The relation between meniscal dynamics and tibiofemoral kinematics

Over the past 30 years, research on meniscal kinematics has been limited by challenges such as low-resolution imaging and capturing continuous motion from static data. This study aimed to develop a computational knee model that overcomes these limitations and enables the continuous assessment of meniscal dynamics. A high-resolution MRI dataset (n = 11) was acquired in 4 configurations of knee flexion. In each configuration, the menisci were modeled based on the underlying osseous anatomy. Principal Polynomial Shape Analysis (PPSA) was employed for continuous meniscal modeling. Maximal medial anterior horn displacement occurred in 60° of flexion, equaling 6.24 mm posteromedial, while the posterior horn remained relatively stable. At 90° of flexion, the lateral anterior and posterior horn displaced posteromedially, amounting 5.70 mm and 6.51 mm respectively. The maximal observed Average Surface Distance (ASD) equaled 0.70 mm for lateral meniscal modeling in 90° of flexion. Based on our results, a strong relation between meniscal dynamics and tibiofemoral kinematics was confirmed. Expanding on static meniscal modeling and employing PPSA, we derived and validated a standardized and systematic methodological workflow.

Characterization of highly active mutational signatures in tumors from a large Chinese population

The majority of mutational signatures have been characterized in tumors from Western countries and the degree to which mutational signatures are similar or different in Eastern populations has not been fully explored. We leveraged a large-scale clinical sequencing cohort of tumors from a Chinese population containing 25 tumor types and found that the highly active mutational signatures were similar to those previously characterized1,2. The aristolochic acid signature SBS22 was observed in four soft tissue sarcomas and the POLE-associated signature SBS10 was observed in a gallbladder carcinoma. In lung adenocarcinoma, the polycyclic aromatic hydrocarbon (PAH) signature SBS4 was significantly higher in males compared to females but not associated with smoking status. The UV-associated signature SBS7 was significantly lower in cutaneous melanomas from the Chinese population compared to a similar American cohort. Overall, these results add to our understanding of the mutational processes that contribute to tumors from the Chinese population.

Personalized statistical modeling of soft tissue structures in the knee

Background and Objective: As in vivo measurements of knee joint contact forces remain challenging, computational musculoskeletal modeling has been popularized as an encouraging solution for non-invasive estimation of joint mechanical loading. Computational musculoskeletal modeling typically relies on laborious manual segmentation as it requires reliable osseous and soft tissue geometry. To improve on feasibility and accuracy of patient-specific geometry predictions, a generic computational approach that can easily be scaled, morphed and fitted to patient-specific knee joint anatomy is presented.

Methods: A personalized prediction algorithm was established to derive soft tissue geometry of the knee, originating solely from skeletal anatomy. Based on a MRI dataset (n = 53), manual identification of soft-tissue anatomy and landmarks served as input for our model by use of geometric morphometrics. Topographic distance maps were generated for cartilage thickness predictions. Meniscal modeling relied on wrapping a triangular geometry with varying height and width from the anterior to the posterior root. Elastic mesh wrapping was applied for ligamentous and patellar tendon path modeling. Leave-one-out validation experiments were conducted for accuracy assessment.

Results: The Root Mean Square Error (RMSE) for the cartilage layers of the medial tibial plateau, the lateral tibial plateau, the femur and the patella equaled respectively 0.32 mm (range 0.14–0.48), 0.35 mm (range 0.16–0.53), 0.39 mm (range 0.15–0.80) and 0.75 mm (range 0.16–1.11). Similarly, the RMSE equaled respectively 1.16 mm (range 0.99–1.59), 0.91 mm (0.75–1.33), 2.93 mm (range 1.85–4.66) and 2.04 mm (1.88–3.29), calculated over the course of the anterior cruciate ligament, posterior cruciate ligament, the medial and the lateral meniscus.

Conclusion: A methodological workflow is presented for patient-specific, morphological knee joint modeling that avoids laborious segmentation. By allowing to accurately predict personalized geometry this method has the potential for generating large (virtual) sample sizes applicable for biomechanical research and improving personalized, computer-assisted medicine.

Characteristics of suicide-related crashes and their potential interventions: A literature review

OBJECTIVE

To develop countermeasures to decrease road trauma, it is essential to increase our understanding of fatal and injury crashes with suicidal intent. As suicide-related crashes can be difficult to identify it seems likely suicide-related road fatalities and injuries are under-reported. Under-reported crashes may lead to two policy issues: these types of casualty crashes may not receive adequate funding for countermeasure development and implementation due to not having a sufficient evidence-basis to justify allocation of resources, and may be miscategorized as having other factors contributing to the crashes, thus resources may be incorrectly allocated to countermeasures to address these other factors. This paper seeks to develop and document characteristics and potential countermeasures to identify and prevent such crashes.

METHODS

Two literature reviews of peer-reviewed journal manuscripts were performed to identify suicide-crash characteristics and potential countermeasures and strategies. Of 61 peer-reviewed journal manuscripts identified from the literature searches, 17 manuscripts fit the criteria and were reviewed. Information regarding the characteristics of suicide-related crashes, as well as potential strategies and countermeasures were gleaned from these manuscripts.

RESULTS

A list of characteristics was developed, underpinning development of a methodology to identify these types of crashes. Strategies and countermeasures recommended by international (road-) agencies to identify and prevent suicide-related crashes were documented and discussed.

CONCLUSION

As suicide-related crashes almost always take place in public space, the grief and pain resulting from such crashes not only relates to the victim, the people who knew the victim, but in many cases also involve the general public. It is therefore paramount to start the discussion about suicide-related crashes to increase awareness, increase willingness to establish a reliable data and knowledge base, and encourage help seeking in individuals at increased risk of attempting suicide using this method.

Phase de consolidation du DES de médecine d’urgence. Enquête nationale sur la première année de Docteur Junior

Introduction : La première promotion d’internes de diplôme d’études spécialisées (DES) de médecine d’urgence est arrivée en novembre 2020 sur un statut inédit de Docteur Junior. De par leur nouveauté, il apparaît intéressant d’évaluer la satisfaction et la formation de cette promotion.

Matériel et méthodes : Une enquête nationale a été réalisée par les membres de la Commission jeunes de la SFMU et diffusée via les réseaux sociaux et les coordonnateurs de DES. Le questionnaire était composé d’une partie sociodémographique, d’une partie sur l’enseignement reçu, une sur les points positifs et négatifs de la maquette et une sur les choix de stage de Docteur Junior. Les variables qualitatives étaient exprimées en pourcentage. Les variables quantitatives étaient exprimées par une moyenne et un écart-type.

Résultats : Sur les 460 étudiants ayant choisi le DESMU en 2017, 142 (31 %) réponses ont été obtenues pour un âge moyen de 28 (± 2) ans, 73 étaient des hommes (51 %), 72 travaillaient en CHU (51 %). Les éléments de choix les plus évoqués sont l’ambiance de l’équipe et la réalisation d’un stage antérieur dans le service. Les étudiants ont bénéficié majoritairement de cours magistraux présentiels et de simulation. Le choix de l’appariement a été respecté pour 86 % des cas. La majorité des étudiants ne souhaite retirer aucun stage de la maquette.

Conclusion : Les internes sont majoritairement satisfaits de leur formation et de l’appariement. Ils choisissent leur lieu de stage de Docteur Junior en fonction de précédents stages dans la structure et d’une bonne ambiance dans l’équipe.

The Mutational Signature Comprehensive Analysis Toolkit (musicatk) for the Discovery, Prediction, and Exploration of Mutational Signatures

Mutational signatures are patterns of somatic alterations in the genome caused by carcinogenic exposures or aberrant cellular processes. To provide a comprehensive workflow for preprocessing, analysis, and visualization of mutational signatures, we created the Mutational Signature Comprehensive Analysis Toolkit (musicatk) package. musicatk enables users to select different schemas for counting mutation types and to easily combine count tables from different schemas. Multiple distinct methods are available to deconvolute signatures and exposures or to predict exposures in individual samples given a pre-existing set of signatures. Additional exploratory features include the ability to compare signatures to the Catalogue Of Somatic Mutations In Cancer (COSMIC) database, embed tumors in two dimensions with uniform manifold approximation and projection, cluster tumors into subgroups based on exposure frequencies, identify differentially active exposures between tumor subgroups, and plot exposure distributions across user-defined annotations such as tumor type. Overall, musicatk will enable users to gain novel insights into the patterns of mutational signatures observed in cancer cohorts. SIGNIFICANCE: The musicatk package empowers researchers to characterize mutational signatures and tumor heterogeneity with a comprehensive set of preprocessing utilities, discovery and prediction tools, and multiple functions for downstream analysis and visualization.

Sex-Related Abnormalities in Substantia Nigra Lipids in Parkinson's Disease

Parkinson’s disease (PD) is a neurodegenerative movement disorder involving the selective loss of dopamine-producing neurons in the substantia nigra (SN). Differences in disease presentation, prevalence, and age of onset have been reported between males and females with PD. The content and composition of the major glycosphingolipids, phospholipids, and cholesterol were evaluated in the SN from 12 PD subjects and in 18 age-matched, neurologically normal controls. Total SN ganglioside sialic acid content and water content (%) were significantly lower in the male PD subjects than in the male controls. The content of all major gangliosides were reduced in the male PD subjects to some degree, but the neuronal-enriched gangliosides, GD1a and GT1b, were most significantly reduced. The distribution of phosphatidylethanolamine, phosphatidylcholine, and phosphatidylinositol was also significantly lower in the male PD subjects than in the male controls. However, the distribution of myelin-enriched cerebrosides and sulfatides was significantly higher in the male PD subjects than in the male controls suggesting myelin sparing in the male PD subjects. No elevation was detected for astrocytosis-linked GD3. These neurochemical changes provide evidence of selective neuronal loss in SN of the males with PD without robust astrocytosis. In contrast to the SN lipid abnormalities found in the male PD subjects, no significant abnormalities were found in the female PD subjects for SN water content or for any major SN lipids. These data indicate sex-related differences in SN lipid abnormalities in PD.

Abstract 5108: Somatic small variant and copy number alteration calling with the Genome Analysis Toolkit

Somatic small mutations, SNVs or Indels, and copy number alterations are the two categories of mutations with the largest impact on cancer tumors. The Broad Institute has released somatic variant calling workflows for small mutations (M2) and copy number alterations (ModelSegments) based on the Genome Analysis Toolkit (GATK). The suite of workflows can call variants in capture or whole-genome sequencing data and will include functional annotations (Funcotator), such as protein change (for small variants) and impacted gene (for all variants). Common artifacts in sequencing data, such as those arising from oxidative DNA damage, FFPE/deamination, or mapping errors, are corrected automatically. Evaluation of the workflows is standardized and repeatable, which allows tracking of performance across versions, both detection performance (e.g. sensitivity, precision), as well as runtime performance (e.g. CPU and RAM usage). A matched normal is not required for a given tumor sample, since the workflows can leverage pre-processed panels of normals (PoNs). The workflows are freely available, are portable (i.e. can be run on local, on-prem, or cloud compute), are optimized for cost reduction, and can be tuned to optimally leverage available compute.The measured sensitivity of M2 was at least 0.93 for small somatic nucleotide variants (SNVs) and 0.83 for small insertions/deletions (Indels) on DREAM1, DREAM2, and DREAM3 challenges, and on a titrated mixture of germline samples (>=100x depth, AF = 0.2). The measured precision of M2 ranged from 0.91 to 0.98 on DREAM1, DREAM2, and DREAM3 for both SNVs and Indels. The false positive rate (FPR) of M2 was between 0.03 and 0.21 FP/Mb for SNVs, and between 0.0 and 0.1 FP/Mb for indels, on twelve paired, replicate normal-normal samples. The cost of the M2 workflow is about USD$1.15 for a pair of 35x WGS matched tumor-normal samples, using Google Cloud Compute, and required about 32 hours of CPU time on a single core with 3GB RAM.

The measured sensitivity of ModelSegments was at least 0.91 for deletions and amplifications across three cohorts of TCGA whole-exome samples (Stomach adenocarcinoma N=39, Thyroid carcinoma N=50, and Lung adenocarcinoma N=60). The measured specificity for the same set of cohorts was at least 0.96 for both deletions and amplifications. All results reported here were using the corresponding SNP Array results as a truth set.

GATK MS cost was approximately USD$0.65 on a 30x WGS pair using Google Cloud Compute and required about 6 hours of CPU time with a single core. The RAM usage was varied automatically in the workflow to minimize cost, but was in the range of 2-13GB.

Citation Format: Lee Lichtenstein, Jonn Smith, David Benjamin, Aaron Chevalier, Kristian Cibulskis, Samuel K. Lee, Eric Banks. Somatic small variant and copy number alteration calling with the Genome Analysis Toolkit [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 5108.

Genomic Evolutionary Patterns of Leiomyosarcoma and Liposarcoma

PURPOSE

Leiomyosarcoma and liposarcoma are common subtypes of soft tissue sarcoma (STS). Patients with metastatic leiomyosarcoma or dedifferentiated liposarcoma (DDLPS) typically have worse outcomes compared with localized leiomyosarcoma or well-differentiated liposarcoma (WDLPS). A better understanding of genetic changes between primary/metastatic leiomyosarcoma and between WDLPS/DDLPS may provide insight into their genetic evolution.

EXPERIMENTAL DESIGN

We interrogated whole-exome sequencing (WES) from "trios" of normal tissue, primary tumor, and metastatic tumor from individual patients with leiomyosarcoma (n = 9), and trios of normal tissue, well-differentiated tumor, and dedifferentiated tumor from individual patients with liposarcoma (n = 19). Specifically, we performed mutational, copy number, and tumor evolution analyses on these cohorts and compared patterns among leiomyosarcoma and liposarcoma trios.

RESULTS

Leiomyosarcoma cases harbored shared drivers through a typical parent/child relationship where the metastatic tumor was derived from the primary tumor. In contrast, while all liposarcoma cases shared the characteristic focal chromosome 12 amplicon, most paired liposarcoma cases did not share additional mutations, suggesting a divergent evolutionary pattern from a common precursor. No highly recurrent genomic alterations from WES were identified that could be implicated as driving the progression of disease in either sarcoma subtype.

CONCLUSIONS

From a genomic perspective, leiomyosarcoma metastases contain genetic alterations that are also found in primary tumors. WDLPS and DDLPS, however, appear to divergently evolve from a common precursor harboring 12q amplification, rather than as a transformation to a higher-grade tumor. Further efforts to identify specific drivers of these distinct evolutionary patterns may inform future translational and clinical research in STS.

Does pre-activating domain knowledge foster elaborated online information search strategies? Comparisons between young and old web user adults

The present study aimed at investigating how pre-activating prior topic knowledge before browsing the web can support information search performance and strategies of young and older users. The experiment focus on analyzing to what extent prior knowledge pre-activation might cope with older users' difficulties when interacting with a search engine. 26 older (age 60 to 77) and 22 young (age 18 to 32) adults performed 6 information search problems related to health and fantastic movies. Overall, results showed that pre-activating prior topic knowledge increased the time spent evaluating the search engine results pages, fostered deeper processing of the navigational paths elaborated (and thus reduced the exploration of different navigational paths) and improved the semantic specificity of queries. Pre-activating prior knowledge helped older adults produced semantically more specific queries when they had lower prior-knowledge than young adults. Moderation analyses indicated that the pre-activation supported older adults' search performance under the condition that participants generated semantically relevant keywords during this pre-activation task. Implications of these results show that prior topic knowledge pre-activation may be a good lead to support the beneficial role of prior knowledge in older users' search behavior and performance. Recommendations for design pre-activation support tool are provided.

Global analysis of protein folding using massively parallel design, synthesis, and testing

Proteins fold into unique native structures stabilized by thousands of weak interactions that collectively overcome the entropic cost of folding. Although these forces are "encoded" in the thousands of known protein structures, "decoding" them is challenging because of the complexity of natural proteins that have evolved for function, not stability. We combined computational protein design, next-generation gene synthesis, and a high-throughput protease susceptibility assay to measure folding and stability for more than 15,000 de novo designed miniproteins, 1000 natural proteins, 10,000 point mutants, and 30,000 negative control sequences. This analysis identified more than 2500 stable designed proteins in four basic folds-a number sufficient to enable us to systematically examine how sequence determines folding and stability in uncharted protein space. Iteration between design and experiment increased the design success rate from 6% to 47%, produced stable proteins unlike those found in nature for topologies where design was initially unsuccessful, and revealed subtle contributions to stability as designs became increasingly optimized. Our approach achieves the long-standing goal of a tight feedback cycle between computation and experiment and has the potential to transform computational protein design into a data-driven science.

Massively parallel de novo protein design for targeted therapeutics

De novo protein design holds promise for creating small stable proteins with shapes customized to bind therapeutic targets. We describe a massively parallel approach for designing, manufacturing and screening mini-protein binders, integrating large-scale computational design, oligonucleotide synthesis, yeast display screening and next-generation sequencing. We designed and tested 22,660 mini-proteins of 37-43 residues that target influenza haemagglutinin and botulinum neurotoxin B, along with 6,286 control sequences to probe contributions to folding and binding, and identified 2,618 high-affinity binders. Comparison of the binding and non-binding design sets, which are two orders of magnitude larger than any previously investigated, enabled the evaluation and improvement of the computational model. Biophysical characterization of a subset of the binder designs showed that they are extremely stable and, unlike antibodies, do not lose activity after exposure to high temperatures. The designs elicit little or no immune response and provide potent prophylactic and therapeutic protection against influenza, even after extensive repeated dosing.

Abstract 3581: GATK ACNV: allelic copy-number variation discovery from SNPs and coverage data

The presence of somatic copy-number alterations in tumor genomes can be used to predict both patient sensitivity to treatments as well as outcomes. The inclusion of allelic data improves statistical power to detect copy-number events and allows for discovery of copy-neutral events. We present GATK ACNV, an allelic copy-number variation method built on the Genome Analysis Toolkit. ACNV is a tool for detecting somatic copy-number activity from whole exome and whole genome sequencing data by segmenting the genome into regions of constant copy number and estimating copy ratio and minor-allele fraction in those regions.

ACNV uses a novel probabilistic model to account for reference bias (optionally using a panel of normals), which improves the estimation of minor-allele fraction. We combine this with the coverage model from GATK CNV by segmenting with a unified hidden Markov model, improving the statistical power to detect copy-number variation.

We validate ACNV using a purity series of the cell line HCC1143 and cancer samples from The Cancer Genome Atlas. Our results show that ACNV is able to discover regions of somatic copy-number activity accurately and with high resolution in both whole exome and whole genome sequencing data.

Citation Format: Aaron Chevalier, Lee Lichtenstein, Andrey Smirnov, Samuel K. Lee, Mehrtash Babidi, David I. Benjamin, Valentin Ruano-Rubio. GATK ACNV: allelic copy-number variation discovery from SNPs and coverage data [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3581. doi:10.1158/1538-7445.AM2017-3581

Rapid Diagnostic Assay for Intact Influenza Virus Using a High Affinity Hemagglutinin Binding Protein

Influenza is a ubiquitous and recurring infection that results in approximately 500 000 deaths globally each year. Commercially available rapid diagnostic tests are based upon detection of the influenza nucleoprotein, which are limited in that they are unable to differentiate by species and require an additional viral lysis step. Sample preprocessing can be minimized or eliminated by targeting the intact influenza virus, thereby reducing assay complexity and leveraging the large number of hemagglutinin proteins on the surface of each virus. Here, we report the development of a paper-based influenza assay that targets the hemagglutinin protein; the assay employs a combination of antibodies and novel computationally designed, recombinant affinity proteins as the capture and detection agents. This system leverages the customizability of recombinant protein design to target the conserved receptor-binding pocket of the hemagglutinin protein and to match the trimeric nature of hemagglutinin for improved avidity. Using this assay, we demonstrate the first instance of intact influenza virus detection using a combination of antibody and affinity proteins within a porous network. The recombinant head region binder based assays yield superior analytical sensitivity as compared to the antibody based assay, with lower limits of detection of 3.54 × 10⁷ and 1.34 × 10⁷ CEID₅₀/mL for the mixed and all binder stacks, respectively. Not only does this work describe the development of a novel influenza assay, it also demonstrates the power of recombinant affinity proteins for use in rapid diagnostic assays.

Genomic landscape of high-grade meningiomas

High-grade meningiomas frequently recur and are associated with high rates of morbidity and mortality. To determine the factors that promote the development and evolution of these tumors, we analyzed the genomes of 134 high-grade meningiomas and compared this information with data from 587 previously published meningiomas. High-grade meningiomas had a higher mutation burden than low-grade meningiomas but did not harbor any statistically significant mutated genes aside from NF2. High-grade meningiomas also possessed significantly elevated rates of chromosomal gains and losses, especially among tumors with monosomy 22. Meningiomas previously treated with adjuvant radiation had significantly more copy number alterations than radiation-induced or radiation-naïve meningiomas. Across serial recurrences, genomic disruption preceded the emergence of nearly all mutations, remained largely uniform across time, and when present in low-grade meningiomas, correlated with subsequent progression to a higher grade. In contrast to the largely stable copy number alterations, mutations were strikingly heterogeneous across tumor recurrences, likely due to extensive geographic heterogeneity in the primary tumor. While high-grade meningiomas harbored significantly fewer overtly targetable alterations than low-grade meningiomas, they contained numerous mutations that are predicted to be neoantigens, suggesting that immunologic targeting may be of therapeutic value.

Predictors of older drivers' involvement in rapid deceleration events

Rapid deceleration occurs when substantial force slows the speed of a vehicle. Rapid deceleration events (RDEs) have been proposed as a surrogate safety measure. As there is concern about crash involvement of older drivers and the effect of age-related declining visual and cognitive function on driving performance, we examined the relationship between RDEs and older driver's vision, cognitive function and driving confidence, using naturalistic driving measures. Participants aged 75 to 94 years had their vehicle instrumented for 12 months. To minimise the chance of identifying false positives, accelerometer data was processed to identify RDEs with a substantial deceleration of >750 milli-g (7.35m/s²). We examined the incidence of RDEs amongst older drivers, and how this behaviour is affected by differences in age; sex; visual function, cognitive function; driving confidence; and declines over the 12 months. Almost two-thirds (64%) of participants were involved in at least one RDE, and 22% of these participants experienced a meaningful decline in contrast sensitivity during the 12 months. We conducted regression modelling to examine associations between RDEs and predictive measures adjusted for (i) duration of monitoring and (ii) distance driven. We found the rate of RDEs per distance increased with age; although, this did not remain in the multivariate model. In the multivariate model, we found older drivers who experienced a decline in contrast sensitivity over the 12 months and those with lower baseline driving confidence were at increased risk of involvement in RDEs adjusted for distance driven. In other studies, contrast sensitivity has been associated with increased crash involvement for older drivers. These findings lend support for the use of RDEs as a surrogate safety measure, and demonstrate an association between a surrogate safety measure and a decline in contrast sensitivity of older drivers.

Landscape of Genomic Alterations in Pituitary Adenomas

Purpose: Pituitary adenomas are the second most common primary brain tumor, yet their genetic profiles are incompletely understood.Experimental Design: We performed whole-exome sequencing of 42 pituitary macroadenomas and matched normal DNA. These adenomas included hormonally active and inactive tumors, ones with typical or atypical histology, and ones that were primary or recurrent.Results: We identified mutations, insertions/deletions, and copy-number alterations. Nearly one-third of samples (29%) had chromosome arm-level copy-number alterations across large fractions of the genome. Despite such widespread genomic disruption, these tumors had few focal events, which is unusual among highly disrupted cancers. The other 71% of tumors formed a distinct molecular class, with somatic copy number alterations involving less than 6% of the genome. Among the highly disrupted group, 75% were functional adenomas or atypical null-cell adenomas, whereas 87% of the less-disrupted group were nonfunctional adenomas. We confirmed this association between functional subtype and disruption in a validation dataset of 87 pituitary adenomas. Analysis of previously published expression data from an additional 50 adenomas showed that arm-level alterations significantly impacted transcript levels, and that the disrupted samples were characterized by expression changes associated with poor outcome in other cancers. Arm-level losses of chromosomes 1, 2, 11, and 18 were significantly recurrent. No significantly recurrent mutations were identified, suggesting no genes are altered by exonic mutations across large fractions of pituitary macroadenomas.Conclusions: These data indicate that sporadic pituitary adenomas have distinct copy-number profiles that associate with hormonal and histologic subtypes and influence gene expression. Clin Cancer Res; 23(7); 1841-51. ©2016 AACR.

The genomic landscape and evolution of endometrial carcinoma progression and abdominopelvic metastasis

Recent studies have detailed the genomic landscape of primary endometrial cancers, but the evolution of these cancers into metastases has not been characterized. We performed whole-exome sequencing of 98 tumor biopsies including complex atypical hyperplasias, primary tumors and paired abdominopelvic metastases to survey the evolutionary landscape of endometrial cancer. We expanded and reanalyzed The Cancer Genome Atlas (TCGA) data, identifying new recurrent alterations in primary tumors, including mutations in the estrogen receptor cofactor gene NRIP1 in 12% of patients. We found that likely driver events were present in both primary and metastatic tissue samples, with notable exceptions such as ARID1A mutations. Phylogenetic analyses indicated that the sampled metastases typically arose from a common ancestral subclone that was not detected in the primary tumor biopsy. These data demonstrate extensive genetic heterogeneity in endometrial cancers and relative homogeneity across metastatic sites.

A Computationally Designed Hemagglutinin Stem-Binding Protein Provides In Vivo Protection from Influenza Independent of a Host Immune Response

Broadly neutralizing antibodies targeting a highly conserved region in the hemagglutinin (HA) stem protect against influenza infection. Here, we investigate the protective efficacy of a protein (HB36.6) computationally designed to bind with high affinity to the same region in the HA stem. We show that intranasal delivery of HB36.6 affords protection in mice lethally challenged with diverse strains of influenza independent of Fc-mediated effector functions or a host antiviral immune response. This designed protein prevents infection when given as a single dose of 6.0 mg/kg up to 48 hours before viral challenge and significantly reduces disease when administered as a daily therapeutic after challenge. A single dose of 10.0 mg/kg HB36.6 administered 1-day post-challenge resulted in substantially better protection than 10 doses of oseltamivir administered twice daily for 5 days. Thus, binding of HB36.6 to the influenza HA stem region alone, independent of a host response, is sufficient to reduce viral infection and replication in vivo. These studies demonstrate the potential of computationally designed binding proteins as a new class of antivirals for influenza.

Influenza is a major public health threat, and pandemics, such as the 2009 H1N1 outbreak, are inevitable. Due to low efficacy of seasonal flu vaccines and the increase in drug-resistant strains of influenza viruses, there is a crucial need to develop new antivirals to protect from seasonal and pandemic influenza. Recently, several broadly neutralizing antibodies have been characterized that bind to a highly conserved site on the viral hemagglutinin (HA) stem region. These antibodies are protective against a wide range of diverse influenza viruses, but their efficacy depends on a host immune effector response through the antibody Fc region (ADCC). Here we show that a small engineered protein computationally designed to bind to the same region of the HA stem as broadly neutralizing antibodies mediated protection against diverse strains of influenza in mice by a distinct mechanism that is independent of a host immune response. Protection was superior to that afforded by oseltamivir, a lead marketed antiviral. Furthermore, combination therapy with low doses of the engineered protein and oseltamivir resulted in enhanced and synergistic protection from lethal challenge. Thus, through computational protein engineering, we have designed a new antiviral with strong biopotency in vivo that targets a neutralizing epitope on the hemagglutinin of influenza virus and inhibits its fusion activity. These results have significant implications for the use of computational modeling to design new antivirals against influenza and other viral diseases.

Genomic Characterization of Brain Metastases Reveals Branched Evolution and Potential Therapeutic Targets

Brain metastases are associated with a dismal prognosis. Whether brain metastases harbor distinct genetic alterations beyond those observed in primary tumors is unknown. We performed whole-exome sequencing of 86 matched brain metastases, primary tumors, and normal tissue. In all clonally related cancer samples, we observed branched evolution, where all metastatic and primary sites shared a common ancestor yet continued to evolve independently. In 53% of cases, we found potentially clinically informative alterations in the brain metastases not detected in the matched primary-tumor sample. In contrast, spatially and temporally separated brain metastasis sites were genetically homogenous. Distal extracranial and regional lymph node metastases were highly divergent from brain metastases. We detected alterations associated with sensitivity to PI3K/AKT/mTOR, CDK, and HER2/EGFR inhibitors in the brain metastases. Genomic analysis of brain metastases provides an opportunity to identify potentially clinically informative alterations not detected in clinically sampled primary tumors, regional lymph nodes, or extracranial metastases.

SIGNIFICANCE

Decisions for individualized therapies in patients with brain metastasis are often made from primary-tumor biopsies. We demonstrate that clinically actionable alterations present in brain metastases are frequently not detected in primary biopsies, suggesting that sequencing of primary biopsies alone may miss a substantial number of opportunities for targeted therapy.

Long-term Benefit of PD-L1 Blockade in Lung Cancer Associated with JAK3 Activation

PD-1 immune checkpoint blockade occasionally results in durable clinical responses in advanced metastatic cancers. However, mechanism-based predictors of response to this immunotherapy remain incompletely characterized. We performed comprehensive genomic profiling on a tumor and germline sample from a patient with refractory lung adenocarcinoma who achieved marked long-term clinical benefit from anti-PD-L1 therapy. We discovered activating somatic and germline amino acid variants in JAK3 that promoted PD-L1 induction in lung cancer cells and in the tumor immune microenvironment. These findings suggest that genomic alterations that deregulate cytokine receptor signal transduction could contribute to PD-L1 activation and engagement of the PD-1 immune checkpoint in lung cancer.

Biogenesis of influenza a virus hemagglutinin cross-protective stem epitopes

Antigenic variation in the globular domain of influenza A virus (IAV) hemagglutinin (HA) precludes effective immunity to this major human pathogen. Although the HA stem is highly conserved between influenza virus strains, HA stem-reactive antibodies (StRAbs) were long considered biologically inert. It is now clear, however, that StRAbs reduce viral replication in animal models and protect against pathogenicity and death, supporting the potential of HA stem-based immunogens as drift-resistant vaccines. Optimally designing StRAb-inducing immunogens and understanding StRAb effector functions require thorough comprehension of HA stem structure and antigenicity. Here, we study the biogenesis of HA stem epitopes recognized in cells infected with various drifted IAV H1N1 strains using mouse and human StRAbs. Using a novel immunofluorescence (IF)-based assay, we find that human StRAbs bind monomeric HA in the endoplasmic reticulum (ER) and trimerized HA in the Golgi complex (GC) with similar high avidity, potentially good news for producing effective monomeric HA stem immunogens. Though HA stem epitopes are nestled among several N-linked oligosaccharides, glycosylation is not required for full antigenicity. Rather, as N-linked glycans increase in size during intracellular transport of HA through the GC, StRAb binding becomes temperature-sensitive, binding poorly to HA at 4°C and well at 37°C. A de novo designed, 65-residue protein binds the mature HA stem independently of temperature, consistent with a lack of N-linked oligosaccharide steric hindrance due to its small size. Likewise, StRAbs bind recombinant HA carrying simple N-linked glycans in a temperature-independent manner. Chemical cross-linking experiments show that N-linked oligosaccharides likely influence StRAb binding by direct local effects rather than by globally modifying the conformational flexibility of HA. Our findings indicate that StRAb binding to HA is precarious, raising the possibility that sufficient immune pressure on the HA stem region could select for viral escape mutants with increased steric hindrance from N-linked glycans.

Optimization of affinity, specificity and function of designed influenza inhibitors using deep sequencing

We show that comprehensive sequence-function maps obtained by deep sequencing can be used to reprogram interaction specificity and to leapfrog over bottlenecks in affinity maturation by combining many individually small contributions not detectable in conventional approaches. We use this approach to optimize two computationally designed inhibitors against H1N1 influenza hemagglutinin and, in both cases, obtain variants with subnanomolar binding affinity. The most potent of these, a 51-residue protein, is broadly cross-reactive against all influenza group 1 hemagglutinins, including human H2, and neutralizes H1N1 viruses with a potency that rivals that of several human monoclonal antibodies, demonstrating that computational design followed by comprehensive energy landscape mapping can generate proteins with potential therapeutic utility.

A CMOS Electrochemical Impedance Spectroscopy (EIS) Biosensor Array

In this paper, we present a fully integrated biosensor 10 × 10 array in a standard complementary metal-oxide semiconducor process, which takes advantage of electrochemical impedance spectroscopy (EIS). We also show that this system is able to detect various biological analytes, such as DNA and proteins, in real time and without the need for molecular labels. In each pixel of this array, we implement a biocompatible Au electrode transducer and embedded sensor circuitry which takes advantage of the coherent detector to measure the impedance of the associated electrode-electrolyte interface. This chip is capable of concurrently measuring admittance values as small as 10(-8) Ω(-1) within the array with the detection dynamic range of more than 90 dB in the frequency range of 10 Hz-50 MHz.

[Sensitivity and specificity of the breast screening program in the Isere region based on positive results between 1991 and 1999]

PURPOSE

The screening program guidelines specify that the call back rate of women for additional imaging (positive mammogram) should not exceed 7% at initial screening, and 5% at subsequent screening. Materials and methods. Results in the Isere region (12%) have prompted a review of the correlation between the call back rate and indicators of quality (detection rate, sensitivity, specificity, positive predictive value) for the radiologists providing interpretations during that time period.

RESULTS

Three groups of radiologists were identified: the group with call back rate of 10% achieved the best results (sensitivity: 92%, detection rate: 0.53%, specificity: 90%). The group with lowest call back rate (7.7%) showed insufficient sensitivity (58%). The last group with call back rate of 18.3%, showed no improvement in sensitivity (82%) and detection rate (0.53%), but showed reduced specificity (82%).

CONCLUSION

The protocol update in 2001 does not resolve this problematic situation and national results continue to demonstrate a high percentage of positive screening mammograms. A significant increase in the number of positive screening examinations compared to recommended guidelines is not advantageous and leads to an overall decrease in the quality of the screening.

Sickness absence as a prognostic marker for common chronic conditions: analysis of mortality in the GAZEL study

OBJECTIVES

To determine whether sickness absence is a prognostic marker in terms of mortality among people with common chronic conditions.

METHODS

Prospective occupational cohort study of 13,077 men and 4871 women aged 37-51 from the National Gas and Electricity Company, France. Records of physician-certified sickness absences over a 3-year period were obtained from employers' registers. Chronic conditions were assessed in annual surveys over the same period. The main outcome measure was all-cause mortality (803 deaths, mean follow-up after assessment of sickness absence: 13.9 years).

RESULTS

In Cox proportional hazard models adjusted for age, sex, socioeconomic position and co-morbidity, >28 annual sickness-absence days versus no absence days was associated with an excess mortality risk among those with cancer (hazard ratio 5.4, 95% CI 2.2 to 13.1), depression (1.7, 1.1 to 2.8), chronic bronchitis or asthma (2.7, 1.6 to 4.6) and hypertension (1.6, 1.0 to 2.6). The corresponding hazard ratios for more than five long (>14 days) sickness-absence episodes per 10 person-years versus no such episodes were 5.4 (2.2 to 13.1), 1.8 (1.3 to 2.7), 2.0 (1.3 to 3.2) and 1.8 (1.2 to 2.7), respectively. Areas under receiver operating characteristics curves for these absence measures varied between 0.56 and 0.73, indicating the potential of these measures to distinguish groups at high risk of mortality. The findings were consistent across sex, age and socioeconomic groups and in those with and without co-morbid conditions.

CONCLUSION

Data on sickness absence may provide useful prognostic information for common chronic conditions at the population level.

Diagnosis-specific sickness absence and all-cause mortality in the GAZEL study

BACKGROUND

This study aims to examine diagnosis-specific sickness absence as a risk marker for all-cause mortality.

METHODS

Prospective occupational cohort (the GAZEL study). Medically certified sickness absence spells >7 days for 15 diagnostic categories, 1990-1992, were examined in relation to all-cause mortality, January 1993-February 2007. The reference group for each diagnostic category was participants with no spell >7 days for that diagnosis. The participants were French public utility workers (5271 women and 13 964 men) aged 37-51 years in 1990, forming the GAZEL study. Over the follow-up period, there were 144 deaths in women and 758 in men.

RESULTS

7875 employees (41.0%) had at least one spell of sickness absence >7 days over the 3-year period. The commonest diagnoses were mental disorders, musculoskeletal diseases, respiratory diseases and external causes in both sexes; genitourinary diseases in women, and digestive and circulatory diseases in men. Of these common diagnoses, mental disorders in women, hazard ratio (95% confidence intervals) 1.24 (1.1 to 1.4), and mental disorders 1.35 (1.3 to 1.5), digestive diseases 1.29 (1.1 to 1.6) and circulatory diseases 1.35 (1.2 to 1.6) in men were associated with mortality after adjustment for age, employment grade and sickness absence in all other diagnostic categories.

CONCLUSIONS

Employees with medically certified absence spells of 1 week or more over a 3-year period had a 60% excess risk of early death. In women and men this excess risk was associated with some of the commonest diagnoses of sickness absence, in particular mental disorders. Sickness absence for mental disorders may be a useful early indicator of groups at increased risk of fatal disease.

Scintigraphic imaging of paediatric thyroid dysfunction

Imaging of thyroid dysfunction is safe and clinically relevant in children. In congenital hypothyroidism (CH), thyroid imaging permits a precise characterization of the aetiology, which is important for genetic counselling and clinical management. CH may be due to thyroid dysgenesis (ectopia, hypoplasia and athyrosis) or occurs in eutopic glands. In the latter, hypothyroidism may be either transient, especially after iodine overload, or due to permanent autosomal recessive dyshormonogenesis. Thyroid scintigraphy (TS) with either 99mTcO4 or 123I will identify ectopic thyroid tissue, which is the commonest cause of CH. However, recent reports favour the use of 123I, which enhances the accuracy of the aetiological classification. In cases of eutopic thyroid, the measurement of 123I uptake before and after perchlorate administration evaluates the organification process. At all ages, colour Doppler ultrasound scanning (CDU) is helpful in assessing thyroid volume, in identifying nodules and in characterizing tissue vascularization. TS and CDU images of most paediatric thyroid dysfunctions are presented.

Home and leisure injuries among the French electricity and gas company active employees: circumstances and short-term consequences

OBJECTIVE

To characterize home and leisure injuries and their immediate consequences among adults aged 20-60 years and to look for homogeneous profiles of injury circumstances to assess the possibility of setting up prevention programs.

DESIGN

Cross-sectional survey by questionnaire completed on the occasion of a medical visit after a first episode of absence for home or leisure injury between 1 January and 31 December 1997 among Electricité de France Gaz de France (EDF GDF) workforce of three geographical areas (47,681 employees). Incidence and relative risks according to sex, age and work grade and a multidimensional classification of injury circumstances.

RESULTS

Eight hundred and fifty four injuries were studied. Risk was estimated at 18.4 injury victims per 1000 employees, of which 13.4 per 1000 employees were home injury victims and 3.7 leisure injury victims. The risk of all injuries was higher among men than women (RR=1.3) and decreased as work grade rose: for men, it was five times higher among operating employees than managers. Multidimensional analysis of injury circumstances ended by distributing into four main classes which may be useful for prevention: gardening and do-it-yourself injuries outdoors (19.9%), coming and going on the streets (6.9%), falling while coming and going in the home on the stairs (13.4%), and do-it-yourself inside the home (13.0%). Injuries induced essentially four types of lesions: sprains (34%), fractures (31.8%), contusions (24.5%) and wounds. The mean sick-leave lasted 32.1 days but half the subjects returned to work in less than 17 days. Hospitalization was necessary in 19.2% of cases.

CONCLUSIONS

This study completed by an analysis of the behavioural factors of injuries led us to propose programs aimed at changing the risk behaviours related to do-it-yourself, stairs falls and gardening.

[A strategy for therapy of depressive disorders and anxiety disorders by a health education intervention in medical consultations: the results of the APRAND program]

BACKGROUND

Studies devoted to the detection and treatment of anxiety and depression in adult populations show that at least 10% meet ICD10 criteria for an anxiety or a depressive disorder, but only half are diagnosed as such and only one third of those receive appropriate treatment. The goal of the APRAND program was to explore the possibility of improving management strategies via health education during doctors' visits.

METHODS

In 2001, EDF-GDF conducted an experimental program in which 21 physicians from its in-house health insurance program used the MINI mental state examination to screen for ICD10 criteria for anxiety and depressive disorders in 9743 employees on sick leave. A "here-elsewhere" epidemiologic study evaluated the program, recording the initial diagnoses and studying a year later the outcome of the persons identified with these disorders in 8 active centers (with prevention activities) and in 13 control centers (without prevention activities). The activities consisted of explanations of the disorders identified, delivery of the test results, delivery of leaflets based on the WHO guidelines, and strong recommendations to see a general practitioner, or a psychiatrist, or the occupational physician, if necessary. Logistic regressions compared the two groups, taking into account sex, age, geographic region, comorbidity, and medical care at screening.

RESULTS

Preventive activities were significantly associated with the disappearance at 1 year of depressive episodes (OR=1.93; CI 95%; 1.3-2.84) and of phobic or panic disorders (OR=1.98; CI 95%; 1.14-3.44). The only other variables affecting prognosis were age and sex. The probability of recovery or remission increased by 10 to 20% at active centers, according to age, sex and disorder. Moreover, the physicians reported that they learned a great deal from the program, which thus also improved their practices.

CONCLUSION

Diagnosis and prognosis of depressive episodes and phobic and panic disorders in adult populations can be improved by a preventive diagnostic and educational approach of the type used by APRAND during doctor's visits.

The Wip1 phosphatase (PPM1D) antagonizes activation of the Chk2 tumour suppressor kinase

We previously demonstrated that type 2C protein phosphatases (PP2C) Ptc2 and Ptc3 are required for DNA checkpoint inactivation after DNA double-strand break repair or adaptation in Saccharomyces cerevisiae. Here, we show the conservation of this pathway in mammalian cells. In response to DNA damage, ataxia telangiectasia mutated (ATM) phosphorylates the Chk2 tumour suppressor kinase at threonine 68 (Thr68), allowing Chk2 kinase dimerization and activation by autophosphorylations in the T-loop. The oncogenic protein Wip1, a PP2C phosphatase, binds Chk2 and dephosphorylates phospho-Thr68. Consequently, Wip1 opposes Chk2 activation by ATM after ionizing irradiation of cells. In HCT15 colorectal cancer cells corrected for functional Chk2 activity, Wip1 overexpression suppressed the contribution of Chk2 to the G2/M DNA damage checkpoint. These results indicate that Wip1 is one of the phosphatases regulating the activity of Chk2 in response to DNA damage.