scholarly journals Gene expression analysis characterizes antemortem stress and has implications for establishing cause of death

2011 ◽  
Vol 43 (16) ◽  
pp. 974-980 ◽  
Author(s):  
David Jardine ◽  
Leanne Cornel ◽  
Mary Emond
Keyword(s):  
Gene Expression ◽  
Cause Of Death ◽  
Expression Analysis ◽  
Liver Tissue ◽  
Gene Expression Analysis ◽  
Expression Patterns ◽  
Gene Expression Patterns ◽  
Sudden Infant ◽  
K Nearest Neighbor ◽  
Diagnostic Laboratory

Within the field of forensic pathology, determination of the cause of death depends upon identifying physical changes in the corpse or finding diagnostic laboratory abnormalities. When such perturbations are absent, definitive assignment of a cause of death may be difficult or impossible. An example of such a problem is sudden infant death syndrome (SIDS), a common cause of neonatal mortality that does not produce physical findings or laboratory abnormalities. Although respiratory failure as a cause of SIDS represents the most widely held hypothesis, sudden cardiac death and hyperthermia have also been advanced as possible causes. We hypothesize that each of these physiological stresses would produce a different pattern of premortem gene expression and that these patterns of gene expression would remain evident in tissues collected postmortem. If these patterns were sufficiently distinctive, they could be used to identify the cause of death. Using an infant mouse model, we compared gene expression patterns in liver tissue after sudden death, lethal hyperthermia, and lethal hypoxia. Each of these conditions produced readily distinguishable differences in gene expression patterns. With the K-nearest neighbor classification algorithm, only 10 genes are necessary to correctly classify samples. If the liver tissue was not harvested immediately after death, additional alteration in gene expression patterns resulted; however, these alterations did not affect the group of genes used to classify the samples. Our findings suggest that gene expression analysis from tissues collected postmortem may provide useful clues about certain physiologic stresses that may precede death.

scholarly journals Gene expression tomography

2002 ◽  
Vol 8 (2) ◽  
pp. 159-167 ◽  
Author(s):  
VANESSA M. BROWN ◽  
ALEX OSSADTCHI ◽  
ARSHAD H. KHAN ◽  
SANJIV S. GAMBHIR ◽  
SIMON R. CHERRY ◽  
...  
Keyword(s):  
Gene Expression ◽  
Image Reconstruction ◽  
Expression Analysis ◽  
Gene Expression Analysis ◽  
Expression Patterns ◽  
Brain Slices ◽  
Axial Rotation ◽  
Gene Expression Patterns ◽  
Rnase Protection ◽  
The Brain

Gene expression tomography, or GET, is a new method to increase the speed of three-dimensional (3-D) gene expression analysis in the brain. The name is evocative of the method’s dual foundations in high-throughput gene expression analysis and computerized tomographic image reconstruction, familiar from techniques such as positron emission tomography (PET) and X-ray computerized tomography (CT). In GET, brain slices are taken using a cryostat in conjunction with axial rotation about independent axes to create a series of “views” of the brain. Gene expression information obtained from the axially rotated views can then be used to recreate 3-D gene expression patterns. GET was used to successfully reconstruct images of tyrosine hydroxylase gene expression in the mouse brain, using both RNase protection and real-time quantitative reverse transcription PCR (QRT-PCR). A Monte-Carlo analysis confirmed the good quality of the GET image reconstruction. By speeding acquisition of gene expression patterns, GET may help improve our understanding of the genomics of the brain in both health and disease.

scholarly journals Comparative uterine gene expression analysis after dioxin and estradiol administration

2004 ◽  
Vol 33 (3) ◽  
pp. 763-771 ◽  
Author(s):  
H Watanabe ◽  
A Suzuki ◽  
M Goto ◽  
S Ohsako ◽  
C Tohyama ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Analysis ◽  
Gene Expression Analysis ◽  
Estrogenic Activity ◽  
Expression Patterns ◽  
Environmental Pollutant ◽  
Abnormal Development ◽  
Gene Expression Patterns ◽  
Endocrine Effects ◽  
Antiestrogenic Activity

The environmental pollutant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) adversely affects many organisms. TCDD exposure is known to be associated with abnormal development, hepatotoxicity and endocrine effects. It has also been reported to have antiestrogenic activity in addition to estrogenic activity. In order to clarify the effects of TCDD in the uterus, we evaluated the patterns of gene expression after TCDD and estradiol administration. Of the 10 000 arrayed genes, only a few were affected by both estradiol and TCDD. Although the subset of genes that responded to estrogen was also activated by TCDD, the response to TCDD was more limited than that observed in response to estradiol. Therefore, according to our analysis of gene expression patterns, TCDD had partial and weak estrogenic activity in the uterus.

scholarly journals Evidence of the Complexity of Gene Expression Analysis in Fish Wild Populations

2017 ◽  
Vol 2017 ◽  
pp. 1-14 ◽  
Author(s):  
Mbaye Tine
Keyword(s):  
Gene Expression ◽  
Differential Expression ◽  
Expression Analysis ◽  
Gene Expression Analysis ◽  
Expression Patterns ◽  
Cell Volume Regulation ◽  
Mitogen Activated Protein Kinase ◽  
Wild Populations ◽  
Natural Habitats ◽  
Evolutionary Forces

The present work examines the induction of theband 3 anion transport protein,mitogen-activated protein kinase, andlactate dehydrogenase, respectively related to osmolyte transport, cell volume regulation, and energy production in the gills of two tilapia strains exposed to either freshwater or hypersaline water. Overall, genes showed similar expression patterns between strains. However, a wild population survey across a range of natural habitats and salinities did not reveal the expected patterns. Although significant, the correlations between gene expression and salinity were slightly ambiguous and did not show any link with phenotypic differences in life history traits previously reported between the same populations. The differential expression was also not associated with the population genetic structure inferred from neutral markers. The results suggest that the differential expression observed is not the result of evolutionary forces such as genetic drift or adaptation by natural selection. Instead, it can be speculated that genes responded to various abiotic and biotic stressors, including factors intrinsic to animals. This study provides clear evidence of the complexity of gene expression analysis in wild populations and shows that more attention needs to be paid when selecting candidates as potential biomarkers for monitoring adaptive responses to a specific environmental perturbation.

Comprehensive genomic analysis in metastatic pancreatic ductal adenocarcinoma (PDAC).

2016 ◽  
Vol 34 (4_suppl) ◽  
pp. 285-285
Author(s):  
Hui-Li Wong ◽  
Martin Jones ◽  
Peter Eirew ◽  
Joanna Karasinska ◽  
Kasmintan A Schrader ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Analysis ◽  
Gene Expression Analysis ◽  
De Novo ◽  
Expression Patterns ◽  
Genomic Analysis ◽  
Ductal Adenocarcinoma ◽  
Tumor Biopsy ◽  
Significant Difference ◽  
Gene Expression Signatures

285 Background: In the absence of defined tumor molecular subtypes and validated predictive markers, PDAC has been largely treated as a single disease. Recent studies of molecular subtyping in PDAC reveal a complex mutational landscape with data suggesting the presence of genomic and gene expression signatures that may have prognostic and therapeutic significance. These studies predominantly focused on resected PDAC and lack data on metastatic tumors. We aim to explore the clinical utility of whole genome sequencing (WGS) and transcriptome analysis from metastatic biopsy samples in patients (pts) with advanced PDAC. Methods: Pts with incurable advanced cancers undergo tumor biopsy for in-depth WGS and RNA sequencing (RNASeq) as part of an ongoing prospective study (NCT02155621). Comprehensive bioinformatics analysis is performed to identify somatic cancer aberrations, gene expression changes and cellular pathway abnormalities. Here we describe clinical and molecular data on the subset of pts with advanced PDAC. Results: Sixteen PDAC pts have been enrolled; median age 59 years, 8 males (50%), 10 with de novo metastases (63%). Full WGS and RNASeq were completed in 11 pts (1 failed biopsy, 4 had insufficient tumor). KRAS codon 12 and TP53 mutations were present in all but one pt. CDKN2A and SMAD4 were also frequently altered (7 and 4 pts respectively). Gene expression analysis for classical and basal subtypes similar to those recently described (PMID 26343385) identified 3 and 6 pts with classical and basal expression patterns respectively, and 2 pts with mixed expression. Overall survival (OS) was significantly worse for the basal subtype vs all others (median OS 7 vs. 13.9 months (ms), p = 0.017). When separated into 3 subtypes a significant difference was still noted (median OS 7 ms in basal, 19.2 ms in classical and 11.8 ms in mixed subtype, p = 0.032). Conclusions: WGS analysis demonstrated a similar mutation pattern to that described in resectable PDAC, with no novel actionable mutations identified. Gene expression analysis demonstrated the presence of distinct gene expression signatures significantly associated with outcome, despite small pt numbers. These results need to be validated prospectively in larger cohorts. Clinical trial information: NCT02155621.

scholarly journals Comparison of phenol-based and alternative RNA isolation methods for gene expression analyses

2010 ◽  
Vol 75 (8) ◽  
pp. 1053-1061 ◽  
Author(s):  
Ksenija Jakovljevic ◽  
Milena Spasic ◽  
Emina Malisic ◽  
Jelena Dobricic ◽  
Ana Krivokuca ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Analysis ◽  
Whole Blood ◽  
Gene Expression Analysis ◽  
Expression Patterns ◽  
Rna Extraction ◽  
Rna Isolation ◽  
Specific Gene ◽  
Isolation Methods ◽  
Gene Expression Analyses

The widespread use of gene expression analyses has been limited by the lack of a critical evaluation of the methods used to extract nucleic acids from human tissues. For evaluating gene expression patterns in whole blood or leukocytes, the method of RNA isolation needs to be considered as a critical variable in the design of the experiment. Quantitative real-time PCR (qPCR) is widely used for the quantification of gene expression in today?s clinical practice. Blood samples as a preferred RNA source for qPCR should be carefully handled and prepared to not inhibit gene expression analyses. The present study was designed to compare the frequently used guanidine thiocyanate-phenol-chloroformbased method (TRI Reagent?) with two alternative RNA isolation methods (6100 PrepStation and QIAamp?) from whole blood or leukocytes for the purpose of gene expression analysis in chronic myeloid leukemia (CML) patients. Based on the results of this study, for the best combination of yield and RNA extraction purity, taking into account the necessary amount of the clinical sample and performance time, the protocol using phenol-based TRI Reagent? for RNA extraction from leukocytes is suggested as the most suitable protocol for this specific gene expression analysis.

scholarly journals Gene Expression Analysis in Four Dogs With Canine Pemphigus Clinical Subtypes Reveals B Cell Signatures and Immune Activation Pathways Similar to Human Disease

2021 ◽  
Vol 8 ◽  
Author(s):  
Haya S. Raef ◽  
Cesar Piedra-Mora ◽  
Neil B. Wong ◽  
Diana Junyue Ma ◽  
Clement N. David ◽  
...  
Keyword(s):  
Gene Expression ◽  
B Cell ◽  
Expression Analysis ◽  
Clinical Characteristics ◽  
Gene Expression Analysis ◽  
Expression Patterns ◽  
Disease Prognosis ◽  
Examine Gene Expression ◽  
Perform Gene Expression ◽  
Activation Pathways

Pemphigus is a group of autoimmune-mediated mucocutaneous blistering diseases characterized by acantholysis. Pemphigus has also been recognized in dogs and shares similar clinical characteristics and variants with human pemphigus. While relationships between human and canine pemphigus have been reported, gene expression patterns across species have not been described in the literature. We sought to perform gene expression analysis of lesional skin tissue from four dogs with various forms of pemphigus to examine gene expression during spontaneous disease in dogs. We found increased T and B cell signatures in canine pemphigus lesions compared to controls, as well as significant upregulation of CCL3, CCL4, CXCL10, and CXCL8 (IL8), among other genes. Similar chemokine/cytokine expression patterns and immune infiltrates have been reported in humans, suggesting that these genes play a role in spontaneous disease. Direct comparison of our dataset to previously published human pemphigus datasets revealed five conserved differentially expressed genes: CD19, WIF1, CXCL10, CD86, and S100A12. Our data expands our understanding of pemphigus and facilitates identification of biomarkers for prediction of disease prognosis and treatment response, which may be useful for future veterinary and human clinical trials.

scholarly journals Genome-Wide Identification and Gene Expression Analysis of ABA Receptor Family Genes in Brassica juncea var. tumida

Genes ◽  
2019 ◽  
Vol 10 (6) ◽  
pp. 470 ◽  
Author(s):  
Cheng ◽  
Zhong ◽  
Cai ◽  
Su ◽  
Li
Keyword(s):  
Gene Expression ◽  
Brassica Juncea ◽  
Expression Analysis ◽  
Gene Expression Analysis ◽  
Expression Patterns ◽  
Plant Response ◽  
Specific Gene ◽  
Cis Elements ◽  
Physiological Processes ◽  
Aba Receptor

Abscisic acid (ABA) plays important roles in multiple physiological processes, such as plant response to stresses and plant development. The ABA receptors pyrabactin resistance (PYR)/ PYR1-like (PYL)/regulatory components of ABA receptor (RCAR) play a crucial role in ABA perception and signaling. However, little is known about the details regarding PYL family genes in Brassica juncea var. tumida. Here, 25 PYL family genes were identified in B. juncea var. tumida genome, including BjuPYL3, BjuPYL4s, BjuPYL5s, BjuPYL6s, BjuPYL7s, BjuPYL8s, BjuPYL10s, BjuPYL11s, and BjuPYL13. The results of phylogenic analysis and gene structure showed that the PYL family genes performed similar gene characteristics. By analyzing cis-elements in the promoters of those BjuPYLs, several hormone and stress related cis-elements were found. The results of gene expression analysis showed that the ABA receptor homologous genes were induced by abiotic and biotic stress. The tissue-specific gene expression patterns of BjuPYLs also suggested those genes might regulate the stem swelling during plant growth. These findings indicate that BjuPYLs are involved in plant response to stresses and organ development. This study provides valuable information for further functional investigations of PYL family genes in B. juncea var. tumida.

scholarly journals Microfluidic Leukocyte Isolation for Gene Expression Analysis in Critically Ill Hospitalized Patients

2008 ◽  
Vol 54 (5) ◽  
pp. 891-900 ◽  
Author(s):  
Aman Russom ◽  
Palaniappan Sethu ◽  
Daniel Irimia ◽  
Michael N Mindrinos ◽  
Steve E Calvano ◽  
...  
Keyword(s):  
Gene Expression ◽  
Critically Ill ◽  
Expression Analysis ◽  
Clinical Setting ◽  
Whole Blood ◽  
Gene Expression Analysis ◽  
Expression Patterns ◽  
Hospitalized Patients ◽  
Genome Wide ◽  
Genome Wide Expression

Abstract Background: Microarray technology is becoming a powerful tool for diagnostic, therapeutic, and prognostic applications. There is at present no consensus regarding the optimal technique to isolate nucleic acids from blood leukocyte populations for subsequent expression analyses. Current collection and processing techniques pose significant challenges in the clinical setting. Here, we report the clinical validation of a novel microfluidic leukocyte nucleic acid isolation technique for gene expression analysis from critically ill, hospitalized patients that can be readily used on small volumes of blood. Methods: We processed whole blood from hospitalized patients after burn injury and severe blunt trauma according to the microfluidic and standard macroscale leukocyte isolation protocol. Side-by-side comparison of RNA quantity, quality, and genome-wide expression patterns was used to clinically validate the microfluidic technique. Results: When the microfluidic protocol was used for processing, sufficient amounts of total RNA were obtained for genome-wide expression analysis from 0.5 mL whole blood. We found that the leukocyte expression patterns from samples processed using the 2 protocols were concordant, and there was less variability introduced as a result of harvesting method than there existed between individuals. Conclusions: The novel microfluidic approach achieves leukocyte isolation in <25 min, and the quality of nucleic acids and genome expression analysis is equivalent to or surpasses that obtained from macroscale approaches. Microfluidics can significantly improve the isolation of blood leukocytes for genomic analyses in the clinical setting.

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