A team of researchers have found 38 genes and molecules that most likely cause HER2+ cancer cells to spread.
The HER2+ subtype accounts for 20 to 30 percent of early-stage breast cancer diagnoses, which are around 200,000 new diagnoses each year in the United States, leading to approximately 40,000 deaths annually. Several cancer chemotherapy drugs do work well at early stages of the disease, destroying 95 to 98 percent of the cancer cells in HER2+ tumors, but patients can develop resistance and the tumors begin to grow again.
In a new study, Ahmad M. Khalil, PhD, assistant professor in the Department of Genetics at Case Western Reserve University School of Medicine, and colleagues went beyond comparing gene expression in normal and in HER2+ cancer-affected breast tissue and compared gene expression differences among HER2+ breast cancer tissues of uncontrolled HER2 activity with those having greatly diminished HER2 activity. Ultimately their work revealed 35 genes and three long intervening noncoding RNA (lincRNAs) molecules were most associated with the active HER2+ cells.
To obtain special breast cancer tissues in HER2-active and HER2-diminished states, Khalil collaborated with oncologist Lyndsay Harris, MD, who had served as correlative science principal investigator for a clinical trial of the drug trastuzumab. Harris obtained the preserved HER2+ breast cancer tissues for the study from two intervals -- before and then during the trastuzumab clinical trial. Trastuzumab works by disrupting HER2 activity, which in turn prevents this recalcitrant protein from launching uncontrolled cell growth.
From this collection of HER2+ breast cancer tissue, they applied RNA sequencing and then compared the sequences in tissues collected before trastuzumab curtailed HER2 activity with those collected later when HER2 activity declined sharply. Next, investigators grew the HER2+ breast cancer tissue cells in the laboratory and examined genes prominent in the cell culture (in vitro) model of the disease. 44 genes stood out during this portion of the investigation. Finally, Khalil and colleagues obtained publicly available RNA-sequence data sets comparing HER2+ breast cancer with matched normal tissue and found that 35 of those 44 genes passed through this third filter.
"In our investigation, we essentially went from thousands of genes and narrowed it down to 35 genes," Khalil said. "A lot of those genes made sense in terms of carcinogenesis. When they become upregulated because of increased HER2 activity, many of these genes are involved in increased transcription and increased cell proliferation, which are hallmarks of cancer cells."
The investigators applied the same comparative analysis -- RNA sequencing, growing cells in culture and inhibiting HER2 protein -- to observe the role of lincRNAs. Khalil and colleagues only discovered this special group of RNA genes in humans in 2009, and scientists now are slowly unraveling the mystery of lincRNAs. For this study, investigators uncovered three standout lincRNAs that are modulated in activity when subjected to increased HER2 activity.