NEW YORK – Researchers at the University of California, Los Angeles School of Dentistry plan to develop a next-generating sequencing (NGS) liquid biopsy assay that analyzes EGFR mutations in ultrashort circulating tumor DNA (usctDNA) from saliva samples for the early detection of lung cancer.
In a recently launched feasibility study sponsored by Spectrum Solutions, the UCLA team is analyzing matched saliva and plasma samples from non-small cell lung cancer (NSCLC) patients in the hopes of showing concordance between the sample types.
David Wong, project leader and professor of oral biology at the UCLA School of Dentistry, explained that his team has been researching methods for sequencing genetic material from saliva since the early 2000s.
However, he pointed out that saliva has held a negative "social, behavioral, and cultural" aspect that has until recently delayed research into its potential for diagnosing diseases like cancer and the coronavirus.
"We came together and established the diagnostic potential [at UCLA]," Wong explained. "Saliva has been a biofluid that has [received] very little attention, but that doesn't mean it has no translational or clinical utility," Wong said.
Wong's team initially published data on using saliva to detect baseline EGFR mutations in NSCLC in 2014, using a method called "electric field-induced release and measurement" (EFIRM). After receiving a $5 million grant from the National Cancer Institute in 2018, the group began building a liquid biopsy technology based on EFIRM.
However, Wong said his team wanted to "go beyond" EFIRM by developing a NGS test that looked at ctDNA in liquid samples, highlighting that saliva directly communicates with the body's vascular system and interacts with the external environment.
Wong's team previously found that sequences of usctDNA in saliva were very similar to plasma usctDNA sequences. Because usctDNA have extremely short base pair lengths (about 30 bp), Wong noted that they cannot be detected by PCR-based methods. Instead, researchers must use sequencing methods to analyze cancer mutations.
Stephen Fanning, president and CEO of Spectrum, said that the firm will help Wong's team by providing its SDNA-1000 Saliva Collection Device, which consists of a plastic tube for collecting human saliva samples.
Wong noted that Spectrum initially reached out to UCLA in late 2020 after the firm had successfully adapted the saliva collection kit for COVID-19 diagnostic tests. He said that Spectrum wanted to explore research avenues for its kit in the liquid biopsy space.
"Many researchers who hadn't considered using saliva as a sample in their areas of research are now taking a closer look at the potential diagnostic power saliva presents," Fanning added. Spectrum's saliva collection kits have demonstrated a "unique ability … to stabilize and preserve viral RNA" since the early days of the COVID-19 pandemic, Fanning said.
Spectrum is also providing an unspecified amount of funding for the research and will further support development of clinical methods and technical innovations.
Wong's team will also partner with UCLA's Thoracic Oncology Group and international academic groups in Asia — such as the National Cheng Kung University Hospital in Taiwan — to gather patient samples for the project.
"NSCLC baseline mutations are much more prevalent in Asian countries, as they have three times the frequency of mutations," Wong said. "It's [thus] more productive, in terms of collection, to work with these groups."
As part of the study, Wong and his colleagues will collect saliva and blood samples from 50 NSCLC patients. After extracting 2 to 4 ml of plasma from blood samples, the researchers will generate single-stranded DNA libraries prior to NGS analysis on cfDNA isolated from plasma and saliva.
Wong's team will then sequence the usctDNA in plasma and attempt to detect the same targets in saliva samples. Wong declined to disclose which sequencing technologies his team will use for the assay.
Wong explained that the ultimate goal of the project is to spot EGFR mutations — including exon 19 deletions and L858R — linked to early-stage NSCLC in extracted usctDNA. The team plans to complete the trial by the end of the year.
"This is a unique opportunity to use a biofluid that is not yet in clinical practice [for cancer]," Wong said. "Saliva will hold somatic mutations that excite us for cancer detection, and yet there is a population of these targets uniquely present in saliva that current technology can't see."
While Wong aims to ultimately use the platform for early detection purposes, his team has not yet mapped out a clear commercial path for the NGS assay.
However, Wong believes that if his team could integrate the envisioned NGS assay into a deployable platform that "could be designed for bedside detection for routine collection of saliva every week … we could find out if [patients] have early detectable EGFR mutations."
Fanning believes Spectrum's SDNA kit will help Wong's team develop the assay because of its ability to process numerous tests from a single "stabilized and inactive" saliva sample. In addition, he noted the firm has engineered the kit to increase testing accuracy, eliminating common user collection errors.
Fanning also highlighted that Spectrum's collection, storage, and transport system can be integrated as part of a direct-to-patient fulfillment workflow into new and existing laboratory-developed tests.
"If a patient can spit into a tube and determine by way of their saliva whether or not they have lung cancer, or [even] what stage they're in, that's a lot easier than determining the stage of disease with current methods," Fanning said. "If this project is efficacious, we will look at other opportunities in the cancer field, as [the project] increases the value of saliva."
"This journey [will] unravel a number of intriguing and clinically impactful outcomes, [including] that saliva can harbor these circulating targets through [somatic] mutations … [that] have not been realized by the scientific community," Wong added. "The technology could lead to earlier detection, and this is where we are heading."