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Cross-Species Immune System Reference

This project has been completed, and this page is no longer being updated. For new project updates, visit MCM Regulatory Science.

Background | Project Description | Project Outcomes | Accomplishments | Additional Reading

Mass cytometer - Mass cytometry enables scientists to take simultaneous measurements of dozens of features located on and in cells and analyze immune cells in far more detail than previously possible.Performer: Stanford University School of Medicine

Principal Investigator: Dr. Garry Nolan

Contract value: $3,030,123

Project duration: October 2012 - June 2016

Image: CyTOF mass cytometer – Mass cytometry enables scientists to take simultaneous measurements of dozens of cell features and analyze immune cells in far more detail than previously possible (Credit: Stanford)

To request access to the antibody screening and cross-species datasets, please contact Zach Bjornson at bjornson@stanford.edu.


Before investigational medical products, such as drugs, can be tested in humans, product sponsors typically conduct animal studies 1  as part of their documentation to support introducing a new drug product into initial testing in humans, and at later stages of product development depending on need.  These animal studies may be important to get a preliminary idea of concerns about potential toxicity in humans, to identify doses that may be suitable for starting human trials, and sometimes to help understand a drug’s action against a disease.

But how do researchers know what models to use?

To successfully translate results from animal models to human trials, researchers must carefully consider the similarities and differences between animal species and humans.  While other mammals have organs similar to our own (heart, liver, kidneys, etc.), their immune systems are similar, but not identical to humans. For example, naturally occurring Ebola viruses do not infect mice, so researchers must use mouse-adapted viruses to research potential Ebola vaccines and treatments in mouse models. 2

In some cases, such as developing medical countermeasures for potential bioterror threats, human challenge studies (exposing people to the threat agent) would not be ethical or feasible. In these cases, FDA may grant approval based on well-controlled animal studies, when the results of those studies establish that the drug or biological product is reasonably likely to produce clinical benefit in humans. The regulations that set forth this path to approval are referred to as the Animal Rule.

By learning more about differences in signaling pathways between humans and model organisms—as this project will do—future medical countermeasure models can be better qualified. This will allow researchers to focus development efforts on investigational products that are more likely to be effective in humans, ultimately helping to deliver safe, high-quality and effective countermeasures more rapidly.

Project Description

Stanford researchers will use mass cytometry to conduct the first single-cell comprehensive cross-species analyses of immune system function.

CyTOF mass cytometry is a new technology combining flow cytometry and mass spectrometry that enables scientists to simultaneously measure dozens of features located on and in cells. Antibodies tagged with rare earth metals bind to cellular targets and results are obtained from time of flight mass spectrometry. Thus, scientists are able to analyze immune cells in far more detail than was previously possible. 3  Given that the immune system is the key “first responder” to disease threats, it follows that how the immune system responds to a new threat in the first minutes and hours can determine the health outcome for the host—be it human or animal.

Stanford will collect data on human and animal immune responses, and use this data to create species-specific immune function maps. Employing advanced computational techniques, they will overlay the maps to highlight differences and similarities, and map immune responses to certain biothreat agents and possible medical countermeasures in humans and animal models.

The resulting data, including analysis tools to evaluate results, will be made available to the research community through a free, open-access website.

Project Outcomes

This project will help FDA and the research community evaluate potential medical countermeasures by enhancing understanding of where immune functions are similar or different in human and animal models.

  • Expand our understanding of the potential toxicity of medical countermeasures in development
  • Enable us to better understand how candidate countermeasures work (for example, what the mechanism of action is and whether there are unanticipated off-target effects that are beneficial)
  • Enable us to examine the potential impact of host factors, such as age or whether the host is male or female
  • Expand our knowledge of how biothreat agents affect host immune physiology
  • Enable comparison of results from experiments conducted in cells from animals to cells from humans, as well in vivo experiments in animals 

Summary of biological responses across species (Credit: Stanford)

The data from these studies may help identify new biomarkers of disease and interpret in vitro, non-clinical and clinical studies performed to support the identification and development of countermeasures against chemical, biological, radiological, and nuclear (CBRN) agents, and emerging infectious diseases.

The toolbox of reagents (substances or compounds that are added to a system to bring about a chemical reaction, or to see if a reaction occurs) being developed under this proposal and the data generated will also inform studies far beyond those focused on CBRN agents. The end result will translate into improved public health and better states of preparedness against emerging diseases and CBRN threats.

Image: Summary of biological responses across species (Credit: Stanford)

Accomplishments (updated July 2016)

Stanford set out to learn more about the immune system and how drugs affect it, but found there was too much data to analyze using existing systems. They then developed computational systems to handle tremendous amounts of data available with the new CyTOF mass cytometry technology. 4

Accomplishments include:

  • Designing and producing universal antibody panels for humans, macaques, African green monkeys and mice. These panels were freeze-dried in single-use packets to ensure consistency and stability.
  • Analyzing almost 1 billion cells from more than 200 donors under approximately 16 conditions, for a total of 3,136 samples.
  • Creating a reference database listing the cross-reactivity of more than 300 antibodies in five species of non-human primates in five blood cell types.
  • Creating a new web-based analysis platform capable of handling this immense volume of data, and providing programmatic access to the data and descriptive statistics extracted from it.
  • Discovery of a large number of differences between the studied species. Publications discussing these differences are in preparation and will be posted on this site in the coming months.

To request access to the antibody screening and cross-species datasets, please contact Zach Bjornson at bjornson@stanford.edu.

Additional Reading

Spitzer, MH, Gherardini, PF, Fragiadakis, GK, et al. An interactive reference framework for modeling a dynamic immune system. Science. 2015 Jul 10;349(6244):155-?. DOI

This project was funded through the MCMi Regulatory Science Extramural Research program.


Related Links

  • 1Animals are sometimes used in the testing of drugs, vaccines and other biologics, and medical devices, mainly to determine the safety of the medical product. This is sometimes referred to as preclinical testing. For drugs and biologics, the focus of animal testing is on the drug’s nature, chemistry, and effects (pharmacology) and on its potential damage to the body (toxicology). For medical devices, the focus of animal testing is on the device’s ability to function with living tissue without harming the tissue (biocompatibility). There are still many areas where animal testing is necessary and non-animal testing is not yet a scientifically valid and available option. However, FDA has supported efforts to reduce animal testing. In addition, FDA has research and development efforts underway to reduce the need for animal testing and to work toward replacement of animal testing.
  • 2Bente, D, Gren, J, Strong JE, et al. Disease modeling for Ebola and Marburg viruses. Dis Model Mech. 2009 Jan-Feb 2(1-2), 12-17. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2615158/
  • 3Researchers can view 50-100 parameters per cell by looking at the ion content with mass spectrometry, vs. a comparable 10 parameters with flow cytometry, an older testing method.
  • 4Collectively, work on this project was funded by various organizations and agencies, including FDA.
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