The Genetic Evidence of Burn-Induced Cardiac Mitochondrial Metabolism Confusion

Burn-induced cardiac dysfunction is thought to involve mitochondrial dysfunction although the mechanisms responsible are unclear. In this study, we used our established model of in vivo burn injury to understand the genetic evidence of burn-induced mitochondrial metabolism confusion by describing cardiac mitochondrial metabolism-related gene expression after burn. Cardiac tissue was collected at 24 hours after burn injury. An O2K respirometer system was utilized to measure cardiac mitochondrial function. Oxidative phosphorylation complex activities were determined using enzyme activity assays. RT Profiler PCR array was used to identify differential regulation of genes involved in mitochondrial biogenesis and metabolism. Quantitative qPCR and Western Blotting were applied to validate differentially expressed genes. Burn-induced cardiac mitochondrial dysfunction was supported by the finding of decreased state 3 respiration and decreased mitochondrial electron transport chain activity in complex I, III, IV, and V following burn injury. Eighty-four mitochondrial metabolism-related gene profiles were measured. The mitochondrial gene profile showed that one third of genes related to mitochondrial energy and metabolism was differentially expressed. Of these 28 genes, 15 were more than 2-fold upregulated and 13 were more than 2-fold downregulated. All genes were validated using qPCR; 4 genes had a protein level which correlated with the observed change in gene expression. This study provides preliminary evidence that a large percentage of mitochondrial metabolism-related genes in cardiomyocytes were significantly affected by burn injury.

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The Genetic Evidence of Burn-Induced Cardiac Mitochondrial Metabolism Dysfunction

Biomedicines ◽

10.3390/biomedicines8120566 ◽

2020 ◽

Vol 8 (12) ◽

pp. 566

Author(s):

Jake J. Wen ◽

Claire B. Cummins ◽

Taylor P. Williams ◽

Ravi S. Radhakrishnan

Keyword(s):

Gene Expression ◽

Mitochondrial Dysfunction ◽

Burn Injury ◽

Mitochondrial Gene ◽

Preliminary Evidence ◽

Mitochondrial Metabolism ◽

Genetic Evidence ◽

Differentially Expressed ◽

Related Gene

Burn-induced cardiac dysfunction is thought to involve mitochondrial dysfunction, although the mechanisms responsible are unclear. In this study, we used our established model of in vivo burn injury to understand the genetic evidence of burn-induced mitochondrial confusion dysfunction by describing cardiac mitochondrial metabolism-related gene expression after burn. Cardiac tissue was collected at 24 hours after burn injury. An O2K respirometer system was utilized to measure the cardiac mitochondrial function. Oxidative phosphorylation complex activities were determined using enzyme activity assays. RT Profiler PCR array was used to identify the differential regulation of genes involved in mitochondrial biogenesis and metabolism. The quantitative qPCR and Western blotting were applied to validate the differentially expressed genes. Burn-induced cardiac mitochondrial dysfunction was supported by the finding of decreased state 3 respiration, decreased mitochondrial electron transport chain activity in complex I, III, IV, and V, and decreased mitochondrial DNA-encoded gene expression as well as decreased levels of the corresponding proteins after burn injury. Eighty-four mitochondrial metabolism-related gene profiles were measured. The mitochondrial gene profile showed that 29 genes related to mitochondrial energy and metabolism was differentially expressed. Of these 29 genes, 16 were more than 2-fold upregulated and 13 were more than 2-fold downregulated. All genes were validated using qPCR and partial genes were correlated with their protein levels. This study provides preliminary evidence that a large percentage of mitochondrial metabolism-related genes in cardiomyocytes were significantly affected by burn injury.

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41 Changes of Mitochondria-related Gene Expression Profile Associated with Burn-induced Cardiomyopathy

Journal of Burn Care & Research ◽

10.1093/jbcr/iraa024.045 ◽

2020 ◽

Vol 41 (Supplement_1) ◽

pp. S27-S28

Author(s):

Jake J Wen ◽

Ravi S Radhakrishnan

Keyword(s):

Mitochondrial Function ◽

Burn Injury ◽

Mitochondrial Gene ◽

Molecular Genetic ◽

Total Body Surface Area ◽

Preliminary Evidence ◽

Related Gene ◽

Complex Activity ◽

Heart Dysfunction ◽

Ann Arbor

Abstract Introduction Burn-related cardiac mitochondria dysfunction (BRMD) is associated with negative health outcomes and decreased health-related quality of life; however, few studies of the molecular-genetic mechanisms of BRMD exist. Methods 60% of total body surface area (TBSA) burned rats was employed. O2K Respirometer system (Innsbruck, Austria) was utilized to measure cardiac mitochondrial function. OXPHOS complex activities were determined by using OXPHOS enzyme complex activity assays (Cayman Chemical, Ann Arbor, Michigan). The Rat Mitochondria RT2 Profiler PCR Array was used to identify differential regulation of genes involved in mitochondrial biogenesis and metabolism function. Results Burn injury induced cardiac mit dysfunction by decreasingOXPHOS oxygen consumption at State 3 energized by malate/pyruvate and succinate and declining mit ETC activity in complex I, III, IV and V. 84 rat mit-related gene profiles were measured. The mitochondrial gene profile showed that 30/84 genes related to mitochondrial function and structure were differentially expressed. Of these 30 genes, 17 (ATP12a, ATP4a, ATP6v0a2, ATP6v1e2, ATP6v1g3, COX8c, LHPP, NDUFA5, SLC25a10, SLC25a15, UCP1, UCP2, UCP3, UQCRFS1, LDHA and RGDC) were more than 2 fold up-regulated, and 13 (ATP5c1, ATP5i, ATP5L, COX17, COX6c, COX7a2, NDUFA8, NDUFB3, NDUFB7, NDUFB9, NDUFS4, NDUFS8, and UQCRB) were greater than 2-fold down-regulated. Furthermore, 8 genes (AIFM2, BCL2, FIS1, IMMP2L, MSTO1, SLC25A23, SLC25A37, SLC25A4) that had significant differentially expression were associated with heart dysfunction. Conclusions This study provides preliminary evidence that 30 mitochondrial function genes were significantly associated with burn-induced heart dysfunction in 24 hpb rats. Applicability of Research to Practice These findings elucidate possible pathways and early biomarkers for targeting novel interventions for burn-induced heart dysfunction.

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

International Journal of Molecular Sciences ◽

10.3390/ijms22052746 ◽

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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CircFAM13B promotes the proliferation of hepatocellular carcinoma by sponging miR-212, upregulating E2F5 expression and activating the P53 pathway

Cancer Cell International ◽

10.1186/s12935-021-02120-6 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Ying Xie ◽

Xiaofeng Hang ◽

Wensheng Xu ◽

Jing Gu ◽

Yuanjing Zhang ◽

...

Keyword(s):

Gene Expression ◽

Hepatocellular Carcinoma ◽

Gene Expression Omnibus ◽

Differentially Expressed ◽

In Vivo Studies ◽

Circular Rnas ◽

Novel Target ◽

Underlying Mechanisms

Abstract Background Most of the biological functions of circular RNAs (circRNAs) and the potential underlying mechanisms in hepatocellular carcinoma (HCC) have not yet been discovered. Methods In this study, using circRNA expression data from HCC tumor tissues and adjacent tissues from the Gene Expression Omnibus database, we identified out differentially expressed circRNAs and verified them by qRT-PCT. Functional experiments were performed to evaluate the effects of circFAM13B in HCC in vitro and in vivo. Results We found that circFAM13B was the most significantly differentially expressed circRNA in HCC tissue. Subsequently, in vitro and in vivo studies also demonstrated that circFAM13B promoted the proliferation of HCC. Further studies revealed that circFAM13B, a sponge of miR-212, is involved in the regulation of E2F5 gene expression by competitively binding to miR-212, inhibits the activation of the P53 signalling pathway, and promotes the proliferation of HCC cells. Conclusions Our findings revealed the mechanism underlying the regulatory role played by circFAM13B, miR-212 and E2F5 in HCC. This study provides a new theoretical basis and novel target for the clinical prevention and treatment of HCC.

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Microtubule Dynamics Plays a Vital Role in Plant Adaptation and Tolerance to Salt Stress

International Journal of Molecular Sciences ◽

10.3390/ijms22115957 ◽

2021 ◽

Vol 22 (11) ◽

pp. 5957

Author(s):

Hyun Jin Chun ◽

Dongwon Baek ◽

Byung Jun Jin ◽

Hyun Min Cho ◽

Mi Suk Park ◽

...

Keyword(s):

Gene Expression ◽

Cell Wall ◽

Salt Stress ◽

Differentially Expressed ◽

Differentially Expressed Proteins ◽

Related Gene ◽

Plant Adaptation ◽

Salt Stress Response ◽

Network Analyses ◽

Cell Wall Biogenesis

Although recent studies suggest that the plant cytoskeleton is associated with plant stress responses, such as salt, cold, and drought, the molecular mechanism underlying microtubule function in plant salt stress response remains unclear. We performed a comparative proteomic analysis between control suspension-cultured cells (A0) and salt-adapted cells (A120) established from Arabidopsis root callus to investigate plant adaptation mechanisms to long-term salt stress. We identified 50 differentially expressed proteins (45 up- and 5 down-regulated proteins) in A120 cells compared with A0 cells. Gene ontology enrichment and protein network analyses indicated that differentially expressed proteins in A120 cells were strongly associated with cell structure-associated clusters, including cytoskeleton and cell wall biogenesis. Gene expression analysis revealed that expressions of cytoskeleton-related genes, such as FBA8, TUB3, TUB4, TUB7, TUB9, and ACT7, and a cell wall biogenesis-related gene, CCoAOMT1, were induced in salt-adapted A120 cells. Moreover, the loss-of-function mutant of Arabidopsis TUB9 gene, tub9, showed a hypersensitive phenotype to salt stress. Consistent overexpression of Arabidopsis TUB9 gene in rice transgenic plants enhanced tolerance to salt stress. Our results suggest that microtubules play crucial roles in plant adaptation and tolerance to salt stress. The modulation of microtubule-related gene expression can be an effective strategy for developing salt-tolerant crops.

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Abstract 286: Long Noncoding RNAs Are Differentially Expressed in Heart Failure

Circulation Research ◽

10.1161/res.111.suppl_1.a286 ◽

2012 ◽

Vol 111 (suppl_1) ◽

Author(s):

Emma L Robinson ◽

Syed Haider ◽

Hillary Hei ◽

Richard T Lee ◽

Roger S Foo

Keyword(s):

Gene Expression ◽

Heart Failure ◽

Significant Proportion ◽

Differentially Expressed ◽

Rna Seq ◽

Control Of Gene Expression ◽

Failing Heart ◽

Novel Transcripts ◽

Non Coding Rnas

Heart failure comprises of clinically distinct inciting causes but a consistent pattern of change in myocardial gene expression supports the hypothesis that unifying biochemical mechanisms underlie disease progression. The recent RNA-seq revolution has enabled whole transcriptome profiling, using deep-sequencing technologies. Up to 70% of the genome is now known to be transcribed into RNA, a significant proportion of which is long non-coding RNAs (lncRNAs), defined as polyribonucleotides of ≥200 nucleotides. This project aims to discover whether the myocardium expression of lncRNAs changes in the failing heart. Paired end RNA-seq from a 300-400bp library of ‘stretched’ mouse myocyte total RNA was carried out to generate 76-mer sequence reads. Mechanically stretching myocytes with equibiaxial stretch apparatus mimics pathological hypertrophy in the heart. Transcripts were assembled and aligned to reference genome mm9 (UCSC), abundance determined and differential expression of novel transcripts and alternative splice variants were compared with that of control (non-stretched) mouse myocytes. Five novel transcripts have been identified in our RNA-seq that are differentially expressed in stretched myocytes compared with non-stretched. These are regions of the genome that are currently unannotated and potentially are transcribed into non-coding RNAs. Roles of known lncRNAs include control of gene expression, either by direct interaction with complementary regions of the genome or association with chromatin remodelling complexes which act on the epigenome.Changes in expression of genes which contribute to the deterioration of the failing heart could be due to the actions of these novel lncRNAs, immediately suggesting a target for new pharmaceuticals. Changes in the expression of these novel transcripts will be validated in a larger sample size of stretched myocytes vs non-stretched myocytes as well as in the hearts of transverse aortic constriction (TAC) mice vs Sham (surgical procedure without the aortic banding). In vivo investigations will then be carried out, using siLNA antisense technology to silence novel lncRNAs in mice.

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Abstract 12567: Circulating Factors Induce Cardiomyopathy After Burn Injury

Circulation ◽

10.1161/circ.142.suppl_3.12567 ◽

2020 ◽

Vol 142 (Suppl_3) ◽

Author(s):

Jake J Wen ◽

◽

Keyword(s):

Mitochondrial Dysfunction ◽

Burn Injury ◽

Membrane Integrity ◽

Bioactive Molecules ◽

Cgmp Level ◽

Heart Dysfunction ◽

Atp Production ◽

Human Cardiomyocytes ◽

Upregulated Genes

Introduction: Our previous results in vivo indicated PDE5-cGMP-PKG was involved in burn-induced heart dysfunction and PDE5A inhibitor restored the dysfunction. It’s unknown if circulating factors after burn would injure cardiomyocytes. Hypothesis: Circulating factors released after burn induce cardiomyopathy. Methods: Human cardiomyocytes (AC16) were treated with sham-serum, burn-serum (24 hpb-serum) and burn/sildenafil-serum (24 hpb/SIL). We performed cut-edged biochemistry technologies and Illumina RNA sequencing (RNA-seq) in this study. GraphPad Prism 8.4.2 was used for statistics. Results: We found a significant decrease of cGMP level and an increase of cTN1 in 24 hpb-serum group. Treatment with the PDE5A inhibitor Sildenafil completely reversed this change similar to our in vivo work. To understand what bioactive molecules would be involved in the alterations by burn injury, human cardiomyocytes (Ac16) were employed to test the cardiomyocyte response to burn-induced circulating factors. We observed that 24 hpb-serum significantly 1) decreased cell viability and cell proliferation; as well as 2) increased cell cytotoxicity, cell apoptosis and cell ROS production. We also found 24 hpb-serum resulted in cell mitochondrial dysfunction by decreasing ATP production and mitochondrial membrane integrity/potential and increasing mitochondrial ROS. Seahorse and O2K approaches confirmed 24 hpb-serum-induced cardiomyocyte mitochondrial dysfunction as evidenced by decreases of mitochondrial basal respiration, proton leak, ATP production, and maximal respiration. 24 hpb/SIL serum rescued 24 hpb serum-induced Ac 16 cell response, at least partially. Advanced bioinformatic analyses identified 1415 upregulated genes and 1091 downregulated genes in 24 hpb-serum group and 776 upregulated genes and 113 downregulated genes restored in 24 hpb/SIL-serum group. We also analyzed and validated the differentially expressed genes. Conclusions: Our study not only confirmed burn induced heart dysfunction, but also provided evidence for understanding the pathogenic mechanism of circulating factors released after burn injury and preliminary genomic evidence for the mechanism for cardiomyopathy after burn injury.

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Mitochondrial gene signature in the prefrontal cortex for differential susceptibility to chronic stress

Scientific Reports ◽

10.1038/s41598-020-75326-9 ◽

2020 ◽

Vol 10 (1) ◽

Author(s):

Meltem Weger ◽

Daniel Alpern ◽

Antoine Cherix ◽

Sriparna Ghosal ◽

Jocelyn Grosse ◽

...

Keyword(s):

Gene Expression ◽

Mitochondrial Dna ◽

Prefrontal Cortex ◽

Mitochondrial Dysfunction ◽

Chronic Stress ◽

Mitochondrial Gene ◽

Brain Regions ◽

Mitochondrial Gene Expression ◽

Data Set ◽

A Genome

Abstract Mitochondrial dysfunction was highlighted as a crucial vulnerability factor for the development of depression. However, systemic studies assessing stress-induced changes in mitochondria-associated genes in brain regions relevant to depression symptomatology remain scarce. Here, we performed a genome-wide transcriptomic study to examine mitochondrial gene expression in the prefrontal cortex (PFC) and nucleus accumbens (NAc) of mice exposed to multimodal chronic restraint stress. We identified mitochondria-associated gene pathways as most prominently affected in the PFC and with lesser significance in the NAc. A more detailed mitochondrial gene expression analysis revealed that in particular mitochondrial DNA-encoded subunits of the oxidative phosphorylation complexes were altered in the PFC. The comparison of our data with a reanalyzed transcriptome data set of chronic variable stress mice and major depression disorder subjects showed that the changes in mitochondrial DNA-encoded genes are a feature generalizing to other chronic stress-protocols as well and might have translational relevance. Finally, we provide evidence for changes in mitochondrial outputs in the PFC following chronic stress that are indicative of mitochondrial dysfunction. Collectively, our work reinforces the idea that changes in mitochondrial gene expression are key players in the prefrontal adaptations observed in individuals with high behavioral susceptibility and resilience to chronic stress.

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Metabolic factors in the development of hepatic steatosis and altered mitochondrial gene expression in vivo

Metabolism ◽

10.1016/j.metabol.2010.12.001 ◽

2011 ◽

Vol 60 (8) ◽

pp. 1090-1099 ◽

Cited By ~ 45

Author(s):

Shaoyun Wang ◽

Amrita Kamat ◽

Pablo Pergola ◽

Anita Swamy ◽

Fermin Tio ◽

...

Keyword(s):

Gene Expression ◽

Hepatic Steatosis ◽

Mitochondrial Gene ◽

Mitochondrial Gene Expression ◽

Metabolic Factors

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3 IN VITRO MATURATION ALTERS GENE EXPRESSION IN MOUSE OOCYTES

Reproduction Fertility and Development ◽

10.1071/rdv20n1ab3 ◽

2008 ◽

Vol 20 (1) ◽

pp. 82

Author(s):

M. Paczkowski ◽

C. Bidwell ◽

D. Spurlock ◽

J. Waddell ◽

R. L. Krisher

Keyword(s):

Gene Expression ◽

Cell Death ◽

Dna Methyltransferase ◽

In Vitro Maturation ◽

Fold Increase ◽

Developmental Competence ◽

Differentially Expressed ◽

Dna Methyltransferase 1

The in vitro culture environment significantly impacts nuclear maturation, fertilization, embryonic development, and epigenetic competence; however, our knowledge of the effects of in vitro maturation on oocyte developmental competence, and specifically cytoplasmic maturation, is limited. The objective of this experiment was to identify alterations in the transcriptome of oocytes matured in vitro compared to those matured in vivo that correlate to developmental competence. Immature oocytes were collected from Day 26 and 7-8-week-old B6D2F1 mice 48 h post-pregnant mare serum gonadotropin (PMSG) administration and matured for 16 h in Gmat supplemented with 0.5 mm citric acid, 0.5 mm cysteamine, 100 ng mL–1 epidermal growth factor (EGF), 0.05% insulin-transferrin-selenium (ITS; v/v), 0.01% recombumin (v/v) and 2 mg mL–1 fetuin. In vivo-matured oocytes from females of the same ages were collected from the oviducts 62 h post-PMSG and 14 h post-hCG and mating to vasectomized males. In vivo- and in vitro-matured oocytes were identified visually by the presence of the first polar body. Mature oocytes were pooled into three groups of 150 oocytes per treatment and lysed; poly A+ RNA was extracted. Samples were processed through two cycles of linear amplification and hybridized to the GeneChip� Mouse Genome 430 2.0 Array (Affymetrix, Inc., Santa Clara, CA, USA), with three arrays per treatment. Microarray data were sorted and filtered to include genes that were classified as having two present calls per treatment. The data were then normalized to the chip median and analyzed using a one-way analysis of variance; the level of significance was calculated at P < 0.01. In total, 2.17% (482/22170) and 1.61% (358/22170) of genes were differentially expressed between in vitro- and in vivo-matured oocytes in Day 26 and 7–8-week-old mice, respectively. However, 72.82% (351/482) and 67.87% (243/358) of differentially expressed genes had increased abundance in the in vitro- and in vivo-matured oocytes, respectively. Transcripts involved in gene expression, cellular growth and proliferation, and cellular development were increased in in vivo-matured oocytes from both age groups compared to those matured in vitro. Cell death was one of the higher ranking functional groups increased in the 7–8-week-old in vitro-matured oocytes compared to the 7–8-week-old in vivo-matured oocytes. Specific genes altered by in vitro maturation conditions in Day 26 oocytes were DNA methyltransferase 1 (>7-fold increase in vivo), caspase 8 (>4-fold increase in vivo), and eukaryotic translation initiation factor 1B (>4-fold increase in vivo). DNA methyltransferase 1 and ubiquitin-conjugating enzyme E2T were significantly increased in in vivo-matured 7–8-week-old oocytes (>3-fold and >5-fold, respectively). These results indicate that gene expression is altered in oocytes matured in vitro compared to those matured in vivo. Based on the functional annotations of genes differentially expressed, dysregulation of gene expression in the oocyte resulting in altered DNA methylation and an up-regulation in cell death pathways are potential developmental mechanisms influenced by in vitro culture conditions that correlate to reduced embryonic developmental potential.

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