How Functional Proteomics Adds New Data Layers to Our Understanding of the Innate Immune Response

  • The innate immune response is the first defense against pathogens, and consists of physical barriers, chemical defenses, and defensive cells. This response system can cause inflammation that can be helpful or damaging. Understanding the mechanisms of inflammation and how to prevent an overactive inflammatory response is essential.
  • Defensive cells such as macrophages and NK cells communicate by releasing cytokines, some of which can release multiple cytokines simultaneously, making them polyfunctional. IsoPlexis identifies these superpowered cell subsets which have been shown to be significantly associated with both disease progression and recovery in many studies.
  • IsoPlexis’ technology has identified an innate immune abnormality in multiple sclerosis patients, a subset of monocytes suppressing T cell function in severe COVID-19 cases, and two subsets of monocytes/macrophages with diverging correlations to prognosis in follicular lymphoma.

How Understanding the Innate Immune Response Helps Researchers Identify and Target the Immune Cells Causing Inflammation and Disease Progression

Previously, we outlined the functions of the adaptive immune system and how the body’s specific immune response can be harnessed to develop better therapeutics and vaccines.  Studying and understanding the innate immune response is an important part of treating cancers and other diseases. Researchers can design immunotherapies to harness cells involved in the innate immune response­, such as macrophages, dendritic cells, and NK cells, which detect and attack cancer cells and other unhealthy cells. IsoPlexis’ platform also allows researchers to identify the highly functional cells driving inflammation which can be either beneficial or detrimental to recovery.

The innate immune system is the body’s first line of defense against a pathogen, consisting of physical barriers (skin and mucous membranes) as well as chemical defenses. Unfortunately, the body’s many physical and chemical immune barriers are imperfect. Broken skin can no longer protect against pathogens, and the mucous membrane can sometimes let pathogens escape, especially if it has been damaged. Luckily, the body has some backup plans for when the barrier system isn’t sufficient, starting with the internal innate defenses, which involve mounting attacks from various defensive cells, such as macrophages, dendritic cells, and natural killer cells.

The cells involved in the innate immune response communicate using cytokines. IsoPlexis’ highly multiplexed functional proteomics (both bulk and single-cell) characterizes the cytokines released by innate immune cells and identifies the polyfunctional cells (those secreting multiple cytokines simultaneously), which may promote inflammation or suppress the immune system, and therefore play a critical role in clinical outcome.

How the Balance of Inflammation Can Help and Hinder Defenses Against Disease Progression

Internal responses, such as inflammation, are also part of the body’s internal innate immune response. While inflammation alerts the body to a problem, in some cases, increased inflammation can lead to an immune-related adverse event (IRAE), lowering the body’s ability to fight off a pathogen. Because inflammation caused by infectious agents such as bacteria, viruses, or parasites is often systemic, it cannot pick and choose which cells to kill. This can be harmful and sometimes fatal when inflammation destroys healthy cells, tissues, and organs. Thus, it is critical to be able to monitor the immune response and predict outcomes to enable early intervention in patients with high risk of chronic systemic inflammation and inflammatory response syndrome.

Cells will release cytokines to carry out their functions. Some cell will have very low function, while others are highly functional, secreting multiple cytokines simultaneosly. These highly functional cells, termed “Supervillain cells”, can do a lot of damage. Identifying these highly damaging cell subsets can allow researchers to design targeted therapies to suppress the effects of those cells. Researchers can use IsoPlexis’ unique functional proteomics to create immunotherapies blocking the innate cells promoting disease progression, inflammation, and immune suppression.

Single-Cell Proteomics Reveals Subsets of “Supervillain” Cells

IsoPlexis’ technology has helped accelerate therapy development by multiplexing and capturing native protein environments to provide meaningful data and show greater connectivity to in vivo biology. When it comes to working with the innate immune system, IsoPlexis can identify the polyfunctional cells inflicting damage, in the cases below, and connect them to clinical outcomes. This technology has predicted durable effective responses in cancer immunology, infectious disease, cellular and regenerative medicine, and more, identifying treatable sources of inflammation for better targeted therapies.

In a study published in Blood Cancer, IsoPlexis’ single-cell secreted proteomics (innate immune panel) revealed a correlation between upregulated CD14+SIRPαhi monocytes/macrophages and inferior survival in follicular lymphoma (FL), while upregulated CD14SIRPαlow monocytes/macrophages correlated with improved chances of survival. The researchers also identified enhanced IL-10 as a mechanism driving inferior outcomes in patients with upregulated polyfunctional CD14+SIRPαhi subsets.1 In this study, IsoPlexis’ platform revealed unique intratumoral monocyte/macrophage subsets with diverging correlations to prognosis, and highlighted monocyte functionality as a key mechanism of FL progression.

In another study, recently published in Cell, researchers Su, et al. used IsoPlexis’ functional single-cell proteomics to characterize the immune profiles of patients with mild, moderate, and severe COVID-19.  IsoPlexis identified a marked upregulation of polyfunctional CD4+ and CD8+ T cells as well as monocytes secreting a variety of inflammatory cytokines in COVID-19 patients with moderate to severe disease.2 The researchers found that the greatest shift in immune profile occurred between mild and moderate COVID-19, where patients with moderate illness had the highest CD8+ T cell polyfunctionality. Monocyte polyfunctionality continued to increase with disease severity, potentially repressing T cell function in severe cases. These findings provided insight into COVID-19 pathogenesis and progression as well as potential biomarkers for the development of effective therapeutics.

In a case where researchers wanted to measure the responses of multiple sclerosis (MS) patients to TLR2 stimulation, including those with progressive forms of the disease, IsoPlexis’ technology identified that over 50% of MS patients exhibited upregulated CD14+ monocyte polyfunctionality in response to TLR2 stimulation, while this response was not seen in the control population. Additionally, IsoPlexis found that a significant subset (over 60%) of patients with progressive MS and relapsing-remitting MS showed enhanced response to TLR2, suggesting that these cohorts may have a TLR2-related innate immune abnormality with significant implications on MS pathogenesis.3

IsoPlexis’ Functional Single-Cell Proteomics Provides Novel Mechanistic Insights into Disease Pathogenesis

IsoPlexis’ walk-away automated functional proteomics platform provides ultra-sensitive, highly multiplexed bulk and single-cell proteomics using re-engineered ELISA technology. IsoPlexis’ unique proteomic barcoding system adds the functional data layer missing from traditional technologies, using ultra-low sample volumes. Researchers across disciplines have used these unique assays to generate novel mechanistic insights into disease pathogenesis, accelerating curative medicine with integrated time-saving technologies that get therapies to the clinic faster.

IsoPlexis offers human panels to study the innate immune system on the single-cell and bulk population level, as well as a variety of panels for other research interests. These fully automated innate immune solutions accelerate the pre-clinical trial testing of novel vaccines and therapeutics, with push-button data analysis provided by the integrated IsoSpeak software. These solutions enable functional biomarker discovery and accelerate development through complete single-cell and bulk population functional characterization.

By studying the innate immune system, researchers can identify the mechanisms of protective and damaging innate responses, enabling the development of immune therapies that activate or suppress elements of the immune system to treat cancers, immunosuppression, immune deficiencies, autoimmune diseases, and more. When a novel immune therapy is being developed, it is critical to test the therapy’s effectiveness and ensure it does not cause any unintended adverse effects. IsoPlexis uniquely reveals how cells are truly functioning and identifies the cells that are most active, providing a direct connection to in vivo function and disease pathogenesis that can’t be obtained with other technologies.

See how highly functional inflammatory monocytes were identified as a driver of COVID-19 severity in our webinar with Dr. Jim Heath of the Institute for Systems Biology.


  1. Chen Y, et al. SIRPα expression delineates subsets of intratumoral monocyte/macrophages with different functional and prognostic impact in follicular lymphoma. Blood Cancer 2019; 9: 84
  2. Su Y, et al. Multi-omics resolves a sharp disease-state shift between mild and moderate COVID-19. Cell 2020.
  3. Fujiwara M, et al. Enhanced TLR2 responses in multiple sclerosis. Clinical & Experimental Immunology 2018; 193(3):313-326.
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