Genes Associated With Prognosis After Surgery For Malignant Pleural Mesothelioma Promote Tumor Cell Survival In Vitro

<p>Abstract</p> <p>Background</p> <p>Mesothelioma is an aggressive neoplasm with few effective treatments, one being cytoreductive surgery. We previously described a test, based on differential expression levels of four genes, to predict clinical outcome in prospectively consented mesothelioma patients after surgery. In this study, we determined whether any of these four genes could be linked to a cancer relevant phenotype.</p> <p>Methods</p> <p>We conducted a high-throughput RNA inhibition screen to knockdown gene expression levels of the four genes comprising the test (ARHGDIA, COBLL1, PKM2, TM4SF1) in both a human lung-derived normal and a tumor cell line using three different small inhibitory RNA molecules per gene. Successful knockdown was confirmed using quantitative RT-PCR. Detection of statistically significant changes in apoptosis and mitosis was performed using immunological assays and quantified using video-assisted microscopy at a single time-point. Changes in nuclear shape, size, and numbers were used to provide additional support of initial findings. Each experiment was conducted in triplicate. Specificity was assured by requiring that at least 2 different siRNAs produced the observed change in each cell line/time-point/gene/assay combination.</p> <p>Results</p> <p>Knockdown of ARHGDIA, COBLL1, and TM4SF1 resulted in 2- to 4-fold increased levels of apoptosis in normal cells (ARHGDIA only) and tumor cells (all three genes). No statistically significant changes were observed in apoptosis after knockdown of PKM2 or for mitosis after knockdown of any gene.</p> <p>Conclusions</p> <p>We provide evidence that ARHGDIA, COBLL1, and TM4SF1 are negative regulators of apoptosis in cultured tumor cells. These genes, and their related intracellular signaling pathways, may represent potential therapeutic targets in mesothelioma.</p

A gene expression ratio-based diagnostic test for bladder cancer

Lingsheng Dong1, Andrew J Bard1, William G Richards1, Matthew D Nitz2, Dan Theodorescu2, Raphael Bueno1, Gavin J Gordon11The Thoracic Surgery Oncology laboratory and the Division of Thoracic Surgery, Brigham and Women&amp;rsquo;s Hospital, Harvard Medical School, Boston, MA, USA; 2Departments of Urology and Molecular Physiology, University of Virginia, Charlottesville, VA, USAPurpose: Bladder cancer is relatively common but early detection techniques such as cystoscopy and cytology are somewhat limited. We developed a broadly applicable, platform-independent and clinically relevant method based on simple ratios of gene expression to diagnose human cancers. In this study, we sought to determine whether this technique could be applied to the diagnosis of bladder cancer.Experimental design: We developed a model for the diagnosis of bladder cancer using expression profiling data from 80 normal and tumor bladder tissues to identify statistically significant discriminating genes with reciprocal average expression levels in each tissue type. The expression levels of select genes were used to calculate individual gene pair expression ratios in order to assign diagnosis. The optimal model was examined in two additional published microarray data sets and using quantitative RT-PCR in a cohort of 13 frozen benign bladder urothelium samples and 13 bladder cancer samples from our institution.Results: A five-ratio test utilizing six genes proved to be 100% accurate (26 of 26 samples) for distinguishing benign from malignant bladder tissue samples (P &amp;lt;&amp;nbsp;10&amp;minus;6).Conclusions: We have provided a proof of principle study for the use of gene expression ratios in the diagnosis of bladder cancer. This technique may ultimately prove to be a useful adjunct to cytopathology in screening urine specimens for bladder cancer.Keywords: bladder cancer, gene expression profiling, and diagnosi

Increased expression of programmed death ligand 1 (PD-L1) in human pituitary tumors

PURPOSE: Subsets of pituitary tumors exhibit an aggressive clinical courses and recur despite surgery, radiation, and chemotherapy. Because modulation of the immune response through inhibition of T-cell checkpoints has led to durable clinical responses in multiple malignancies, we explored whether pituitary adenomas express immune-related biomarkers that could suggest suitability for immunotherapy. Specifically, programmed death ligand 1 (PD-L1) has emerged as a potential biomarker whose expression may portend more favorable responses to immune checkpoint blockade therapies. We thus investigated the expression of PD-L1 in pituitary adenomas. METHODS: PD-L1 RNA and protein expression were evaluated in 48 pituitary tumors, including functioning and non-functioning adenomas as well as atypical and recurrent tumors. Tumor infiltrating lymphocyte populations were also assessed by immunohistochemistry. RESULTS: Pituitary tumors express variable levels of PD-L1 transcript and protein. PD-L1 RNA and protein expression were significantly increased in functioning (growth hormone and prolactin-expressing) pituitary adenomas compared to non-functioning (null cell and silent gonadotroph) adenomas. Moreover, primary pituitary adenomas harbored higher levels of PD-L1 mRNA compared to recurrent tumors. Tumor infiltrating lymphocytes were observed in all pituitary tumors and were positively correlated with increased PD-L1 expression, particularly in the functional subtypes. CONCLUSIONS: Human pituitary adenomas harbor PD-L1 across subtypes, with significantly higher expression in functioning adenomas compared to non-functioning adenomas. This expression is accompanied by the presence of tumor infiltrating lymphocytes. These findings suggest the existence of an immune response to pituitary tumors and raise the possibility of considering checkpoint blockade immunotherapy in cases refractory to conventional management

Thermodynamic Computing System for AI Applications

Recent breakthroughs in artificial intelligence (AI) algorithms have highlighted the need for novel computing hardware in order to truly unlock the potential for AI. Physics-based hardware, such as thermodynamic computing, has the potential to provide a fast, low-power means to accelerate AI primitives, especially generative AI and probabilistic AI. In this work, we present the first continuous-variable thermodynamic computer, which we call the stochastic processing unit (SPU). Our SPU is composed of RLC circuits, as unit cells, on a printed circuit board, with 8 unit cells that are all-to-all coupled via switched capacitances. It can be used for either sampling or linear algebra primitives, and we demonstrate Gaussian sampling and matrix inversion on our hardware. The latter represents the first thermodynamic linear algebra experiment. We also illustrate the applicability of the SPU to uncertainty quantification for neural network classification. We envision that this hardware, when scaled up in size, will have significant impact on accelerating various probabilistic AI applications.Comment: 26 pages, 22 figure

Fifteen-year prospective longitudinal cohort study of outcomes following single radius total knee arthroplasty: patient reported outcome measures, response attrition and survival

AimsThis prospective study reports longitudinal, within-patient, patient-reported outcome measures (PROMs) over a 15-year period following cemented single radius total knee arthroplasty (TKA). Secondary aims included reporting PROMs trajectory, 15-year implant survival, and patient attrition from follow-up.MethodsFrom 2006 to 2007, 462 consecutive cemented cruciate-retaining Triathlon TKAs were implanted in 426 patients (mean age 69 years (21 to 89); 290 (62.7%) female). PROMs (12-item Short Form Survey (SF-12), Oxford Knee Score (OKS), and satisfaction) were assessed preoperatively and at one, five, ten, and 15 years. Kaplan-Meier survival and univariate analysis were performed.ResultsAt 15 years, 28 patients were lost to follow-up (6.1%) and 221 patients (51.9%) had died, with the mean age of the remaining cohort reducing by four years. PROMs response rates among surviving patients were: one-year 63%; five-year 72%; ten-year 94%; and 15-year 59%. OKS and SF-12 scores changed significantly over 15 years (p &lt; 0.001). The mean improvement in OKS was 18.8 (95% confidence (CI) 16.7 to 19.0) at one year. OKS peaked at five years (median 43 years) declining thereafter (p &lt; 0.001), though at 15 years it remained 17.5 better than preoperatively. Age and sex did not alter this trajectory. A quarter of patients experienced a clinically significant decline (≥ 7) in OKS from five to ten years and from ten to 15 years. The SF-12 physical component score displayed a similar trajectory, peaking at one year (p &lt; 0.001). Patient satisfaction was 88% at one, five, and ten years, and 94% at 15 years. In all, 15-year Kaplan-Meier survival was 97.6% (95% CI 96.0% to 99.2%) for any revision, and 98.9% (95% CI 97.9% to 99.9%) for aseptic revision.ConclusionImprovements in PROMs were significant and maintained following single radius TKA, with OKS peaking at five years, and generic physical health peaking at one year. Patient satisfaction remained high at 15 years, at which point 2.4% had been revise

Role of multicellular aggregates in biofilm formation

In traditional models of in vitro biofilm development, individual bacterial cells seed a surface, multiply, and mature into multicellular, three-dimensional structures. Much research has been devoted to elucidating the mechanisms governing the initial attachment of single cells to surfaces. However, in natural environments and during infection, bacterial cells tend to clump as multicellular aggregates, and biofilms can also slough off aggregates as a part of the dispersal process. This makes it likely that biofilms are often seeded by aggregates and single cells, yet how these aggregates impact biofilm initiation and development is not known. Here we use a combination of experimental and computational approaches to determine the relative fitness of single cells and preformed aggregates during early development of Pseudomonas aeruginosa biofilms. We find that the relative fitness of aggregates depends markedly on the density of surrounding single cells, i.e., the level of competition for growth resources. When competition between aggregates and single cells is low, an aggregate has a growth disadvantage because the aggregate interior has poor access to growth resources. However, if competition is high, aggregates exhibit higher fitness, because extending vertically above the surface gives cells at the top of aggregates better access to growth resources. Other advantages of seeding by aggregates, such as earlier switching to a biofilm-like phenotype and enhanced resilience toward antibiotics and immune response, may add to this ecological benefit. Our findings suggest that current models of biofilm formation should be reconsidered to incorporate the role of aggregates in biofilm initiation

The molecular basis of thioalcohol production in human body odour

This work was supported by the BBSRC Grant BB/N006615/1.Body odour is a characteristic trait of Homo sapiens, however its role in human behaviour and evolution is poorly understood. Remarkably, body odour is linked to the presence of a few species of commensal microbes. Herein we discover a bacterial enzyme, limited to odour-forming staphylococci that are able to cleave odourless precursors of thioalcohols, the most pungent components of body odour. We demonstrated using phylogenetics, biochemistry and structural biology that this cysteine-thiol lyase (C-T lyase) is a PLP-dependent enzyme that moved horizontally into a unique monophyletic group of odour-forming staphylococci about 60 million years ago, and has subsequently tailored its enzymatic function to human-derived thioalcohol precursors. Significantly, transfer of this enzyme alone to non-odour producing staphylococci confers odour production, demonstrating that this C-T lyase is both necessary and sufficient for thioalcohol formation. The structure of the C-T lyase compared to that of other related enzymes reveals how the adaptation to thioalcohol precursors has evolved through changes in the binding site to create a constrained hydrophobic pocket that is selective for branched aliphatic thioalcohol ligands. The ancestral acquisition of this enzyme, and the subsequent evolution of the specificity for thioalcohol precursors implies that body odour production in humans is an ancient process.Publisher PDFPeer reviewe

The \u27Pseudomonas aeruginosa\u27 PSL Polysaccharide Is a Social but Noncheatable Trait in Biofilms

Extracellular polysaccharides are compounds secreted by microorganisms into the surrounding environment, and they are important for surface attachment and maintaining structural integrity within biofilms. The social nature of many extracellular polysaccharides remains unclear, and it has been suggested that they could function as either cooperative public goods or as traits that provide a competitive advantage. Here, we empirically tested the cooperative nature of the PSL polysaccharide, which is crucial for the formation of biofilms in Pseudomonas aeruginosa. We show that (i) PSL is not metabolically costly to produce; (ii) PSL provides populationlevel benefits in biofilms, for both growth and antibiotic tolerance; (iii) the benefits of PSL production are social and are shared with other cells; (iv) the benefits of PSL production appear to be preferentially directed toward cells which produce PSL; (v) cells which do not produce PSL are unable to successfully exploit cells which produce PSL. Taken together, this suggests that PSL is a social but relatively nonexploitable trait and that growth within biofilms selects for PSL-producing strains, even when multiple strains are on a patch (low relatedness at the patch level)