into a Microsoft Excel cleaned, reviewed, and analyzed. We used descriptive statistics to summarize results into frequency and proportion and displayed results in tables, graphs, and maps.

Results

During the study period, 4737 dog bite cases were identified from a population of 1,907,529 (incidence of 248 per 100,000). Twelve (0.25%) humans were confirmed for rabies with a 100% case fatality rate. Males accounted for 2455 (51.8%) of dog bite cases. The age group between 10 and 19 years (21.9%) was most affected. About 35.0% (1640/4737) were administered with the anti-rabies vaccine, and 25.3% (1200/4737) were administered anti-tetanus toxoid. Keta district (550 per 100000) reported the highest incidence of dog bites. Dog bite cases were highest in the third and fourth quarters of 2016 and the first quarter of 2017.

Conclusion

The incidence of dog bites and rabies was high in the Volta region. Children and adolescents were mostly affected. There was a low coverage rate of anti-rabies vaccine and anti-tetanus toxoids usage. We recommended that the Regional Health Directorates and the Regional Veterinary Department develop robust strategies to control stray or free-roaming dogs in the Volta region.

SARS-CoV-2 antibody prevalence in Sierra Leone, March 2021: a cross-sectional, nationally representative, age-stratified serosurvey

Background As of 26 March 2021, the Africa CDC had reported 4,159,055 cases of COVID-19 and 111,357 deaths among the 55 African Union Member States; however, no country has published a nationally representative serosurvey as of May 2021. Such data are vital for understanding the pandemic's progression on the continent, evaluating containment measures, and policy planning. Methods We conducted a cross-sectional, nationally representative, age-stratified serosurvey in Sierra Leone in March 2021 by randomly selecting 120 Enumeration Areas throughout the country and 10 randomly selected households in each of these. One to two persons per selected household were interviewed to collect information on socio-demographics, symptoms suggestive of COVID-19, exposure history to laboratory-confirmed COVID-19 cases, and history of COVID-19 illness. Capillary blood was collected by fingerstick, and blood samples were tested using the Hangzhou Biotest Biotech RightSign COVID-19 IgG/IgM Rapid Test Cassette. Total seroprevalence was was estimated after applying sampling weights. Findings The overall weighted seroprevalence was 2.6% (95% CI 1.9-3.4). This is 43 times higher than the reported number of cases. Rural seropositivity was 1.8% (95% CI 1.0-2.5), and urban seropositivity was 4.2% (95% CI 2.6-5.7). Interpretation Although overall seroprevalence was low compared to countries in Europe and the Americas (suggesting relatively successful containment in Sierra Leone), our findings indicate enormous underreporting of active cases. This has ramifications for the country's third wave (which started in June 2021), where the average number of daily reported cases was 87 by the end of the month: this could potentially be on the order of 3,700 actual infections, calling for stronger containment measures in a country with only 0.2% of people fully vaccinated. It may also reflect significant underreporting of incidence and mortality across the continent.

Supersonic plasma turbulence in the laboratory

The properties of supersonic, compressible plasma turbulence determine the behavior of many terrestrial and astrophysical systems. In the interstellar medium and molecular clouds, compressible turbulence plays a vital role in star formation and the evolution of our galaxy. Observations of the density and velocity power spectra in the Orion B and Perseus molecular clouds show large deviations from those predicted for incompressible turbulence. Hydrodynamic simulations attribute this to the high Mach number in the interstellar medium (ISM), although the exact details of this dependence are not well understood. Here we investigate experimentally the statistical behavior of boundary-free supersonic turbulence created by the collision of two laser-driven high-velocity turbulent plasma jets. The Mach number dependence of the slopes of the density and velocity power spectra agree with astrophysical observations, and supports the notion that the turbulence transitions from being Kolmogorov-like at low Mach number to being more Burgers-like at higher Mach numbers.

Turbulence and jet-driven zonal flows: Secondary circulation in rotating fluids due to asymmetric forcing

We report on experiments and modeling on a rotating confined liquid that is forced by circumferential jets coaxial with the rotation axis, wherein system-scale secondary flows are observed to emerge. The jets are evenly divided in number between inlets and outlets and have zero net mass transport. For low forcing strengths the sign of this flow depends on the sign of a sloped end cap, which simulates a planetary β plane. For increased forcing strengths the secondary flow direction is insensitive to the slope sign, and instead appears to be dominated by an asymmetry in the forcing mechanism, namely, the difference in radial divergence between the inlet and outlet jet profiles. This asymmetry yields a net radial velocity that is affected by the Coriolis force, inducing secondary zonal flow.

Magneto-immutable turbulence in weakly collisional plasmas

We propose that pressure anisotropy causes weakly collisional turbulent plasmas to self-organize so as to resist changes in magnetic-field strength. We term this effect "magneto-immutability" by analogy with incompressibility (resistance to changes in pressure). The effect is important when the pressure anisotropy becomes comparable to the magnetic pressure, suggesting that in collisionless, weakly magnetized (high-β) plasmas its dynamical relevance is similar to that of incompressibility. Simulations of magnetized turbulence using the weakly collisional Braginskii model show that magneto-immutable turbulence is surprisingly similar, in most statistical measures, to critically balanced MHD turbulence. However, in order to minimize magnetic-field variation, the flow direction becomes more constrained than in MHD, and the turbulence is more strongly dominated by magnetic energy (a nonzero "residual energy"). These effects represent key differences between pressure-anisotropic and fluid turbulence, and should be observable in the β ≳ 1 turbulent solar wind.

The factors affecting household transmission dynamics and community compliance with Ebola control measures: a mixed-methods study in a rural village in Sierra Leone

Background

Little is understood of Ebola virus disease (EVD) transmission dynamics and community compliance with control measures over time. Understanding these interactions is essential if interventions are to be effective in future outbreaks. We conducted a mixed-methods study to explore these factors in a rural village that experienced sustained EVD transmission in Kailahun District, Sierra Leone.

Methods

We reconstructed transmission dynamics using a cross-sectional survey conducted in April 2015, and cross-referenced our results with surveillance, burial, and Ebola Management Centre (EMC) data. Factors associated with EVD transmission were assessed with Cox proportional hazards regression. Following the survey, qualitative semi-structured interviews explored views of community informants and households.

Results

All households (n = 240; 1161 individuals) participated in the survey. 29 of 31 EVD probable/confirmed cases died (93·5% case fatality rate); six deaths (20·6%) had been missed by other surveillance systems. Transmission over five generations lasted 16 weeks. Although most households had ≤5 members there was a significant increase in risk of Ebola in households with > 5 members. Risk of EVD was also associated with older age. Cases were spatially clustered; all occurred in 15 households.

EVD transmission was better understood when the community experience started to concord with public health messages being given. Perceptions of contact tracing changed from invading privacy and selling people to ensuring community safety. Burials in plastic bags, without female attendants or prayer, were perceived as dishonourable. Further reasons for low compliance were low EMC survival rates, family perceptions of a moral duty to provide care to relatives, poor communication with the EMC, and loss of livelihoods due to quarantine. Compliance with response measures increased only after the second generation, coinciding with the implementation of restrictive by-laws, return of the first survivor, reduced contact with dead bodies, and admission of patients to the EMC.

Conclusions

Transmission occurred primarily in a few large households, with prolonged transmission and a high death toll. Return of a survivor to the village and more effective implementation of control strategies coincided with increased compliance to control measures, with few subsequent cases. We propose key recommendations for management of EVD outbreaks based on this experience.

Pressure-anisotropy-induced nonlinearities in the kinetic magnetorotational instability

In collisionless and weakly collisional plasmas, such as hot accretion flows onto compact objects, the magnetorotational instability (MRI) can differ significantly from the standard (collisional) MRI. In particular, pressure anisotropy with respect to the local magnetic-field direction can both change the linear MRI dispersion relation and cause nonlinear modifications to the mode structure and growth rate, even when the field and flow perturbations are very small. This work studies these pressure-anisotropy-induced nonlinearities in the weakly nonlinear, high-ion-beta regime, before the MRI saturates into strong turbulence. Our goal is to better understand how the saturation of the MRI in a low-collisionality plasma might differ from that in the collisional regime. We focus on two key effects: (i) the direct impact of self-induced pressure-anisotropy nonlinearities on the evolution of an MRI mode, and (ii) the influence of pressure anisotropy on the 'parasitic instabilities' that are suspected to cause the mode to break up into turbulence. Our main conclusions are: (i) The mirror instability regulates the pressure anisotropy in such a way that the linear MRI in a collisionless plasma is an approximate nonlinear solution once the mode amplitude becomes larger than the background field (just as in magnetohyrodynamics). This implies that differences between the collisionless and collisional MRI become unimportant at large amplitudes. (ii) The break up of large-amplitude MRI modes into turbulence via parasitic instabilities is similar in collisionless and collisional plasmas. Together, these conclusions suggest that the route to magnetorotational turbulence in a collisionless plasma may well be similar to that in a collisional plasma, as suggested by recent kinetic simulations. As a supplement to these findings, we offer guidance for the design of future kinetic simulations of magnetorotational turbulence.

Publisher's Note: Kinetic Simulations of the Interruption of Large-Amplitude Shear-Alfvén Waves in a High-β Plasma [Phys. Rev. Lett. 119, 155101 (2017)]

This corrects the article DOI: 10.1103/PhysRevLett.119.155101.

Kinetic Simulations of the Interruption of Large-Amplitude Shear-Alfvén Waves in a High-β Plasma

Using two-dimensional hybrid-kinetic simulations, we explore the nonlinear "interruption" of standing and traveling shear-Alfvén waves in collisionless plasmas. Interruption involves a self-generated pressure anisotropy removing the restoring force of a linearly polarized Alfvénic perturbation, and occurs for wave amplitudes δB_{⊥}/B_{0}≳β^{-1/2} (where β is the ratio of thermal to magnetic pressure). We use highly elongated domains to obtain maximal scale separation between the wave and the ion gyroscale. For standing waves above the amplitude limit, we find that the large-scale magnetic field of the wave decays rapidly. The dynamics are strongly affected by the excitation of oblique firehose modes, which transition into long-lived parallel fluctuations at the ion gyroscale and cause significant particle scattering. Traveling waves are damped more slowly, but are also influenced by small-scale parallel fluctuations created by the decay of firehose modes. Our results demonstrate that collisionless plasmas cannot support linearly polarized Alfvén waves above δB_{⊥}/B_{0}∼β^{-1/2}. They also provide a vivid illustration of two key aspects of low-collisionality plasma dynamics: (i) the importance of velocity-space instabilities in regulating plasma dynamics at high β, and (ii) how nonlinear collisionless processes can transfer mechanical energy directly from the largest scales into thermal energy and microscale fluctuations, without the need for a scale-by-scale turbulent cascade.

Assessment of the MSF triage system, separating patients into different wards pending Ebola virus laboratory confirmation, Kailahun, Sierra Leone, July to September 2014

Prevention of nosocomial Ebola virus (EBOV) infection among patients admitted to an Ebola management centre (EMC) is paramount. Current Médecins Sans Frontières (MSF) guidelines recommend classifying admitted patients at triage into suspect and highly-suspect categories pending laboratory confirmation. We investigated the performance of the MSF triage system to separate patients with subsequent EBOV-positive laboratory test (true-positive admissions) from patients who were initially admitted on clinical grounds but subsequently tested EBOV-negative (false-positive admissions). We calculated standard diagnostic test statistics for triage allocation into suspect or highly-suspect wards (index test) and subsequent positive or negative laboratory results (reference test) among 433 patients admitted into the MSF EMC Kailahun, Sierra Leone, between 1 July and 30 September 2014. 254 (59%) of admissions were classified as highly-suspect, the remaining 179 (41%) as suspect. 276 (64%) were true-positive admissions, leaving 157 (36.3%) false-positive admissions exposed to the risk of nosocomial EBOV infection. The positive predictive value for receiving a positive laboratory result after being allocated to the highly-suspect ward was 76%. The corresponding negative predictive value was 54%. Sensitivity and specificity were 70% and 61%, respectively. Results for accurate patient classification were unconvincing. The current triage system should be changed. Whenever possible, patients should be accommodated in single compartments pending laboratory confirmation. Furthermore, the initial triage step on whether or not to admit a patient in the first place must be improved. What is ultimately needed is a point-of-care EBOV diagnostic test that is reliable, accurate, robust, mobile, affordable, easy to use outside strict biosafety protocols, providing results with quick turnaround time.

Successful Control of Ebola Virus Disease: Analysis of Service Based Data from Rural Sierra Leone

Introduction

The scale and geographical distribution of the current outbreak in West Africa raised doubts as to the effectiveness of established methods of control. Ebola Virus Disease (EVD) was first detected in Sierra Leone in May 2014 in Kailahun district. Despite high case numbers elsewhere in the country, transmission was eliminated in the district by December 2014. We describe interventions underpinning successful EVD control in Kailahun and implications for EVD control in other areas.

Methods

Internal service data and published reports from response agencies were analysed to describe the structure and type of response activities, EVD case numbers and epidemic characteristics. This included daily national situation reports and District-level data and reports of the Sierra Leone Ministry of Health and Sanitation, and Médecins Sans Frontières (MSF) patient data and internal epidemiological reports. We used EVD case definitions provided by the World Health Organisation over the course of the outbreak. Characteristics assessed included level of response activities and epidemiological features such as reported exposure (funeral-related or not), time interval between onset of illness and admission to the EVD Management Centre (EMC), work-related exposures (health worker or not) and mortality. We compared these characteristics between two time periods—June to July (the early period of response), and August to December (when coverage and quality of response had improved). A stochastic model was used to predict case numbers per generation with different numbers of beds and a varying percentage of community cases detected.

Results

There were 652 probable/confirmed EVD cases from June-December 2014 in Kailahun. An EMC providing patient care opened in June. By August 2014 an integrated detection, treatment, and prevention strategy was in place across the district catchment zone. From June-July to August-December 2014 surveillance and contact tracing staff increased from 1.0 to 8.8 per confirmed EVD case, EMC capacity increased from 32 to 100 beds, the number of burial teams doubled, and health promotion activities increased in coverage. These improvements in response were associated with the following changes between the same periods: the proportion of confirmed/probable cases admitted to the EMC increased from 35% to 83% (χ² p-value<0·001), the proportion of confirmed patients admitted to the EMC <3 days of symptom onset increased from 19% to 37% (χ² p-value <0·001), and reported funeral contact in those admitted decreased from 33% to 16% (χ² p-value <0·001). Mathematical modelling confirmed the importance of both patient management capacity and surveillance and contact tracing for EVD control.

Discussion

Our findings demonstrate that control of EVD can be achieved using established interventions based on identification and appropriate management of those who are at risk of and develop EVD, including in the context of ongoing transmission in surrounding regions. Key attributes in achieving control were sufficient patient care capacity (including admission to specialist facilities of suspect and probable cases for assessment), integrated with adequate staffing and resourcing of community-based case detection and prevention activities. The response structure and coverage targets we present are of value in informing effective control in current and future EVD outbreaks.

Ebola Virus Disease (EVD) is a severe illness that is usually spread from person to person through caring for someone who is sick, or if they die, contact with their body during their funeral. The recent EVD outbreak in West Africa caused illness and death in many thousands in Guinea, Sierra Leone and Liberia. It has been the largest and most difficult to control of any EVD outbreak in history, and this led to doubts as to the effectiveness of established control measures. Our study describes the successful control of EVD in a rural district of Sierra Leone. As in previous outbreaks, we found that control was achieved by working with communities to identify people who may have been exposed to EVD; if they then became sick, their early admission for testing and care to specialised centres that have equipment and procedures to prevent EVD passing on to staff or other patients, and safe burial of those who die of EVD by trained workers with appropriate protective equipment. We describe the resources and response structure needed to implement such measures effectively, information that will assist in controlling future outbreaks.

Electromotive force due to magnetohydrodynamic fluctuations in sheared rotating turbulence

This article presents a calculation of the mean electromotive force arising from general small-scale magnetohydrodynamical turbulence, within the framework of the second-order correlation approximation. With the goal of improving understanding of the accretion disk dynamo, effects arising through small-scale magnetic fluctuations, velocity gradients, density and turbulence stratification, and rotation, are included. The primary result, which supplements numerical findings, is that an off-diagonal turbulent resistivity due to magnetic fluctuations can produce large-scale dynamo action-the magnetic analog of the "shear-current" effect. In addition, consideration of α effects in the stratified regions of disks gives the puzzling result that there is no strong prediction for a sign of α, since the effects due to kinetic and magnetic fluctuations, as well as those due to shear and rotation, are each of opposing signs and tend to cancel each other.

Generation of Large-Scale Magnetic Fields by Small-Scale Dynamo in Shear Flows

We propose a new mechanism for a turbulent mean-field dynamo in which the magnetic fluctuations resulting from a small-scale dynamo drive the generation of large-scale magnetic fields. This is in stark contrast to the common idea that small-scale magnetic fields should be harmful to large-scale dynamo action. These dynamos occur in the presence of a large-scale velocity shear and do not require net helicity, resulting from off-diagonal components of the turbulent resistivity tensor as the magnetic analogue of the "shear-current" effect. Given the inevitable existence of nonhelical small-scale magnetic fields in turbulent plasmas, as well as the generic nature of velocity shear, the suggested mechanism may help explain the generation of large-scale magnetic fields across a wide range of astrophysical objects.

Understanding the emergence of ebola virus disease in sierra leone: stalking the virus in the threatening wake of emergence

Since Ebola Virus Disease (EVD) was first identified in 1976 in what is now the Democratic Republic of Congo, and despite the numerous outbreaks recorded to date, rarely has an epidemic origin been identified. Indeed, among the twenty-one most documented EVD outbreaks in Africa, an index case has been identified four times, and hypothesized in only two other instances. The initial steps of emergence and spread of a virus are critical in the development of a potential outbreak and need to be thoroughly dissected and understood in order to improve on preventative strategies. In the current West African outbreak of EVD, a unique index case has been identified, pinpointing the geographical origin of the epidemic in Guinea. Herein, we provide an accounting of events that serve as the footprint of EVD emergence in Sierra Leone and a road map for risk mitigation fueled by lessons learned.

Statistical simulation of the magnetorotational dynamo

Turbulence and dynamo induced by the magnetorotational instability (MRI) are analyzed using quasilinear statistical simulation methods. It is found that homogenous turbulence is unstable to a large-scale dynamo instability, which saturates to an inhomogenous equilibrium with a strong dependence on the magnetic Prandtl number (Pm). Despite its enormously reduced nonlinearity, the dependence of the angular momentum transport on Pm in the quasilinear model is qualitatively similar to that of nonlinear MRI turbulence. This demonstrates the importance of the large-scale dynamo and suggests how dramatically simplified models may be used to gain insight into the astrophysically relevant regimes of very low or high Pm.

Nonmodal growth of the magnetorotational instability

We analyze the linear growth of the magnetorotational instability (MRI) in the short-time limit using nonmodal methods. Our findings are quite different from standard results, illustrating that shearing wave energy can grow at the maximum MRI rate -dΩ/dlnr for any choice of azimuthal and vertical wavelengths. In addition, by comparing the growth of shearing waves with static structures, we show that over short time scales shearing waves will always be dynamically more important than static structures in the ideal limit. By demonstrating that fast linear growth is possible at all wavelengths, these results suggest that nonmodal linear physics could play a fundamental role in MRI turbulence.

Phase II study of temsirolimus (CCI-779) in women with recurrent, unresectable, locally advanced or metastatic carcinoma of the cervix. A trial of the NCIC Clinical Trials Group (NCIC CTG IND 199)

OBJECTIVE

HPV infection has been associated with deregulation of the PI3K-Akt-mTOR pathway in invasive cervical carcinomas. This 2-stage phase II study assessed the activity of the mTOR inhibitor, temsirolimus, in patients with measurable metastatic and/or locally advanced, recurrent carcinoma of the cervix.

METHODS

Temsirolimus 25mg i.v. was administered weekly in 4 week cycles. One response among the first 18 patients was required to proceed to the second stage of accrual. Correlative molecular studies were performed on archival tumor tissue.

RESULTS

Thirty-eight patients were enrolled. Thirty-seven patients were evaluable for toxicity and 33 for response. One patient experienced a partial response (3.0%). Nineteen patients had stable disease (57.6%) [median duration 6.5 months (range 2.4-12.0mo)]. The 6-month progression free survival rate was 28% (95% CI: 14-43%). The median progression free survival was 3.52 months [95% CI (1.81-4.70)]. Adverse effects were mild-moderate in most cases and similar to other temsirolimus studies. No toxicity>grade 3 was observed. Assessment of PTEN and PIK3CA by IHC, copy number analyses and PTEN promoter methylation status did not reveal subsets associated with disease stability.

CONCLUSION

Single agent temsirolimus has modest activity in cervical carcinoma with about two-thirds of patients exhibiting stable disease. Molecular markers for treatment benefit remain to be identified.

Topographical analysis of telomere length and correlation with genomic instability in whole mount prostatectomies

11107

Background: Many critical events in prostatic carcinogenesis appear to relate to the emergence of chromosomal instability and acquisition of genomic rearrangements. Characteristic abnormalities such as 8p loss, 8q gain, trisomy 7, PTEN microdeletions and TMPRSS2-ERG gene fusions appear to mediate mechanisms to increase neoplastic transformation in prostate cancer. Current evidence suggests that telomere dysfunction is a likely causative factor for some of these abnormalities on the basis of its relationship to mechanisms such as the break-fusion-bridge cycle that can lead to the onset of chromosomal instability. Methods: In this study, we correlated telomere length in various prostatic histologies by quantitative FISH with genomic markers of chromosomal instability by standard FISH and immunohistochemical measures of proliferation in 3 whole mount prostatectomies. Results: After analysing approximately 25,000 cells, we found that telomere shortening was correlated with an increase in the number of cells with abnormalities on chromosome 8, such as an increase in the average number of c-myc signals (r∼0.35, p∼0.02). However, there were no significant correlations with abnormalities such as trisomy 7 or abnormalities of the PTEN locus in any sample. Additional findings included; associations found with the probability of C-MYC aberrations in stroma with greater proximity to cancer (<1,000 um), a correlation between telomere length in a number of prostatic histologies (normal, atrophy, HPIN and cancer) with the adjacent stroma, and a lack of correlation between the Ki67 index of various histologies and their telomere length - all suggesting the importance of microenvironmental effects on telomere maintenance in the prostate. Finally, we also report significant telomere shortening in BPH in 2 cases, a phenomenon that has not been noted previously. Conclusions: This is the first study to directly link a mechanism of chromosomal instability with specific chromosomal abnormalities in prostatic carcinogenesis and also suggests that the microenvironmental milieu is of critical importance in the evolution of in vivo telomere homeostasis.

No significant financial relationships to disclose.

Mechanisms of Plk4 haploinsufficiency in hepatocellular carcinogenesis

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Background: The pathogenesis of hepatocellular carcinoma (HCC) is multifactorial and includes genetic predisposition, though the precise nature of the latter is as yet poorly understood. Mice heterozygous for the polo like kinase Plk4 develop spontaneous HCC and human HCC cases show a high rate of LOH (loss of heterozygosity) at the Plk4 locus. We hypothesize that Plk4 is a haploinsufficient tumor suppressor in man. The purpose of this study was to investigate the mechanisms by which a 50% reduction of Plk4 leads to carcinogenesis. Methods: We established Plk4± and Plk4+/+ murine embryonic fibroblast cell lines (MEFs) in vitro. 5 of 5 Plk4+/+ MEF lines senesced at passage 7–8 as expected, while 9 of 9 Plk4±MEF lines immortalized in culture under NIH 3T3 protocol. The latter were used at passage 15–20 for in vivo tumorigenesis studies. Results: Plk4± MEFs demonstrated increased ploidy with increased passage number. By passage 4, Plk4± MEFs showed a near tetraploid karyotype as well as multiple chromosomal rearrangements and deletions, as assessed by Spectral Karyotype (SKY) Analysis. 5 out of 9 late passage Plk4± MEF lines injected into NOD-SCID mice grew tumors, with a latency of 3 to 12 weeks. By contrast, injection of Plk4+/+ MEFs yielded no tumors. Tumors generated from injection of Plk4± MEFs were harvested, cultured and submitted to SKY analysis; this showed increased clonal rearrangements and deletions compared to the parent cell lines. Conclusion: A 50% reduction in Plk4 expression results in immortalization, aneuploidy and chromosomal instability in vitro, and tumorigenicity in vivo. These results demonstrate that insufficient levels of Plk4, whether due to mutation or LOH, can contribute to the pathogenesis of HCC.

No significant financial relationships to disclose.

Updated molecular analyses of exons 19 and 21 of the epidermal growth factor receptor (EGFR) gene and codons 12 and 13 of the KRAS gene in non-small cell lung cancer (NSCLC) patients treated with erlotinib in National Cancer Institute of Cancer

7571

Background: BR.21 demonstrated significant survival benefit from erlotinib for NSCLC patients (Shepherd, NEJM 2005). EGFR gene point mutations in exon 21 and deletions in exon 19 predict response to EGFR TKIs, but the predictive value of EGFR mutations (Mut) or high copy number (Amp) on survival remains unclear. Methods: The sensitivity of PCR-sequencing to detect EGFR mutations may be suboptimal. Thus, we re-analyzed all BR.21 samples with available material using a fluourescent-based PCR technique (Pan, JMD 2005;7:396) and ScorpionIM kits (DxS, Manchester, UK) as they may detect mutations in samples with only 5–10% tumor DNA. 204 samples were analyzed successfully for EGFR Mut, 206 for KRAS Mut and 159 by FISH for EGFR Amp. Results: Exon 19 deletion and/or exon 21 L858R Mut were identified in 34 patients (overall Mut rate 17%). EGFR high polysomy or true amplification was present in 61 patients (38%), and 30 patients (15%) had KRAS Mut. Overall response rates were EGFR wildtype (WT)/Mut: 7%/27%, p=0.03; KRAS WT/Mut: 10%/5%, p=0.69; No Amp/Amp: 5%/21%, p=0.02. Hazard ratios for survival benefit were EGFR WT: 0.74 (0.52–1.05, p=0.09), Mut: 0.55 (0.25–1.19, p=0.12); KRAS WT: 0.69 (0.9–0.97, p=0.03), Mut: 1.67 (0.62–4.50, p=0.31); no Amp: 0.80 (0.49–1.29, p=0.35), Amp: 0.43 0.23–0.78, p=0.004). The test for interaction was borderline for KRAS Mut (0.09) but was not significant for EGFR Mut (p=0.47) or EGFR Amp (0.12). It was significant only for non-smokers with EGFR Amp (p=0.04). In the multiple Cox regression model, including all markers, EGFR Amp was both prognostic for poorer survival (p=0.005) and predictive of a differential survival benefit from erlotinib (p=0.009). EGFR and KRAS Mut were not significant prognostic or predictive markers. Conclusion: EGFR genotype and copy number are predictive of objective response to erlotinib. In BR.21, EGFR gene copy number is the strongest molecular prognostic marker and the only significant molecular predictor of a differential survival benefit from treatment.

[Table: see text]

The relationship of K-ras mutations and EGFR gene copy number to outcome in patients treated with Erlotinib on National Cancer Institute of Canada Clinical Trials Group trial study PA.3

4521

Background: The National Cancer Institute of Canada Clinical Trials Group (NCIC CTG) PA.3 study compared treatment with the EGFR tyrosine kinase inhibitor erlotinib to placebo in patients with advanced stage pancreatic carcinoma who were receiving gemcitabine. This study demonstrated a significant advantage in survival [HR=0.82; P<0.04] and in progression free survival [HR=0.77; P<0.004] for patients who received erlotinib [Moore MJ et al, J Clin Oncol 2007]. While high-level expression of EGFR is common in pancreatic cancer, EGFR protein expression level as evaluated by immunohistochemistry did not predict which patients might benefit from erlotinib. In non- small cell lung cancer (NSCLC) where erlotinib has shown a survival benefit; the use of EGFR copy number measured by FISH is a better predictive factor for benefit, and patients whose tumor had a K-ras mutation do not respond nor benefit. Methods: The NCIC-CTG PA.3 trial had a sample size of 569 and NCIC.CTG has collected 280 archival formalin-fixed and paraffin embedded tumor biopsy or primary resection specimens from patients randomized on study. Many were fine needle aspirates and a total of 181 had sufficient tissue to allow molecular analysis. We performed a K-ras mutation analysis by PCR of exon 2 followed by sequencing, with negative results being validated by DHPLC. EGFR gene copy number was analysed by fluorescent in situ hybridization. Both methods were performed on all tumor samples adequate for analysis. Results: Overall 146 cases were suitable for K-ras mutation analysis and preliminary results have identified K-ras mutation in 90 patients [76%] and wild type KRAS in 29 patients; the remainder are pending. A total of 118 cases are suitable for EGFR FISH analysis, results have been obtained in 73 patients, and the remaining cases are pending. The correlations between K-ras mutational status and EGFR copy number, and outcomes [survival and disease control] in patients randomized to both erlotinib and placebo will be presented.

[Table: see text]

Detection of novel variant TMPRSS2 /ERG fusion transcripts suggests independent genomic alterations may underlie origin of multi-centric prostate cancer

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Background: Most of the early successes in identifying chromosomal translocations in neoplasias came from the study of hematological malignancies and sarcomas, with limited evidence that consistent genomic rearrangements were present in epithelial malignancies. Recently it was reported that ∼75% of prostate cancers carry a genomic rearrangement leading to fusion of the TMPRSS2 locus to either the ERG or ETV1 genes (both ETS transcription factors). In the fusion gene, the androgen-sensitive promoter elements of TMPRSS2 are thought to mediate over-expression of these ETS transcription factors. Over-activity of the ETS family of transcription factors has been suggested to be involved in the transition from pre-neoplasia to carcinoma as they regulate genes involved in processes such as adhesion, motility, invasion and angiogenesis. Methods: Using both RT-PCR and FISH with published primers and BACs respectively we analyzed 15 samples of prostatic carcinoma from radical prostatectomies and sequenced a subset of the TMPRSS2/ERG fusions. Results: We have found ERG-TMPRSS2 fusion transcripts in 6 samples and no ETV1-TMPRSS2 fusions. Of the 6 fusion tumours, 5 were Gleason 7 and 1 was Gleason 9. Tumour stages ranged from T2a-T3b. One sample with multi-centric carcinoma exhibited 2 distinct in-frame rearrangements generating novel TMPRSS2 /ERG fusion transcripts. Variant I TMPRSS2/ERG transcript was 430 bp and it led to fusion of exons 1 and 2 of the TMPRSS2 gene with exons 5 and 6 of the ERG gene. Variant II TMPRSS2/ERG fusion transcript was slightly smaller at 350 bp and it led to fusion of exon 1 of the TMPRSS2 gene to exons 5 and 6 of the ERG gene. These novel transcripts appear to be smaller than the published fusion proteins but preliminary analysis suggests that all known regulatory and functional protein domains are maintained. Conclusions: The demonstration of two new TMPRSS2/ERG variant fusion transcripts in prostate cancer deserves further study to evaluate their functional impact and prognostic and pathological importance. Moreover the presence of two distinct transcripts within a single multi-centric tumor provides genomic evidence that independent clonal neoplasms can arise synchronously in prostate cancer.

No significant financial relationships to disclose.

Prognostic impact of chromosomal aberrations in Ewing tumours

Although greater than 50% of Ewing tumours contain non-random cytogenetic aberrations in addition to the pathognomonic 22q12 rearrangements, little is known about their prognostic significance. To address this question, tumour samples from 134 Ewing tumour patients were analysed using a combination of classical cytogenetics, comparative genomic and fluorescence in situ hybridisation. The evaluation of the compiled data revealed that gain of chromosome 8 occurred in 52% of Ewing tumours but was not a predictive factor for outcome. Gain of 1q was associated with adverse overall survival and event-free survival in all patients, irrespective of whether the tumour was localised or disseminated (overall survival: P=0.002 and P=0.029; event-free survival: P=0.018 and P=0.010). Loss of 16q was a significant predictive factor for adverse overall survival in all patients (P=0.008) and was associated with disseminated disease at diagnosis (P=0.039). Gain of chromosome 12 was associated with adverse event-free survival (P=0.009) in patients with localised disease. These results indicate that in addition to a 22q12 rearrangement confirmation in Ewing tumours it is important to assess the copy number of 1q and 16q to identify patients with a higher probability of adverse outcome.

Tumor development in the Beckwith-Wiedemann syndrome is associated with a variety of constitutional molecular 11p15 alterations including imprinting defects of KCNQ1OT1

Dysregulation of imprinted genes on human chromosome 11p15 has been implicated in Beckwith-Wiedemann syndrome (BWS), an overgrowth syndrome associated with congenital malformations and tumor predisposition. The molecular basis of BWS is complex and heterogeneous. The syndrome is associated with alterations in two distinct imprinting domains on 11p15: a telomeric domain containing the H19 and IGF2 genes and a centromeric domain including the KCNQ1OT1 and CDKNIC genes. It has been postulated that disorders of imprinting in the telomeric domain are associated with overgrowth and cancer predisposition, whereas those in the centromeric domain involve malformations but not tumor development. In this study of 125 BWS cases, we confirm the association of tumors with constitutional defects in the 11p15 telomeric domain; six of 21 BWS cases with uniparental disomy (UPD) of 11p15 developed tumors and one of three of the rare BWS subtype with hypermethylation of the H19 gene developed tumors. Most importantly, we find that five of 32 individuals with BWS and imprinting defects in the centromeric domain developed embryonal tumors. Furthermore, the type of tumors observed in BWS cases with telomeric defects are different from those seen in BWS cases with defects limited to the centromeric domain. Whereas Wilms' tumor was the most frequent tumor seen in BWS cases with UPD for 11p15 or H19 hypermethylation, none of the embryonal tumors with imprinting defects at KCNQ1OT1 was a Wilms' tumor. This suggests that distinct tumor predisposition profiles result from dysregulation of the telomeric domain versus the centromeric domain and that these imprinting defects activate distinct genetic pathways for embryonal tumorigenesis.

GPC3 mutation analysis in a spectrum of patients with overgrowth expands the phenotype of Simpson-Golabi-Behmel syndrome

Simpson-Golabi-Behmel syndrome (SGBS) is an X-linked overgrowth syndrome caused by deletions in glypican 3 (GPC3). SGBS is characterized by pre- and postnatal overgrowth, a characteristic facial appearance, and a spectrum of congenital malformations which overlaps that of other overgrowth syndromes. We performed GPC3 deletion screening on 80 male patients with somatic overgrowth in the following categories: SGBS (n = 19), possible SGBS (n = 26), including families in which individuals had previously been diagnosed with other overgrowth syndromes, and Wiedemann-Beckwith syndrome (WBS) (n = 35). Using exon-specific PCR and Southern blot analysis, we identified seven GPC3 deletions. In most cases a clear X-linked family history was not present. In two cases, GPC3 deletions were identified in patients belonging to pedigrees published previously as other overgrowth syndromes: one with a diagnosis of Sotos syndrome and the other Perlman syndrome with nephroblastomatosis. A third patient developed hepatoblastoma, a tumor type not previously described in SGBS. No GPC3 deletions were identified among the WBS patients. Direct sequencing of all GPC3 exons in the remaining 13 SGBS patients without GPC3 deletions did not identify any further mutations, raising the possibility of alternative silencing mechanisms and/or other genes in the pathogenesis of SGBS. Our results validate the clinical specificity of the facial appearance, skeletal/hand anomalies, and supernumerary nipples in patients with GPC3 deletions. Our data also suggest that nephroblastomatosis and hepatoblastoma are included in the phenotypic spectrum of GPC3 deletions and SGBS, underscoring the importance of tumor surveillance in these children.

Fusion of two novel genes, RBM15 and MKL1, in the t(1;22)(p13;q13) of acute megakaryoblastic leukemia

t(1;22) is the principal translocation of acute megakaryoblastic leukemias. Here we show this chromosomal rearrangement to result in the fusion of two novel genes, RNA-binding motif protein-15 (RBM15), an RNA recognition motif-encoding gene with homology to Drosophila spen, and Megakaryoblastic Leukemia-1 (MKL1), a gene encoding an SAP (SAF-A/B, Acinus and PIAS) DNA-binding domain.

Imprinting status of 11p15 genes in Beckwith-Wiedemann syndrome patients with CDKN1C mutations

Beckwith-Wiedemann syndrome (BWS) is an imprinting disorder characterized by somatic overgrowth, congenital malformations, and predisposition to childhood tumors. Aberrant expression of multiple imprinted genes, including H19, IGF2, KCNQ1OT1, and CDKN1C, has been observed in BWS patients. It has been estimated that mutations in CDKN1C occur in 12-17% of BWS patients. We have screened 10 autosomal dominant pedigrees and 65 sporadic BWS cases by PCR/heteroduplex analysis and DNA sequencing and have identified four mutations, two of which were associated with biallelic IGF2 expression and normal H19 and KCNQ1OT1 imprinting. One patient demonstrated phenotypic expression of paternally transmitted mutation in this maternally expressed gene, a second proband is the child of one of a pair of monozygotic twin females who carry the mutation de novo, and a third patient exhibited unusual skeletal changes more commonly found in other overgrowth syndromes. When considered with other studies published to date, this work reveals the frequency of CDKN1C mutations in BWS to be only 4.9%. This is the first report of an analysis of the imprinting status of genes in the 11p15 region where CDKN1C mutations were associated with loss of IGF2 imprinting and maintenance of H19 and KCNQ1OT1 imprinting.

Immortal human pancreatic duct epithelial cell lines with near normal genotype and phenotype

Immortal epithelial cell lines were previously established after transduction of the HPV16-E6E7 genes into primary cultures of normal pancreatic duct epithelial cells. Single clones were isolated that demonstrated near normal genotype and phenotype. The proliferation of HPDE6-E6E7c7 and c11 cells is anchorage-dependent, and they were nontumorigenic in SCID mice. The cell lines demonstrated many phenotypes of normal pancreatic duct epithelium, including mRNA expression of carbonic anhydrase II, MUC-1, and cytokeratins 7, 8, 18, and 19. These cells have normal Ki-ras, p53, c-myc, and p16(INK4A) genotypes. Cytogenetic studies demonstrated losses of 3p, 10p12, and 13q14, the latter included the Rb1 gene. The wild-type p53 protein was detectable at very low levels consistent with the presence of E6 gene product, and the lack of functional p53 pathway was confirmed by the inability for gamma-irradiation to up-regulate p53 and p21waf1/cip1 protein. The p110/Rb protein level was also not detectable consistent with the expression of E7 protein and haploid loss of Rb1 gene. Despite this, the proliferation of both c7 and c11 cells were markedly inhibited by transforming growth factor-beta1. This was associated with up-regulation of p21cip1/waf1 but not p27kip1. Further studies showed that p130/Rb2 and cyclin D3 were expressed, suggesting that p130/Rb2 may have partially assumed the maintenance of G(1) cell cycle checkpoint regulation. These results indicate that except for the loss of p53 functional pathway, the two clones of HPDE6-E6E7 cells demonstrated a near normal genotype and phenotype of pancreatic duct epithelial cells. These cell lines will be useful for future studies on the molecular basis of pancreatic duct cell carcinogenesis and islet cell differentiation.

Use of multicolor spectral karyotyping in genetic analysis of pleuropulmonary blastoma

Pleuropulmonary blastoma (PPB) is a rare, malignant intrathoracic pediatric tumor. It arises from the lung, pleura, or mediastinum and its pathogenesis and relationship to other pediatric solid tumors is not well understood. In this study, a case of PPB in a 3-year-old girl was studied using a combination of molecular genetic methods and cytogenetics. Molecular analysis of the commonly encountered fusion translocation gene products of pediatric solid tumors failed to detect a rearrangement. Cytogenetic analysis, supplemented by multicolor spectral karyotyping (SKY), identified an unbalanced translocation between chromosomes 1 and X, resulting in additional copies of 1q, an extra copy of Xq, and loss of part of Xp. In addition, trisomy 8 was detected. The identification of new chromosomal alterations and confirmation of previously reported ones in this rare neoplasm helps to improve our understanding of its pathogenesis and association with other pediatric tumors.

Brca1 required for T cell lineage development but not TCR loci rearrangement

Brca1 (breast cancerl, early onset) deficiency results in early embryonic lethality. As Brca1 is highly expressed in the T cell lineage, a T cell-specific disruption of Brca1 was generated to assess the role of Brca1 in relation to T lymphocyte development. We found that thymocyte development in Brca1-/- mice was impaired not as a result of V(D)J T cell receptor (TCR) recombination but because thymocytes had increased expression of tumor protein p53. Chromosomal damage accumulation and abnormal cell death were observed in mutant cells. We found that cell death inhibitor Bcl-2 overexpression, or p53-/- backgrounds, completely restored survival and development of Brca1-/- thymocytes; peripheral T cell numbers were not totally restored in Brcal-/- p53-/- mice; and that a mutant background for p21 (cyclin-dependent kinase inhibitor 1A) did not restore Brca1-/- thymocyte development, but partially restored peripheral T cell development. Thus, the outcome of Brca1 deficiency was dependent on cellular context, with the major defects being increased apoptosis in thymocytes, and defective proliferation in peripheral T cells.

Recurrent anomalies of 6q25 in chondromyxoid fibroma

Chondromyxoid fibroma is a rare benign bone tumor most commonly arising in the metaphysis of long bones in young adults. Histopathologically, chondromyxoid fibroma may be difficult to distinguish from other cartilaginous neoplasms. Recently, a pericentric inversion of chromosome 6 [inv(6)(p25q13)] has been proposed as a specific genetic marker for chondromyxoid fibroma. In this study, cytogenetic and spectral karyotypic analyses of 2 chondromyxoid fibroma cases showed clonal abnormalities of chromosome 6 but at a breakpoint on the long arm (q25) distal to that described in the pericentric inversion. These findings suggest that several distinct breakpoints on chromosome 6 are nonrandomly involved in chondromyxoid fibroma.

Comparative genomic hybridization analysis of clear cell sarcoma of the kidney

BACKGROUND

Clear cell sarcoma of the kidney (CCSK) is a rare malignant pediatric tumor, distinguished from the Wilms tumor by its characteristic histologic features and a more aggressive clinical behavior with a tendency to metastasize to bone. Genetic studies on CCSK are limited and no consistent findings have been reported.

PROCEDURE

We examined four cases of CCSK for presence of consistent genetic alterations using comparative genomic hybridization (CGH). This is the first report concerning CGH analysis of CCSK.

RESULTS

Three of the tumors showed no chromosome gains or losses. One of the tumors had gains of 1 q and the terminal end of 11 q.

CONCLUSIONS

These results are consistent with previous findings of limited chromosomal changes in CCSK karyotypes. Gain of 1 q in CCSK warrants further investigation. Copy number gains of 1 q have been repeatedly demonstrated in soft tissue and bone sarcomas, as well as other tumors, implying the presence of genes involved in tumor development and/or progression.

Oncogene amplification in medulloblastoma: analysis of a case by comparative genomic hybridization and fluorescence in situ hybridization

We describe amplification of the MYCC oncogene in a medulloblastoma with aggressive clinical behavior. The patient was a six year old boy who underwent gross total surgical excision of a cerebellar tumor. Despite chemotherapy and total neuraxis radiation, the clinical course was one of relentless progression, with extensive subarachnoid spread and death within eight months of presentation. The pathological features were consistent with the recently described, "large cell variant" of medulloblastoma. Tumor cells exhibited large vesicular nuclei, prominent nucleoli and strong immunoreactivity for synaptophysin. Polymerase chain reaction (PCR) and fluorescence in situ hybridization (FISH) assay revealed no evidence of MYCN amplification or 1p deletion in the tumor. FISH analysis revealed evidence of MYCC amplification in the 20- to 30-fold range. Comparative genomic hybridization (CGH) revealed regions of gains and amplification in three locations, with gains of chromosome 7, amplification of 8q24 (corresponding to the MYCC locus) and gains of the long arm of chromosome 17 (suggestive of isochromosome 17q). While conventional karyotypic analysis was not successful in the present case, CGH provided invaluable information about gene amplification and losses/gains of chromosomes and chromosomal regions. Thus, CGH is a powerful technique applicable to frozen or paraffin-embedded material which helps to ascertain the presence of gene amplification even without prior knowledge of the gene to be tested.

Attribution of intent and role-taking: cognitive factors as mediators of aggression with people who have mental retardation

An assessment task was devised to explore the attributional style and role-taking ability of 22 aggressive and 22 nonaggressive adults with moderate to mild mental retardation. Aggressive participants showed a hostile bias in their interpretation of others' intentions towards themselves within ambiguous interpersonal situations, although no difference was found across groups within clearly provocative situations. Furthermore, the role-taking ability of the aggressive participants was superior to the nonaggressive group, undermining the focus on global problems of interpersonal understanding as a causal factor of aggression for people with mental retardation.