The immunome is the set of

gene In biology, the word gene has two meanings. The Mendelian gene is a basic unit of heredity. The molecular gene is a sequence of nucleotides in DNA that is transcribed to produce a functional RNA. There are two types of molecular genes: protei ...

s that

code In communications and information processing, code is a system of rules to convert information—such as a letter, word, sound, image, or gesture—into another form, sometimes shortened or secret, for communication through a communicati ...

for

protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residue (biochemistry), residues. Proteins perform a vast array of functions within organisms, including Enzyme catalysis, catalysing metab ...

s which constitute the

immune system The immune system is a network of biological systems that protects an organism from diseases. It detects and responds to a wide variety of pathogens, from viruses to bacteria, as well as Tumor immunology, cancer cells, Parasitic worm, parasitic ...

, excluding those that are widespread in other cell types, and not involved in the immune response itself. It is further defined as the set of peptides derived from the

proteome A proteome is the entire set of proteins that is, or can be, expressed by a genome, cell, tissue, or organism at a certain time. It is the set of expressed proteins in a given type of cell or organism, at a given time, under defined conditions. P ...

that interact with the immune system. There are numerous ongoing efforts to characterize and sequence the immunomes of

human Humans (''Homo sapiens'') or modern humans are the most common and widespread species of primate, and the last surviving species of the genus ''Homo''. They are Hominidae, great apes characterized by their Prehistory of nakedness and clothing ...

mice A mouse (: mice) is a small rodent. Characteristically, mice are known to have a pointed snout, small rounded ears, a body-length scaly tail, and a high breeding rate. The best known mouse species is the common house mouse (''Mus musculus' ...

, and elements of non-human primates. Typically, immunomes are studied using

immunofluorescence Immunofluorescence (IF) is a light microscopy-based technique that allows detection and localization of a wide variety of target biomolecules within a cell or tissue at a quantitative level. The technique utilizes the binding specificity of anti ...

microscopy to determine the presence and activity of immune-related

enzyme An enzyme () is a protein that acts as a biological catalyst by accelerating chemical reactions. The molecules upon which enzymes may act are called substrate (chemistry), substrates, and the enzyme converts the substrates into different mol ...

s and pathways. Practical applications for studying the immunome include

vaccine A vaccine is a biological Dosage form, preparation that provides active acquired immunity to a particular infectious disease, infectious or cancer, malignant disease. The safety and effectiveness of vaccines has been widely studied and verifi ...

s, therapeutic proteins, and further treatment of other diseases. The study of the immunome falls under the field of

immunomics Immunomics is the study of immune system regulation and response to pathogens using genome-wide approaches. With the rise of genomic and proteomic technologies, scientists have been able to visualize biological networks and infer interrelationship ...

Etymology

The word immunome is a

portmanteau In linguistics, a blend—also known as a blend word, lexical blend, or portmanteau—is a word formed by combining the meanings, and parts of the sounds, of two or more words together.

of the words "

immune In biology, immunity is the state of being insusceptible or resistant to a noxious agent or process, especially a pathogen or infectious disease. Immunity may occur naturally or be produced by prior exposure or immunization. Innate and adaptive ...

" and "

chromosome A chromosome is a package of DNA containing part or all of the genetic material of an organism. In most chromosomes, the very long thin DNA fibers are coated with nucleosome-forming packaging proteins; in eukaryotic cells, the most import ...

." See

omics Omics is the collective characterization and quantification of entire sets of biological molecules and the investigation of how they translate into the structure, function, and dynamics of an organism or group of organisms. The branches of scien ...

for a further discussion.

History

The exact size of the human immunome has been a topic of study for decades. However, the amount of information it encodes is said to exceed the size of the human genome by several orders of magnitude due to, at least in part,

somatic hypermutation Somatic hypermutation (or SHM) is a cellular mechanism by which the immune system adapts to the new foreign elements that confront it (e.g. microbes). A major component of the process of affinity maturation, SHM diversifies B cell receptors used t ...

and

junctional diversity Junctional diversity describes the DNA sequence variations introduced by the improper joining of gene segments during the process of V(D)J recombination. This process of V(D)J recombination has vital roles for the vertebrate immune system, as it ...

. Several efforts are attempting to characterize the immunomes of humans and other species. The Human Immunome Program is a major effort, launched in 2016, as a collaborative project between The Human Vaccines Project,

Vanderbilt University Medical Center The Vanderbilt University Medical Center (VUMC) is a medical provider with multiple hospitals in Nashville, Tennessee, as well as clinics and facilities throughout Middle Tennessee. VUMC is an independent non-profit organization, but maintains a ...

, and Illumina, Inc. Its goal is to decipher the complete collection of human B and T immune cell receptors. Thousands of individuals will be studied, representing the range of age, gender, ethnicity, geographical origin, health status, and vaccination status. The results will be shared as an

open-source Open source is source code that is made freely available for possible modification and redistribution. Products include permission to use and view the source code, design documents, or content of the product. The open source model is a decentrali ...

database In computing, a database is an organized collection of data or a type of data store based on the use of a database management system (DBMS), the software that interacts with end users, applications, and the database itself to capture and a ...

. The sequencing project will continue until unique sequences stop appearing within B and T cell receptors and is expected to take ten years. The Immunological Genome Project's stated goal is to characterize the immunome of the mouse, generating "a complete microarray dissection of gene expression and its regulation in the immune system". This project is intended to function as a primary resource. The project engages more than 20 research labs, studying T cells, B cells, and

dendritic cell A dendritic cell (DC) is an antigen-presenting cell (also known as an ''accessory cell'') of the mammalian immune system. A DC's main function is to process antigen material and present it on the cell surface to the T cells of the immune system ...

s, along with many other cell types. The project began in 2008. Non-human primate immunomes are studied because of their genetic similarity to humans. In 2025, the Mal-ID project first sequenced B (BCR) and T cell receptors (TCR) at scale across multiple diagnoses using three

machine learning Machine learning (ML) is a field of study in artificial intelligence concerned with the development and study of Computational statistics, statistical algorithms that can learn from data and generalise to unseen data, and thus perform Task ( ...

models, achieving an area under the receiver operative characteristic curve value of 0.986.

Methods of study

In order to gain useful knowledge about the immunome and its characteristics, the cells and components of the immune system must be phenotyped in a quick and pragmatic manner. There are hundreds of known cell types within the immune system and the possibility of detecting and characterizing them without the use of recent advances in immunophenotyping technology was remote because large amounts of an individual's blood would have been required. This outdated method is called low-dimensional immunophenotyping. However, high-dimensional immunophenotyping is now a possibility. The types of high-dimensional immunophenotyping can be broadly grouped into two categories: the use of

isotope Isotopes are distinct nuclear species (or ''nuclides'') of the same chemical element. They have the same atomic number (number of protons in their Atomic nucleus, nuclei) and position in the periodic table (and hence belong to the same chemica ...

s of

lanthanide The lanthanide () or lanthanoid () series of chemical elements comprises at least the 14 metallic chemical elements with atomic numbers 57–70, from lanthanum through ytterbium. In the periodic table, they fill the 4f orbitals. Lutetium (el ...

and the use of

fluorophore A fluorophore (or fluorochrome, similarly to a chromophore) is a fluorescent chemical compound that can re-emit light upon light excitation. Fluorophores typically contain several combined aromatic groups, or planar or cyclic molecules with se ...

s. These advanced technologies allow for up to 100 parameters to be measured at one time.

Applications

There are potentially far-reaching applications for studying the immunome. Some scientists believe that knowledge gained from the immunome could lead to the discovery of differences in the absolute number of T cell

epitope An epitope, also known as antigenic determinant, is the part of an antigen that is recognized by the immune system, specifically by antibodies, B cells, or T cells. The part of an antibody that binds to the epitope is called a paratope. Although e ...

s, and could reveal antigenic relationships between different but immunologically similar pathogens, potentially unlocking

autoimmune disease An autoimmune disease is a condition that results from an anomalous response of the adaptive immune system, wherein it mistakenly targets and attacks healthy, functioning parts of the body as if they were foreign organisms. It is estimated tha ...

therapies and

organ transplantation Organ transplantation is a medical procedure in which an organ is removed from one body and placed in the body of a recipient, to replace a damaged or missing organ. The donor and recipient may be at the same location, or organs may be trans ...

. Immunome investigation has proven useful in determining the symptoms and potential causes of

pulmonary fibrosis Pulmonary fibrosis is a condition in which the lungs become scarred over time. Symptoms include shortness of breath, a dry cough, feeling tired, weight loss, and nail clubbing. Complications may include pulmonary hypertension, respiratory ...

on a molecular level. The development of vaccines is also an application of immunome study as shown by Carlos F. Suárez and his colleagues. They were able to find components of a malaria vaccine that could be readily used in humans as a result of having characterized the cell surface receptor of an immune cell from an

owl monkey Night monkeys, also known as owl monkeys or douroucoulis (), are nocturnal New World monkeys of the genus ''Aotus'', the only member of the family Aotidae (). The genus comprises eleven species which are found across Panama and much of South Am ...

. These monkeys have been shown to be highly susceptible to human malaria, so they serve as a good model for the disease. It could also be possible to develop an influenza vaccine that would provide protection from several strains of the virus. Furthermore, analyzation of the immunomes of non-human primates and other species can reflect the evolutionary history of species as shown by David F. Plaza and his colleagues. This immunome data can also be helpful when testing antibody therapies on non-human primates to ensure they are safe for humans. This can be accomplished by being able to interpret results in the context of the slight differences in ortholog structure between the human and non-human primate immunomes.

Databases

There are a number of databases corresponding to the different facets of the human immunome and the immunomes of other species.

Immunome Knowledge Base (IKB)

An effort is being made to assemble immunological information into a singular database called the Immunome Knowledge Base(IKB). The two scientists behind the effort, Csaba Ortutay & Mauno Vihinen, have integrated data from three separate databases into IKB. These three databases, Immunome, ImmTree, and ImmunomeBase, all have separate, but related information pertaining to the immunome. Immunome contains entries to official gene names according to the

HUGO Gene Nomenclature Committee The HUGO Gene Nomenclature Committee (HGNC) is a committee of the Human Genome Organisation (HUGO) that sets the standards for human gene nomenclature. The HGNC approves a ''unique'' and ''meaningful'' name for every known human gene, based on a ...

, alternative names, and locations of genes on the chromosomes. ImmTree contains entries related to the molecular evolution of the immune system, including orthologous genes and

phylogenetic tree A phylogenetic tree or phylogeny is a graphical representation which shows the evolutionary history between a set of species or taxa during a specific time.Felsenstein J. (2004). ''Inferring Phylogenies'' Sinauer Associates: Sunderland, MA. In ...

s. Finally, ImmunomeBase is a multi-species database related to immunity. Altogether, as of 2009, IKB has entries for more than 100,000 data items, including 893 entries for genes in the immunome.

Immune Epitope Database (IEDB)

This database serves as a resource for data on antibody and T cell epitopes studied in humans, non-human primates, and other species as it relates to disease, allergies, autoimmunity, and transplantation. The database also has tools to assist in the prediction and analysis of epitopes.

Immunome Database for Marsupials and Monotremes (IDMM)

This database has data for every known marsupial and monotreme immune gene. It serves as a resource for immunologists and researchers studying the evolution of mammalian immunity.

Immunology Database and Analysis Portal (ImmPort)

A database developed for the purpose of promoting the re-use of immunological data. It is a partnership between researchers at the University of California-San Francisco, Stanford University, the University of Buffalo, the Technion - Israel Institute of Technology, and Northrop Grumman. It encompasses results from over 400 studies related to immunology.

Immunological Genome Project (ImmGen)

This database is a public resource containing the data relating to the study of the immune system of the mouse.

Other databases

* Reference Database of Immune Cells (RefDIC) * Innate Immune Database (IIDB) * Immunogenetic Related Information Source (IRIS) * DC ATLAS * Human Immunome Project

References

{{Reflist Systems biology