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    First Steps of the Genetic Monitorization in Primary Immune Deficiencies in the Lead of Prof. Dr. Isil Barlan in Turkey
    (Turkish Soc Immunology, 2015) Ng, Yuk Yin; Sisko, Sinem; Ng, Ozden Hatirnaz; Tatonyan, Suzin Catal; Kaya, Dilek Sever; Firtina, Sinem; Sayitoglu, Muge
    [Abstract Not Available]
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    High TUBB2A expression in childhood T-ALL is correlated with the clinical outcome
    (Wiley, 2020) Khodzhaev, Khusan; Ng, Ozden Hatirnaz; Tugcu, Deniz; Erbilgin, Yucel; Ng, Yuk Yin; Celkan, Tiraje; Timur, Cetin
    Introduction Microtubules are polymers that perform functions such as mitosis, intracellular transport, cell morphology, and ciliary and flagellar motility. Since microtubules are taking active part in cell division, they are among direct targets of several antimitotic drugs. Methods Expression levels of tubulin isotypes were analyzed in microarray data of childhood diagnostic T-ALL samples (n = 31) and healthy thymocytes (n = 7). Findings were validated with qPCR in separate T-ALL cohort (n = 48), and clinical correlation analyses were performed.TUBB2A's effects were tested with siRNA-mediated knockdown in MOLT4 cell line, and apoptosis assay was carried out at 24, 48, and 72 hours time points. Results In microarray data,TUBB2Awas found to be the only differentially expressed tubulin isotype (adj.Pvalue = .01), which was validated by qPCR (P = .02). Samples representing differentiation stages of T cell showed an increasing trend ofTUBB2Atoward mature T-cell stage.TUBB2Aexpression was significantly higher in high-risk group patients (P = .026) and in a group with WBC counts >100 (x10(9)cells/L) (P = .029). HighTUBB2Awas also found to be a predictor of shorter OS (P = .029) and RFS (P = .042). Conclusion Aberrant expression of TUBB isotypes can affect the balance of microtubules or microtubule-associated proteins, which might lead to drug resistance/relapse. Contribution of cytoskeleton proteins to drug resistance needs further investigation, and understanding aberrant expression and mode of action of microtubules will improve therapy strategies.
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    Lymphoma Predisposing Gene in an Extended Family: CD70 Signaling Defect
    (Springer/Plenum Publishers, 2020) Khodzhaev, Khusan; Bay, Sema Buyukkapu; Kebudi, Rejin; Altindirek, Didem; Kaya, Aysenur; Erbilgin, Yucel; Ng, Ozden Hatirnaz
    Genome-wide sequencing studies in pediatric cancer cohorts indicate that about 10% of patients have germline mutations within cancer predisposition genes. Within this group, primary immune deficiencies take the priority regarding the vulnerability of the patients to infectious agents and the difficulties of cancer management. On the other hand, early recognition of these diseases may offer specific targeted therapies and hematopoietic stem cell transplantation as an option. Besides therapeutic benefits, early diagnosis will provide genetic counseling for the family members. Within this context, an extended family with multiple consanguineous marriages and affected individuals, who presented with combined immune deficiency (CID) and/or Hodgkin lymphoma phenotype, were examined by exome sequencing. A pathogenic homozygous missenseCD70variation was detected (NM_001252.5:c332C>T) in concordance withCD70phenotype and familial segregation was confirmed.CD70variations in patients with CID and malignancy have very rarely been reported. This paper reports extended family with multiple affected members with CID and malignancy carrying a missenseCD70variation, and reviews the rare cases reported in the literature. Primary immune deficiencies appear to be a potential cause for pediatric cancers. Better focusing on these inborn disorders to prevent or make an early diagnosis of malignant transformation and reduce mortalities is important.
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    Mutational landscape of severe combined immunodeficiency patients from Turkey
    (Wiley, 2020) Firtina, Sinem; Ng, Yuk Yin; Ng, Ozden Hatirnaz; Kiykim, Ayca; Aydiner, Elif; Nepesov, Serdar; Camcioglu, Yildiz
    Severe combined immunodeficiency (SCID) has a diverse genetic aetiology, where a clinical phenotype, caused by single and/or multiple gene variants, can give rise to multiple presentations. The advent of next-generation sequencing (NGS) has recently enabled rapid identification of the molecular aetiology of SCID, which is crucial for prognosis and treatment strategies. We sought to identify the genetic aetiology of various phenotypes of SCIDs and assessed both clinical and immunologic characteristics associated with gene variants. An amplicon-based targeted NGS panel, which contained 18 most common SCID-related genes, was contumely made to screen the patients (n = 38) with typical SCID, atypical SCID or OMENN syndrome. Allelic segregations were confirmed for the detected gene variants within the families. In total, 24 disease-causing variants (17 known and 7 novel) were identified in 23 patients in 9 different SCID genes: RAG1 (n = 5), RAG2 (n = 2), ADA (n = 3), DCLRE1C (n = 2), NHEJ1 (n = 2), CD3E (n = 2), IL2RG (n = 3), JAK3 (n = 4) and IL7R (n = 1). The overall success rate of our custom-made NGS panel was 60% (39.3% for NK+ SCID and 100% for NK- SCID). Incidence of autosomal-recessive inherited genes is more frequently found in our cohort than the previously reported populations probably due to the high consanguineous marriages in Turkey. In conclusion, the custom-made sequencing panel was able to identify and confirm the previously known and novel disease-causing variants with high accuracy.
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    A Novel FOXN1 Variant Is Identified in Two Siblings with Nude Severe Combined Immunodeficiency
    (Springer/Plenum Publishers, 2019) Firtina, Sinem; Cipe, Funda; Ng, Yuk Yin; Kiykim, Ayca; Ng, Ozden Hatirnaz; Sudutan, Tugce; Aydogmus, Cigdem
    [Abstract Not Available]
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    A novel pathogenic frameshift variant of CD3E gene in two T-B plus NK plus SCID patients from Turkey
    (Springer, 2017) Firtina, Sinem; Ng, Yuk Yin; Ng, Ozden Hatirnaz; Nepesov, Serdar; Yesilbas, Osman; Kilercik, Meltem; Burtecene, Nihan
    Severe combined immunodeficiency (SCID) is the most severe form of primary immunodeficiency, which is characterized by the dysfunction and/or absence of T lymphocytes. Early diagnosis of SCID is crucial for overall survival, and if it remains untreated, SCID is often fatal. Next-generation sequencing (NGS) has become a rapid, high-throughput technology, and has already been proven to be beneficial in medical diagnostics. In this study, a targeted NGS panel was developed to identify the genetic variations of SCID by using SmartChip-TE technology, and a novel pathogenic frameshift variant was found in the CD3E gene. Sanger sequencing has confirmed the segregation of the variant among patients. We found a novel deletion in the CD3E gene (NM000733.3:p.L58Hfs*9) in two T-B+ NK+ patients. The variant was not found in the databases of dbSNP, ExAC, and 1000G. One sibling in family I was homozygous and the rest of the family members were heterozygous for this variant. T cell receptor excision circle (TREC) and kappa-deleting recombination excision circle (KREC) analyses were performed for T and B cell maturation. TRECs were not detected in both patients and the KREC copy numbers were similar to the other family members. In addition, heterozygous family members showed decreased TREC levels when compared with the wild-type sibling, indicating that carrying this variant in one allele does not cause immunodeficiency, but does effect T cell proliferation. Here, we report a novel pathogenic frameshift variant in CD3E gene by using targeted NGS panel.