1.Identification of biomarkers in laryngeal cancer by weighted gene co-expression network analysis.
Fengyu ZHANG ; Li SHE ; Donghai HUANG
Journal of Central South University(Medical Sciences) 2023;48(8):1136-1151
OBJECTIVES:
Laryngeal cancer (LC) is a globally prevalent and highly lethal tumor. Despite extensive efforts, the underlying mechanisms of LC remain inadequately understood. This study aims to conduct an innovative bioinformatic analysis to identify hub genes that could potentially serve as biomarkers or therapeutic targets in LC.
METHODS:
We acquired a dataset consisting of 117 LC patient samples, 16 746 LC gene RNA sequencing data points, and 9 clinical features from the Cancer Genome Atlas (TCGA) database in the United States. We employed weighted gene co-expression network analysis (WGCNA) to construct multiple co-expression gene modules. Subsequently, we assessed the correlations between these co-expression modules and clinical features to validate their associations. We also explored the interplay between modules to identify pivotal genes within disease pathways. Finally, we used the Kaplan-Meier plotter to validate the correlation between enriched genes and LC prognosis.
RESULTS:
WGCNA analysis led to the creation of a total of 16 co-expression gene modules related to LC. Four of these modules (designated as the yellow, magenta, black, and brown modules) exhibited significant correlations with 3 clinical features: The age of initial pathological diagnosis, cancer status, and pathological N stage. Specifically, the yellow and magenta gene modules displayed negative correlations with the age of pathological diagnosis (r=-0.23, P<0.05; r=-0.33, P<0.05), while the black and brown gene modules demonstrated negative associations with cancer status (r=-0.39, P<0.05; r=-0.50, P<0.05). The brown gene module displayed a positive correlation with pathological N stage. Gene Ontology (GO) enrichment analysis identified 77 items, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis identified 30 related signaling pathways, including the calcium signaling pathway, cytokine-cytokine receptor interaction, neuro active ligand-receptor interaction, and regulation of lipolysis in adipocytes, etc. Consequently, central genes within these modules that were significantly linked to the overall survival rate of LC patients were identified. Central genes included CHRNB4, FOXL2, KCNG1, LOC440173, ADAMTS15, BMP2, FAP, and KIAA1644.
CONCLUSIONS
This study, utilizing WGCNA and subsequent validation, pinpointed 8 genes with potential as gene biomarkers for LC. These findings offer valuable references for the clinical diagnosis, prognosis, and treatment of LC.
Humans
;
Laryngeal Neoplasms/genetics*
;
Rosaniline Dyes
;
Biomarkers
;
Adipocytes
;
Gene Regulatory Networks
;
Gene Expression Profiling
2.Comparison of the Microleakage and Shear Bond Strength to Dentine of Different Tricalcium Silicate-based Pulp Capping Materials
Miri KIM ; Wansun JO ; Myeongkwan JIH ; Sangho LEE ; Nanyoung LEE
Journal of Korean Academy of Pediatric Dentistry 2019;46(1):76-84
This study evaluated the microleakage of three restorative materials and three tricalcium silicate-based pulp capping agents. The restorative materials were composite resin (CR), resin-reinforced glass ionomer cement (RMGI), and traditional glass ionomer cement (GIC) and the pulp capping agents were TheraCal LC® (TLC), Biodentine® (BD), and ProRoot® white MTA (WMTA). Additionally, shear bond strengths between the pulp-capping agents and dentine were compared.Class V cavities were made in bovine incisors and classified into nine groups according to the type of pulp-capping agent and final restoration. After immersion in 0.5% fuchsin solution, each specimen was observed with a stereoscopic microscope to score microleakage level. The crowns of the bovine incisors were implanted into acrylic resin, cut horizontally, and divided into three groups. TLC, BD and WMTA blocks were applied on dentine, and the shear bond strengths were measured using a universal testing machine.The microleakage was lowest in TLC + GIC, TLC + RMGI, TLC + CR, and BD + GIC groups and highest in WMTA + RMGI and WMTA + CR groups. The shear bond strength of BD group was the highest and that of WMTA group was significantly lower than the others.
Crowns
;
Dental Pulp Capping
;
Dentin
;
Glass Ionomer Cements
;
Immersion
;
Incisor
;
Pemetrexed
;
Pulp Capping and Pulpectomy Agents
;
Rosaniline Dyes
3.P2X7 Receptor Antagonism Attenuates the Intermittent Hypoxia-induced Spatial Deficits in a Murine Model of Sleep Apnea Via Inhibiting Neuroinflammation and Oxidative Stress.
Yan DENG ; Xue-Ling GUO ; Xiao YUAN ; Jin SHANG ; Die ZHU ; Hui-Guo LIU
Chinese Medical Journal 2015;128(16):2168-2175
BACKGROUNDThe mechanism of the neural injury caused by chronic intermittent hypoxia (CIH) that characterizes obstructive sleep apnea syndrome (OSAS) is not clearly known. The purpose of this study was to investigate whether P2X7 receptor (P2X7R) is responsible for the CIH-induced neural injury and the possible pathway it involves.
METHODSEight-week-old male C57BL/6 mice were used. For each exposure time point, eight mice divided in room air (RA) and IH group were assigned to the study of P2X7R expression. Whereas in the 21 days-Brilliant Blue G (BBG, a selective P2X7R antagonist) study, 48 mice were randomly divided into CIH group, BBG-treated CIH group, RA group and BBG-treated RA group. The hippocampus P2X7R expression was determined by Western blotting and real-time polymerase chain reaction (PCR). The spatial learning was analyzed by Morris water maze. The nuclear factor kappa B (NFκB) and NADPH oxidase 2 (NOX2) expressions were analyzed by Western blotting. The expressions of tumor necrosis factor α, interleukin 1β (IL-β), IL-18, and IL-6 were measured by real-time PCR. The malondialdehyde and superoxide dismutase levels were detected by colorimetric method. Cell damage was evaluated by Hematoxylin and Eosin staining and Terminal Transferase dUTP Nick-end Labeling method.
RESULTSThe P2X7R mRNA was elevated and sustained after 3-day IH exposure and the P2X7R protein was elevated and sustained after 7-day IH exposure. In the BBG study, the CIH mice showed severer neuronal cell damage and poorer performance in the behavior test. The increased NFκB and NOX2 expressions along with the inflammation injury and oxidative stress were also observed in the CIH group. BBG alleviated CIH-induced neural injury and consequent functional deficits.
CONCLUSIONSThe P2X7R antagonism attenuates the CIH-induced neuroinflammation, oxidative stress, and spatial deficits, demonstrating that the P2X7R is an important therapeutic target in the cognition deficits accompanied OSAS.
Animals ; Disease Models, Animal ; Hypoxia ; Male ; Metabolic Networks and Pathways ; Mice ; Mice, Inbred C57BL ; Purinergic P2 Receptor Antagonists ; pharmacology ; Receptors, Purinergic P2X7 ; analysis ; physiology ; Rosaniline Dyes ; pharmacology ; Sleep Apnea, Obstructive ; metabolism
4.Blue dye, blue skin.
Nanthini PILLAY ; Qing Yan CHEN ; Sharon LAM ; Chin Ted CHONG
Annals of the Academy of Medicine, Singapore 2014;43(1):66-67
Coloring Agents
;
adverse effects
;
Female
;
Humans
;
Middle Aged
;
Rosaniline Dyes
;
adverse effects
;
Skin
;
pathology
5.Enamel pretreatment with Er:YAG laser: effects on the microleakage of fissure sealant in fluorosed teeth.
Mahtab MEMARPOUR ; Nasrin KIANIMANESH ; Bahareh SHAYEGHI
Restorative Dentistry & Endodontics 2014;39(3):180-186
OBJECTIVES: The purpose of this in vitro study was to evaluate the microleakage and penetration of fissure sealant in permanent molar teeth with fluorosis after pretreatment of the occlusal surface. MATERIALS AND METHODS: A total of 120 third molars with mild dental fluorosis were randomly divided into 6 groups (n = 20). The tooth surfaces were sealed with an unfilled resin fissure sealant (FS) material. The experimental groups included: 1) phosphoric acid etching (AE) + FS (control); 2) AE + One-Step Plus (OS, Bisco) + FS; 3) bur + AE + FS; 4) bur + AE + OS + FS; 5) Er:YAG laser + AE + FS; and 6) Er:YAG laser + AE + OS + FS. After thermocycling, the teeth were immersed in 0.5% fuchsin and sectioned. Proportions of mircoleakage (PM) and unfilled area (PUA) were measured by digital microscope. RESULTS: Overall, there were significant differences among all groups in the PM (p = 0.00). Group 3 showed the greatest PM, and was significantly different from groups 2 to 6 (p < 0.05). Group 6 showed the lowest PM. Pretreatment with Er:YAG with or without adhesive led to less PM than bur pretreatment. There were no significant differences among groups in PUA. CONCLUSIONS: Conventional acid etching provided a similar degree of occlusal seal in teeth with fluorosis compared to those pretreated with a bur or Er:YAG laser. Pretreatment of pits and fissures with Er:YAG in teeth with fluorosis may be an alternative method before fissure sealant application.
Adhesives
;
Dental Enamel*
;
Fluorosis, Dental
;
Molar
;
Molar, Third
;
Rosaniline Dyes
;
Tooth*
6.Effect of 38% carbamide peroxide on the microleakage of silorane-based versus methacrylate-based composite restorations.
Sedighe Sadat HASHEMI KAMANGAR ; Maryam GHAVAM ; Nazanin MAHINFAR ; Seyed Jalal POURHASHEMI
Restorative Dentistry & Endodontics 2014;39(3):172-179
OBJECTIVES: This study aimed to assess the effect of 38% carbamide peroxide on the microleakage of class V cavities restored with either a silorane-based composite or two methacrylate-based composites. MATERIALS AND METHODS: A total of 96 class V cavities were prepared on the buccal surface of extracted human teeth with both enamel and dentin margins and were randomly assigned into three groups of Filtek P90 (3M-ESPE) + P90 system adhesive (3M-ESPE)(group A), Filtek Z250 (3M-ESPE) + Adper Prompt L-Pop (3M-ESPE)(group B) and Filtek Z350XT (3M-ESPE) + Adper Prompt L-Pop (group C). Half of the teeth were randomly underwent bleaching (38% carbamide peroxide, Day White, Discus Dental, applying for 15 min, twice a day for 14 day) while the remaining half (control) were not bleached. Dye penetration was measured following immersion in basic fuchsine. Data were statistically analyzed using Kruskal-Wallis and Mann-Whitney U tests at a level of 0.05. RESULTS: No significant differences were found between composites in the control groups in enamel (p = 0.171) or dentin (p = 0.094) margins. After bleaching, microleakage of Z250 (in enamel [p = 0.867] or dentin [p = 0.590] margins) and Z350 (in enamel [p = 0.445] or dentin [p = 0.591] margins) did not change significantly, but the microleakage of P90 significantly increased in both enamel (p = 0.042) and dentin (p = 0.002) margins. CONCLUSIONS: No significant differences were noted between the bleached and control subgroups of two methacrylate-based composites in enamel or dentin margins. Microleakage of silorane-based composite significantly increased after bleaching.
Adhesives
;
Dental Enamel
;
Dentin
;
Humans
;
Immersion
;
Rosaniline Dyes
;
Tooth
;
Tooth Bleaching
;
Urea*
7.The Revised Edition of Korean Calendar for Allergenic Pollens.
Jae Won OH ; Ha Baik LEE ; Im Joo KANG ; Seong Won KIM ; Kang Seo PARK ; Myung Hee KOOK ; Bong Seong KIM ; Hey Sung BAEK ; Joo Hwa KIM ; Ja Kyung KIM ; Dong Jin LEE ; Kyu Rang KIM ; Young Jin CHOI
Allergy, Asthma & Immunology Research 2012;4(1):5-11
The old calendar of pollens did not reflect current pollen distribution and concentrations that can be influenced by changes of weather and environment of each region in South Korea. A new pollen calendar of allergenic pollens was made based on the data on pollen concentrations obtained in eight regions nationwide between 1997 and 2009. The distribution of pollen was assessed every day at 8 areas (Seoul, Guri, Busan, Daegu, Jeonju, Kwangju, Kangneung, and Jeju) for 12 years between July 1, 1997 and June 30, 2009. Pollens were collected by using Burkard 7-day sampler (Burkard Manufacturing Co Ltd, UK). Pollens which were stained with Calberla's fuchsin staining solution were identified and counted. Pine became the highest pollen in May, and the pollen concentrations of oak and birch also became high. Ragweed appeared in the middle of August and showed the highest pollen concentration in the middles of September. Japanese hop showed a high concentration between the middle of August and the end of September, and mugwort appeared in the middles of August and its concentration increased up until early September. In Kangneung, birch appeared earlier, pine showed a higher pollen concentration than in the other areas. In Daegu, Oriental thuja and alder produced a large concentration of pollens. Pine produced a large concentration of pollens between the middle of April and the end of May. Weeds showed higher concentrations in September and mugwort appeared earlier than ragweed. In Busan the time of flowering is relatively early, and alder and Oriental thuja appeared earliest among all areas. In Kwangju, Oriental thuja and hazelnut appeared in early February. Japanese cedar showed the highest pollen concentration in March in Jeju. In conclusion, update information on pollen calendar in South Korea should be provided for allergic patients through the website to manage and prevent the pollinosis.
Allergens
;
Alnus
;
Ambrosia
;
Artemisia
;
Asian Continental Ancestry Group
;
Betula
;
Corylus
;
Cryptomeria
;
Flowers
;
Humans
;
Humulus
;
Pollen
;
Republic of Korea
;
Rhinitis, Allergic, Seasonal
;
Rosaniline Dyes
;
Thuja
;
Weather
8.Heterologous Expression of Phanerochaete chrysoporium Glyoxal Oxidase and its Application for the Coupled Reaction with Manganese Peroxidase to Decolorize Malachite Green.
Yu Lim SON ; Hyoun Young KIM ; Saravanakumar THIYAGARAJAN ; Jing Jing XU ; Seung Moon PARK
Mycobiology 2012;40(4):258-262
cDNA of the glx1 gene encoding glyoxal oxidase (GLX) from Phanerochaete chrysosporium was isolated and expressed in Pichia pastoris. The recombinant GLX (rGLX) produces H2O2 over 7.0 nmol/min/mL using methyl glyoxal as a substrate. Use of rGLX as a generator of H2O2 improved the coupled reaction with recombinant manganese peroxidase resulting in decolorization of malachite green up to 150 microM within 90 min.
Alcohol Oxidoreductases
;
DNA, Complementary
;
Glyoxal
;
Manganese
;
Organometallic Compounds
;
Oxidoreductases
;
Peroxidase
;
Peroxidases
;
Phanerochaete
;
Pichia
;
Rosaniline Dyes
9.Exploitation of Culture Medium for Mycobacterium tuberculosis.
Journal of Bacteriology and Virology 2011;41(4):237-244
The culture media for Mycobacterium tuberculosis (MTB) were contrived from both egg-based and agar based ingredients. In 1903, Dorset introduced the first egg-based medium. It was followed by the invention of Lowenstein-Jensen and Ogawa media that contain whole eggs as nutrient and malachite green to inhibit the growth of contaminants. These media have been used worldwide for their usefulness and inexpensiveness. However they have a fundamental disadvantage that the cultivation time for mycobacterial growth takes more than 4 weeks. In 1947, Dubos introduced the first agar medium and followed by the invention of the 7H10 by Middlebrook and Cohn. A powder base of these media contains agar, combination of seven salts, L-glutamic acid, pyridoxine, biotin, and malachite green. This requires the addition of the oleic acid, albumin, dextrose, and catalase (OADC) growth supplement. BACTEC MGIT960 has recently been introduced for rapid cultivation of MTB, which is fully automated liquid culture system with modified 7H9 broth. Agar-based medium developed by Middlebrook has a number of advantages over egg-based medium. One of them is transparency, which enables earlier detection of growing colonies. The major disadvantages of agar media are the high cost of OADC and the need for a CO2 incubator. In conclusion, there is a need for a new agar medium, which can be produced at a lower cost and earlier growth detection. In this review, we introduced the growth promoting factors which can be used as an alternative new growth supplement, cAMP and resuscitation-promoting factor (Rpf). These factors may abrogate a lag in adaption of the bacilli in culture media.
Agar
;
Biotin
;
Catalase
;
Culture Media
;
Eggs
;
Glucose
;
Glutamic Acid
;
Incubators
;
Inventions
;
Mycobacterium
;
Mycobacterium tuberculosis
;
Oleic Acid
;
Ovum
;
Pyridoxine
;
Rosaniline Dyes
;
Salts
10.A Case of Carbol Fuchsin Poisoning Successfully Treated with Hemoperfusion and Continuous Venovenous Hemodiafiltration.
Eun Jung HWANG ; Wi Jung KOOK ; Sul Ra LEE ; Ju Young MOON ; Kyung Whan JEONG ; Sang Ho LEE ; Chun Gyoo IHM ; Tae Won LEE
Korean Journal of Nephrology 2011;30(5):565-569
Carbol fuchsin is a mixture of phenol and basics fuchsin, used in bacterial staining procedures. It is a component of Ziehl-Neelsen stain. Phenol in Carbol fuchsin is a toxic agent which can lead to various gastrointestinal, ocular, skin, neurologic and renal side effects. We hereby report a case of Carbol fuchsin poisoned patient. Acute renal failure with metabolic acidosis was rapidly progressed. However, she was treated successfully by continuous veno-venous hemodiafiltration.
Acidosis
;
Acute Kidney Injury
;
Dialysis
;
Hemodiafiltration
;
Hemoperfusion
;
Humans
;
Phenol
;
Rosaniline Dyes
;
Skin

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