Expression profiling by high throughput sequencing
Summary
Immune class in hepatocellular carcinoma (HCC) has been shown to possess immunogenic power; however, how preestablished immune landscapes in premalignant and early HCC stages impact the clinical outcomes of HCC patients remains unexplored. We sequenced bulk transcriptomes for 62 malignant tumor samples from a Korean HCC cohort in which 38 patients underwent total hepatectomy, as well as for 15 normal and 47 adjacent nontumor samples. Using in-silico deconvolution of expression mixtures, 22 immune cell fractions for each sample were inferred, and validated with immune cell counting by immunohistochemistry. Cell type-specific immune signatures dynamically shifted from premalignant stages to the late HCC stage. Total hepatectomy patients displayed elevated immune infiltration and prolonged disease-free survival compared to the partial hepatectomy patients. However, patients who exhibited an infiltration of regulatory T cells (Tregs) during the pretransplantation period displayed a high risk of tumor relapse with suppressed immune responses, and pretreatment was a potential driver of Treg infiltration in the total hepatectomy group. Treg infiltration appeared to be independent of molecular classifications based on transcriptomic data. Our study provides not only comprehensive immune signatures in adjacent nontumor lesions and early malignant HCC stages but also clinical guidance for HCC patients who will undergo liver transplantation.
Overall design
HCC and premalignant samples were collected from HCC or chronic liver disease patients who had undergone surgical resection at Seoul National University Hospital from 2004 to 2009. 15 nontumor samples were collected from patients who received partial hepatectomy for metastatic cancer, cholangiocarcinoma, and polycystic liver disease. Tissue samples were immediately snap-frozen and stored in liquid nitrogen and matched formalin fixed paraffine block were made for histologic diagnosis and immunohistochemical staining. In total, 128 samples (62 malignant tumors, 47 premalignant lesions, 15 nontumor samples and 4 replicates) from 98 patients were collected. Of 54 HCC patients available with clinical information, 35 patients received total hepatectomy for transplantation and remaining 19 patients received partial hepatectomy. All nontumor liver tissues were histologically confirmed to have no evidence of hepatic fibrosis on glass slide and clinical evidence of chronic liver disease, such as viral hepatitis.
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