Clinical and molecular evaluation of MEFV gene variants in the Turkish population: a study by the National Genetics Consortium.

Familial Mediterranean fever (FMF) is a monogenic autoinflammatory disorder with recurrent fever, abdominal pain, serositis, articular manifestations, erysipelas-like erythema, and renal complications as its main features. Caused by the mutations in the MEditerranean FeVer (MEFV) gene, it mainly affects people of Mediterranean descent with a higher incidence in the Turkish, Jewish, Arabic, and Armenian populations. As our understanding of FMF improves, it becomes clearer that we are facing with a more complex picture of FMF with respect to its pathogenesis, penetrance, variant type (gain-of-function vs. loss-of-function), and inheritance. In this study, MEFV gene analysis results and clinical findings of 27,504 patients from 35 universities and institutions in Turkey and Northern Cyprus are combined in an effort to provide a better insight into the genotype-phenotype correlation and how a specific variant contributes to certain clinical findings in FMF patients. Our results may help better understand this complex disease and how the genotype may sometimes contribute to phenotype. Unlike many studies in the literature, our study investigated a broader symptomatic spectrum and the relationship between the genotype and phenotype data. In this sense, we aimed to guide all clinicians and academicians who work in this field to better establish a comprehensive data set for the patients. One of the biggest messages of our study is that lack of uniformity in some clinical and demographic data of participants may become an obstacle in approaching FMF patients and understanding this complex disease.

The effect of neoadjuvant chemotherapy on tumor-infiltrating lymphocytes in patients with breast cancer.

Aim: This study investigated the effect of neoadjuvant chemotherapy (NAC) on stromal tumor-infiltrating lymphocytes (sTILs) and their treatment response. Materials & methods: 115 patients with pre-NAC core biopsies and post-NAC surgical resection specimens were reviewed. Results: There was no significant change between pre- and post-treatment sTILs. Both pre- and post-NAC sTILs were significantly lower in patients with luminal A subtype. An increase in sTILs was observed in 21 (25.9%) patients after NAC, a decrease in 29 (35.8%) and no change in 31 (38.3%; p = 0.07). Pretreatment sTIL density was independent predictor of pathological complete response in multivariate analyses (odds ratio: 1.025, 95% CI: 1.003-1.047; p = 0.023). Conclusion: High sTIL density in core biopsies was independently related to pathological complete response. In addition, ER appears to be the most crucial factor determining the rate of sTIL.

New studies have shown that the tumor microenvironment is critical in tumor behavior. Immune cells surrounding tumor cells are the main components of the tumor microenvironment. Our study aimed to investigate the change in immune cells before and after chemotherapy in breast cancer patients. Our study included 115 patients. All patients underwent chemotherapy before surgery to shrink the tumor. Tru-cut biopsy pieces and the breast tissue obtained after surgery were examined. The presence of estrogen or progesterone receptors on tumor cells decreased the number of immune cells surrounding the tumor cells. The number of immune cells did not decrease after chemotherapy. Another finding was that the greater the number of immune cells around the tumor, the more likely that the tumor would disappear after chemotherapy.

Unusual Chromosomal Rearrangement Resulted in Interstitial Monosomy 9p: Case Report.

We report on a 4.5-year-old boy with interstitial monosomy 9p in a unique and complex de novo rearrangement. The patient had been referred for craniofacial dysmorphism, delayed psychomotor development, and various congenital malformations. We combined cytogenetic studies and FISH analyses to delineate the deletion. The result of our cytogenetic studies was 46,XY,der(9)(p22pter). In order to confirm the deletion, we also performed FISH analysis, which showed that the 9p subtelomeric region was inserted into chromosome 13. Molecular karyotyping was performed to describe the exact genomic breakpoints of the rearrangement. In conclusion, this case is a complex insertion/deletion abnormality which has not been reported before.

AUTS2 Syndrome in a 68-year-old female: Natural history and further delineation of the phenotype.

Here we summarize the clinical and molecular findings in a 68-year-old female with dysmorphic features, mild-to-moderate intellectual disability, and behavioral findings suggesting autism spectrum disorder. SNP array analysis demonstrated a 257 kb deletion comprising exon 6 of AUTS2. This clinical report provides the natural history in the eldest patient yet to be reported, and complements the existing evidence suggesting that disruption of the AUTS2 leads to a recently delineated neurodevelopmental phenotype with a wide spectrum, namely "AUTS2 Syndrome." © 2016 Wiley Periodicals, Inc.

First Co-Occurrence of Griscelli Syndrome Type 2 and Neurofibromatosis Type 1.

Introduction: Griscelli syndrome type 2 (GS2) and neurofibromatosis type 1 (NF1) are both rare genetic disorders, but their coexistence has not been documented prior to this report. Case Presentation: We present the case of a 4-year-old girl initially diagnosed with GS2 due to albinism and immunodeficiency, and later with NF1, manifested by the development of multiple café-au-lait macules (CALMs) and MRI findings. The patient was the second child of consanguineous parents and exhibited symptoms early, with silver-gray hair at birth and subsequent health complications at 9 months. GS2 was confirmed via the identification of a homozygous frameshift variant in the RAB27A gene, and a de novo heterozygous splice site mutation in the NF1 gene established the NF1 diagnosis. Her treatment included hematopoietic stem cell transplantation and ongoing surveillance for NF1-associated complications. Discussion/Conclusion: This case emphasizes the importance of considering the potential for concurrent rare genetic diseases in clinical evaluations, especially with progressive or evolving symptomatology.

MCM-2 Levels as a Potential Biomarker for Predicting High-Risk Breast Cancer Patients According to TAILORx Classification.

Background: The minichromosome maintenance protein-2 (MCM-2) is a more sensitive proliferation marker than Ki-67. This study aimed to evaluate the relationship between MCM-2 and Oncotype DX recurrence score (ODX-RS) and determine an MCM-2 cutoff value in high-risk patients according to TAILORx risk categorization. Methods: Hormone receptor (HR) positive HER-2 negative early-stage breast cancer patients (pT1-2, pN0-N1, M0) who had ODX-RS were included in the study. According to the TAILORx trial, patients were divided into two groups with high (ODX-RS ≥26) and low risk (ODX-RS <26) in terms of ODX-RS. Formalin-fixed-paraffin-embedded tissues of patients were re-evaluated, and 3 µm sections were prepared for MCM-2 immuno-histochemical staining. The relationship between ODX-RS and the percentage of MCM-2 staining was evaluated in two groups. The ROC curve analysis was performed to determine the MCM-2 cut-off value for the TAILORx high-risk group (ODX-RS ≥26). Results: The mean MCM-2 value was significantly higher in the high-risk group [(60.2 ± 11.2 vs 34.4 ± 13.8, p < 0.001)]. In the multivariate analysis, MCM-2 (OR: 1.27, 95% CI: 1.08-1.49, p = 0.003) and progesterone receptor (PR) levels ≤10% (OR: 60.9, 95% CI: 4.1-89.7, p = 0.003) were found to be independent factors indicating a high-risk group. A one-unit increase in MCM-2 level increased the likelihood of being in the high-risk group by 1.27 times. In the ROC curve analysis, the optimal MCM-2 cut-off level was 50 (AUC: 0.921, sensitivity: 86.7%, specificity: 96.0%, p < 0.001). Conclusion: Our study is the first study in the literature to investigate the relationship between ODX-RS and MCM-2 levels in HR-positive HER-2 negative early breast-cancer patients. In this study, MCM-2 was an independent risk factor in identifying high-risk patients according to TAILORx risk classification. MCM 2 cut-off value (50) may help the decision on adjuvant chemotherapy in patients where the Oncotype DX test cannot be performed.

Clinical and inflammation marker features of cancer patients with COVID-19: data of Istanbul, Turkey multicenter cancer patients (2020-2022).

OBJECTIVE: We aimed to identify a rapid, accurate, and accessible biomarker in the early stages of COVID-19 that can determine the prognosis of the disease in cancer patients. METHODS: A total number of 241 patients with solid cancers who had a COVID-19 diagnosis between March 2020 and February 2022 were included in the study. Factors and ten different markers of inflammation were analyzed by year of diagnosis of COVID-19 and grouped by severity of infection. RESULTS: Hospitalization, referral to the intensive care unit (ICU), mechanical ventilation, and death were more frequent in 2020 than in 2021 and 2022 (mortality rates, respectively, were 18.8%, 3.8%, and 2.5%). Bilateral lung involvement and chronic lung disease were independent risk factors for severe disease in 2020. In 2021-2022, only bilateral lung involvement was found as an independent risk factor for severe disease. The neutrophil-to-lymphocyte platelet ratio (NLPR) with the highest area under the curve (AUC) value in 2020 had a sensitivity of 71.4% and specificity of 73.3% in detecting severe disease (cut-off > 0.0241, Area Under the Curve (AUC) = 0.842, p <.001). In 2021-2022, the sensitivity of the C-reactive protein-to-lymphocyte ratio (CRP/L) with the highest AUC value was 70.0%, and the specificity was 73.3% (cut-off > 36.7, AUC = 0.829, p = .001). CONCLUSIONS: This is the first study to investigate the distribution and characteristics of cancer patients, with a focus on the years of their COVID-19 diagnosis. Based on the data from our study, bilateral lung involvement is an independent factor for severe disease, and the CRP/L inflammation index appears to be the most reliable prognostic marker.

Survival results according to Oncotype Dx recurrence score in patients with hormone receptor positive HER-2 negative early-stage breast cancer: first multicenter Oncotype Dx recurrence score survival data of Turkey.

Background: The Oncotype Dx recurrence score (ODx-RS) guides the adjuvant chemotherapy decision-making process for patients with early-stage hormone receptor-positive, HER-2 receptor-negative breast cancer. This study aimed to evaluate survival and its correlation with ODx-RS in pT1-2, N0-N1mic patients treated with adjuvant therapy based on tumor board decisions. Patients and methods: Estrogen-positive HER-2 negative early-stage breast cancer patients (pT1-2 N0, N1mic) with known ODx-RS, operated on between 2010 and 2014, were included in this study. The primary aim was to evaluate 5-year disease-free survival (DFS) rates according to ODX-RS. Results: A total of 203 eligible patients were included in the study, with a median age of 48 (range 26-75) and median follow-up of 84 (range 23-138) months. ROC curve analysis for all patients revealed a recurrence cut-off age of 45 years, prompting evaluation by grouping patients as ≤45 years vs. >45 years. No significant difference in five-year DFS rates was observed between the endocrine-only (ET) and chemo-endocrine (CE) groups. However, among the ET group, DFS was higher in patients over 45 years compared to those aged ≤45 years. When stratifying by ODx-RS as 0-17 and ≥18, DFS was significantly higher in the former group within the ET group. However, such differences were not seen in the CE group. In the ET group, an ODx-RS ≥18 and menopausal status were identified as independent factors affecting survival, with only an ODx-RS ≥18 impacting DFS in patients aged ≤45 years. The ROC curve analysis for this subgroup found the ODx-RS cut-off to be 18. Conclusion: This first multicenter Oncotype Dx survival analysis in Turkey demonstrates the importance of Oncotype Dx recurrence score and age in determining treatment strategies for early-stage breast cancer patients. As a different aproach to the literature, our findings suggest that the addition of chemotherapy to endocrine therapy in young patients (≤45 years) with Oncotype Dx recurrence scores of ≥18 improves DFS.

Evaluation of Anti-Mullerian Hormone Levels, Antral Follicle Counts, and Mean Ovarian Volumes in Chemotherapy-Induced Amenorrhea among Breast Cancer Patients: A Prospective Clinical Study.

Estradiol (E2), a follicle-stimulating hormone (FSH), AMH, and inhibin B levels, along with AFC and MOV, are used to determine ovarian reserve in pre-menopausal women. Studies have shown that AMH levels are more sensitive than those of E2, FSH, and inhibin B and that AFC and MOV can be used to evaluate ovarian reserve. AMH, AFC, and MOV measurements were performed before and after adjuvant SC in 3-month periods for one year. Patients were classified as experiencing chemotherapy-induced amenorrhea (CIA) if they did not have menstrual cycles for a period of six months or longer following the conclusion of their chemotherapy treatment. We aimed to evaluate the factors affecting chemotherapy-induced amenorrhea in breast cancer patients treated with adjuvant chemotherapy and the performance of baseline measurements of AMH, AFC, and MOV to predict chemotherapy-induced amenorrhea. The effects of different chemotherapy regimens on the AMH level, AFC, and MOV in CIA patients were investigated. Seventy-one patients were eligible for this study, and the median age was 38 years (range: 23-45). The median follow-up was 37 months (range: 20-51), and CIA developed in 62% of the patients. The AMH level and AFC were significantly decreased one year after SC (p < 0.0001), whereas MOV was not (p = 0.507). AMH levels before chemotherapy (median: 1.520 vs. 0.755, p = 0.001) and at the end of the first year (median: 0.073 vs. 0.010, p = 0.030) and pre-treatment AFC (median: 12 vs. 4.50, p = 0.026) were lower in patients with CIA compared to those without CIA. The AMH levels before SC were the most valuable and earliest factor for predicting CIA development. In addition, there was no difference between the chemotherapy regimens (including or not including taxane) in terms of CIA development.

Hypomyelinating spastic dyskinesia and ichthyosis caused by a homozygous splice site mutation leading to exon skipping in ELOVL1.

INTRODUCTION: Next generation sequencing technologies allow detection of very rare pathogenic gene variants and uncover cerebral palsy. Herein, we describe two siblings with cerebral palsy due to ELOVL1 splice site mutation in autosomal recessive manner. ELOVL1 catalyzes fatty acid elongation to produce very long-chain fatty acids (VLCFAs; ≥C21), most of which are components of sphingolipids such as ceramides and sphingomyelins. Ichthyotic keratoderma, spasticity, hypomyelination, and dysmorphic facies (MIM: 618527) stem from ELOVL1 gene deficiency in human. METHODS: We have studied a consanguineous family with whole exome sequencing (WES) and performed in depth analysis of cryptic splicing on the molecular level using RNA. Comprehensive analysis of ceramides in the skin stratum corneum of patients using liquid chromatography-tandem mass spectrometry (LC-MS/MS). ELOVL1 protein structure was computationally modelled. RESULTS: The novel c.376-2A > G (ENST00000372458.8) homozygous variant in the affected siblings causes exon skipping. Comprehensive analysis of ceramides in the skin stratum corneum of patients using LC-MS/MS demonstrated significant shortening of fatty acid moieties and severe reduction in the levels of acylceramides. DISCUSSION: It has recently been shown that disease associated variants of ELOVL1 segregate in an autosomal dominant manner. However, our study for the first time demonstrates an alternative autosomal recessive inheritance model for ELOVL1. In conclusion, we suggest that in ultra-rare diseases, being able to identify the inheritance patterns of the disease-associated gene or genes can be an important guide to identifying the molecular mechanism of genetic cerebral palsy.

Importance of multigene panel test in patients with consanguineous marriage and family history of breast cancer.

Next-generation sequencing (NGS) technology is used to evaluate hereditary cancer risks of patients worldwide; however, information concerning the germline multigene mutational spectrum among patients with breast cancer (BC) with consanguineous marriage (CM) is limited. Therefore, this prospective study aimed to determine the molecular characteristics of patients with BC who were tested with multigene hereditary cancer predisposition NGS panel and to show the effect of CM on cancer-related genes. Patients with BC with or without CM and family history (FH) of BC treated in our breast center were selected according to The National Comprehensive Cancer Network (NCCN) criteria for hereditary BC. In these patients, the analysis of a panel of 33 genes involved in hereditary cancer predisposition was performed after genetic counseling by using NGS. The pathogenic variant (PV) and the variant of uncertain significance (VUS) were found to be 15.8 and 47.4%, respectively. PVs were identified in 10/33 genes in 34 patients; 38.2% in BRCA1/2 genes; 6, 24, and 14% in other high, moderate and low-risk genes, respectively. The CM rate was 17.7% among the 215 patients with BC. The PV rate was 13.2% in patients with CM and 16.4% in patients without CM (P=0.80). When PV and VUS were evaluated together, the PV+VUS ratio was significantly higher in patients with CM and FH of BC than patients without CM and FH of BC (88.2 vs. 63.3%, P=0.045). Analysis of multigene panel provided 9.76% additional PVs in moderate/low-risk genes. The PV rate was similar in patients with BC with or without CM. A high PV+VUS ratio in patients with CM and FH of BC suggests that genes whose importance are unknown are likely to be pathogenic genes later.

Rapid molecular diagnosis of ALB gene variants prevents unnecessary interventions in familial dysalbuminemic hyperthyroxinemia.

OBJECTIVES: Familial dysalbuminemic hyperthyroxinemia (FDH) is an autosomal dominant condition caused by heterozygous gain-of-function mutations in the human ALB gene. CASE PRESENTATION: We report, a three-year-old boy with FDH due to p.R242P (or p.R218P without signal peptide) mutation in the ALB gene with a phenotype characterized by extremely high serum total and free thyroxine concentrations. His parents had normal thyroid function tests (TFT), so the mutation detected in this patient is assumed "de novo". Although the most frequent variant was p.R242H in Caucasians and p.R242P in Japanese, our patient had p.R242P variant. CONCLUSIONS: Early identification of FDH is fundamental to prevent unnecessary repeats of TFT with different methods. We encourage the ALB gene hot spot sequencing initially and indicate that this molecular diagnosis is a rapid and simple method to diagnose FDH in individuals with euthyroid hyperthyroxinemia.

The miRNA content of circulating exosomes in DLBCL patients and in vitro influence of DLBCL-derived exosomes on miRNA expression of healthy B-cells from peripheral blood.

BACKGROUND: Due to the heterogeneous nature of Diffuse Large B-cell Lymphoma (DLBCL), the mechanisms underlying tumor development and progression have not yet been fully elucidated. OBJECTIVE: This study aimed to compare the characteristics of plasma exosomes of DLBCL patients and healthy individuals and to evaluate the exosomal interactions between DLBCL cell lines and normal B-cells. METHODS: Exosome isolation was performed using an ultracentrifugation-based protocol from plasma of 20 patients with DLBCL and 20 controls. The expression of miRNAs from exosome samples was analyzed using a miRNA expression microarray. The presence of exosome-mediated communication between the lymphoma cells and normal B-cells was determined by the co-culture model. RESULTS: A significant increase in plasma exosome concentrations of DLBCL patients was observed. There was also a significant decrease in the expression of 33 miRNAs in plasma exosomes of DLBCL patients. It was determined that normal B-cells internalize DLBCL-derived exosomes and then miRNA expression differences observed in normal B-cells are specific to lymphoma-subtypes. CONCLUSIONS: MiR-3960, miR-6089 and miR-939-5p can be used as the miRNA signature in DLBCL diagnosis. We suppose that the exosomes changed the molecular signature of the target cells depending on the genomic characterization of the lymphoma cells they have originated.

Prevalence and clinical/molecular characteristics of PTEN mutations in Turkish children with autism spectrum disorders and macrocephaly.

BACKGROUND: Phosphatase and tensin homolog (PTEN) germline mutations are associated with cancer syndromes (PTEN hamartoma tumor syndrome; PHTS) and in pediatric patients with autism spectrum disorder (ASD) and macrocephaly. The exact prevalence of PTEN mutations in patients with ASD and macrocephaly is uncertain; with prevalence rates ranging from 1% to 17%. Most studies are retrospective and contain more adult than pediatric patients, there is a need for more prospective pediatric studies. METHODS: We recruited 131 patients (108 males, 23 females) with ASD and macrocephaly between the ages of 3 and 18 from five child and adolescent psychiatry clinics in Turkey from July 2018 to December 2019. We defined macrocephaly as occipito-frontal HC size at or greater than 2 standard deviations (SD) above the mean for age and sex on standard growth charts. PTEN gene sequence analysis was performed using a MiSeq next generation sequencing (NGS) platform, (Illumina). CONCLUSION: PTEN gene sequence analyses identified three pathogenic/likely pathogenic mutations [NM_000314.6; p.(Pro204Leu), (p.Arg233*) and novel (p.Tyr176Cys*8)] and two variants of uncertain significance (VUS) [NM_000314.6; p.(Ala79Thr) and c.*10del]. We also report that patient with (p.Tyr176Cys*8) mutation has Grade 1 hepatosteatosis, a phenotype not previously described. This is the first PTEN prevalence study of patients with ASD and macrocephaly in Turkey and South Eastern Europe region with a largest homogenous cohort. The prevalence of PTEN mutations was found 3.8% (VUS included) or 2.29% (VUS omitted). We recommend testing for PTEN mutations in all patients with ASD and macrocephaly.

Prenatal diagnsis of intracardiac hamartoma and Turner syndrome.

Turner syndrome is associated with a higher frequency of heart defects detected prenatally when compared to postnatal reports. The most common heart defects detected prenatally are hypoplastic left heart syndrome and coarctation of the aorta. We report a case involving a fetus at 16 gestational weeks with a septated cystic hygroma located on the neck and head, an interventricular septal mass, a hypoplastic left ventricle due to aortic stenosis, mitral stenosis, and a hypoplastic aortic arch with a karyotype of mos 45, X, [47 cells]/47, XXX [3 cells]. The autopsy findings confirmed our prenatal diagnosis with a final diagnosis of Turner syndrome and congenital cardiac vascular malformation.

Prenatal diagnosis of VACTERL syndrome and partial caudal regression syndrome: a previously unreported association.

We describe a case of VACTERL syndrome associated with type 1 unilateral caudal regression syndrome. The abnormal sonographic findings at 26 weeks included hemivertebrae, scoliosis, hypoplastic and deformed lumbar spine and sacrum, preaxial polydactyly on the left hand, duplicated hallux on the left foot and hemihypoplasia of the left lower limb, bilateral club foot, and single umbilical artery. Postmortem examination confirmed prenatal sonographic findings with additional findings of supernumerary rib at the lumbar level and anal atresia.

DNA fragmentation index and human papilloma virus in males with previous assisted reproductive technology failures.

OBJECTIVE: This study was designed to evaluate the prevalence of Human Papilloma Virus (HPV) in semen and document the cycle outcomes in couples with previous intra-cytoplasmic sperm injection (ICSI) failures. MATERIAL AND METHODS: One hundred and seventeen couples with at least two ICSI attempts were included in the study. HPV infection in semen and DNA fragmentation in samples were analyzed by commercially available kits. The percentage of spermatozoa with fragmented DNA (DNA fragmentation index: DFI) was determined during fluorescence microscopic examination as previously described. The cycle outcomes of couples with or without HPV infected male partners were recorded. RESULTS: According to our results, the prevalence of HPV was 7.7% in asymptomatic males with at least two previous ICSI failures. The increased DFI (>30%) was observed in 82.9% of the cases. In HPV-positive cases significantly lower number of good quality embryos were obtained. The implantation and pregnancy rates were similar in infected and non-infected males (p>0.05). The early miscarriage rate was slightly higher in HPV- positive group (33% vs. 10%, p>0.05). CONCLUSION: In cases with previous ICSI failures, the prevalence of HPV infection in semen is not higher than previously reported infertile populations. The reproductive outcome might be impaired in HPV-positive semen due to lower number of good quality embryos, which needs to be clarified by further large population-based studies.

Clonal evolution of monosomy 7 in acquired severe aplastic anemia: Two cases treated with allogeneic hematopoietic stem cell transplantation.

Aplastic anemia (AA) may evolve into clonal diseases like myelodysplastic syndrome (MDS) and acute myeloblastic leuke¬mia (AML). Monosomy 7 is a poor prognostic chromosomal abnormality commonly associated with therapy related MDS and secondary AML. It has also been associated with leukomogenic transformation in AA. We present here two adult ma¬le patients with acquired severe AA. Both patients had received immunosuppressive therapy (IST) as first line treatment and had monosomy 7 positive clone at transformation to MDS with refractory anemia and excess of blast (RAEB-II) and AML, respectively. Both patients have undergone allogeneic hematopoietic stem cell (HSC) transplantation from their HLA identical donors (unrelated and sibling).