Manish Butte

Genes (Basel). 2024 Dec 26;16(1):18. doi: 10.3390/genes16010018.

ABSTRACT

Background: The advent of next-generation sequencing (NGS) has revolutionized the analysis of genetic data, enabling rapid identification of pathogenic variants in patients with inborn errors of immunity (IEI). Sometimes, the use of NGS-based technologies is associated with challenges in the evaluation of the clinical significance of novel genetic variants. Methods: In silico prediction tools, such as SpliceAI neural network, are often used as a first-tier approach for the primary examination of genetic variants of uncertain clinical significance. Such tools allow us to parse through genetic data and emphasize potential splice-altering variants. Further variant assessment requires precise RNA assessment by agarose gel electrophoresis and/or cDNA Sanger sequencing. Results: We found two novel heterozygous variants in the coding region of the LYST gene (c.10104G>T, c.10894A>G) in an individual with a typical clinical presentation of Chediak-Higashi syndrome (CHS). The SpliceAI neural network predicted both variants as probably splice-altering. cDNA assessment by agarose gel electrophoresis revealed the presence of abnormally shortened splicing products in each variant’s case, and cDNA Sanger sequencing demonstrated that c.10104G>T and c.10894A>G substitutions resulted in a shortening of the 44 and 49 exons by 41 and 47 bp, respectively. Both mutations probably lead to a frameshift and the formation of a premature termination codon. This, in turn, may disrupt the structure and/or function of the LYST protein. Conclusions: We identified two novel variants in the LYST gene, predicted to be deleterious by the SpliceAI neural network. Agarose gel cDNA electrophoresis and cDNA Sanger sequencing allowed us to verify inappropriate splicing patterns and establish these variants as disease-causing.

PMID:39858566 | DOI:10.3390/genes16010018

J Clin Immunol. 2025 Jan 24;45(1):67. doi: 10.1007/s10875-025-01857-3.

ABSTRACT

BACKGROUND: Ataxia telangiectasia mutated (ATM) kinase plays a critical role in DNA double-strand break (DSB) repair. Ataxia telangiectasia (A-T) patients exhibit abnormalities in immunoglobulin isotype expression and class switch recombination (CSR). This study investigates the role of residual ATM kinase expression and activity in the severity of A-T disease.

METHODS: A-T patients with defined genetic diagnoses were classified based on CSR and based on the severity of their medical complications. Isolated peripheral blood mononuclear cells from any patient were evaluated before and after exposure to 0.5 Gy ionizing radiation for one minute. Western blotting was performed to identify the expression of ATM and phosphorylated ATM (p-ATM) proteins compared to age-sex-matched healthy controls.

RESULTS: In severe A-T patients (n = 6), the majority (66.7%) had frameshift mutations, while 33.3% had nonsense mutations in the ATM gene. The mild group (n = 3) had two cases of splice errors and one missense mutation. All patients with CSR defect had elevated IgM serum levels, whereas all switched immunoglobulins were reduced in them. Expression of ATM and p-ATM proteins was significantly lower (p = 0.01) in all patients compared to healthy controls, both pre-and post- and post-radiation. Additionally, low ATM and p-ATM protein expression levels were linked with the clinical severity of patients but were not correlated with CSR defects.

CONCLUSION: Expression and activation of ATM protein were defective in A-T patients compared to healthy controls. Altered expression of ATM and p-ATM proteins may have potential clinical implications for prognostic evaluation and symptom severity assessment in individuals with A-T.

PMID:39853455 | DOI:10.1007/s10875-025-01857-3

Vet Sci. 2025 Jan 9;12(1):35. doi: 10.3390/vetsci12010035.

ABSTRACT

The primary aim of this study was to determine the accuracy of saliva as a proxy for blood in cats using Anigen Rapid^® FIV point-of-care (PoC) kits and as an easy collection technique applicable for all veterinary clinics and shelters. A secondary aim was to report FIV prevalence in various Australian states/territories and key cat risk factors associated with FIV infection. In total, 382 cats were recruited from patients presenting to private, shelter and teaching hospital veterinary clinics in Australia. Information collected for each cat included age, sex, neuter status, postcode, and health status (‘healthy’ versus ‘sick’). The traditional blood testing technique with Anigen Rapid^® was used to determine the FIV status of cats. Comparative saliva testing found 48/382 (12.5%) cats were FIV-positive. Test sensitivity for Anigen Rapid^® FIV using saliva was 84.2% (48/57; 95% CI 80.6 to 87.9). Test specificity for Anigen Rapid^® FIV using saliva was 100% (325/325). The two significant cat risk factors for FIV infection were sex (male) and health status (sick). In terms of demographic information, prevalence in Tasmania and the Northen Territory was reported for the first time. This study proves the ability to utilise cheap and readily available consumables for less invasive FIV testing purposes by using saliva instead of blood, for example, when screening cat before adoption in shelters and in cats prior to annual FIV re-vaccination.

PMID:39852909 | DOI:10.3390/vetsci12010035

Zool Res. 2025 Jan 18;46(1):249-260. doi: 10.24272/j.issn.2095-8137.2024.195.

ABSTRACT

Severe combined immunodeficiency disease (SCID), characterized by profound immune system dysfunction, can lead to life-threatening infections and death. Animal models play a pivotal role in elucidating biological processes and advancing therapeutic strategies. Recent advances in gene-editing technologies, including zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), CRISPR/Cas9, and base editing, have significantly enhanced the generation of SCID models. These models have not only deepened our understanding of disease pathophysiology but have also driven progress in cancer therapy, stem cell transplantation, organ transplantation, and infectious disease management. This review provides a comprehensive overview of current SCID models generated using novel gene-editing approaches, highlighting their potential applications in translational medicine and their role in advancing biomedical research.

PMID:39846200 | DOI:10.24272/j.issn.2095-8137.2024.195

Fetal Pediatr Pathol. 2025 Jan 23:1-7. doi: 10.1080/15513815.2025.2449948. Online ahead of print.

ABSTRACT

Background:Pseudomonas aeruginosa (PA), a gram-negative bacillus, has varied clinical manifestations with septicemia as the most lethal. PA infection is usually regarded as opportunistic and often nosocomial. Case Presentation: We present a case of a “healthy” pediatric patient presenting with upper respiratory symptoms who rapidly deteriorated. Blood cultures grew Pseudomonas aeruginosa shortly after death. The postmortem examination revealed Pseudomonal vasculopathy of the central nervous system and genetic testing detected an autosomal recessive pathogenic variant in IRAK-4. Discussion: Community-acquired Pseudomonal sepsis in previously healthy children is rare. Studies have found that up to 20% of children presenting with sepsis have an underlying immune defect. Deficiency of IRAK-4 predisposes patients to recurrent, life-threatening, microbial infections, notably Streptococcus pneumoniae, Staphylococcus aureus, and PA. Conclusion: A primary immunodeficiency should be suspected in a “healthy” child presenting with sepsis by an unexpected bacterium as the clinical consequences may be severe and the findings may have reproductive implications for the parents.

PMID:39846126 | DOI:10.1080/15513815.2025.2449948

Front Immunol. 2025 Jan 8;15:1475448. doi: 10.3389/fimmu.2024.1475448. eCollection 2024.

ABSTRACT

BACKGROUND: With recent advances in clinical practice, including the use of reduced-toxicity conditioning regimens and innovative approaches such as ex vivo TCRαβ/CD19 depletion of haploidentical donor stem cells or post-transplant cyclophosphamide (PTCY), hematopoietic stem cell transplantation (HSCT) has emerged as a curative treatment option for a growing population of patients with inborn errors of immunity (IEI). However, despite these promising developments, graft failure (GF) remains a significant concern associated with HSCT in these patients. Although a second HSCT is the only established salvage therapy for patients who experience GF, there are no uniform, standardized strategies for performing these second transplants. Furthermore, even less data is available regarding the outcomes and best practices for a third HSCT as a salvage measure when a second HSCT fails to achieve engraftment.

CASE PRESENTATION: A 6-year-old boy with leukocyte adhesion deficiency type I (LAD-I) experienced GF after the first and second HSCT from a matched unrelated donor. As a salvage measure, the patient received a dual in vivo T-cell depleted haploidentical HSCT. The conditioning regimen for this third HSCT included anti-thymocyte globulin (ATG) and PTCY. Complete donor chimerism was assessed using the short tandem repeat (STR) PCR technique. By day +28 after the transplant, the expression of the leukocyte adhesion molecules CD18, CD11b, and CD11c on the patient’s peripheral blood neutrophils had recovered to over 99%. It remained stable throughout the 18-month follow-up period.

CONCLUSION: T-cell replete haploidentical HSCT with ATG and PTCY may be a viable salvage option for LAD patients who have rejected prior HSCT.

PMID:39845947 | PMC:PMC11751042 | DOI:10.3389/fimmu.2024.1475448

Biomedica. 2024 Dec 23;44(Sp. 2):51-62. doi: 10.7705/biomedica.7398.

ABSTRACT

INTRODUCTION: Predominant antibody deficiency is the most frequent group of innate immunity errors, but information about patients’ nutritional status is scarce.

OBJECTIVES: To characterize the nutritional status of Colombian patients with predominant antibody deficiencies.

MATERIAL AND METHODS: Material and methods. We analyzed medical charts of patients with predominant antibody deficiency in a pediatric hospital in Bogotá.

RESULTS: We analyzed 55 medical charts. The most frequent diagnoses were specific deficiencies of polysaccharide antibodies and immunoglobulin A, common variable immunodeficiency, and agammaglobulinemia. More than 70% of the patients had sinopulmonary infections, with pneumonia being the most frequent, followed by otitis and sinusitis. In children under five years, 45% had adequate weight for their height, 18% had a risk of malnutrition, and 18% had moderate acute malnutrition. Four-point-five percent had obesity, 4.5% showed overweight, and 9% had a risk of being overweight. Of those older than five years, 54% had an adequate body mass index, 22.5% showed overweight, 9.6% were at risk of thinness, and 9.6% were thin. We found that the risk of short stature and short stature per se were more frequent than the expected height in these patients. The percentages of patients with short stature were higher than those reported nationally.

CONCLUSIONS: Due to the epidemic of childhood obesity, it will be more frequent to find overweight or obesity in children above five years. Therefore, finding short stature could be a more sensitive alarm sign for predominant antibody deficiency.

PMID:39836854 | DOI:10.7705/biomedica.7398

Biomedica. 2024 Dec 23;44(Sp. 2):16-21. doi: 10.7705/biomedica.7414.

ABSTRACT

Cernunnos/XLF deficiency is a rare, severe combined immunodeficiency, inherited in an autosomal recessive pattern (OMIM number: 611290), related to the NHEJ1 gene. This gene participates in the DNA non-homologous end-joining pathway, repairing double-strand breaks in the DNA of mammalian cells. The clinical features include growth retardation, microcephaly, triangle-shaped face, recurrent infections, fibroblast’s excessive sensitivity to gamma-ionizing radiation, and hypogammaglobulinemia; also, low counts of subpopulations of B and T lymphocytes, with normal values of natural-killer cells. This manuscript aims to present an extremely rare case of combined immunodeficiency in a twenty-years-old man with non-consanguineous parents and a homozygote variant of the NHEJ1 gene. This case is the fiftieth reported in the literature and the first in Colombia, given the low prevalence of NHEJ1-related immunodeficiency and its difficult diagnosis due to scarce knowledge.

PMID:39836852 | DOI:10.7705/biomedica.7414

Biomedica. 2024 Dec 23;44(Sp. 2):10-15. doi: 10.7705/biomedica.7436.

ABSTRACT

Activated phosphoinositide 3-kinase δ syndrome is an inborn error of immunity due to mutations within the genes responsible for encoding PI3Kδ subunits. This syndrome results in an excessive activation of the phosphoinositide 3-kinase signaling pathway. Gainof-function mutations in the gene PIK3R1 (encoding p85α, p55α, and p50α) lead to the development of the activated PI3K δ syndrome. Notably, the clinical presentations of this syndrome often closely resemble those of other primary immunodeficiencies. We present a case involving a 15-year-old male who displayed an immunological phenotype that bore a striking resemblance to hyper-IgM syndrome. Whole exome sequencing was undertaken to pinpoint the underlying genetic mutation. Our investigation successfully identified a heterozygous splice site mutation previously reported within the well-established hotspot of the PIK3R1 gene (GRCh37, c.1425+1 G>T). The diverse spectrum of inborn errors of immunity underscores the pivotal role of identifying gene mutations, particularly in patients presenting clinical manifestations spanning autoimmune disorders, lymphoproliferative conditions, and antibody deficiencies. Such precise genetic diagnoses hold significant potential for improving patient care and management.

PMID:39836850 | DOI:10.7705/biomedica.7436

Biomedica. 2024 Dec 23;44(Sp. 2):39-47. doi: 10.7705/biomedica.7636.

ABSTRACT

INTRODUCTION: Common variable immunodeficiency is a diagnosis of exclusion in immunodeficient patients with increased susceptibility to infections, hypogammaglobulinemia, deficient response to vaccination, or low percentages of switched memory B cells. In low- and middle-income countries, the elucidation and study of molecular defects in these patients may take decades.

OBJECTIVE: To elucidate the genetic defect conferring impaired immunity in a patient diagnosed with common variable immunodeficiency.

MATERIALS AND METHODS: The clinical phenotype was extracted from the clinical records. NKG2D expression in natural killer cells was evaluated by flow cytometry. The whole exome sequencing was performed in the patient and his parents. Sanger sequencing confirmed the pathogenic variant.

RESULTS: The patient suffered from upper respiratory and urinary tract infections, autoimmune hemolytic anemia, and hepatopathy. NKG2D was decreased in the different blood subpopulations of natural killer cells. Serologic and viral load studies for Epstein-Barr virus were positive, but no B-cell malignancies have been documented. The patient presented a nonsense variant in the exon 3 of the MAGT1 gen (c.409C>T, rs387906724) in the X chromosome, resulting in an amino acid substitution of arginine for a stop codon in the position 137 of the protein (R137X). The mother also carried the pathogenic variant in a heterozygous state.

CONCLUSIONS: We report the clinical case of the first Colombian male patient with a pathogenic variant in MAGT1 associated with XMEN disease. Genetic counseling and followup are recommended for families with similar cases to allow prompt detection of new cases.

PMID:39836832 | DOI:10.7705/biomedica.7636