Bioanalyzer results for total RNA isolated from (A) AS-FFPE HCC tissues, and (B) good, intermediate, and poor quality FC-FFPE tissues.

<p>The AS- and FC-FFPE RNA samples were extracted from different samples. AS: archived section, FFPE: formalin-fixed paraffin-embedded, HCC: hepatocellular carcinoma, FC: freshly cut, RIN: RNA Integrity Number.</p

Comparison of (A) %P-call and (B) inter-sample correlation between AS-FFPE and FC-FFPE profiles.

<p>AS: archived section, FFPE: formalin-fixed paraffin-embedded, HCC: hepatocellular carcinoma, FC: freshly cut, %P-call: % present call.</p

HL60 (A) or OCI-AML3 cells stably expressing shRNA silencing p53 (B) were treated with Nutlin 3a for 24–96 hrs and analyzed by flow cytometry for AnnV/MDC staining.

<p>HL60 (A) or OCI-AML3 cells stably expressing shRNA silencing p53 (B) were treated with Nutlin 3a for 24–96 hrs and analyzed by flow cytometry for AnnV/MDC staining.</p

Quality of genome-wide transcriptome profiles of (A) AS-FFPE HCC and (B) liver cirrhosis tissues.

<p>Inter-sample correlation is plotted against %P-call. Green lines indicate quality cut-off of %P-call (20%). AS: archived section, FFPE: formalin-fixed paraffin-embedded, HCC: hepatocellular carcinoma, %P-call: % present call.</p

OCI-AML3 cells transduced with LC3-GFP-mCherry construct were treated with 5 μM Nutlin 3a and visualized by confocal microscopy.

<p>Increase in proportion of red ‘puncta’ at 96 hrs compared to 48 hrs (merge images) in Nutlin 3a treated cells indicate completion of autophagic flux.</p

Comparison of transcriptome-based prediction of cirrhosis prognosis between FC-FFPE DASL and AS-FFPE nCounter profiles generated on the same tissue blocks (n = 24).

<p>(A) Cirrhosis prognosis prediction result for each sample. (B) Contingency table of prediction results comparing FC-FFPE and AS-FFPE. (C) Contingency table of prediction results in 13 samples with statistically more confident prediction (prediction confidence p-value <0.05). AS: archived section, FFPE: formalin-fixed paraffin-embedded, FC: freshly cut.</p

Reproducibility of genome-wide transcriptome profiles in (A) AS-FFPE HCC tissues, and (B) good, intermediate, and poor quality FC-FFPE tissues.

<p>Scatter plots of technical replicates are shown for each sample. The AS- and FC-FFPE RNA samples were extracted from different samples. AS: archived section, FFPE: formalin-fixed paraffin-embedded, HCC: hepatocellular carcinoma, FC: freshly cut.</p

Comparison of transcriptome-based prediction of HCC subclass between FC-FFPE and AS-FFPE RNA extracted from the same tissue blocks (n = 64).

<p>(A) HCC subclass prediction result for each sample. Top panel indicates prediction confidence p-values for AS-FFPE (black diamond) and FC-FFPE (green diamond). Middle and bottom panels show prediction results made by using FC-FFPE and AS-FFPE profiles, respectively. (B) Contingency table of prediction results comparing FC-FFPE and AS-FFPE. (C) Contingency table of prediction results in 37 samples with statistically more confident prediction (prediction confidence p-value <0.05). AS: archived section, FFPE: formalin-fixed paraffin-embedded, FC: freshly cut, HCC: hepatocellular carcinoma.</p

OCI-AML3 cells were treated with Nutlin 3a for indicated time and Western blots done for p53, LC3B, Atg 5/12, p62.

<p>OCI-AML3 cells were treated with Nutlin 3a for indicated time and Western blots done for p53, LC3B, Atg 5/12, p62.</p

OCI-AML3 (p53 wild type) or HL–60 (p53 null) cells were treated with DMSO or Nutlin 3a for 72 hours and imaged using transmission electron microscopy.

<p>While OCI-AML3 cells showed numerous electron-dense ‘mitophagic’ vacuoles at 72 hrs of Nutlin 3a treatment, such vacuoles were absent in HL–60 cells (lower panel).</p