Primary Immunodeficiencies: principles of genetic diagnosis

When a person has recurrent infections that do not respond to treatment or frequent episodes of autoimmune diseases, there is a possibility that the underlying cause is a primary immunodeficiency. Early diagnosis of patients with these diseases is essential in order to initiate personalized management and achieve a better prognosis.

The immune system

The immune system is our defense system against possible external attacks and is made up of a complex network of organs, cells, and proteins. This complex network has two operating systems to defend against external agents. On the one hand, we differentiate between the innate immune system, which protects us in a non-specific way from birth, and on the other hand, the adaptive immune system, which becomes more specialized as the body faces different external agents.

Within adaptive immunity, it is possible to distinguish two types of responses: cellular immunity and humoral immunity. The former specializes in fighting intracellular pathogens, such as viruses or pathogens that have been phagocytosed. The main effector cells of cellular immunity are T lymphocytes. On the other hand, humoral immunity acts against extracellular pathogens through molecules such as antibodies. In this case, B lymphocytes are involved, which, upon recognizing antigens, transform into plasma cells responsible for producing antibodies.

When the immune system does not function properly, the individual has an immunodeficiency that can be primary or secondary. Primary immunodeficiencies are due to genetic alterations, while secondary immunodeficiencies are caused by external factors such as treatment with immunosuppressants or other diseases that result in the loss of antibodies. In this article, we focus on primary immunodeficiencies and how genetics can be a useful tool for their medical management.

What are primary immunodeficiencies?

Primary immunodeficiencies (PIDs) are a heterogeneous group of genetic disorders that compromise the immune system from birth, although some of these disorders may appear in adulthood. PIDs cause increased susceptibility to recurrent or severe infections that can affect the skin, ears, lungs, intestines, and other parts of the body. It is estimated that these conditions affect 1 in every 2,000 people, yet recent studies indicate that many of them may be underdiagnosed and could affect up to 1-2% of the population when all types and variants are considered.

PIDs tend to present with infections that are more frequent, longer lasting, or more difficult to treat than infections in people with normal immune systems. These infections are often treated without addressing the underlying cause, leading to recurrence of the disease and increased vulnerability of the patient. If not properly identified and treated, people with IP are at risk of serious, prolonged, and sometimes life-threatening infections. IP can also predispose patients to allergies, autoimmune diseases, and cancer.

In most cases, IPs appear during the first years of life. However, it is important to note that they can also manifest in adults, either due to a misdiagnosis during childhood or because it is a late-onset IP in adulthood.

Classification of PIDs

Although there are numerous types of PIDs, the Primary Immunodeficiency Classification Committee of the International Union of Societies for Immunology (IUIS) has established classification criteria that organize these conditions into 10 main groups depending on the immunological and phenotypic characteristics of each PID:

• Combined immunodeficiencies are those caused by a defect predominantly in T lymphocytes that affects many other components of the patient’s immune system, impacting both cellular and humoral immunity. The most important form is severe combined immunodeficiency (SCID), which encompasses a group of disorders characterized by a poor or absent immune response. Also known as “bubble boy” disease, individuals with SCID are highly susceptible to severe bacterial, viral, and fungal infections. Symptoms include common pneumonia, chickenpox, meningitis, recurrent diarrhea, and growth retardation. SCID is fatal within the first 2 years of life if not treated with hematopoietic stem cell transplantation or gene therapy.
• Combined immunodeficiencies with syndromic features are also included among the pathologies that affect cellular and humoral immunity, in which, in addition to the defect in the immune system, the patient also has alterations in other organs or body systems. One of the most relevant examples is DiGeorge syndrome, in which patients also have cardiac malformations and facial dysmorphia, among other features.
• Antibody-predominant immunodeficiencies are the most common IPs worldwide, accounting for approximately half of all IPs. Selective IgA deficiency is the most common IP, in which serum IgA levels are decreased, but normal levels of other immunoglobulins are maintained. In most cases, patients are asymptomatic. Another common PI within this group is common variable immunodeficiency, which is mostly diagnosed in adulthood.
• Immune dysregulation diseases are a group characterized by autoimmune manifestations with the presence of autoantibodies. In these cases, treatment with immunosuppressants is key to patient management.
• Congenital defects in the number and function of phagocytic cells are pathologies that affect phagocytes, immune system cells that include neutrophils and macrophages. These cells are responsible for phagocytosing (engulfing) pathogens, making them a fundamental pillar of the innate immune system.
• Defects in innate immunity are caused by genetic alterations that expose patients to serious infections by certain microorganisms, such as mycobacteria, viruses, and fungi.
• Autoinflammatory diseases are characterized by abnormal stimulation of the innate immune system, in which the individual frequently experiences recurrent inflammatory episodes with fever as the main sign.
• Complement system defects are a group of rare IPs caused by genetic alterations in the innate immune system, resulting in increased susceptibility to recurrent infections and autoimmune diseases. The complement system comprises a group of proteins that help phagocytes find, identify, and phagocytose microorganisms, with the ability to directly eliminate bacteria and viruses.
• Phenocopies of congenital immunodeficiencies are a recently defined type of IP in which the genetic alteration is somatic, i.e., not inherited.
• Bone marrow failure represents a heterogeneous group of diseases resulting from an underlying dysfunction of hematopoietic cells.

Warning signs: when we need to look further

PI encompasses a heterogeneous group of disorders that manifest themselves in a wide variety of clinical presentations, but which share a number of characteristics that enable specialists to recognize primary immunodeficiency and establish appropriate management for the patient. When an individual presents two or more of the characteristic signs of PIDs, it is essential to initiate a study to determine whether there is any underlying PID. Depending on whether we are dealing with a child or an adult, the signs to recognize are:

Diagnosis of IPs and genetics as a fundamental tool

IPs are rare diseases, but once identified, many of them are treatable, and in some cases, even curable. This is possible thanks to established advanced treatments such as gene therapy or hematopoietic precursor transplantation, especially when it comes to primary bone marrow disease. Without proper diagnosis and treatment, these immune system defects can be chronic, severe, or even fatal. Due to general ignorance, complexity, and the uniqueness of some IPs, their diagnosis can be very complicated.

When a patient presents any of the warning signs mentioned above, a series of tests must be performed to determine whether these signs and symptoms are indicative of IP. Generally, the first step is to conduct a thorough medical history and a series of laboratory tests to make an initial diagnosis. These tests include a blood test to assess the levels of immunoglobulins or immune system cells, such as lymphocytes, and a precise study of the immune system’s cell populations using flow cytometry.

This initial assessment makes it possible to narrow down the differential diagnosis and target genetic testing at a specific group of genes. However, due to the high clinical and genetic heterogeneity of some IPs, the same molecular defect can manifest itself very differently in different individuals, or the patient may have a phenotype that is not fully characterized, making it difficult to select the gene or genes to be analyzed.

Today, Next-Generation Sequencing (NGS) allows us to sequence both the exome and the genome of an individual quickly and affordably, enabling the analysis of a broad set of genes targeted to the patient’s symptoms and clinical manifestations. Genetic diagnosis reveals the cause of the patient’s immune dysregulation, allowing for the establishment of clinical management with personalized treatments and monitoring strategies.

Despite advances in genetic knowledge of IPs, it is not always possible to obtain a genetic diagnosis for all patients. This may be due to the fact that the gene-disease association has not yet been established, to epigenetics, or to other variables. The diagnostic yield of genetic analysis of IPs is around 29%, reaching 38% when using studies based on whole exome sequencing. In this regard, it remains important to integrate genetic information with clinical history and functional studies in order to establish a diagnosis.

Veritas is committed to diagnosing these types of pathologies and making them accessible to as many patients as possible. With this goal in mind, Veritas has a collaboration agreement with the Jeffrey Modell Foundation for the early diagnosis of children with primary immunodeficiencies. In addition to working with the foundation, Veritas offers any specialist the JMF PRIMARY IMMUNODEFICIENCY PANEL, a comprehensive panel that includes the analysis of 575 genes associated with immune system disorders. The panel is based on whole exome sequencing, which allows, in the event that no genetic variants are detected in the genes on the panel, the study to be extended to the whole exome with a diagnostic approach.