Genomic analysis of liver cancer reveals unexpected genetic players

June 16, 2017, Baylor College of Medicine
Cancer cell during cell division. Credit: National Institutes of Health

Liver cancer has the second-highest worldwide cancer mortality, and yet there are limited therapeutic options to manage the disease. To learn more about the genetic causes of this cancer, and to identify potential new therapeutic targets for HCC, a nation-wide team of genomics researchers co-led by David Wheeler, Director of Cancer Genomics and Professor in the Human Genome Sequencing Center (HGSC) at Baylor College of Medicine, and Lewis Roberts, Professor of Medicine at the Mayo Clinic, analyzed 363 liver cancer cases from all over the world gathering genome mutations, epigenetic alteration through DNA methylation, RNA expression and protein expression. The research appears in Cell.

Part of the larger Cancer Genome Atlas project (TCGA), this work represents the first large scale, multi-platform analysis of HCC looking at numerous dimensions of the tumor. "There have been large-cohort studies in in the past, but they have been limited mainly to one aspect of the tumor, genome mutation. By looking at a wide variety of the tumor's molecular characteristics we get substantially deeper insights into the operation of the cancer cell at the molecular level," Wheeler said.

The research team made a number of interesting associations, including uncovering a major role of the . Through a combination of p53 mutation, DNA methylation and viral integrations, this pathway becomes aberrantly activated. The sonic hedgehog pathway, the role of which had not been full appreciated in liver cancer previously, is activated in nearly half of the samples analyzed in this study.

"We have a very active liver cancer community here at Baylor, so we had a great opportunity to work with them and benefit from their insights into liver cancer," Wheeler said. Among the many critical functions of the liver, hepatocytes expend a lot of energy in the production of albumin and urea. It was fascinating to realize how the liver cancer cell shuts these functions off, to its own purpose of tumor growth and cell division.

"Intriguingly, we found that the urea cycle enzyme carbamyl phosphate synthase is downregulated by hypermethylation, while cytoplasmic carbamyl phosphate synthase II is upregulated," said Karl-Dimiter Bissig, Assistant Professor of Molecular and Cellular Biology at Baylor and co-author of the study. "This might be explained by the anabolic needs of liver cancer, reprogramming glutamine pathways to favor pyrimidine production potentially facilitating DNA replication, which is beneficial to the cancer cell."

"Albumin and apolipoprotein B are unexpected members on the list of genes mutated in liver cancer. Although neither has any obvious connection to cancer, both are at the top of the list of products that the liver secretes into the blood as part of its ordinary functions," explained Dr. David Moore, professor of molecular and cellular biology at Baylor. "For the cancer cell, this secretion is a significant loss of raw materials, amino acids and lipids that could be used for growth. We proposed that mutation of these genes would give the a growth advantage by preventing this expensive loss."

Multiple data platforms coupled with clinical data allowed the researchers to correlate the molecular findings with clinical attributes of the tumor, leading to insights into the roles of its molecules and genes to help design new therapies and identify prognostic implications that have the potential to influence HCC clinical management and survivorship.

"This is outstanding research analyzing a cancer that's increasing in frequency, especially in Texas. Notably, the observation of gene expression signatures that forecast patient outcome, which we validate in external cohorts, is a remarkable achievement of the study. The results have the potential to mark a turning point in the treatment of this cancer," said Dr. Richard Gibbs, director of the HGSC at Baylor. The HGSC was also the DNA sequence production Center for the project.

Wheeler says they expect the data produced by this TCGA study to lead to new avenues for therapy in this difficult cancer for years to come. "There are inhibitors currently under development for the sonic hedgehog pathway, and our results suggest that those inhibitors, if they pass into phase one clinical trials, could be applied in patients, since the pathway is frequently activated in these patients," added Wheeler.

Explore further: Study identifies a role for the metabolism regulator PPAR-gamma in liver cancer

More information: Adrian Ally et al. Comprehensive and Integrative Genomic Characterization of Hepatocellular Carcinoma, Cell (2017). DOI: 10.1016/j.cell.2017.05.046

Related Stories

Study identifies a role for the metabolism regulator PPAR-gamma in liver cancer

April 10, 2017
Liver cancers are a major cause of cancer-related deaths. Large-scale genetic analyses have associated liver cancer with dysregulation of numerous molecular pathways, but disruptions in insulin signaling pathways appear to ...

Scrib protein identified as a natural suppressor of liver cancer

May 8, 2017
A protein that typically helps keep cells organized and on task becomes a tumor suppressor in the face of liver cancer, scientists say.

Monitoring sugar metabolism in liver may be a key to cancer diagnosis

April 18, 2016
Scientists may have discovered a significant new diagnostic marker for liver cancer, according to a paper published in the April 18 online issue of Nature Cell Biology.

Researchers develop algorithm to find precise cancer treatments

August 9, 2016
University of Hawai'i Cancer Center researchers developed a computational algorithm to analyze "Big Data" obtained from tumor samples to better understand and treat cancer.

Genome of Sezary syndrome points to potential treatment targets

November 10, 2015
A genomic analysis of 37 patients with Sézary syndrome, a rare form of T-cell lymphoma that affects the skin and causes large numbers of atypical T-lymphocytes (an immune system disease) to circulate, reveals mutations in ...

New subtypes of lung cancer can lead to personalized therapies with better outcome

October 24, 2016
Personalized therapies can potentially improve the outcomes of patients with lung cancer, but how to best design such an approach is not always clear. A team of scientists from Baylor College of Medicine and the University ...

Recommended for you

Single-cell study in a childhood brain tumor affirms the importance of context

April 20, 2018
In defining the cellular context of diffuse midline gliomas, researchers find the cells fueling their growth and suggest a potential approach to treating them: forcing their cells to be more mature.

Aggressive breast cancer already has resistant tumour cells prior to chemotherapy

April 20, 2018
Difficult to treat and aggressive "triple-negative" breast cancer is chemoresistant even before chemotherapy begins, a new study by researchers from Karolinska Institutet and the University of Texas MD Anderson Cancer Center ...

Mechanism that drives development of liver cancer brought on by non-alcoholic fatty liver disease discovered

April 19, 2018
A team of researchers from several institutions in China has found a mechanism that appears to drive the development of a type of liver cancer not caused by alcohol consumption. In their paper published in the journal Science ...

Discovery adds to evidence that some children are predisposed to develop leukemia

April 19, 2018
St. Jude Children's Research Hospital researchers have made a discovery that expands the list of genes to include when screening individuals for possible increased susceptibility to childhood leukemia. The finding is reported ...

Scientists identify 170 potential lung cancer drug targets using unique cellular library

April 19, 2018
After testing more than 200,000 chemical compounds, UT Southwestern's Simmons Cancer Center researchers have identified 170 chemicals that are potential candidates for development into drug therapies for lung cancer.

Chip-based blood test for multiple myeloma could make bone biopsies a relic of the past

April 19, 2018
The diagnosis and treatment of multiple myeloma, a cancer affecting plasma cells, traditionally forces patients to suffer through a painful bone biopsy. During that procedure, doctors insert a bone-biopsy needle through an ...

0 comments

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.