The liver cancer proteome


Liver cancer is the 6th most common cancer and the third leading in cancer death worldwide. It is associated with poor prognosis due to the lack of early detection.

Hepatocellular carcinoma is the most common type of primary liver cancer. The overall median survival is 4 months and the overall 5-year survival rate is 3%. The tumor predominantly affects males who are over 50 years of age. Risk factors include infection with hepatotropic viruses such as hepatitis B and C viruses, liver cirrhosis, liver cell dysplasia, exposure to aflatoxins and inborn errors of metabolism. Serum elevation of α-fetoprotein occurs in a large proportion of patients (up to 75%) with hepatocellular carcinoma. Most tumors are detected at an advanced stage are not suitable for liver transplantation.

Cholangiocarcinomas (intrahepatic bile duct cancers) are relatively rare and account for 10-20% of all cases. Cholangiocarcinomas occur in older individuals, usually after the age of 60, and have an overall mean survival time of less than 2 years. This type of tumor have been associated with parasitic infestation of the liver (Clonorchis sinensis), multiple bile duct hamartomas, intrahepatic lithiasis and congenital hepatic fibrosis. Most patients with cholangiocarcinoma show no symptoms until the disease has progressed to a late stage with local spread or metastasis.

Here, we explore the liver cancer proteome using TCGA transcriptomics data and antibody based protein data. 2881 genes are suggested as prognostic based on transcriptomics data from 365 patients; 2618 genes associated with unfavourable prognosis and 263 genes associated with favourable prognosis.

TCGA data analysis


In this metadata study we used data from TCGA where transcriptomics data was available from 365 patients in total with 119 female and 246 male patients. A majority of patients (235 patients) were still alive at the time of data collection. The stage distribution was stage i) 170 patients, stage ii) 84 patients, stage iii) 83 patients, stage iv) 4 patients and 24 patients with missing stage information.

Unfavourable prognostic genes in liver cancer


For unfavourable genes, higher relative expression levels at diagnosis gives significantly lower overall survival for the patients. There are 2618 genes associated with unfavourable prognosis in liver cancer. In Table 1, the top 20 most significant genes related to unfavourable prognosis are listed.

PES1 is a gene associated with unfavourable prognosis in liver cancer. The best separation is achieved by an expression cutoff at 16.6 fpkm which divides the patients into two groups with 30% 5-year survival for patients with high expression versus 55% for patients with low expression, p-value:1.84e-9. Immunohistochemical staining using an antibody targeting PES1 (HPA062439) shows differential expression pattern in liver cancer samples.

PES1 - survival analysis p<0.001
PES1 - high expression
PES1 - low expression

RPA1 is another gene associated with unfavourable prognosis in liver cancer. The best separation is achieved by an expression cutoff at 10.5 fpkm which divides the patients into two groups with 26% 5-year survival for patients with high expression versus 53% for patients with low expression, p-value: 9.00e-9. Immunohistochemical staining using an antibody targeting RPA1 (HPA006914) shows differential expression pattern in liver cancer samples.

RPA1 - survival analysis p<0.001
RPA1 - high expression
RPA1 - low expression

Table 1. The 20 genes with highest significance associated with unfavourable prognosis in liver cancer.

Gene Description Predicted localization mRNA (cancer) p-value
SFPQ splicing factor proline and glutamine rich Intracellular 18.7 7.91e-13
G6PD glucose-6-phosphate dehydrogenase Intracellular 13.5 9.45e-13
KIF20A kinesin family member 20A Intracellular 2.9 2.14e-12
KDM1A lysine demethylase 1A Intracellular,Secreted 7.0 4.47e-12
TRMT6 tRNA methyltransferase 6 Intracellular 3.6 4.70e-12
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Favourable prognostic genes in liver cancer


For favourable genes, higher relative expression levels at diagnosis gives significantly higher overall survival for the patients. There are 263 genes associated with favourable prognosis in liver cancer. In Table 2, the top 20 most significant genes related to favourable prognosis are listed.

IVD is a gene associated with favourable prognosis in liver cancer. The best separation is achieved by an expression cutoff at 27.5 fpkm which divides the patients into two groups with 63% 5-year survival for patients with high expression versus 40% for patients with low expression, p-value: 2.30e-7. Immunohistochemical staining using an antibody targeting IVD (HPA044250) shows differential expression pattern in liver cancer samples.

IVD - survival analysis p<0.001
IVD - high expression
IVD - low expression

Table 2. The 20 genes with highest significance associated with favourable prognosis in liver cancer.

Gene Description Predicted localization mRNA (cancer) p-value
MARC2 mitochondrial amidoxime reducing component 2 Intracellular,Membrane 35.9 1.40e-10
BTNL9 butyrophilin like 9 Membrane 1.4 1.55e-9
CLEC3B C-type lectin domain family 3 member B Intracellular,Secreted 7.3 9.99e-9
RBP4 retinol binding protein 4 Intracellular,Secreted 3135.4 1.74e-8
LCAT lecithin-cholesterol acyltransferase Intracellular,Secreted 17.0 4.21e-8
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The liver cancer transcriptome


The transcriptome analysis shows that 65% (n=12745) of all human genes (n=19479) are expressed in liver cancer. All genes were classified according to the liver cancer-specific expression into one of five different categories, based on the ratio between mRNA levels in liver cancer compared to the mRNA levels in the other 16 analyzed cancer tissues. 467 genes show some level of elevated expression in liver cancer compared to other cancers (Figure 1). The elevated category is further subdivided into three categories as shown in Table 3.

Figure 1. The distribution of all genes across the five categories based on transcript abundance in liver cancer as well as in all other cancer tissues.

Table 3. Number of genes in the subdivided categories of elevated expression in liver cancer.

Category Number of genes Description
Tissue enriched 242 At least five-fold higher mRNA levels in a particular cancer as compared to all other cancers
Group enriched 128 At least five-fold higher mRNA levels in a group of 2-7 cancers
Tissue enhanced 97 At least five-fold higher mRNA levels in a particular cancer as compared to average levels in all cancers
Total 467 Total number of elevated genes in liver cancer

Additional information


Liver transplantation is considered to be the best treatment for hepatocellular carcinoma and also for the underlying cirrhosis. Tumors of late stage are however not eligible for transplantation.Other therapeutic options include surgical resection, targeted systemic chemotherapy and radiotherapy. Early stages of the disease have a much better prognosis with various treatment options.

Histologically, hepatocellular carcinomas present a range of appearances. A common feature is the presence of fibrosis and inflammation as hepatocellular carcinoma often develops in the liver of patients with late stages of chronic hepatitis. Well-differentiated tumors may be difficult to discriminate from normal liver tissues since tumor cells have a similar appearance to normal hepatocytes. The more poorly differentiated tumors display marked pleomorphism, with tumor giant cells showing little resemblance to normal hepatocytes. Characteristic features of hepatocellular carcinomas include a sinusoidal growth pattern and absence of intracellular mucin and wells as lack of bile production. Immunohistochemically, hepatocellular carcinomas are immunoreactive for α-fetoprotein, various keratins, α-1 antitrypsin, various integrins, villin and CD15.

Diagnosis of cholangiocarcinoma is made using biochemical tests, immunohistochemical tumor markers and different types imaging techniques. Early stages of cholangiocarcinoma are treated with surgery while the more advanced tumors are not suitable for surgery and for these cases chemotherapy is used instead.

Cholangiocarcinomas are adenocarcinomas and typical histological features include gland formation, heterogeneity of neoplastic epithelial cells and positive mucin stains. Cholangiocarcinomas are also immunoreactive for various keratins, epithelial membrane antigen and carcinoembryonic antigen. Keratins are used for discrimination of cholangiocarcinoma from hepatocellular carcinoma.

Relevant links and publications


Uhlen M et al, 2017. A pathology atlas of the human cancer transcriptome. Science.
PubMed: 28818916 DOI: 10.1126/science.aan2507

Cancer Genome Atlas Research Network et al, 2013. The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet.
PubMed: 24071849 DOI: 10.1038/ng.2764

UhlĂ©n M et al, 2015. Tissue-based map of the human proteome. Science
PubMed: 25613900 DOI: 10.1126/science.1260419

Kampf C et al, 2014. The human liver-specific proteome defined by transcriptomics and antibody-based profiling. FASEB J.
PubMed: 24648543 DOI: 10.1096/fj.14-250555

Raza A et al, 2014. Hepatocellular carcinoma review: current treatment, and evidence-based medicine. World J Gastroenterol.
PubMed: 24764650 DOI: 10.3748/wjg.v20.i15.4115

Van Beers BE. 2008. Diagnosis of cholangiocarcinoma. HPB (Oxford).
PubMed: 18773062 DOI: 10.1080/13651820801992716

Zhao DY et al, 2017. Current biologics for treatment of biliary tract cancers. J Gastrointest Oncol.
PubMed: 28736630 DOI: 10.21037/jgo.2017.05.04

El-Serag HB. 2012. Epidemiology of viral hepatitis and hepatocellular carcinoma. Gastroenterology.
PubMed: 22537432 DOI: 10.1053/j.gastro.2011.12.061

Histology dictionary - Liver cancer