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Mucopolysaccharidosis IVA (MPS IVA; Morquio A syndrome) is caused by a deficiency of the N-acetylgalactosamine-6-sulfate-sulfatase (GALNS) enzyme, leading to the accumulation of glycosaminoglycans (GAG), keratan sulfate (KS) and chondroitin-6-sulfate (C6S), mainly in cartilage and bone. This lysosomal storage disorder (LSD) is characterized by severe systemic skeletal dysplasia. To this date, none of the treatment options for the MPS IVA patients correct bone pathology. Enzyme replacement therapy with elosulfase alpha provides a limited impact on bone growth and skeletal lesions in MPS IVA patients. To improve bone pathology, we propose a novel gene therapy with a small peptide as a growth-promoting agent for MPS IVA. A small molecule in this peptide family has been found to exert biological actions over the cardiovascular system. This work shows that an AAV vector expressing a C-type natriuretic (CNP) peptide induces bone growth in the MPS IVA mouse model. Histopathological analysis showed the induction of chondrocyte proliferation. CNP peptide also changed the pattern of GAG levels in bone and liver. These results suggest the potential for CNP peptide to be used as a treatment in MPS IVA patients.

The association between hypertensive retinopathy and left atrial (LA) impairment is unknown. Accordingly, it was aimed to investigate the possible relationship between hypertensive retinopathy and LA phasic functions by means of two-dimensional speckle-tracking echocardiography (2D-STE).A total of 124 hypertensive patients and 27 control subjects were included in the study. LA reservoir strain (LAHypertensive patients (with and without retinopathy) displayed an obvious reduction in the LA reservoir strain (LAImpaired LA reservoir and conduit strain may be used to predict hypertensive patients at higher risk of developing hypertensive retinopathy, and to determine which patients should be followed more closely for hypertensive retinopathy.

Objectives To find BRCA1/2 test selection criteria unique to the Turkish population, as well as to provide the BRCA1/2 gene mutation distributions of patient population to the literature. Methods Genetic counseling was given to 2,373 cases with a family history of high-risk breast and/or ovarian cancer who applied to Istanbul University, Oncology Institute, Department of Cancer Genetics between 1994 and 2021 and selected by NCCN Guidelines for the BRCA1/2 test criteria. In our clinic, mutation screenings in BRCA1/2 genes were performed by Sanger sequencing method in patients admitted between 1994 and 2014 and by NGS method in patients admitted between 2015 and 2021. Results The overall mutation rate in our patient group selected from high-risk patients was 16.5% (391/2,373) after BRCA1/2 gene mutation screening performed in 2,373 cases who applied to the Cancer Genetics clinic. Of the patients with mutations, 57.5% (225/391) had BRCA1 mutation, 41.9% (164/391) had BRCA2 mutation, and 0.6% (2/391) had both BRCA1 and BRCA2 pathogenic mutations. People diagnosed before the age of 60 who have a history of triple-negative breast cancer had a 28.5% overall mutation rate. Conclusions BRCA1/2 mutation in Turkish population were evaluated in accordance with NCCN BRCA1/2 genetic test selection criteria; we discovered that all of our study results were statistically significant (p

Angiolipofibroma is an extremely rare triphasic mesenchymal lesion. It consists of mature adipose tissue, fibrous tissue, and vessels. Very few cases reported in the current literature. This report presents a case of a polyp-like mass in detected in routine colonoscopy screening. We also present comprehensive data of previously reported cases found throughout the world.

Introduction: To compare performance of indivisual categories between the Johns Hopkins template and the Paris system for reporting urinary cytology. Methods: Medical records of patients with bladder biopsy and relevant cytology slides were obtained from archived material. Slides were reclassified according to Johns Hopkins Template and the Paris. Results were compared to histologic diagnoses. Results: BD SurePath preparations from 205 cases with biopsy follow up (118 benign, 5 dysplasia, 23 low-and 59 malignant urothelial carcinoma (UC)) were reviewed. There were 2 inadequate specimens in each system. According to the Johns Hopkins Template, there were 96 (46.8%) no urothelial atypia or malignancy, 37 (18%) atypical urothelial cells of uncertain significance (AUC-US), 21 (10.2%) atypical urothelial cells, cannot exclude HGUC (AUC-H), 38 (18.5%) high grade urothelial carcinoma (HGUC) , and 11 (5.4%) low grade urothelial carcinoma (LGUC). The Paris System categorized 111 (54.1%) negative for high grade urothelial carcinoma, 29 (14.1%) atypical urothelial cells (AUC), 25 (12.2%) suspicious for HGUC (SHGUC), 36 (17.6%) HGUC and 2 (1%) LGUC. The Johns Hopkins Template had a sensitivity of 95.6%, specificity of 73.6%, Positive Predictive Value of 61.5%, Negative Predictive Value of 96.3, with an overall diagnostic accuracy of 79.8%. The Paris System had a sensitivity of 93.6%, specificity of 77.9%, Positive Predictive Value of 65.6%, Negative Predictive Value of 96.5, with an overall diagnostic accuracy of 82.8%. The Risk of Malignancy (ROM) for atypical category (AUC-US/AUC) in the Johns Hopkins Template was 43.2%, while it has been 24.1% for the Paris System. The ROM for suspicious category was 47.6% and 68.0% respectively. There was a statistically significant differences between negative and atypical, suspicious, and HGUC categories in each system (p

OBJECTIVE: Osteoarthritis is the most prevalent joint disease worldwide and the primary cause of musculoskeletal dysfunction. Epigenetic changes in various genes, particularly methylation, have been implicated as possible underlying causes of primary osteoarthritis. The aim of our study was to investigate the promoter methylation status of the calcium voltage-gated channel alpha 1 subunit G (CACNA1G) and interleukin-16 (IL-16) genes, which are strongly associated with calcium channel activity and antigen presentation, respectively, in primary osteoarthritis patients. PATIENTS AND METHODS: Twenty-one patients with primary osteoarthritis and 25 healthy controls were included in our study. The methylation status of CACNA1G and IL-16 genes was analyzed with methylation-specific Polymerase Chain Reaction (PCR), and the serum levels of IL-16 were determined with Enzyme-Linked Immunosorbent Assay (ELISA). RESULTS: The age of the patients was 63.95±8.41 years, and they were 15 females and 6 males. The promoter of the CACNA1G gene was found to be hypermethylated in primary osteoarthritis patients (p

Background: Inflammatory bowel disease (IBD), which is an umbrella term used for ulcerative colitis (UC) and Crohn's disease (CD), is associated with an increased risk for atherosclerotic cardiovascular disease (CVD). We aimed to investigate the association of local and systemic biomarkers of inflammation and gut microbiota-derived metabolite trimethylamine N-oxide (TMAO) with endothelial and coronary microvascular dysfunction in IBD. Methods: A total of 56 patients with IBD (20 with UC and 36 with CD) and 34 age and gender matched controls were included. For all participants, samples were collected to analyze faecal calprotectin, and TMAO concentrations. Ultrasound-based examinations were done to measure flow-mediated vasodilatation (FMD) and coronary flow velocity reserve (CFVR). Results: Patients with IBD had lower CFVR (2.07 (1.82–2.40)) and FMD (8.7 ± 3.7) as compared to controls (2.30 (2.07–2.74), p = 0.005 and 11.9 ± 6.8, p = 0.03). In patients with IBD, TMAO concentration (r = −0.30, p = 0.03), C-reactive protein (r = −0.29, p = 0.03) and WBC count (r = −0.37, p = 0.006) had a significant negative correlation with CFVR, and TMAO (β = −0.27, 95 % CI: −0.23 to −0.02) and WBC count (β = −0.31, 95 % CI: −0.56 to −0.06) were significant predictors of CFVR after multivariate adjustment. None of the biomarkers of inflammation or TMAO showed significant correlations with FMD. In patients with UC, TMAO showed a significant correlation with both CFVR (r = −0.55, p = 0.01) and FMD (r = −0.60, p = 0.005) while only WBC count had a statistically significant correlation with CFVR (r = −0.49, p = 0.004) in patients with CD. Conclusions: Gut microbiota-derived metabolite TMAO and biomarkers of systemic inflammation are associated with measures of endothelial/coronary microvascular dysfunction in patients with IBD. © 2022

The aim of the study was to investigate the frequency and types of mutations on the RB1 gene at the familial, clinical, and ethnic levels which are known to have an important role in the genetics of retinoblastoma in Turkish population. RB1 gene mutation analysis was performed in 219 people (122 probands, 14 family members with retinoblastoma and 83 clinically healthy family members) in total. All 27 exons and close intronic regions of the RB1 gene were sequenced for small deletions and insertions using both the Sanger sequencing or NGS methods, and also the large deletions and duplications were investigated by both the Multiplex Ligation Probe Amplification (MLPA) analysis and the Copy Number Variation (CNV) algorithm. The general RB1 gene mutation frequency of the patients with retinoblastoma was 41.9%. The bilateral retinoblastoma rate was 34.5% in our study population. It was striking that approximately 51.5% of our patients were diagnosed 12 months earlier, and de novo mutation occurred in 90.4% of the patients. Small genetic rearrangement mutations were detected in 78.9% of patients and Large Genetic Rearrangement (LGR) was detected in 21.1% of patients. There was a relationship between the eye color of the RB patients and RB1 mutations. As a conclusion, the familial, clinical and ethnical level of the RB1 gene mutations which are known to have a significant role in genetics of retinoblastoma were investigated, and different RB1 mutations, 10 of which are novel, have been identified on the RB1 gene sequence.

Purpose: Ovarian cancer is the seventh most frequent cancer in women worldwide and the eighth leading cause of death from cancer. Approximately 5–10% of all diagnosed cancer cases are caused by hereditary cancer risk syndromes. The aim of this study was investigate the prevalence of pathogenic variants associated with hereditary ovarian cancer propensity inTurkish people. Methods:630 patients with personal or a family history of breast and/or ovarian cancer and other cancers included in the study. The Illumina NGS technology was used to enrich genomic DNA. Results:118 of the 630 tested people have pathogenic mutation (20.0%). The mutation distribution detected in a total of 130 patients was 131. 1 mutation (1,315%) in ATM , 40 different mutations (52.630%) in BRCA1, 29 different mutations in BRCA2 (38.165%), 2 different mutations (2,630) in CHEK2, 1 mutation (1,315%) in ERCC2, 1 mutation (1,315%) in MUTYH, 1 mutation (1,315%) in RAD51C, and 1 mutation (1,315%) were detected in TP53.Notably, in a patient with ovarian cancer both BRCA1 and BRCA2 mutations; BRCA1 NM_007294.3Ex1c.135-2A>Gp.?rs80358065 and BRCA2 NM_000059.3 Ex 11 c.6466_6469delTCTC p.Ser2156Asnfs*11rs879255330 were found, respectively. Conclusion: Analysis of gene panels demonstrate the clinical importance of multigene panel analysis in hereditary cancer predisposition meeting the BRCA1/2 NCCN criteria in Turkish population.

It is challenging to determine whether Bacillus species other than Bacillus anthracis cause infections. Pseudo and true outbreaks of Bacillus spp. have been noted. Here, we present a molecular analysis of a Bacillus spp. pseudo-outbreak caused by contaminated culture tubes containing Stuart medium.Between January and March 2015, a high percentage of Bacillus spp. was isolated from the wound samples of inpatients at the Karabuk University Hospital, and an outbreak was suspected. Environmental and staff nasal samples were cultured aerobically, and Bacillus spp. were isolated from some of them. However, the isolation of Bacillus spp. in throat cultures of outpatients suggested contamination caused by culture tubes containing Stuart medium. We examined two lots of culture tubes used in the hospital. Although the culture tubes' expiry date and storage conditions were suitable, Bacillus spp. grew in one of these lots. A total of 47 Bacillus spp. isolated during this period were identified, and the clonal relationship among the isolates was investigated by arbitrarily primed polymerase chain reaction.Twenty-seven strains were identified as Bacillus megaterium and 20 as Bacillus firmus. Of the four strains isolated from the Stuart medium, two were identified as B. firmus and the other two were B. megaterium. Two B. firmus strains isolated from the Stuart medium and two B. firmus strains obtained from the coronary intensive care environmental samples were matched and clustered within the same genotype. We recalled all culture tubes containing Stuart medium. After another brand's culture tubes were distributed, no growth was observed. It was then understood that the pseudo-outbreak source was contaminated culture tubes containing Stuart medium.Microbiological controls of medical materials and equipment should be regularly checked to prevent outbreaks (true or pseudo).

Mucopolysaccharidoses (MPSs) constitute a heterogeneous group of lysosomal storage disorders characterized by the lysosomal accumulation of glycosaminoglycans (GAGs). Although lysosomal dysfunction is mainly affected, several cellular organelles such as mitochondria, endoplasmic reticulum, Golgi apparatus, and their related process are also impaired, leading to the activation of pathophysiological cascades. While supplying missing enzymes is the mainstream for the treatment of MPS, including enzyme replacement therapy (ERT), hematopoietic stem cell transplantation (HSCT), or gene therapy (GT), the use of modulators available to restore affected organelles for recovering cell homeostasis may be a simultaneous approach. This review summarizes the current knowledge about the cellular consequences of the lysosomal GAGs accumulation and discusses the use of potential modulators that can reestablish normal cell function beyond ERT-, HSCT-, or GT-based alternatives.

The most common gynecologic cancers detected in women in Turkey are uterine cancer, ovarian cancer, and cervical cancer. These data reported that a mean of 3800 individuals were diagnosed with uterine cancer, 2790 were diagnosed with ovarian cancer, and 1950 were diagnosed with cervical cancer, and 400 individuals were diagnosed with other gynecologic cancers each year in Turkey. A mean of 14.270 individuals were detected to have been diagnosed with gynecologic cancers each year in the United States of America(USA). Ovarian cancer treatment is generally composed of chemotherapy, and surgery. In general, chemotherapy is administered after surgery. The identification of the molecular pathogenesis of ovarian cancer, and discovery of new moleculer biomarkers which facilitate the ovarian cancer treatment are required for an effective ovarian cancer treatment in clinics. miRNAs are reported to be the possible biologic indicators for various cancer types. We aimed to investigate 2 miRNAs which were suggested to have effect in ovarian cancer in our (previous)monozygotic twin study from miR-1260 microRNA family whose association with ovarian cancer yet has not been reported in the literature. We investigated the expression levels of miR-1260a, and miR-1260b miRNAs, in the peripheral blood lymphocytes of 150 familial and sporadic ovarian cancer patients, and of 100 healthy individuals of the control group who were matched for age, sex, and ethnicity with the patient group, and investigated their possible property of being a biologic indicator for ovarian cancer. The expression results of ovarian cancer patients were evaluated by comparison of the results of the control group in the study. The expression levels of miR-1260a, and miR-1260b in ovarian cancer patients were found highly increased compared with the levels in the control group. miR-1260a expression level in ovarian cancer patients was detected to have increased approximately 17 fold compared with the control group, and miR-1260b expression level in ovarian cancer patients was detected to have increased approximately 33 fold compared with the levels in the control group. The String Analyses showed that the miR-1260a was associated with the ribosomal protein family which was known to be effective in the translation stage of cell and that miR-1260b was associated with CHEK2 protein which was a member of the serine/threonine-protein kinase family. It should be investigated for larger cohorts in benign ovarian diseases and in different stages of patients receiving ovarian cancer treatment whether these two molecules are a noninvasive biomarker and therapeutic target to be used especially in the early diagnosis and prognosis of ovarian cancer in future.

Glycosaminoglycans (GAGs) are present in proteoglycans, which play critical physiological roles in various tissues. They are known to be elevated in mucopolysaccharidoses (MPS), a group of rare inherited metabolic diseases in which the lysosomal enzyme required to break down one or more GAG is deficient. In a previous study, we found elevation of GAGs in a subset of patients without MPS. In the current study, we aim to investigate serum GAG levels in patients with conditions beyond MPS. In our investigated samples, the largest group of patients had a clinical diagnosis of viral or non-viral encephalopathy. Clinical diagnoses and conditions also included epilepsy, fatty acid metabolism disorders, respiratory and renal disorders, liver disorders, hypoglycemia, developmental disorders, hyperCKemia, myopathy, acidosis, and vomiting disorders. While there was no conclusive evidence across all ages for any disease, serum GAG levels were elevated in patients with encephalopathy and some patients with other conditions. These preliminary findings suggest that serum GAGs are potential biomarkers in MPS and other disorders. In conclusion, we propose that GAGs elevated in blood can be used as biomarkers in the diagnosis and prognosis of various diseases in childhood, however, further designed experiments with larger sample sizes are required.

Background Mucopolysaccharidosis IVA (MPS IVA, also called Morquio A syndrome) is caused by a deficiency of N‐acetylglucosamine‐6‐sulfate sulfatase (GALNS) and results in skeletal dysplasia symptoms such as short stature and abnormal gait. Treatments include enzyme replacement therapy (ERT) and hematopoietic stem cell transplantation (HSCT), but the effects are limited depending on the age of initiation and clinical phenotype. Thus, this study aims to assess the effects of treatments on MPS IVA patients compared to untreated MPS IVA patients and an age‐matched control group. Methods We used activity of daily living (ADL) survey with 4 sections: “movement,” “movement with cognition,” “cognition,” and “other MPS symptoms.” Lower scores indicate more assistance required. This study included 161 patients, 270 total surveys, and 70 patients with longitudinal data. Results We describe 134 severe patients and 25 attenuated patients. ERT and HSCT treatment improved only the “other MPS symptoms” section in severe patients. There were no differences between ERT and HSCT severe patient scores. A 19‐year‐old male patient, who had robust physical training, provided a significant increase in “movement” without treatment, suggesting the importance of exercise. Conclusion Overall, this ADL questionnaire has demonstrated validation and reliability in assessing the MPS IVA patients and therapeutic efficacy., We have evaluated activity of daily living in mucopolysaccharidosis IVA patients from 161 patients. This is the first manuscript to evaluate therapeutic efficacy in both HSCT and ERT.

The most prevalent malignant bone tumor, osteosarcoma, affects the growth plates of long bones in adolescents and young adults. Standard chemotherapeutic methods showed poor response rates in patients with recurrent and metastatic phases. Therefore, it is critical to develop novel and efficient targeted therapies to address relapse cases. In this regard, RNA interference technologies are encouraging options in cancer treatment, in which small interfering RNAs regulate the gene expression following RNA interference pathways. The determination of target tissue is as important as the selection of tissue-specific promoters. Moreover, small interfering RNAs should be delivered effectively into the cytoplasm. Lentiviral vectors could encapsulate and deliver the desired gene into the cell and integrate it into the genome, providing long-term regulation of targeted genes. Silencing overexpressed genes promote the tumor cells to lose invasiveness, prevents their proliferation, and triggers their apoptosis. The uniqueness of cancer cells among patients requires novel therapeutic methods that treat patients based on their unique mutations. Several studies showed the effectiveness of different approaches such as microRNA, drug- or chemotherapy-related methods in treating the disease; however, identifying various targets was challenging to understanding disease progression. In this regard, the patient-specific abnormal gene might be targeted using genomics and molecular advancements such as RNA interference approaches. Here, we review potential therapeutic targets for the RNA interference approach, which is applicable as a therapeutic option for osteosarcoma patients, and we point out how the small interfering RNA method becomes a promising approach for the unmet challenge.

We assess the potential of rotational ground motions to resolve time-dependent near surface structural heterogeneities using noise correlations. Recent studies reveal an increased sensitivity of gradient related observations to near surface structural heterogeneities (e.g., material contrast, cavities) compared to directly measured wavefields (and their time derivatives). The development of new sensing technologies, such as rotational ground motion sensors and distributing acoustic sensing (DAS), enable measurements of strain and rotations and motivate this study. Combining gradient related observations with ambient noise-based monitoring methods has the potential to increase both spatial and temporal resolution. In order to investigate the suggested benefits, we perform a numerical study in 2D, where we simulate seismic noise with random sources at random locations. We apply interferometric principles and calculate cross-correlations of the resulting noise traces recorded at different receiver locations for multiple realizations of the noise field. After analysing the convergence of the correlation functions in terms of simulation length and number of simulations, we compare noise correlations of acceleration and rotation rate for a homogenous reference and a perturbed model. Ultimately, we establish that noise correlations of wavefield gradients are more sensitive than noise correlations of wavefields to small-scale heterogeneity.

Mucopolysaccharidoses (MPS) are a group of lysosomal storage disorders caused by a lysosomal enzyme deficiency or malfunction, which leads to the accumulation of glycosaminoglycans in tissues and organs. If not treated at an early stage, patients have various health problems, affecting their quality of life and life-span. Two therapeutic options for MPS are widely used in practice: enzyme replacement therapy and hematopoietic stem cell transplantation. However, early diagnosis of MPS is crucial, as treatment may be too late to reverse or ameliorate the disease progress. It has been noted that the prevalence of MPS and each subtype varies based on geographic regions and/or ethnic background. Each type of MPS is caused by a wide range of the mutational spectrum, mainly missense mutations. Some mutations were derived from the common founder effect. In the previous study, Khan et al. 2018 have reported the epidemiology of MPS from 22 countries and 16 regions. In this study, we aimed to update the prevalence of MPS across the world. We have collected and investigated 189 publications related to the prevalence of MPS via PubMed as of December 2020. In total, data from 33 countries and 23 regions were compiled and analyzed. Saudi Arabia provided the highest frequency of overall MPS because of regional or consanguineous marriages (or founder effect), followed by Portugal, Brazil, the Netherlands, and Australia. The newborn screening is an efficient and early diagnosis for MPS. MPS I has been approved for newborn screening in the United States. After the newborn screening of MPS I, the frequency of MPS I increased, compared with the past incidence rates. Overall, we conclude that the current identification methods are not enough to recognize all MPS patients, leading to an inaccurate incidence and status. Differences in ethnic background and/or founder effects impact on the frequency of MPS, which affects the prevalence of MPS. Two-tier newborn screening has accelerated early recognition of MPS I, providing an accurate incidence of patients.

e22007 Background: Retinoblastoma (RB) is the most common intraocular malignancy in children, caused by mutations in the tumor suppressor RB1 gene. Patients with bilateral/trilateral/familial RB are considered to have hereditary RB (1 germline, 1 somatic mutation); although most unilateral RB are nonhereditary (2 somatic mutations), some have germline RB1 mutation. Identification of RB1 mutations and genetic counseling is essential to assess the risk of developing RB in the patients´ relatives and to prevent the disease. The aim of this study is to assess the frequency/type of RB1 gene mutations in a large cohort of Turkish RB cases. Methods: RB1 gene mutation screening was performed in peripheral blood samples of 219 individuals (122 children with RB/14 family members with RB/83 healthy family members of 47 probands with RB1 mutations) followed in the Istanbul University, Oncology Institute. All 27 exons and close intronic regions of the RB1 gene were sequenced for small deletions and insertions using the Sanger sequencing (2013-2018) or Next Generation Sequencing (2019-2021); large deletions and duplications were investigated both by Multiplex Ligation Probe Amplification (MLPA) and copy number variation (CNV). Correlation with demographic and clinical data were evaluated. Results: After RB1 mutation screening, mutations were detected in 57 (41.9%) of 136 patients. RB1 mutations was observed in 23/84 (27.4%) patients with unilateral RB, in 30/47 (63.8%) bilateral RB, in 3/3 trilateral RB, and1/2 unilateral retinoma. Of these mutations, 45 (78.9%) were small genetic rearrangements and 12 (21.1%) large genetic rearrangements. Frameshift mutations were found in 11, nonsense in 18, splice error in 11, and missense mutation in 1, synonymous substitution in 2, upstream substitution in 2 patients. Ten novel mutations were found. Three of 83 healthy family members also had germline RB1 mutation. The disease was hereditary in 13 (22.8%); and de novo (77.2 %) in 44 of the 57 patients with mutations. Three siblings were found to have RB1 mutation, while their parents did not. Patients diagnosed as infants (RB1 mutation found in 63.2% of 70 infants vs in 36.8% of older ones, p:0.021); those with bilateral/trilateral RB (66 vs 27.4%, p:0.0001); those with light (green-blue) iris color vs dark color (71.4% vs 36.5%. p:0.003) had higher frequency of RB1 gene mutation. There was no significant correlation regarding gender or ICRB stage and RB1 mutation frequency. Conclusions: RB1 gene mutation was found in 41.9% of Turkish children with RB, in 63.8% of bilateral and 27.4% of unilateral RB. 10 novel mutations of the RB1 gene were found according to the Leiden Open Variation Database and the Human Gene Mutation Database.The mutation frequency was significantly higher in patients with bilateral/trilateral RB, in infants, in those with light iris color. In bilateral RB with no RB1 mutation, other genes/RB1 gene methylation and expression status may play a role in the pathogenesis.

Background The most common cancers detected in women are breast, thyroid, colorectal, uterine corpus, lung, and ovarian cancer. Ovarian cancer is responsible from more than 150.000 death annually worldwide. This cancer is detected in the late stage, and is characterised with poor prognosis, therefore most cases result with death. The fact that this cancer manifests itself in the late stage and is characterized by a poor prognosis, is caused death in the majority of cases. Therefore, the diagnosis and the treatment of the disease have to be improved for a better quality of life for patients. MicroRNAs are the noncoding RNAs in the length of 19–24 nucleotides which show suppressor effect on target genes. miRNAs are included in the pathology of various diseases including cancer. miRNAs being as the biomarker candidates in diagnosis, and their use in treatment as the inhibitors of the molecules mimicking the miRNA showed that they may be used as the new therapeutic target and agents. Methods We detected with our group in our prior study conducted with disconcordant ovarian cancer twins that many miRNA molecules were different in ovarian cancer compared with the molecules in healthy sibling. The expression level of miR-142-3p that was selected from the miRNAs detected in the previous study was compared, and investigated in a wider ovarian cancer group, and in healthy control group. miR-142-3p expression level was investigated using the real-time PCR method in the present study involving 147 patients, and 100 healthy control group. The differences in the expression levels of miR-142-3p detected in the peripheral blood lymphocytes of ovarian cancer patients, and healthy control were statisticaly evaluated. Results The expression level of miR-142-3p was detected to have increased 3.11 fold in ovarian cancer patients compared with the levels in healthy controls, and the difference was statistically significant (p:0.00). These results suggest that miR-142-3p that was found significantly increased in the peripheral blood samples of ovarian cancer patients compared with the healthy controls might be used as a sensitive, noninvasive biomarker in the early diagnosis, and treatment and follow up of ovarian cancer.

BRCA1/2 gene testing is a difficult, expensive, and time-consuming test which requires excessive work load. The identification of the BRCA1/2 gene mutations is significantly important in the selection of treatment and the risk of secondary cancer. We aimed to develop an algorithm considering all the clinical, demographic, and genetic features of patients for identifying the BRCA1/2 negativity in the present study. An experimental dataset was created with the collection of the all clinical, demographic, and genetic features of breast cancer patients for 20 years. This dataset consisted of 125 features of 2070 high-risk breast cancer patients. All data were numeralized and normalized for detection of the BRCA1/2 negativity in the machine learning algorithm. The performance of the algorithm was identified by studying the machine learning model with the test data. k nearest neighbours (KNN) and decision tree (DT) accuracy rates of 9 features involving Dataset 2 were found to be the most effective. The removal of the unnecessary data in the dataset by reducing the number of features was shown to increase the accuracy rate of algorithm compared with the DT. BRCA1/2 negativity was identified without performing the BRCA1/2 gene test with 92.88% accuracy within minutes in high-risk breast cancer patients with this algorithm, and the test associated result waiting stress, time, and money loss were prevented. That algorithm is suggested be useful in fast performing of the treatment plans of patients and accurately in addition to speeding up the clinical practice. Scientific Research Projects Coordination Unit of Istanbul UniversityIstanbul University [TSA-2019-34244] This study was funded by the Scientific Research Projects Coordination Unit of Istanbul University (project number: TSA-2019-34244).

MicroRNAs (miRNAs), are endogenous noncoding single strand RNA molecules with approximate length of 22 nucleotides. Ovarian cancer is a heterogenous disease which includes different biologic behaviors in the clinical, and molecular level. miRNAs have roles in the early diagnosis, prognosis, and chemotherapy sensitivity for ovarian cancer, and in the regulation of reproduction by being expressed in the ovaries. The expression level of two miRNAs of miR-423-5p, and miR-664b-5p selected from the miRNAs which were detected to be important for the ovarian cancer etiology in our previous studies were investigated in the peripheral blood of familial and sporadic ovarian cancer patients, and in healthy individuals. The expression analyses were statistically evaluated with SPSS v21.0 program using the Quantitative Real-Time PCR technique. A statistically significant difference was detected for both miRNAs between the healthy controls and ovarian cancer patient groups (p:0.000). The miR-423-5p expression was detected to increase 2.35 fold, and miR-664b-5p was detected to increase 2.47 fold in ovarian cancer patients compared with the levels in the control group. miR-423-5p was reported to be overexpressed in various cancer types, and in different disease stages in previous study, and miR-423-5p was demonstrated to have increased in the lymphocytes in the peripheral circulation of ovarian cancer patients first in our literature. The miR-664b-5p expression level was detected in high levels in ovarian cancer patient group, however was detected to have decreased in 64% of ovarian cancer patients with BRCA mutation carrier. The expressions of both miRNA molecules were detected to have decreased in the ovarian cancer subgroups in patients with ovarian cancer with addition of a second primary cancer of endometrium cancer, however, were detected in the highest level in ovarian cancer patients in addition to another secondary cancer except breast and endometrium cancer. The results obtained from the study showed that the increased expression of both miRNA molecules were suggested to be associated with ovarian cancer, and decrease was suggested to be associated with endometrium cancer. In summary, the miRNA molecules in the present study might be the non-invasive biological indicator in ovarian cancer, and the demonstration of these molecules on the tumor tissue, and their change during treatment in future studies will be beneficial.

Background Ovarian cancer is the second most common gynecologic cancer with high mortality rate and generally diagnosed in advanced stages. The 5-year disease-free survival is below 40%. MicroRNAs, subset of the non-coding RNA molecules, regulate the translation in post transcriptional level by binding to specific mRNAs to promote or degrade the target oncogenes or tumor suppressor genes. Abnormal expression of miRNAs were found in numerous human cancer, including ovarian cancer. Investigating the miRNAs derived from the peripheral blood samples can be used as a marker in the diagnose, treatment and prognosis of ovarian cancer. We aimed to find biological markers for early diagnosis of ovarian cancer by investigating BRCA1 gene mutation carrier monozygotic discordant twins and their high risk healthy family individual’s miRNAs. Methods The study was conducted on monozygotic twins discordant for ovarian cancer, and the liquid biopsy exploration of miRNAs was performed on mononuclear cells that were isolated from the peripheral blood samples. The miRNA expression profile changes in the study were found by using microarray analysis. miRNA isolation procedure performed from the lymphocyte in accordance with the kit protocol. The presence and quality of the isolated miRNAs screened by electrophoresis. Raw data logarithmic analysis was studied by identifying the threshold, normalization, correlation, mean and median values. Target proteins were detected for each miRNA by using different algorithms. Results After the comparison of monozygotic discordant twins for epithelial ovarian carcinoma upregulation of the 4 miRNAs, miR-6131, miR-1305, miR-197-3p, miR-3651 and downregulation of 4 miRNAs, miR-3135b, miR-4430, miR-664b-5p, miR-766-3p were found statically significant. Conclusions The detected 99 miRNAs out of 2549 miRNAs might be used in the clinic as new biological indicators in the diagnosis and follow up of epithelial ovarian cancer with complementary studies. The miRNA expression profiles were identified to be statistically significant in the evaluation of ovarian cancer etiology, BRCA1 mutation status, and ovarian cancer risk in accordance with the obtained data. There is a need for validation of the miRNAs which were particularly detected between monozygotic twins and its association with ovarian cancer was emphasized in our study in wider cohorts including ovarian cancer patients, and healthy individuals.

Matrix Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) is a new method that is increasingly used in microbiology laboratories due to its ability of reliable and rapid identification (ID) of bacteria and fungi. However, some problems emerge in the routine clinical diagnosis since only one gram-negative selective medium has been suggested up to date. Though EMB agar is one of the traditional gram-negative selective media, there is no data in the scientific literature, about the ID performance of MALDI TOF MS with the gram-negative bacteria grown on this medium. In this study, we tested the ID performance of MALDI-TOF MS for gram-negative isolates on EMB agar and aimed to develop a rapid and easy sample preparation method for improving this performance. A total of 468 clinical isolates of gram-negative bacteria, consisting of 37 different species from 20 genera, were included in this study. The isolates were identified using the Vitek MS MALDI-TOF MS (Bio Merieux, France) both directly from EMB agar, and also through a two-step colony washing (once with physiologic saline, and three times with 70% ethanol) method. The performances of these two IDs were compared. In the direct reading from EMB medium, 382 (81.6%) of 468 studied isolates were correctly identified at species level; no ID was detected for 80 (17%) isolates, and 6 (1.2%) isolates (four at the genus level) were misidentified Performance of MALDI-TOF MS directly from EMB agar was excellent (100%) for 14 species including Stenotrophomonas maltophilia, Klebsiella oxytoca, Salmonella spp., and Proteus mirabilis; and lowest for Providencia spp. (62.5%), Escherichia coli (70.5%) and Acinetobacter spp. (70.7%). Following the washing procedure which was performed about 20 min with simple laboratory equipment, 434 (92.7%) isolates were correctly identified at species level; 30 (6.4%) strains could not be identified, and four (0.85%) isolates (two at the genus level) were misidentified. Statistical analyses indicated that the washing procedure defined here significantly increased the overall ID performance of MALDI-TOF MS with EMB agar (p= 0.001), particularly with improving the IDs of those markedly dye-absorbing genera, such as E.coli and A.baumannii. In this study, EMB agar which has no data until today on its suitability for mass spectrometric identification has been shown to be useful for bacterial identification with MALDI-TOF MS. In addition, the unidentified gram-negative bacteria in the direct reading from the EMB medium have been shown to be identified after the colony washing method as described here. Determination of the different medium alternatives will contribute to effective usage of MALDI-TOF MS in microbiology laboratories.

MicroRNAs (miRNAs) have major roles in nearly all cellular process including gene expression, and may behave as oncogene or tumor suppressor gene by binding to complementary sequences in the target mRNA. The circulating microRNA-15a (miRNA-15a) and microRNA-16-1 (miRNA-16-1) of 15 healthy adults and of 40 untreated patients diagnosed with diffuse large B-cell lymphoma (DLBC) were recruited to investigate the expression levels. The expression levels of miRNA-15a, and miRNA-16-1 genes of the untreated DLBCL patients, and healthy individuals with matched age, sex and ethnicity were examined. MicroRNA expression profiles obtained from peripheral blood were investigated. The samples were collected from 40 patients diagnosed with DLBC patients, and from 15 healthy controls. Two miRNAs were selected, and expression profile was examined using a quantitative real-time polymerase chain reaction (qPCR) based on the previous studies. Statistically significant expression level differences (p 0.05) were detected for miRNA-16-1 in DLBCL patients and healthy control groups. miRNA-16-1 gene expression level was found approximately ninefold higher in the patient group compared to the controls; however, no statistical difference was detected in the expression profile of miRNA-15a between the both groups. On the other hand, the decreased gene expression in miRNA16-1 was observed in 88.3% of DLBCL patients. These results suggested that there was no statistically significant decrease in the miRNA-15a gene expression in DLBCL patients (p 0.05). On the contrary to the literature, miRNA-16-1 expression level was suppressed in DLBCL group in our study, however no whole gene silencing was performed. MicroRNA-16-1 might be suggested to behave as a tumor suppressor in DLBCL in our study.

Objective: We aimed to review the influence of host genetic factors on the clinical course, treatment response as well as fibrosis progression in patients with viral hepatitis C genotype 1. Materials and Methods: Ninety-five patients with chronic hepatitis C virus (HCV) infection and 97 controls were enrolled. The patients received pegylated interferon (Peg-IFN)+ribavirin therapy for 48 weeks and were followed up for the next 48 weeks. Aspartat aminotransferase/platelet ratio (APRI) was used to detect liver fibrosis DNA specimens were extracted from the peripheral blood mononuclear cells and the tumor necrosis factor-alpha (TNF-α) 308 rs3091256 was genotyped by the polymerase chain reaction-restriction fragment length polymorphism method. Results: All patients included in the study were infected with HCV genotype 1. of the 95 HCV-positive patients, spontaneous viral clearence was observed in 25.5%, rapid viral response in 44.2%, early viral response in 91.8%, and sustained viral response was found in 73.3% of patients. The allele and genotype were not significant between patients and controls. There was no significant difference in virologic response as well. However, TNF-α-308 single nucleotide polymorphisms (SNP) rs3091256 GG genotype was strongly associated with fibrosis and alanine aminotransferase (ALT) levels (p=0.006 and p=0.017, respectively). Conclusion: TNF-α-308 polymorphisms may reveal different results among countries. Patients having SNP rs3091256 GG are prone to have higher ALT levels and fibrosis score but have better treatment outcome.

Human epididymis protein 4 (HE4) acts as a protease inhibitor. It has been detected in the serum of patients with lung cancer patients and its utility for lung cancer screening was found in different studies. Nevertheless, little is known regarding the expression of HE4 in lung carcinoma subtypes. The aim of the present study was to investigate whether HE4 expression is a reliable marker for detecting any lung carcinoma subtypes, including small cell lung cancer (SCLC), non-small cell lung cancer (NSCLC) and adenocarcinoma (AC). In total, 141 lung carcinoma patients were enrolled in the study. Biopsy samples were obtained from bronchoscopic biopsy. The tumors were classified as SCLC (group 1, 54 cases) or NSCLC (group 2, 87 cases) based on histology and immunohistochemistry. The latter was sub-grouped as adenocarcinoma (group 2a, AC) and squamous cell carcinoma (group 2b, SCC). The immunohistochemical expression of HE4 was compared between the groups. The study revealed that the majority of the SCLC and SCC cases were devoid of HE4 (90.1 and 89.65%, respectively). Approximately 10% of cases had HE4 immune expression and the staining was focal and moderate throughout the tumor tissue. On the other hand, 78.8% of AC expressed HE4 and the staining was diffuse and strong. The overall HE4 expression in the lung cancer patients was 33.7%. In conclusion, the results of the present study have shown that HE4 is expressed in adenocarcinoma of the lung but it is not frequent in SCC and SCLC. The value of HE4 as a screening biomarker for lung cancer is limited but its presence exclusively in adenocarcinoma may provide new insight for targeted therapy.

Purpose. Various molecular variations are known to result in different gene variants in the FGFR4 gene, known for its oncogenic transformation activity. The goal of this study was to investigate the FGFR4 p.Gly388Arg variant that plays role in the progression of cancer and retinal growth and may be an effective candidate variant in the Turkish population in retinoblastoma patients with no RB1 gene mutation. Methods. Using the Sanger sequencing methods, the FGFR4 p.Gly388Arg variant was bidirectionally sequenced in 49 patients with non-RB1 gene mutation in retinoblastoma patients and 13 healthy first-degree relatives and 146 individuals matched by sex and age in the control group. Results. In Turkish population-specific study, the FGFR4 p.Gly388Arg variant was found in 27 (55.1 percent) of 49 patients; mutation was found in 7 (53.8 percent) of these patients’ 13 healthy relatives screened. When FGFR4 p.Gly388Arg mutation status is evaluated in terms of 146 healthy controls, in 70 (47.9 percent) individuals, mutation was observed. Our analysis showed that the FGFR4 p.Gly388Arg allele frequency, which according to different databases is seen as 30 percent in the general population, is 50 percent common in the Turkish population. Conclusions. In patients with advanced retinoblastoma who were diagnosed with retinoblastoma prior to 24 months, the FGFR4 p.Gly388Arg allele was found to be significantly higher. As a result, these results indicate that the polymorphism of FGFR4 p.Gly388Arg may play a role in both the development of tumors and the progression of aggressive tumors.

Additional file 2. BRCA1 mutation carriage and epithelial ovarian cancer etiology related upregulated and downregulated miRNAs, target molecules.

Additional file 1. BRCA1 gene mutation positivity related upregulated and downregulated miRNAs and target molecules.

Ovarian cancer is a disease that is generally diagnosed at an advanced stage, and has poor survival. Monozygotic (MZ) twins are considered to be good research models for investigating the epigenetic changes associated with diseases. In the present study, the involvement of epigenetic mechanisms in ovarian cancer etiology were evaluated using the MZ twin model. Whole-genome methylation patterns were investigated in a BRCA1 gene mutation-carrying family comprising MZ twins, only one of whom had ovarian cancer, and other healthy siblings. Whole-genome methylation patterns were assessed in peripheral blood DNA using Infinium MethylationEPIC BeadChips on an Illumina iScan device. The hypermethylated and hypomethylated genes were detected between cases and controls in four different comparison groups in order to evaluate the differences in methylation levels according to cancer diagnosis and BRCA mutation status. The obtained results showed that the differential methylations in 12 different genes, namely PR/SET domain 6, cytochrome B5 reductase 4, ZNF714, OR52M1, SEMA4D, CHD1L, CAPZB, clustered mitochondria homolog, RB-binding protein 7, chromatin repair factor, ankyrin repeat domain 23, RIB43A domain with coiled-coils 1 and C6orf227, were associated with ovarian cancer. Biological functional analysis of the genes detected in the study using the PANTHER classification system revealed that they have roles in biological processes including 'biologic adhesion', 'regulation', 'cellular components organization', 'biogenesis', 'immune system functioning', 'metabolic functioning' and 'localization'. Overall, the present study suggested that epigenetic differences, such as methylation status, could be used as a non-invasive biological markers for the early diagnosis and follow-up of ovarian cancer. © 2020 Spandidos Publications. All rights reserved. Istanbul Üniversitesi: 59477 This study was supported by the Scientific Research Projects Unit of Istanbul University (project no. 59477). In the study, the funding body has no role in the preparation, data collection, analysis and interpretation of the manuscript.

Additional file 3. Epithelial ovarian cancer predisposition associated upregulated and downregulated miRNAs, target molecules.