Cancer testis antigen burden (CTAB): a novel biomarker of tumor-associated antigens in lung cancer.

BACKGROUND: Cancer-testis antigens (CTAs) are tumor antigens that are normally expressed in the testes but are aberrantly expressed in several cancers. CTA overexpression drives the metastasis and progression of lung cancer, and is associated with poor prognosis. To improve lung cancer diagnosis, prognostic prediction, and drug discovery, robust CTA identification and quantitation is needed. In this study, we examined and quantified the co-expression of CTAs in lung cancer to derive cancer testis antigen burden (CTAB), a novel biomarker of immunotherapy response. METHODS: Formalin fixed paraffin embedded (FFPE) tumor samples in discovery cohort (n = 5250) and immunotherapy and combination therapy treated non-small cell lung cancer (NSCLC) retrospective (n = 250) cohorts were tested by comprehensive genomic and immune profiling (CGIP), including tumor mutational burden (TMB) and the mRNA expression of 17 CTAs. PD-L1 expression was evaluated by IHC. CTA expression was summed to derive the CTAB score. The median CTAB score for the discovery cohort of 170 was applied to the retrospective cohort as cutoff for CTAB "high" and "low". Biomarker and gene expression correlation was measured by Spearman correlation. Kaplan-Meier survival analyses were used to detect overall survival (OS) differences, and objective response rate (ORR) based on RECIST criteria was compared using Fisher's exact test. RESULTS: The CTAs were highly co-expressed (p < 0.05) in the discovery cohort. There was no correlation between CTAB and PD-L1 expression (R = 0.011, p = 0.45) but some correlation with TMB (R = 0.11, p = 9.2 × 10-14). Kaplan-Meier survival analysis of the immunotherapy-treated NSCLC cohort revealed better OS for the pembrolizumab monotherapy treated patients with high CTAB (p = 0.027). The combination group demonstrated improved OS compared to pembrolizumab monotherapy group (p = 0.04). The pembrolizumab monotherapy patients with high CTAB had a greater ORR than the combination therapy group (p = 0.02). CONCLUSIONS: CTA co-expression can be reliably measured using CGIP in solid tumors. As a biomarker, CTAB appears to be independent from PD-L1 expression, suggesting that CTAB represents aspects of tumor immunogenicity not measured by current standard of care testing. Improved OS and ORR for high CTAB NSCLC patients treated with pembrolizumab monotherapy suggests a unique underlying aspect of immune response to these tumor antigens that needs further investigation.

Tumor Inflammation, Obesity, and Proliferative Status as Biomarkers in Gastroesophageal Adenocarcinoma.

Recent epidemiological studies have shown that obesity, typically measured by increased body mass index (BMI), is associated with an increased risk of gastroesophageal adenocarcinoma (GEAC), but the contributing molecular and immune mechanisms remain unknown. Since obesity is known to promote chronic inflammation, we hypothesized that obesity leads to inflammation-related immune dysfunction, which can be reversed by immune-modulating therapy. To test our hypothesis, we examined the clinical and molecular data from advanced GEAC patients. To this end, 46 GEAC tumors were evaluated for biomarkers representing tumor inflammation, cell proliferation, and PD-L1 expression. A CoxPH regression model with potential co-variates, followed by pairwise post hoc analysis, revealed that inflammation in the GEAC tumor microenvironment is associated with improved overall survival, regardless of BMI. We also observed a significant association between cell proliferation and progression-free survival in overweight individuals who received immune-modulating therapy. In conclusion, our data confirm the role of the immune system in the natural course of GEAC and its responses to immunotherapies, but do not support the role of BMI as an independent clinically relevant biomarker in this group of patients.

A scalable high-throughput targeted next-generation sequencing assay for comprehensive genomic profiling of solid tumors.

Timely and accurate identification of molecular alterations in solid tumors is essential for proper management of patients with advanced cancers. This has created a need for rapid, scalable comprehensive genomic profiling (CGP) systems that detect an increasing number of therapeutically-relevant variant types and molecular signatures. In this study, we assessed the analytical performance of the TruSight Oncology 500 High-Throughput assay for detection of somatic alterations from formalin-fixed paraffin-embedded tissue specimens. In parallel, we developed supporting software and automated sample preparation systems designed to process up to 70 clinical samples in a single NovaSeq 6000TM sequencing run with a turnaround time of <7 days from specimen receipt to report. The results demonstrate that the scalable assay accurately and reproducibly detects small variants, copy number alterations, microsatellite instability (MSI) and tumor mutational burden (TMB) from 40ng DNA, and multiple gene fusions, including known and unknown partners and splice variants from 20ng RNA. 717 tumor samples and reference materials with previously known alterations in 96 cancer-related genes were sequenced to evaluate assay performance. All variant classes were reliably detected at consistent and reportable variant allele percentages with >99% overall accuracy and precision. Our results demonstrate that the high-throughput CGP assay is a reliable method for accurate detection of molecular alterations in support of precision therapeutics in oncology. The supporting systems and scalable workflow allow for efficient interpretation and prompt reporting of hundreds of patient cancer genomes per week with excellent analytical performance.

Integration of tumor inflammation, cell proliferation, and traditional biomarkers improves prediction of immunotherapy resistance and response.

BACKGROUND: Contemporary to the rapidly evolving landscape of cancer immunotherapy is the equally changing understanding of immune tumor microenvironments (TMEs) which is crucial to the success of these therapies. Their reliance on a robust host immune response necessitates clinical grade measurements of immune TMEs at diagnosis. In this study, we describe a stable tumor immunogenic profile describing immune TMEs in multiple tumor types with ability to predict clinical benefit from immune checkpoint inhibitors (ICIs). METHODS: A tumor immunogenic signature (TIGS) was derived from targeted RNA-sequencing (RNA-seq) and gene expression analysis of 1323 clinical solid tumor cases spanning 35 histologies using unsupervised analysis. TIGS correlation with ICI response and survival was assessed in a retrospective cohort of NSCLC, melanoma and RCC tumor blocks, alone and combined with TMB, PD-L1 IHC and cell proliferation biomarkers. RESULTS: Unsupervised clustering of RNA-seq profiles uncovered a 161 gene signature where T cell and B cell activation, IFNg, chemokine, cytokine and interleukin pathways are over-represented. Mean expression of these genes produced three distinct TIGS score categories: strong (n = 384/1323; 29.02%), moderate (n = 354/1323; 26.76%), and weak (n = 585/1323; 44.22%). Strong TIGS tumors presented an improved ICI response rate of 37% (30/81); with highest response rate advantage occurring in NSCLC (ORR = 36.6%; 16/44; p = 0.051). Similarly, overall survival for strong TIGS tumors trended upward (median = 25 months; p = 0.19). Integrating the TIGS score categories with neoplastic influence quantified via cell proliferation showed highly proliferative and strong TIGS tumors correlate with significantly higher ICI ORR than poorly proliferative and weak TIGS tumors [14.28%; p = 0.0006]. Importantly, we noted that strong TIGS and highly [median = not achieved; p = 0.025] or moderately [median = 16.2 months; p = 0.025] proliferative tumors had significantly better survival compared to weak TIGS, highly proliferative tumors [median = 7.03 months]. Importantly, TIGS discriminates subpopulations of potential ICI responders that were considered negative for response by TMB and PD-L1. CONCLUSIONS: TIGS is a comprehensive and informative measurement of immune TME that effectively characterizes host immune response to ICIs in multiple tumors. The results indicate that when combined with PD-L1, TMB and cell proliferation, TIGS provides greater context of both immune and neoplastic influences on the TME for implementation into clinical practice.

Integrated in silico and 3D in vitro model of macrophage migration in response to physical and chemical factors in the tumor microenvironment.

Macrophages are abundant in the tumor microenvironment (TME), serving as accomplices to cancer cells for their invasion. Studies have explored the biochemical mechanisms that drive pro-tumor macrophage functions; however the role of TME interstitial flow (IF) is often disregarded. Therefore, we developed a three-dimensional microfluidic-based model with tumor cells and macrophages to study how IF affects macrophage migration and its potential contribution to cancer invasion. The presence of either tumor cells or IF individually increased macrophage migration directedness and speed. Interestingly, there was no additive effect on macrophage migration directedness and speed under the simultaneous presence of tumor cells and IF. Further, we present an in silico model that couples chemokine-mediated signaling with mechanosensing networks to explain our in vitro observations. In our model design, we propose IL-8, CCL2, and ß-integrin as key pathways that commonly regulate various Rho GTPases. In agreement, in vitro macrophage migration remained elevated when exposed to a saturating concentration of recombinant IL-8 or CCL2 or to the co-addition of a sub-saturating concentration of both cytokines. Moreover, antibody blockade against IL-8 and/or CCL2 inhibited migration that could be restored by IF, indicating cytokine-independent mechanisms of migration induction. Importantly, we demonstrate the utility of an integrated in silico and 3D in vitro approach to aid the design of tumor-associated macrophage-based immunotherapeutic strategies.

Synchronous crop failures and climate-forced production variability.

Large-scale modes of climate variability can force widespread crop yield anomalies and are therefore often presented as a risk to food security. We quantify how modes of climate variability contribute to crop production variance. We find that the El Niño Southern Oscillation (ENSO), the Indian Ocean Dipole (IOD), tropical Atlantic variability (TAV), and the North Atlantic Oscillation (NAO) together account for 18, 7, and 6% of globally aggregated maize, soybean, and wheat production variability, respectively. The lower fractions of global-scale soybean and wheat production variability result from substantial but offsetting climate-forced production anomalies. All climate modes are important in at least one region studied. In 1983, ENSO, the only mode capable of forcing globally synchronous crop failures, was responsible for the largest synchronous crop failure in the modern historical record. Our results provide the basis for monitoring, and potentially predicting, simultaneous crop failures.

Solid dissolution in a fluid solvent is characterized by the interplay of surface area-dependent diffusion and physical fragmentation.

The processes of dissolution and fragmentation have high relevance in pharmaceutical research, medicine, digestive physiology, and engineering design. Experimentally, dissolution and fragmentation are observed to occur simultaneously, yet little is known about the relative importance of each of these processes and their impact on the dissolution process as a whole. Thus, in order to better explain these phenomena and the manner in which they interact, we have developed a novel mathematical model of dissolution, based on partial differential equations, taking into consideration the two constituent processes of surface area-dependent diffusive mass removal and physical fragmentation of the solid particles, and the basic physical laws governing these processes. With this model, we have been able to quantify the effects of the interplay between these two processes and determine the optimal conditions for rapid solid dissolution in liquid solvents. We were able to reproduce experimentally observed phenomena and simulate dissolution under a wide range of experimentally occurring conditions to give new perspectives into the kinetics of this common, yet complex process. Finally, we demonstrated the utility of this model to aid in experiment and device design as an optimisation tool.

Dynamic interplay between tumour, stroma and immune system can drive or prevent tumour progression.

In the tumour microenvironment, cancer cells directly interact with both the immune system and the stroma. It is firmly established that the immune system, historically believed to be a major part of the body's defence against tumour progression, can be reprogrammed by tumour cells to be ineffective, inactivated, or even acquire tumour promoting phenotypes. Likewise, stromal cells and extracellular matrix can also have pro-and anti-tumour properties. However, there is strong evidence that the stroma and immune system also directly interact, therefore creating a tripartite interaction that exists between cancer cells, immune cells and tumour stroma. This interaction contributes to the maintenance of a chronically inflamed tumour microenvironment with pro-tumorigenic immune phenotypes and facilitated metastatic dissemination. A comprehensive understanding of cancer in the context of dynamical interactions of the immune system and the tumour stroma is therefore required to truly understand the progression toward and past malignancy.

Internal ocean-atmosphere variability drives megadroughts in Western North America.

Multidecadal droughts that occurred during the Medieval Climate Anomaly represent an important target for validating the ability of climate models to adequately characterize drought risk over the near-term future. A prominent hypothesis is that these megadroughts were driven by a centuries-long radiatively forced shift in the mean state of the tropical Pacific Ocean. Here we use a novel combination of spatiotemporal tree-ring reconstructions of Northern Hemisphere hydroclimate to infer the atmosphere-ocean dynamics that coincide with megadroughts over the American West, and find that these features are consistently associated with ten-to-thirty year periods of frequent cold El Niño Southern Oscillation conditions and not a centuries-long shift in the mean of the tropical Pacific Ocean. These results suggest an important role for internal variability in driving past megadroughts. State-of-the art climate models from the Coupled Model Intercomparison Project phase 5, however, do not simulate a consistent association between megadroughts and internal variability of the tropical Pacific Ocean, with implications for our confidence in megadrought risk projections.

Effect of training on accumulated oxygen deficit and shuttle run performance.

BACKGROUND: The purpose of the present study was to investigate changes in physiological, metabolic and performance parameters resulting from an intense 6 week training programme. METHODS: Sixteen volunteers were divided into a control (CN; 4 men and 2 women) and training group (TR; 6 men and 4 women). Laboratory measures included maximal aerobic power (VO2max), submaximal oxygen uptake (10.5 percent or 6 degrees treadmill inclination) and accumulated oxygen deficit (AOD). Performance was assessed during 20 metre shuttle run tests (PST, progressive shuttle run test; HIST, high intensity shuttle run test). RESULTS: TR improved their HIST performance (m) significantly compared with CN, identified by a significant "group-by-training" interaction (p<0.01). Similarly, AOD values improved more in TR compared with CN (p<0.01). There was a trend for TR to further reduce blood pH values after training compared with CN, although this decrease (approximately 0.05 units) did not attain statistical significance. The change in AOD was strongly correlated with the change in run time to exhaustion (r=0.76, p<0.01) and the change in estimated total work output (r=0.69, p<0.01) during 10.5 percent gradient running and modestly correlated with the change in HIST performance (r=0.49, p<0.05, assuming a directional test). CONCLUSIONS: The results of the present study suggest changes in the anaerobic capacity, determined as AOD, due to training may be reflected in corresponding changes in laboratory and field performance.

Twentieth-Century Sea Surface Temperature Trends

An analysis of historical sea surface temperatures provides evidence for global warming since 1900, in line with land-based analyses of global temperature trends, and also shows that over the same period, the eastern equatorial Pacific cooled and the zonal sea surface temperature gradient strengthened. Recent theoretical studies have predicted such a pattern as a response of the coupled ocean-atmosphere system to an exogenous heating of the tropical atmosphere. This pattern, however, is not reproduced by the complex ocean-atmosphere circulation models currently used to simulate the climatic response to increased greenhouse gases. Its presence is likely to lessen the mean 20th-century global temperature change in model simulations.

A comparison of the psychosocial needs of hospice patients with AIDS and those with other diagnoses.

We compared the amount of psychosocial support required and received by patients with AIDS and without AIDS at Cedar Valley Hospice, Waterloo, Iowa. Hospice patients with AIDS (N = 11) required significantly more psychosocial support than non-AIDS patients (N = 36) of the same average age. The amount of non-hospice social support--family, congregation, and neighbors--received by AIDS patients was significantly less than that received by those with other diagnoses due to a virtual lack of neighbor support. There were no significant differences in family or congregational support. The high level of family support and lack of neighbor support may have been a result of many (8) of the AIDS patients having moved back to the area to die. A survey of hospice staff showed they felt working with AIDS patients was both more time consuming and more stressful than working with patients with other diagnoses.

Chromosome interactions in Drosophila melanogaster. I. Viability studies.

The nature of fitness interactions is an important, yet unsolved, question in population genetics. We compare the egg-to-adult viability of individuals homozygous for either a second or a third chromosome with the viability of individuals homozygous for both chromosomes simultaneously. On the average, the viability of the two-chromosome homozygotes is somewhat greater than expected assuming that the fitnesses of the single-chromosome homozygotes interact in a multiplicative fashion. This result differs from previous observations that indicate either no significant deviations from the expectation or lower-than-expected average fitnesses for the double homozygotes.

Chromosome interactions in Drosophila melanogaster. II. Total fitness.

In a large experiment, using nearly 200 population cages, we have measured the fitness of Drosophila melanogaster homozygous (1) for the second chromosome, (2) for the third chromosome, and (3) for both chromosomes. Twenty-four second chromosomes and 24 third chromosomes sampled from a natural population were tested. The mean fitness of the homozygous flies is 0.081 +/- 0.014 for the second chromosome, 0.080 +/- 0.017 for the third chromosome, and 0.079 +/- 0.024 for both chromosomes simultaneously. Assuming that fitnesses are multiplicative (the additive fitness model makes no sense in the present case because of the large selection coefficients involved), the expected mean fitness of the homozygotes for both chromosomes is 0.0066; their observed fitness is more than ten times greater. Thus, it appears that synergistic interactions between loci are considerable; and that, consequently, the fitness function substantially departs from linearity. Two models are tentatively suggested for the fitness function: a "threshold" model and a "synergistic" model.--The experiments reported here confirm previous results showing that the concealed genetic load present in natural populations of Drosophila is sufficient to account for the selective maintenance of numerous polymorphisms (of the order of 1000).