• Biomedical Science Letters
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• v.18 no.1
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• pp.49-55
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• 2012

Numerous biochemical molecules have been implicated in the development of muscular atrophy. However, control mechanisms associated with muscular disease are not clear. The present study was conducted to investigate gene expression profiles of rat muscle during the denervation to atrophy transition processes. We isolated total RNA from rats suffering from partial muscle atrophy (P) and electromyostimulated atrophy (PE) and synthesized cDNA using annealing control primers. Using 20 ACPs for PCR, we cloned 18 DEGs using TOPO TA cloning vector, sequenced, and analyzed their identities using BLAST search. Sequences of 14 clones significantly matched database entries, while one clone was ESTs, and 3 clones were unidentified. Different expression profiles of selected DEGs between P and PE were confirmed. The troponin T, Fkbp1a, RGD1307554, Phtf1, Atp1a1 and Commd3 were highly expressed genes in the P and PE groups, while Krox-25 and TCOX2 were only expressed genes in the P group, the Sv2b and Marcks were only expressed genes in PE group. also, Cox8h was highly expressed genes in PE groups. The ASPH, ND1, and ARPL1 were highly expressed genes in the P and PE groups. List of genes obtained from the present study might provide an insight for the study of mechanism regulating muscle atrophy and electrostimulated muscle atrophy transitions. These data suggest that troponin T, Fkbp1a, RGD1307554, Phtf1, Atp1a1, and Commd3 are potentially useful as clinical biomarkers of age-related muscle atrophy and dysfunction.

• Biomolecules & Therapeutics
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• v.29 no.2
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• pp.154-165
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• 2021

This study aimed to investigate whether the antidiabetic drugs dipeptidyl peptidase 4 (DPP4) inhibitors such as evogliptin and sitagliptin affect the membrane DPP4 (mDPP4) enzymatic activity and immune function of T helper1 (Th1) cells in terms of cytokine expression and cell profiles. The mDPP4 enzymatic activity, cytokine expression, and cell profiles, including cell counts, cell viability, DNA synthesis, and apoptosis, were measured in pokeweed mitogen (PWM)-activated CD4+CD26+ H9 Th1 cells with or without the DPP4 inhibitors, evogliptin and sitagliptin. PWM treatment alone strongly stimulated the expression of mDPP4 and cytokines such as interleukin (IL)-2, IL-10, tumor necrosis factor-alpha, interferon-gamma, IL-13, and granulocyte-macrophage colony stimulating factor in the CD4+CD26+ H9 Th1 cells. Evogliptin or sitagliptin treatment potently inhibited mDPP4 activity in a dose-dependent manner but did not affect either the cytokine profile or cell viability in PWM-activated CD4+CD26+ H9 Th1 cells. These results suggest that, following immune stimulation, Th1 cell signaling pathways for cytokine expression function normally after treatment with evogliptin or sitagliptin, which efficiently inhibit mDPP4 enzymatic activity in Th1 cells.

• BMB Reports
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• v.54 no.12
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• pp.601-607
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• 2021

Odorant receptors (ORs) account for about 60% of all human G protein-coupled receptors (GPCRs). OR expression outside of the nose has functions distinct from odor perception, and may contribute to the pathogenesis of disorders including brain diseases and cancers. Glioma is the most common adult malignant brain tumor and requires novel therapeutic strategies to improve clinical outcomes. Here, we outlined the expression of brain ORs and investigated OR expression levels in glioma. Although most ORs were not ubiquitously expressed in gliomas, a subset of ORs displayed glioma subtype-specific expression. Moreover, through systematic survival analysis on OR genes, OR51E1 (mouse Olfr558) was identified as a potential biomarker of unfavorable overall survival, and OR2C1 (mouse Olfr15) was identified as a potential biomarker of favorable overall survival in isocitrate dehydrogenase (IDH) wild-type glioma. In addition to transcriptomic analysis, mutational profiles revealed that somatic mutations in OR genes were detected in > 60% of glioma samples. OR5D18 (mouse Olfr1155) was the most frequently mutated OR gene, and OR5AR1 (mouse Olfr1019) showed IDH wild-type-specific mutation. Based on this systematic analysis and review of the genomic and transcriptomic profiles of ORs in glioma, we suggest that ORs are potential biomarkers and therapeutic targets for glioma.

• Entomological Research
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• v.48 no.5
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• pp.416-428
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• 2018

To gain an insight into the function of heat shock proteins (HSPs) in insects during thermal stress, three HSP cDNAs were identified in the transcriptome of adult Heortia vitessoides, one of the most destructive defoliating pests in Aquilaria sinensis (Loureiro) Sprenger forests. The open reading frames of HvHsp60, HvHsp70, and HvHsp90 were 1,719, 2,070, and 2,151 bp in length, respectively, and encoded proteins with molecular weights of 61.05, 75.02, and 82.23 kDa, respectively. Sequence analysis revealed that all three HSPs were highly conserved in structure. Regarding the stage-specific expression profiles, HvHsp60, HvHsp70, and HvHsp90 mRNAs were detected in all developmental stages. Regarding the tissue-specific expression profiles, the expression levels of the three HSP genes were different in various larval and adult tissues. Moreover, the expression patterns of heat-stressed larvae, pupae, and adults indicated that HvHsp60, HvHsp70, and HvHsp90 were heat-inducible. In particular, HvHsp60 transcripts increased dramatically in larvae and pupae that were heat-stressed at $40^{\circ}C$ and were upregulated in adults that were heat-stressed at $35^{\circ}C$ and $40^{\circ}C$. The expression of HvHsp70 significantly increased in all of the three different developmental stages at $35^{\circ}C$, $40^{\circ}C$, and $45^{\circ}C$. The expression of HvHsp90 obviously increased at $30^{\circ}C$, $35^{\circ}C$, and $40^{\circ}C$ in larvae and could be induced at $35^{\circ}C$ in pupae and adults. The results suggest that HSP60, HSP70, and HSP90 play a major role in protecting H. vitessoides against high-temperature stress.

• Asian-Australasian Journal of Animal Sciences
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• v.33 no.2
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• pp.294-304
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• 2020

Objective: The study was conducted to evaluate the effects of the absorbent (a mixture of activated carbon and hydrated sodium calcium aluminosilicate) on growth performance, blood profiles and hepatic genes expression in broilers fed diets naturally contaminated with aflatoxin. Methods: A total of 1,200 one-day-old male chicks were randomly assigned to 6 treatments with 10 replicate cages per treatment. The dietary treatments were as follows: i) control (basal diets); ii) 50% contaminated corn; iii) 100% contaminated corn; iv) control+1% adsorbent; v) 50% contaminated corn+1% absorbent; vi) 100% contaminated corn+1% absorbent. Results: During d 1 to 21, feeding contaminated diets reduced (p<0.05) body weight (BW), average daily gain (ADG), and average daily feed intake (ADFI), but increased (p<0.05) feed-to-gain ratio (F/G). The absorbent supplementation increased (p<0.05) BW, ADG, and ADFI. There were interactions (p<0.05) in BW, ADG, and ADFI between contaminated corn and absorbent. Overall, birds fed 100% contaminated diets had lower (p<0.05) final BW and ADG, but higher (p<0.05) F/G compared to those fed control diets. The absorbent addition increased (p<0.05) serum albumin concentration on d 14 and 28 and total protein (TP) level on d 28, decreased (p<0.05) alanine transaminase activity on d 14 and activities of aspartate aminotransferase and alkaline phosphatase on d 28. Feeding contaminated diets reduced (p<0.05) hepatic TP content on d 28 and 42. The contaminated diets upregulated (p<0.05) expression of interleukin-6, catalase (CAT), and superoxide dismutase (SOD), but downregulated (p<0.05) glutathione S-transferase (GST) expression in liver. The absorbent supplementation increased (p<0.05) interleukin-1β, CAT, SOD, cytochrome P450 1A1 and GST expression in liver. There were interactions (p<0.05) in the expression of hepatic CAT, SOD, and GST between contaminated corn and absorbent. Conclusion: The results suggest that the naturally aflatoxin-contaminated corn depressed growth performance, while the adsorbent could partially attenuate the adverse effects of aflatoxin on growth performance, blood profiles and hepatic genes expression in broilers.

• Molecular & Cellular Toxicology
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• v.1 no.3
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• pp.209-215
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• 2005

Recently, a large number of clinical experiments have shown that exposure of organic pollutants lead to various cancers through the abnormal cell growth. Environmental pollutants, such as 2, 3, 7, 8-Tetrachloro dibenzo-p-dioxin (TCDD) and polycyclic aromatic hydrocarbons (PAHs), are carcinogen and are known to cause the cognitive disability and motor dysfunction in the developing of brain. The effects of these pollutants on neurodevelopmental disorder is well established, but the underlying mechanism(s) and similarity of gene expression profiles in human brain tumors with organic pollutants still remain unclear. In this study, we first examined the gene expression profiles in glioblastomas compared with meningioma that are kinds of primary human brain tumor by using human cDNA microarray. The results of cDNA microarray analysis revealed that 26 genes were upregulated (Z-ratio>2.0) and 14 genes were downregulated (Z-ratio<-2.0) in glioblastoma compared with meningioma. From the altered gene patterns, mitogen-activated protein kinase (MAPK) signaling related genes, such as MAP2K3, MAP3K11 and jun activated domain binding protein, and transcription factors, such as UTF2 and TF12, were upregulated in glioblastoma. Also, we tried to investigate the relation between important genes up- and down-regulated in giloblastoma and various organic pollutants. Therefore, the identification of changes in the patterns of gene expression may provide a better understanding of the molecular mechanisms involved in human primary brain tumors and of the relation between gene expression profiles and organic pollutants in brain tissue.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.16
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• pp.7277-7284
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• 2015

Background: The Wnt/${\beta}$-catenin signaling pathway is an important regulator of cellular functions such as proliferation, survival and cell adhesion. Wnt/${\beta}$-catenin signaling is associated with tumor initiation and progression; ${\beta}$-catenin mutations explain only 30% of aberrant signaling found in breast cancer, indicating that other components and/or regulation of the Wnt/${\beta}$-catenin pathway may be involved. Objective: We evaluated AXIN2 rs2240308 and rs151279728 polymorphisms, and expression profiles of ${\beta}$-catenin destruction complex genes in breast cancer patients. Materials and Methods: We collected peripheral blood samples from 102 breast cancer and 102 healthy subjects. The identification of the genetic variation was performed using PCR-RFLPs and DNA sequencing. RT-qPCR was used to determine expression profiles. Results: We found significant association of AXIN2 rs151279728 and rs2240308 polymorphisms with breast cancer risk. Significant increase was observed in AXIN2 level expression in breast cancer patients. Further analyses showed APC, ${\beta}$-catenin, CK1${\alpha}$, GSK3${\beta}$ and PP2A gene expression to be associated to clinic-pathological characteristics. Conclusions: The present study demonstrated, for the first time, that AXIN2 genetic defects and disturbance of ${\beta}$-catenin destruction complex expression may be found in breast cancer patients, providing additional support for roles of Wnt/${\beta}$-catenin pathway dysfunction in breast cancer tumorigenesis. However, the functional consequences of the genetic alterations remain to be determined.

• Molecular & Cellular Toxicology
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• v.1 no.3
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• pp.164-171
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• 2005

Toxicological studies have an object of detecting adverse effects of a chemical on an organism based on observed toxicity marker (i.e., serum biochemical markers and chemical-specific gene expression) or phenotypic outcome. To date, most toxicogenomic studies concentrated on hepatic toxicity. cDNA microarray analysis enable discrimination of the responses in animals exposed to different classes of hepatotoxicants. In an effort to further characterize the mechanisms of 2, 3, 7, 8,-Tetrachlorodibenzo-p-dioxin (TCDD or dioxin)-mediated toxicity, comprehensive temporal-responsive microarray analyses were performed on hepatic tissue from Sprague-Dawley rats treated with TCDD. Hepatic gene expression profiles were monitored using custom DNA chip containing 490 cDNA clones related with toxicology. Gene expression analysis identified 26 features which exhibited a significant change. In this study, we observed that the genes related with oxidative stress in rats exposed to Dioxin, such as CYPIIA3 and glutathione S-transferase, were up-regulated at 24hr after exposure. In this study, we carried out to discover novel evidence for previously unknown gene expression patterns related to mechanism of hepatic toxicity in rats exposed to dioxin, and to elucidate the effects of dioxin on the gene expression after exposure to dioxin.

• Journal of fish pathology
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• v.35 no.2
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• pp.141-155
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• 2022

Rock bream iridovirus (RBIV) causes high mortality and economic losses in the rock bream (Oplegnathus fasciatus) aquaculture industry in Korea. Viral open reading frames (ORFs) expression profiling at different RBIV infection stages was investigated using microarray approaches. Rock bream were exposed to the virus and held for 7 days at 23 ℃ before the water temperature was reduced to 17 ℃. Herein, 28% mortality was observed from 24 to 35 days post infection (dpi), after which no mortality was observed until 70 dpi (end of the experiment). A total of 27 ORFs were significantly up- or down-regulated after RBIV infection. In RBIV-infected rock bream, four viral genes were expressed after 2 dpi. Most RBIV ORFs (26 genes, 96.2%) were significantly elevated between 7 and 20 dpi. Among them, 12 ORF (44.4%) transcripts reached their peak expression intensity at 15 dpi, and 14 ORFs (51.8%) were at peak expression intensity at 20 dpi. Expression levels began to decrease after 25 dpi, and 92.6% of ORFs (25 genes) were expressed below 1-fold at 70 dpi. From the microarray data, in addition to the viral infection, viral gene expression profiles were categorized into three infection stages, namely, early (2 dpi), middle (7 to 20 dpi), and recovery (25 and 70 dpi). RBIV ORFs 009R, 023R, 032L, 049L, and 056L were remarkably expressed during RBIV infection. Furthermore, six ORFs (001L, 013R, 052L, 053L, 058L, and 061L) were significantly expressed only at 20 dpi. To verify the cDNA microarray data, we performed quantitative real-time PCR, and the results were similar to that of the microarray. Our results provide novel observations on broader RBIV gene expression at different stages of infection and the development of control strategies against RBIV infection.

• Communications for Statistical Applications and Methods
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• v.22 no.2
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• pp.181-199
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• 2015

In a short history, RNA-seq data have established a revolutionary tool to directly decode various scenarios occurring on whole genome-wide expression profiles in regards with differential expression at gene, transcript, isoform, and exon specific quantification, genetic and genomic mutations, and etc. RNA-seq technique has been rapidly replacing arrays with seq-based platform experimental settings by revealing a couple of advantages such as identification of alternative splicing and allelic specific expression. The remarkable characteristics of high-throughput large-scale expression profile in RNA-seq are lied on expression levels of read counts, structure of correlated samples and genes, larger number of genes compared to sample size, different sampling rates, inevitable systematic RNA-seq biases, and etc. In this study, we will comprehensively review how robust Bayesian and non-parametric methods have a better performance than classical statistical approaches by explicitly incorporating such intrinsic RNA-seq specific features with flexible and more appropriate assumptions and distributions in practice.