Mustafa Altan

Objective: Early embryonic development is orchestrated by transcriptional and epigenetic mechanisms that regulate pluripotency and differentiation. This study aimed to investigate the stage-specific expression of key transcription factors (Oct-3/-4, Sox-2, Nanog, SSEA-1, and c-Myc) and DNA methylation enzymes (Dnmt1 and Dnmt3) during the pre-implantation period in a rat model. Materials and Methods: Embryos were collected at the 2-8 cell, 8-16 cell, and blastocyst stages. Gene expression levels were assessed using real-time PCR, while protein localisation was evaluated via immunofluorescence staining. Results: Oct-3/-4 and Sox-2 exhibited the highest levels of expression at the 2–8 cell stage, which suggests that they play an important role in the maintenance of pluripotency at an early stage. Nanog, c-Myc, and Dnmt3 were significantly upregulated at the blastocyst stage, indicating their involvement in lineage commitment. Dnmt-1 was consistently expressed across all stages, which supports its role in epigenetic memory. Discrepancies between SSEA-1 gene expression and protein detection suggested post-transcriptional regulation. Conclusion: These findings emphasise the dynamic and coordinated functions of transcriptional and epigenetic regulators during the early stages of embryogenesis. Combined mRNA and protein analysis provides a comprehensive molecular profile that is relevant to reproductive medicine and developmental biology.

Mandibuloacral dysplasia (MAD) is a rare genetic disorder characterized by distinctive skeletal abnormalities, metabolic issues, and skin changes, often linked to pathogenic variants in the LMNA gene, which encodes lamin A/C. This study investigates a specific founder mutation within a Turkish cohort and explores its impact on phenotypic expressivity. We conducted a comprehensive analysis involving genetic testing for LMNA variants in patients diagnosed with MAD. Clinical evaluations documented a wide range of phenotypic features, including facial dysmorphism, skeletal anomalies, and metabolic abnormalities. We also collected family histories to assess inheritance patterns and potential environmental influences. Our findings identified a common founder mutation in the LMNA gene among the cohort, which was present in a significant percentage of participants. Notably, phenotypic expressivity varied significantly, with some individuals exhibiting classic MAD features, while others showed atypical manifestations, such as additional endocrine disorders and variable severity of skeletal anomalies. This variability underscores the complexity of the genotype-phenotype relationship. This study highlights the significance of the founder mutation in LMNA and its diverse phenotypic outcomes in MAD. Our results contribute to the understanding of how genetic mutations can lead to a spectrum of clinical presentations, emphasizing the necessity for personalized clinical approaches in managing this condition. Further research is warranted to elucidate the underlying mechanisms of phenotypic variability and to improve diagnostic and therapeutic strategies.

Background: Molecular testing is recommended to refine risk stratification in indeterminate thyroid nodules (Bethesda III–IV), but data on dual-gene (BRAF and RAS) testing using fresh FNA washout specimens are limited. We aimed to evaluate the performance of BRAF and RAS mutation analysis from fresh thyroid FNA washout material, with a focus on indeterminate cytology. Methods: We retrospectively analyzed 1139 patients who underwent washout-based molecular testing between May 2022 and October 2024 at a tertiary endocrine center. Of these, 307 had available histopathologic results after surgery. Primary outcomes were sample adequacy, mutation spectrum, and diagnostic metrics (sensitivity, specificity, PPV, NPV, and accuracy). Analyses were repeated under two assumptions that classified borderline/low-risk neoplasms as benign vs. malignant, and within the Bethesda III–IV subset. Results: Adequate material for molecular analysis was obtained in 1037/1139 samples (90.9%). In the operated cohort (n = 307), malignant lesions comprised 31.9% and low-risk neoplasms 8.5%. When borderline lesions were considered benign, mutation positivity yielded a sensitivity of 48.0%, a specificity of 89.6%, a PPV of 75.9%, an NPV of 71.9%, and an accuracy of 72.9%. In Bethesda III–IV nodules (n = 153), sensitivity, specificity, and accuracy were 41.0%, 85.2%, and 66.0% (malignant assumption). Isolated BRAF positivity showed high specificity (~96.7%) with modest sensitivity. Conclusions: Our findings extend current diagnostic approaches by showing that dual-gene (BRAF and RAS) testing from fresh FNA washouts is technically feasible (≥90% adequacy) and provides high specificity with modest sensitivity for malignancy in indeterminate nodules. In settings lacking comprehensive commercial panels, this low-complexity approach offers a practical adjunct to cytology and imaging for preoperative decision-making.

Neurofibromatosis Type 1 (NF1) is a common genetic disorder of childhood, characterized by highly variable expressivity. In addition to café-au-lait spots, it shows multisystemic involvement and may cause skeletal abnormalities, tumor predisposition, and neurodevelopmental delay during childhood. This study aims to investigate the clinical and molecular characteristics of pediatric NF1 patients and to explore possible genotype–phenotype correlations. This study retrospectively evaluated the clinical and molecular findings of 148 pediatric NF1 patients, identifying genotype–phenotype correlations through Next-Generation Sequencing (NGS) and multiplex ligation-dependent probe amplification (MLPA) analysis. The mean age at diagnosis was 8.7 years (1 month to 17 years), with a male-to-female ratio of 0.8. Cafe-au-lait spots were the most common finding (99.3%), followed by freckling (46.6%) and Lisch nodules (28.4%). Additional findings included short stature (29.3%), scoliosis (11.4%), neurodevelopmental delay (14.9%), cutaneous neurofibromas (6.8%), plexiform neurofibromas (6.8%), and optic pathway gliomas (6.7%). Magnetic Resonance Imaging revealed T2 hyperintensities in 72.6% of cases. NGS identified NF1 variants in 94.5% of patients, and MLPA detected full-gene deletions in 2 additional cases. With a molecular diagnostic yield of 95.9%, this study identifies 14 novel variants. Conclusion: This study expands the NF1 variant spectrum in children and emphasizes the value of molecular testing for early diagnosis, especially in infants and those with atypical features. Age-stratified clinical data from a large pediatric cohort revealed a potential link between truncating variants and axillary/inguinal freckling. Beyond diagnosis, molecular testing also supports surveillance and genetic counseling, highlighting its clinical utility in managing pediatric NF1. What is Known: • NF1 is a well-known genetic disorder with highly variable expressivity. It shows a wide range of clinical findings, even among patients with the same genetic variant. While some specific genotype–phenotype links have been reported, most NF1 variants do not show clear clinical patterns. Certain features, like café-au-lait macules, appear early in infancy, but others, such as freckling or neurofibromas, often appear later. What is New: • In our pediatric NF1 cohort, axillary/inguinal freckling was found to be significantly more common in patients with truncating variants. For Lisch nodules, cutaneous neurofibromas, tumor presence, and especially T2 hyperintensities, point estimates suggested a non-significant trend toward higher frequencies in the truncating group. This suggests that some features may differ depending on the type of mutation. A total of 14 novel variants in NF1 were identified through NGS.

Objective: Small for gestational age (SGA) is a heterogeneous condition influenced by fetal, placental, maternal, and genetic factors. While most SGA children experience catch-up growth within the first two years, up to 10-15% remain short-statured and may require growth hormone (GH) therapy. This study evaluated the clinical characteristics, genetic factors, and responses to recombinant GH (rGH) therapy in non-syndromic SGA children with persistent short stature. Material and Methods: We retrospectively analyzed 36 non-syndromic short-statured children born SGA who were evaluated in a tertiary center. Genetic testing, including karyotyping and microarray analysis for copy number variations (CNVs), was performed. Growth response to rGH therapy was assessed in 19 patients over a three-year period. Results: Among the 19 patients receiving rGH therapy, the mean height SDS improved from -3.04±0.58 at baseline to -2.07±0.67 after three years, with an average gain of 0.97 SDS. CNVs were identified in 6 patients (16.66%), with several pathogenic or likely pathogenic variants, including deletions and duplications in regions associated with growth and developmental disorders. Conclusion: A significant proportion of non-syndromic SGA children with persistent short stature exhibit CNVs, underscoring the genetic complexity of this condition. rGH therapy effectively improves growth outcomes, but individual responses vary. These findings highlight the need for routine genetic screening and personalized treatment strategies to optimize care for SGA children.

Background/Objectives: Inherited platelet disorders (IPDs) are diverse conditions characterized by abnormalities in platelet count and function. Next-Generation Sequencing (NGS) shows promise as a diagnostic tool in the diagnosis of IPDs. This study aims to assess the clinical value and limitations of using a targeted NGS panel in diagnosing children with suspected IPDs. Methods: We conducted a retrospective study of 93 children evaluated for suspected IPDs. A targeted NGS panel of 14 IPD-associated genes (RUNX1, WAS, ADAMTS13, ANKRD26, CYCS, GATA1, GP1BA, GB1BB, GP9, ITGA2B, ITGB3, MASTL, MPL, MYH9) was performed. Results: Genetic variants were identified in 30 patients (32.3% of the cohort). A total of 37 variants, of which 15 (40.5%) were novel, were found across 11 of the 14 genes on the panel (all except MPL, CYCS, and RUNX1). Variants were most frequently found in ITGB3 (18.9% of variants), GP1BA (16.2%), and ADAMTS13 (16.2%) genes. The majority of variants (64.9%) were classified as variants of uncertain significance (VUS), followed by likely pathogenic (LP) (27%) and pathogenic (8.1%) variants. Most variants were in a heterozygous state (73%). Specific cases highlighted complex genetic scenarios, such as co-occurring variants, and the identification of pathogenic and LP variants in patients initially presenting with immune thrombocytopenia. Conclusions: NGS helps to identify genetic causes, assess risk, manage, and provide genetic counseling in the management of IPDs. However, the prevalence of VUS underscores the need for a multidisciplinary approach to evaluate NGS results accurately.

Onkoloji alanındaki tüm dünyanın yakın takip ettiği bilimsel gelişmeler ışığında günümüzde artık sistemik kemoterapi gibi konvansiyonel tedaviler yerlerini büyük ölçüde immünoterapi, moleküler hedefli ilaçlar ve gen tedavilerine bırakmaya başlamıştır. Bu tedavi stratejilerinin geliştirilmesi, yeni ilaçların keşifleri ve mevcut ilaçlara karşı gelişen direnç mekanizmalarının anlaşılması ve tümörlerin detaylı kimliklendirilmelerinin önemi tartışılmaz bir gerçek ve gereklilik haline gelmiştir. Moleküler ve genetik temelli çalışmalar bize bu imkanları sağlama konusunda çok önemli katkılar sağlamaktadır.