Background/Objectives: Mesenchymal stem cells (MSCs) offer promising prospects for novel treatment modalities in cellular therapies and artificial organ production. Despite a surge in artificial tissue research, there is a dearth of comprehensive studies detailing the entire process from stem cells to tissue production, coupled with a scarcity. This study, however, presents the utility of extra-embryonic MSCs derived from placental tissue, traditionally considered as medical waste. Methods: Within a 3-dimensional cell culture system, histological assessments, and comprehensive optimization studies, the entire process required for artificial tissue production is addressed. Results: The results obtained are encouraging regarding the advancement of cellular therapies and artificial tissue engineering. However, challenges such as biopolymer degradation highlight the necessity for multistep approaches. Each analysis within this study delves into the discussion and optimization of key steps in artificial tissue production. Conclusions: Consequently, this study not only represents one of the first of its kind but also lays the groundwork for future investigations into relevant clinical applications.

e15060 Background: Next generation sequencing (NGS) makes it possible to identify the specific molecular biomarkers to define patient eligibility for targeted therapies via multigene panels. Since then, even though the interpretation of data is complex and not all tumors have genomic alterations within actionable genes, using somatic sequencing for cancer patients becomes a daily routine in clinical oncology. Thus, here we present the data derived from our experience in NGS testing of different cancer patients and biological samples over the course of 7 years in our genetic diagnosis center. Methods: The cohort was consisted of total 5511 cases. While 2590 (46.99%) of them were formalin fixed paraffin embedded (FFPE) tissues, 2906 (52.73%) were liquid biopsies and 15 (0.27%) were other types of biological samples. Total of 15 different cancers were classified (Table 1) and were sequenced using 3 different multigene NGS panels (additional Table 1, BRCAs’ testing for breast/ovarian cancer is not included). NGS was performed via GeneReader NGS System (Qiagen, Germany). Bioinformatics analyzes and variant classification were performed using QCI-Analyze and QCI-Interpret interfaces. Results: As a result, the cases of 93.36% (n = 5145) among all samples were successfully sequenced. The lung cancer group was the most frequent with 47.96% (n = 2643 patients), followed by 491 (%8.9) colorectal 288 (5.23%) and breast cancer patients respectively, while 781 cases (14.17%) grouped as other including many rare cancers. Overall positivity rate was 42.57% (n = 2346) and 366 samples (6.64%) were not sufficient enough to be sequenced. The distribution of positivity rates in relation to cancer type and biological samples used were listed in Table 1. Classification and diagnosis of all tested cases, specimens and Tier 1-2 variants included in this cohort are available on the Additional Table 2. Conclusions: This report is a comprehensive review of the aggregate data across the entire cohort of cancer patients referred to a genetics diagnosis center. While our findings highlight the importance of NGS testing in the somatic setting for cancer patients, also these data stress the importance of diagnosis, biological sample types tested and test results. [Table: see text]

Objective: Breast cancer (BC) is the most common cancer type in women and may be inherited, mostly in an autosomal dominant pattern.The clinical diagnosis of BC relies on the published diagnostic criteria, and analysis of two genes, BRCA1 and BRCA2, which are strongly associated with BC, are included in these criteria.The aim of this study was to compare BC index cases with non-BC individuals in terms of genotype and diagnostic features to investigate the genotype/demographic information association. Materials and Methods:Mutational analyses for the BRCA1/BRCA2 genes was performed in 2475 individuals between 2013-2022 from collaborative centers across Turkey, of whom 1444 with BC were designated as index cases.Results: Overall, mutations were identified in 17% (421/2475), while the percentage of mutation carriers in cases of BC was similar, 16.6% (239/1444).BRCA1/BRCA2 gene mutations were detected in 17.8% (131/737) of familial cases and 12% (78/549) of sporadic cases.Mutations in BRCA1 were found in 4.9%, whereas 12% were in BRCA2 (p<0.05).Meta-analyses were performed to compare these results with other studies of Mediterranean-region populations. Conclusion:Patients with BRCA2 mutations were significantly more common than those with BRCA1 mutations.In sporadic cases, there was a lower proportion with BRCA1/BRCA2 variants, as expected, and these results were consistent with the data of Mediterranean-region populations.However, the present study, because of the large sample size, revealed more robust findings than previous studies.These findings may be helpful in facilitating the clinical management of BC for both familial and non-familial cases.

Integration of new technologies in cancer research in medicine provides an opportunity to do more comprehensive studies on more specified areas. One of the major study fields of clinical cancer research is the drug design and targeting studies together with the microenvironment in which most of them are performed on experimental animals. However, there are distinct differences when it comes between animal models and humans: metabolic, immunologic, and genetic. Thus, traditional (2D) cell culture techniques are not insufficient enough in cancer research due to the limitations of not showing the characteristic features as in vivo. Therefore, 3D cell culture techniques were developed to overcome these problems. In the comparison of 3D to 2D cell cultures, the most important advantage is that the 3D culture of cells/tissues presents more likely real in vivo patterns such as drug metabolism, proliferation, and responses to the stimuli. According to the most recent developments in 3D cell culture techniques bioreactor-based 3D cell technologies have been designed. Moreover, these methodologies can also be utilized in combination with biopolymers, microcarriers, spheroids, and organoids. Among these 3D cell culture techniques, the most remarkable one is the rotary cell culture systems (RCCS), because providing microgravity reduces the shear stress caused by the mixing force. In addition to bioreactors, microfluidic chips were also developed as a result of the most innovative approach. Microfluidic chips can also be used in any cancer study depending on the researchers’ needs, providing a study-specific modification and 3D cell culturing with accessible manipulations. Hence, improvements in bioreactors lead to the population and acceleration of cancer-related drug response, immunological and genetic studies as an alternative to experimental animal models.

Purpose SARS-CoV-2-infected individuals may be asymptomatic, and therefore, the virus is highly contagious. We aimed to develop an agent to control viral replication in the upper respiratory tract and to prevent progression of the disease into the lower airways as well as inter-individual transmission. For this purpose, we investigated the antibacterial and antiviral activities of our novel nanobubble ozonated hyaluronic acid-decorated liposomal (NOHAL) solution, developed by using nanotechnology. Methods The MIC levels of NOHAL solution were determined on blood agar cultures of Staphylococcus aureus (ATCC 6538), Streptococcuspneumoniae (ATCC 49619) and Escherichia coli (ATCC 25922). The in vitro anti-viral activity of NOHAL solution was studied using recombinant SARS-CoV-2 copies of the original virus, grown in Vero cells generated by reverse genetic technology. Human primary lung epithelial cells obtained by bronchoscopy or lung resection were used for cell viability tests using flow cytometry analysis. The cytotoxicity testing was performed using the BALB/c 3T3 (CCL-163) cell line. Skin, oral, nasal and ocular irritation tests were performed using New Zealand albino rabbits, Syrian hamsters, BALB c mice and New Zealand albino rabbits of both sexes. Results Bacterial growth was prevented by NOHAL solution in a time-/dose-dependent manner. In vivo or in vitro experiments did not show any toxicity of NOHAL solution. No cytotoxicity was recorded on cell viability. No skin, oral, nasal or ocular toxicities were recorded. In addition, in a SARS-CoV-2 mouse infection model, NOHAL solution diminished the viral RNA levels effectively in nasopharyngeal and lung samples after its prophylactic intranasal application. Conclusion NOHAL solution has the potential to reduce or prevent the spread of SARS-CoV-2 through the nose and/or oral cavity. The clinical efficacy of this solution needs to be tested in order to determine its efficacy in the early phase of COVID-19.

BRCA1/2 mutations play a significant role in cancer pathogenesis and predisposition particularly in breast, ovarian and prostate cancers. Thus, germline analysis of BRCA1 and BRCA2 is essential for clinical management strategies aiming at the identification of recurrent and novel mutations that could be used as a first screening approach. We analyzed germline variants of BRCA1/2 genes for 2168 individuals who had cancer diagnosis or high risk assessment due to BRCAs related cancers, referred to 10 health care centers distributed across 7 regions covering the Turkish landscape. Overall, 68 and 157 distinct mutations were identified in BRCA1 and BRCA2, respectively. Twenty-two novel variants were reported from both genes while BRCA2 showed higher mutational heterogeneity. We herein report the collective data as BRCA Turkish consortium that confirm the molecular heterogeneity in BRCAs among Turkish population, and also as the first study presenting the both geographical, demographical and gene based landscape of all recurrent and novel mutations which some might be a founder effect in comparison to global databases. This wider perspective leads to the most accurate variant interpretations which pave the way for the more precise and efficient management affecting the clinical and molecular aspects.

Ahead of Print article withdrawn by publisher. AIM:The aim of this study is to determine the mutation spectrums and clinical characteristics of NF1 patients followed up in our center and to investigate whether there is a genotype-phenotype relationship. MATERIAL AND METHODS:Sixty-three children and 34 relatives diagnosed with NF1 were included in the study. Age, gender, family history, clinical features, tumors detected in the patient at the time of diagnosis or during follow-up, orbital and cerebral magnetic resonance imaging (MRI) findings were recorded. Also results of the NF1 gene analysis results were recorded. RESULTS:Fifty-three different mutations were found as a result of the NF1 gene analysis studied from patients and their family members. Among these 53 mutations, stop codon mutation was the most frequently detected mutations. Sixteen out of 50 (32%) mutations were found to be novel mutations. Twenty-eight tumors developed in our patients. Twenty of them were optic gliomas and others were medullary thyroid carcinoma, glioblastome multiforme, pons glioma, acute lymphoblastic leukemia, pilocytic astrositoma, hypothalamic glioma, cerebral hamartoma and cardiac fibroma. No genotype-phenotype relationship was detected in patients Conclusion: Comprehensive mutation analysis of NF1 will increase our knowledge due to its different phenotypic characteristics even in the same mutation.

Background Neuroendocrine tumours (NETs) arise from hormone-producing or nervous system cells and can develop from anywhere in the body. They have heterogeneous origins from skin to gastrointestinal track and a complicated histology. Thus, there is an inevitable need for genomic profiling to determine the exact genetics of each tumour for prognosis and treatment strategies to overcome the disease’s complexity. For this purpose, next-generation-sequencing (NGS) is the most reliable methodology for both germ-line and somatic studies to make a clinical diagnosis. In this study, we analyse liquid biopsies, formalin fixed paraffin embedded (FFPE) tissues, and peripheral blood samples for their ability to provide information for actionability. Methods A customized multi-gene panel comprised of Succinate Dehydrogenase Complex Iron Sulfur Subunit B ( SDHB), Succinate Dehydrogenase Complex Subunit C (SDHC), Cell Division Cycle 73 (CDC73), Calcium Sensing Receptor (CASR), Platelet Derived Growth Factor Receptor Alpha (PDGFRA), Succinate Dehydrogenase Complex Flavoprotein Subunit A (SDHA), Ret Proto-Oncogene (RET), Succinate Dehydrogenase Complex Assembly Factor 2(SDHAF2), Menin 1 (MEN1), Succinate Dehydrogenase Complex Subunit D (SDHD), MYC Associated Factor X (MAX) and Protein Kinase CAMP-Dependent Type I Regulatory Subunit Alpha (PRKAR1A) genes was constructed to assess multiple specimen types including: 3 liquid biopsies, 6 FFPE tissues, and 26 peripheral blood samples from 35 unique NET patients. Quality-control and bioinformatics analyses were performed using QCI-Analyze and QCI-Interpret. Results The three liquid biopsies and the 6 FFPE tissue samples were evaluated for somatic mutations; while the 26 peripheral blood samples were analysed using the germ-line pipeline. Five (55.6%) of the nine patients that were studied for somatic changes carried actionable mutations related to therapy sensitivities. Through the germ-line studies, we observed a 50% positivity rate for disease predisposition with 16 variants classified according to ACMG (American College of Medical Genetics) Standards and Guidelines. Conclusions Genomic profiling medicine is an emerging area of clinical oncology and has become crucial for disease and patient management by providing a precision approach; this is especially true for rare diseases including rare cancers such as NETs. Notably, this study emphasized the relevance of multiple distinctive biological sample types for use in the genetic testing of cancers to help with the choice of therapy to maximize the likelihood of a positive clinical outcome.

BACKGROUND:Cystic fibrosis (CF) is the most common worldwide, life-shortening multisystem hereditary disease, with an autosomal recessive inheritance pattern caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. The national newborn screening (NBS) program for CF has been initiated in Turkey since 2015. If the immunoreactive trypsinogen (IRT) is elevated (higher than 70 μg/L in the second control) and confirmed by sweat test or clinical findings, genetic testing is performed. The aims of this study are to emphasize the effect of NBS on the status of genetic diagnosis centers with the increasing numbers of molecular testing methods, and to determine the numbers and types of CFTR mutations in Turkey.METHODS:The next-generation sequencing (NGS) and multiplex ligation-dependent probe amplification (MLPA) results of 1595 newborns, who were referred to Cukurova University Adana Genetic Diseases Diagnosis and Treatment Center (AGENTEM) for molecular genetic testing, were evaluated with positive CF NBS program results since 2017.RESULTS:According to the results; 560 (35.1%) of the 1595 patients carried at least 1 (one) CF-related variant, while 1035 patients (64.9%) had no mutation. Compound heterozygosity for two mutations was the most common in patients, while two detected variants were homozygote in 14 patients. A total of 161 variants were detected in 561 patients with mutations. Fifteen novel variants that have not been previously reported were found. Moreover, p.L997F was identified as the most frequent pathogenic mutation that might affect the IRT measurements used for the NBS. The distribution of mutation frequencies in our study showed a difference from those previously reported; for example, the well-known p.F508del was the third most common (n = 42 alleles), rather than the first. The most striking finding is that 313 cases had a pathogenic variant together with the V470M variant, which might have a cumulative effect on CF perpetuation.CONCLUSION:This study is the first to determine the mutational spectrum of CFTR in correlation with the NBS program in the Turkish population. NBS for CF raises issues regarding screening in diverse populations, both medical and non-medical benefits, and carrier identification. Through the lens of NBS, we focused on the integrated diagnostic algorithms and their effect on the results of genetic testing.

Abstract Neuroendocrine tumors (NET) can develop everywhere in the body which have heterogeneous origins and complicated histology. Thus, genomic profiling becomes inevitable to overcome the disease's complexity through the determination of hereditary predisposition and treatment actionability. For this purpose, next generation sequencing as the most reliable methodology for both germ-line and somatic studies, can be utilized in clinical oncology as we present in this study which liquid biopsy, FFPE tissue and peripheral blood samples in terms of actionability and predisposition for various types of neuroendocrine tumors have been analyzed. A customized multi-gene panel (consists of SDHB, SDHC, CDC73, CASR, PDGFRA, SDHA, RET, SDHAF2, MEN1, SDHD, MAX and PRKAR1A genes) have been used from 3 liquid biopsy, 6 FFPE tissue and 26 peripheral blood samples of 35 distinctive NET patients. Quality control and bioinformatics analysis were performed using QCI-Analyze and QCI-Interpret. Three liquid biopsy and 6 FFPE samples were evaluated for somatic analysis while 26 peripheral blood samples were included in germ-line pipeline. Five (55.6%) of the 9 patients that were studied for somatic changes carry actionable mutations related to therapy sensitivity. While through the germ-line studies, we observed 50% positivity rate for disease predisposition in germ-line studies with sixteen variants in 13 patients. Variant classification criteria were given in details in Table 1 according to the ACMG (American College of Medical Genetics) Standards and Guidelines. Genomic profiling medicine as the emerging area of clinical oncology in this era becomes crucial for disease and patient management properly in terms of a precise approach especially in rare diseases including the rare cancers such as NETs. Most notably, our study emphasizes the relevance of distinctive biological samples in the use of genetic testing for cancer care. Table 1.Implemented variant classification criteria of detected germ-line mutations in our study.PatientGeneVariant (amino acid change)ACMG criteria (doi: 10.1038/gim.2015.30)P1KITM541L (Heterozygote)PM2, BP4, BP6P2SDHCR72H (Heterozygote)PM1, PM2, PP3P3SDHBG19FS*57 (Heterozygote)PVS1, PM1, PM2P4PDGFRAS66R (Heterozygote)PM2, BP1, BP4P5RETA96V (Heterozygote)PM2, PP2, BP4P6KITR946* (Heterozygote)PM2, PP2, BP4P7RETG691S (Heterozygote)PP2, BA1, BS3, BP4P8RETG691S (Heterozygote)PP2, BA1, BS3, BP4P9RETG691S (Heterozygote)PP2, BA1, BS3, BP4P10RETG691S (Heterozygote)PP2, BA1, BS3, BP4P11RETG691S (Heterozygote)PP2, BA1, BS3, BP4KITA431E (Heterozygote)PM1, PM2, BP4P12RETG691S (Heterozygote)PP2, BA1, BS3, BP4RETA1051V (Heterozygote)PM1, PP2, PP3P13KITM541L (Heterozygote)PM2, BP4, BP6SDHDG12S (Heterozygote)PP2, BS1, BS3, BP4, BP6 Citation Format: Ozge Sonmezler, Isa B. Guney, Cem Mujde, Atil Bisgin. The emerging clinical relevance of genomic profiling medicine in neuroendocrine tumors [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4154.

e13611 Background: The detection of BRCA1 and BRCA2 mutations both somatic and germ-line became essential for the clinical management strategies of different cancers. Aiming at the identification of common and recurrent mutations that answer the questions about the association between a variant and phenotype, we collected the data of 1126 probands with pathogenic, likely pathogenic variants and variants of uncertain significance (VUS) distributed across 22 Turkish cities. Methods: Peripheral blood samples from 1126 individuals were collected and sequenced via the GeneReader (Qiagen, Hilden, Germany) and MiSeq (Illumina, San Diego, USA) NGS systems for BRCA1/ BRCA2 genes. QCI-Analyze and QCI-Interpret bioinformatics tools were used for bioinformatics analyses. Results: Total of 68 and 108 distinct variants were identified in BRCA1 and BRCA2 genes, respectively. Twenty novel variants were identified in both genes, while BRCA2 had higher heterogeneity. However, there had been no any recurrent mutations identified in any certain geographic region. Among all distinct mutations identified 11.9% were novel, corresponding to 12.8% of all carriers and 28.4% were VUS, corresponding to 32.1% of all carriers. Conclusions: This study presented with three important outcomes. First, a significant molecular heterogeneity in BRCAs among Turkish carriers were confirmed with 15.63% positivity rate. Most notably as the second, this is the first study showing the profiles of recurrent and common mutations that might be unique to Turkish landscape. In conclusion, it is critical to identify all the genetic variants, to aid in diagnosis, prevention, prognosis and treatment. Third and the last, the identification of novel mutations in BRCAs is a vital information that should be shared with mutation databases, in order to use for further clinical interpretation of Turkish population. Key words: Landscape of BRCA1/2, genetic testing, BRCA profiling, population data.

Abstract Background: In terms of precision medicine, not only tumoral tissue samples but also with liquid biopsy for somatic variants detection, have been used routinely. It also helps to overcome the resampling difficulties that require an invasive procedure with the problem of tumor heterogeneity. With the Next Generation Sequencing (NGS) method which is accepted as the gold standard in molecular genetic testing, colorectal cancer patients ccfDNA (Circulating Cell-Free DNA) samples were next generation sequenced via a targeted multigene panel. Methods: In our study, liquid biopsy samples of 63 colorectal cancer patients whom referred to Cukurova University AGENTEM (Adana Genetic Diseases Diagnosis and Treatment Center) were sequenced via GeneReader NGS Systems (Qiagen). The multi-gene panel which includes cancer related actionable 11 genes (KRAS, NRAS, KIT, BRAF, PDGFRA, ALK, EGFR, ERBB2, ERBB3, ESR1 and RAF1) were used to identify the variants of drug sensitivity and resistance. Sequencing data were analyzed by QCI-Analyze and QCI-Interpret bioinformatics tools. Results: Forty-three clinically significant variants detected in 53.96% (n=34) of 63 patients. Total of 43 clinically significant variants in 7 genes (KRAS, NRAS, KIT, BRAF, EGFR, PDGFRA and ERBB2) were detected according to the ACMG (American College of Medical Genetics) and AMP (Association for Molecular Pathology) criteria in which 13.95%, 41.86% and 41.86% prospectively related to drug resistance, treatment sensitivity, and both treatment sensitivity and drug resistance. Moreover, 2.33% were classified as uncertain clinical significance due to data mining. Variants detected upon gene names were listed in Table 1. Table 1:Genes and variants distribution in colorectal cancer patientsGene NameVariantsTotal %KRASp.G12A,p.G12C,p.G12D,p.G12V,p.G13S,p.G15S,p.A18V,p.I21M,p.A59T,p.A146T32.56KITp.M541L20.93BRAFp.T559I,p.V600E,p.K601R,p.R603*,p.P632S,p.639I20.93EGFRp.E282K,p.H773R,p.H773P,p.V834A,p.G863D11.63PDGFRAp.E241A,p.Y555H4.65NRASp.G13C,p.E31V,p.Q61R6.98ERBB2p.P1170V2.33 Conclusion: In terms of identifying potential target therapy options without the need of a invasive intervention becomes available with NGS multigene panel studies within high reliability that also have an effect on the quality of life in colorectal cancer patients. Citation Format: Cem Mujde, Abdullah Hanta, Ozge Sonmezler, Ahmet Rencuzogullari, Ibrahim Boga, Atil Bisgin. The significance of liquid biopsy in colorectal cancer via GeneReader NGS Systems [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1972.

Molecular profiling helps to diagnose, classify and guide the treatment of hematologic neoplasms. Thus NGS is the most powerful diagnostics tool to serve clinical management needs. In this study, we analyzed a multi-gene panel for genes associated with diagnostic, prognostic and therapeutic utilities for hematologic neoplasms. A total of 37 samples of myeloid and lenfoid were analyzed in GeneReader NGS system through a targeted multi-gene panel consisting of ASXL1, CALR, CBL, CEBPA, CSF3R, DNMT3A, EZH2, FLT3, IDH1, IDH2, JAK2, KIT, KRAS, MPL, NPM1, NRAS, RUNX1, SETBP1, SF3B1, SH2B3, SRSF2, TET2, TP53, U2AF1, ZRSR2. QCI-Analyze and QCI-Interpret were used for bioinformatic analyses. Each sample generated 2.176.058 million reads on average, and minimum of 99.5 % mapped reads to the reference reads. Total of 38 reportable variants of 16 genes were detected in 21 patients. The positivity rate was 70.5% (12 of 17) in myeloid group while its 90% (9 of 10 patients) in lymphoid group.In conclusion, our study shows the high sensitivity and specificity of the NGS technology that facilitates the identification of actionable genetic alterations on multiple genes simultaneously to avoid time-consuming multi-step procedures in hematologic malignancies. Citation Format: Sevcan Tug Bozdogan, Cagla Rencuzogullari, Cem Mujde, Atil Bisgin. Clinical utility of a multigene panel for hematologic malignancies [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5294.

In this study, it was aimed to investigate the presence of extended-spectrum beta-lactamase (ESBL) producing Escherichia coli in caged birds. A total of 139 fecal swab samples were collected from cage birds from 14 different aviaries in Adana. ESBL producing E. coli was detected in 4.3% (n=6) of the fecal samples and these isolates harbored blaCTX-M-15 gene. ERIC-PCR analysis revealed three different band patterns among the isolates. These results indicate that cage birds are carrier of ESBL-producing E. coli. Therefore, further epidemiological studies are needed to determine the presence of resistant bacteria including ESBL producing E. coli in various animal species.