Correlation of Plasma FL Expression with Bone Marrow Irradiation Dose

<div><p>Purpose</p><p>Ablative bone marrow irradiation is an integral part of hematopoietic stem cell transplantation. These treatment regimens are based on classically held models of radiation dose and the bone marrow response. Flt-3 ligand (FL) has been suggested as a marker of hematopoiesis and bone marrow status but the kinetics of its response to bone marrow irradiation has yet to be fully characterized. In the current study, we examine plasma FL response to total body and partial body irradiation in mice and its relationship with irradiation dose, time of collection and pattern of bone marrow exposure.</p> <p>Materials/Methods</p><p>C57BL6 mice received a single whole body or partial body irradiation dose of 1–8 Gy. Plasma was collected by mandibular or cardiac puncture at 24, 48 and 72 hr post-irradiation as well as 1–3 weeks post-irradiation. FL levels were determined via ELISA assay and used to generate two models: a linear regression model and a gated values model correlating plasma FL levels with radiation dose.</p> <p>Results</p><p>At all doses between 1–8 Gy, plasma FL levels were greater than control and the level of FL increased proportionally to the total body irradiation dose. Differences in FL levels were statistically significant at each dose and at all time points. Partial body irradiation of the trunk areas, encompassing the bulk of the hematopoietically active bone marrow, resulted in significantly increased FL levels over control but irradiation of only the head or extremities did not. FL levels were used to generate a dose prediction model for total body irradiation. In a blinded study, the model differentiated mice into dose received cohorts of 1, 4 or 8 Gy based on plasma FL levels at 24 or 72 hrs post-irradiation.</p> <p>Conclusion</p><p>Our findings indicate that plasma FL levels might be used as a marker of hematopoietically active bone marrow and radiation exposure in mice.</p> </div

FL Levels Following TBI.

<p>FL levels correlate with dose of irradiation and time of collection. A) Plasma FL levels in TBI C57BL6 mice at 24, 48 and 72 hrs post-IR at doses between 0 and 8 Gy. B) Extended time course of plasma FL expression in TBI C57BL6 mice at 0, 4 and 8 Gy at time points between 24 hrs and 3wks post-IR. Values reflect the mean ± SEM.</p

miRNAs module use case – mir-34a profile by survivorship stratification.

<p>We compare the expression levels of mir-34a in samples stratified by length of survival. Panels A–D shows comparison of 1–3 Quartiles (short survivors) versus 4th Quartile (long survivors). Panels E–H shows comparison of 1st Quartile (short survivors) versus 4th Quartile (long survivors). A, E show the histogram of expression distribution for all GBM patients. B, F show the p-values of the t-tests comparing expression of mir-34a in short and long survivors. C, G show the boxplots of expression for short and long survivors, and D, H show barplots of expressions mean-centered around the mean of the two groups. In both stratifications, long survivors (4th Quartile patients) express significantly lower levels of mir-34a compared to short survivors (p-val 0.041 when compared to 1–3 Quartile patients, and p-val 0.033 when compared to 1st Quartile patients).</p

GBM-BioDP overall architecture.

<p>The diagram represents a runtime view of the architecture of GBM-BioDP. The lower tier represents the sources of experimental and meta data, and external tools that are invoked to visualize the data. The middle tier represents how the data are processed, stored, and made available to the user. The right hand side of the middle tier represents the visualization “services” that are available at runtime to the user. These services are made available as web-services and are hosted on an Apache server. The higher tier represents the user interface, and is organized in a tabbed interface.</p

Use case from miRNAs module – miRNA targets.

<p>Correlation of mir-34a predicted targets, and p53. Color red represent positive correlation, whereas blue color represent negative correlation. The cells are annotated with the correlation values. p53 and mir-34a expression are anti-correlated, which indicates a possible suppressor role of mir-34a.</p

Hypothesis generation – Molecular classification of GBM clinical data.

<p>A. Model depicting parallels between tumor subtypes and stages in neurogenesis <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0101239#pone.0101239-Phillips1" target="_blank">[28]</a>. B. Main features of tumor subtypes <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0101239#pone.0101239-Verhaak1" target="_blank">[6]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0101239#pone.0101239-Phillips1" target="_blank">[28]</a>. C. Random forest model “out of bag” error rates for training data using 201 samples from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0101239#pone.0101239-Verhaak1" target="_blank">[6]</a> and the corresponding 768 gene expression measurements common between the training and validated data. D. Summary of error rates for the predicted subtypes of validated data. Abbreviations RF: random forest, C: classical, M: mesenchymal, N: neural, P: proneural.</p

Partial Body Irradiation Patterns and FL Response.

<p>Plasma FL expression following heterogeneous partial body irradiation patterns in C57BL6 mice. A) Mice were partially shielded to irradiation using the represented partial body diagrams with either the head, limbs, trunk, or trunk+limbs exposed. B) Plasma FL expression in partial body exposed mice at 0, 2, and 8 Gy at 24 hrs post-IR. C) Plasma FL expression in partial body exposed mice at 0, 2, and 8 Gy at 72 hrs post-IR. Values reflect the mean ± SEM.</p

Results of Blinded Dose Prediction Analysis Using Plasma FL at 24 hrs and 72 hrs following Total Body Irradiation.

α<p>#Correct represents the number of correct predictions over # of total animals in that group. 72 hr time point prediction analysis includes evaluation of 24 hr/72 hr FL trend as described in the text.</p>β<p>Samples pooled from the stated treatment groups and evaluated as a single cohort.</p

Additional file 3: of Computational analysis of the mesenchymal signature landscape in gliomas

Kaplan Meier plots of 20 genes selected by LASSO based gene prioritization, showing the prognostic relevance of each gene in LGG and GBM. (PPTX 1298 kb

Additional file 1: of Computational analysis of the mesenchymal signature landscape in gliomas

Table showing the summary of clinical characteristics of independent data (XLSX 9 kb