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NIH Using Fluidigm Mass Cytometry, Other Omics Technologies to Profile COVID-19 Patients


NEW YORK – The National Institutes of Health has launched a clinical trial in which it aims to generate immune profiles of up to 2,000 adults hospitalized with confirmed or presumptive cases of COVID-19.

Fluidigm's mass cytometry platform and its Maxpar Direct Immune Profiling Assay will be one of the primary technologies used in the study, allowing researchers to measure multiplexed panels of immune proteins at the single-cell level.

Fluidigm has been active in SARS-CoV-2 research, as users of its mass cytometry technology have shifted focus from areas like immune oncology to investigating questions around the immune response to the virus.

The NIH study, called the Immunophenotyping Assessment in a COVID-19 Cohort (IMPACC) study, decided to include mass cytometry among its methods upon the suggestion of trial researcher Adeeb Rahman, associate professor and director of technology development at the Icahn School of Medicine at Mount Sinai's Human Immune Monitoring Center.

Rahman has been "an avid user of the mass cytometry technology, and so when the NIH group was pulled together to consider the different types of technology… he was a big promoter of the technology to NIH," said Andrew Quong, Fluidigm's chief science officer.

The IMPACC study is enrolling COVID-19 patients at ten medical centers across the US with researchers collecting a variety of clinical, molecular, proteomic, and other data on them over the course of their hospital stay and during the year following their infection.

Fluidigm's CyTOF platform will be used to look at the immune cell populations and their activation status in blood and endotracheal aspirate samples taken longitudinally over the initial 28 days following a patient's admission and then in blood samples taken longitudinally over the next 12 months.

"The purpose of the study is to really understand the dynamics of how immune cells respond in a very large population of individuals," Quong said. "And you want to look at not just one single time point when, say, they are at the peak of their symptoms, but you also want to look at the recovery of the immune system over time."

He noted that in addition to the long duration, the study would also have the advantage of looking at a much larger patient cohort than have many of the COVID-19 studies done to date.

"I think that is what is really important about this study," he said. "It's very easy to make conclusions from a small number of patients that don't necessarily hold up to a larger group. You may have bias because of the small number of patients you looked at either because they were all from one site or they were from a relatively homogeneous population."

"What's really nice about this study is if you look at the different clinical sites you are going to have a very diverse population," he said. "That will hopefully allow [researchers] to draw conclusions that will be important for helping the larger population."

In addition to Mount Sinai, the participating institutions include Drexel University, Oregon Health & Science University, University Hospitals Case Medical Center, Brigham and Women's Hospital, Emory University, Yale University, Stanford University, the University of California, San Francisco, and the University of California, Los Angeles.

The study will also be using Olink Proteomics' proximity extension assay (PEA) approach to measure circulating protein markers of immune function throughout the 12 months the patients are followed. Olink has a co-marketing deal with Fluidigm through which it offers its protein assays on Fluidigm's BioMark HD rtPCR system, which allows users to measure up to 92 proteins across 96 samples, though the company announced in June that it is adopting next-generation sequencing for readout of large-scale PEA experiments.

The researchers will also collect transcriptomic data from patient blood and respiratory epithelium over the course of the year following infection and will conduct PCR testing through day 28 to assess patient viral load and serology testing to collect information on initial exposure to the virus as well as possibly the progression of the infection.

A number of researchers have been using the CyTOF technology for SARS-CoV-2 research prior to the launch of the NIH study, Quong noted.

Ruth Montgomery, professor of medicine and epidemiology at Yale University and director of the university's CyTOF facility, is currently using a custom protein panel designed with Fluidigm to analyze cells from the airways of patients collected at 10 sites around the country to investigate how their different immune responses correlate with the course of their infections.

At Belgium's KU Leuven, researchers have launched a study that is using CyTOF as well as single-cell RNA sequencing and fluorescence-activated cell sorting to profile COVID-19 patients' immune response in peripheral blood, bronchial alveolar lavage samples, and lung tissue, and compare them to the immune profiles of patients suffering other respiratory infections like influenza.

In March, a team led by researchers at Shanghai University published a paper in Aging and Disease in which they used CyTOF to investigate whether mesenchymal stem cell therapy might help patients with COVID-19 pneumonia. In the study, the researchers looked at 36 protein markers to assess the immune cell profile in patients' peripheral blood before and after stem cell transplantation, finding that in severe infections, the stem cell transplants led to a decrease in cytokine-secreting immune cells and an increase in regulatory T and dendritic cells, which they suggested could have helped modulate the cytokine response.

In May, researchers at the University of Paris used the platform to profile the immune cell populations of 50 COVID-19 patients.

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