Interactions between ploidy and resource availability shape clonal interference at initiation and recurrence of glioblastoma

Glioblastoma (GBM) is the most aggressive form of primary brain tumor. Complete surgical resection of GBM is almost impossible due to the infiltrative nature of the cancer. While no evidence for recent selection events have been found after diagnosis, the selective forces that govern gliomagenesis are strong, shaping the tumor's cell composition during the initial progression to malignancy with late consequences for invasiveness and therapy response. We present a mathematical model that simulates the growth and invasion of a glioma, given its ploidy level and the nature of its brain tissue micro-environment (TME), and use it to make inferences about GBM initiation and response to standard-of-care treatment. We approximate the spatial distribution of resource access in the TME through integration of in-silico modelling, multi-omics data and image analysis of primary and recurrent GBM. In the pre-malignant setting, our in-silico results suggest that low ploidy cancer cells are more resistant to starvation-induced cell death. In the malignant setting, between first and second surgery, simulated tumors with different ploidy compositions progressed at different rates. Whether higher ploidy predicted fast recurrence, however, depended on the TME. Historical data supports this dependence on TME resources, as shown by a significant correlation between the median glucose uptake rates in human tissues and the median ploidy of cancer types that arise in the respective tissues (Spearman r = -0.70; P = 0.026). Taken together our findings suggest that availability of metabolic substrates in the TME drives different cell fate decisions for cancer cells with different ploidy and shapes GBM disease initiation and relapse characteristics.

Mathematical Modeling of Clonal Interference by Density-Dependent Selection in Heterogeneous Cancer Cell Lines

Many cancer cell lines are aneuploid and heterogeneous, with multiple karyotypes co-existing within the same cell line. Karyotype heterogeneity has been shown to manifest phenotypically, thus affecting how cells respond to drugs or to minor differences in culture media. Knowing how to interpret karyotype heterogeneity phenotypically would give insights into cellular phenotypes before they unfold temporally. Here, we re-analyzed single cell RNA (scRNA) and scDNA sequencing data from eight stomach cancer cell lines by placing gene expression programs into a phenotypic context. Using live cell imaging, we quantified differences in the growth rate and contact inhibition between the eight cell lines and used these differences to prioritize the transcriptomic biomarkers of the growth rate and carrying capacity. Using these biomarkers, we found significant differences in the predicted growth rate or carrying capacity between multiple karyotypes detected within the same cell line. We used these predictions to simulate how the clonal composition of a cell line would change depending on density conditions during in-vitro experiments. Once validated, these models can aid in the design of experiments that steer evolution with density-dependent selection.

Abstract 6549: Investigating the effects of density and frequency-dependent selection on subpopulations of cancer cells defined by copy number

Intratumoral heterogeneity is a major obstacle for many cancer therapies. Treatment modalities which target a particular phenotype select for cells with different phenotypes. For example, chemotherapy which targets fast-dividing cells may select for a tumor composed of slower-dividing cells which cannot be effectively targeted by the drug. We hypothesize that subpopulations (SPs) of cells defined by somatic copy number alterations (sCNAs) differ in how quickly they divide and how well they can compete at high population densities. Additionally, we expect that sCNA-defined SPs affect the fitness of one another through cooperative (e.g., exchange of growth factors) and competitive (resource depletion) interactions. To test these hypotheses and compare the relative effects of (i) density and (ii) frequency-dependent selection on tumor evolution, we have developed two mathematical models integrated with experimental and computational techniques. In both models, we evaluate the growth dynamics of cancer cell SPs defined by sCNAs detected in single cell RNA/DNA-sequencing data from 4 gastric cancer cell lines (HGC-27, KATOIII, NUGC-4, SNU-16). To investigate the effects of density dependent selection (i), we start by growing the cell lines in our lab in order to infer growth rate (r) and carrying capacity (K). Next, linear models are built correlating pathway expression levels with r/K values. We tested 50 KEGG pathways previously identified as differentially expressed between r and K-selected cells as transcriptomic biomarkers of growth parameters. The best fitting models are then used to infer SP-specific r/K values. For growth, we found r as a function of the KEGG pathway ‘RNA Polymerase’ (R2 = 0.9636, p-val=0.0019). For carrying capacity, we used ‘Pathways in Cancer’ (R2 = 0.7898, p-val=0.0629). In each cell line, an r/K tradeoff existed between at least one pair of SPs, suggesting sCNAs indeed have effect on r/K parameters. For frequency-dependent selection (ii), we use an inverse game theory algorithm which takes SP frequencies over time as input and outputs a parameterization for the replicator equation to recapitulate detected frequencies and predict future growth. The algorithm uses a penalized least squares method that takes the error to be the difference between replicator equation output and SP frequency input. SP growth over time can then be modeled with the replicator equation to characterize conditions for co-existence or dominance. These approaches reveal the dynamics of heterogeneous tumor growth, and make it possible to compare the relative influence of different selective pressures. We can examine how the growth of a tumor would change with the elimination of a given SP. This greater understanding can contribute to a better design of evolution-based therapies that avoid, or at least delay, the evolution of resistance to treatment.

Citation Format: Thomas A. Veith, Andrew Schultz, Noemi Andor, Saeed Alahmari. Investigating the effects of density and frequency-dependent selection on subpopulations of cancer cells defined by copy number. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6549.

Evaluating the genetic consequences of population subdivision as it unfolds and how to best mitigate them: A rare story about koalas

The genetic consequences of the subdivision of populations are regarded as significant to long-term evolution, and research has shown that the scale and speed at which this is now occurring is critically reducing the adaptive potential of most species which inhabit human-impacted landscapes. Here, we provide a rare and, to our knowledge, the first analysis of this process while it is happening and demonstrate a method of evaluating the effect of mitigation measures such as fauna crossings. We did this by using an extensive genetic data set collected from a koala population which was intensely monitored during the construction of linear transport infrastructure which resulted in the subdivision of their population. First, we found that both allelic richness and effective population size decreased through the process of population subdivision. Second, we predicted the extent to which genetic drift could impact genetic diversity over time and showed that after only 10 generations the resulting two subdivided populations could experience between 12% and 69% loss in genetic diversity. Lastly, using forward simulations we estimated that a minimum of eight koalas would need to disperse from each side of the subdivision per generation to maintain genetic connectivity close to zero but that 16 koalas would ensure that both genetic connectivity and diversity remained unchanged. These results have important consequences for the genetic management of species in human-impacted landscapes by showing which genetic metrics are best to identify immediate loss in genetic diversity and how to evaluate the effectiveness of any mitigation measures.

The EcpD Tip Adhesin of the Escherichia coli Common Pilus Mediates Binding of Enteropathogenic E. coli to Extracellular Matrix Proteins

The attachment of enteropathogenic Escherichia coli (EPEC) to intestinal epithelial cells is facilitated by several adhesins; however, the individual host-cell receptors for pili-mediated adherence have not been fully characterized. In this study, we evaluated the hypothesis that the E. coli common pilus (ECP) tip adhesin protein EcpD mediates attachment of EPEC to several extracellular matrix (ECM) glycoproteins (fibronectin, laminin, collagens I and IV, and mucin). We found that the ΔecpA mutant, which lacks production of the EcpA filament but retains EcpD on the surface, adhered to these glycoproteins below the wild-type levels, while the ΔecpD mutant, which does not display EcpA or EcpD, bound significantly less to these host glycoproteins. In agreement, a purified recombinant EcpD subunit bound significantly more than EcpA to laminin, fibronectin, collagens I and IV, and mucin in a dose-dependent manner. These are compelling data that strongly suggest that ECP-producing EPEC may bind to host ECM glycoproteins and mucins through the tip adhesin protein EcpD. This study highlights the versatility of EPEC to bind to different host proteins and suggests that the interaction of ECP with the host’s ECM glycoproteins may facilitate colonization of the intestinal mucosal epithelium.

Abstract A030: Characterizing cytotoxic therapy induced shifts in the cost-to-benefit ratio of high ploidy

Analyses of intra-tumor heterogeneity across multiple cancer types suggest that tumor cell fitness declines once aneuploidy exceeds a certain limit. A significant difference in outcome between tumors above and below the limit however is only evident among therapy-naïve patients, not among patients who subsequently underwent cytotoxic therapy. Our hypothesis is that the context-dependent ambivalence of high ploidy is what accounts for both of these observations. On one hand, high ploidy ameliorates the deleterious effects of missegregation-induced genome-dosage imbalances, on the other hand a high ploidy cell has higher energetic demands as it has to replicate and express more genetic material. We performed a series of in-vitro and in-silico experiments to quantify both, (i) the costs and (ii) benefits of high ploidy. We developed and used mathematical models to predict differences in S phase duration between high and low ploidy cells (i), and to evaluate the possibility of mis-segregation induced population extinction (ii). Model predictions include critical curves that separate viable from non-viable populations as a function of their turnover- and mis-segregation rates. Missegregation- and turnover rates estimated for nine cancer types are then compared to these predictions for various biological assumptions. For (i), we evaluated three key building blocks of dNTP synthesis –PO4, O2 and Glucose– as candidate cell-extrinsic resources that cap ploidy in Glioblastoma and stomach cancers. We predict that at limiting dNTP concentrations, high-ploidy cells will take longer to replicate their DNA than low-ploidy cells. In-vitro experiments support these predictions showing that PO4 depletion imposes a higher fitness cost on near-tetraploid than on near-diploid breast cancer cells. For (ii), the majority of tumors across all nine cancer types had missegregation- and turnover rates that were within viable regions of the parameter space. When a dependency of mis-segregation rate on ploidy was introduced, ploidy states associated with low mis-segregation rates rendered MIE impossible at low turnover rates. Exposing a heterogeneous stomach cancer cell line to the microtubule-targeting drug Vinblastine confirmed that the high ploidy subpopulation had a fitness advantage. If our hypothesis is true, the implications are broad. It would explain vast differences in the extent of inter-tumor karyotype heterogeneity. It may contribute to explain why agents that block dNTP production work well in combination with DNA damaging agents. It would also explain differences in ploidy across different primary and metastatic sites. As solid tumors progress, resources in the tumor microenvironment become scarcer than the resources available in normal surrounding tissues. These resource-poor environments may push high-ploidy cells to leave the primary tumor and thrive at locations with abundant nutrients. Understanding the resource cost of high ploidy can help uncover its therapeutic vulnerabilities across tissue sites with versatile energy supplies.

Citation Format: Noemi Andor, Ana Gomes, Gregory Kimmel, Andriy Marusyk, Richard Beck, Daria Miroshnychenko, Andrew Schultz, Samuel Bakhoum, Philipp Altrock, Thomas Veith. Characterizing cytotoxic therapy induced shifts in the cost-to-benefit ratio of high ploidy [abstract]. In: Proceedings of the AACR Special Conference on the Evolutionary Dynamics in Carcinogenesis and Response to Therapy; 2022 Mar 14-17. Philadelphia (PA): AACR; Cancer Res 2022;82(10 Suppl):Abstract nr A030.

Abstract A014: Models of neighbors and space: frequency and density dependent dynamics of tumor evolution

Mutations matter in cancer. Loss of function in a gene such as tp53 is advantageous for tumor progression. However, we also know that cells can share similar mutational burdens but exhibit starkly different phenotypes. The heterogeneous nature of cancer cell populations that comprise a tumor compounds this problem, and is a known source of treatment failure. We hypothesize that density conditions in the tumor microenvironment select for particular cellular phenotypes. Additionally, we posit that a cell’s neighbor can affect its phenotypes through interactions such as the exchange of growth factors or competition for resources – a phenomenon known as frequency-dependent selection. To test these hypotheses and compare the relative effects of density and frequency dependent selection on tumor evolution, we have developed two mathematical models integrated with experimental and computational techniques. In both models, we investigate the growth dynamics of subclonal populations defined by somatic copy number alterations detected by single cell RNA/DNA-sequencing data in 5 gastric cancer cell lines. For density dependence, we have identified transcriptomic biomarkers of growth rate (r) and carrying capacity (K). These r/K biomarkers are used to parameterize logistic, power-law, and Gompertzian models to evaluate which best captures the observed growth. In the case of frequency dependent selection, we have deployed an inverse game theory algorithm which takes the subclonal frequencies and finds parameterizations for the replicator equation which can recapitulate the detected frequencies. The algorithm uses a penalized least squares method that takes the error in parameterization to be the difference between replicator equation output and detected subclonal frequencies. For density dependence, we tested 25 KEGG pathways as transcriptomic biomarkers of cell line growth parameters. Of these, ‘Pathways in cancer’ fit best for growth rate (R2 = 0.9965) and ‘p53 signaling pathway’ fit best for carrying capacity (R2 = 0.9701). In 4 out of 5 cells lines, all 3 growth models that were tested fit the data well (R2 ≥ 0.93), with logistic being the best fit or tied for best fit. In each cell line, an r/K tradeoff existed between at least 2 subclones, suggesting density conditions will indeed select for certain subclones. In the case of frequency dependence, we found the best fit parameterizations for the replicator equation indicate competition is less intense between different subclones than when a subclone competes with itself. This suggests a cell’s neighbor will have an effect on its growth. Taken together, these approaches reveal the dynamics of heterogeneous tumor growth, and make it possible to compare the relative influence of different types of evolutionarily selective pressures. For example, we can examine how the growth of a tumor would change with the elimination of one subclone. This greater understanding can contribute to a better design of evolution-based therapies that avoid, or at least delay, the evolution of resistance to treatment.

Citation Format: Thomas Veith, Andrew Schultz, Saeed Alahmari, Noemi Andor. Models of neighbors and space: frequency and density dependent dynamics of tumor evolution [abstract]. In: Proceedings of the AACR Special Conference on the Evolutionary Dynamics in Carcinogenesis and Response to Therapy; 2022 Mar 14-17. Philadelphia (PA): AACR; Cancer Res 2022;82(10 Suppl):Abstract nr A014.

Coupling the immunomodulatory properties of the HDAC6 inhibitor ACY241 with Oxaliplatin promotes robust anti-tumor response in Non-small cell lung cancer

Although immunotherapy provides durable therapeutic response in a subset of Non-small cell lung cancer (NSCLC) patients, there is still a need for broadly applicable therapeutic strategies. HDAC inhibitors are a promising class of drugs whose immunomodulatory properties are now being appreciated. In the present study, we evaluated the immunomodulatory properties of the HDAC6 inhibitor, Citarinostat (ACY241) on lung tumor immune compartment and its therapeutic potential in combination with Oxaliplatin. Lung adenocarcinoma-bearing mice were treated with ACY241 or vehicle after which immune profiling and RNA-sequencing were conducted in tumor-associated T cells and macrophages. Ex vivo T cell functional studies, tumor growth assessment and survival of tumor-bearing mice treated with ACY241 and/or Oxaliplatin were also conducted. ACY241 treatment promoted increased presence of T and NK cells as well as activation, proliferation, and effector profile of T cells in the lung tumors of treated mice. Furthermore, tumor-associated macrophages exhibited increased expression of MHC and co-stimulatory molecules while expression of inhibitory ligands were reduced. RNA-sequencing of tumor-associated T cells and macrophages revealed significant genomic changes that is consistent with ACY241-mediated enhancement of immune priming. Finally, ACY241 treatment led to significantly enhanced tumor-associated T cell effector functionality in lung cancer-bearing mice and in patient-derived tumors when combined with the chemotherapy drug Oxaliplatin. Collectively, our studies support ACY241 as a promising HDAC6 inhibitor which coupled with Oxaliplatin promotes robust therapeutic outcomes in a pre-clinical model of NSCLC.

Coupling the immunomodulatory properties of the HDAC6 inhibitor ACY241 with Oxaliplatin promotes robust anti-tumor response in non-small cell lung cancer

While HDAC inhibitors have shown promise in hematologic cancers, their efficacy remains limited in solid cancers. In the present study, we evaluated the immunomodulatory properties of the HDAC6 inhibitor, Citarinostat (ACY241) on lung tumor immune compartment and its therapeutic potential in combination with Oxaliplatin. As a single agent, ACY241 treatment promoted increased infiltration, activation, proliferation, and effector function of T cells in the tumors of lung adenocarcinoma-bearing mice. Furthermore, tumor-associated macrophages exhibited downregulated expression of inhibitory ligands in favor of increased MHC and co-stimulatory molecules in addition to higher expression of CCL4 that favored increased T cell numbers in the tumors. RNA-sequencing of tumor-associated T cells and macrophages after ACY241 treatment revealed significant genomic changes that is consistent with improved T cell viability, reduced inhibitory molecular signature, and enhancement of macrophage capacity for improved T cell priming. Finally, coupling these ACY241-mediated effects with the chemotherapy drug Oxaliplatin led to significantly enhanced tumor-associated T cell effector functionality in lung cancer-bearing mice and in patient-derived tumors. Collectively, our studies highlight the molecular underpinnings of the expansive immunomodulatory activity of ACY241 and supports its suitability as a partner agent in combination with rationally selected chemotherapy agents for therapeutic intervention in NSCLC.

SARS-CoV-2 prevalence and immunity: a hospital-based study from Malawi

Background

COVID-19 transmission and disease dynamics in sub-Saharan Africa are not well understood. Our study aims to provide insight into COVID-19 epidemiology in Malawi by estimating SARS-CoV-2 prevalence and immunity after SARS-CoV-2 infection in a hospital-based setting.

Methods

We conducted a hospital-based, convenience sampling, cross-sectional survey for SARS-CoV-2 in Lilongwe, Malawi. Participants answered a questionnaire and were tested for SARS-CoV-2 by enzyme-linked immunosorbent assay and real-time reverse-transcription polymerase chain reaction (RT-PCR). A surrogate virus neutralization test (sVNT) was performed in seropositive samples to estimate immunity. Poisson regression was used to assess SARS-CoV-2 point prevalence association with demographic and behavioral variables.

Findings

The study included 930 participants. We found a combined point prevalence of 10.1%. Separately analyzed, RT-PCR positivity was 2.0%, and seropositivity was 9.3%. Of tested seropositive samples, 90.1% were sVNT positive. We found a high rate (45.7%) of asymptomatic SARS-CoV-2 infection. SARS-CoV-2 point prevalence was significantly associated with being a healthcare worker.

Interpretation

Our study suggests that official data underestimate COVID-19 transmission. Using sVNTs to estimate immunity in Malawi is feasible and revealed considerable post-infection immunity in our cohort. Subclinical infection and transmission are probably a game-changer in surveillance, mitigation and vaccination strategies.

RASAL2 Confers Collateral MEK/EGFR Dependency in Chemoresistant Triple-Negative Breast Cancer

PURPOSE

While chemotherapy remains the standard treatment for triple-negative breast cancer (TNBC), identifying and managing chemoresistant tumors has proven elusive. We sought to discover hallmarks and therapeutically actionable features of refractory TNBC through molecular analysis of primary chemoresistant TNBC specimens.

EXPERIMENTAL DESIGN

We performed transcriptional profiling of tumors from a phase II clinical trial of platinum chemotherapy for advanced TNBC (TBCRC-009), revealing a gene expression signature that identified de novo chemorefractory tumors. We then employed pharmacogenomic data mining, proteomic and other molecular studies to define the therapeutic vulnerabilities of these tumors.

RESULTS

We reveal the RAS-GTPase-activating protein (RAS-GAP) RASAL2 as an upregulated factor that mediates chemotherapy resistance but also an exquisite collateral sensitivity to combination MAP kinase kinase (MEK1/2) and EGFR inhibitors in TNBC. Mechanistically, RASAL2 GAP activity is required to confer kinase inhibitor sensitivity, as RASAL2-high TNBCs sustain basal RAS activity through suppression of negative feedback regulators SPRY1/2, together with EGFR upregulation. Consequently, RASAL2 expression results in failed feedback compensation upon co-inhibition of MEK1/2 and EGFR that induces synergistic apoptosis in vitro and in vivo. In patients with TNBC, high RASAL2 levels predict clinical chemotherapy response and long-term outcomes, and are associated via direct transcriptional regulation with activated oncogenic Yes-Associated Protein (YAP). Accordingly, chemorefractory patient-derived TNBC models exhibit YAP activation, high RASAL2 expression, and tumor regression in response to MEK/EGFR inhibitor combinations despite well-tolerated intermittent dosing.

CONCLUSIONS

These findings identify RASAL2 as a mediator of TNBC chemoresistance that rewires MAPK feedback and cross-talk to confer profound collateral sensitivity to combination MEK1/2 and EGFR inhibitors.

Abstract PR18: The immune landscape of prostate cancer in African-American patients is skewed towards inhibitory signatures relative to Caucasian-American patients

Prostate Cancer is a leading cause of cancer-related deaths among men in the United States. Within the general population, African-Americans who constitute a minority group suffer a higher burden of the disease compared to other racial groups. Given that immune cells recruited to the tumor micro-environment shape tumor behavior, an outstanding issue is whether the immunological landscape of prostate cancer in African-American patients is a contributory factor to disease disparity seen in this minority patient population. In this regard, the present study sought to investigate whether prostate cancer in African-American men harbor distinctive immunological features compared to their Caucasian counterparts. Fresh prostate cancer specimens were obtained from consented African-American and Caucasian patients after prostatectomy. Gleason scores were comparable between the two demographics with an average score of 7 for African-American patients and 7.5 for Caucasian patients. We analyzed both tumor and matched peripheral blood mononuclear cells from each patient using comprehensive, multi-parameter flow cytometry. We found that both CD4+ and CD8+ T cells in African-American prostate cancer displayed upregulated expression of a number of inhibitory proteins that restrain T cell response. These cells also expressed reduced levels of co-stimulatory receptors and a less activated phenotype compared to equivalent cells in the tumors of Caucasian patients. Furthermore, analysis of serum from patients in each demographic revealed an enrichment of cytokines skewed towards immunosuppressive profile which may support reduced immune cell function against tumor-associated antigens. These findings suggest that the immunological profile of prostate cancer in African-American men harbors intrinsic signatures that may contribute to muting of potential anti-tumor responses in this patient demographic, enabling tumor immune evasion to support aggressive tumor growth and progression. Collectively, our data is in support of the contributory role of immunological factors to disease behavior and associated disparity in African-American prostate cancer patients.

Citation Format: Andrew Schultz, David Noyes, Arup Bag, Dennis Adeegbe. The immune landscape of prostate cancer in African-American patients is skewed towards inhibitory signatures relative to Caucasian-American patients [abstract]. In: Proceedings of the AACR Virtual Conference: Thirteenth AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2020 Oct 2-4. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2020;29(12 Suppl):Abstract nr PR18.

Dissecting the Financial Relationship Between Industry and Academic Neurosurgery

BACKGROUND

Established by the Centers for Medicare and Medicaid Services (CMS), the Open Payments Database (OPD) has reported industry payments to physicians since August 2013.

OBJECTIVE

To evaluate the frequency, type, and value of payments received by academic neurosurgeons in the United States over a 5-yr period (2014-2018).

METHODS

The OPD was queried for attending neurosurgeons from all neurosurgical training programs in the United States (n = 116). Information from the OPD was analyzed for the entire cohort as well as for comparative subgroup analyses, such as career stage, subspecialty, and geographic location.

RESULTS

Of all identified neurosurgeons, 1509 (95.0%) received some payment from industry between 2014 and 2018 for a total of 106 171 payments totaling $266 407 458.33. A bimodal distribution was observed for payment number and total value: 0 to 9 (n = 438) vs > 50 (n = 563) and 0-$1000 (n = 418) vs >$10 000 (n = 653), respectively. Royalty/License was the most common type of payment overall (59.6%; $158 723 550.57). The median number (40) and value ($8958.95) of payments were highest for mid-career surgeons. The South-Central region received the most money ($117 970 036.39) while New England received the greatest number of payments (29 423). Spine surgeons had the greatest median number (60) and dollar value ($20 551.27) of payments, while pediatric neurosurgeons received the least (8; $1108.29). Male neurosurgeons received a greater number (31) and value ($6395.80) of payments than their female counterparts (11, $1643.72).

CONCLUSION

From 2014 to 2018, payments to academic neurosurgeons have increased in number and value. Dollars received were dependent on geography, career stage, subspecialty and gender.

A pilot study of the performance of captive-reared delta smelt Hypomesus transpacificus in a semi-natural environment

A captive breeding programme was developed in 2008 for delta smelt Hypomesus transpacificus in reaction to dramatic population decline over several decades. We took 526 sub-adult captive-reared delta smelt and cultured them for 200 days without providing artificial food or water quality management to assess their performance once released in the wild. The results indicated captive-reared sub-adult delta smelt could survive in a semi-natural environment with uncontrolled water quality and naturally produced wild prey through spawning and into their post spawning phase.

Evaluation of VIDAS Listeria monocytogenes II (LMO2) Immunoassay Method for the Detection of Listeria monocytogenes in Foods: Collaborative Study

A multilaboratory study was conducted to compare the VIDAS®Listeria monocytogenes II (LMO2) immunoassay and the standard cultural methods for the detection of Listeria monocytogenes in foods. Five food types—vanilla ice cream, brie cheese, cooked roast beef, frozen green beans, and frozen tilapia fish—at 3 levels were analyzed by each method. A total of 26 laboratories representing government and industry participated. In this study, 1404 test portions were analyzed of which 1152 were used in the statistical analysis. There were 448 positive by the VIDAS LMO2 assay and 457 positive by the standard culture methods. A χ2 analysis of each of the 5 food types, at the 3 inoculation levels tested, was performed. The resulting χ2 value, 0.36, indicates that overall, there are no statistical differences between the VIDAS LMO2 assay and the standard methods at the 5% level of significance.

Evaluation of the VIDAS® Listeria (LIS) Immunoassay for the Detection of Listeria in Foods Using Demi-Fraser and Fraser Enrichment Broths, as Modification of AOAC Official Method 999.06 (AOAC Official Method 2004.06)

A multilaboratory study was conducted to compare the VIDAS® LIS immunoassay with the standard cultural methods for the detection of Listeria in foods using an enrichment modification of AOAC Official Method 999.06. The modified enrichment protocol was implemented to harmonize the VIDAS LIS assay with the VIDAS LMO2 assay. Five food types—brie cheese, vanilla ice cream, frozen green beans, frozen raw tilapia fish, and cooked roast beef—at 3 inoculation levels, were analyzed by each method. A total of 15 laboratories representing government and industry participated. In this study, 1206 test portions were tested, of which 1170 were used in the statistical analysis. There were 433 positive by the VIDAS LIS assay and 396 positive by the standard culture methods. A Chi-square analysis of each of the 5 food types, at the 3 inoculation levels tested, was performed. The resulting average Chi square analysis, 0.42, indicated that, overall, there are no statistical differences between the VIDAS LIS assay and the standard methods at the 5% level of significance.

Evaluation of the BAX® System for Detection of Listeria monocytogenes in Foods: Collaborative Study

A multilaboratory study was conducted to compare the automated BAX® system and the standard cultural methods for detection of Listeria monocytogenes in foods. Six food types (frankfurters, soft cheese, smoked salmon, raw, ground beef, fresh radishes, and frozen peas) were analyzed by each method. For each food type, 3 inoculation levels were tested: high (average of 2 CFU/g), low (average of 0.2 CFU/g) and uninoculated controls. A total of 25 laboratories representing government and industry participated. Of the 2335 samples analyzed, 1109 were positive by the BAX system and 1115 were positive by the standard method. A Chi square analysis of each of the 6 food types, at the 3 inoculation levels tested, was performed. For all foods, except radishes, the BAX system performed as well as or better than the standard reference methods based on the Chi square results.

Evaluation of VIDAS® Immuno-Concentration Salmonella/VIDAS Salmonella Immunoassay Method for Detection of Salmonella in Selected Foods: Collaborative Study

The VIDAS Immuno-concentration Salmonella (ICS)/VIDAS Salmonella (SLM) immunoassay method for the detection of Salmonella was compared to the Bacteriological Analytical Manual (BAM)/AOAC culture method in a collaborative study. Thirty-two laboratories participated in the evaluation. Each laboratory tested one or more of the 6 test products: milk chocolate, nonfat dry milk, dried whole egg, soy flour, ground black pepper, and ground raw turkey. The 2 methods were in agreement for 1266 of the 1440 samples. Of the 174 samples not in agreement, 69 were VIDAS ICS/SLM-positive and BAM/AOAC-negative and 105 were VIDAS ICS/SLM-negative and BAM/AOAC-positive.

Evaluation of VIDAS® Immuno-Concentration Salmonella Assay Plus Selective Plate Method (Hektoen Enteric, Bismuth Sulfite, Salmonella Identification) for Detection of Salmonella in Selected Foods: Collaborative Study

The VIDAS Immuno-concentration Salmonella (ICS) plus selective plate method (Hektoen enteric, bismuth sulfite, Salmonella identification) method for the detection of Salmonella was compared to the Bacteriological Analytical Manual (BAM)/AOAC culture method in a collaborative study. Thirty-two laboratories participated in the evaluation. Each laboratory tested one or more of the 6 test products: milk chocolate, nonfat dry milk, dried whole egg, soy flour, ground black pepper, and ground raw turkey. The 2 methods were in agreement for 1283 of the 1440 test samples. Of the 157 test samples not in agreement, 82 were VIDAS ICS plus selective plate-positive and BAM/AOAC-negative, and 75 were VIDAS ICS plus selective plate-negative and BAM/AOAC-positive.

Salmonella in Selected Foods by VIDAS® Immuno-Concentration Salmonella Plus Selective Plate Method (Hektoen Enteric, Xylose Lysine Desoxycholate, Bismuth Sulfite): Collaborative Study

The VIDAS Immuno-concentration Salmonella (ICS) plus selective plate method (Hektoen enteric, xylose lysine desoxycholate, bismuth sulfite) method for the detection of Salmonella was compared to the Bacteriological Analytical Manual (BAM)/AOAC culture method in a collaborative study. Thirty-two laboratories participated in the evaluation. Each laboratory tested one or more of the 6 test products: milk chocolate, nonfat dry milk, dried whole egg, soy flour, ground black pepper, and ground raw turkey. The 2 methods were in agreement for 1297 of the 1455 samples. Of the 158 samples not in agreement, 82 were VIDAS ICS plus selective plate-positive and BAM/AOAC-negative, and 76 were VIDAS ICS plus selective plate-negative and BAM/AOAC-positive.

VIDAS® Enzyme-Linked Immunofluorescent Assay for Detection of Listeria in Foods: Collaborative Study

The VIDAS LIS method and the traditional culture methods for detection of Listeria species in food were evaluated in a multilaboratory comparative study. The 6 foods tested were either naturally contaminated or inoculated with 3 different concentrations of Listeria. Results for each food and each contamination level with the VIDAS LIS method were as good as or better than those obtained with the traditional culture method. Of 1558 samples tested, 935 were positive: 839 by the VIDAS method and 809 by standard culture methods. Overall false negative rates were 10.3 and 13.5% for the VIDAS LIS and culture methods, respectively. The false positive rate for the VIDAS LIS assay was 1.4% based on 9 VIDAS LIS positive assays that did not confirm positive by isolation of Listeria. The agreement between the VIDAS LIS and culture methods for all samples tested was 86%.

An introduction to clinical trial design

Clinicians and other decision makers in healthcare use results from clinical trials to inform practice. Interpretation of clinical trial results can be challenging, as weaknesses in trial design, data collection, analysis or reporting, can compromise the usefulness of results. A good working knowledge of clinical trial design is essential to expertly interpret and determine the validity and generalizability of the results. This manuscript will give a brief overview of clinical trial design including the strengths and limitations of various approaches. The focus will be on confirmatory clinical trials.

Postgraduate publishing output in pediatric neurosurgery: correlation with fellowship site and individual scholars

OBJECTIVE

The objective of this study was to analyze the publication output of postgraduate pediatric neurosurgery fellows for a 10-year period as well as identify 25 individual highly productive pediatric neurosurgeons. The correlation between academic productivity and the site of fellowship training was studied.

METHODS

Programs certified by the Accreditation Council for Pediatric Neurosurgery Fellowships that had 5 or more graduating fellows from 2006 to 2015 were included for analysis. Fellows were queried using Scopus for publications during those 10 years with citation data through 2017. Pearson correlation coefficients were calculated, comparing program rankings of faculty against fellows using the revised Hirsch index (r-index; primary) and Hirsch index (h-index; secondary). A list of 25 highly accomplished individual academicians and their fellowship training locations was compiled.

RESULTS

Sixteen programs qualified with 152 fellows from 2006 to 2015; 136 of these surgeons published a total of 2009 articles with 23,735 citations. Most publications were pediatric-specific (66.7%) clinical articles (93.1%), with middle authorship (55%). Co-investigators were more likely from residency than fellowship. There was a clustering of the top 7 programs each having total publications of around 120 or greater, publications per fellow greater than 12, more than 1200 citations, and adjusted ir10 (revised 10-year institutional h-index) and ih10 (10-year institutional h-index) values of approximately 2 or higher. Correlating faculty and fellowship program rankings yielded correlation coefficients ranging from 0.53 to 0.80. Fifteen individuals (60%) in the top 25 (by r5 index) list completed their fellowship at 1 of these 7 institutions.

CONCLUSIONS

Approximately 90% of fellowship-trained pediatric neurosurgeons have 1 or more publications, but the spectrum of output is broad. There is a strong correlation between where surgeons complete their fellowships and postgraduate publications.

How Does the Media Portray Neurosurgeons?

BACKGROUND

It is not unusual to find neurosurgeons in the news and entertainment. The present study examined the portrayal of neurosurgeons by major print and online media sources.

METHODS

Two search strategies identified articles from October 1, 2012 to October 1, 2017 containing the keyword "neurosurgeon." The top 25 newspapers in the United States, determined by their circulation, were searched using the LexisNexis Academic or NewsBank databases; a layman's Google News search was used to collect online stories. Each identified article was evaluated to confirm the relevance and then examined for content. Relevant characteristics for each article and neurosurgeon were determined and analyzed.

RESULTS

Our searches returned 1005 articles comprising 561 unique stories about 203 different neurosurgeons. One particular neurosurgeon had 459 reports (45.7%). More articles were reported in 2015 (405; 40.3%) than any other single year. Most articles featured male neurosurgeons (879; 87.1%) and neurosurgeons who had been practicing for >20 years (636; 63.0%), with just 10 institutions accounting for the training of most of them (733; 72.6%). The articles were classified as positive (270; 26.9%), negative (356; 35.4%), or neutral (379; 37.7%) in terms of their reflection on the field of neurosurgery. The odds of a negative story were greater for male neurosurgeons, within 10 years of residency completion, and in a nonacademic position.

CONCLUSIONS

Neurosurgeons are naturally subject to media coverage, and we must be cognizant that this predilection can serve as both an occupational advantage and an occupational hazard.

The Differential Anti-HIV Effect of a New Humic Substance-Derived Preparation in Diverse Cells of the Immune System

The anti-HIV activity of a new humic substance-derived preparation has been studied in individual pools of immune cells (CD4+ T lymphocytes, macrophages, dendritic cells). Near-complete inhibition of the HIV infection (by more than 90%) was achieved by treating each of the abovementioned cell types with non-toxic concentrations of the preparation. The inhibitory effect demonstrates the possibility of preventing the depletion of a significant portion of functionally important immune cells. A comparative study of infection inhibition in individual cell pools has allowed us to reveal the differences in the preparation's effectiveness in each of the cell populations. A R5-tropic HIV-1 infection in macrophages exhibited maximum sensitivity to the preparation: 90% and 50% inhibition of the infection were observed in the presence of concentrations as low as 1.4 and 0.35 μg/ml, respectively. A 15- and 19-fold higher concentration was required to achieve the same extent of inhibition in dendritic cells infected with the same strain. The effectiveness of the drug in CD4 + T lymphocytes is quite comparable to its effectiveness in macrophages. The drug is universally effective for both the T- and M-tropic variants of HIV-1.

Testing the Gaussianity of the Human EEG During Anesthesia

The Gaussian properties of human EEGs, which were measured over various stages of general anesthesia, were tested. The basis of the method was to describe the EEG signals by autoregressive models and to test the normality of the regression residuals with the Shapiro-Wilk statistic. The results show that in general the human EEG during anesthesia can be considered as a realization of a Gaussian stochastic process.

Application of Adjusted Survival Curves to Renal Transplant Data

An important means in the analysis of survival time data is the estimation and graphical representation of survival probabilities. In this paper unifactorial parametric and non-parametric survival curve estimators and two types of adjusted survival curves based on a parametric multifactorial approach are applied to renal transplant data. It is shown that the resulting survival curves can differ substantially. The unifactorial survival curves yield biased results in case of serious disequilibrium in the data. This drawback of the unifactorial methods has been overcome by the use of adjusted survival curves which take possible distortions in the data set into account. The benefits of adjusted survival curves in assessing potentially prognostic factors are elucidated by the application to data from renal transplantation.

Expressed Gene Fusions as Frequent Drivers of Poor Outcomes in Hormone Receptor-Positive Breast Cancer

We sought to uncover genetic drivers of hormone receptor-positive (HR⁺) breast cancer, using a targeted next-generation sequencing approach for detecting expressed gene rearrangements without prior knowledge of the fusion partners. We identified intergenic fusions involving driver genes, including PIK3CA, AKT3, RAF1, and ESR1, in 14% (24/173) of unselected patients with advanced HR⁺ breast cancer. FISH confirmed the corresponding chromosomal rearrangements in both primary and metastatic tumors. Expression of novel kinase fusions in nontransformed cells deregulates phosphoprotein signaling, cell proliferation, and survival in three-dimensional culture, whereas expression in HR⁺ breast cancer models modulates estrogen-dependent growth and confers hormonal therapy resistance in vitro and in vivo Strikingly, shorter overall survival was observed in patients with rearrangement-positive versus rearrangement-negative tumors. Correspondingly, fusions were uncommon (<5%) among 300 patients presenting with primary HR⁺ breast cancer. Collectively, our findings identify expressed gene fusions as frequent and potentially actionable drivers in HR⁺ breast cancer.Significance: By using a powerful clinical molecular diagnostic assay, we identified expressed intergenic fusions as frequent contributors to treatment resistance and poor survival in advanced HR⁺ breast cancer. The prevalence and biological and prognostic significance of these alterations suggests that their detection may alter clinical management and bring to light new therapeutic opportunities. Cancer Discov; 8(3); 336-53. ©2017 AACR.See related commentary by Natrajan et al., p. 272See related article by Liu et al., p. 354This article is highlighted in the In This Issue feature, p. 253.

Current options in aerosolised drug therapy for children receiving respiratory support

Inhalation of aerosolised medications are the mainstay of treatment for a number of chronic lung diseases and have several advantages over systemically-administered medications. These include more rapid onset of action for drugs such as β-adrenergic agonists when compared with oral medication, high luminal doses for inhaled antibiotics when used to treat endobronchial infection, and an improved therapeutic index compared with systemic delivery for these and other classes of drugs such as corticosteroids. The use of aerosolised drugs to treat patients whose tracheas are intubated is less well established, in part because systemic delivery via the intravenous route can be a simpler alternative for many drugs. Consequently, research in this area is largely limited to a number of in vitro studies and very few clinical trials. Unfortunately, a lack of focus in this area has resulted in a number of practices which at best are ineffective, and at worst dangerous for the patient. Although there have been some attempts to re-invigorate research in order to improve delivery systems, current devices are, to a great extent, based on long-standing technology developed more than 50 years ago. In this review, we explore current knowledge and provide guidance as to when and how the inhaled route may be of value when treating patients whose tracheas are intubated, and we set out the challenges facing those attempting to advance the topic. We conclude by reviewing current areas of interest that may lead to more effective and widespread use of aerosols in the treatment of intubated patients.

IDENTIFYING CANCER SPECIFIC METABOLIC SIGNATURES USING CONSTRAINT-BASED MODELS

Cancer metabolism differs remarkably from the metabolism of healthy surrounding tissues, and it is extremely heterogeneous across cancer types. While these metabolic differences provide promising avenues for cancer treatments, much work remains to be done in understanding how metabolism is rewired in malignant tissues. To that end, constraint-based models provide a powerful computational tool for the study of metabolism at the genome scale. To generate meaningful predictions, however, these generalized human models must first be tailored for specific cell or tissue sub-types. Here we first present two improved algorithms for (1) the generation of these context-specific metabolic models based on omics data, and (2) Monte-Carlo sampling of the metabolic model ux space. By applying these methods to generate and analyze context-specific metabolic models of diverse solid cancer cell line data, and primary leukemia pediatric patient biopsies, we demonstrate how the methodology presented in this study can generate insights into the rewiring differences across solid tumors and blood cancers.

Hypoxia-induced metabolic stress in retinal pigment epithelial cells is sufficient to induce photoreceptor degeneration

Photoreceptors are the most numerous and metabolically demanding cells in the retina. Their primary nutrient source is the choriocapillaris, and both the choriocapillaris and photoreceptors require trophic and functional support from retinal pigment epithelium (RPE) cells. Defects in RPE, photoreceptors, and the choriocapillaris are characteristic of age-related macular degeneration (AMD), a common vision-threatening disease. RPE dysfunction or death is a primary event in AMD, but the combination(s) of cellular stresses that affect the function and survival of RPE are incompletely understood. Here, using mouse models in which hypoxia can be genetically triggered in RPE, we show that hypoxia-induced metabolic stress alone leads to photoreceptor atrophy. Glucose and lipid metabolism are radically altered in hypoxic RPE cells; these changes impact nutrient availability for the sensory retina and promote progressive photoreceptor degeneration. Understanding the molecular pathways that control these responses may provide important clues about AMD pathogenesis and inform future therapies.

DOI:http://dx.doi.org/10.7554/eLife.14319.001

Cells use a sugar called glucose as fuel to provide energy for many essential processes. The light-sensing cells in the eye, known as photoreceptors, need tremendous amounts of glucose, which they receive from the blood with the help of neighboring cells called retinal pigment epithelium (RPE) cells. Without a reliable supply of this sugar, the photoreceptors die and vision is lost.

As we age, we are at greater risk of vision loss because RPE cells become less efficient at transporting glucose and our blood vessels shrink so that the photoreceptors may become starved of glucose. To prevent age-related vision loss, we need new strategies to keep blood vessels and RPE cells healthy. However, it was not clear exactly how RPE cells supply photoreceptors with glucose, and what happens when blood supplies are reduced.

To address this question, Kurihara, Westenskow et al. used genetically modified mice to investigate how cells in the eye respond to starvation. The experiments show that when nutrients are scarce the RPE cells essentially panic, radically change their diet, and become greedy. That is to say that they double in size and begin burning fuel faster while also stockpiling extra sugar and fat for later use. In turn, the photoreceptors don’t get the energy they need and so they slowly stop working and die.

Kurihara, Westenskow et al. also show that there is a rapid change in the way in which sugar and fat are processed in the eye during starvation. Learning how to prevent these changes in patients with age-related vision loss could protect their photoreceptors from starvation and death. The next step following on from this research is to design drugs to improve the supply of glucose and nutrients to the photoreceptors by repairing aging blood vessels and/or preventing RPE cells from stockpiling glucose for themselves.

DOI:http://dx.doi.org/10.7554/eLife.14319.002

The effect of mild and moderate renal impairment on the pharmacokinetics of pridopidine, a new drug for Huntington's disease

Aim

Pridopidine, a new oral drug for treatment of patients with motor symptoms associated with Huntington's Disease (HD) is currently under development. In steady‐state conditions, pridopidine elimination is mediated primarily through renal excretion. This study evaluated single dose and steady‐state pharmacokinetics (PK) of a daily dose of pridopidine in subjects with mild and moderate renal impairment and matched healthy subjects.

Methods

Subjects with mild renal impairment (n = 12), moderate impairment (n = 12), or their matched healthy controls (n = 25) participated in this study. Subjects received a single dose of pridopidine (45 mg) on day 1 and a multiple dose cycle of 45 mg once daily on days 5–18. Blood and urine samples were collected on days 1 and 18 for PK analysis.

Results

Mild renal impairment did not affect the PK of pridopidine whilst an increase in exposure was seen in subjects with moderate renal impairment. Subjects with moderate impairment showed reduced plasma clearance (by 44%) and had 68% higher AUC (90% CI 1.22, 2.30) and 26% higher C_max (90% CI 1.02, 1.56) values than those with normal renal function at steady‐state. Pridopidine was safe and well tolerated in healthy subjects and in subjects with mild and moderate renal impairment.

Conclusions

Mild renal impairment has no impact on exposure to pridopidine while moderately impaired renal function resulted in higher pridopidine concentrations.