The Relationship Between Controlling Nutritional Assessment Score and Mortality in Patients with Chronic Coronary Syndrome: A Retrospective Study from Türkiye

BACKGROUND

Controlling Nutritional Assessment (CONUT) score has been shown to have a higher predictive value compared to other nutritional scores in acute coronary syndrome.

AIM

To determine the relationship between CONUT score and long-term mortality in patients with chronic coronary syndrome (CCS).

METHODS

Between 2017 and 2020, 585 consecutive patients newly diagnosed and proven to have CCS by coronary angiography were included in the study. CONUT score and demographic and laboratory data of all patients were evaluated. The relationship between results and mortality was evaluated.

RESULTS

The mean age of the patients was 64 years and 75% were male. Mortality was observed in 56 (9.6%) patients after a median follow-up period of 3.5 years. The median CONUT score was significantly higher in patients with mortality (P < 0.001). In multivariate regression analysis, the CONUT score was associated with mortality (Hazard ratio (HR): 1.63 (95% confidence interval (CI): 1.34-1.98 P < 0.001)). The area under curve (AUC) for long-term mortality estimation for the CONUT score was 0.75 (95% CI 0.67-0.82 P < 0.001). When the CONUT score value was accepted as 0.5, the sensitivity was 78% and the specificity was 60.

CONCLUSION

CONUT score was found to be predictive of mortality in long-term follow-up of patients with CCS.

A DNA Extraction Method for Nondestructive Testing and Evaluation of Cotton Seeds (Gossypium L.)

Kernels of cotton provide lint and linter for textiles, oil and protein for food and feed. Cotton seed is formed following fertilization between an ovule and a pollen grain. The seed coat is maternal in origin, whereas the embryo and attached cotyledonary leaves are hybrids of parental lines. The extraction of genomic DNA from an ungerminated whole, a portion or mixed seeds are prerequisite in genetic and genomic studies of cotton. As far as our knowledge, there is only one method of nondescriptive DNA extraction from ungerminated cotton seeds without affecting the seed germination capability, but it has technical difficulties and requires special equipment. Furthermore, the amount of DNA extracted using the published method is low and, therefore, it is only suitable for routine marker assisted selection studies. In this study, a DNA extraction protocol referred to as the CTAB-LiCl was developed for single whole cotton seed, a portion of cotton seed and bulked cotton seeds. This protocol uses a combination of CTAB and LiCl to lyse cells and deplete RNAs simultaneously. The CTAB-LiCl DNA extraction method was evaluated in ninety-six individuals of six different cotton cultivars along with two genetic standards of cotton, TM-1 (G. hirsutum L.), Pima 3-79 (G. barbadense L.), and several other plant species of different plant genera. Results revealed that this method produced high quality and amounts of DNA as confirmed by spectrophotometry, agarose gel, restriction enzyme digestion, polymerase chain reaction, and library production for next generation sequencing studies of whole genome bisulfite sequencing. It does not require the use of liquid nitrogen, RNase, proteinase K, or beta-mercaptoethanol and can be completed in approximately 2 h. Small tissues of the chalaza ends of ungerminated cotton seeds could be used to obtain high quality and quantity of DNA ranging from 14 to 28 µg without affecting the seeds' germination ability, allowing marker-assisted selection before planting and flowering.

Investigation of the effects of in ovo taurine injection on hatching characteristics and stress reduction potential

BACKGROUND

In ovo application is the process of administering some nutrients or components into the egg. The main purpose of this application is to ensure that some nutrients are provided to chicks with a short incubation period. Few studies were conducted with taurine in fertile eggs; especially, no observation of hatchability and chick quality has been found. In addition, taurine has an anti-stress impact that fights oxidative factors.

OBJECTIVE

To assess the hatchability and chick quality after in ovo taurine administration. To determine the stress that may occur as a result of in ovo application and whether taurine has a stress-reducing effect.

METHODS

A total of 1200 fertile eggs from a 34-week-old broiler breeder (Ross 308) flock were categorized into 4 groups with 75 eggs per replicate: control (uninjected), taurine group (0.30 mL dissolved taurine in distilled water), sham control (sterile distilled water) and perforation (eggs perforated and then waxed). On day 14 of incubation, an in ovo injection was administered to the albumen. Data on hatching parameters and hepatic HSP70 levels were obtained using relevant formulas and western blotting, respectively.

RESULTS

Control chicks exhibited higher hatchability than other groups, with the taurine group showing the lowest hatchability. The HSP70 levels were the highest in the perforation group compared to the control group. An increase of 21.37% in the taurine group and 83.45% in the sham control group was observed compared to the control group.

CONCLUSIONS

The findings suggest that in ovo application may induce increased stress, whereas taurine may have positive effects in mitigating the stress caused by in ovo application.

Investigation of some acute phase proteins, cytokines and hepcidin values in feline enteric corona virus antibodies and feline infectious peritonitis antigen positive cats

Feline Infectious Peritonitis (FIP) is a fatal disease caused by feline coronaviruses. The causative agent is Feline Infectious Peritonitis Virus, a mutation of Feline Enteric Coronavirus. Feline Corona Virus is very common in the cat population. In Feline Corona Virus infected cats, the development of FIP depends on the cat's immune response. FIP disease is more common in young and old cats because young and old animals have a weaker immune system. The acute phase response is a complex systemic reaction that occurs as a response to acute or chronic inflammatory processes such as infection, neoplasia or immunological disorders, tissue damage, trauma and surgery. The study material included 15 cat with presumptive FIP (study group) and 10 healthy cats (control group). Of the 15 cats, 9 (60%) showed dry and 6 (40%) effusive form. Serum amyloid A (SAA), haptoglobin (Hp),  α1-acid glycoprotein (AGP), albumin, interleukin-6 (IL-6), hepcidin, alanine-amino transferase (ALT), aspartate aminotransferase (AST), alkaline phosphatase (ALP), blood urea nitrogen(BUN), and creatinine levels were measured in the serum collected from both groups. There were no difference between the wet and dry FIP in albumin values; haptoglobin, α1-acid glycoprotein, SAA and hepcidin values were significantly different between the two groups. IL-6, showed significant difference in both wet and dry FIP groups. It was also concluded that hepcidin may be used as a biomarker in Feline Infectious Peritonitis disease like other acute phase proteins.

Cardio-protective effect of dapagliflozin against doxorubicin induced cardiomyopathy in rats

OBJECTIVE

Cancer is the second most common non-communicable disease group in the world and its frequency is increasing. In parallel, side effects of drugs used in cancer treatment are frequently encountered. Doxorubicin (DOX) is one of the most effective multi-purpose anticancer drugs. However, its use is significantly limited due to the risk of cardiotoxicity. Sodium-glucose cotransporter-2 inhibitors are a group of antidiabetic drugs that have been shown to reduce cardiovascular events. Our aim is to examine the preventive effect of dapagliflozin on DOX-induced cardiac damage.

SUBJECTS AND METHODS

We used 30 albino rats. 20 of 30 rats were administered doxorubicin for cardiomyopathy model. The rats in the DOX arm were divided into two groups: those given penicillin and placebo. After the rats were terminated, tissues were prepared for histopathological and immunohistochemical examination. TNF-α, pro-BNP, troponin T and plasma FGF-21 levels were also measured in plasma.

RESULTS

The mean concentrations of cTnT and pro-BNP in the plasma of the DOX treated rats demonstrated a significantly higher value compared to the control group. Treatment with dapagliflozin caused a significant reduction in plasma cTnT, pro-BNP and TNF-α levels concentrations compared to the DOX control group (p < 0.001). The group of rats treated with dapagliflozin was effective in significantly decreasing the FGF-21 concentration and the percentage of fibronectin immunoexpression compared to the DOX control group (p  < 0.0001).

CONCLUSIONS

This study revealed, for the first time, that dapagliflozin can improve DOX-induced cardiac dysfunction and pathological changes in non-diabetic rats. This result has shown that dapaglifozin, may be promising in terms of preventing cardiac damage that may develop in cancer treatment.

Correlation of Preoperative Serum and Intraoperative Peritoneal Lavage Fluid Ca-125 Levels with Postoperative Tumor Histology in Patients with Endometrial Cancer: A Prospective-Controlled Study

BACKGROUND

The role of Ca-125 in endometrial cancer is not fully known. Some authors have reported high Ca-125 levels in patients with recurrent or advanced endometrial cancer, whereas others have stated that Ca-125 levels and the advance of the disease were not correlated in endometrial cancer. This makes it inevitable for clinicians to search for different measurement methods or interpretation of the present tumor markers. The aim of this study was to evaluate the relationship between Ca-125 values of the serum and abdominal lavage fluid and postoperative histopathological parameters in patients with endometrial carcinoma.

METHODS

The study included patients who were diagnosed with endometrial cancer in the Gynecology Clinic and were planned to undergo surgery. The correlations of clinicopathological parameters with preoperative values of Ca-125 measured from serum and abdominal lavage fluid were investigated. The Spearman correlation test was applied in the analysis of correlations of serum and abdominal lavage fluid Ca-125 values with postoperative tumor characteristics.

RESULTS

The serum Ca-125 values were determined to be positively correlated with surgical stage, tumor diameter, and lymph node involvement (p = 0.03; p = 0.04; and p = 0.01, respectively). No correlation was determined between tumor grade and serum Ca-125 level. The level of Ca-125 in the abdominal lavage fluid was observed to be correlated with surgical stage and tumor grade, but not with tumor diameter or lymph node involvement (p = 0.01, p = 0.04, respectively).

CONCLUSIONS

The value of Ca-125 in the abdominal lavage fluid has a positive correlation with the surgical stage and tumor grade in patients with endometrial carcinoma.

Tissue and/or developmental stage specific methylation of nrDNA in Capsicum annuum

The nuclear ribosomal DNA (nrDNA) sequences are often used for phylogenetic analysis among organisms. Because DNA cytosine methylation and nucleolar dominancy are two common epigenetic mechanisms of nrDNA, we hypothesized that internal transcribed spacer 1 (ITS1), 5.8S rRNA and ITS2 of nrDNA sequences could be used as epigenetic biomarkers. Thus, this research was undertaken to study level and pattern of site-specific cytosine methylation of ITS1, 5.8S and ITS2 in nine tissues and/or developmental stage of pepper Capsicum annuum L. cultivar Demre Sivrisi. Tissues studied consisted of young and old roots at 30 and 90 days after sowing (das), mature dry seeds and seeds at 26 days of post anthesis (dpa), flowering buds at 1 day before flowering, pericarps at 3, 15 and 65 dpa. Levels and patterns of DNA cytosine methylation were identified at single base resolution using bisulfite conversion sequencing. Results of this study revealed that DNA cytosine level and pattern of ITS1, 5.8S and ITS2 were different in most tissues and/or developmental stages studied. In addition, methylation levels of CG, CHG and CHH contexts were also significantly different among the regions. Based on the findings of this study, it was concluded that high level of methylation of nrDNA sequences was relatively higher as observed in transposable element and promoter. On the other hand, its tissue-specific gene expression was effective as that of gene body and promoter methylation. Overall findings revealed that methylation levels of nrDNA could be used as biomarkers for tissue identification or age estimation in plants.

Performance of neutrophil to lymphocyte ratio for the prediction of long-term morbidity and mortality in coronary slow flow phenomenon patients presented with non-ST segment elevation acute coronary syndrome

Introduction: In this study, we aimed to determine if neutrophil to lymphocyte ratio could predict long term morbidity and mortality in patients who hospitalized for non-ST segment elevation acute coronary syndrome (NSTE-ACS) and had coronary slow flow on coronary angiography.

Methods: In this observational study, 111 patients who presented with NSTE-ACS and diagnosed with coronary slow flow phenomenon on angiographic examination were included. Neutrophil to lymphocyte ratio (NLR) calculated as the ratio of the number of neutrophils to the number of lymphocytes. Patients classified into three groups according to NLR values. The term coronary slow flow phenomenon was depicted by calculating Thrombolysis in Myocardial Infarction frame count.Patients were followed up and the occurrence of recurrent angina, recurrent myocardial infarction, and long-term mortality was determined using medical records, phone calls, or face-to-face interviews. P values <0.05 considered to indicate statistical significance.

Results: Recurrent angina and myocardial infarction occurred more frequently in the highest NLR tertile compared with middle and lowest NLR tertiles. High NLR group (NLR≥ 3.88 n=38) was significantly associated with younger age and smoking status. WBC, troponin I and CRP levels increased as the NLR tertile increased. Recurrent myocardial infarction and angina showed strong relationship with increasing NLR values. In multivariate regression analyses smoking and high NLR levels were independent predictors of recurrent myocardial infarction (HR:4.64 95%CI 0.95-22.52 P=0.04, HR: 1.48 95%CI 1.16-1.90 P<0.01 respectively) in the long term follow up.

Conclusion: Our study demonstrated that high NLR values can be a valuable prognostic tool in the long term follow up of patients who presented with NSTE-ACS and diagnosed with slow flow phenomenon on coronary angiography.

Phenotypic and Molecular Characterization of Risk Loci Associated With Asthma and Lung Function

Purpose

Respiratory diseases have a highly multifactorial etiology where different mechanisms contribute to the individual's susceptibility. We conducted a deep characterization of loci associated with asthma and lung function by previous genome-wide association studies (GWAS).

Methods

Sixteen variants were selected from previous GWAS of childhood/adult asthma and pulmonary function tests. We conducted a phenome-wide association study of these loci in 4,083 traits assessed in the UK Biobank (n = 361,194 participants). Data from the Genotype-Tissue Expression (GTEx) project were used to conduct a transcriptomic analysis with respect to tissues relevant for asthma pathogenesis. A pediatric cohort assessed with the International Study of Asthma and Allergies in Children (ISAAC) Phase II tools was used to further explore the association of these variants with 116 traits related to asthma comorbidities.

Results

Our phenome-wide association studies (PheWAS) identified 206 phenotypic associations with respect to the 16 variants identified. In addition to the replication of the phenotypes tested in the discovery GWAS, we observed novel associations related to blood levels of immune cells (eosinophils, neutrophils, monocytes, and lymphocytes) for the asthma-related variants. Conversely, the lung-function variants were associated with phenotypes related to body fat mass. In the ISAAC-assessed cohort, we observed that risk alleles associated with increased fat mass can exacerbate allergic reactions in individuals affected by allergic respiratory diseases. The GTEx-based analysis showed that the variants tested affect the transcriptomic regulation of multiple surrounding genes across several tissues.

Conclusions

This study generated novel data regarding the genetics of respiratory diseases and their comorbidities, providing a deep characterization of loci associated with asthma and lung function.

Genotypic-phenotypic features and enzyme replacement therapy outcome in patients with mucopolysaccharidosis VI from Turkey

Mucopolysaccharidosis type VI (MPS VI) is a lysosomal storage disorder (LSD) characterized by a chronic, progressive course with multiorgan involvement. In our study, clinical, biochemical, molecular findings, and response to enzyme replacement therapy (ERT) for at least 6 months were evaluated in 20 patients with MPS VI. Treatment effects on clinical findings such as liver and spleen sizes, cardiac and respiratory parameters, visual and auditory changes, joints' range of motions, endurance tests and changes in urinary glycosaminoglycan excretions, before and after ERT were analyzed. ERT caused increased physical endurance and decreased urinary dermatan sulfate/chondroitin sulfate ratios. Changes in growth parameters, cardiac, respiratory, visual, auditory findings, and joint mobility were not significant. All patients and parents reported out an increased quality of life, which were not correlated with clinical results. The most prevalent mutation was p.L321P, accounting for 58.8% of the mutant alleles and two novel mutations (p.G79E and p.E390 K) were found. ERT was a safe but expensive treatment for MPS VI, with mild benefits in severely affected patients. Early treatment with ERT is mandatory before many organs and systems are involved.

Abstract 5406: Low-input transcript profiling with enhanced sensitivity using a highly efficient, low-bias and strand-specific RNA-Seq library preparation method

RNA-seq has become the most popular method for transcriptome analysis and is widely used to study gene expression, detect mutations, fusion transcripts, alternative splicing, and post-transcriptional modifications. It is becoming the method of choice to detect alterations in diseases, especially cancer, to provide insights on the various molecular pathways perturbed by changes in the transcriptome and study their implications. As RNA-seq is being adopted in molecular diagnostics and biomarker identifications, the need for good quality, reproducible library preparation methods using very low amounts of RNA input, or precious clinical samples, is increasing. To address these challenges, we have developed a strand-specific RNA-seq library preparation method that retains information about which strand of DNA is transcribed, from as low as 5 ng total RNA input. Strand specificity is important for correct annotation of genes, identification of antisense transcripts with potential regulatory roles, and accurate determination of gene expression levels in the presence of antisense transcripts. Enhanced sensitivity to detect transcripts with even coverage across their length offers a non-biased approach for accurate quantification of transcript levels.

Methods: Enriched poly-A mRNA or ribo-depleted RNA (Universal Human Reference RNA) was used to make libraries with our strand specific library preparation method. Library quality and quantity were analyzed on an Agilent Bioanalyzer, pooled at equimolar ratio and sequenced on Illumina’s Nextseq 500. Paired end reads were mapped to a human reference genome (hg19) using Hisat2 and sequencing metrics were calculated using Picard's RNA-seq Metrics and RSeqC tools. Transcript abundance was measured using Salmon and the Ensembl GRCh38 CDS sequences.

Results: Libraries prepared with our streamlined method using inputs that range from 5ng to 1ug show greater than 98% directionality at all input levels. GC content analysis, gene body coverage and gene expression correlation are similar for all inputs tested (5ng to 1ug), even though input amounts vary by over three orders of magnitude. These consistent results are recapitulated with the spiked-in ERCC controls at all inputs.

Conclusions: Our library preparation method is streamlined and can be used for a wide range of input RNA without any major modifications to the protocol, making it an easy to follow, convenient method for RNA-seq library preparation. In addition, our method has increased sensitivity and specificity, especially for low-abundance transcripts, reduced PCR duplicates and sequence bias, delivering high quality strand-specific data even for low input RNA. Finally, our method is compatible with both poly A-tail enriched and ribosomal RNA depleted samples, and is amenable to large-scale library construction and automation.

Citation Format: Keerthana Krishnan, Erbay Yigit, Mehmet Karaca, Deyra Rodriguez, Bradley Langhorst, Timur Shtatland, Daniela Munafo, Pingfang Liu, Lynne Apone, Vaishnavi Panchapakesa, Karen Duggan, Christine Sumner, Christine Rozzi, Fiona Stewart, Laurie Mazzola, Joanna Bybee, Danielle Rivizzigno, Eileen T. Dimalanta, Theodore B. Davis. Low-input transcript profiling with enhanced sensitivity using a highly efficient, low-bias and strand-specific RNA-Seq library preparation method [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5406. doi:10.1158/1538-7445.AM2017-5406