Data released at the Society of Gynecologic Oncology's 2017 Annual Meeting on Women's Cancer suggests that understanding the impact of chemotherapy on gene expression could play a key role in therapy decisions (Abstract 19).
“Analysis of matched tumors showed significant alterations in cell cycle, DNA damage, chromatin modification, and Wnt, TGFB, and JAK-STAT signaling,” according to the research team, led by Rebecca C. Arend, MD, Assistant Professor in Gynecologic Oncology at the University of Alabama at Birmingham. “These changes likely reflect tumor dysregulation caused by neoadjuvant chemotherapy (NACT).”
Seeking to evaluate genetic variations in high-grade serous carcinoma (HGSC) pre- and post-NACT, researchers collected plasma and tumor specimens from 19 patients at the time of initial diagnosis when they underwent diagnostic laparoscopy and then again at interval debulking.
Additionally, the investigative team “aimed to observe how gene expression affects specific pathways and to assess the utility of using cell-free DNA (cfDNA) to molecularly profile patients.”
The median age of participants was 74 years (range 47-85) and 70 percent of patients had stage IIIC HGSC.
“Genetic sequencing was conducted on matched samples utilizing the NanoString panel, which looks at the RNA of 770 genes and 13 canonical pathways,” explained Arend. “This allowed us to look at specific, cancer-related pathways during that time period.
“Subsequently, we conducted next-generation sequencing of a panel of 50 genes on both plasma cfDNA and tumor DNA in order to determine the correlation between the tumor mutations and the cfDNA,” she continued.
According to researchers, the top pathways affected by NACT were the cell cycle and DNA damage pathways; the top 5 upregulated genes were NR4A3, NR4A1, THBS4, SFRP2, and RASGRF2.
Analysis of the next-generation sequencing of cfDNA detected more mutations in cancer-related genes than in tumor DNA. “The cfDNA pre-NACT contained 19 mutated genes with 57 specific mutations; the tumor DNA contained six mutated genes with 38 specific mutations,” the authors reported.
When comparing post-NACT mutations, researchers noted similar findings; more genetic diversity was demonstrated by the cfDNA after NACT. “Of the 57 mutations in the plasma pre-NACT, only six persisted, whereas 33 of 38 mutations in the tumor DNA remained unchanged.
“Interestingly, the data revealed that the top genes included nuclear receptor subfamily genes, which help control both apoptosis and the proliferation of cancer cells,” Arend noted. “Another significant gene identified was the WNT pathway gene, a stem cell pathway.”
Additionally, an unexpected finding was the significant downregulation of the DNA damaged pathway and associated genes, reported Arend. Specific genes involved in this pathway included E2F1, CHEK1, and BRCA2.
Arend noted that the major limitation of the study is the sample size. Other limitations, which Arend plans to address, are the need for whole genome sequencing as well as complete RNA sequencing and analysis of protein expression.
As clinical practice continues to evolve, the results of this study have a number of implications for the future.
“Interesting to note, the majority of mutations identified in the cfDNA were not found in the tumor, which highlights the fact that the cfDNA is likely picking up some non-neoplastic DNA,” Arend noted. However, when four patients recurred, researchers collected a plasma sample and found that, in the cfDNA of three out of the four individuals, the mutations previously seen in the tumor were still found by researchers.
In Arend's opinion, this suggests that, with a better mechanism for capturing cfDNA, there is the potential to one day follow these mutations over time instead of having to rebiospy patients repeatedly to make a decision about future treatment or enrollment in clinical trials. “This is one step toward the idea of utilizing cfDNA as liquid biopsy,” she explained.
Arend reiterated that the field is not there yet in terms of being able to utilize this for clinical decision-making, but just the suggestion that these mutations can be followed by clinicians is a noteworthy observation.
Additionally, Arend found that one patient, who had a known BRCA mutation, had the lowest DNA damage pathway score at the time of interval debulking. “While there are not enough numbers at this time, this is hypothesis-generating,” she noted. “There is the possibility that we can look at the RNA expression rather than just the DNA BRCA and that, in turn, could be a surrogate for homologous recombination deficiency, suggesting that those patients could potentially be responders to PARP inhibitors.
“These observations led me to the conclusion that we can potentially use some of these genetic changes to help tailor therapy or make decisions based on the RNA expression changes,” she added.
With these clinical implications in mind, Arend and her team have plans to continue to build upon the promising results of this study.
Arend is committed to looking at the big picture when it comes to what is happening in both the tumor and the blood system. “In order to capture all of the changes that are happening, we need to do whole exome sequencing, complete RNA sequencing, protein analysis, and also look at the immune signature or changes in the immune cells,” she said.
“Ongoing research in my lab includes looking at how some of these pathway changes correlate with immune signature changes in the tumor,” Arend continued. “There have been suggestions in melanoma that an increase or upregulation of the WNT pathway is inversely related to tumor-infiltrating lymphocytes, so that is a particular area of interest of mine moving forward.”
These research areas are key to tailoring targeting therapies for patients, Arend noted. “We are focused on personalized medicine and developing therapies that best serve our patients and their individual needs,” she emphasized. “So, as we move forward, it is my hope to continue to develop this research with a larger patient sample, more time points, and longer follow-up.
“A large portion of research conducted in personalized medicine focuses on the DNA mutations and I believe it is important to look at the RNA expression to determine the functionality of what these mutations mean,” Arend concluded. “As we move forward with tailoring specific treatments for specific patients, it is going to be important to be able to utilize more functional assays that focus on RNA expression.”
Catlin Nalley is associate editor.
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