Ladner develops method to detect complete history of viral exposures with a single test
Funding for a Pilot Project Program through Northern Arizona University’s Southwest Health Equity Research Collaborative (SHERC) allowed Jason Ladner, assistant professor in the Department of Biological Sciences, to develop a unique “technological toolbox” that can identify and characterize antibodies against many different viruses simultaneously rather than only one at a time.
Called PepSeq, for peptide sequencing, Ladner’s technological toolbox was developed in close collaboration with John Altin, assistant professor in the Pathogen and Microbiome Division at the Translational Genomics Research Institute, or TGen, along with a team of researchers.
PepSeq is being applied to many viral antibody response projects already, including those involving SARS-CoV-2, and will be used more broadly in future research that assists in containing and combating viruses.
“A large part of this [PPP] project was focused on technology development, and this technology for highly-multiplexed serology [PepSeq] forms the basis for many of my ongoing and planned projects,” Ladner said.
PepSeq’s distinctive advancement in identifying and characterizing antibodies
Ladner, who works in NAU’s Pathogen and Microbiome Institute, said that during the past few decades, researchers have made great strides in understanding DNA––the molecule that carries genetic instructions in all living things.
“As a result, there has been a boom in genetic sequencing, which has included a big focus on the characterization of viral infections using molecular diagnostics and genome sequencing,” Ladner said. “Technologies associated with serological characterization, which identify antibodies circulating in the blood, have not advanced at the same rate, and can only detect antibodies against a single virus at a time rather than characterizing multiple viral exposures, as PepSeq does.”
Other complicating factors according to Ladner have been that “molecular [diagnostic] approaches … are limited to detecting active viral infections,” so “exactly the right sample type at the right time must be collected to allow for detection.”
Ladner said that antibodies, on the other hand, provide long-lived records of exposures to pathogens, including viruses, thus allowing for a more comprehensive view of viral exposure history.
Ladner’s PepSeq work
PepSeq uses large libraries of peptides tagged with DNA sequences to precisely identify particular peptides that are recognized by antibodies.
PepSeq technology was used to develop a highly-multiplexed assay, which is a biochemical test that uses protein-bound magnetic beads and high-throughput sequencing—a technology that quickly and successfully sequences DNA—to characterize an individual’s nearly complete history of viral exposures within a single test.Ladner’s project results include:
- A 244,000 peptide assay for highly-multiplexed serology, which broadly covers the full diversity of viruses known to infect humans.
- A streamlined methodology for conducting PepSeq assays in the lab.
- A custom, open source software package for processing the high-dimensional data generated from these assays.
PepSeq’s connection to health equity
Ladner said that despite well-documented disparities in infection rates for particular viruses, scientists still do not have a complete picture of virus-associated health disparities.
“Although these diseases are a global burden, there are also important gender and ethnicity-based health disparities associated with viral infections and therefore, viral-associated disease,” he said.
From his work, Ladner and his colleagues have already released two publications: “Epitope-resolved Profiling of the SARS-CoV-2 Antibody Response Identifies Cross-reactivity with Endemic Human Coronaviruses” and “PepSIRF: A Flexible and Comprehensive Tool for the Analysis of Data from Highly-multiplexed DNA-barcoded Peptide Assays.”
To connect this tool with health equity, Ladner also mentored NAU graduate Alejandra Piña with her Master of Science thesis, “Mapping Virus-Associated Health Disparities Utilizing Highly Multiplexed Serology.”
“We used this approach to broadly characterize differences in viral infection rates among Hispanic and non-Hispanic individuals in Phoenix,” Ladner said.
Ladner said following this study, he is now applying PepSeq to broadly characterize viral exposures in non-human animals.
“Our current understanding of the diversity and ecology of viruses in animals is very limited and expanding knowledge in this area is critical for future pandemic prevention,” Ladner said.
SHERC (U54MD012388), is sponsored by the National Institute on Minority Health and Health Disparities (NIMHD).