scholarly journals Investigation of Ifosfamide Toxicity Induces Common Upstream Regulator in Liver and Kidney

2021 ◽  
Vol 22 (22) ◽  
pp. 12201
Author(s):  
Hyoung-Yun Han ◽  
Mi-Sun Choi ◽  
Seokjoo Yoon ◽  
Je-Won Ko ◽  
Sang-Kyum Kim ◽  
...  
Keyword(s):  
Target Genes ◽  
Intraperitoneal Administration ◽  
Microarray Experiment ◽  
Pcr Analysis ◽  
Synthetic Analogue ◽  
Organ Toxicity ◽  
Upstream Regulator ◽  
Liver And Kidney ◽  
Adenosyl Methionine ◽  
Good Laboratory

Ifosfamide is an alkylating agent, a synthetic analogue of cyclophosphamide, used to treat various solid cancers. In this study, the toxicity of ifosfamide was evaluated using single-and multiple-dose intraperitoneal administration in rats under Good Laboratory Practice guidelines, and an additional microarray experiment was followed to support toxicological findings. A single dose of ifosfamide (50 mg/kg) did not induce any pathological changes. Meanwhile, severe renal toxicity was observed in the 7 and 28 days consecutively administered groups, with significant increases in blood urea nitrogen and creatinine levels. In the tox-list analysis, cholesterol synthesis-related genes were mostly affected in the liver and renal failure-related genes were affected in the kidney after ifosfamide administration. Moreover, interferon regulatory factor 7 was selected as the main upstream regulator that changed in both the liver and kidney, and was found to interact with other target genes, such as ubiquitin specific peptidase 18, radical S-adenosyl methionine domain containing 2, and interferon-stimulated gene 15, which was further confirmed by real-time RT-PCR analysis. In conclusion, we confirmed kidney-biased ifosfamide organ toxicity and identified identically altered genes in both the liver and kidney. Further comprehensive toxicogenomic studies are required to reveal the exact relationship between ifosfamide-induced genes and organ toxicity.

scholarly journals Reproductive failure in mice lacking inter-alpha-trypsin inhibitor (ITI) – ITI target genes in mouse ovary identified by microarray analysis

2004 ◽  
Vol 183 (1) ◽  
pp. 29-38 ◽  
Author(s):  
Mika Suzuki ◽  
Hiroshi Kobayashi ◽  
Yoshiko Tanaka ◽  
Naohiro Kanayama ◽  
Toshihiko Terao
Keyword(s):  
Real Time ◽  
Trypsin Inhibitor ◽  
Target Genes ◽  
Reproductive Function ◽  
Pcr Analysis ◽  
Rt Pcr ◽  
Reproductive Process ◽  
Female Mice ◽  
Retinoid Metabolism ◽  
Regulatory Effects

Bikunin, a Kunitz-type protease inhibitor, is found in blood and urine. It has been established by two laboratories independently that the bikunin knockout female mice display a severe reduction in fertility: the cumulus oophorus has a defect in forming the extracellular hyaluronan-rich matrix during expansion. Proteins of the inter-alpha-trypsin inhibitor (ITI) family are eliminated in mice in which the bikunin gene has been inactivated, since bikunin is essential for their biosynthesis. Proteins of the ITI family may contribute to the microenvironment in which ovulation takes place. It is not clear, however, whether a single mechanism affects the reproductive function including ovulation. For identifying the full repertoire of the ITI deficiency-related genes, a cDNA microarray hybridization screening was conducted using mRNA from ovaries of wild-type or bik−/− female mice. A number of genes were identified and their regulation was confirmed by real-time RT-PCR analysis. Our screen identified that 29 (0.7%) and 5 genes (0.1%) of the genes assayed were, respectively, up- and down-regulated twofold or more. The identified genes can be classified into distinct subsets. These include stress-related, apoptosis-related, proteases, signaling molecules, aging-related, cytokines, hyaluronan metabolism and signaling, reactive oxygen species-related, and retinoid metabolism, which have previously been implicated in enhancing follicle development and/or ovulation. Real-time RT-PCR analysis confirmed that these genes were up- and down-regulated two- to tenfold by bikunin knockout. These studies demonstrate that proteins of the ITI family may exert potent regulatory effects on a major physiological reproductive process, ovulation.

REACTIVE CHANGES OF LIVER AND KIDNEY HISTOLOGICAL ELEMENTS IN MURINE MODELS OF SEPSIS CAUSED BY ADMINISTRATION OF DIFFERENT STRAINS TO MICE

2020 ◽  
pp. 66-71
Author(s):  
Татьяна Геннадьевна Боровая ◽  
Владимир Григорьевич Жуховицкий ◽  
Мария Николаевна Черкасова
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Morphological Changes ◽  
Blood Stasis ◽  
Intraperitoneal Administration ◽  
Liver Parenchyma ◽  
Experimental Models ◽  
Control Group ◽  
Reactive Changes ◽  
Liver And Kidney ◽  
Different Strains

Цель - выявление реактивных изменений гистологических элементов печени и почек у мышей в экспериментальных моделях сепсиса, вызванного штаммами 1840 и 1623 Pseudomonas aeruginosa (PsA1840, 1623). Материал и методы. Сепсис моделировали на двух группах половозрелых самцов мышей линии C57Bl/6 интраперитонеальным введением Pseudomonas aeruginosa. Животным 1-й группы (8 особей) вводили штамм 1840, животным 2-й группы (12 особей) - штамм 1623. Контрольная группа состояла из 3 животных. Перед началом опыта штаммы тестировали на присутствие генов экзотоксинов U, S, T, Y (ExoU, ExoS, ExoT, ExoY) с помощью полимеразной цепной реакции (ПЦР). Для визуализации продуктов ПЦР применяли электрофорез в горизонтальном 1,5 % агарозном геле. Животных вскрывали на терминальной стадии сепсиса. Серийные парафиновые срезы печени и почек толщиной 4 мкм окрашивали гематоксилином - эозином, анализировали особенности гистоструктуры органов и фотографировали в световом микроскопе «AxioPlus» (фирма Zeiss, Германия). Результаты. Штамм PsA 1840, имеющий ген exoU, вызывал выраженные деструктивные изменения пластинок гепатоцитов и замещение участков паренхимы печени гомогенным эозинофильным веществом. Присутствовали признаки стаза крови в синусоидных капиллярах, расширение и тромбоз центральных вен, немногочисленные скопления лейкоцитов. Морфологические изменения нефронов состояли в локальных деструктивных изменениях проксимальных канальцев на периферии коркового вещества почек. При введении PsA1623, имеющего ген exoS, возникали массовая гибель почечных телец и дегенерация канальцев нефронов. В печени дольковая гистоархитектура в основном сохранялась. Выводы. Предполагается связь выявленных различий в реактивных изменениях гистологических элементов печени и почек в подопытных группах с особенностями геномов штаммов PsA, использованных для моделирования сепсиса. Objective - to identify reactive changes of liver and kidney histological elements in experimental models of sepsis in mice caused by 1840 and 1623 Pseudomonas aeruginosa strains (PsA1840, 1623). Material and methods. Sepsis was modeled in two groups of mature male C57Bl/6 mice by intraperitoneal administration of Pseudomonas aeruginosa. Strain 1840 was administered to animals of the first group (n=8), animals of the second group (n=12) were administered strain 1623; the control group consisted of 3 animals. Before the experiment, the strains were tested for the presence of genes of exotoxins U, S, T, Y (ExoU, ExoS, ExoT, ExoY) using polymerase chain reaction (PCR). Electrophoresis in horizontal 1,5 % agarose gel was used to visualize PCR products. The animals were euthanized at the terminal stage of sepsis. The extracted liver and kidneys were fixed according to the generally accepted histological method, and embedded into paraffin blocks. Serial 4 μm thick sections of organs were stained with hematoxylin and eosin, analyzed and photographed using «AxioPlus» light microscope (Zeiss, Germany). Results. Strain PsA 1840, carrying the gene of exotoxin U (ExoU), caused severe destructive changes of hepatocytes plates and the replacement of the liver parenchyma with homogeneous eosinophilic substance. There were signs of blood stasis in sinusoidal capillaries, expansion and thrombosis of central veins, a few accumulations of leukocytes. Morphological changes of nephrons consisted of local destructive changes in the proximal tubules at the periphery of kidney cortical substance. After the introduction of PsA1623, carrying the gene of exotoxin S (ExoS), the massive death of renal corpuscles and degeneration of nephron tubules were registered. However, the lobular histoarchitecture in the liver remained mostly unaltered. Conclusions. It is supposed that there is a possible connection of the observed differences in reactive changes of liver and kidney histological elements in two experimental groups with genome features of PsA strains used for the sepsis modeling.

Discovery and Characterization of Differentially Expressed Soybean MiRNAs and Their Targets During Soybean Mosaic Virus Infection Unveils Novel Insight Into Soybean-SMV Interaction

2021 ◽  
Author(s):  
Bowen Li ◽  
Adhimoolam Karthikeyan ◽  
Liqun Wang ◽  
Jinlong Yin ◽  
Tongtong Jin ◽  
...  
Keyword(s):  
Virus Infection ◽  
Mosaic Virus ◽  
Target Genes ◽  
Soybean Mosaic Virus ◽  
Expression Patterns ◽  
Defense Responses ◽  
Pcr Analysis ◽  
Functional Annotations ◽  
Additional Information ◽  
Insight Into

Abstract Background: Soybean mosaic virus (SMV) is the most devastating pathogen of soybean. MicroRNAs (miRNAs) are a class of non-coding RNAs (21-24 nucleotides) and play important roles in regulating defense responses against pathogens. However, miRNA's response to SMV in soybean is not as well documented. Result: In this study, we analyzed 18 miRNA libraries, including three biological replicates from two soybean lines (Resistant and susceptible lines to SMV strain SC3 selected from the near-isogenic lines of Qihuang No. 1× Nannong1138-2) after virus infection at three different time intervals (0 dpi, 7 dpi, and 14 dpi). A total of 1,092 miRNAs, including 608 known miRNAs and 484 novel miRNAs were detected. Differential expression analyses identified the miRNAs responded during soybean-SMV interaction. Then, miRNAs potential target genes were predicted via data mining, and functional annotation was done by Gene Ontology (GO) analysis. Eventually, the expression patterns of several miRNAs validated by quantitative real-time PCR analysis are consistent with sequencing results. Conclusion: We have identified a large number of miRNAs and their target genes and also functional annotations. Our study provides additional information on soybean miRNAs and an insight into the role of miRNAs during SMV-infection in soybean.

scholarly journals Key Regulatory Pathways, MicroRNAs, and Target Genes Participate in Adventitious Root Formation of Acer Rubrum L

2021 ◽  
Author(s):  
Wenpeng Zhu ◽  
Manyu Zhang ◽  
Jianyi Li ◽  
Hewen Zhao ◽  
Kezhong Zhang ◽  
...  
Keyword(s):  
Transcriptional Activation ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Seedling Survival ◽  
Expression Patterns ◽  
Economic Value ◽  
Acer Rubrum ◽  
Pcr Analysis ◽  
Asexual Propagation ◽  
Regulatory Pathways

Abstract BackgroundAcer rubrum L. is a colorful ornamental tree with great economic value. Because this tree is difficult to root under natural conditions and the seedling survival rate is low, vegetative propagation methods are often used. Because the formation of adventitious roots (ARs) is essential for the survival of asexual propagation of A. rubrum, it is necessary to investigate the molecular regulatory mechanisms in the formation of ARs of A. ruburm. To address this knowledge gap, we sequenced the transcriptome and sRNA of the A. rubrum variety ‘Autumn Fantasy’ using high-throughput sequencing and explored changes in gene and microRNA (miRNA) expression in response to exogenous auxin treatment. ResultsWe identified 82,468 differentially expressed genes between the treated and untreated ARs, as well as 48 known and 95 novel miRNAs. We also identified 172 target genes of the known miRNAs using degradome sequencing. Two regulatory pathways (ubiquitin mediated proteolysis and plant hormone signal transduction), Ar-miR160a and the target gene ArARF10 were shown to be involved in the auxin response. We further investigated the expression patterns and regulatory roles of ArARF10 through subcellular localization, transcriptional activation, plant transformation, qRT-PCR analysis, and GUS staining. ConclusionsDifferential expression patterns indicated the Ar-miR160a-ArARF10 interaction might play a significant role in the regulation of AR formation in A. rubrum. Our study provided new insights into mechanisms underlying the regulation of AR formation in A. rubrum.

scholarly journals Chorionic villus-derived mesenchymal stem cell-mediated autophagy promotes proliferation and invasiveness of trophoblasts under hypoxia by activating the JAK2/STAT3 signalling pathway

2020 ◽  
Author(s):  
Yijing Chu ◽  
Chongyu Yue ◽  
Wei Peng ◽  
Weiping Chen ◽  
Yan Zhang ◽  
...  
Keyword(s):  
Stem Cells ◽  
Mesenchymal Stem Cells ◽  
Chorionic Villus ◽  
Pcr Analysis ◽  
Rna Seq ◽  
Protein Levels ◽  
Hypoxic Conditions ◽  
Upstream Regulator ◽  
Pathway Analyses ◽  
Stat3 Signalling

Abstract Objectives Trophoblast dysfunction during pregnancy is fundamentally involved in preeclampsia. The aim of this study was to understand how human chorionic villous mesenchymal stem cells (CV-MSCs) operate in regulation of trophoblast function.Materials and Methods We treated trophoblasts with CV-MSC supernatant under hypoxic conditions, and transcriptome and pathway analyses of trophoblasts were performed. Western blotting and PCR analysis were used to examine the JAK2, STAT3 and autophagy associated protein expression levels in trophoblasts.Results The CV-MSC supernatant treatment markedly enhanced proliferation, invasion and autophagy. The RNA-seq revealed JAK2/STAT3 signalling as an upstream regulator, and STAT3 mRNA and protein levels increased during CV-MSC treatment. Inhibition of JAK2/STAT3 signalling reduced autophagy, survival and invasion of trophoblasts even in the presence of CV-MSCs, and blocking autophagy did not affect STAT3 activation in trophoblasts treated with CV-MSCs. Importantly, overexpression of STAT3 increased the levels of autophagy in trophoblasts; thus, it regulated positively autophagy in hypoxic trophoblasts. Human placental explants also proved our finding, in which STAT3 was activated and LC3B-II levels were increased by CV-MSC treatment.Conclusions Our data suggest that CV-MSC-dependent activation of JAK2/STAT3 signalling is a prerequisite for upregulation of autophagy in trophoblasts.

Dysregulation of tRNA-derived small RNAs and their potential roles in lupus nephritis

Lupus ◽  
2021 ◽  
pp. 096120332110614
Author(s):  
Yan Liang ◽  
Ji Zhang ◽  
Wenxian Qiu ◽  
Bo Chen ◽  
Ying Zhou ◽  
...  
Keyword(s):  
Lupus Nephritis ◽  
Signaling Pathway ◽  
Small Rnas ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Expression Profiles ◽  
Mapk Signaling ◽  
Pcr Analysis ◽  
Clinical Indicators ◽  
Qrt Pcr

Objective Lupus nephritis (LN) is a major end-organ complication of systemic lupus erythematosus (SLE), and the molecular mechanism of LN is not completely clear. Accumulating pieces of evidence indicate the potential vital role of tRNA-derived small RNAs (tsRNAs) in human diseases. Current study aimed to investigate the potential roles of tsRNAs in LN. Methods We herein employed high‐throughput sequencing to screen the expression profiles of tsRNAs in renal tissues of the LN and control groups. To validate the sequencing data, we performed quantitative real-time PCR (qRT-PCR) analysis. Correlational analysis of verified tsRNAs expression and clinical indicators was conducted using linear regression. The potential target genes were also predicted. The biological functions of tsRNAs were annotated by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Results Our findings revealed that the expression profiles of tsRNAs were significantly altered in the kidney tissues from LN patients compared with control. Overall, 160 tsRNAs were significantly dysregulated in the LN group, of which 79 were upregulated, whereas 81 were downregulated. Subsequent qRT-PCR results confirmed the different expression of candidate tsRNAs. Correlation analysis results found that expression of verified tsRNAs were correlated to clinical indicators. The target prediction results revealed that verified tsRNAs might act on 712 target genes. Further bioinformatics analysis uncovered tsRNAs might participate in the pathogenesis of LN through several associated pathways, including cell adhesion molecules, MAPK signaling pathway, PI3K-Akt signaling pathway and B cell receptor signaling pathway. Conclusion This study provides a novel insight for studying the mechanism of LN.

F. nucleatum targets lncRNA ENO1-IT1 to promote glycolysis and oncogenesis in colorectal cancer

Gut ◽  
2020 ◽  
pp. gutjnl-2020-322780
Author(s):  
Jie Hong ◽  
Fangfang Guo ◽  
Shi-Yuan Lu ◽  
Chaoqin Shen ◽  
Dan Ma ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Glucose Metabolism ◽  
Target Genes ◽  
Colorectal Carcinogenesis ◽  
Pcr Analysis ◽  
Positron Emission ◽  
Non Coding Rna ◽  
Cancer Models ◽  
Chromatin Immunoprecipitation Sequencing ◽  
Rna Immunoprecipitation

ObjectiveMicrobiota disorder promotes chronic inflammation and carcinogenesis. High glycolysis is associated with poor prognosis in patients with colorectal cancer (CRC). However, the potential correlation between the gut microbiota and glucose metabolism is unknown in CRC.Design18F-FDG (18F-fluorodeoxyglucose) PET (positron emission tomography)/CT image scanning data and microbiota PCR analysis were performed to measure the correlation between metabolic alterations and microbiota disorder in 33 patients with CRC. Multiple colorectal cancer models, metabolic analysis and Seahorse assay were established to assess the role of long non-coding RNA (lncRNA) enolase1-intronic transcript 1 (ENO1-IT1) in Fusobacterium (F.) nucleatum-induced glucose metabolism and colorectal carcinogenesis. RNA immunoprecipitation and chromatin immunoprecipitation sequencing were conducted to identify potential targets of lncRNA ENO1-IT1.ResultsWe have found F. nucleatum abundance correlated with high glucose metabolism in patients with CRC. Furthermore, F. nucleatum supported carcinogenesis via increasing CRC cell glucose metabolism. Mechanistically, F. nucleatum activated lncRNA ENO1-IT1 transcription via upregulating the binding efficiency of transcription factor SP1 to the promoter region of lncRNA ENO1-IT1. Elevated ENO1-IT behaved as a guider modular for KAT7 histone acetyltransferase, specifying the histone modification pattern on its target genes, including ENO1, and consequently altering CRC biological function.ConclusionF. nucleatum and glucose metabolism are mechanistically, biologically and clinically connected to CRC. Targeting ENO1 pathway may be meaningful in treating patients with CRC with elevated F. nucleatum.

scholarly journals Genomewide analysis of circular RNA in pituitaries of normal and heat-stressed sows

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Haojie Zhang ◽  
Baoyu Hu ◽  
Jiali Xiong ◽  
Ting Chen ◽  
Qianyun Xi ◽  
...  
Keyword(s):  
Heat Stress ◽  
Heat Shock ◽  
Heat Shock Protein ◽  
Noncoding Rna ◽  
Target Genes ◽  
Hormone Secretion ◽  
Circular Rna ◽  
Differentially Expressed ◽  
Pcr Analysis ◽  
Pituitary Hormone

Abstract Background As a newly characterized type of noncoding RNA, circular RNA (circRNA) has been shown to have functions in diverse biological processes of animals. It has been reported that several noncoding RNAs may regulate animals’ response to heat stress which can be easily induced by hyperthermia in summer. However, the expression and functions of circRNAs in the pituitary of sows and whether they participate in heat stress adaption are still unclear. Results In this study, we found that high temperature over the thermoneutral zone of sows during the summer increased the serum heat shock protein 70 (HSP70) level, decreased the superoxide dismutase (SOD) vitality and prolactin (PRL) concentration, and induced heat stress in sows. Then, we explored circRNA in the pituitary of heat-stressed and normal sows using RNA sequencing and bioinformatics analysis. In total, 12,035 circRNAs were detected, with 59 circRNAs differentially expressed, including 42 up-regulated and 17 down-regulated circRNAs in pituitaries of the heat-stressed sows. Six randomly selected circRNAs were identified through reverse transcription PCR followed by DNA sequencing and other 7 randomly selected differentially expressed circRNAs were verified by quantitative real-time PCR analysis. The predicted target genes regulated by circRNAs through sponging microRNAs (miRNAs) were enriched in metabolic pathway. Furthermore, the predicted circRNA–miRNA–mRNA interactions showed that some circRNAs might sponge miRNAs to regulate pituitary-specific genes and heat shock protein family members, indicating circRNA’s roles in pituitary hormone secretion and heat stress response. Conclusions Our results provided a meaningful reference to understand the functions of circRNA in the porcine pituitary and the mechanisms by which circRNA may participate in animals’ response to heat stress.

scholarly journals Identification of microRNAs and relative target genes in Moringa oleifera leaf and callus

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Stefano Pirrò ◽  
Ivana Matic ◽  
Arianna Guidi ◽  
Letizia Zanella ◽  
Angelo Gismondi ◽  
...  
Keyword(s):  
Stress Response ◽  
Moringa Oleifera ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Pcr Analysis ◽  
Microrna Target ◽  
Sequencing Technology ◽  
Important Addition ◽  
Non Coding Rnas ◽  
Growth Development

Abstract MicroRNAs, a class of small, non-coding RNAs, play important roles in plant growth, development and stress response by negatively regulating gene expression. Moringa oleifera Lam. plant has many medical and nutritional uses; however, little attention has been dedicated to its potential for the bio production of active compounds. In this study, 431 conserved and 392 novel microRNA families were identified and 9 novel small RNA libraries constructed from leaf, and cold stress treated callus, using high-throughput sequencing technology. Based on the M. oleifera genome, the microRNA repertoire of the seed was re-evaluated. qRT-PCR analysis confirmed the expression pattern of 11 conserved microRNAs in all groups. MicroRNA159 was found to be the most abundant conserved microRNA in leaf and callus, while microRNA393 was most abundantly expressed in the seed. The majority of predicted microRNA target genes were transcriptional factors involved in plant reproduction, growth/development and abiotic/biotic stress response. In conclusion, this is the first comprehensive analysis of microRNAs in M. oleifera leaf and callus which represents an important addition to the existing M. oleifera seed microRNA database and allows for possible exploitation of plant microRNAs induced with abiotic stress, as a tool for bio-enrichment with pharmacologically important phytochemicals.

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