Microarray analysis of miRNA expression profiles following whole body irradiation in a mouse model

<p><b>Context:</b> Accidental exposure to life-threatening radiation in a nuclear event is a major concern; there is an enormous need for identifying biomarkers for radiation biodosimetry to triage populations and treat critically exposed individuals.</p> <p><b>Objective:</b> To identify dose-differentiating miRNA signatures from whole blood samples of whole body irradiated mice.</p> <p><b>Methods:</b> Mice were whole body irradiated with X-rays (2 Gy–15 Gy); blood was collected at various time-points post-exposure; total RNA was isolated; miRNA microarrays were performed; miRNAs differentially expressed in irradiated vs. unirradiated controls were identified; feature extraction and classification models were applied to predict dose-differentiating miRNA signature.</p> <p><b>Results:</b> We observed a time and dose responsive alteration in the expression levels of miRNAs. Maximum number of miRNAs were altered at 24-h and 48-h time-points post-irradiation. A 23-miRNA signature was identified using feature selection algorithms and classifier models. An inverse correlation in the expression level changes of miR-17 members, and their targets were observed in whole body irradiated mice and non-human primates.</p> <p><b>Conclusion:</b> Whole blood-based miRNA expression signatures might be used for predicting radiation exposures in a mass casualty nuclear incident.</p

Table S1 from Multiomic-Based Molecular Landscape of FaDu Xenograft Tumors in Mice after a Combinatorial Treatment with Radiation and an HSP90 Inhibitor Identifies Adaptation-Induced Targets of Resistance and Therapeutic Intervention

Supplementary Table of phosphoproteomic data</p

Figure S3 from Multiomic-Based Molecular Landscape of FaDu Xenograft Tumors in Mice after a Combinatorial Treatment with Radiation and an HSP90 Inhibitor Identifies Adaptation-Induced Targets of Resistance and Therapeutic Intervention

Supplemental Figure S3: IPA pathway highlights genes relevant to, Cell Migration, Angiogenesis and Morbidity or mortality for Treatment groups at Week 2 compared to Untreated Week 2. Significantly altered genes ([2-fold change, p < 0.01) are shown. White indicates no significant changes, Red indicates upregulation, Blue indicates downregulation. Black arrows indicate genes of interest. More genes exist in these pathways than are displayed, for ease of visualization only genes which showed significant changes in expression in at least 2 treatment groups are presented. Genes may be relevant to more than one pathway (PLAUR) is relevant to Organismal Death and Vasculogenesis, but to avoid redundancy is shown once.</p

Figure S6 from Multiomic-Based Molecular Landscape of FaDu Xenograft Tumors in Mice after a Combinatorial Treatment with Radiation and an HSP90 Inhibitor Identifies Adaptation-Induced Targets of Resistance and Therapeutic Intervention

Supplemental Figure S6: Graphs of proteins and phosphoproteins that previously showed impact on cancer proliferation or death. Trends towards significance only. Normalized to intensity. For JUN, microarray data showed that Drug Week 2 and Drug+Rad Week 1 were significantly decreased ([FC} > 2, p < 0.05) compared to respective Untreated tumors.</p

Figure S5 from Multiomic-Based Molecular Landscape of FaDu Xenograft Tumors in Mice after a Combinatorial Treatment with Radiation and an HSP90 Inhibitor Identifies Adaptation-Induced Targets of Resistance and Therapeutic Intervention

Supplemental Figure S5. Proteomic and Phospho-proteomic comparison of changes observed comparing UT_Wk1 to UT_Wk2 (A), Treated Week 1 to UT_Wk1 (B) and Treated Week 2 to UT_Wk2 (C). Trends towards significance only. Normalized to intensity. No notable change is shown in white, upregulation is red, downregulation is blue. Supplemental Figure 4A indicates change in UT_Wk2 compared to UT_Wk1, interestingly p53 and PDL-1 protein expression decrease over three days. Supplemental Figure 6A indicates change in Untreated Week 2 compared to Untreated Week 1, interestingly p53 and PDL-1 protein expression show a decreasing trend.</p

Figure S1 from Multiomic-Based Molecular Landscape of FaDu Xenograft Tumors in Mice after a Combinatorial Treatment with Radiation and an HSP90 Inhibitor Identifies Adaptation-Induced Targets of Resistance and Therapeutic Intervention

Supplemental Figure S1: IPA pathway highlights genes relevant to Organismal Death, Viral infection and Vasculogenesis for Untreated groups at Week 1 and Week 2 compared to Control Day 1. Significantly altered genes (2-fold change, p < 0.01) are shown. White indicates no significant change, Red indicates upregulation, Blue indicates downregulation. Black arrows indicate genes of interest.</p

Figure S4 from Multiomic-Based Molecular Landscape of FaDu Xenograft Tumors in Mice after a Combinatorial Treatment with Radiation and an HSP90 Inhibitor Identifies Adaptation-Induced Targets of Resistance and Therapeutic Intervention

Supplemental Figure S4: Heat Shock protein gene expression was significantly modified by treatment over time. Statistical difference (2-fold change, p < 0.01) indicated with (*). No radiation samples showed statistically significant changes compared to time-matched Untreated tumors, though there was a trend towards significant downregulation for HSPB11 and HSP90AA1 in Rad Week 2 samples compared to UT_Wk2. HSPA1A was significantly upregulated in Drug+Rad Week 1 and Week 2 samples compared to respective UT_Wk1 and 2 samples. HSPA1B was also upregulated in Drug and Drug+Rad at Week 1 and Week 2 compared to respective UT_Wk1 and UT_Wk2. HSP90AA1 was only significantly downregulated at Drug Week 2. For HSPB11 only Drug+Rad Week 1 and Week 2 were significantly downregulated. HSPA14 showed significant downregulation at Drug and Drug+Rad Week 1 and Drug Week 2 compared to respective controls.</p

Figure S2 from Multiomic-Based Molecular Landscape of FaDu Xenograft Tumors in Mice after a Combinatorial Treatment with Radiation and an HSP90 Inhibitor Identifies Adaptation-Induced Targets of Resistance and Therapeutic Intervention

Supplemental Figure S2: IPA pathway highlights genes relevant to Organismal Death, Viral Infection and Vasculogenesis for Treatment groups at Week 1 compared to Control Day 1. Significantly altered genes (2-fold change, p < 0.01) are shown. White indicates no significant change, Red indicates upregulation, Blue indicates downregulation. Black arrows indicate genes of interest. Drug+Rad and Drug alone caused significantly more gene up/down regulation than Rad alone. More genes exist in these pathways than are displayed, for ease of visualization only genes which showed significant changes in expression in at least 2 treatment groups are presented. Genes may be relevant to more than one pathway (PLAUR) is relevant to Organismal Death and Vasculogenesis, but to avoid redundancy is shown once.</p