Journal News

MCP: Proteome profiling dissects variations in tumors

Saddiq Zahari
April 01, 2018

It is well established that tumors, even those of the same type, exhibit differences in genetics and morphology. This heterogeneity not only exists for tumors from different patients but also across regions within the same tumor. The latter, termed intratumoral heterogeneity, is of particular interest because it directly affects diagnosis and prognosis.

This microscopic photo shows tumor cells from a fine needle aspiration cytology smear of a liver mass. Tumor cells exhibit nuclear enlargement, opened chromatin and multiple nucleoli.Courtesy of Jian-Hua Qiao/NIH flickr

Martin Beck and others at the European Molecular Biology Laboratory study intratumoral heterogeneity. “This has important implications for tumor development because certain cells might be more aggressive than others,” Beck said.

Most studies have looked at intratumoral heterogeneity at the genomic level. It remains largely unknown to what extent the local proteome of tumors intrinsically varies. In a new study in Molecular & Cellular Proteomics, Beck and a group of researchers at the EMBL attempt to answer this question. “We were interested to find out if the proteins contained within individual cells of the tumor are the same or different,” Beck said. Since heterogeneity in the tumor microenvironment, such as the presence of a neighboring blood vessel, may drive genetic changes, he reasoned that it might also be reflected on the level of proteins.

The researchers looked at hepatocellular carcinoma, or HCC, the most common type of liver cancer. They used HCC samples biopsied from patients and then formalin-fixed and paraffin-embedded on microscope slides. Such samples, commonly referred to as FFPE, preserve the integrity of the tissue architecture of the original tumor, allowing the researchers to study the spatial differences in protein expression.

FFPE samples, however, present technical challenges for proteomic analysis, particularly because only a limited amount of proteins can be extracted. To overcome this problem, the researchers developed a novel method that efficiently extracts proteins from FFPE samples. To profile the spatial expression of proteins, they combined this method with a technique called laser-capture microdissection to carve out microscopic regions within the tumor. The extracted proteins then were run on a mass spectrometer for identification.

The researchers first looked at the differences of protein expression between the tumor tissue and the normal tissue immediately adjacent to it. They detected consistent changes of multiple proteins known to be associated with HCC. More importantly, they also identified a few proteins that previously were not known to be HCC-related, opening possibilities for candidate biomarker development. Among these were members of the NADH dehydrogenase complex I. This finding was striking because the researchers showed that the changes were not reflected at the gene expression level, underscoring the importance of proteome profiling.

The researchers went deeper and dissected different regions within the tumor bulk. Here they found significant variations in expression of multiple proteins between areas from the center and the periphery of the tumor. “We could show that even between seemingly identical cells, with the same morphology and the same genome, there are surprisingly pronounced differences on the level of the proteins,” Beck said.

These spatial differences of protein expression include proteins that have previously been identified as HCC biomarkers. “In our analysis, we saw that even proteins that have been proposed as such biomarkers are not evenly distributed across the tumor,” Beck said.

This finding is of immediate clinical importance. Only a small fraction of a tumor can be obtained in a diagnostic or pretreatment biopsy, and thus the region of withdrawal could have a direct impact on the acquired expression profile. “It is possible that the tissue sample taken during biopsy does not reflect the actual state of the entire tumor,” Beck said.

Beck believes the method developed in this study not only allows for studying intratumoral heterogeneity but also can improve cancer proteomics research in general. “Proteomic intratumoral heterogeneity should be taken into account for future cancer research,” he said, “for example in the design of biomarker discovery experiments.”

Saddiq Zahari

Saddiq Zahari is the editor for manuscript integrity at MCP.

Join the ASBMB Today mailing list

Sign up to get updates on articles, interviews and events.

Latest in Science

Science highlights or most popular articles

Lessons from how the polio vaccine
News

Lessons from how the polio vaccine

September 26, 2020

Despite the polio vaccine’s long-term success, manufacturers, government leaders and the nonprofit that funded the vaccine’s development made several missteps.

From the journals: MCP
Journal News

From the journals: MCP

September 25, 2020

How marine iguanas mark their turf. A new way to study Parkinson’s disease. Glycosylation in influenza A. Read about recent papers on these topics in the journal Molecular & Cellular Proteomics.

Gut microbiome shaped by dietary sphingolipids
Journal News

Gut microbiome shaped by dietary sphingolipids

September 22, 2020

A new tracing method described in the Journal of Lipid Research offers clues on how a macronutrient interacts with the microbes that live inside us.

From the journals: JBC
Journal News

From the journals: JBC

September 21, 2020

Proteases that fire up the flu. A sulfate pocket to take out MRSA. Proteins that prompt cancer protrusions. Read about recent papers on these topics and more.

AeroNabs promise powerful, inhalable protection against COVID-19
News

AeroNabs promise powerful, inhalable protection against COVID-19

September 20, 2020

As the world awaits vaccines to bring the COVID-19 pandemic under control, UC San Francisco scientists have devised a novel approach to halting the spread of SARS-CoV-2, the virus that causes the disease.

Keeping bone and muscle strong on the ISS
News

Keeping bone and muscle strong on the ISS

September 19, 2020

Researchers helped mice stay mighty with an experiment to counter the effects of microgravity. The gene treatment might also enhance muscle and bone health on Earth — and in humans.