Investigation of Transcription Factor and Cytokine Gene Expression Levels in Helper T Cell Subsets Among Turkish Patients Diagnosed with ICF2 (Novel ZBTB24 gene Variant) and ICF3 (CDCA7 Variant) Syndrome.

Immunodeficiency, centromeric region instability, facial anomalies syndrome (ICF), is a rare disease with autosomal recessive inheritance. ICF syndrome. It has been reported that ICF syndrome is caused by mutations in the DNMT3B (ICF1), ZBTB24 (ICF2), CDCA7 (ICF3), and HELLS (ICF4) genes. As a result of literature research, there are no studies on transcription factor and cytokine expressions of helper T cell subsets in ICF syndrome. In the study; Th1 (TBET, STAT1, STAT4), Th2 (GATA3, STAT6), Th17 (RORgt, STAT3), Treg (FoxP3, STAT5) transcription factors and the major cytokines of these cells (Th1; IFNG, Th2; IL4, Th17; IL17A-21-22, Treg; IL10, TGFß) expressions were aimed to be evaluated by qRT-PCR. Patients (ICF3: three patients; ICF2: two patients), six heterozygous individual and five healthy controls were included in the study. All patients had hypogammaglobulinemia. Except for the CD19 cells of P2 from patients diagnosed with ICF3, the CD3, CD4, CD8, and CD19 cells in the other ICF3 patients were normal. However, the rates of these cells were low in patients with ICF2 syndrome. Factors belonging to patients' Th1, Th17 and Treg cells were significantly lower than the control. Additionally, novel mutation was detected in ZBTB24 gene (c.1121-2 A > T). Our study is the first molecular study on Th cell subsets in patients with ICF syndrome and a new mutation that causes ICF2 syndrome has been identified.

Characteristics of Endemic Mycoses Talaromyces marneffei Infection Associated with Inborn Errors of Immunity.

BACKGROUND: Talaromyces marneffei (T. marneffei) is an opportunistic pathogen that causes endemic mycoses, which could lead to multiple organ damage. Talaromycosis is frequently disregarded as an early cautionary sign of immune system disorders in non-HIV-infected children. OBJECTIVE: We conduct a comprehensive review of the genotypes and clinical features of talaromycosis in patients with IEI to enhance clinical awareness regarding T. marneffei as a potential opportunistic pathogen in individuals with immune deficiencies. METHODS: A systematic literature review was performed by searching PubMed, Cochrane Central Register of Controlled Trials, Web of Science, EMBASE, and Scopus. Data on IEI patients with talaromycosis, including genotypes and their immunological and clinical features, were collected. RESULTS: Fifty patients with talaromycosis and IEI were included: XHIM (30.0%), STAT3-LOF deficiency (20.0%), STAT1-GOF (20.0%), IL2RG (6.00%), IFNGR1 (6.0%), IL12RB1 (4.0%), CARD9 (4.0%), COPA (4.0%), ADA (2.0%), RELB deficiency (2.0%), and NFKB2 (2.0%). Common symptoms of respiratory (43/50, 86.0%), skin (17/50, 34.0%), lymph node (31/50, 62.0%), digestive (34/50, 68.0%), and hematologic (22/50, 44.0%) systems were involved. The CT findings of the lungs may include lymph node calcification (9/30), interstitial lesions (8/30), pulmonary cavities (8/30), or specific pathogens (4/30), which could be easily misdiagnosed as tuberculosis infection. Amphotericin B (26/43), Voriconazole (24/43) and Itraconazole (22/43) were used for induction therapy. Ten patients were treated with Itraconazole sequentially and prophylaxis. 68.0% (34/50) of patients were still alive, and 4.0% (2/50) of were lost to follow-up. The disseminated T. marneffei infection resulted in the deaths of 14 individuals. CONCLUSIONS: The XHIM, STAT1-GOF, and STAT3-LOF demonstrated the highest susceptibility to talaromycosis, indicating the potential involvement of cellular immunity, IL-17 signaling, and the IL-12/IFN-γ axis in T. marneffei defense. T. marneffei infection may serve as an early warning indicator of IEI. For IEI patients suspected of T. marneffei, metagenomic next-generation sequencing (mNGS) could rapidly and effectively identify the causative pathogen. Prompt initiation of antifungal therapy is crucial for optimizing patient outcomes.

Primary Immunodeficiency: Specific antibody deficiency with normal IgG.

Specific antibody deficiency (SAD) is a common primary immunodeficiency disorder that should be considered in older children and adults with recurrent and/or severe sinopulmonary infections. The diagnosis is characterized by inadequate antibody response to polysaccharide vaccine, specifically, pneumococcal, with normal responses to protein antigens and normal levels of serum immunoglobulins as well as immunoglobulin G (IgG) subclasses. The underlying mechanism for SAD is not completely elucidated. It is understood that young children have limited polysaccharide responsiveness, which develops with increased age. Due to this phenomenon, the consensus is that there is adequate immune maturity after age 2 years, which is the earliest for the SAD diagnosis to be established. There remains a lack of consensus on thresholds for polysaccharide nonresponse, and there are several commercial laboratories that measure a range of serotypes, with the recommendation for patients to have their diagnostic evaluation with serotype testing both before vaccination and after vaccination to be conducted by the same laboratory. Once a diagnosis has been made, the management of SAD is based on the clinical severity. Clinicians may consider prophylactic antibiotics as well as immunoglobulin replacement. These patients should be closely followed up, with the possibility of discontinuation of IgG replacement after 12 to 24 months. Children are more likely to demonstrate resolution of SAD than are adolescents and adults. Patients with SAD may also progress to a more severe immunodeficiency; therefore, continued monitoring remains a crucial principle of practice in the care of patients with SAD.

Immunodeficiency: Complement disorders.

The complement system is an important component of innate and adaptive immunity that consists of three activation pathways. The classic complement pathway plays a role in humoral immunity, whereas the alternative and lectin pathways augment the innate response. Impairment, deficiency, or overactivation of any of the known 50 complement proteins may lead to increased susceptibility to infection with encapsulated organisms, autoimmunity, hereditary angioedema, or thrombosis, depending on the affected protein. Classic pathway defects result from deficiencies of complement proteins C1q, C1r, C1s, C2, and C4, and typically manifest with features of systemic lupus erythematosus and infections with encapsulated organisms. Alternative pathway defects due to deficiencies of factor B, factor D, and properdin may present with increased susceptibility to Neisseria infections. Lectin pathway defects, including Mannose-binding protein-associated serine protease 2 (MASP2) and ficolin 3, may be asymptomatic or lead to pyogenic infections and autoimmunity. Complement protein C3 is common to all pathways, deficiency of which predisposes patients to severe frequent infections and glomerulonephritis. Deficiencies in factor H and factor I, which regulate the alternative pathway, may lead to hemolytic uremic syndrome. Disseminated Neisseria infections result from terminal pathway defects (i.e., C5, C6, C7, C8, and C9). Diagnosis of complement deficiencies involves screening with functional assays (i.e., total complement activity [CH50], alternative complement pathway activity [AH50], enzyme-linked immunosorbent assay [ELISA]) followed by measurement of individual complement factors by immunoassay. Management of complement deficiencies requires a comprehensive and individualized approach with special attention to vaccination against encapsulated bacteria, consideration of prophylactic antibiotics, treatment of comorbid autoimmunity, and close surveillance.

Diagnostic tests for primary immunodeficiency disorders: Classic and genetic testing.

Primary immunodeficiency diseases encompass a variety of genetic conditions characterized by a compromised immune system and typically results in increased susceptibility to infection. In fact, they also manifest as autoimmunity, autoinflammation, atopic diseases, and malignancy. Currently, the number of recognized monogenic primary immunodeficiency disorders is set at ∼500 different entities, owing to the exponential use of unbiased genetic testing for disease discovery. In addition, the prevalence of secondary immunodeficiency has also been on the rise due to the increased use of immunosuppressive drugs to treat diseases based on immune dysregulation, an increase in the number of individuals undergoing hematopoietic stem cell transplantation, and other chronic medical conditions, including autoimmunity. Although the clinical symptoms of immunodeficiency disorders are broad, an early diagnosis and tailored management strategies are essential to mitigate the risk of infections and prevent disease-associated morbidity. Generally, the medical history and physical examination can provide useful information that can help delineate the possibility of immune defects. In turn, this makes it feasible to select focused laboratory tests that identify immunodeficiency disorders based on the specific immune cells and their functions or products that are affected. Laboratory evaluation involves quantitative and functional classic testing (e.g., leukocyte counts, serum immunoglobulin levels, specific antibody titers in response to vaccines, and enumeration of lymphocyte subsets) as well as genetic testing (e.g., individual gene evaluation via Sanger sequencing or unbiased evaluation based on next-generation sequencing). However, in many cases, a diagnosis also requires additional advanced research techniques to validate genetic or other findings. This article updates clinicians about available laboratory tests for evaluating the immune system in patients with primary immunodeficiency disorders. It also provides a comprehensive list of testing options, organized based on different components of host defense.

Immunodeficiency: Overview of primary immune regulatory disorders (PIRDs).

Primary immune regulatory disorders (PIRD) comprise a heterogeneous group of monogenic disorders that impact homeostatic control of inflammation and immune tolerance. Patients with a PIRD typically present to medical care with symptoms of autoimmunity or hyperinflammation as the dominant clinical feature, symptoms that include fever, rash, lymphadenopathy, organomegaly, arthritis, and colitis are commonplace. Notably, PIRDs are a distinct entity from primary immune deficiency disorders (PIDD), which are primarily defined by a qualitative or quantitative defect in immunity, which manifests as a susceptibility to recurrent infections. PIDDs and PIRDs can be challenging to differentiate because the clinical presentations can be similar. Red flags for PIRDs include multiple autoimmune diagnoses in the same patient, chronic lymphadenopathy, hepatomegaly, and/or splenomegaly, chronic colitis, hemophagocytic lymphohistiocytosis (HLH), Epstein Barr virus (EBV) susceptibility, recurrent or persistent fever, vasculitis, and sterile inflammation. For simplicity in this brief review, we limit our discussion of PIRDs to the following categories multiple autoimmune diseases, immune dysregulation with colitis, disorders with HLH and/or EBV susceptibility, autoinflammatory syndromes, type 1 interferonopathies, and disorders of sterile inflammation. Diagnosing a PIRD requires a broad immune evaluation for both immune system deficiencies and inflammation, along with genetic testing. Given the complex nature of these diseases, treatment often requires a team of subspecialists. Treatment, depending on the specific diagnosis, may be somewhat empiric with nonspecific immune modulators, symptom-directed therapies, and, in severe cases, hematopoietic stem cell transplantation; however, with the increasing number of biologics available, we are often able to use targeted immune therapy or even gene therapy.

Isotype deficiencies (IgG subclass and selective IgA, IgM, IgE deficiencies).

Background: Immunoglobulin G (IgG) subclass deficiencies and isolated IgA, IgM, IgE deficiencies have all been described in the literature with variable prevalence. Methods: These isotype deficiencies have a variable presentation from asymptomatic to recurrent infections resistant to prophylactic antibiotics. Results: Atopic disorders and autoimmune diseases are common comorbidities. IgE deficiency has been associated with impaired vaccine response and an increased risk of malignancy, particularly in patients with no allergic comorbidities and those with non-common variable immunodeficiency (CVID) humoral immunodeficiency, IgM deficiency, IgG2 deficiency, and CD4 lymphopenia. Conclusion: Close monitoring for malignancy should be strongly considered for these patients who are at risk. Treatment is variable and may include antimicrobial therapies for illnesses and prophylactic antibiotics in select patients, and immunoglobulin replacement can be considered for patients with refractory, recurrent infections.

Overview of secondary immunodeficiency.

In contrast to inborn errors of immunity (IEI), which are inherited disorders of the immune system that predispose to infections, malignancy, atopy, and immune dysregulation, secondary immunodeficiencies and immune dysregulation states (SID) are acquired impairments in immune cell function and/or regulation, and may be transient, reversible, or permanent. SIDs can derive from a variety of medical comorbidities, including protein-losing conditions, malnutrition, malignancy, certain genetic syndromes, prematurity, and chronic infections. Medications, including immunosuppressive and chemotherapeutic drugs, can have profound effects on immunity and biologic agents used in rheumatology, neurology, and hematology/oncology practice are increasingly common causes of SID. Iatrogenic factors, including surgical procedures (thymectomy, splenectomy) can also contribute to SID. A thorough case history, medication review, and laboratory evaluation are necessary to identify the primary driver and determine proper management of SID. Careful consideration should be given to whether a primary IEI could be contributing to autoimmunity, malignancy, and posttreatment complications (e.g., antibody deficiency). SID management consists of addressing the driving condition and/or removing the offending agent if feasible. If SID is suspected to be permanent, then antibiotic prophylaxis, additional immunization, and immunoglobulin replacement should be considered.

Hematopoietic stem cell transplantation for primary immunodeficiency.

Primary immunodeficiencies, also commonly called inborn errors of immunity (IEI), are commonly due to developmental or functional defects in peripheral blood cells derived from hematopoietic stem cells. In light of this, for the past 50 years, hematopoietic stem cell transplantation (HSCT) has been used as a definitive therapy for IEI. The fields of both clinical immunology and transplantation medicine have had significant advances. This, in turn, has allowed for both an increasing ability to determine a monogenic etiology for many IEIs and an increasing ability to successfully treat these patients with HSCT. Therefore, it has become more common for the practicing allergist/immunologist to diagnose and manage a broad range of patients with IEI before and after HSCT. This review aims to provide practical guidance for the clinical allergist/immunologist on the basics of HSCT and known outcomes in selected forms of IEI, the importance of pre-HSCT supportive care, and the critical importance of and guidance for life-long immunologic and medical monitoring of these patients.

Primary antibody deficiencies.

Primary antibody deficiencies are characterized by the inability to effectively produce antibodies and may involve defects in B-cell development or maturation. Primary antibody deficiencies can occur at any age, depending on the disease pathology. Certain primary antibody deficiencies affect males and females equally, whereas others affect males more often. Patients typically present with recurrent sinopulmonary and gastrointestinal infections, and some patients can experience an increased risk of opportunistic infections. Multidisciplinary collaboration is important in the management of patients with primary antibody deficiencies because these patients require heightened monitoring for atopic, autoimmune, and malignant comorbidities and complications. The underlying genetic defects associated with many primary antibody deficiencies have been discovered, but, in some diseases, the underlying genetic defect and inheritance are still unknown. The diagnosis of primary antibody deficiencies is often made through the evaluation of immunoglobulin levels, lymphocyte levels, and antibody responses. A definitive diagnosis is obtained through genetic testing, which offers specific management options and may inform future family planning. Treatment varies but generally includes antibiotic prophylaxis, vaccination, and immunoglobulin replacement. Hematopoietic stem cell transplantation is also an option for certain primary antibody deficiencies.

Inborn Errors of Immunity in Early Childhood: Essential Insights for the Neonatologist.

BACKGROUND: Inborn errors of immunity (IEI), formerly referred to as primary immunodeficiencies, manifest with a wide range of symptoms such as increased susceptibility to infections, immune dysregulation, and autoinflammation. Although most cases manifest in childhood, onset during the neonatal period is rare but potentially critical. SUMMARY: In this review, we discuss the diverse clinical presentations of IEI and the specific challenges they pose to neonatologists. Rather than detailing every molecular defect, we focus on common clinical scenarios in neonates and young infants, providing practical diagnostic strategies to ensure timely and effective therapeutic interventions. KEY MESSAGES: Clinical presentations of IEI in neonates may include delayed separation of the umbilical cord, skin rashes such as eczema and erythroderma, and recurrent episodes of inflammation. We also highlight immunological emergencies that require urgent medical attention, such as hyperinflammatory activity mimicking acute neonatal liver failure, sometimes seen in hemophagocytic lymphohistiocytosis. We also discuss appropriate medical action in the case of a positive newborn screening for severe T-cell defects. Early medical intervention in such circumstances may significantly improve outcomes.

Early Onset Inflammatory Bowel Disease Due to Immunodeficiency as a Result of ICOS Gene Homozygous Mutation.

INTRODUCTION: Inflammatory bowel disease (IBD) is classified as very early-onset IBD (VEO-IBD) if it occurs before age six. VEO-IBD may progress with more severe and resistant inflammation findings in the gastrointestinal and non-gastrointestinal systems. CASE REPORT: We describe the clinical presentation of a 4-year-old female presenting with recurring episodes of bloody diarrhea, vomiting, abdominal pain, fever, arthritis, erysipelas, and bilateral ankle pain. Monogenic primary immunodeficiency (PID) was suspected due to her age, different clinical findings and the presence of atypical gastroscopic findings and deep transmural ulcerations resembling Crohn's disease. The gene analysis showed a homozygous mutation in the inducible T cell co-stimulator (ICOS) deficiency genes. DISCUSSION/CONCLUSION: This case presentation shares our clinical experience and demonstrates the link between IBD progression and ICOS deficiency.

Allogeneic Hematopoietic Stem Cell Transplantation in Immunodeficiency-Centromeric Instability-Facial Dysmorphism (ICF) Syndrome: an EBMT/ESID Inborn Errors Working Party Study.

Immunodeficiency-Centromeric instability-Facial dysmorphism (ICF) syndrome is an inborn error of immunity characterized by progressive immune dysfunction and multi-organ disease usually treated with antimicrobial prophylaxis and immunoglobulin substitution. Allogeneic hematopoietic stem cell transplantation (HSCT) is the only curative treatment, but data on outcome are scarce. We provide a detailed description of disease characteristics and HSCT outcome in an international cohort of ICF syndrome patients. Eighteen patients (including all four genotypes) were enrolled. Main HSCT indications were infections (83%), enteropathy/failure to thrive (56%), immune dysregulation (22%) and myelodysplasia/haematological malignancy (17%). Two patients underwent pre-emptive HSCT after early diagnosis. Patients were transplanted between 2003-2021, at median age 4.3 years (range 0.5-19), after myeloablative or reduced-intensity conditioning, from matched sibling or matched family donors, matched unrelated or mismatched donors in 39%, 50% and 12% of cases respectively. Overall survival was 83% (all deaths occurred within the first 5 months post-HSCT; mean follow-up 54 months (range 1-185)). Acute GvHD occurred in 35% of patients, severe (grade III) in two (12%), while none developed chronic GvHD. At latest follow-up (median 2.2 years (range 0.1-14)), complete donor chimerism was achieved in 15/17 surviving patients. All survivors demonstrated normalized T and B cell numbers. Immunoglobulin substitution independence was achieved in all but two patients. All survivors recovered from pre-transplant infections, enteropathy/failure to thrive and immune dysregulation. All three patients transplanted at young age (≤ 3 years), after early diagnosis, survived. The favourable clinical and immunological HSCT outcome in this cohort of patients supports the timely use of this curative treatment in ICF syndrome.

Flow Cytometry-based Immune Phenotyping of T and B Lymphocytes in the Evaluation of Immunodeficiency and Immune Dysregulation.

There are approximately 500 congenital disorders that impair immune cell development and/or function. Patients with these disorders may present with a wide range of symptoms, including increased susceptibility to infection, autoimmunity, autoinflammation, lymphoproliferation, and/or atopy. Flow cytometry-based immune phenotyping of T and B lymphocytes plays an essential role in the evaluation of patients with these presentations. In this review, we describe the clinical utility of flow cytometry as part of a comprehensive evaluation of immune function and how this testing may be used as a diagnostic tool to identify underlying aberrant immune pathways, monitor disease activity, and assess infection risk.

Flow cytometry-based diagnostic approach for inborn errors of immunity: experience from Algeria.

Purpose: In this study, we retrospectively reviewed the use of flow cytometry (FCM) in the diagnosis of inborn errors of immunity (IEIs) at a single center in Algeria. Sharing insights into our practical experience, we present FCM based diagnostic approaches adapted to different clinical scenarios. Methods: Between May 2017 and February 2024, pediatric and adult patients presenting with clinical features suggestive of immunodeficiency were subjected to FCM evaluation, including lymphocyte subset analysis, detection of specific surface or intracellular proteins, and functional analysis of immune cells. Results: Over a nearly seven-year period, our laboratory diagnosed a total of 670 patients (372 (55.5%) males and 298 (44.5%) females), distributed into 70 different IEIs belonging to 9 different categories of the International Union of Immunological Societies classification. FCM was used to diagnose and categorize IEI in 514 patients (76.7%). It provided direct diagnostic insights for IEIs such as severe combined immunodeficiency, Omenn syndrome, MHC class II deficiency, familial hemophagocytic lymphohistiocytosis, and CD55 deficiency. For certain IEIs, including hyper-IgE syndrome, STAT1-gain of function, autoimmune lymphoproliferative syndrome, and activated PI3K delta syndrome, FCM offered suggestive evidence, necessitating subsequent genetic testing for confirmation. Protein expression and functional assays played a crucial role in establishing definitive diagnoses for various disorders. To setup such diagnostic assays at high and reproducible quality, high level of expertise is required; in house reference values need to be determined and the parallel testing of healthy controls is highly recommended. Conclusion: Flow cytometry has emerged as a highly valuable and cost-effective tool for diagnosing and studying most IEIs, particularly in low-income countries where access to genetic testing can be limited. FCM analysis could provide direct diagnostic insights for most common IEIs, offer clues to the underlying genetic defects, and/or aid in narrowing the list of putative genes to be analyzed.

Unexpected diagnosis of WHIM syndrome in refractory autoimmune cytopenia.

ABSTRACT: WHIM (warts, hypogammaglobulinemia, infections, and myelokathexis) syndrome is a rare primary immunodeficiency predominantly caused by heterozygous gain-of-function mutations in the C-terminus of the gene CXCR4. These CXCR4 variants display impaired receptor trafficking with persistence of the CXCR4 receptor on the surface, resulting in hyperactive downstream signaling after CXCL12 stimulation. In turn, this results in defective lymphoid differentiation, and reduced blood neutrophil and lymphocyte numbers. Here, we report a CXCR4 mutation that in 2 members of a kindred, led to life-long autoimmunity and lymphoid hypertrophy as the primary clinical manifestations of WHIM syndrome. We examine the functional effects of this mutation, and how these have affected phosphorylation, activation, and receptor internalization.

Genetic Evaluation of the Patients with Clinically Diagnosed Inborn Errors of Immunity by Whole Exome Sequencing: Results from a Specialized Research Center for Immunodeficiency in Türkiye.

Molecular diagnosis of inborn errors of immunity (IEI) plays a critical role in determining patients' long-term prognosis, treatment options, and genetic counseling. Over the past decade, the broader utilization of next-generation sequencing (NGS) techniques in both research and clinical settings has facilitated the evaluation of a significant proportion of patients for gene variants associated with IEI. In addition to its role in diagnosing known gene defects, the application of high-throughput techniques such as targeted, exome, and genome sequencing has led to the identification of novel disease-causing genes. However, the results obtained from these different methods can vary depending on disease phenotypes or patient characteristics. In this study, we conducted whole-exome sequencing (WES) in a sizable cohort of IEI patients, consisting of 303 individuals from 21 different clinical immunology centers in Türkiye. Our analysis resulted in likely genetic diagnoses for 41.1% of the patients (122 out of 297), revealing 52 novel variants and uncovering potential new IEI genes in six patients. The significance of understanding outcomes across various IEI cohorts cannot be overstated, and we believe that our findings will make a valuable contribution to the existing literature and foster collaborative research between clinicians and basic science researchers.