Fig 1.
Genomic alterations are common in FL-HCC.
(A) Cumulative average number of genomic segment amplifications and deletions in primary liver tumors, recurrent liver tumors, metastatic lymph nodes, and distant metastases. (B) Total number of genes amplified or deleted (C) in patients with primary and metastatic lesions. (D) Number of amplifications (amp) and deletions (del) gained, lost, or retained in metastatic tumors of the liver (L), peritoneum (P), or lymph nodes (N). Amp ↔ del refers to genes amplified in primary but deleted in metastatic tumors, or deleted in primary but amplified in metastatic tumors. Number of genes amplified or deleted in primary or metastatic tumors for all patients (E,F) and distribution of genomic alterations in primary tumors (G). Lines on dot plots represent medians. *, p<0.05.
Table 1.
Clinicopathologic characteristics of 28 patients and 73 specimens.
Fig 2.
RAE analysis of genomic amplifications and deletions in FL-HCC.
The frequency of genomic gain (red) or loss (blue) in primary (A) and metastatic (B) tumors is indicated on the y-axis, with relative chromosomal location on x-axis. Corresponding genetic elements are indicated in Table 2. Of note, several regions shown of high genomic gain or loss do not encompass gene coding regions and therefore do not appear in Table 2.
Fig 3.
Transcriptome analysis demonstrates intrapatient tumor similarity.
(A) PAM analysis of RNA sequencing data from normal liver and tumor specimens. (B) PAM analysis of RNA sequencing data from 6 patients, matched by data point color, who have multiple tumor specimens available for comparison. (C) Relative tumor mRNA expression compared with normal liver is shown for the 50 most frequently amplified and deleted genes. Lines on dot plot represent medians.
Fig 4.
Differential gene expression reveals similarity between primary and metastatic FL-HCC.
(A) Comparison of upregulated and downregulated genes in primary tumors (Prim), metastases (Met), and normal liver (NL). (B) Gene clustering diagram calculated using normalized expression values from RNA sequencing of specimens from normal liver, primary liver tumors (P), metastatic lymph nodes (N), distant metastases (M), or recurrent liver tumors (R). The 50 most significantly up-regulated and down-regulated genes between normal liver and all tumors are depicted.
Table 2.
Top 20 significantly dysregulated genes in FL-HCC tumors compared with normal liver.