Analysis Of Genomic DNA Research Articles

Sensitive and reliable detection of KIT p.D816V mutation in decalcified archival bone marrow trephines.

The majority of mastocytosis cases are characterized by an activating mutation in the KIT gene in codon 816. The detection of this alteration is of importance for proper diagnostic workup. Therefore, reliable and sensitive methods for the detection of KIT Codon 816 hotspot mutations in various types of patient samples are required. Since mutated cancer genes are often overexpressed, we evaluated the feasibility and sensitivity of KIT p.D816V detection by analysing mRNA/cDNA instead of genomic DNA. From 80 bone marrow trephines harboring a KIT p.D816 mutation, seven were only mutated by mRNA/cDNA pyrosequencing and 11 only by digital PCR analysis of genomic DNA. These results clearly demonstrate that detection of clinically relevant mutations in mRNA extracted from routinely processed decalcified archival bone marrow trephines is not only possible in a reliable fashion but under many circumstances advantageous. This enables the direct correlation of genomic data with high-quality morphological evaluation.

Abstract 4133040: Cardiac Favored Transcription of the Exogenous Gene in Mice after A Single Systemic Delivery of AAV9-cBIN1

Introduction: Heart failure (HF) is associated with high mortality and morbidity, and there are limited therapeutic options available to improve cardiac muscle function. Recent studies suggest that the impairment of cardiomyocyte T-tubule microdomains is a key factor in HF pathophysiology. AAV9-cBIN1 gene therapy effectively addresses this impairment. However, the kinetics and biodistribution of AAV9-cBIN1 have not been explored, limiting the knowledge of the transcription efficiency and organ specificity of cBIN1 gene therapy when delivered systemically. Aim: This study aims to elucidate the kinetics and biodistribution of AAV9-cBIN1 in a murine model. Method: Adult male C57BL/6J mice (n=20) were administered a single retro-orbital injection of AAV9-CMV-cBIN1-V5 at a dose (2x10^12 vg/kg) known to effectively transduce the majority of cardiomyocytes. Mice were sacrificed at pre-determined time points: prior to injection (Day 0, n=2) and post-injection at Days 3, 7, 14, 28, 56, and 84 (n=3/group). Tissues were harvested from the heart, lung, liver, kidney, skeletal muscle, and spleen. Genomic DNA was extracted and analyzed using qPCR to determine vector genome (vg) copies. For transcriptional analysis of the AAV9-transduced exogenous gene, mRNA was extracted and converted to cDNA for qRT-PCR quantification of cBin1-V5 , normalized to the housekeeping gene Hprt1 . Results: All mice survived to their designated sacrifice times. Kinetic analysis demonstrated a time-dependent expression of the exogenous cBin1-V5 gene, with peak expression observed at 4 weeks in both the heart and liver, with expression declining in the liver after this peak (Figure 1A). Genomic DNA analysis showed a gradual increase and plateau of viral genome distribution in the heart between 2-4 weeks, while in the liver, distribution peaked sharply between Days 3-7 and then decreased. When correcting the gene transcription of cBin1-V5 (ΔCq of V5/Hprt1 ) for vector DNA vg copies in the tissue, the transcription efficiency in the heart was higher than in the liver (Figure 1B). Outside of the liver and heart, cBin1-V5 mRNA expression was undetectable in all other tissues by Day 56. Conclusion: In adult male mice, a single systemic administration of AAV9-cBIN1 results in robust transduction and higher transcription efficiency in the heart compared to the liver. AAV9-cBIN1 holds promise for targeted gene therapy in cardiac tissues, with minimal off-target expression in other organs.

Artificial Intelligence-Enhanced Analysis of Genomic DNA Visualized with Nanoparticle-Tagged Peptides under Electron Microscopy.

DNA visualization has advanced across multiple microscopy platforms, albeit with limited progress in the identification of novel staining agents for electron microscopy (EM), notwithstanding its ability to furnish a broad magnification range and high-resolution details for observing DNA molecules. Herein, a non-toxic, universal, and simple method is proposed that uses gold nanoparticle-tagged peptides to stain all types of naturally occurring DNA molecules, enabling their visualization under EM. This method enhances the current DNA visualization capabilities, allowing for sequence-specific, genomic-scale, and multi-conformational visualization. Importantly, an artificial intelligence (AI)-enabled pipeline for identifying DNA molecules imaged under EM is presented, followed by classification based on their size, shape, or conformation, and finally, extraction of their significant dimensional features, which to the best of authors' knowledge, has not been reported yet. This pipeline strongly improved the accuracy of obtaining crucial information such as the number and mean length of DNA molecules in a given EM image for linear DNA (salmon sperm DNA) and the circumferential length and diameter for circular DNA (M13 phage DNA), owing to its image segmentation capability. Furthermore, it remained robust to several variations in the raw EM images arising from handling during the DNA staining stage.

Genomic and epigenomic analysis of plasma cell-free DNA identifies stemness features associated with worse survival in lethal prostate cancer.

Metastatic castration-resistant prostate cancer (mCRPC) resistant to androgen receptor signaling inhibitors (ARSIs) is often lethal. Liquid biopsy biomarkers for this deadly form of disease remain under investigation, and underpinning mechanisms remain ill-understood. We applied targeted cell-free DNA sequencing to 126 mCRPC patients from three academic cancer centers, and separately performed genome-wide cell-free DNA methylation sequencing on 43 plasma samples collected prior to the initiation of first-line ARSI treatment. To analyze the genome-wide sequencing data, we performed nucleosome-positioning and differential methylated region analysis. We additionally analyzed single-cell and bulk RNA sequencing data from 14 and 80 mCRPC patients, respectively, to develop and validate a stem-like signature, which we inferred from cell-free DNA. Targeted cell-free DNA sequencing detected AR/enhancer alterations prior to first-line ARSIs which correlated with significantly worse PFS (p = 0.01; HR = 2.12) and OS (p = 0.02; HR = 2.48). Plasma methylome analysis revealed that AR/enhancer lethal mCRPC patients have significantly higher promoter-level hypomethylation than AR/enhancer wild-type mCRPC patients (p < 0.0001). Moreover, gene ontology and CytoTRACE analysis of nucleosomally more accessible transcription factors in cell-free DNA revealed enrichment for stemness-associated transcription factors in lethal mCRPC patients. The resulting stemness signature was then validated in a completely held-out cohort of 80 mCRPC patients profiled by tumor RNA sequencing. We analyzed a total of 220 mCRPC patients, validated the importance of cell-free AR/enhancer alterations as a prognostic biomarker in lethal mCRPC and showed that the underlying mechanism for lethality involves reprogramming developmental states toward increased stemness.

Establishment and biological characteristics of a human buccal mucosa squamous cell carcinoma cell line SCC117

Objective: To establish a human buccal mucosa squamous cell carcinoma (BMSCC) cell line SCC117 in China, analyze and identify its basic biological characteristics. Methods: A 59-year-old Chinese male patient with BMSCC in the Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology in January 2011 was included in this study, his surgical specimens were primary cultured in vitro by improved tissue block culture method. The BMSCC cell line SCC117 was established after continuous passage and stable growth. The morphological characteristics of the cells were observed by light and electron microscope, and their basic biological characteristics were analyzed by growth curve, chromosome karyotype and xenotransplantation tumorigenicity in nude mice experiment. The expressions of cytokeratin (CK14), tumor-related proteins retinoblastoma tumor suppressor protein (RB), P53, E-cadherin, P21, phosphatase and tensin homolog deleted on chromosome ten (PTEN) were detected by immunohistochemical and human papilloma virus (HPV) were tested by PCR. SCC117 was identified by short tandem repeat (STR) analysis of genomic DNA. Results: SCC117, a human BMSCC cell line, had been continuously subcultured in vitro for more than 150 generations. The cells grew in polygonal mosaic and lost contact inhibition, the typical desmosomes and tensional fibrils were observed by electron microscope, and CK14 was positive by immunohistochemistry. The doubling time was 40.16 h, the chromosome mode of the cell line was concentrated between 67 and 69, hypo-triploid. All 4 nude mice inoculated with SCC117 cells developed tumors, indicating that the SCC117 cell line had the ability of xenogeneic tumorigenesis. The histopathological type of the transplanted tumor in nude mice was consistent with that of the primary tumor tissue, both of which were squamous cell carcinoma. The immunohistochemical results showed that in both human primary tumor and the transplanted tumor tissue in nude mice, RB, P53, and E-cadherin were all positive, P21 was weakly positive, while PTEN was negative. SCC117 was tested negative for the presence of HPV. STR sequence analysis showed that SCC117 cell line originated from primary tumor tissue and was not cross-contaminated by other cell lines. Conclusions: The human BMSCC cell line SCC117 was successfully established in China, which could provide a new experimental model for the study of oral SCC without HPV infection, especially BMSCC.

Pheno- and Genotypic Epidemiological Characterization of Vancomycin-Resistant Enterococcus faecium Isolates from Intensive Care Unit Patients in Central Türkiye.

Vancomycin-resistant Enterococcus faecium (VRE) has been detected in Türkiye. Only limited information is available on its dissemination in the central regions of the country. This study describes the first epidemiological characterization of VRE clinical isolates detected in patients in a hospital in the province of Aksaray. In this one-year study conducted between 2021 and 2022, stool samples from intensive care unit patients were screened for VRE using the phenotypic E-test method, and the antibiotic sensitivity test was analyzed by using the VITEK® 2 system. A molecular assay for confirmation of species level was carried out by 16S rRNA gene-based sequencing and testing for antibiotic resistance (vanA or vanB) and virulence factor-encoding genes (esp, asa1, and hyl). Further, genotypic characterization was determined by macro-restriction fragment pattern analysis (MRFPA) of genomic DNA digested with SmaI restriction enzyme. Of the total 350 Enterococcus positive patients from different hospital intensive care units, 22 (6.3%) were positive for VRE using the phenotypic E-test method. All isolates showed resistance to ampicillin, ciprofloxacin, vancomycin, and teicoplanin and positive amplification for the vanA gene. However, none of the isolates was positive for the vanB gene. The most prevalent virulence gene was esp. The results indicate that the isolates are persistent in the hospital environment and subsequently transmitted to hospitalized patients, thus representing challenges to an outbreak and infection control. These study results would also help formulate more effective strategies to reduce the transmission and propagation of VRE contamination in various hospital settings.

AGTR1 A1166C gene polymorphism is associated with the effectiveness of valsartan monotherapy in Chinese patients with essential hypertension: A retrospective analysis

Objective: To investigate whether angiotensin II type 1 receptor (AGTR1 A1166C) gene polymorphism was associated with the effectiveness of valsartan monotherapy in Chinese patients with essential hypertension. Methods: This retrospective analysis included 198 patients (⩾18 years of age) who received valsartan monotherapy (80 mg/day) for newly developed essential hypertension at the authors’ center between January 1, 2020 and December 31, 2023. Genotyping for AGTR1 A1166C gene polymorphism was done by polymerase chain reaction (PCR)-melting curve analysis of genomic DNA from peripheral blood samples. A dominant genetic model for AGTR1 A1166C (AA genotype versus AC + CC genotype) was used. Multivariate regression analysis of baseline variables and AGTR1 polymorphism was conducted to identify predictors of target blood pressure attainment (&lt;140/90 mmHg) at the 4-week follow-up. Results: The median age of the 198 patients was (53.7±13.5) years, and 58% were men. Genotyping assays showed that 164 patients had the AA genotype, and 34 patients were of the AC/CC genotype, including 30 with the AC genotype and 4 with the CC genotype. Allele distribution was consistent with Hardy Weinberg equilibrium. 109 Patients (55.1%) attained the blood pressure target. Multivariate analysis showed that smoking (versus no smoking, HR 0.314, 95% CI 0.159-0.619, P=0.001) and AGTR1 A1166C AA genotype (versus AC/CC, HR 2.927, 95% CI 1.296-6.611, P=0.023) were significant and independent predictors of target attainment. 25 Patients (73.5%) with AGTR1 A1166C AC/CC genotype attained the target versus 51.2% (51/164) of patients with AGTR1 A1166C AA genotype (P=0.017). Patients with AGTR1 A1166C AC/CC genotype had a significantly greater reduction in systolic blood pressure [(33.1±10.8) mmHg versus (29.2±11.7) mmHg in AA carriers; P=0.029)]. Conclusions: Hypertensive patients carrying one or two C alleles of the AGTR1 A1166C gene were more responsive to valsartan treatment.

Remarkable genetic variability and high antigenicity of the octapeptide-repeat region in an Entamoeba nuttalli-specific surface protein.

Entamoeba nuttalli is genetically the closest to Entamoeba histolytica, the causative agent of human amebiasis. E. nuttalli is found in Macaca species, exhibiting no symptoms while potentially virulent. Using comparative genomics of Entamoeba species, we identified a gene encoding an E. nuttalli-specific protein containing 42 repeats of an octapeptide (PTORS). In the present study, we analyzed the genes in E. nuttalli strains derived from various geographic locations and host species. Sequence analysis of genomic DNA from four strains indicated 43, 44, and 48 repeat types in addition to 42 repeats and remarkable genetic diversity in the repeat region, although all nucleotide substitutions were synonymous. In contrast, the sequences of the N-terminal side region and C-terminus were identical among the strains. Monoclonal antibodies prepared against recombinant PTORS were reactive to the repeat regions but not to the N-terminal side regions. Polyclonal antibodies did not react with the N-terminal region, demonstrating that the repeat region had higher antigenicity. Analysis using synthetic peptides revealed that the two repeats of the octapeptide functioned as epitopes. Immunofluorescence microscopy using monoclonal antibodies demonstrated the surface localization of PTORS. These results suggest that the repeat region of PTORS plays an important role in host-parasite interactions.

Next generation triplex-forming PNAs for site-specific genome editing of the F508del CFTR mutation

BackgroundCystic Fibrosis (CF) is an autosomal recessive genetic disease caused by mutations in the gene encoding the cystic fibrosis transmembrane conductance regulator (CFTR) protein for which there is no cure. One approach to cure CF is to correct the underlying mutations in the CFTR gene. We have used triplex-forming peptide nucleic acids (PNAs) loaded into biodegradable nanoparticles (NPs) in combination with donor DNAs as reagents for correcting mutations associated with genetic diseases including CF. Previously, we demonstrated that PNAs induce recombination between a donor DNA and the CFTR gene, correcting the F508del CFTR mutation in human cystic fibrosis bronchial epithelial cells (CFBE cells) and in a CF murine model leading to improved CFTR function with low off-target effects, however the level of correction was still below the threshold for therapeutic cure. MethodsHere, we report the use of next generation, chemically modified gamma PNAs (γPNAs) containing a diethylene glycol substitution at the gamma position for enhanced DNA binding. These modified γPNAs yield enhanced gene correction of F508del mutation in human bronchial epithelial cells (CFBE cells) and in primary nasal epithelial cells from CF mice (NECF cells). ResultsTreatment of CFBE cells and NECF cells grown at air-liquid interface (ALI) by NPs containing γtcPNAs and donor DNA resulted in increased CFTR function measured by short circuit current and improved gene editing (up to 32 %) on analysis of genomic DNA. ConclusionsThese findings provide the basis for further development of PNA and NP technology for editing of the CFTR gene.

Simultaneous profiling of chromatin accessibility and DNA methylation in complete plant genomes using long-read sequencing.

Epigenetic regulations, including chromatin accessibility, nucleosome positioningand DNA methylation intricately shape genome function. However, current chromatin profiling techniques relying on short-read sequencing technologies fail to characterise highly repetitive genomic regions and cannot detect multiple chromatin features simultaneously. Here, we performed Simultaneous Accessibility and DNA Methylation Sequencing (SAM-seq) of purified plant nuclei. Thanks to the use of long-read nanopore sequencing, SAM-seq enables high-resolution profiling of m6A-tagged chromatin accessibility together with endogenous cytosine methylation in plants. Analysis of naked genomic DNA revealed significant sequence preference biases of m6A-MTases, controllable through a normalisation step. By applying SAM-seq to Arabidopsis and maize nuclei we obtained fine-grained accessibility and DNA methylation landscapes genome-wide. We uncovered crosstalk between chromatin accessibility and DNA methylation within nucleosomes of genes, TEs, and centromeric repeats. SAM-seq also detects DNA footprints over cis-regulatory regions. Furthermore, using the single-molecule information provided by SAM-seq we identified extensive cellular heterogeneity at chromatin domains with antagonistic chromatin marks, suggesting that bivalency reflects cell-specific regulations. SAM-seq is a powerful approach to simultaneously study multiple epigenetic features over unique and repetitive sequences, opening new opportunities for the investigation of epigenetic mechanisms.

Abstract 7248: Simultaneous isolation and parallel analysis of genomic DNA and RNA for gene therapy

Abstract Introduction Viral vectors, such as adeno-associated vector (AAV), play a crucial role in delivering transgenes for gene therapy research. The success of vector transduction is vital for efficacy, which is measured through vector copy number (VCN) and transgene expression. In preclinical studies, both VCN and transgene expression are commonly tested from the same sample to ensure accuracy. We have reported a method for simultaneous high-quality genomic DNA and RNA extraction without splitting the sample, utilizing SPRI bead-based technology that has consistent performance across diverse tissue types and brain regions. Methods AAV was administered to mouse and non-human primate (NHP) models. At the conclusion of each experiment, tissue samples from the adrenal gland, brain, gonads, heart, kidney, liver, lung, skeletal muscle, spinal cord, and spleen were harvested. All tissue samples that demonstrated around 15 mm3 were snap-frozen in liquid nitrogen before nucleic acid extraction. The extraction process was carried out manually or on an automated liquid handler. The quality and quantity of DNA and RNA were then assessed from all tested tissues before downstream assay. Results Our study found that all mouse tissue types (n=72/tissue type) and NHP (n=11/tissue type) had an average gDNA and RNA yield that exceeded the minimum yield cutoff of 25 ng/μL for DNA and 6.25 ng/μL for RNA. We also analyzed DNA from tissues treated with two different AAV serotype-treated tissues in the mouse model, which showed that transduction across all the tissues was highly efficient for both AAV serotypes. Furthermore, we observed variations in transgene expression levels (copies/1 μg RNA) among different tissue types. Similar patterns of VCN and transgene expression were also observed in NHP models. Conclusions Efficient gene therapy depends on a safe and effective viral vector. The simultaneous extraction of gDNA and RNA simplifies the process, saves time, ensures quality, and facilitates integration into existing lab automation. This leads to consistent and error-resistant performance in analyzing vector copy and transgene levels. Citation Format: Han Wei. Simultaneous isolation and parallel analysis of genomic DNA and RNA for gene therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7248.

Abstract 3662: Cell-free DNA dynamics following neuroblastoma resection

Abstract Introduction: Prior studies have demonstrated the utility of circulating tumor DNA (ctDNA) as a biomarker in the postoperative period for oncologic risk stratification. However, its utility may be limited in the early postoperative period by surgical trauma causing an increase in total cell-free DNA (cfDNA) due to tissue destruction, inflammation, and wound healing. No studies have identified the optimal timing of postoperative sample collection in pediatric patients undergoing resection of high-risk neuroblastoma. The purpose of this study is to assess the postoperative dynamics of cfDNA following neuroblastoma resection to determine optimal timing for ctDNA investigations. Methods: An institutional database of banked cell-free DNA samples was retrospectively queried for patients with a diagnosis of neuroblastoma who had blood samples collected prior to resection and postoperative samples collected within 2 months of the operation. Plasma was collected from whole blood samples. cfDNA was extracted from plasma samples using the QIAGEN QIAsymphony SP system, and samples were quantified using the Advanced Analytical Fragment Analyzer Automated CE System with the High Sensitivity Genomic DNA Analysis Kit. Results: Seventeen patients were identified undergoing 18 total operations and 37 total blood draws yielding cfDNA. There were 12 male and 5 female patients. Median age at operation was 5.5 years (range 1.4y to 20.5y). Two patients were INRG stage L2, and 15 patients were stage M. Operative indications were primary tumor resection in 10 patients and resection of recurrence/progression in 8 patients. Three postoperative samples were drawn within 10 days of the operation, and 16 samples were collected between postoperative weeks 4 and 6. There was a statistically significant difference (p=0.029) in cfDNA yield between each timepoint sampled: preoperative (median 6ng/mL, range 2-30ng/mL), 0-10 days postop (median 34ng/mL, range 15 - 85 ng/mL), and 4-6 weeks postop (median 6ng/mL, range 2 - 17ng/mL). Pairing the pre- and post-operative samples for each patient, those drawn within 10 days had a median increased yield of 180% (range +67% to +652%) while the samples collected at 4-6 weeks had a median decreased yield of 23% (range -55% to +491%; p = 0.047). Of note, there were three outliers in the 4-6 week group who had increases in cfDNA yield of &amp;gt;200%. On further review of these charts, each patient was being treated for obstructive uropathy at the time the postoperative sample was collected. Conclusion: Plasma cfDNA yield increases in the early postoperative period before dropping by postoperative week 6. Tumor resection may be associated with an overall decrease in total cfDNA. Postoperative renal pathology may cause a persistent elevation in cfDNA. Further studies are necessary to clarify the role of ctDNA in the management of patients with neuroblastoma. Citation Format: Joshua N. Honeyman, Andrew Chi, Shakeel Modak, Fiorella Iglesias Cardenas, Michael P. La Quaglia, Neerav N. Shukla, J. Ted Gerstle. Cell-free DNA dynamics following neuroblastoma resection [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3662.

New Genetic Variants of RUNX2 in Mexican Families Cause Cleidocranial Dysplasia.

Cleidocranial dysplasia (CCD) is an autosomal dominant skeletal dysplasia characterized by persistent open skull sutures with bulging calvaria, hypoplasia, or aplasia of clavicles permitting abnormal opposition of the shoulders; wide public symphysis; short middle phalanx of the fifth fingers; and vertebral, craniofacial, and dental anomalies. It is a rare disease, with a prevalence of 1-9/1,000,000, high penetrance, and variable expression. The gene responsible for CCD is the Runt-related transcription factor 2 (RUNX2) gene. We characterize the clinical, genetic, and bioinformatic results of four CCD cases: two cases within Mexican families with six affected members, nine asymptomatic individuals, and two sporadic cases with CCD, with one hundred healthy controls. Genomic DNA analyses of the RUNX2 gene were performed for Sanger sequencing. Bioinformatics tools were used to predict the function, stability, and structural changes of the mutated RUNX2 proteins. Three novel heterozygous mutations (c.651_652delTA; c.538_539delinsCA; c.662T>A) and a previously reported mutation (c.674G>A) were detected. In silico analysis showed that all mutations had functional, stability-related, and structural alterations in the RUNX2 protein. Our results show novel mutations that enrich the pool of RUNX2 gene mutations with CCD. Moreover, the proband 1 presented clinical data not previously reported that could represent an expanded phenotype of severe expression.

Novel electroporation-based genome editing of carnation plant tissues using RNPs targeting the anthocyanidin synthase gene.

A novel electroporation method for genome editing was performed using plant tissue samples by direct RNPs-introduction in carnation. Genome editing is becoming a very useful tool in plant breeding. In this study, a novel electroporation method was performed for genome editing using plant tissue samples. The objective was to create a flower color mutant using the pink-flowered carnation 'Kane Ainou 1-go'. For this purpose, a ribonucleoprotein consisting of guide RNA and clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9 (Cas9) was introduced into the stem tissue to induce mutations in the anthocyanidin synthase (ANS) gene, which is involved in anthocyanin biosynthesis. As the ANS of 'Kane Ainou 1-go' has not been previously isolated, we initially isolated the ANS gene from 'Kane Ainou 1-go' for characterization. Southern hybridization analysis confirmed that the ANS gene was present in the genome as a two-allele gene with a pair of homologous sequences (ANS-1 and 2); these sequences were used as the target for genome editing. Genome editing was performed by introducing #2_single-guide RNA into the stem tissue using the ribonucleoprotein. This molecule was used because it exhibited the highest efficiency in an analysis of cleavage activity against the target sequence in vitro. Cleaved amplified polymorphic sequence analysis of genomic DNA extracted from 85 regenerated individuals after genome editing was performed. The results indicated that mutations in the ANS gene may have been introduced into two lines. Cloning of the ANS gene in these two lines confirmed the introduction of a single nucleotide substitution mutation for ANS-1 in both lines, and a single amino acid substitution in one line. We discussed the possibility of color change by the amino acid substitution, and also the future applications of this technology.

(058) Evaluation of Pathway Expression Following Down-Regulation of NELL1, a Potential Gene of Interest in Peyronie’s Disease

Abstract Introduction Peyronie’s Disease (PD) is a superficial fibrosing disorder characterized by inelastic fibrous plaques within the tunica albuginea. We previously performed high-resolution array comparative genomic hybridization analysis of genomic DNA from men with both PD and Dupuytren’s Disease (DD), yielding candidate genes, including NELL1, with potential involvement in these conditions. NELL1 is a secreted growth factor that enhances osteoblastic differentiation and chondrogenesis and may contribute to calcification and inflammation in fibrotic plaques via its interaction with bone morphogenetic protein (BMP) within the TGF-β signaling pathway. Here, we report on pathway analysis following up- and down-regulation of NELL1 using CRISPR modification in an in vitro setting. Objective This study aimed to investigate the influence of NELL1 modification on downstream gene regulation, focusing on pathways that were significantly regulated following NELL1 down-regulation. Methods For down-regulation of NELL1, gRNAs were delivered to HEK293 cells with a nuclease deficient (d) dCas9-KRAB system adapted from Streptococcus pyogenes. Gene regulation was assessed using qRT-PCR. Results For down-regulation of NELL1, PCR analysis confirmed a 95% reduction in expression. Non-target vectors did not change NELL1 expression levels. RNA sequencing results found over 5,000 differentially expressed genes between, with significant changes in multiple pathways, including the HIF-1α pathway, which promotes keloid development by activating the TGF-β/Smad pathways. Additionally, we identified pathways related to ECM-receptor interaction, inflammation, apoptosis, and cell cycle regulation that are mediated by TGF-β/Smad signaling, which plays a crucial role in fibrosis. Our analysis also demonstrated upregulation of the PI3K-Akt pathway, which is involved in regulating type I collagen expression in response to TGF-β1. These results highlight the significance of NELL1 in fibrotic regulation and suggest its potential involvement in the development of PD. Conclusions We have created guides for and successfully down-regulated the expression of NELL1, a gene of interest in Peyronie’s disease. We have also demonstrated, through RNA sequencing, that changes in NELL1 lead to large changes in gene and pathway expression. The identified modified pathways, including HIF-1α-mediated, TGF-β/Smad and PI3K-Akt, provide valuable insights into the potential molecular mechanisms underlying NELL1's role in regulation of fibrosis, and further investigation of these pathways may reveal potential therapeutic targets for fibrosis-related disorders. Disclosure Any of the authors act as a consultant, employee or shareholder of an industry for: Contraline, Techfields Inc, Alto Neurosciences, Curebase.

Comparison of genomic DNA sequencing to anerobic cultures to detect efficacy of hydrogen peroxide at reducing cutibacterium acnes bacterial burden during primary shoulder arthroplasty

BackgroundThe purpose of this investigation is to compare Cutibacterium acnes diagnosis using culturing vs. genomic DNA sequencing (NextGen) at various timepoints and locations during primary total shoulder arthroplasty. Additionally, we intend to compare the effects of hydrogen peroxide on standard culture technique results with genomic DNA sequencing. MethodsA prospective diagnostic study of 40 patients undergoing primary total shoulder arthroplasty was performed. Intraoperatively, 4 tissue samples were collected per patient: subdermal skin edge following initial skin incision, subdermal skin edge following hydrogen peroxide soak for 5 minutes, glenohumeral joint capsule, and subdermal skin edge prior to wound closure. Each tissue specimen was collected twice (one for culture analysis and the other for genomic (NextGen) DNA sequencing analysis) for a total of 8 specimens per patient and 320 tissue specimens in total. All anaerobic cultures were held for 14 days. Each culture plate was divided into quadrants and the amount of growth was quantified. Tissue samples were collected for genomic sequencing DNA analysis. Genomic sequencing results provided relative percentage of bacteria for each specimen detected. ResultsThere were 18/40 males (45%) and no postoperative complications. Average age was 72.2 ± 11.8. Overall, 18% (29/160) of standard anaerobic cultures were positive for C. Acnes and 26% (942/160) were positive with genomic (Nextgen) DNA sequencing. When comparing the NextGen results with anaerobic standard cultures, there was a calculated negative predictive value of 85.6% and positive predictive value of 28.6%. Sensitivity of the NextGen was 41.4% and specificity was 77.1%. Bacterial culture rates did not significantly change from the beginning to the end of surgery as demonstrated on standard culturing and the NextGen analysis (P > .05). After treatment with hydrogen peroxide, the standard culturing technique showed no significant difference between the samples; however, there was a significant increase in bacterial burden (12.4%) noted with NextGen analysis (P = .0147). ConclusionNextGen culturing is a novel technique to help identify shoulder prosthetic joint infections. These results show that, NextGen is better at identifying the absence of infection, but has a high false positive rate indicative of its ability to identify contaminants as compared to standard anaerobic culturing methods. The increase in bacterial burden after peroxide treatment noted with NextGen could also be secondary to the test’s increased ability to identify both living and dead bacterial pathogens.

Human buccal epithelial cells as a model system for molecular analysis of DNA, RNA and protein

We report use of human buccal epithelial cells as an easy model system for isolation and molecular analysis of genomic DNA, RNA, and protein to study any gene of interest by Polymerase Chain Reaction (PCR), RNA expression by Reverse Transcription-PCR (RT-PCR), protein-profiling, and expression by western blot as well as DNA-methylation by Msp I/Hpa II-restriction digestion. We used simple methods to isolate genomic DNA, RNA and protein from human buccal cells collected by oral swab and cultured them in-vitro. The microscopic observation of haematoxylin and eosin (EA-50) stained cells, genomic PCR of house-keeping genes (GAPDH and β-actin), RT-PCR of GAPDH and β-actin mRNAs and whole cell protein-profiling by Sodium Dodecyl Sulphate-Polyacrylamide Gel Electrophoresis (SDS-PAGE) were carried out. Expression of β-actin protein in supernatant and pellet fractions of the cells was determined by western blot analysis. MTT-assay was carried out to assess the cell viability and cell growth. Green Fluorescence Protein (GFP)-DNA was expressed in these cells by transient transfection. DNA-methylation in the genome was analyzed by Msp I/ Hpa II restriction digestion and agarose gel electrophoresis. Thus these methods can be used for molecular analysis of DNA, RNA and protein from the human buccal epithelial cells for studying and monitoring health, disease, population genetics/genomics and epidemiology under different conditions.

MACULOPAPULAR CUTANEOUS MASTOCYTOSIS HARBORING A KIT MUTATION (ASP419DEL): A CASE REPORT

A 2-year-old, male patient presented with an 18-month history of scattered, brown macules and nodules up to 2 cm in size on his trunk and extremities. These macules were accompanied by pruritus and were positive for Darier's sign. A skin biopsy of a brown macule on the left thigh revealed a dense accumulation of CD117-positive, round or oval cells with amphophilic cytoplasm within the upper to middle dermis. The patient was otherwise healthy and had normal laboratory and imaging test results. Sequence analysis of genomic DNA from a skin biopsy demonstrated the presence of an Asp419del mutation in exon 8 of the KIT gene. Based on these findings, maculopapular cutaneous mastocytosis (MPCM) was diagnosed. The patient received H 1-antihistamine. Although the pruritus resolved, the brown macules remained for one year after the initial treatment. To the best of our knowledge, only three cases of cutaneous mastocytosis (CM) with an Asp419del mutation, including the present case, have been reported in the Japanese literature to date; moreover, while the previous two cases were of DCM, the present case was the first instance of MPCM. Normally, the symptoms of childhood-onset MPCM are dormant until puberty. However, a recent study reported that many MPCM patients may experience persistent or exacerbated symptoms. The present study therefore evaluated 53 Japanese cases of childhood onset MPCM with a KIT gene mutation and discussed the patients' clinical outcomes.

Türkiye’deki kanser hastalarında kalıtsal PALB2 gen varyantlarının yeni nesil dizileme yöntemiyle araştırılması

Aim: The study aimed to investigate germline PALB2 gene variants in 1056 cancer patients in Türkiye, selected based on the National Comprehensive Cancer Network guidelines for genetic/familial high-risk assessment related to breast, ovarian, and pancreatic cancer. Materials and Methods: The next-generation sequencing analysis of genomic DNA was performed using a Sophia Hereditary Cancer Solutions Panel for PALB2 gene mutation screening. Results: The PALB2 genetic variants were detected in 48 patients, including 20 patients with pathogenic or likely pathogenic variants and 28 patients with variants of uncertain significance. The most common PALB2 mutations were the frameshift mutations c.557dupA p.(Asn186Lysfs*4) and c.509_510del p.(Arg170Ilefs*14), found in 0.57% and 0.28% of patients, respectively. Conclusion: The findings of the study emphasize the importance of PALB2 gene analysis for breast cancer predisposition in Türkiye.

Detection of APP gene recombinant in human blood plasma

The pathogenesis of Alzheimer’s disease (AD) is believed to involve the accumulation of amyloid-β in the brain, which is produced by the sequential cleavage of amyloid precursor protein (APP) by β-secretase and γ-secretase. Recently, analysis of genomic DNA and mRNA from postmortem brain neurons has revealed intra-exonic recombinants of APP (gencDNA), which have been implicated in the accumulation of amyloid-β. In this study, we computationally analyzed publicly available sequence data (SRA) using probe sequences we constructed to screen APP gencDNAs. APP gencDNAs were detected in SRAs constructed from both genomic DNA and RNA obtained from the postmortem brain and in the SRA constructed from plasma cell-free mRNA (cf-mRNA). The SRA constructed from plasma cf-mRNA showed a significant difference in the number of APP gencDNA reads between SAD and NCI: the p-value from the Mann–Whitney U test was 5.14 × 10−6. The transcripts were also found in circulating nucleic acids (CNA) from our plasma samples with NGS analysis. These data indicate that transcripts of APP gencDNA can be detected in blood plasma and suggest the possibility of using them as blood biomarkers for Alzheimer's disease.