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Biochemistry, Autoimmunity

Editor: Alexander Pozun Updated: 12/19/2022 6:50:18 PM


Autoimmunity refers to an aberration in the body's normal development such that the immune system mounts an attack against its own cells.[1] The etiology behind autoimmune diseases is multifactorial, with genetic, hormonal, and environmental factors all playing a role. This review will discuss basic fundamentals of the antigen self-tolerance process, cellular and molecular processes contributing to autoimmunity, diagnostic indicators, and key diseases.


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The immune system has two arms, the more ancient innate immune system and the more recently evolved adaptive immune system. The innate immune system is non-specific to individual pathogens and cannot build memory. It is a first-line defense that consists of the skin, saliva, tears, bacterial flora, and numerous cells and proteins, including complement, lysozyme, white blood cells, red blood cells, and platelets. 

On the other hand, the adaptive immune system is capable of mounting specific immune responses against pathogens encountered in the past due to its capability to build memory. The adaptive immune system utilizes B- and T- lymphocytes and their products, immunoglobulins, and cytokines to generate a highly specific response that becomes more efficient at attacking a certain pathogen with each subsequent exposure.[2] 

To protect against a wide variety of pathogens, host receptors on lymphocytes undergo extensive gene rearrangement and somatic mutation processes to create a repertoire of receptors that recognize a vast amount of antigens. Upon recognition, the adaptive immune system delivers a message of either immunity or tolerance. Tolerance refers to the process where "self" antigens found normally in the body are prevented from mounting an immune response, while "non-self" antigens mount the appropriate response. When the tolerance process fails, autoimmunity can manifest. Both central and peripheral tolerance are crucial in preventing autoimmunity.[3]


Central Tolerance

The central regions of maturation for T-lymphocytes and B-lymphocytes are in the thymus and bone marrow, respectively. Therefore, mechanisms of tolerance present in these locations are referred to as central tolerance.

T-cell Central Tolerance

The process for immature T-cells begins when they arrive in the thymus from the bone marrow and encounter proteins bound to major histocompatibility complexes (MHC).[4] MHC molecules are cell-surface antigens present in vertebrates, and in humans, they are called human leukocyte antigens (HLA). There are three subtypes, HLA-A, HLA-B, and HLA-C, that comprise MHC Class I. MHC I antigens are expressed on almost every cell type in the body. Other subtypes, namely HLA-DP, HLA-DQ, and HLA-DR, belong to MHC Class II. MHC II molecules are found less ubiquitously, namely in cells of the reticuloendothelial system such as macrophages and B-lymphocytes. The significance of MHC molecules lies in the type of T-lymphocyte with which each type interacts. MHC I molecules bind with CD8+-T lymphocytes initiating a cytotoxic response, and MHC II molecules bind with CD4+-T cells initiating a helper T-cell response.[5]

The central tolerance process begins in the cortical epithelial region of the thymus. Endogenous proteins are bound either to MHC I or MHC II molecules, which then interact with immature double-positive T-lymphocytes that express both CD4+ and CD8+. T-lymphocytes that bind with an intermediate affinity are signaled to survive and mature into single-positive lymphocytes, thus creating lymphocytes that are either CD4+ or CD8+. This is known as positive selection. These cells then move to the corticomedullary junction region, where each CD4+ or CD8+ T-lymphocyte becomes exposed to MHC molecules that are bound to self-peptides. If binding at this stage is of high affinity, the respective T-cell will undergo death by apoptosis. This is known as negative selection.

Central tolerance is the initial way in which autoreactive T-cells are prevented from making it out into the systemic circulation. This is an effective process largely due to the medullary epithelial cells in the thymus. To present a comprehensive array of self-peptides found in all organs of the body, these cells express autoimmune regulator transcription factors (AIRE) that cause increased expression of tissue-restricted antigens found in other parts of the body. Expression of tissue-restricted antigens aids with efficient negative selection. Autoimmunity can develop in cases where mutations arise in AIRE, causing less expression of tissue-restricted antigens. An example of this is the disease autoimmune polyglandular syndrome type I (APECED), characterized by at least two of the following three conditions: candidiasis, hypoparathyroidism, and Addison disease.

B-cell Central Tolerance

The central tolerance process for immature B-cells occurs in the bone marrow. B-cells play a significant role in the immune response to various pathogens through the production of antibodies, also known as immunoglobulins. These antibodies are glycoprotein molecules with a heavy chain and a light chain that bind to antigens, such as those of microbial origin, and facilitate their destruction. There are five classes of immunoglobulins- IgG, IgM, IgA, IgE, and IgD- which play various roles in protecting the body against acute and chronic infections and from pathogens of various types, including bacteria, viruses, parasites, and fungi.[6] In cases where individuals cannot produce certain or all antibodies, recurrent infections are likely to occur.

Activation of the B-cell occurs via interaction of the membrane-bound form of its antibody with the antigen present on the antigen-presenting cell. When this interaction occurs, the B-cell differentiates into a plasma cell and secretes large quantities of specific immunoglobulins targeted to attack the antigen. This process is vital in protecting from foreign antigens. However, when B-cells recognize and destroy self-antigens, autoimmunity arises. Similar to T-cells, there are tolerance mechanisms in place to prevent this from occurring.

Clonal deletion and receptor editing are two main central tolerance mechanisms in B-cell development. To discuss these mechanisms, a brief overview of B-cell development from the immature stage follows.[7] 

The common lymphoid progenitor cell gives rise to pro-B cells in the bone marrow. The pro-B cell does not have any membrane-bound immunoglobulin on its surface. Expression of recombination-activating genes (RAG1 and RAG2) leads to rearrangement and expression of the IgM heavy chain (H-chain) on the immature B-cell. The pro-B cell becomes a larger pre-B cell when this initial IgM heavy chain receptor is expressed on its surface.

The heavy chain locus is composed of smaller gene regions known as the V (variable), D (diversity), and J (joining) gene segments. Rearrangement of these segments, known as VDJ recombination, leads to the generation of unique antigen recognition sites on the immunoglobulin. Pre-B cells then express the immunoglobulin light chain (L-chain) segments, that together with the H-chain, form the initial surface IgM molecule capable of detecting antigens. The antigen detecting site spans over both the heavy chain and light chain. At this stage, central tolerance mechanisms come into play.[7] 

Immature B-cells with surface IgM expressing the H-chain and L-chain are exposed to broadly expressed housekeeping antigens expressed by stromal cells of the bone marrow. If a B-cell binds to self-antigen too strongly, it can undergo receptor editing of the B-cell receptor, the surface IgM molecule. Receptor editing involves VDJ recombination described earlier. If the BCR remains self-reactive after receptor editing, negative selection occurs, and the cell dies by apoptosis. However, if receptor editing leads to the production of a B-cell that is not self-reactive, positive selection occurs, and the immature B-cell is permitted to leave the bone marrow. Therefore, receptor editing is a mechanism that can alter the BCR's specificity before entering the peripheral circulation.[8] 

Another mechanism of central tolerance is that of clonal deletion. Certain immature B-cells may encounter antigens in the bone marrow that cross-link surface immunoglobulins with very high avidity. This interaction causes subsequent downregulation of surface immunoglobulins, which triggers deletion of the B-cell by apoptosis. Aberrations in either clonal deletion or receptor editing can lead to leakage of self-reactive B-cells in the periphery. While peripheral tolerance mechanisms are present that can prevent the development of autoimmunity, most of these mechanisms are reversible. Therefore, central tolerance is key in preventing the development of autoimmunity.

Peripheral Tolerance

After T-lymphocytes and B-lymphocytes leave the thymus and bone marrow, they enter peripheral immune organs and tissues such as the spleen and lymph nodes. In these regions, peripheral tolerance mechanisms prevent autoimmunity from arising in the case that autoreactive lymphocytes made it through all central tolerance processes. There are many different types of peripheral tolerance, and the main subtypes will be discussed here.[9]

Anergy is the first main peripheral tolerance mechanism. Anergy refers to a lack of immune response due to the absence of costimulatory signals. This process in T-lymphocytes is as follows. Mounting an immune response requires not only the MHC: T-cell receptor interaction but also a second signal delivered via costimulatory molecules. There are many costimulatory pathways, but one major axis is that of CD28:B7. CD28 is a receptor present on the T-lymphocyte, which binds B7, a ligand present on the antigen-presenting cell. The MHC: TCR and CD28:B7 interaction together promote growth and survival of the T-lymphocyte via production of the cytokine interleukin-2. Therefore, if the second costimulatory signal is not given, the immune response will not proceed further.

Two proteins that aid in maintaining anergy are cytotoxic T-lymphocyte-associated antigen 4 (CTLA4) and programmed cell death protein 1 (PD-1). CTLA4 is a receptor present on T-lymphocytes, and it binds to B7 with greater affinity than CD28. When a T-lymphocyte recognizes a self-antigen, CTLA4 will bind B7 and cause clathrin-mediated removal of B7, thus preventing the costimulatory signal from occurring. PD-1 works similarly. It is expressed on various classes of T-cells and recognizes the ligands PD-L1, and PD-L2 found on antigen-presenting cells. The binding of PD-1 with either of its ligands causes phosphorylation of tyrosine motifs present on PD-1 with the ultimate downstream effect of downregulation of TCR signaling. Any aberration in the peripheral tolerance process can result in autoimmunity.

Clonal ignorance is another mechanism of peripheral tolerance. This is the process in which autoreactive T-lymphocytes ignore self-antigen through various mechanisms. The ignorance can be due to a physical barrier, such as the blood-brain barrier, preventing lymphocytes from reaching self-antigens. It can also be due to lymphocytes not being presented with a sufficient quantity of self-antigen to result in an autoimmune response.

In other cases, peripheral tolerance occurs via apoptosis. The association of autoreactive T-cells with self-antigen complexes triggers activation of the Fas-Fas ligand system. Both Fas and its ligand are found on T-lymphocytes, and their interaction induces cell death of the T-lymphocyte by triggering the caspase cascade. Therefore, a mutation in the Fas gene can lead to both autoimmunity and lymphoproliferative disorders. This is the pathogenesis of the condition autoimmune lymphoproliferative syndrome (ALPS).[10]


Diagnosing an autoimmune condition requires a multistep approach, as many laboratory tests on their own are not specific to a particular disease. Obtaining a complete blood count (CBC) and comprehensive metabolic panel (CMP) is an initial part of the work-up. Immunologic studies, acute-phase reactant levels, cytokine analysis, and HLA-typing are all techniques that can be utilized as well. Autoimmune conditions are associated with inflammation, and key inflammatory markers assessed are erythrocyte sedimentation rate (ESR), C-reactive protein (CRP), and ferritin. Less frequently, ceruloplasmin, fibrinogen, haptoglobin, and albumin levels are also obtained to assess the inflammatory state. Inflammatory markers, while not specific to a particular autoimmune disease, are helpful in monitoring disease activity.[11] 

Enzyme-linked immunosorbent assay (ELISA) is a tool used to detect specific antibodies. Many autoimmune diseases have strong associations with the presence of certain antibodies. Rheumatoid factor, an autoantibody that attacks the Fc region of the IgG immunoglobulin, is one such molecule found in many autoimmune conditions. It is associated with rheumatoid arthritis, systemic lupus erythematosus (SLE), Sjogren syndrome, cryoglobulinemia, and interstitial fibrosis, among others. A more specific autoantibody for rheumatoid arthritis that can be tested for is anti-cyclic citrullinated peptide (anti-CCP). Several more examples of key autoantibodies and associated diseases are listed below. While this list is not exhaustive, it reflects very common, high-yield autoantibody associations.[11]

  • Anti-nuclear antibody (ANA): SLE, Sjogren syndrome, scleroderma, polymyositis, dermatomyositis, Hashimoto's thyroiditis, autoimmune hepatitis, Graves disease, primary pulmonary hypertension, primary autoimmune cholangitis
  • Anti-double-stranded DNA (anti-dsDNA): SLE
  • Anti-signal recognition particle (anti-SRP), anti-JO-1, anti-PM/Scl: polymyositis and dermatomyositis
  • Antineutrophil cytoplasmic antibody (ANCA): Wegener Granulomatosis, Churg-Strauss syndrome, microscopic polyangiitis 
  • Anti-cardiolipin (aCL)/antiphospholipid (aPL): anti-phospholipid antibody syndrome

Flow cytometry is another laboratory technique that can be used to study certain cell populations based on the presence or absence of various cell-surface markers. For example, it serves to quantify CD4+ T-lymphocytes in patients with human immunodeficiency virus (HIV), which is used to gauge the severity of infection.[11] 

HLA-typing studies examine MHC class I and II genes, which are implicated in various autoimmune diseases. Gel electrophoresis and polymerase chain reaction, along with ELISA, are some of the techniques used to analyze certain types of HLA molecules. Strong associations of certain HLA alleles with autoimmune conditions are listed below. 

  • HLA-B27: ankylosing spondylitis
  • HLA-DR1, HLA-DR4: polyarticular juvenile idiopathic arthritis
  • HLA-DR3, HLA-DR2: lupus 
  • HLA-DRB1: rheumatoid arthritis
  • HLA-DQ2, HLA-DQ8: celiac disease[12]

Utilizing one or more of these techniques is common in the diagnostic approach toward autoimmune diseases. 

Clinical Significance

An estimated 7.6- to 9.5% of the U.S. population reported one of 29 common autoimmune diseases in 2009.[13] The prevalence may potentially be even higher today. Furthermore, autoimmune diseases disproportionately affect females compared to males.[14] An abnormal response to self-antigen recognition at the cellular level translates to a wide variety of clinical manifestations, many of which are debilitating and have a significant impact on quality of life. Autoimmune conditions can have both systemic effects and localized effects. Major clinical features of several major autoimmune diseases in both categories are listed below. It is important to note that this is not an exhaustive list, and even organ-based autoimmune diseases can have varying systemic manifestations as the disease progresses. 

Systemic Autoimmune Diseases

  • Systemic Lupus Erythematosus: at least four of the following eleven criteria must be present: malar rash, discoid rash, photosensitivity, oral ulcers, arthritis, serositis, kidney disorder [most often lupus nephritis], hematologic disorder, neurologic disorder, immunologic disorder, and antinuclear antibody positivity[15]
  • Sjogren Syndrome: xerophthalmia and xerostomia with various renal, pulmonary, dermatologic, and nervous system manifestations possible[16]
  • Scleroderma: excessive deposition of collagen in the skin and internal organs; can present in both local and systemic forms (limited cutaneous systemic and diffuse cutaneous systemic); limited cutaneous systemic form is associated with CREST syndrome of calcinosis, Raynaud phenomenon, esophageal involvement, scleroderma, and telangiectasia [17]
  • Sarcoidosis: noncaseating granulomas in organs throughout the body, most commonly manifesting in the lungs as bilateral hilar lymphadenopathy but can also have ocular, dermatologic, cardiac, gastrointestinal, neurologic, and endocrine manifestations[18]
  • Rheumatoid Arthritis: symmetric synovial inflammation and morning stiffness > 30 minutes, and various extra-articular manifestations including rheumatoid nodules, amyloidosis, and systemic vasculitis[16] 
  • Celiac Disease: duodenal villous atrophy and associated foul-smelling diarrhea and malabsorption upon consumption of gluten-containing foods[19]

Organ-Based Autoimmune Diseases

  • Type 1 Diabetes: autoantibodies to pancreatic islet cells leads to lack of production of insulin, resulting in hyperglycemia, polyuria, and polydipsia[16]
  • Crohn Disease: inflammatory bowel disease characterized by patchy, transmural lesions that can affect the entire gastrointestinal tract, with the possibility of fistulas, erythema nodosum, and pyoderma gangrenosum[20][16][20]
  • Bullous Pemphigoid: a subepidermal blistering disease caused by autoantibodies attacking the hemidesmosome; associated with symmetric tense bullae on the trunk, inner thigh, and flexures as well as urticaria, pruritus, and eczema [21][16][21]
  • Ankylosing Spondylitis: sacroiliac joint tenderness, lower back pain, peripheral arthritis, dactylitis[22]
  • Henoch-Schonlein Purpura: vasculitis associated with purpuric rash, arthralgia, gastrointestinal bleeding, abdominal pain, and nephritis[16]
  • Multiple Sclerosis: demyelination caused by chronic inflammation of the central nervous system results in spinal cord syndromes, optic neuritis, brainstem and cerebellar syndromes, and cognitive impairment[23]



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