The COVID-19 pandemic raised urgent calls from health experts worldwide for governments to form a cohesive strategy to prepare for future pandemics—while also putting measures in place to prevent them. Towards that end, the World Health Organization is leading negotiations for a global pandemic preparedness treaty, and it’s set to present its findings at the World Health Assembly in 2025.1
Regardless of the specifics of the pandemic preparedness plan, there’s no doubt immunology researchers will play a prominent role in carrying out its goals. There has already been an uptick in studies aimed at improving the understanding of the human immune system and applying that knowledge to prepare for future pandemics. This work is centered around sophisticated and rapidly evolving genomics technologies. For example, RNA researchers can now use single-cell transcriptomics to study gene expression of individual cells in the immune system, deriving much more precise knowledge than they could if they relied on traditional technologies that only allowed them to average data derived from many different cell populations.
Insights gained from this rapidly evolving field, dubbed “immunomics,” will improve the scientific understanding of the human response to novel pathogens, including how people contract and spread viruses, who is most susceptible to life-threatening complications, and how the response to vaccines can vary among patients. Armed with this information, health systems will be able to react faster and more effectively to emerging pathogens in the future.
Automation of RNA sequencing is key to immunomics, because it enables researchers to collect more data and process it faster than they ever could before. This helps scientists ask and answer more complex questions so they can build a toolkit for pandemic preparedness.
Improving Single-Cell Techniques to Probe Immune Response
Immunomics involves mapping the genes of immune cells with exquisite detail, capturing RNA, proteins and all of the other components of the cell types that govern the immune response to pathogens. This level of immune profiling is difficult to do in traditional cell culture, because the activation of immune cells happens in the context of multiple other cell types and antigens. Until recently, researchers isolated individual antigens and tested them against immune cells to measure responses—a costly, time-consuming approach that limited their ability to visualize the whole immune system.
Laboratory automation combined with single-cell transcriptomics technology is enabling much more sophisticated immunomics studies. For example, an automated method for library preparation can support up to 96 samples per run and reduce hands-on time from 7.5 hours to 40 minutes. In a 2024 experiment comparing manually prepared DNA from 20,000 human kidney cells and 500 blood cells, this automated method generated 216 libraries, vs. just 80 libraries generated from three manual methods. The complexity and sensitivity of the results were comparable between the automated and manual workflows.2 What’s more, researchers who had never used the automated workflow before were able to learn it quickly and generate comparable results to those using a more manual technique.
There are several potential uses for immunomics research that will help improve future pandemic responses. One example is vaccine design. Researchers who are developing RNA vaccines against emerging pathogens need a quick way to analyze the effectiveness of the vaccines in being absorbed by the body and generating the desired immune response. Automated immunomics workflows that can quickly churn out results from 96 patient samples simultaneously help achieve that outcome, while at the same time reducing errors and the risk of contamination that comes from manual processes.
Immunomics can also help drive vaccination strategies during pandemics. By shedding light on “immune memory”—the length of time vaccine-induced antibodies stay in the body and continue fighting the infection—researchers can help government officials and health authorities make recommendations for booster strategies. Immunomics research is also critical for adjusting vaccines to tackle evolving strains of novel viruses.3
The COVID-19 pandemic prompted calls from the WHO and other health authorities to improve the prevention of “zoonotic spillover,” the transmission of viruses from animals to people.4 Here, too, immunomics research is critical. Single-cell analysis and other advanced techniques can uncover biomarkers and environmental vectors that allow authorities to closely track viral transmission. For example, by studying viral DNA collected from minks on two farms and from the people working with them, a team of Dutch researchers showed in 2020 that the novel coronavirus was being transmitted among the animals, and that one farm worker likely caught the disease from a mink.5 The ability to track inter-species transmission of novel pathogens could help authorities better understand the evolution and spread of diseases, thereby improving prevention and containment strategies.6
What You Need to Know
Single-cell transcriptomics and automation are driving advances in immunomics, enabling researchers to analyze gene expression, immune responses, and vaccine effectiveness more efficiently.
Immunomics also aids in vaccine design, tracking immune memory, and adapting to evolving virus strains. It has applications in preventing zoonotic spillovers by identifying viral transmission patterns, as demonstrated by studies on COVID-19 transmission between animals and humans.
Proactive pandemic strategies rely on deeper immune system understanding. Initiatives like the Human Immunome Project aim to use advanced technologies to build publicly available datasets and AI models, accelerating vaccine development and containment strategies.
The effort to better track and control the spread of emerging viruses in densely populated areas is another priority for health systems, and automating sample-processing workflows will be critical to reaching that goal. The value of automation in that process was demonstrated in a study carried out at Cornell University starting in 2020. Anticipating the need to process at least 8,000 COVID-19 tests per day, researchers used robotics and electronic data-transfer methods to automate processes that had been done manually, including sample and reagent transfer for 96-well plates, and pooling and labeling specimens. By the end of February 2023, the lab was processing up to 10,300 samples per day, exceeding the university’s surveillance needs.7
Shifting to Proactive Pandemic Preparedness
Ideally, our understanding of the immune system will improve to the point where in the future, vaccines can be developed and widely distributed well before novel pathogens become pandemics. To achieve that goal, researchers will need to uncover many more molecular details of how the immune system responds to foreign invaders.
One organization that’s contributing to that effort is the Human Immunome Project, a global network of research sites that are building diverse datasets of the human immune system. Their goal is to use advanced omics technologies, including single-cell transcriptomics, to generate datasets and make artificial-intelligence models of the immune system. The models will be publicly available in the hopes of accelerating medical discovery.8
Ultimately, immunomics advances will allow the world’s health authorities to stay ahead of emerging pathogens, more effectively containing their spread, while developing vaccines much faster than they ever could before. To get there, researchers will need advanced, efficient tools for generating and analyzing hundreds of thousands of immunomics datapoints, enhanced by automation. This will be key to shifting from a reactive approach to pandemics—as we saw after the COVID-19 outbreak—to a more proactive approach that’s sure to save lives.
This is the second in a series on preparedness. Check back in tomorrow as we discuss a potential new approach to biocontainment.
References
1.Governments progress on negotiations for a pandemic agreement to boost global preparedness for future emergencies. World Health Organization website. https://www.who.int/news/item/20-09-2024-governments-progress-on-negotiations-for-a-pandemic-agreement-to-boost-global-preparedness-for-future-emergencies. Published September 20, 2024. Accessed December 13, 2024.
2.Zhao A., et al. Accelerating Single Cell Research by Automating Gene Expression Library Construction for 10x Genomics GEM-X Chemistry on the Biomek i7 Hybrid Workstation. 10X Genomics, Beckman Coulter Life Sciences. 2024.
3.Gao J, Zhang C, Wheelock A, et al. Immunomics in one health: understanding the human, animal, and environmental aspects of COVID-19. Frontiers in Immunology. 2024 Sep 4;15:1450380. doi: 10.3389/fimmu.2024.1450380.
4.Prevention of zoonotic spillover. World Health Organization website. https://www.who.int/publications/m/item/prevention-of-zoonotic-spillover. Published February 22, 2023. Accessed December 13, 2024.
5.Oreshkova N, Molenaar RJ, Vreman S, et al. SARS-CoV-2 infection in farmed minks, the Netherlands, April and May 2020. Eurosurveillance. 2020 Jun 11;25(23):2001005. doi: 10.2807/1560-7917.ES.2020.25.23.2001005.
6.Gao J, Zhang C, Wheelock A, et al. Immunomics in one health: understanding the human, animal, and environmental aspects of COVID-19. Frontiers in Immunology. 2024 Sep 4;15:1450380. doi: 10.3389/fimmu.2024.1450380.
7.Laverack M, Tallmadge RL, Venugopalan R, et al. The Cornell COVID-19 Testing Laboratory: A Model to High-Capacity Testing Hubs for Infectious Disease Emergency Response and Preparedness. Viruses 2023, 15, 1555. https://doi.org/10.3390/v15071555.
8.Human Immunome Project: Vision, Mission, & Values. Human Immunome Project website. https://www.humanimmunomeproject.org/about/mission-vision/. Accessed December 13, 2024.
