scholarly journals Proteomics in Deaths by Drowning: Diagnostic Efficacy of Apolipoprotein A1 and α-1 Antitrypsin, Pilot Study

Diagnostics ◽  
2020 ◽  
Vol 10 (10) ◽  
pp. 747
Author(s):  
Diana Hernández-Romero ◽  
Encarnación Sánchez-Rodríguez ◽  
Eduardo Osuna ◽  
Agustín Sibón ◽  
Miriam Martínez-Villanueva ◽  
...  
Keyword(s):  
Roc Curves ◽  
Apolipoprotein A1 ◽  
Differentially Expressed ◽  
Correct Classification ◽  
Postmortem Diagnosis ◽  
Diagnostic Efficacy ◽  
Proteomic Approach ◽  
Validation Experiment ◽  
Diagnosis Criteria

Drowning is one of the leading causes of death worldwide. The pathophysiology of drowning is complex and, sometimes, interpretation of the circumstances of death in the autopsy becomes the main source of information in its diagnosis. New advances in medical research, such as proteomics, especially in forensic pathology, are still in the development. We proposed to investigate the application of Mass Spectrometry-based technologies, to identify differentially expressed proteins that may act as potential biomarkers in the postmortem diagnosis of drowning. We performed a pilot proteomic experiment with the inclusion of two drowned and two control forensic cases. After applying restrictive parameters, we identified apolipoprotein A1 (ApoA1) and α-1 antitrypsin as differentially expressed between the two diagnostic groups. A validation experiment, with the determination of both proteins in 25 forensic cases (16 drowned and 9 controls) was performed, and we corroborated ApoA1 higher values in the drowning group, whereas α-1 antitrypsin showed lower levels. After adjusting by confounder factors, both remained as predictive independent factors for diagnosis of drowning (p = 0.010 and p = 0.022, respectively). We constructed ROC curves for biomarkers’ levels attending at the origin of death and established an ApoA1 cut-off point of 100 mg/dL. Correct classification based on the diagnosis criteria was reached for 73.9% of the cases in a discriminant analysis. We propose apolipoprotein A1 (with our cutoff value for correct classification) and α-1 antitrypsin as valuable biomarkers of drowning. Our study, based on forensic cases, reveals our proteomic approach as a new complementary tool in the forensic diagnosis of drowning and, perhaps, in clinical future implications in drowned patients. However, this is a pilot approach, and future studies are necessary to consolidate our promising preliminary data.

scholarly journals Comprehensive Analysis of Hub Genes Associated With Competing Endogenous RNA Networks in Stroke Using Bioinformatics Analysis

2022 ◽  
Vol 12 ◽  
Author(s):  
Xiuqi Chen ◽  
Danhong Wu
Keyword(s):  
Expression Profiles ◽  
Area Under The Curve ◽  
Roc Curves ◽  
Diagnostic Value ◽  
Differentially Expressed ◽  
Competing Endogenous Rna ◽  
Diagnostic Efficacy ◽  
Go Analysis ◽  
Cerna Network ◽  
Neutrophil Degranulation

Background: Acute ischemic stroke (AIS) is the second leading cause of death and the third leading cause of disability worldwide. Long noncoding RNAs (lncRNAs) are promising biomarkers for the early diagnosis of AIS and closely participate in the mechanism of stroke onset. However, studies focusing on lncRNAs functioning as microRNA (miRNA) sponges to regulate the mRNA expression are rare and superficial.Methods: In this study, we systematically analyzed the expression profiles of lncRNA, mRNA (GSE58294), and miRNA (GSE110993) from the GEO database. Gene ontology (GO) analysis was performed to reveal the functions of differentially expressed genes (DEGs), and we used weighted gene co-expression network analysis (WGCNA) to investigate the relationships between clinical features and expression profiles and the co-expression of miRNA and lncRNA. Finally, we constructed a lncRNA–miRNA–mRNA competing endogenous RNA (ceRNA) network with selected DEGs using bioinformatics methods and obtained ROC curves to assess the diagnostic efficacy of differentially expressed lncRNAs (DElncRNAs) and differentially expressed mRNAs (DEmRNAs) in our network. The GSE22255 dataset was used to confirm the diagnostic value of candidate genes.Results: In total, 199 DElncRNAs, 2068 DEmRNAs, and 96 differentially expressed miRNAs were detected. The GO analysis revealed that DEmRNAs primarily participate in neutrophil activation, neutrophil degranulation, vacuolar transport, and lysosomal transport. WGCNA screened out 16 lncRNAs and 195 mRNAs from DEGs, and only eight DElncRNAs maintained an area under the curve higher than 0.9. By investigating the relationships between lncRNAs and mRNAs, a ceRNA network containing three lncRNAs, three miRNAs, and seven mRNAs was constructed. GSE22255 confirmed that RP1-193H18.2 is more advantageous for diagnosing stroke, whereas no mRNA showed realistic diagnostic efficacy.Conclusion: The ceRNA network may broaden our understanding of AIS pathology, and the candidate lncRNA from the ceRNA network is assumed to be a promising therapeutic target and diagnostic biomarker for AIS.

Identification of differentially expressed proteins in retinoblastoma tumors using mass spectrometry-based comparative proteomic approach

2017 ◽  
Vol 159 ◽  
pp. 77-91 ◽  
Author(s):  
Jasmine Naru ◽  
Ritu Aggarwal ◽  
Ashok Kumar Mohanty ◽  
Usha Singh ◽  
Deepak Bansal ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Differentially Expressed ◽  
Differentially Expressed Proteins ◽  
Proteomic Approach

scholarly journals Comprehensive Analysis of Differentially Expressed Long Noncoding RNA-mRNA in the Adenoma-Carcinoma Sequence of DNA Mismatch Repair Proficient Colon Cancer

2021 ◽  
Vol 2021 ◽  
pp. 1-15
Author(s):  
Wenkun Li ◽  
Qian Li ◽  
Jiang Ge ◽  
Yun Wang ◽  
Nanshan Li ◽  
...  
Keyword(s):  
Colon Cancer ◽  
Mismatch Repair ◽  
Noncoding Rna ◽  
Intraepithelial Neoplasia ◽  
Roc Curves ◽  
Differentially Expressed ◽  
Low Grade ◽  
Large Set ◽  
Network Analyses ◽  
Qrt Pcr

DNA proficient mismatch repair colon cancer (pMMR CC) is the most common subtype of sporadic CC. We aimed to investigate the role of long noncoding RNAs (lncRNAs) in pMMR CC carcinogenesis. In the present study, we conducted transcriptomic analysis of lncRNAs-mRNAs in five low-grade intraepithelial neoplasia (LGIN), five high-grade intraepithelial neoplasia (HGIN), four pMMR CC, and five normal control (NC) tissues. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment pathway, and coexpression network analyses were performed to elucidate the functions of lncRNAs and mRNAs as well as their interactions. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to validate five dysregulated lncRNAs in a large set of colon tissues. Receiver-operating characteristic (ROC) curves were employed to evaluate the performance of the candidate lncRNAs. A set of 5783 differentially expressed lncRNAs and 4483 differentially expressed mRNAs were detected among the LGIN, HGIN, pMMR CC, and NC samples. These differentially expressed lncRNAs and mRNAs were assigned to 275 significant GO terms and 179 significant KEGG enriched pathways. qRT-PCR confirmed that the expression of five selected lncRNAs (ENST00000521815, ENST00000603052, ENST00000609220, NR_026543, and ENST00000545920) were consistent with the microarray data. ROC analysis showed that four lncRNAs (ENST00000521815, ENST00000603052, ENST00000609220, and NR_026543) had larger area under the ROC curve (AUC) values compared to serum carcinoembryonic antigens, thereby distinguishing NC from pMMR CC. In conclusion, several lncRNAs play various roles in the adenoma-carcinoma sequence and may serve as potential biomarkers for the early diagnosis of pMMR CC.

scholarly journals Profiling of Differentially Expressed MicroRNAs in Saliva of Parkinson's Disease Patients

2021 ◽  
Vol 12 ◽  
Author(s):  
Yanyan Jiang ◽  
Jing Chen ◽  
Yunchuang Sun ◽  
Fan Li ◽  
Luhua Wei ◽  
...  
Keyword(s):  
Parkinson’S Disease ◽  
Parkinson's Disease ◽  
Microarray Analysis ◽  
Target Genes ◽  
Characteristic Curve ◽  
Differentially Expressed ◽  
Diagnostic Efficacy ◽  
Mirna Microarray ◽  
Candidate Mirnas ◽  
Diagnostic Potential

Objective: This study aims to identify differentially expressed salivary miRNAs and validate the diagnostic potential for idiopathic Parkinson's disease (PD). Also, the disease specificity of candidate miRNAs was evaluated between PD, multiple system atrophy (MSA), and essential tremor (ET).Methods: We collected salivary samples from 50 PD, 20 ET, and 20 MSA patients, as well as 30 healthy controls (HCs). In the discovery phase, salivary miRNA microarray analysis was performed. In-silico analysis was used to investigate the target genes of differentially expressed miRNAs and clustered pathways. In validation phase, RT-qPCR was performed with samples from 30 PD patients and 30 HCs. Subsequently, we investigated candidate miRNAs in all recruited subjects. Receiver operating characteristic curve and Spearman correlation analysis was performed to determine diagnostic usefulness.Results: We identified 43 miRNAs that were differentially expressed between 5 PD patients and 5 HCs by miRNA microarray analysis. Computational analysis revealed the target genes were clustered in the pathways associated with ubiquitin protein ligase activity. The result of RT-qPCR showed that the miR-29a-3p and miR-29c-3p were found to be significantly downregulated (p = 0.004, p = 0.027), whereas the miR-6756-5p was significantly upregulated in 30 PD patients compared with 30 HCs (p = 0.032). The miR-29a-3p expression level in PD patients was significantly lower than ET patients (p = 0.035), but higher than MSA patients (p < 0.0001). The diagnostic efficacy reached a little higher when the combination of miR-29a-3p and miR-29c-3p.Conclusion: The miRNA combination of salivary miR-29a-3p and miR-29c-3p has potential to be a diagnostic biomarker for idiopathic PD.

Determination of non-enzymatically glycated apolipoprotein A1

1989 ◽  
Vol 22 (4) ◽  
pp. 285-287 ◽  
Author(s):  
Patrick S. Caines ◽  
Roger J. Thibert ◽  
Thomas F. Draisey ◽  
Craig C. Foreback ◽  
Jau W. Chu
Keyword(s):  
Apolipoprotein A1

Proteomic analysis of the effects of lutein on mammary gland metabolism in dairy cows

2018 ◽  
Vol 85 (2) ◽  
pp. 152-156
Author(s):  
Caihong Wang ◽  
Chong Wang ◽  
Jianxin Liu ◽  
Hongyun Liu
Keyword(s):  
Blood Flow ◽  
Mammary Gland ◽  
Fatty Acid ◽  
Dairy Cows ◽  
Control Diet ◽  
Differentially Expressed ◽  
Acid Oxidation ◽  
Differentially Expressed Proteins ◽  
Proteomic Approach ◽  
Increased Blood Flow

The aim of the research reported in this Research Communication was to identify differentially expressed proteins in dairy cows with normal and lutein diet and to elucidate the mechanisms of lutein-induced effects on bovine mammary gland metabolism using a comparative proteomic approach. Thirty-three differentially expressed proteins were identified from mammary gland of control diet-fed and lutein diet-fed dairy cows. Among these proteins, 15 were upregulated and 18 were downregulated in the lutein group. Functional analysis of the differentially expressed proteins showed that increased blood flow, depressed glycolysis, enhanced lactose anabolism, decreased fatty acid oxidation and up-regulated beta lactoglobulin expression were connected with lutein addition. These results suggested that the increased blood flow, reduced glucose catabolism, enhanced capacity for milk lactose synthesis, depressed fatty acid catabolism and increased expression of antioxidantion related protein may be the prime factors contributing to the increased milk production and enhanced immune status in lutein-fed dairy cows. This study provides molecular mechanism of dietary lutein in regulating lactation of dairy cows.

Ultrasound grayscale ratio: a reliable parameter for differentiating papillary thyroid microcarcinoma from micronodular goiter

2020 ◽  
Author(s):  
Chenke Xu ◽  
Lifang Yu ◽  
Jianhua Fang ◽  
Zhijiang Han ◽  
Dingcun Luo ◽  
...  
Keyword(s):  
Operating Characteristic ◽  
Roc Curves ◽  
Mean Value ◽  
Papillary Thyroid ◽  
Diagnostic Efficacy ◽  
Receiver Operating Characteristic Curves ◽  
Thyroid Microcarcinoma ◽  
Reliable Parameter ◽  
The Mean ◽  
Reading System

Abstract Background: To evaluate the reliability and diagnostic efficacy of the ultrasound grayscale ratio (UGSR) for differentiating papillary thyroid microcarcinomas (PTMC) from micronodular goiters (diameter ≤ 1.0cm).Methods: The ultrasound data of 241 pathologically-confirmed cases of patients with 265 PTMC and 141 patients with 168 micronodular goiters were retrospectively reviewed. All patients underwent outpatient ultrasonic examination and preoperative ultrasonic positioning. The RADinfo radiograph reading system (Zhejiang RAD Information Technology Co., Ltd., China) was used to measure and calculated the UGSR of PTMC, micronodular goiters. Patients were divided into the outpatient examination, preoperative positioning, and mean value groups, and the receiver operating characteristic curves (ROC) were calculated to obtain the optimal UGSR threshold for distinguishing PTMC from micronodular goiters.Results: The UGSR values of the PTMC and micronodular goiters were 0.56±0.14 and 0.80±0.19 (t=5.84, P<0.01) in the outpatient examination group, 0.55±0.14 and 0.80±0.19 (t=18.74, P<0.01) in the preoperative positioning group, and 0.56±0.12 and 0.80±0.18 (t=16.49, P<0.01) in the mean value group. The areas under the ROC curves in the outpatient examination, preoperative positioning, and mean value groups were 0.860, 0.856, and 0.875, respectively. When the cut-off UGSR values for the outpatient examination, preoperative positioning, and mean value groups were 0.649, 0.646, and 0.657, the sensitivity and specificity for predicting PTMC were 78.9% and 86.9%, 79.2% and 83.9%, 82.6%, and 85.7%, respectively. A reliable UGSR value was obtained between the outpatient examination and preoperative positioning groups (ICC=0.79, P=0.68).Conclusion: The UGSR is an accurate and feasible tool for differentiating PTMC from micronodular goiters with better diagnostic efficacy.

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