Researchers analyze precursor lesions to define earliest genetic changes in lung cancer

Despite significant advances in lung cancer treatment, new approaches for early detection and prevention remain limited because the earliest stages of lung cancer development remain unclear. In a recent study, published in Cancer Research, MD Anderson researchers have uncovered gene mutation and expression changes in lung cancer precursor cells to define the earliest events driving tumor progression.

Lung cancer is the leading cause of cancer mortality in the United States, with more than 220,000 new cases and 155,000 deaths expected in 2017, according to the American Cancer Society. Non-small cell lung cancer is the most common type of lung cancer, with lung adenocarcinoma (LUAD) being the most frequent subtype.

Because lung cancer symptoms often don’t appear until advanced stages at disease, there is a need for improve early detection and prevention strategies to reduce the significant impact of this disease. Understanding the catalog of genetic changes that drive normal tissue toward malignancy, termed the “precancer atlas,” may offer insight into new screening or intervention approaches.

Atypical adenomatous hyperplasias (AAHs) are the only known precursors to LUAD, and therefore offer a rare opportunity to characterize the premalignant landscape, explains Paul Scheet, Ph.D., associate professor of Epidemiology and a corresponding author of the study.

For the current study, led by Scheet and Humam Kadara, Ph.D., who is now at the American University of Beirut, researchers performed deep DNA and RNA sequencing on matched samples of normal tissue, AAH and malignant LUAD taken from lung cancer patients. This study is among the few to have to have performed such characterization of AAHs.

The researchers analyzed 67 normal, AAH and LUAD samples from 22 patients evaluated at Aichi Cancer Center (Nagoya, Japan) and Nagasaki University (Nagasaki, Japan) between 2011 and 2015. All but one of the patients had stage I lung cancers.

Among the AAH samples, 23 percent (5/22) had mutations in the oncogene BRAF, known to have a role in lung cancer development. Interestingly, the matched LUAD samples did not exhibit BRAF mutations, but rather 4/5 displayed mutations in EGFR, another oncogene. These samples comprised both smokers and non-smokers.

The second-most common mutated oncogene in AAH samples was KRAS, with 18% (4/22) of samples harboring mutations, all of which were ever-smokers. The matched malignant tissues exhibited mutations in other tumor drivers, including TP53.

Notably, the KRAS and BRAF mutations showed mutual exclusivity in the AAH samples analyzed. The researchers discovered additional mutations in a number of additional oncogenes and tumor suppressors across the samples.

“Our findings reveal potentially divergent pathways driving lung cancer progression from precursor to malignancy,” says Smruthy Sivakumar, M.S., graduate trainee and the study’s lead author. “This indicates there may be distinct subgroups of AAHs with driver mutations in KRAS or BRAF, each with different biological implications.”

In addition to genetic mutations, the researchers performed RNA sequencing in a subset of samples (based on sample availability and quality) to characterize expression profiles throughout the process of LUAD development.

Genes involved in immune-cell trafficking and WNT/β-catenin signaling were elevated in AAHs, compared to normal lung tissue, whereas inflammatory response and TGFB1 pathway genes were repressed. Further, the researchers discovered sets of differentially expressed genes in AAHs with KRAS mutations compared to those with BRAF mutations, underscoring their distinct pathways to tumor development.

LUAD samples displayed gene expression changes associated with increased cell proliferation and decreased cell death, including those regulated by the EGFR, MYC and CSF2 pathways.

Based on known roles for the immune response in tumor development, the researchers looked more closely at known markers of immune function in their samples, explains Scheet.

Generally, the findings suggest activation of pro-tumor immune pathways and inhibition of anti-tumor immune response genes in AAHs compared to normal tissue. LUAD samples displayed gene expression changes suggestive of decreased T-cell activation, including elevated expression of the major immune checkpoint protein, CTLA-4.

“There is clearly a role for immune dysregulation early in the path of lung cancer development, as indicated by our results,” says Scheet. “This highlights a need to pursue research on immune-based intervention strategies at the earliest stages, before lung cancer has progressed to an aggressive malignancy.”

While limited by a small number of samples, this study sheds light on some of the earliest changes occurring in lung cancer precursors. The researchers hope to continue investigation with more samples to better characterize mechanisms driving tumor progression, in the hopes of identifying better markers for detection or strategies for personalized prevention in patients with early stage disease.