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Additional file 2: Supplementary Fig. S1. Altered miR-146a expression influences BRAF/MEKi sensitivity and apoptosis in melanoma. A) Boxplots representing IC50 values of 6 matched PLX4032-resistant (R) and sensitive (S) melanoma cell lines to PLX4032 (vemurafenib), BRAFi (dabrafenib), MEKi (trametinib), to the combined treatment BRAF/MEKi, and to sTRAIL-induced apoptosis. B) Inverse correlation between miR-146a expression levels and IC50 values of PLX4032, BRAFi and MEKi in melanoma cell lines (Spearman analysis). C) Forced expression of miR-146a (+m-miR-146a) in LM16R cell line and in LM69 and LM70 short term cultures increased the effects of PLX4032 treatment as shown by reduced cell growth and increased cell cytotoxicity and apoptosis, evaluated by CCK8, LDH and caspase 8 and 3/7 activity. D) Inhibition of miR-146a expression (i-miR-146a) in LM16 cells increased cell proliferation and decreased the release of LDH and the apoptosis rate as evaluated by CCK8, LDH and caspase 3/7 activity. E) Overexpression of miR-146a (m-miR-146a) upon PLX4032, BRAF/MEKi and sTRAIL treatments in LM47R cells increased cell cytotoxicity and apoptosis, as evaluated by LDH and caspase 8 and 3/7 activity. Data are plotted compared to scrambled control. *: p < 0.05, **: p < 0.01, ***: p < 0.0001 by Student’s unpaired t test. Supplementary Fig. S2. COX2 inhibition increases sensitivity to PLX4032 and to BRAF/MEKi and reduces PGE2 release. A) Relative luciferase activity after co-transfection of PTGS2 3’UTR luciferase reporter vector or control vector with miR-146a mimic or mimic negative control. Experiment was performed in LM16R cells. B) Inverse correlation between miR-146a expression levels and IC50 values of PLX4032 in melanoma cell lines (Spearman analysis). C) Western blot analyses showing downregulation of COX2 after transfection with siRNA against COX2 (siCOX2) compared to scrambled control (S). COX2 protein levels were downregulated to 15%, as determined by quantification of the signal and expressed as the ratio of COX2/Actin intensity. Experiment was performed with LM47R cells. D) Silencing of COX2 by siRNA transfection enhanced cell growth inhibition and increased cell cytotoxicity and apoptosis upon treatment with PLX4032 compared to scrambled control. E) PGE2 release in culture supernatants following 24 h treatment with the COX2 inhibitors celecoxib and NS398, alone or in combination with BRAF/MEKi. F) Combined treatment with celecoxib increased cell growth inhibition and cytotoxicity by PLX4032. ●: interaction index = 1. G) Dose-dependent effect of celecoxib alone (5, 10, 20, 40, 50 and 80 μM) and combined with PLX4032 (3 μM) on cell growth. ●: interaction index = 1 at the dose of 50 μM of celecoxib combined with PLX4032. P values were calculated by Student’s unpaired t test in A, D and F, by one-way ANOVA followed by Bonferroni correction in E, and by two-way ANOVA followed by Bonferroni correction in G. *: p < 0.05, **: p < 0.01, ***: p < 0.0001. Supplementary Fig. S3. miR-146a expression levels are inversely correlated with levels of target genes. Analysis of correlation between miR-146a expression and its target genes EGFR, CCL2 and BCL2L1 in metastatic melanoma specimens. The rp and p values resulting from Pearson analysis are shown. Supplementary Fig. S4. Dynamic culture in bioreactor preserves TME architecture of 3D tumor explants. Representative histological images of H&E-stained 3D tumor sections after 3 days culture in bioreactor. The marked areas in the left panels are shown at higher magnification in the right panels to display the preserved cellularity and tumor tissue histo-architecture. Scale bar 80 μM. Supplementary Fig. S5. miR-146a overexpression increases drug sensitivity in 3D cultures of tumor explants. A) Modulation of direct and indirect miR-146a target genes upon transfection of miR-146a mimic (m-miR-146a) compared to scrambled-transfected control (S) in 3D cultures of BRAF-mutated melanoma tumors from naïve patients. AU: arbitrary units. B) Decreased staining for Ki67 and pERK proliferating cells and increased Caspase 3 positive cells in 3D cultures upon treatment with BRAF/MEKi and transfection with miR-146a (m-miR-146a) or scrambled control (S). Scale bar 10 um.

RATIONALE AND OBJECTIVES: Our goal was to prospectively determine the value of perfusion computed tomography (CT) in the quantitative assessment of tumor-related angiogenesis in cirrhotic patients with hepatocellular carcinoma (HCC). MATERIALS AND METHODS: Forty-seven patients met all the following inclusion criteria: 1) Child-Pugh class A or B liver cirrhosis; 2) presence of a single lesion suspected as HCC at screening ultrasound examination; and 3) lesion diameter between 1 and 3 cm. All patients underwent contrast-enhanced ultrasound, pre- and post-contrast triple-phase CT, and perfusion computed tomographic study using multidetector 16-slice CT. Six parameters related to the blood microcirculation and tissue perfusion were measured for the focal liver lesion and cirrhotic parenchyma: perfusion (P), tissue blood volume (BV), hepatic perfusion index (HPI), arterial perfusion (AP), portal perfusion (PP), and time to peak (TTP). Perfusion parameters were described with quartile values of their distribution; univariate paired and unpaired Wilcoxon signed rank tests were used for statistical analysis. RESULTS: HCC was diagnosed in 21 of the 47 patients; in the remaining 26, HCC was not found at contrast-enhanced ultrasound and multidetector 16-slice computed tomographic study. The values of perfusion parameters measured within tumor tissue were: P (ml/s/100 g): median = 47.0 (first quartile = 36.0, third quartile = 61.4); BV (ml/100 mg): median = 24.0 (first quartile = 18.7, third quartile = 29.3); HPI (%): median = 78.4 (first quartile = 62.9, third quartile = 100); AP (ml/min): median = 45.9 (first quartile = 39.0, third quartile = 60.1); PP (ml/min): median = 9.0 (first quartile = 0.0, third quartile = 24.5); and TTP (seconds): median = 18.7 (first quartile = 16.3, third quartile = 26.5). The corresponding values calculated in cirrhotic surrounding parenchyma were P (ml/s/100 g): median = 11.5 (first quartile = 9.4, third quartile = 13.9); BV (ml/100 mg): median = 10.7 (first quartile = 7.1, third quartile = 14.2); HPI (%): median = 10.6 (first quartile = 8.7, third quartile = 11.9); AP (ml/min): median = 13.2 (first quartile = 10.1, third quartile = 15.5); PP (ml/min) median = 55.2 (first quartile = 40.1, third quartile = 79.5); and TTP (seconds): median = 41.7 (first quartile = 38.9, third quartile = 44.6). P, BV, HPI, and AP values were higher (P < .001), whereas PP and TTP were lower (P < .001) in HCC relative to the surrounding liver. Values of perfusion parameters in the cirrhotic liver of patients with and without HCC were not significantly different (P > .001). CONCLUSION: In cirrhotic patients with HCC, perfusion computed tomographic technique can provide quantitative information about tumor-related angiogenesis.