Molecular Profiling Yields Insights into Glioblastoma

Antonio Iavarone, MD

Glioblastoma is one of the most enigmatic and difficult-to-treat tumor types. Patients with the most common form of this brain cancer, IDH-wildtype glioblastoma, have a median survival of only 14.6 months, a number that has barely budged for decades.

Two new studies seek to understand the disease more fully at the molecular level, with the ultimate aim of developing new treatments. Scientists molecularly profiled IDH-wildtype tumors and their nearby cellular microenvironment, using RNA sequencing on single cells and DNA analysis bulk tumor samples.

“Our goal is to understand what really happens to these tumor cells, individually, before and after therapy,” said Antonio Iavarone, MD, deputy director of Sylvester Comprehensive Cancer Center, part of the University of Miami Miller School of Medicine, and Sylvester Brain Tumor Institute (SBTI) director.

Dr. Iavarone, also a professor of neurological surgery, biochemistry and molecular biology at the Miller School, is a corresponding author on the studies. The work was undertaken as part of a larger research consortium and published in Nature Genetics.

The Glioblastoma Study

The study examined a total of 121 tumor samples from 59 patients. Scientists molecularly profiled glioblastoma tumors and their nearby microenvironments, using RNA sequencing on single cells and DNA analysis on bulk tumor samples.

Samples were obtained from surgeries before and after treatment, which typically consists of surgery, radiation and chemotherapy. The regimen has changed little over the years.

It was an immense undertaking. Single-cell RNA sequencing data was obtained on about 430,000 cell nuclei in total. The resulting data was complex and required deep, computational expertise to analyze.

he effort leveraged the combined capability of multiple institutions including Sylvester, which banded together to form the GBM Cellular Analysis of Resistance and Evolution (CARE) consortium.

Examining tumors from diagnosis to relapse enables researchers “to extract the consistent characteristics of glioblastoma evolution and resistance to therapies,” said Anna Lasorella, MD, professor of biochemistry and molecular biology at the Miller School, director of the Precision Medicine Initiative at Sylvester and SBTI co-director. Dr. Lasorella is a corresponding author on the studies.

Cellular Diversity and Tumor Resilience

The new findings back up glioblastoma’s reputation for being difficult. As with previous studies, the findings show a high degree of heterogeneity between and within tumors. At the cellular and molecular level, each tumor is highly distinct from other tumors. Even the cells within each tumor typically show a high degree of dissimilarity.

“Even though you can call these tumors the same name, glioblastoma, the truth is that, when you look at individual tumors and individual cells within each tumor, you find very different types of cells,” said Dr. Iavarone.

Cellular heterogeneity makes tumors resilient and is thought to underly the disease’s resistance to treatment. Standard treatments can initially kill a lot of cells, but other cells will not respond and seed tumor re-growth.

Finding Patterns, Finding Treatments

Despite observing a high degree of heterogeneity, the researchers found a few consistent, underlying patterns in the data.

Some of the untreated tumors could be divided into subtypes, with distinct molecular states resembling that of neurons, supportive cells called glia or a neuronal projection called a cilium.

The researchers also observed shifts in molecular profiles after treatment. One particularly common change was an increase in cells with neuron-like characteristics. The researchers speculate that this shift might support tumor integration into the neuronal architecture of the brain, including through active connections with healthy neurons.

“We believe this is a way in which tumor cells become resistant to therapy,” said Dr. Iavarone.

By bringing such mechanisms to light, the study might lead to drugs that can interfere with them.

Drs. Lasorella, Iavarone and their colleagues took a step in this direction with a previous study, published last year in Cancer Cell. In that study, they examined glioblastoma cells that had become resistant to therapy through transitioning to a neuronal-like state.

The researchers zeroed in on a highly active cellular regulator in these cells, called BRAF, and targeted it with the drug vemurafenib. Vemurafenib combined with chemotherapy killed such tumor cells in a petri dish and extend lifespan in a preclinical cancer model.

The researchers are now considering designing a clinical trial to test the approach in people. Dr. Iavarone will also be leading an educational session on emerging therapeutics for patients with brain tumors and rare oncogenic drivers at the annual meeting of the American Society of Clinical Oncology.