Manish Butte

Math Biosci Eng. 2023 Mar 31;20(6):10264-10283. doi: 10.3934/mbe.2023450.

ABSTRACT

BACKGROUND: Epigenetic changes, such as DNA methylation and miRNA-target gene mechanisms, have recently emerged as key provokers in Ischemic stroke (IS) onset. However, cellular and molecular events harboring these epigenetic alterations are poorly understood. Therefore, the present study aimed to explore the potential biomarkers and therapeutic targets for IS.

METHODS: miRNAs, mRNAs and DNA methylation datasets of IS were derived from the GEO database and normalized by PCA sample analysis. Differentially expressed genes (DEGs) were identified, and GO and KEGG enrichment analyses were performed. The overlapped genes were utilized to construct a protein-protein interaction network (PPI). Meanwhile, differentially expressed mRNAs and miRNAs interaction pairs were obtained from the miRDB, TargetScan, miRanda, miRMap and miTarBase databases. We constructed differential miRNA-target gene regulatory networks based on mRNA-miRNA interactions.

RESULTS: A total of 27 up-regulated and 15 down-regulated differential miRNAs were identified. Dataset analysis identified 1053 and 132 up-regulated and 1294 and 9068 down-regulated differentially expressed genes in the GSE16561 and GSE140275 datasets, respectively. Moreover, 9301 hypermethylated and 3356 hypomethylated differentially methylated sites were also identified. Moreover, DEGs were enriched in terms related to translation, peptide biosynthesis, gene expression, autophagy, Th1 and Th2 cell differentiation, primary immunodeficiency, oxidative phosphorylation and T cell receptor signaling pathway. MRPS9, MRPL22, MRPL32 and RPS15 were identified as hub genes. Finally, a differential miRNA-target gene regulatory network was constructed.

CONCLUSIONS: RPS15, along with hsa-miR-363-3p and hsa-miR-320e have been identified in the differential DNA methylation protein interaction network and miRNA-target gene regulatory network, respectively. These findings strongly posit the differentially expressed miRNAs as potential biomarkers to improve ischemic stroke diagnosis and prognosis.

PMID:37322932 | DOI:10.3934/mbe.2023450

Transplant Cell Ther. 2023 Jun 13:S2666-6367(23)01354-4. doi: 10.1016/j.jtct.2023.06.006. Online ahead of print.

ABSTRACT

Overall survival rate after Hematopoietic stem cell transplantation (HSCT) for Inborn Errors of Immunity (IEI) has improved considerably and its indications have broadened. As a consequence, addressing the issue of long-term health-related quality of life (HRQoL) has become crucial. Our study focuses on the health and HRQoL of post-HSCT survivors. We conducted a multicenter prospective follow-up study enrolling IEI patients transplanted in childhood, before 2009. Self-reported data from the French Childhood Immune Deficiency Long-term Cohort (F-CILC) and 36-item Short Form (SF-36) questionnaires were compiled. 112 survivors were included with a median duration period from HSCT of 15 years (range: 5-37), of whom 55 were transplanted for a combined immunodeficiency. We show that in patients evaluated at least 5 years after HSCT, 55% are still affected by a poor or very poor health status. Poor and very poor health status correlated with an abnormal graft function defined as host or mixed chimerism and/or abnormal CD3+ count and/or diagnosis of chronic GVHD (Poor health: OR 2,6 CI 95%: 1,1-5,9 p:0,028; Very poor health: OR 3,6 CI 95%: 1,1-13, p:0,049). Poor health directly linked to a poorer HRQoL. Significant improvements in graft procedures have translated in better survival rates, but we show here that about half of the transplanted patients remain affected by an altered health status with a correlation to both abnormal graft function and impaired HRQoL. Additional studies are needed to confirm the impact of those improvements on long-term health status and HRQoL.

PMID:37321401 | DOI:10.1016/j.jtct.2023.06.006

BMC Bioinformatics. 2023 Jun 15;24(1):251. doi: 10.1186/s12859-023-05361-6.

ABSTRACT

Hennekam Lymphangiectasia-Lymphedema Syndrome 3 (HKLLS3) is a rare genetical disorder caused by mutations in a few genes including ADAMTS3. It is characterized by lymphatic dysplasia, intestinal lymphangiectasia, severe lymphedema and distinctive facial appearance. Up till now, no extensive studies have been conducted to elucidate the mechanism of the disease caused by various mutations. As a preliminary investigation of HKLLS3, we sorted out the most deleterious nonsynonymous single nucleotide polymorphisms (nsSNPs) that might affect the structure and function of ADAMTS3 protein by using a variety of in silico tools. A total of 919 nsSNPs in the ADAMTS3 gene were identified. 50 nsSNPs were predicted to be deleterious by multiple computational tools. 5 nsSNPs (G298R, C567Y, A370T, C567R and G374S) were found to be the most dangerous and can be associated with the disease as predicted by different bioinformatics tools. Modelling of the protein shows it can be divided into segments 1, 2 and 3, which are connected by short loops. Segment 3 mainly consists of loops without substantial secondary structures. With prediction tools and molecular dynamics simulation, some SNPs were found to significantly destabilize the protein structure and disrupt the secondary structures, especially in segment 2. The deleterious effects of mutations in segment 1 are possibly not from destabilization but from other factors such as the change in phosphorylation as suggested by post-translational modification (PTM) studies. This is the first-ever study of ADAMTS3 gene polymorphism, and the predicted nsSNPs in ADAMST3, some of which have not been reported yet in patients, will serve for diagnostic purposes and further therapeutic implications in Hennekam syndrome, contributing to better diagnosis and treatment.

PMID:37322437 | DOI:10.1186/s12859-023-05361-6

J Clin Immunol. 2023 Jun 14. doi: 10.1007/s10875-023-01530-7. Online ahead of print.

ABSTRACT

The transcription factor STAT6 (Signal Transducer and Activator of Transcription 6) is a key regulator of Th2 (T-helper 2) mediated allergic inflammation via the IL-4 (interleukin-4) JAK (Janus kinase)/STAT signalling pathway. We identified a novel heterozygous germline mutation STAT6 c.1255G > C, p.D419H leading to overactivity of IL-4 JAK/STAT signalling pathway, in a kindred affected by early-onset atopic dermatitis, food allergy, eosinophilic asthma, anaphylaxis and follicular lymphoma. STAT6 D419H expression and functional activity were compared with wild type STAT6 in transduced HEK293T cells and to healthy control primary skin fibroblasts and peripheral blood mononuclear cells (PBMC). We observed consistently higher STAT6 levels at baseline and higher STAT6 and phosphorylated STAT6 following IL-4 stimulation in D419H cell lines and primary cells compared to wild type controls. The pSTAT6/STAT6 ratios were unchanged between D419H and control cells suggesting that elevated pSTAT6 levels resulted from higher total basal STAT6 expression. The selective JAK1/JAK2 inhibitor ruxolitinib reduced pSTAT6 levels in D419H HEK293T cells and patient PBMC. Nuclear staining demonstrated increased STAT6 in patient fibroblasts at baseline and both STAT6 and pSTAT6 after IL-4 stimulation. We also observed higher transcriptional upregulation of downstream genes (XBP1 and EPAS1) in patient PBMC. Our study confirms STAT6 gain of function (GOF) as a novel monogenetic cause of early onset atopic disease. The clinical association of lymphoma in our kindred, along with previous data linking somatic STAT6 D419H mutations to follicular lymphoma suggest that patients with STAT6 GOF disease may be at higher risk of lymphomagenesis.245 words.

PMID:37316763 | DOI:10.1007/s10875-023-01530-7

Front Immunol. 2023 May 29;14:1155883. doi: 10.3389/fimmu.2023.1155883. eCollection 2023.

ABSTRACT

INTRODUCTION: ZAP-70, a protein tyrosine kinase recruited to the T cell receptor (TCR), initiates a TCR signaling cascade upon antigen stimulation. Mutations in the ZAP70 gene cause a combined immunodeficiency characterized by low or absent CD8+ T cells and nonfunctional CD4+ T cells. Most deleterious missense ZAP70 mutations in patients are located in the kinase domain but the impact of mutations in the SH2 domains, regulating ZAP-70 recruitment to the TCR, are not well understood.

METHODS: Genetic analyses were performed on four patients with CD8 lymphopenia and a high resolution melting screening for ZAP70 mutations was developed. The impact of SH2 domain mutations was evaluated by biochemical and functional analyses as well as by protein modeling.

RESULTS AND DISCUSSION: Genetic characterization of an infant who presented with pneumocystis pneumonia, mycobacterial infection, and an absence of CD8 T cells revealed a novel homozygous mutation in the C-terminal SH2 domain (SH2-C) of the ZAP70 gene (c.C343T, p.R170C). A distantly related second patient was found to be compound heterozygous for the R170C variant and a 13bp deletion in the ZAP70 kinase domain. While the R170C mutant was highly expressed, there was an absence of TCR-induced proliferation, associated with significantly attenuated TCR-induced ZAP-70 phosphorylation and a lack of binding of ZAP-70 to TCR-ζ. Moreover, a homozygous ZAP-70 R192W variant was identified in 2 siblings with combined immunodeficiency and CD8 lymphopenia, confirming the pathogenicity of this mutation. Structural modeling of this region revealed the critical nature of the arginines at positions 170 and 192, in concert with R190, forming a binding pocket for the phosphorylated TCR-ζ chain. Deleterious mutations in the SH2-C domain result in attenuated ZAP-70 function and clinical manifestations of immunodeficiency.

PMID:37313400 | PMC:PMC10258307 | DOI:10.3389/fimmu.2023.1155883

BMC Immunol. 2023 Jun 13;24(1):9. doi: 10.1186/s12865-023-00545-4.

ABSTRACT

BACKGROUND: Common Variable Immunodeficiency (CVID) is a primary immunodeficiency syndrome resulting in recurrent infections, autoimmunity, and granulomatous manifestations.

METHODS AND MATERIALS: This retrospective study was conducted on an Iranian national registry of immunodeficient patients from 2010 to 2021. The frequency of first presentations of CVID and its association with sex, age of onset, and family history of CVID was evaluated.

RESULTS: A total of 383 patients entered the study, 164 of whom were female, and the rest were male. The mean age of the patients was 25.3 ± 14.5 years. The most frequent first presentations of CVID were pneumonia (36.8%) and diarrhea (19.1%). Patient sex, age of onset, and family history did not make significant differences in first presentations of this disease.

CONCLUSION: pneumonia is the most common first presentation of CVID. Family history of CVID, the age of symptom onset, and sex made no differences in the first presentations of CVID.

PMID:37312036 | DOI:10.1186/s12865-023-00545-4

Orphanet J Rare Dis. 2023 Jun 12;18(1):147. doi: 10.1186/s13023-023-02758-7.

ABSTRACT

BACKGROUND AND OBJECTIVES: Cartilage-hair hypoplasia (CHH) is a rare chondrodysplasia with associated primary immunodeficiency. The aim of this cross-sectional study was to examine oral health indicators in individuals with CHH.

METHODS: In total, 23 individuals with CHH, aged between 4.5 and 70 years, and 46 controls aged between 5 and 76 years were clinically examined for periodontal disease, presence of oral mucosal lesions, tooth decay, masticatory system function, and malocclusions. A chairside lateral flow immunoassay test of active-matrix metalloproteinase was obtained from all the adult participants with a permanent dentition. Laboratory signs of immunodeficiency were recorded for individuals with CHH.

RESULTS: Individuals with CHH and controls had similar prevalence of gingival bleeding on probing (median 6% vs. 4%). Oral fluid active-matrix metalloproteinase concentration was greater than 20 ng/ml in 45% of study subjects in both groups. However, deep periodontal pockets, 4 mm or deeper, were more common in individuals with CHH as compared to the controls (U = 282.5, p = 0.002). Similarly mucosal lesions were significantly more common in individuals with CHH (30% vs. 9%, OR = 0.223, 95%CI 0.057-0.867). The median sum of the number of decayed, missing due to caries, and filled teeth was nine for the individuals with CHH and four for controls. In the CHH cohort, 70% displayed an ideal sagittal occlusal relationship. Malocclusion and temporomandibular joint dysfunction prevalence were similar in both study groups.

CONCLUSIONS: Individuals with CHH have more frequently deep periodontal pockets and oral mucosal lesions than general population controls. Routine intraoral examination by a dentist at regular intervals should be recommended to all individuals with CHH.

PMID:37308912 | DOI:10.1186/s13023-023-02758-7

Int J Immunogenet. 2023 Jun 12. doi: 10.1111/iji.12624. Online ahead of print.

ABSTRACT

Severe combined immunodeficiency (SCID) is an inborn errors of immunity (IEI) disorder characterized by impairment in the development and function of lymphocytes and could be fatal if not treated with hematopoietic stem cell transplant in the first 2 years of life. There are various diagnostic criteria for SCID among different primary immunodeficiency societies. We retrospectively evaluated clinical and laboratory findings of 59 patients followed up with the diagnosis of SCID at our clinic over the past 20 years in order to develop an algorithm that would help diagnosis of SCID for the countries where a high ratio of consanguineous marriage is present because these countries have not launched TREC assay in their newborn screening programs. The mean age at diagnosis was 5.80 ± 4.90 months, and the delay was 3.29 ± 3.99 months. The most common complaint and physical examination findings were cough (29.05%), eczematous rash (63%) and organomegaly (61%). ADA (17%), Artemis (14%), RAG1/2 (15%), MHC Class II (12%) and IL-2R (12%) deficiencies were the most common genetic defects. Lymphopenia (87.5%) was the most frequent abnormal laboratory finding and below 3000/mm³ in 95% of the patients. The CD3⁺ T cell count was 300/mm³ and below in 83% of the patients. As a result, a combination of low lymphocyte count and CD3 lymphopenia for SCID diagnosis would be more reliable for countries with high rate of consanguineous marriage. Physicians should consider diagnosis of SCID in a patient presenting with severe infections and lymphocyte counts below 3000/mm³ under 2 years of age.

PMID:37308802 | DOI:10.1111/iji.12624

Front Immunol. 2023 May 25;14:1192690. doi: 10.3389/fimmu.2023.1192690. eCollection 2023.

ABSTRACT

Primary complement system (C) deficiencies are rare but notably associated with an increased risk of infections, autoimmunity, or immune disorders. Patients with terminal pathway C-deficiency have a 1,000- to 10,000-fold-higher risk of Neisseria meningitidis infections and should be therefore promptly identified to minimize the likelihood of further infections and to favor vaccination. In this paper, we performed a systematic review about clinical and genetic patterns of C7 deficiency starting from the case of a ten-year old boy infected by Neisseria meningitidis B and with clinical presentation suggestive of reduced C activity. Functional assay via Wieslab ELISA Kit confirmed a reduction in total C activity of the classical (0.6% activity), lectin (0.2% activity) and alternative (0.1% activity) pathways. Western blot analysis revealed the absence of C7 in patient serum. Sanger sequencing of genomic DNA extracted from peripheral blood of the patient allowed the identification of two pathogenetic variants in the C7 gene: the already well-characterized missense mutation G379R and a novel heterozygous deletion of three nucleotides located at the 3’UTR (c.*99_*101delTCT). This mutation resulted in an instability of the mRNA; thus, only the allele containing the missense mutation was expressed, making the proband a functional hemizygote for the expression of the mutated C7 allele.

PMID:37304269 | PMC:PMC10248053 | DOI:10.3389/fimmu.2023.1192690

J Allergy Clin Immunol Pract. 2023 Jun 8:S2213-2198(23)00645-1. doi: 10.1016/j.jaip.2023.05.046. Online ahead of print.

NO ABSTRACT

PMID:37301434 | DOI:10.1016/j.jaip.2023.05.046