A management perspective on resilience in healthcare: a framework and avenues for future research

Recent major health shocks, such as the 2014-16 Ebola, the Zika outbreak, and, last but not least, the COVID-19 pandemic, have strongly contributed to drawing attention to the issue of resilience in the healthcare domain. Nevertheless, the scientific literature appears fragmented, creating difficulties in developing incremental research in this relevant managerial field.To fill this gap, this systematic literature review aims to provide a clear state of the art of the literature dealing with resilience in healthcare. Specifically, from the analysis of the theoretical articles and reviews, the key dimensions of resilience are identified, and a novel classification framework is proposed. The classification framework is then used to systematize extant empirical contributions. Two main dimensions of resilience are identified: the approach to resilience (reactive vs. proactive) and the type of crisis to deal with (acute shocks vs. chronic stressors). Four main streams of research are thus identified: (i) proactive approaches to acute shocks; (ii) proactive approaches to chronic stressors; (iii) reactive approaches to acute shocks; and (iv) reactive approaches to chronic stressors. These are scrutinised considering three additional dimensions: the level of analysis, the resources to nurture resilience, and the country context. The classification framework and the associated mapping contribute to systematising the fragmented literature on resilience in healthcare, providing a clear picture of the state of the art in this field and drawing a research agenda that opens interesting paths for future research.

Erratum: Sequence data and association statistics from 12,940 type 2 diabetes cases and controls

This corrects the article DOI: 10.1038/sdata.2017.179.

Sequence data and association statistics from 12,940 type 2 diabetes cases and controls

To investigate the genetic basis of type 2 diabetes (T2D) to high resolution, the GoT2D and T2D-GENES consortia catalogued variation from whole-genome sequencing of 2,657 European individuals and exome sequencing of 12,940 individuals of multiple ancestries. Over 27M SNPs, indels, and structural variants were identified, including 99% of low-frequency (minor allele frequency [MAF] 0.1-5%) non-coding variants in the whole-genome sequenced individuals and 99.7% of low-frequency coding variants in the whole-exome sequenced individuals. Each variant was tested for association with T2D in the sequenced individuals, and, to increase power, most were tested in larger numbers of individuals (>80% of low-frequency coding variants in ~82 K Europeans via the exome chip, and ~90% of low-frequency non-coding variants in ~44 K Europeans via genotype imputation). The variants, genotypes, and association statistics from these analyses provide the largest reference to date of human genetic information relevant to T2D, for use in activities such as T2D-focused genotype imputation, functional characterization of variants or genes, and other novel analyses to detect associations between sequence variation and T2D.

A Low-Frequency Inactivating AKT2 Variant Enriched in the Finnish Population Is Associated With Fasting Insulin Levels and Type 2 Diabetes Risk

To identify novel coding association signals and facilitate characterization of mechanisms influencing glycemic traits and type 2 diabetes risk, we analyzed 109,215 variants derived from exome array genotyping together with an additional 390,225 variants from exome sequence in up to 39,339 normoglycemic individuals from five ancestry groups. We identified a novel association between the coding variant (p.Pro50Thr) in AKT2 and fasting plasma insulin (FI), a gene in which rare fully penetrant mutations are causal for monogenic glycemic disorders. The low-frequency allele is associated with a 12% increase in FI levels. This variant is present at 1.1% frequency in Finns but virtually absent in individuals from other ancestries. Carriers of the FI-increasing allele had increased 2-h insulin values, decreased insulin sensitivity, and increased risk of type 2 diabetes (odds ratio 1.05). In cellular studies, the AKT2-Thr50 protein exhibited a partial loss of function. We extend the allelic spectrum for coding variants in AKT2 associated with disorders of glucose homeostasis and demonstrate bidirectional effects of variants within the pleckstrin homology domain of AKT2.

Identification and functional characterization of G6PC2 coding variants influencing glycemic traits define an effector transcript at the G6PC2-ABCB11 locus

Genome wide association studies (GWAS) for fasting glucose (FG) and insulin (FI) have identified common variant signals which explain 4.8% and 1.2% of trait variance, respectively. It is hypothesized that low-frequency and rare variants could contribute substantially to unexplained genetic variance. To test this, we analyzed exome-array data from up to 33,231 non-diabetic individuals of European ancestry. We found exome-wide significant (P<5×10-7) evidence for two loci not previously highlighted by common variant GWAS: GLP1R (p.Ala316Thr, minor allele frequency (MAF)=1.5%) influencing FG levels, and URB2 (p.Glu594Val, MAF = 0.1%) influencing FI levels. Coding variant associations can highlight potential effector genes at (non-coding) GWAS signals. At the G6PC2/ABCB11 locus, we identified multiple coding variants in G6PC2 (p.Val219Leu, p.His177Tyr, and p.Tyr207Ser) influencing FG levels, conditionally independent of each other and the non-coding GWAS signal. In vitro assays demonstrate that these associated coding alleles result in reduced protein abundance via proteasomal degradation, establishing G6PC2 as an effector gene at this locus. Reconciliation of single-variant associations and functional effects was only possible when haplotype phase was considered. In contrast to earlier reports suggesting that, paradoxically, glucose-raising alleles at this locus are protective against type 2 diabetes (T2D), the p.Val219Leu G6PC2 variant displayed a modest but directionally consistent association with T2D risk. Coding variant associations for glycemic traits in GWAS signals highlight PCSK1, RREB1, and ZHX3 as likely effector transcripts. These coding variant association signals do not have a major impact on the trait variance explained, but they do provide valuable biological insights.

Understanding how FI and FG levels are regulated is important because their derangement is a feature of T2D. Despite recent success from GWAS in identifying regions of the genome influencing glycemic traits, collectively these loci explain only a small proportion of trait variance. Unlocking the biological mechanisms driving these associations has been challenging because the vast majority of variants map to non-coding sequence, and the genes through which they exert their impact are largely unknown. In the current study, we sought to increase our understanding of the physiological pathways influencing both traits using exome-array genotyping in up to 33,231 non-diabetic individuals to identify coding variants and consequently genes associated with either FG or FI levels. We identified novel association signals for both traits including the receptor for GLP-1 agonists which are a widely used therapy for T2D. Furthermore, we identified coding variants at several GWAS loci which point to the genes underlying these association signals. Importantly, we found that multiple coding variants in G6PC2 result in a loss of protein function and lower fasting glucose levels.

Epidermal growth factor receptor inhibition attenuates liver fibrosis and development of hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is the most rapidly increasing cause of cancer-related mortality in the United States. Because of the lack of viable treatment options for HCC, prevention in high-risk patients has been proposed as an alternative strategy. The main risk factor for HCC is cirrhosis and several lines of evidence implicate epidermal growth factor (EGF) in the progression of cirrhosis and development of HCC. We therefore examined the effects of the EGF receptor (EGFR) inhibitor erlotinib on liver fibrogenesis and hepatocellular transformation in three different animal models of progressive cirrhosis: a rat model induced by repeated, low-dose injections of diethylnitrosamine (DEN), a mouse model induced by carbon tetrachloride (CCl4 ), and a rat model induced by bile duct ligation (BDL). Erlotinib reduced EGFR phosphorylation in hepatic stellate cells (HSC) and reduced the total number of activated HSC. Erlotinib also decreased hepatocyte proliferation and liver injury. Consistent with all these findings, pharmacological inhibition of EGFR signaling effectively prevented the progression of cirrhosis and regressed fibrosis in some animals. Moreover, by alleviating the underlying liver disease, erlotinib blocked the development of HCC and its therapeutic efficacy could be monitored with a previously reported gene expression signature predictive of HCC risk in human cirrhosis patients.

CONCLUSION

These data suggest that EGFR inhibition using Food and Drug Administration-approved inhibitors provides a promising therapeutic approach for reduction of fibrogenesis and prevention of HCC in high-risk cirrhosis patients who can be identified and monitored by gene expression signatures.

Somatic mutation of CDKN1B in small intestine neuroendocrine tumors

The diagnosed incidence of small intestine neuroendocrine tumors (SI-NETs) is increasing, and the underlying genomic mechanisms have not yet been defined. Using exome- and genome-sequence analysis of SI-NETs, we identified recurrent somatic mutations and deletions in CDKN1B, the cyclin-dependent kinase inhibitor gene, which encodes p27. We observed frameshift mutations of CDKN1B in 14 of 180 SI-NETs, and we detected hemizygous deletions encompassing CDKN1B in 7 out of 50 SI-NETs, nominating p27 as a tumor suppressor and implicating cell cycle dysregulation in the etiology of SI-NETs.

Mutational heterogeneity in cancer and the search for new cancer-associated genes

Major international projects are underway that are aimed at creating a comprehensive catalogue of all the genes responsible for the initiation and progression of cancer. These studies involve the sequencing of matched tumour-normal samples followed by mathematical analysis to identify those genes in which mutations occur more frequently than expected by random chance. Here we describe a fundamental problem with cancer genome studies: as the sample size increases, the list of putatively significant genes produced by current analytical methods burgeons into the hundreds. The list includes many implausible genes (such as those encoding olfactory receptors and the muscle protein titin), suggesting extensive false-positive findings that overshadow true driver events. We show that this problem stems largely from mutational heterogeneity and provide a novel analytical methodology, MutSigCV, for resolving the problem. We apply MutSigCV to exome sequences from 3,083 tumour-normal pairs and discover extraordinary variation in mutation frequency and spectrum within cancer types, which sheds light on mutational processes and disease aetiology, and in mutation frequency across the genome, which is strongly correlated with DNA replication timing and also with transcriptional activity. By incorporating mutational heterogeneity into the analyses, MutSigCV is able to eliminate most of the apparent artefactual findings and enable the identification of genes truly associated with cancer.

Prognostically relevant gene signatures of high-grade serous ovarian carcinoma

Because of the high risk of recurrence in high-grade serous ovarian carcinoma (HGS-OvCa), the development of outcome predictors could be valuable for patient stratification. Using the catalog of The Cancer Genome Atlas (TCGA), we developed subtype and survival gene expression signatures, which, when combined, provide a prognostic model of HGS-OvCa classification, named "Classification of Ovarian Cancer" (CLOVAR). We validated CLOVAR on an independent dataset consisting of 879 HGS-OvCa expression profiles. The worst outcome group, accounting for 23% of all cases, was associated with a median survival of 23 months and a platinum resistance rate of 63%, versus a median survival of 46 months and platinum resistance rate of 23% in other cases. Associating the outcome prediction model with BRCA1/BRCA2 mutation status, residual disease after surgery, and disease stage further optimized outcome classification. Ovarian cancer is a disease in urgent need of more effective therapies. The spectrum of outcomes observed here and their association with CLOVAR signatures suggests variations in underlying tumor biology. Prospective validation of the CLOVAR model in the context of additional prognostic variables may provide a rationale for optimal combination of patient and treatment regimens.

Melanoma genome sequencing reveals frequent PREX2 mutations

Melanoma is notable for its metastatic propensity, lethality in the advanced setting, and association with ultraviolet (UV) exposure early in life¹. To obtain a comprehensive genomic view of melanoma, we sequenced the genomes of 25 metastatic melanomas and matched germline DNA. A wide range of point mutation rates was observed: lowest in melanomas whose primaries arose on non-UV exposed hairless skin of the extremities (3 and 14 per Mb genome), intermediate in those originating from hair-bearing skin of the trunk (range = 5 to 55 per Mb), and highest in a patient with a documented history of chronic sun exposure (111 per Mb). Analysis of whole-genome sequence data identified PREX2 - a PTEN-interacting protein and negative regulator of PTEN in breast cancer² - as a significantly mutated gene with a mutation frequency of approximately 14% in an independent extension cohort of 107 human melanomas. PREX2 mutations are biologically relevant, as ectopic expression of mutant PREX2 accelerated tumor formation of immortalized human melanocytes in vivo. Thus, whole-genome sequencing of human melanoma tumors revealed genomic evidence of UV pathogenesis and discovered a new recurrently mutated gene in melanoma.

The mutational landscape of head and neck squamous cell carcinoma

Head and neck squamous cell carcinoma (HNSCC) is a common, morbid, and frequently lethal malignancy. To uncover its mutational spectrum, we analyzed whole-exome sequencing data from 74 tumor-normal pairs. The majority exhibited a mutational profile consistent with tobacco exposure; human papillomavirus was detectable by sequencing DNA from infected tumors. In addition to identifying previously known HNSCC genes (TP53, CDKN2A, PTEN, PIK3CA, and HRAS), our analysis revealed many genes not previously implicated in this malignancy. At least 30% of cases harbored mutations in genes that regulate squamous differentiation (for example, NOTCH1, IRF6, and TP63), implicating its dysregulation as a major driver of HNSCC carcinogenesis. More generally, the results indicate the ability of large-scale sequencing to reveal fundamental tumorigenic mechanisms.

Abstract 923: Separating the wheat from the chaff: A first look at the Cancer Cell Lines Encyclopedia sequencing data

Comprehensive characterization of cancer genomic alterations and understanding their functional roles are important steps in the development of personalized cancer treatments. The Cancer Cell Lines Encyclopedia project aims to relate genomic alterations to drug sensitivity of cancer cells. Cancer cell lines are indispensable resource for researchers because of their convenience for high-throughput profiling and availability for follow-up experiments.

We sequenced the coding regions of 1645 genes in over 800 cancer cell lines representing 32 different tumor types. Genes were selected on their likelihood to be cancer-related and sequenced using next-generation Illumina technology after hybrid selection of exonic regions. Although, the absence of matched normal cell lines precludes direct distinction of somatic from germline mutations, we were able to select a subset of mutations highly enriched in somatic events combining the following three approaches: subtraction of known polymorphisms, prediction of strongly detrimental mutations (including computational predictions of amino acid substitutions’ effects on protein function) and detection of abnormal linkage disequilibrium patterns for recurring mutations.

We then searched for the three independent indicators of the potential involvement of mutated genes in cancer: the presence of an unusually high fraction of strongly damaging mutations within a gene, statistically significant deviation of distribution of mutations between cancer types from random expectation and clustering of mutations within a gene. Combined analysis of these lines of evidence revealed both known and novel potential tumor suppressors and oncogenes.

These data should become an import resource for cancer researchers in their search for personalized cancer therapies.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 923. doi:10.1158/1538-7445.AM2011-923

The genomic complexity of primary human prostate cancer

Prostate cancer is the second most common cause of male cancer deaths in the United States. However, the full range of prostate cancer genomic alterations is incompletely characterized. Here we present the complete sequence of seven primary human prostate cancers and their paired normal counterparts. Several tumours contained complex chains of balanced (that is, 'copy-neutral') rearrangements that occurred within or adjacent to known cancer genes. Rearrangement breakpoints were enriched near open chromatin, androgen receptor and ERG DNA binding sites in the setting of the ETS gene fusion TMPRSS2-ERG, but inversely correlated with these regions in tumours lacking ETS fusions. This observation suggests a link between chromatin or transcriptional regulation and the genesis of genomic aberrations. Three tumours contained rearrangements that disrupted CADM2, and four harboured events disrupting either PTEN (unbalanced events), a prostate tumour suppressor, or MAGI2 (balanced events), a PTEN interacting protein not previously implicated in prostate tumorigenesis. Thus, genomic rearrangements may arise from transcriptional or chromatin aberrancies and engage prostate tumorigenic mechanisms.

Screening for familial APP mutations in sporadic cerebral amyloid angiopathy

BACKGROUND

Advances in genetic technology have revealed that variation in the same gene can cause both rare familial and common sporadic forms of the same disease. Cerebral amyloid angiopathy (CAA), a common cause of symptomatic intracerebral hemorrhage (ICH) in the elderly, can also occur in families in an autosomal dominant pattern. The majority of affected families harbor mutations in the Beta amyloid Peptide (Aβ) coding region of the gene for amyloid precursor protein (APP) or have duplications of chromosomal segments containing APP.

METHODOLOGY/PRINCIPAL FINDINGS

A total of 58 subjects with a diagnosis of probable or definite CAA according to validated criteria were included in the present study. We sequenced the Aβ coding region of APP in 58 individuals and performed multiplex ligation-dependent probe amplification to determine APP gene dosage in 60. No patient harbored a known or novel APP mutation or gene duplication. The frequency of mutations investigated in the present study is estimated to range from 0% to 8% in individuals with probable CAA in the general population, based on the ascertained sample size.

CONCLUSIONS/SIGNIFICANCE

We found no evidence that variants at loci associated with familial CAA play a role in sporadic CAA. Based on our findings, these rare highly-penetrant mutations are unlikely to be seen in sporadic CAA patients. Therefore, our results do not support systematic genetic screening of CAA patients who lack a strong family history of hemorrhage or dementia.

Abstract 2925: Gene expression analysis to monitor erlotinib prevention of hepatocellular transformation during cirrhosis

Background: Hepatocellular carcinoma (HCC) is the sixth most common solid tumor worldwide and due to its poor prognosis it is the third leading cause of cancer-related death. Given the lack of successful treatment options, chemoprevention in high-risk patients has been proposed as an alternative strategy. Mounting evidence supports a role for epidermal growth factor (EGF) during chronic liver disease and hepatocellular transformation. Based on these findings, we address the hypothesis that blocking the EGF-EGF receptor (EGFR) pathway may be an effective strategy for inhibiting fibrogenesis and hepatocarcinogenesis. Methods: A rat model of diethylnitrosamine (DEN)-induced cirrhosis was used to examine the effects of erlotinib on underlying chronic liver disease and HCC formation. DEN (50 mg/kg) was administered weekly throughout the study while erlotinib (either 0.5 or 2 mg/kg) was administered 5 days per week for 6 weeks beginning at the onset of cirrhosis. At the end of the study, rats were sacrificed and tumor nodules were counted. Disease progression was assessed by H&E and trichrome staining. The effects of erlotinib on EGFR signaling were examined by western blot analysis. Activation of hepatic stellate cells was assessed by alpha-smooth muscle actin staining and blood tests were performed to determine hepatotoxicity and overall liver function. Finally, genome-wide gene expression profiling was used to compare the similarities between rat cirrhosis and human cirrhosis as well as to monitor the response to erlotinib. Results: The DEN-induced rat model closely resembles disease progression in humans. Liver fibrosis and cirrhosis were pathologically observed after 8 and 12 weeks, respectively, and multiple well-differentiated HCCs formed only in cirrhotic livers after 18 weeks. Microarray analysis revealed that DEN-induced rat cirrhosis recapitulates genome-wide gene expression observed in human cirrhosis. Erlotinib significantly prevented the development of HCC tumor nodules in a dose-dependent fashion. Erlotinib was shown to inhibit EGFR signaling more profoundly in the surrounding non-tumoral tissue than in residual tumors. Further, erlotinib inhibited the activation of hepatic stellate cells and prevented fibrogenesis. Erlotinib also reduced hepatotoxicity and improved liver function. Finally, a gene expression signature predictive of poor survival in human cirrhosis patients was reversed in response to erlotinib. Conclusions: Our data demonstrate for the first time that EGFR inhibition prevents liver fibrogenesis. Further, our results suggest that erlotinib is a potentially effective HCC chemoprevention agent that prevents progression of cirrhosis and its effects can be monitored using gene expression signatures.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2925.

Abstract 2620: The Cancer Cell Line Encyclopedia project: From integrative cancer genomics to personalized cancer therapy

Cancer genome characterization efforts such as The Cancer Genome Atlas project are rapidly improving our knowledge of tumor genetic alterations. With the expanded use of massively parallel sequencing, the catalogue of known genetic alterations in cancer is expected to expand at an accelerating rate. In this context, the emphasis is shifting towards systematic identification of the genes and pathways targeted by recurrent genetic alterations, their functional impact in tumor biology, and the resulting cellular dependencies that might be exploited therapeutically. Anticipating the need for a companion resource to systematically probe tumor biology armed with cancer genomics knowledge, we have assembled a compendium of experimentally tractable cancer model systems consisting of ∼1000 human cancer cell lines and performed extensive genomic analysis (at the level of gene expression, DNA copy number and mutations) coupled with pharmacological profiling. This resource, which we call the Cancer Cell Line Encyclopedia (CCLE), is being used not only to identify the putative targets of prevalent genetic alterations, but also to systematically link the presence or absence of certain genetic alterations to drug sensitivity or resistance.

To date, we have identified several previously unappreciated genomic predictors of response or intrinsic resistance to targeted anticancer agents. For instance, through integrative analysis, we have discovered additional mechanisms that may underlie sensitivity to MET inhibitors, beyond amplification of the MET receptor, highlighting the fact that response prediction in the clinic may require assessment of multiple variables. We have also broadened the potential relevance of known predictive biomarkers that might provide a rationale for future genotype-driven clinical trials. As an example, we have expanded on existing knowledge of resistance to receptor tyrosine kinase (RTK) inhibitors, showing that the presence of RAS mutations may predict lack of response to a broad spectrum of RTK inhibitors in addition to EGFR inhibitors. This work demonstrates that pharmacological profiling of large, genomically-annotated cancer model systems may uncover new tumor dependencies as well as positive and negative predictors of drug response. The results of this study are being made publicly available at a CCLE online portal, with the hope they will become a valuable resource for the cancer community to propel translation of the knowledge generated through in vitro integrative genomics into personalized cancer medicine.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2620.

Genome sequence, comparative analysis, and population genetics of the domestic horse

We report a high-quality draft sequence of the genome of the horse (Equus caballus). The genome is relatively repetitive but has little segmental duplication. Chromosomes appear to have undergone few historical rearrangements: 53% of equine chromosomes show conserved synteny to a single human chromosome. Equine chromosome 11 is shown to have an evolutionary new centromere devoid of centromeric satellite DNA, suggesting that centromeric function may arise before satellite repeat accumulation. Linkage disequilibrium, showing the influences of early domestication of large herds of female horses, is intermediate in length between dog and human, and there is long-range haplotype sharing among breeds.

Three functional variants of IFN regulatory factor 5 (IRF5) define risk and protective haplotypes for human lupus

Systematic genome-wide studies to map genomic regions associated with human diseases are becoming more practical. Increasingly, efforts will be focused on the identification of the specific functional variants responsible for the disease. The challenges of identifying causal variants include the need for complete ascertainment of genetic variants and the need to consider the possibility of multiple causal alleles. We recently reported that risk of systemic lupus erythematosus (SLE) is strongly associated with a common SNP in IFN regulatory factor 5 (IRF5), and that this variant altered spicing in a way that might provide a functional explanation for the reproducible association to SLE risk. Here, by resequencing and genotyping in patients with SLE, we find evidence for three functional alleles of IRF5: the previously described exon 1B splice site variant, a 30-bp in-frame insertion/deletion variant of exon 6 that alters a proline-, glutamic acid-, serine- and threonine-rich domain region, and a variant in a conserved polyA+ signal sequence that alters the length of the 3' UTR and stability of IRF5 mRNAs. Haplotypes of these three variants define at least three distinct levels of risk to SLE. Understanding how combinations of variants influence IRF5 function may offer etiological and therapeutic insights in SLE; more generally, IRF5 and SLE illustrates how multiple common variants of the same gene can together influence risk of common disease.

A genome-wide map of diversity in Plasmodium falciparum

Genetic variation allows the malaria parasite Plasmodium falciparum to overcome chemotherapeutic agents, vaccines and vector control strategies and remain a leading cause of global morbidity and mortality. Here we describe an initial survey of genetic variation across the P. falciparum genome. We performed extensive sequencing of 16 geographically diverse parasites and identified 46,937 SNPs, demonstrating rich diversity among P. falciparum parasites (pi = 1.16 x 10(-3)) and strong correlation with gene function. We identified multiple regions with signatures of selective sweeps in drug-resistant parasites, including a previously unidentified 160-kb region with extremely low polymorphism in pyrimethamine-resistant parasites. We further characterized 54 worldwide isolates by genotyping SNPs across 20 genomic regions. These data begin to define population structure among African, Asian and American groups and illustrate the degree of linkage disequilibrium, which extends over relatively short distances in African parasites but over longer distances in Asian parasites. We provide an initial map of genetic diversity in P. falciparum and demonstrate its potential utility in identifying genes subject to recent natural selection and in understanding the population genetics of this parasite.

Epidermal growth factor receptor activation in glioblastoma through novel missense mutations in the extracellular domain

BACKGROUND

Protein tyrosine kinases are important regulators of cellular homeostasis with tightly controlled catalytic activity. Mutations in kinase-encoding genes can relieve the autoinhibitory constraints on kinase activity, can promote malignant transformation, and appear to be a major determinant of response to kinase inhibitor therapy. Missense mutations in the EGFR kinase domain, for example, have recently been identified in patients who showed clinical responses to EGFR kinase inhibitor therapy.

METHODS AND FINDINGS

Encouraged by the promising clinical activity of epidermal growth factor receptor (EGFR) kinase inhibitors in treating glioblastoma in humans, we have sequenced the complete EGFR coding sequence in glioma tumor samples and cell lines. We identified novel missense mutations in the extracellular domain of EGFR in 13.6% (18/132) of glioblastomas and 12.5% (1/8) of glioblastoma cell lines. These EGFR mutations were associated with increased EGFR gene dosage and conferred anchorage-independent growth and tumorigenicity to NIH-3T3 cells. Cells transformed by expression of these EGFR mutants were sensitive to small-molecule EGFR kinase inhibitors.

CONCLUSIONS

Our results suggest extracellular missense mutations as a novel mechanism for oncogenic EGFR activation and may help identify patients who can benefit from EGFR kinase inhibitors for treatment of glioblastoma.

Measurement of the Casimir force between parallel metallic surfaces

We report on the measurement of the Casimir force between conducting surfaces in a parallel configuration. The force is exerted between a silicon cantilever coated with chromium and a similar rigid surface and is detected by looking at the shifts induced in the cantilever frequency when the latter is approached. The scaling of the force with the distance between the surfaces was tested in the 0.5-3.0 microm range, and the related force coefficient was determined at the 15% precision level.

Observation of superfluid flow in a bose-einstein condensed Gas

We have studied the hydrodynamic flow in a Bose-Einstein condensate stirred by a macroscopic object, a blue-detuned laser beam, using nondestructive in situ phase contrast imaging. A critical velocity for the onset of a pressure gradient has been observed, and shown to be density dependent. The technique has been compared to a calorimetric method used previously to measure the heating induced by the motion of the laser beam.

Surface excitations of a bose-einstein condensate

Surface modes in a Bose-Einstein condensate of sodium atoms have been studied. We observed excitations of standing and rotating quadrupolar and hexadecapolar modes. The modes were excited with high spatial and temporal resolution using the optical dipole force of a rapidly scanning laser beam. This novel technique is very flexible and should be useful for the study of rotating Bose-Einstein condensates and vortices.

Clinical aspects of granulomatous orchitis

Granulomatous orchitis can present in a variety of forms varying from acute to chronic. Clinically, testicular neoplasm is usually diagnosed and radical orchiectomy is performed, with the correct diagnosis being made on microscopic examination. In this article 6 cases of granulomatous orchitis are presented, with a variety of clinical presentations varying from acute to the more chronic forms.