A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

10.3791/61633 ◽  
2021 ◽  
Author(s):  
Aide Macias-Muñoz ◽  
Ali Mortazavi
Keyword(s):  
Gene Expression ◽  
Molecular Evolution ◽  
Rna Seq ◽  
Bioinformatics Pipeline

scholarly journals Transcriptomics of Type 2 Diabetic and Healthy Human Neutrophils

2019 ◽  
Author(s):  
Sarah E. Kleinstein ◽  
Jamison McCorrison ◽  
Alaa Ahmed ◽  
Hatice Hasturk ◽  
Thomas E. Van Dyke ◽  
...  
Keyword(s):  
Gene Expression ◽  
Inflammatory Diseases ◽  
Differentially Expressed ◽  
Human Neutrophils ◽  
Rna Seq ◽  
Bioinformatics Pipeline ◽  
Healthy Human ◽  
Significant Differential Expression ◽  
The Impact

ABSTRACTObjectivesChronic inflammatory diseases, including diabetes and cardiovascular disease, are heterogeneous and often co-morbid, with increasing global prevalence. Uncontrolled type 2 diabetes (T2D) can result in severe inflammatory complications. As neutrophils are essential to inflammation, we conducted RNA-seq transcriptomic analyses to investigate the association between neutrophil gene expression and T2D phenotype. Further, as specialized pro-resolving lipid mediators, including resolvin E1 (RvE1), can actively resolve inflammation, we further surveyed the impact of RvE1 on isolated neutrophils.MethodsCell isolation and RNA-seq analysis of neutrophils from N=11 T2D and N=7 healthy individuals with available clinical data was conducted. Additionally, cultured neutrophils (N=3 T2D, N=3 healthy) were perturbed with increasing RvE1 doses (0nM, 1nM, 10nM, or 100nM) prior to RNA-seq. Data was evaluated through a bioinformatics pipeline including pathway analysis and post hoc false-discovery rate (FDR)-correction.ResultsWe observed significant differential expression of 50 genes between T2D and healthy neutrophils (p<0.05), including decreased T2D gene expression in inflammatory- and lipid-related genes SLC9A4, NECTIN2 and PLPP3 (p<0.003). RvE1 treatment induced dose-dependent differential gene expression (uncorrected p<0.05) across groups, including 59 healthy and 216 T2D neutrophil genes. Comparing T2D to healthy neutrophils, 1097 genes were differentially expressed across RvE1 doses, including two significant genes, LILRB5 and AKR1C1, involved in inflammation (p<0.05).ConclusionsInflammatory- and lipid-related genes were differentially expressed between T2D and healthy neutrophils, and RvE1 dose-dependently modified gene expression in both groups. Unraveling the mechanisms regulating abnormalities in diabetic neutrophil responses could lead to better diagnostics and therapeutics targeting inflammation and inflammation resolution.

scholarly journals Transcriptomics of type 2 diabetic and healthy human neutrophils

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Sarah E. Kleinstein ◽  
Jamison McCorrison ◽  
Alaa Ahmed ◽  
Hatice Hasturk ◽  
Thomas E. Van Dyke ◽  
...  
Keyword(s):  
Gene Expression ◽  
Inflammatory Diseases ◽  
Differentially Expressed ◽  
Human Neutrophils ◽  
Rna Seq ◽  
Bioinformatics Pipeline ◽  
Healthy Human ◽  
Significant Differential Expression ◽  
The Impact

Abstract Objectives Chronic inflammatory diseases, including diabetes and cardiovascular disease, are heterogeneous and often co-morbid, with increasing global prevalence. Uncontrolled type 2 diabetes (T2D) can result in severe inflammatory complications. As neutrophils are essential to normal and aberrant inflammation, we conducted RNA-seq transcriptomic analyses to investigate the association between neutrophil gene expression and T2D phenotype. As specialized pro-resolving lipid mediators (SPM) act to resolve inflammation, we further surveyed the impact of neutrophil receptor binding SPM resolvin E1 (RvE1) on isolated diabetic and healthy neutrophils. Methods Cell isolation and RNA-seq analysis of neutrophils from N = 11 T2D and N = 7 healthy individuals with available clinical data was conducted. Additionally, cultured neutrophils (N = 3 T2D, N = 3 healthy) were perturbed with increasing RvE1 doses (0 nM, 1 nM, 10 nM, or 100 nM) prior to RNA-seq. Data was evaluated through a bioinformatics pipeline including pathway analysis and post hoc false discovery rate (FDR)-correction. Results We observed significant differential expression of 50 genes between T2D and healthy neutrophils (p < 0.05), including decreased T2D gene expression in inflammatory- and lipid-related genes SLC9A4, NECTIN2, and PLPP3 (p < 0.003). RvE1 treatment induced dose-dependent differential gene expression (uncorrected p < 0.05) across groups, including 59 healthy and 216 T2D neutrophil genes. Comparing T2D to healthy neutrophils, 1097 genes were differentially expressed across RvE1 doses, including two significant genes, LILRB5 and AKR1C1, involved in inflammation (p < 0.05). Conclusions The neutrophil transcriptomic database revealed novel chronic inflammatory- and lipid-related genes that were differentially expressed between T2D cells when compared to controls, and cells responded to RvE1 dose-dependently by gene expression changes. Unraveling the mechanisms regulating abnormalities in diabetic neutrophil responses could lead to better diagnostics and therapeutics targeting inflammation and inflammation resolution.

scholarly journals A benchmark of gene expression tissue-specificity metrics

2015 ◽  
Author(s):  
Nadezda Kryuchkova ◽  
Marc Robinson-Rechavi
Keyword(s):  
Gene Expression ◽  
Molecular Evolution ◽  
Expression Pattern ◽  
Tissue Specificity ◽  
Evolutionary Rate ◽  
Evolutionary Conservation ◽  
Rna Seq ◽  
Functional Feature ◽  
Tissue Specific

One of the major properties of genes is their expression pattern. Notably, genes are often classified as tissue-specific or housekeeping. This property is of interest to molecular evolution as an explanatory factor of, e.g., evolutionary rate, as well as a functional feature which may in itself evolve. While many different methods of measuring tissue specificity have been proposed and used for such studies, there has been no comparison or benchmarking of these methods to our knowledge, and little justification of their use. In this study we compare nine measures of tissue-specificity. Most methods were established for ESTs and microarrays, and several were later adapted to RNA-seq. We analyze their capacity to distinguish gene categories, their robustness to the choice and number of tissues used, and their capture of evolutionary conservation signal.

scholarly journals Transcriptomics of Type 2 Diabetic and Healthy Human Neutrophils

2020 ◽  
Author(s):  
Sarah E Kleinstein ◽  
Jamison McCorrison ◽  
Alaa Ahmed ◽  
Hatice Hasturk ◽  
Thomas E. Van Dyke ◽  
...  
Keyword(s):  
Gene Expression ◽  
Inflammatory Diseases ◽  
Differentially Expressed ◽  
Human Neutrophils ◽  
Rna Seq ◽  
Bioinformatics Pipeline ◽  
Healthy Human ◽  
Significant Differential Expression ◽  
The Impact

Abstract Objectives: Chronic inflammatory diseases, including diabetes and cardiovascular disease, are heterogeneous and often co-morbid, with increasing global prevalence. Uncontrolled type 2 diabetes (T2D) can result in severe inflammatory complications. As neutrophils are essential to inflammation, we conducted RNA-seq transcriptomic analyses to investigate the association between neutrophil gene expression and T2D phenotype. Further, as specialized pro-resolving lipid mediators, including resolvin E1 (RvE1), can actively resolve inflammation, we further surveyed the impact of RvE1 on isolated neutrophils.Methods: Cell isolation and RNA-seq analysis of neutrophils from N=11 T2D and N=7 healthy individuals with available clinical data was conducted. Additionally, cultured neutrophils (N=3 T2D, N=3 healthy) were perturbed with increasing RvE1 doses (0nM, 1nM, 10nM, or 100nM) prior to RNA-seq. Data was evaluated through a bioinformatics pipeline including pathway analysis and post hoc false-discovery rate (FDR)-correction. Results: We observed significant differential expression of 50 genes between T2D and healthy neutrophils (p<0.05), including decreased T2D gene expression in inflammatory- and lipid-related genes SLC9A4, NECTIN2 and PLPP3 (p<0.003). RvE1 treatment induced dose-dependent differential gene expression (uncorrected p<0.05) across groups, including 59 healthy and 216 T2D neutrophil genes. Comparing T2D to healthy neutrophils, 1097 genes were differentially expressed across RvE1 doses, including two significant genes, LILRB5 and AKR1C1, involved in inflammation (p<0.05). Conclusions: Inflammatory- and lipid-related genes were differentially expressed between T2D and healthy neutrophils, and RvE1 dose-dependently modified gene expression in both groups. Unraveling the mechanisms regulating abnormalities in diabetic neutrophil responses could lead to better diagnostics and therapeutics targeting inflammation and inflammation resolution.

scholarly journals Transcriptomics of Type 2 Diabetic and Healthy Human Neutrophils

2020 ◽  
Author(s):  
Sarah E Kleinstein ◽  
Jamison McCorrison ◽  
Alaa Ahmed ◽  
Hatice Hasturk ◽  
Thomas E. Van Dyke ◽  
...  
Keyword(s):  
Gene Expression ◽  
Inflammatory Diseases ◽  
Differentially Expressed ◽  
Human Neutrophils ◽  
Rna Seq ◽  
Bioinformatics Pipeline ◽  
Healthy Human ◽  
Significant Differential Expression ◽  
The Impact

Abstract Objectives: Chronic inflammatory diseases, including diabetes and cardiovascular disease, are heterogeneous and often co-morbid, with increasing global prevalence. Uncontrolled type 2 diabetes (T2D) can result in severe inflammatory complications. As neutrophils are essential to inflammation, we conducted RNA-seq transcriptomic analyses to investigate the association between neutrophil gene expression and T2D phenotype. Further, as specialized pro-resolving lipid mediators, including resolvin E1 (RvE1), can actively resolve inflammation, we further surveyed the impact of RvE1 on isolated neutrophils. Methods: Cell isolation and RNA-seq analysis of neutrophils from N=11 T2D and N=7 healthy individuals with available clinical data was conducted. Additionally, cultured neutrophils (N=3 T2D, N=3 healthy) were perturbed with increasing RvE1 doses (0nM, 1nM, 10nM, or 100nM) prior to RNA-seq. Data was evaluated through a bioinformatics pipeline including pathway analysis and post hoc false-discovery rate (FDR)-correction. Results: We observed significant differential expression of 50 genes between T2D and healthy neutrophils (p<0.05), including decreased T2D gene expression in inflammatory- and lipid-related genes SLC9A4, NECTIN2 and PLPP3 (p<0.003). RvE1 treatment induced dose-dependent differential gene expression (uncorrected p<0.05) across groups, including 59 healthy and 216 T2D neutrophil genes. Comparing T2D to healthy neutrophils, 1097 genes were differentially expressed across RvE1 doses, including two significant genes, LILRB5 and AKR1C1 , involved in inflammation (p<0.05). Conclusions: Inflammatory- and lipid-related genes were differentially expressed between T2D and healthy neutrophils, and RvE1 dose-dependently modified gene expression in both groups. Unraveling the mechanisms regulating abnormalities in diabetic neutrophil responses could lead to better diagnostics and therapeutics targeting inflammation and inflammation resolution.

scholarly journals Rewired Pathways and Disrupted Pathway Crosstalk in Schizophrenia Transcriptomes by Multiple Differential Coexpression Methods

Genes ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 665
Author(s):  
Hui Yu ◽  
Yan Guo ◽  
Jingchun Chen ◽  
Xiangning Chen ◽  
Peilin Jia ◽  
...  
Keyword(s):  
Gene Expression ◽  
Focal Adhesion ◽  
Biological Pathways ◽  
Postmortem Brain ◽  
Rna Seq ◽  
Hub Genes ◽  
Differential Coexpression ◽  
Pathway Crosstalk ◽  
Microarray Datasets ◽  
Transcriptomic Studies

Transcriptomic studies of mental disorders using the human brain tissues have been limited, and gene expression signatures in schizophrenia (SCZ) remain elusive. In this study, we applied three differential co-expression methods to analyze five transcriptomic datasets (three RNA-Seq and two microarray datasets) derived from SCZ and matched normal postmortem brain samples. We aimed to uncover biological pathways where internal correlation structure was rewired or inter-coordination was disrupted in SCZ. In total, we identified 60 rewired pathways, many of which were related to neurotransmitter, synapse, immune, and cell adhesion. We found the hub genes, which were on the center of rewired pathways, were highly mutually consistent among the five datasets. The combinatory list of 92 hub genes was generally multi-functional, suggesting their complex and dynamic roles in SCZ pathophysiology. In our constructed pathway crosstalk network, we found “Clostridium neurotoxicity” and “signaling events mediated by focal adhesion kinase” had the highest interactions. We further identified disconnected gene links underlying the disrupted pathway crosstalk. Among them, four gene pairs (PAK1:SYT1, PAK1:RFC5, DCTN1:STX1A, and GRIA1:MAP2K4) were normally correlated in universal contexts. In summary, we systematically identified rewired pathways, disrupted pathway crosstalk circuits, and critical genes and gene links in schizophrenia transcriptomes.

scholarly journals Mitochondrial Mistranslation in Brain Provokes a Metabolic Response Which Mitigates the Age-Associated Decline in Mitochondrial Gene Expression

2021 ◽  
Vol 22 (5) ◽  
pp. 2746
Author(s):  
Dimitri Shcherbakov ◽  
Reda Juskeviciene ◽  
Adrián Cortés Sanchón ◽  
Margarita Brilkova ◽  
Hubert Rehrauer ◽  
...  
Keyword(s):  
Gene Expression ◽  
Metabolic Response ◽  
Mitochondrial Gene ◽  
Tca Cycle ◽  
Brain Mitochondria ◽  
Mitochondrial Gene Expression ◽  
Rna Seq ◽  
The Tca Cycle ◽  
Neurological Phenotype

Mitochondrial misreading, conferred by mutation V338Y in mitoribosomal protein Mrps5, in-vivo is associated with a subtle neurological phenotype. Brain mitochondria of homozygous knock-in mutant Mrps5V338Y/V338Y mice show decreased oxygen consumption and reduced ATP levels. Using a combination of unbiased RNA-Seq with untargeted metabolomics, we here demonstrate a concerted response, which alleviates the impaired functionality of OXPHOS complexes in Mrps5 mutant mice. This concerted response mitigates the age-associated decline in mitochondrial gene expression and compensates for impaired respiration by transcriptional upregulation of OXPHOS components together with anaplerotic replenishment of the TCA cycle (pyruvate, 2-ketoglutarate).

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