Epitope Discovery Program

New contracts awarded for Epitope Discovery

In September 2024, NIAID awarded six contracts under the Innovations in Functional B Cell Immune Epitope Discovery Program and five contracts under the T Cell Immune Epitope Discovery and Mechanisms of T Cell Protection Program.

The Epitope Discovery Program is comprised of two complementary programs: 1) Innovations in Functional B Cell Epitope Discovery, and 2) T Cell Immune Epitope Discovery and Mechanisms of T Cell Protection. Together, these programs support the following areas of research:

  • Discovery of novel epitopes associated with human responses to pathogens that cause chronic or acute infection, including pathogens with pandemic potential
  • Discovery of novel epitopes associated with human allergic responses, development of autoimmune disease, and transplant rejection
  • Structural characterization of epitopes: monoclonal antibody binding and MHC-peptide: TCR binding
  • Validation of the functional role of epitopes in human disease (i.e., participation in immune protection or pathogenesis)
  • Deposition of epitope data into the Immune Epitope Database and Analysis Resource (IEDB)

Additionally, NIAID funds two supporting resources that are available to the biomedical community: the Immune Epitope Database and Analysis Resource (IEDB) and the Tetramer Core Facility.

Contact Information

Email Epitope Discovery for questions or help.

NIH Tetramer Core Facility (TCF)

Reagents to detect and quantify antigen-specific T cells.

Immune Epitope Database and Analysis Resource (IEDB)

Catalog of B cell- and T cell-specific epitopes and MHC ligands for infectious and immune-mediated diseases (allergy, autoimmunity, transplant rejection).

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Introduction

NIAID supports research to enhance understanding of basic immunology, including immunity to infectious pathogens and the etiology, treatment, and prevention of immune-mediated diseases. Critical to this mission is the discovery and characterization of novel epitopes targeted by B and T lymphocyte cells.

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Using the NIAID Data Ecosystem Discovery Portal to Search Across Data Repositories

Data Science Dispatch |

NIAID has developed a platform to help researchers find data related to infectious and immune-mediated disease (IID) across multiple data repositories. The NIAID Data Ecosystem Discovery Portal is a centralized hub cataloging millions of datasets from over 50 sources.

Researchers can use the Discovery Portal to find data, resources, and computational tools from different repositories. This can save them time otherwise spent combing through multiple sources and help them find datasets they weren’t aware of previously.

The Discovery Portal includes resources from IID and generalist repositories. Representative resources include NIAID-sponsored repositories such as AccessClinicalData@NIAID, ImmPort, and VDJServer, as well as repositories funded outside of NIAID but relevant to IID research. Resources in the Discovery Portal include a diverse array of data types spanning multiple domains of IID research, including -omics data, clinical data, epidemiological data, pathogen-host interaction data, flow cytometry, imaging, and other experimental data.

The Discovery Portal supports NIAID objectives of maximizing the impact of scientific data, reducing duplication of efforts in research, and promoting data reuse, data transparency and compliance with data-sharing policies. The portal aligns with many of the principles of findable, accessible, interoperable, and reusable (FAIR) data practices by making data easier to find and access.

Using metadata to drive discovery

The NIAID Data Ecosystem Discovery Portal does not contain data itself. Instead, it contains detailed information about IID datasets and resources drawn from metadata. Users can then access the resources through external links.

The portal uses metadata to support several key features:

  • Search and Discovery: Users can rapidly search millions of datasets across both IID and generalist repositories using the Search or Advanced Search options. Metadata categories such as funding source, repository, and conditions of access help filter search results and identify relevant research data.
  • Metadata Compatibility: Each individual dataset in the Discovery Portal has a “metadata compatibility score,” which displays specific metadata elements collected for a given resource.  Additionally, the Discovery Portal has metadata compatibility visualizations which capture the breadth of metadata at the repository level. This information can help researchers and data contributors quickly understand a repository’s metadata structure, aiding in decisions about where to deposit or retrieve resources.
  • Downloadable Metadata: The portal has buttons that allow users to download metadata to perform meta-analyses.

The Discovery Portal is working to fill missing or incomplete metadata fields (such as Pathogen Species, Health Condition, and Host Species) by augmenting and standardizing metadata fields to provide more of this necessary information for users.

New Program Collection tool and other features

One of the new features of the NIAID Data Ecosystem Discovery Portal is the “Program Collection” filter. These are groups of datasets contributed by specialized NIAID research programs and initiatives. The Discovery Portal displays the Program Collection filter on the search page, and current efforts are focused on expanding Program Collection data.

The Program Collection filter allows researchers to discover high-quality, program-specific data relevant to their area of interest and find collections that align with the broader objectives of NIAID’s strategic research efforts. The feature also amplifies the scientific contributions of participating networks and increases the likelihood of researchers using these datasets. 

Using the Sources page of the Discovery Portal can also help researchers and data providers make informed decisions about different repositories where they can deposit their data.

The Discovery Portal is now connected to National Center for Biotechnology Information (NCBI) databases through NCBI LinkOut. When NCBI database content is linked to data described in the Portal, a link to the related Portal entry can be found on the NCBI page.

Learn more by visiting the Discovery Portal, reviewing the Getting Started page, and exploring the Knowledge Center

Understanding Metadata: A Key to Data Sharing and Reuse

Data Science Dispatch |

Metadata plays a crucial role in sharing and reusing scientific data. Understanding what metadata is and how it is used can accelerate your research and increase the visibility of your work. It can also help to advance the field of infectious and immune-mediated disease (IID) research.

What is metadata?

Metadata is data about data. It provides additional information to help people understand the data, such as its origin, structure, and context. 

For example, for a genome sequence, the data is the actual sequence of nucleotides. The metadata is the author of the data, the date the data was collected, the measurement techniques used, the health condition at the focus of dataset (like asthma or autoimmune diseases), and more. You can see another example of data versus metadata in the video on the right (data management and sharing webinar from the National Institute of Diabetes and Digestive and Kidney Diseases, 4:22-6:28).

Examples of common metadata elements that describe IID research data are available at the NIAID Data Ecosystem’s list of common fundamental and recommended metadata elements

Why is metadata important? When you share scientific data, metadata provides the context that allows others to understand, trust, reproduce, or reuse data. This is particularly important in studies or secondary analyses where data is integrated from multiple sources; comprehensive metadata enables a scientist to combine data from different sources.

Using metadata effectively can also help your data get discovered, reused, and cited—thereby maximizing the value and impact of your research.

Collecting rich metadata during research

Effective metadata use starts with collecting rich metadata throughout the research process. “Rich” metadata is detailed and structured, making it easier for people to quickly learn about your data. 

Including standardized formats and schemas makes it clear which metadata components are present and where they can be found. Using common terminologies, ontologies, and data formats takes this a step further by defining specific metadata elements for both people and computers. Machine-readable metadata allows users to learn about and use data using code, helping them quickly learn about many data files.

Some common examples of collecting metadata in a structured way include defining standardized date and time formats and using ORCID IDs for authors to ensure precise identification.

Biomedical researchers can follow some basic steps to ensure that they are collecting comprehensive and standardized metadata. 

1. Determine necessary metadata content and formats

Collecting data in the format you intend to share it in is more efficient than reformatting everything at the end. Here are some questions to help you determine data and metadata formats:

  • Who will use these data and how will they use it? What information do they need to understand the data?
  • Many research areas have standardized metadata formats that researchers can follow. What metadata standards or schemas do other researchers in your field use? Would using these standards and schemas help researchers understand and reuse these data?
  • Does the target repository or scientific journal have any specific metadata or formatting requirements? If the repository where you plan to share your data has specific guidance, follow that guidance from the start of your research.

2. Create metadata throughout the data lifecycle

Before data collection, collect protocol documentation and set up systems for data and metadata collection. These systems can collect information using the standards, formats, vocabularies, and ontologies selected, and will save you time when preparing data and metadata for publication.

During the data collection phase, document anything that fits into the target metadata fields. These may include the dates data was collected, variables measured, the units of measurement, the instruments used, and the conditions under which the data was collected.

After data collection, add any remaining metadata elements from your plan. These elements may focus more on describing data processing steps, versioning, authors, or related topics. 

3. Prepare to share data and metadata 

Verify that metadata meets requirements for where you would like to share your data, and add any elements that you may finalize late in the data lifecycle, like associated publications, license for reuse, or a data author list prior to sharing.

Throughout the process, you can seek guidance from your program officer or the repositories where you intend to share data to ensure that metadata is collected and shared effectively.

Sharing data and metadata

The NIH Data Management and Sharing Policy encourages sharing metadata that describes or supports your scientific data. NIH recommends data management and sharing practices consistent with the FAIR (Findable, Accessible, Interoperable, and Reusable) data principles, and it strongly encourages the use of established data repositories for preserving and sharing data

In some instances, the full scientific data cannot be shared easily. This may be due to large file sizes — particularly with imaging-related research — or data privacy regulations. However, even if the actual scientific data cannot be shared, sharing metadata is still valuable. This practice ensures that there is a public record of the data's existence and provides important background information that can be used by other researchers.

Metadata is also a powerful tool for finding scientific data in repositories. Researchers can use metadata to search for data sets that match specific criteria. One tool that can help researchers find relevant data is the NIAID Data Ecosystem Discovery Portal, which uses metadata present in data stored in repositories to search across over 50 different IID repositories and data sources. 

Learn more about developing a data management and sharing plan and compliance with relevant NIH data sharing policies by reviewing the Data Policy and Guidance page

Study of the ITK Inhibitor Soquelitinib to Reduce Lymphoproliferation and Improve Cytopenias in Autoimmune Lymphoproliferative Syndrome (ALPS)-FAS Patients

Autoimmune lymphoproliferative syndrome (ALPS) is a rare disorder of the immune system caused by a mutation in the FAS gene. The objective of this study is to determine the efficacy of soquelitinib in reducing spleen volume or target lymph node volume in people with ALPS-FAS.

Contact Information

Office/Contact: Alanvin Orpia, B.S.N.
Phone: 240-669-2935
Email: alanvin.orpia@nih.gov
 

Antibodies Targeting Gut Bacteria Associated with Development of Rheumatoid Arthritis

NIAID Now |

Rheumatoid arthritis (RA) is an autoimmune disease characterized by inflammation and joint destruction. As with many autoimmune diseases, RA disproportionally affects females. The development of RA is believed to involve complex interactions that include both environmental and genetic factors, and understanding the contributions of these factors continues to evolve. Many people with RA have detectable circulating autoantibodies—immune proteins that react to an individual’s own proteins—in their serum for years before experiencing any symptoms. The presence of these autoantibodies prior to joint inflammation suggests that the autoimmune process is initiated elsewhere in the body. 

Recent studies have pointed to an imbalance of commensal bacteria in mucosal sites as a possible cause of inflammation leading to the initiation of the autoimmune process. In particular, expansion of Prevotella copri in stool was associated with new-onset RA, and additional studies found that people living with RA were more likely to have immune reactivity against P. copri, making this an opportune candidate to further investigate. Given that several previous studies using samples from people with RA reported immune reactivity to a P. copri protein called Pc-p27, this study aimed to further characterize the development and timing of antibody responses to this protein in people at risk for or with RA. 

Researchers examined levels of immunoglobulin (Ig)G, an antibody associated with systemic immune responses, and IgA, an antibody associated with immune responses at mucosal sites, in individuals at risk for developing RA, those with early-onset RA, and those with established RA. Overall, people with RA had higher levels of both IgA and IgG anti-Pc-p27 antibodies than their matched healthy controls. When participants were stratified into early and established RA groups, there were notable differences in antibody level trends. Those in the early RA group had trending increases in IgG anti-Pc-p27 antibody levels, while participants with established RA had a significant elevation in IgA anti-Pc-p27 antibody levels. Furthermore, at-risk participants did not have higher IgA or IgG anti-Pc-p27 levels than their matched controls. In the 23 participants in the at-risk group who developed RA during the study, there was no significant increase in either IgA or IgG anti-Pc-p27 antibody levels between the visits before and after receiving their RA diagnosis.

Additional analysis was done to further interrogate the connection between the two known autoantibodies associated with the development of RA, anti-CCP and RF, and the observed differences in IgA and IgG anti-Pc-p27 antibody levels between the RA groups. All RA participants who were positive for both autoantibodies had significantly higher IgA and IgG anti-Pc-p27 antibody levels compared to matched healthy participants in the control group. In addition, at-risk participants who were anti-CCP positive but RF negative had higher IgG anti-Pc-p27 antibody levels than those in the control group.

Taken together, the findings of this study extend the conclusions of previous studies associating immune activity against P. copri with the development of RA. Additional work is needed to understand how P. copri and other microorganisms may contribute to disease pathogenesis, which may ultimately lead to the development of novel interventions to prevent disease in individuals at risk of developing RA. A thorough understanding of the underlying mechanisms that lead to increased susceptibility to autoimmune diseases in women is a critical step in prevention.

References:

Seifert, JA et al. Association of Antibodies to Prevotella copri in Anti–Cyclic Citrullinated Peptide-Positive Individuals At Risk of Developing Rheumatoid Arthritis and in Patients With Early or Established Rheumatoid Arthritis. Arthritis & Rheumatology. DOI 10.1002/art.42370

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Existing Drug Shows Promise as Treatment for Rare Genetic Disorder

A drug approved to treat certain autoimmune diseases and cancers successfully alleviated symptoms of a rare genetic syndrome called autoimmune polyendocrine syndrome type 1 (APS-1).

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In People with Stable Lupus, Tapering Immunosuppressant Linked to Low Flare Risk

NIAID Now |

NIH Trial Gives People with Lupus Data to Inform Treatment Decisions 

In people with a form of lupus called systemic lupus erythematosus (SLE), the risk for a severe flare-up of disease was low for both individuals who tapered off long-term immunosuppressive therapy and those who remained on it, a clinical trial has found. The National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institutes of Health, sponsored and funded the trial. The findings were reported today in the journal The Lancet Rheumatology.

SLE is a chronic autoimmune disease in which the immune system attacks healthy tissues and organs.  An estimated 450,000 people in the United States have the disease. Medications that doctors prescribe for people with SLE help suppress or tamp down their overactive immune systems. One of the most prescribed immunosuppressants for SLE, mycophenolate mofetil or MMF, effectively treats moderate and severe forms of the disease but also increases the risk of infections, cancers, severe birth defects, miscarriage, and impaired responses to vaccines when the drug is used long-term. Tapering off MMF once SLE symptoms subside reduces these side effects but could risk exposing the individual to a disease flare with the potential to cause a range of symptoms, including fatigue, rash, arthritis, and internal organ damage. 

Until today's report, little evidence existed to help people with SLE and their physicians understand the likelihood of a flare after tapering off MMF. The new findings will help people with SLE make informed decisions about withdrawing treatment based on their personal circumstances and risk tolerance. 

The NIAID-funded Autoimmunity Centers of Excellence network conducted the trial under the leadership of Judith A. James, M.D., Ph.D., and Eliza F. Chakravarty, M.D. Dr. James is professor and chair of the Arthritis & Clinical Immunology Research Program at the Oklahoma Medical Research Foundation. Dr. Chakravarty was an associate professor in the same program during the study. The National Institute of Arthritis and Musculoskeletal and Skin Diseases, part of NIH, supports the database for the biological samples processed during the trial.

The trial involved 102 people with SLE ages 18 to 70 whose symptoms had subsided after treatment with MMF. Participants had been taking the drug for an average of 6.6 years. Eighty-four percent of participants were female, reflecting the disproportionate prevalence of lupus in women. Seventy-six percent of participants had a history of lupus nephritis—kidney inflammation that can harm kidney function. Forty-one percent of participants were Black, 40% were White, 21% were Hispanic/Latino, 10% were Asian, and 2% were American Indian/Alaska Native.

The study team assigned participants at random to either taper off MMF over a 12-week period or to remain on their baseline MMF dose. Investigators followed the participants for 60 weeks to monitor if and when they experienced a flare severe or persistent enough to require either new immunosuppressive therapy or higher doses of it. 

By week 60, 9 of 51 participants in the MMF withdrawal group and 5 of 49 in the MMF maintenance group had severe or persistent flares requiring new or increased immunosuppressive therapy. The estimated risk of such flares by week 60—a metric that reflected both occurrence and timing—was up to 18% in the withdrawal group and 11% in the maintenance group. The investigators also looked at five different measures of lupus flares and found that treatment withdrawal consistently led to a 6% to 8% increase in the risk for flares. For participants with a history of kidney disease, the increase in risk was higher, at 14%. One benefit of MMF withdrawal, however, was a reduction in infections. Forty-six percent of the withdrawal group had at least one infection compared with 64% of the maintenance group. 

This study is the first clinical trial of therapy withdrawal in people with SLE who no longer experience symptoms on long-term MMF, according to the researchers. Their findings suggest that MMF may be safely withdrawn in many people with stable SLE, they write, but larger studies and longer follow-up are still needed.

Reference: EF Chakravarty, et al. Mycophenolate mofetil withdrawal in systemic lupus erythematosus patients. The Lancet Rheumatology DOI: 10.1016/S2665-9913(23)00320-X (2024).

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Promising Advances for Antibody Treatment of Viruses that Cause Neurologic and Arthritic Diseases

NIAID Now |

NIAID scientists and colleagues are one step closer to developing a safe and effective therapy against alphaviruses with the identification of SKT05, a monoclonal antibody (mAb) derived from macaques vaccinated with virus-like particles (VLPs) representing three encephalitic alphaviruses.

Spread by mosquitos, alphaviruses primarily affect people in one of two ways: causing severe neurological impairment such as encephalitis (brain swelling) or crippling muscle pain similar to arthritis. Western, eastern and Venezuelan equine encephalitis viruses (EEV) are examples of the former, while chikungunya and Ross River viruses are examples of the latter.

Building on studies from the past decade, scientists in NIAID’s Vaccine Research Center and colleagues knew that macaques produce dozens of different protective antibodies when experimentally vaccinated against the EEVs. In a new study published in Cell, the research team identified 109 mAbs in macaques immunized with the experimental western, eastern, and Venezuelan EEV VLP vaccine. All antibodies were individually tested for binding and neutralization against the three EEVs, with the best ones also assessed against arthritogenic alphaviruses not included in the vaccine. Collaborators included scientists from NIAID’s Laboratory of Viral Diseases, USAMRIID’s Virology Division, and Columbia University.

Their work identified SKT05 as the most broadly reactive antibody – remarkably, it also provided protection against both types of alphaviruses, those that cause encephalitis and those that cause arthritic-like disease. High-resolution structural studies further revealed that the way SKT05 binds to alphaviruses could make it resistant to surface changes that can occur in viruses – which means the mAb is likely to have lasting effectiveness.

Further studies are planned to investigate potential clinical development of SKT05. They aim to better define how SKT05 interacts with viruses and whether it can confer protective benefits against additional alphaviruses.

References:
M Sutton et al. Vaccine elicitation and structural basis for antibody protection against alphaviruses. Cell DOI: https://doi.org/10.1016/j.cell.2023.05.019 (2023).

EE Coates, et al. Safety and immunogenicity of a trivalent virus-like particle vaccine against western, eastern, and Venezuelan equine encephalitis viruses: a phase 1, open-label, dose-escalation, randomised clinical trial. Lancet Infectious Diseases (2022).

SY Ko, et al. A virus-like particle vaccine prevents equine encephalitis virus infection in nonhuman primates. Science Translational Medicine (2019).

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T Cells Can Activate Themselves to Fight Tumors

Immunotherapy Eliminates Disease-Causing Cells in Mice with MS-Like Disease

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Washington University School of Medicine in St. Louis
Short Title
Immunotherapy Eliminates Disease-Causing Cells in Mice with MS-Like Disease
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