Convergence of Logic of Cellular Regulation in Different Premalignant Cells by an Information Theoretic Approach

Abstract Background Surprisal analysis is a thermodynamic-like molecular level approach that identifies biological constraints that prevents the entropy from reaching its maximum. To examine the significance of altered gene expression levels in tumorigenesis we apply surprisal analysis to the WI-38 model through its precancerous states. The constraints identified by the analysis are transcription patterns underlying the process of transformation. Each pattern highlights the role of a group of genes that act coherently to define a transformed phenotype. Results We identify a major transcription pattern that represents a contraction of signaling networks accompanied by induction of cellular proliferation and protein metabolism, which is essential for full transformation. In addition, a more minor, "tumor signature" transcription pattern completes the transformation process. The variation with time of the importance of each transcription pattern is determined. Midway through the transformation, at the stage when cells switch from slow to fast growth rate, the major transcription pattern undergoes a total inversion of its weight while the more minor pattern does not contribute before that stage. Conclusions A similar network reorganization occurs in two very different cellular transformation models: WI-38 and the cervical cancer HF1 models. Our results suggest that despite differences in a list of transcripts expressed in different cancer models the rationale of the network reorganization remains essentially the same

31st Annual Meeting and Associated Programs of the Society for Immunotherapy of Cancer (SITC 2016) : part two

Background The immunological escape of tumors represents one of the main ob- stacles to the treatment of malignancies. The blockade of PD-1 or CTLA-4 receptors represented a milestone in the history of immunotherapy. However, immune checkpoint inhibitors seem to be effective in specific cohorts of patients. It has been proposed that their efficacy relies on the presence of an immunological response. Thus, we hypothesized that disruption of the PD-L1/PD-1 axis would synergize with our oncolytic vaccine platform PeptiCRAd. Methods We used murine B16OVA in vivo tumor models and flow cytometry analysis to investigate the immunological background. Results First, we found that high-burden B16OVA tumors were refractory to combination immunotherapy. However, with a more aggressive schedule, tumors with a lower burden were more susceptible to the combination of PeptiCRAd and PD-L1 blockade. The therapy signifi- cantly increased the median survival of mice (Fig. 7). Interestingly, the reduced growth of contralaterally injected B16F10 cells sug- gested the presence of a long lasting immunological memory also against non-targeted antigens. Concerning the functional state of tumor infiltrating lymphocytes (TILs), we found that all the immune therapies would enhance the percentage of activated (PD-1pos TIM- 3neg) T lymphocytes and reduce the amount of exhausted (PD-1pos TIM-3pos) cells compared to placebo. As expected, we found that PeptiCRAd monotherapy could increase the number of antigen spe- cific CD8+ T cells compared to other treatments. However, only the combination with PD-L1 blockade could significantly increase the ra- tio between activated and exhausted pentamer positive cells (p= 0.0058), suggesting that by disrupting the PD-1/PD-L1 axis we could decrease the amount of dysfunctional antigen specific T cells. We ob- served that the anatomical location deeply influenced the state of CD4+ and CD8+ T lymphocytes. In fact, TIM-3 expression was in- creased by 2 fold on TILs compared to splenic and lymphoid T cells. In the CD8+ compartment, the expression of PD-1 on the surface seemed to be restricted to the tumor micro-environment, while CD4 + T cells had a high expression of PD-1 also in lymphoid organs. Interestingly, we found that the levels of PD-1 were significantly higher on CD8+ T cells than on CD4+ T cells into the tumor micro- environment (p < 0.0001). Conclusions In conclusion, we demonstrated that the efficacy of immune check- point inhibitors might be strongly enhanced by their combination with cancer vaccines. PeptiCRAd was able to increase the number of antigen-specific T cells and PD-L1 blockade prevented their exhaus- tion, resulting in long-lasting immunological memory and increased median survival

Surprisal Analysis of Transcripts Expression Levels in the Presence of Noise: A Reliable Determination of the Onset of a Tumor Phenotype

<div><p>Towards a reliable identification of the onset in time of a cancer phenotype, changes in transcription levels in cell models were tested. Surprisal analysis, an information-theoretic approach grounded in thermodynamics, was used to characterize the expression level of mRNAs as time changed. Surprisal Analysis provides a very compact representation for the measured expression levels of many thousands of mRNAs in terms of very few - three, four - transcription patterns. The patterns, that are a collection of transcripts that respond together, can be assigned definite biological phenotypic role. We identify a transcription pattern that is a clear marker of eventual malignancy. The weight of each transcription pattern is determined by surprisal analysis. The weight of this pattern changes with time; it is never strictly zero but it is very low at early times and then rises rather suddenly. We suggest that the low weights at early time points are primarily due to experimental noise. We develop the necessary formalism to determine at what point in time the value of that pattern becomes reliable. Beyond the point in time when a pattern is deemed reliable the data shows that the pattern remain reliable. We suggest that this allows a determination of the presence of a cancer forewarning. We apply the same formalism to the weight of the transcription patterns that account for healthy cell pathways, such as apoptosis, that need to be switched off in cancer cells. We show that their weight eventually falls below the threshold. Lastly we discuss patient heterogeneity as an additional source of fluctuation and show how to incorporate it within the developed formalism.</p></div

Reliability of weights of phenotypes during tumerogenesis.

<p>The upper bound on the fractional error in the Lagrange multipliers, , at different successive time points in the WI-38 cancer model of Rotter et al <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0061554#pone.0061554-Tabach1" target="_blank">[11]</a>. A constraint is warranted by the data when the fractional error is below unity, see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0061554#pone.0061554.e066" target="_blank">equation (14</a>). is the tumor signature and it is seen that it is only valid in later times but well before the cell is cancerous that is observed at time point 12. Note that the error in the steady state constraint is minimal.</p

The importance of patient variability.

<p>The statistical error bound in the Lagrange multipliers for steady state () and the next 2 constraints calculated taking into account patient variability by using equation (16). Renal cancer data for 3 patients as reported in Stevanović et al <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0061554#pone.0061554-Stickel1" target="_blank">[13]</a>. The error bound for the 2^nd constraint is high at all time points.</p

Reliability of weights of phenotypes for a renal cancer patient.

<p>The error bound in the Lagrange multipliers for steady state () and the next 2 constraints calculated for the 2^nd patient of renal carcinoma, using the data reported measured by Stevanović et al <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0061554#pone.0061554-Stickel1" target="_blank">[13]</a> for patient number 2. Quite similar results are obtained for the other two patients.</p

Soundness of weights of phenotypes during tumerogenesis.

<p>The bound for the fractional error of the Lagrange multipliers, , for steady state () and the next 3 constraints calculated for the four time points measured in the HPV-16 model <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0061554#pone.0061554-KravchenkoBalasha3" target="_blank">[12]</a>.</p

Phytolith-rich layers from the Late Bronze and Iron Ages at Tel Dor (Israel): mode of formation and archaeological significance

The presence of many phytolith-rich layers in late Bronze and Iron Age deposits at Tel Dor, Israel, are indicative of specific locations where plants were concentrated. Detailed studies of six of these phytolith-rich layers and associated sediments from Tel Dor show that the phytoliths were derived mainly from wild and domestic grasses. The most common domestic grass was the cereal Triticum aestivum (bread wheat). Three of these layers have a microlaminated microstructure, associated dung spherulites and phosphate nodules; characteristics that all point to the phytolith-rich layers having formed from dung in animal enclosures. In two of the layers, the microlaminated structure is absent while dung spherulites and phosphate nodules are present, suggesting that these too originate from dung that was not deposited in an enclosure. The sixth layer is microlaminated but does not contain spherulites. We thus cannot suggest a parsimonious explanation of its observed properties. Concentrations of burnt phytoliths are present in three locations, implying that dung was either burnt in situ or the ashes from burnt dung were redeposited. The transformation of dung accumulations into phytolith-rich layers involves a loss of organic material and hence a significant reduction in sediment volume, which is clearly apparent in the stratigraphy of some of the locations examined. The volume reduction can be observed in the macrostratigraphy and has important implications with regard to macrostratigraphic interpretation. The presence of abundant phytolith-rich layers on the tell has significant implications for the concept of ‘urbanism’ during these periods.We also thank the Berman Center for Biblical Archaeology, Mr George Schwartzmann, Sarasota, Florida, and the Kimmel Center for Archaeological Science for their financial support. R.S.G. would like to thank Liora Kolska-Horowitz for providing a sample of dung plastered wall from South Africa, reported in this study. S.W. is the incumbent of the Dr Trude Burchardt Professorial Chair of Structural Biology. The Fundacio´n Atapuerca financed the research performed by D. Cabanes.Peer reviewe

Sediments exposed to high temperatures: reconstructing pyrotechnological processes in Late Bronze and Iron Age Strata at Tel Dor (Israel)

Journal of Archaeological Science 34: 358–73Sediments from Phases 12-9 (covering the end of the Late Bronze to the later part of Iron Age I) were examined to establish to what temperatures they were heated and what that might signify. The Phase 12-11 material suggested redeposition of materials from ovens or kilns. The material from Phase 10 indicated on-site heating to temperatures over 1000 degress C consistent with resmelting activities. The Phase 9 sediments reflected the high heat to which they were subjected in the conflagration that destoryed the building