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1.
Braz. j. med. biol. res ; 54(3): e10152, 2021. tab, graf
Article in English | LILACS | ID: biblio-1153522

ABSTRACT

The goal of this study was to identify potential transcriptomic markers in pediatric septic shock prognosis by an integrative analysis of multiple public microarray datasets. Using the R software and bioconductor packages, we performed a statistical analysis to identify differentially expressed (DE) genes in pediatric septic shock non-survivors, and further performed functional interpretation (enrichment analysis and co-expression network construction) and classification quality evaluation of the DE genes identified. Four microarray datasets (3 training datasets and 1 testing dataset, 252 pediatric patients with septic shock in total) were collected for the integrative analysis. A total of 32 DE genes (18 upregulated genes; 14 downregulated genes) were identified in pediatric septic shock non-survivors. Enrichment analysis revealed that those DE genes were strongly associated with acute inflammatory response to antigenic stimulus, response to yeast, and defense response to bacterium. A support vector machine classifier (non-survivors vs survivors) was also trained based on DE genes. In conclusion, the DE genes identified in this study are suggested as candidate transcriptomic markers for pediatric septic shock prognosis and provide novel insights into the progression of pediatric septic shock.


Subject(s)
Humans , Child , Shock, Septic/diagnosis , Shock, Septic/genetics , Transcriptome , Biomarkers , Computational Biology , Gene Expression Profiling , Microarray Analysis
2.
Article in Chinese | WPRIM | ID: wpr-879621

ABSTRACT

OBJECTIVE@#To explore the value of chromosomal microarray analysis (CMA) for the diagnosis of fetuses with high risk signaled by non-invasive prenatal testing (NIPT).@*METHODS@#From June 2017 to August 2019, 628 pregnant women with high risk signaled by NIPT underwent invasive prenatal diagnosis. Amniotic fluid or cord blood samples were subjected to chromosomal karyotyping analysis or CMA. Pregnancy outcome and postnatal conditions of the fetuses were followed up.@*RESULTS@#The positive predictive value for trisomy 21, trisomy 18, trisomy 13, sex chromosome aneuploidy, other rare trisomies and copy number variants (CNVs) among the 628 women were 86.4% (127/147), 41.7% (30/72), 12.9% (4/31), 43.7% (101/231), 16.5% (14/85) and 52.2% (35/67), respectively. In 218 samples with normal karyotype, 5.5% (12/218) of additional pathogenic CNVs and 2.3% (5/218) of loss of heterozygosity were detected by CMA.@*CONCLUSION@#CMA combined with karyotyping analysis can be used as first-tier test for prenatal diagnosis for women with high-risk signaled by NIPT.


Subject(s)
Female , Humans , Karyotyping , Microarray Analysis , Pregnancy , Prenatal Diagnosis , Trisomy 13 Syndrome/genetics , Trisomy 18 Syndrome
3.
Article in Chinese | WPRIM | ID: wpr-879594

ABSTRACT

Chromosome microarray analysis (CMA) has become the first-tier testing for chromosomal abnormalities and copy number variations (CNV). This review described the clinical validation of CMA, the development and updating of technical standards and guidelines and their diagnostic impacts. The main focuses were on the development and updating of expert consensus, practice resources, and a series of technical standards and guidelines through systematic review of case series with CMA application in the literature. Expert consensus and practice resource supported the use of CMA as the first-tier testing for detecting chromosomal abnormalities and CNV in developmental and intellectual disabilities, multiple congenital anomalies and autism. The standards and guidelines have been applied to pre- and postnatal testing for constitutional CNV and tumor testing for acquired CNV. CMA has significantly improved the diagnostic yields but still needs to overcome its technical limitations and face challenges of new technologies. Guiding and governing CMA through expert consensus, practice resource, standards and guidelines in the United States has provided effective and safe diagnostic services to patients and their families, reliable diagnosis on related genetic diseases for clinical database and basic research, and references for clinical translation of new technologies.


Subject(s)
Child , Chromosome Aberrations , Chromosomes , DNA Copy Number Variations , Developmental Disabilities/genetics , Humans , Intellectual Disability/genetics , Microarray Analysis , United States
4.
Article in Chinese | WPRIM | ID: wpr-879568

ABSTRACT

OBJECTIVE@#To assess the value of chromosomal microarray analysis (CMA) for the prenatal diagnosis of a fetus with structural anomaly detected by ultrasonography.@*METHODS@#The fetus and its parents were subjected to chromosomal karyotyping and CMA analysis.@*RESULTS@#The fetus was found to carry a 46,XN,t(8;11)(q21.2;q13) translocation which was inherited from its mother. CMA has found no copy number variations (CNVs) in both parents but a de novo 2.00 Mb microdeletion in the fetus at 8q13.3.@*CONCLUSION@#CMA is capable of detecting microdeletions and microduplications in fetuses with translocations detected by karyotyping analysis.


Subject(s)
Chromosome Aberrations , Chromosome Deletion , Chromosomes, Human, Pair 8 , DNA Copy Number Variations , Female , Fetus , Humans , Karyotyping , Microarray Analysis , Pregnancy , Prenatal Diagnosis
5.
Article in Chinese | WPRIM | ID: wpr-879555

ABSTRACT

OBJECTIVE@#To assess the value of chromosomal microarray analysis (CMA) for fetal duodenal obstruction (DO).@*METHODS@#Fifty-one fetuses with DO identified by prenatal ultrasound were divided into DO only group and DO with other anomaly group. CMA was carried out on amniotic fluid or umbilical blood samples, and the outcome of pregnancy of all cases were followed up.@*RESULTS@#Eight fetuses (15.7%) were found with genomic abnormalities, which included 3 chromosomal aneuploidies and 5 copy number variations (CNVs), including one 17q12 microduplication syndrome, one 13q21.33q31.1 microdeletion, one 13q21.32q22.3 deletion, one 13q21.2q31.1 deletion and one 1q43q44 duplication. EDNRB from 13q and HNF1B from 17q12 are candidate genes for fetal DO. No significant difference was found in the detection rate of pathogenic CNVs between the DO only and DO with other anomaly groups (9.5% vs.11.1%, P> 0.05). There were 39 live borns, 1 stillbirth, and 11 artificial abortions (8 with abnormal CMA results).@*CONCLUSION@#There is a correlation between fetal DO and abnormal copy number of the genome, for which prenatal diagnosis is necessary. CMA not only can detect microdeletions/microduplications, but also identify pathogenic genes, which can facilitate prenatal diagnosis, genetic counseling and prognosis for the fetus.


Subject(s)
Chromosome Aberrations , DNA Copy Number Variations , Duodenal Obstruction/genetics , Female , Fetus , Humans , Microarray Analysis , Pregnancy , Prenatal Diagnosis
6.
Article in Chinese | WPRIM | ID: wpr-888398

ABSTRACT

OBJECTIVE@#To investigate the association of fetal cardiac structural abnormalities with chromosomal aneuploidies and copy number variations (CNVs) in amniocytes.@*METHODS@#328 pregnant women were subjected to fetal ultrasonography and chromosomal microarray analysis (CMA). Based on the fetal heart structure, the subjects were divided into normal (n=273) and abnormal groups (n=55). The detection rates of chromosomal aneuploidies and CNVs were compared between the two groups. Spearman method was used to assess the association between the results and fetal cardiac structural abnormalities.@*RESULTS@#The detection rates for chromosomal aneuploidies and CNVs in the abnormal group were significantly higher than that in the normal group (P< 0.05), and the incidence of fetal cardiac structural abnormalities was strongly associated with chromosomal aneuploidies and CNVs (P< 0.05).@*CONCLUSION@#Fetal chromosomal aneuploidies and CNVs are strongly associated with cardiac structural abnormalities.


Subject(s)
Aneuploidy , Chromosome Aberrations , DNA Copy Number Variations , Female , Fetus , Humans , Microarray Analysis , Pregnancy , Prenatal Diagnosis , Ultrasonography, Prenatal
7.
Article in Chinese | WPRIM | ID: wpr-888369

ABSTRACT

OBJECTIVE@#To analyze the prenatal diagnosis, parental verification and pregnancy outcome of 6 fetuses with 22q11.2 microdeletion syndrome.@*METHODS@#Copy number variation sequencing (CNV-seq)and chromosomal microarray analysis (CMA) were carried out for the fetuses.@*RESULTS@#The fetuses were found to harbor 2.54-3.2 Mb microdeletions of the 22q11.2 region, among which one was maternally inherited and one was paternally inherited. Two parents opted to continue with the pregnancy, and 4 chose induced labor. One fetus was found to have tetralogy of Fallot, while two carrier parents and one fetus appeared to have normal phenotype.@*CONCLUSION@#22q11.2 microdeletions identified upon prenatal diagnosis should be treated carefully, with ultrasonic scan and parental verification taken into account.


Subject(s)
DNA Copy Number Variations , Female , Fetus , Humans , Microarray Analysis , Pregnancy , Pregnancy Outcome , Prenatal Diagnosis , Ultrasonography, Prenatal
8.
Article in Chinese | WPRIM | ID: wpr-922036

ABSTRACT

OBJECTIVE@#To assess the correlation of borderline fetal ventriculomegaly with genomic copy number variations (CNVs) and outcome of pregnancy.@*METHODS@#For 84 singleton pregnancies diagnosed with VM, chromosomal microarray analysis (CMA) was carried out to detect the CNVs of the fetal genome. Outcome of the pregnancy and neonatal development were analyzed. The pregnant women were divided into mild group (10-12 mm), moderate group (12-15 mm) and severe group (>= 15 mm) based on the severity of fetal ventriculomegaly. The detection rate of pathogenic CNVs and pregnancy outcome were compared. Multivariate logistic regression was carried out to analyze the predictors for pregnancy outcome.@*RESULTS@#Respectively, 24, 28 and 32 fetuses were assigned into the mild, moderate and severe groups. CMA has detected 15 cases of chromosomal abnormalities, including 11 pathogenic CNVs and 4 abnormal karyotypes. Abnormal pregnancy outcomes were found in 20 fetuses, including 12 with hydrocephalus and 8 with chromosomal microdeletion syndromes. A significant difference was found in the detection rate of fetal pathogenic CNVs and abnormal pregnancy outcome among the three groups (P<0.05). Multivariate logistic regression analysis showed that the largest change of lateral ventricle width (OR = 1.868, 95%CI = 1.120-3.116) and the extent of lateral ventricle widening (OR = 1.571, 95%CI = 1.120-2.206) were the key factors affecting the outcome of pregnancy (P<0.05).@*CONCLUSION@#Borderline fetal VM is associated with the risk of pathogenic CNVs and adverse pregnancy outcome. A comprehensive examination is required after prenatal ultrasound diagnosis, which is conducive to prenatal consultation and prognostic evaluation of the fetus.


Subject(s)
Chromosome Aberrations , DNA Copy Number Variations , Female , Fetus , Humans , Hydrocephalus/genetics , Infant, Newborn , Microarray Analysis , Pregnancy , Pregnancy Outcome , Prenatal Diagnosis
9.
Article in Chinese | WPRIM | ID: wpr-921996

ABSTRACT

OBJECTIVE@#To analyze the prenatal ultrasound phenotypes of copy number variations (CNVs) in different regions of 22q11.2, their parental original, and pregnancy outcome.@*METHODS@#Prenatal phenotypes of 25 cases with CNVs of the 22q11.2 region detected by chromosomal microarray analysis (CMA) was reviewed, which including There were 13 deletions and 12 duplications. Multiplex ligation-dependent probe amplification(MLPA) was carried out to determine their parental origin. All cases were followed up for their pregnancy outcome and postnatal growth.@*RESULTS@#Among the 25 cases, the ultrasound phenotypes of those involving the TBX1 gene were mostly cardiovascular system abnormalities, the ultrasound phenotypes of cases involving CRKL gene are mostly polycystic renal dysplasia. The ultrasound phenotypes of CNVs in the distal region (involving the SMARCB1 gene) are nervous system abnormalities. 12 cases (48%) of CNVs were de novo in origin. Five cases were lost during follow-up,12 had opted to terminate the pregnancy, 8 fetuses were born,7 with normal growth and development, 1 case with CNV in A-D region was abnormal.Prenatal ultrasound showed abnormalities in the cardiovascular system consistent with postnatal ultrasound, in addition with dysphagia and growth retardation.@*CONCLUSION@#Prenatal phenotypes of the 22q11.2 region CNVs are diverse, which may be related to gene function. NT thickening may be used as an early ultrasound finding of proximal 22q11.2 CNV. More research is still required to delineate the nature of CNVs and gene function, so as to facilitate genetic counseling.


Subject(s)
DNA Copy Number Variations , Female , Fetus , Genetic Counseling , Humans , Microarray Analysis , Phenotype , Pregnancy , Prenatal Diagnosis
10.
Chinese Journal of Biotechnology ; (12): 4111-4123, 2021.
Article in Chinese | WPRIM | ID: wpr-921492

ABSTRACT

In case/control gene expression data, differential expression (DE) represents changes in gene expression levels across various biological conditions, whereas differential co-expression (DC) represents an alteration of correlation coefficients between gene pairs. Both DC and DE genes have been studied extensively in human diseases. However, effective approaches for integrating DC-DE analyses are lacking. Here, we report a novel analytical framework named DC&DEmodule for integrating DC and DE analyses and combining information from multiple case/control expression datasets to identify disease-related gene co-expression modules. This includes activated modules (gaining co-expression and up-regulated in disease) and dysfunctional modules (losing co-expression and down-regulated in disease). By applying this framework to microarray data associated with liver, gastric and colon cancer, we identified two, five and two activated modules and five, five and one dysfunctional module(s), respectively. Compared with the other methods, pathway enrichment analysis demonstrated the superior sensitivity of our method in detecting both known cancer-related pathways and those not previously reported. Moreover, we identified 17, 69, and 11 module hub genes that were activated in three cancers, which included 53 known and three novel cancer prognostic markers. Random forest classifiers trained by the hub genes showed an average of 93% accuracy in differentiating tumor and adjacent normal samples in the TCGA and GEO database. Comparison of the three cancers provided new insights into common and tissue-specific cancer mechanisms. A series of evaluations demonstrated the framework is capable of integrating the rapidly accumulated expression data and facilitating the discovery of dysregulated processes.


Subject(s)
Gene Expression Profiling , Gene Regulatory Networks , Humans , Microarray Analysis , Neoplasms/genetics
11.
Article in English | WPRIM | ID: wpr-921385

ABSTRACT

OBJECTIVES@#To identify the differentially expressed genes (DEGs) during the pathogenesis of periodontitis by bioinformatics analysis.@*METHODS@#GEO2R was used to screen DEGs in GSE10334 and GSE16134. Then, the overlapped DEGs were used for further analysis. g:Profiler was used to perform Gene Ontology analysis and pathway analysis for upregulated and downregulated DEGs. The STRING database was used to construct the protein-protein interaction (PPI) network, which was further visua-lized and analyzed by Cytoscape software. Hub genes and key modules were identified by cytoHubba and MCODE plug-ins, respectively. Finally, transcription factors were predicted via iRegulon plug-in.@*RESULTS@#A total of 196 DEGs were identified, including 139 upregulated and 57 downregulated DEGs. Functional enrichment analysis showed that the upregulated DEGs were mainly enriched in immune-related pathways including immune system, viral protein interaction with cytokine and cytokine receptor, cytokine-cytokine receptor interaction, leukocyte transendothelial migration, and chemokine receptors bind chemokines. On the contrary, the downregulated DEGs were mainly related to the formation of the cornified envelope and keratinization. The identified hub genes in the PPI network were CXCL8, CXCL1, CXCR4, SEL, CD19, and IKZF1. The top three modules were involved in chemokine response, B cell receptor signaling pathway, and interleukin response, respectively. iRegulon analysis revealed that IRF4 scored the highest.@*CONCLUSIONS@#The pathogenesis of periodontitis was closely associated with the expression levels of the identified hub genes including CXCL8, CXCL1, CXCR4, SELL, CD19, and IKZF1. IRF4, the predicted transcription factor, might serve as a dominant upstream regulator.


Subject(s)
Computational Biology , Gene Expression Profiling , Humans , Microarray Analysis , Periodontitis , Protein Interaction Maps
12.
Chinese Medical Journal ; (24): 268-275, 2021.
Article in English | WPRIM | ID: wpr-921236

ABSTRACT

BACKGROUND@#Chromosomal abnormalities are important causes of ventriculomegaly (VM). In mild and isolated cases of fetal VM, obstetricians rarely give clear indications for pregnancy termination. We aimed to calculate the incidence of chromosomal abnormalities and incremental yield of chromosomal microarray analysis (CMA) in VM, providing more information on genetic counseling and prognostic evaluation for fetuses with VM.@*METHODS@#The Chinese language databases Wanfang Data, China National Knowledge Infrastructure, and China Biomedical Literature Database (from January 1, 1991 to April 29, 2020) and English language databases PubMed, Embase, and Cochrane Library (from January 1, 1945 to April 29, 2020) were systematically searched for articles on fetal VM. Diagnostic criteria were based on ultrasonographic or magnetic resonance imaging (MRI) assessment of lateral ventricular atrium width: ≥10 to <15 mm for mild VM, and ≥15 mm for severe VM. Isolated VM was defined by the absence of structural abnormalities other than VM detected by ultrasonography or MRI. R software was used for the meta-analysis to determine the incidence of chromosomal abnormalities and incremental yield of CMA in VM, and the combined rate and 95% confidence interval (CI) were calculated.@*RESULTS@#Twenty-three articles involving 1635 patients were included. The incidence of chromosomal abnormalities in VM was 9% (95% CI: 5%-12%) and incremental yield of CMA in VM was 11% (95% CI: 7%-16%). The incidences of chromosomal abnormalities in mild, severe, isolated, and non-isolated VM were 9% (95% CI: 4%-16%), 5% (95% CI: 1%-11%), 3% (95% CI: 1%-6%), and 13% (95% CI: 4%-25%), respectively.@*CONCLUSIONS@#Applying CMA in VM improved the detection rate of abnormalities. When VM is confirmed by ultrasound or MRI, obstetricians should recommend fetal karyotype analysis to exclude chromosomal abnormalities. Moreover, CMA should be recommended preferentially in pregnant women with fetal VM who are undergoing invasive prenatal diagnosis. CMA cannot completely replace chromosome karyotype analysis.


Subject(s)
Chromosome Aberrations , Chromosomes , Female , Fetus , Humans , Hydrocephalus , Karyotyping , Microarray Analysis , Pregnancy , Prenatal Diagnosis , Retrospective Studies , Ultrasonography, Prenatal
13.
J. appl. oral sci ; 29: e20201074, 2021. tab, graf
Article in English | LILACS | ID: biblio-1340110

ABSTRACT

Abstract Hyperglycemia, a major characteristic of diabetes, is considered to play a vital role in diabetic complications. High glucose levels have been found to inhibit the mineralization of dental pulp cells. However, gene expression associated with this phenomenon has not yet been reported. This is important for future dental therapeutic application. Objective Our study aimed to investigate the effect of high glucose levels on mineralization of human dental pulp-derived cells (hDPCs) and identify the genes involved. Methodology hDPCs were cultured in mineralizing medium containing 25 or 5.5 mM D-glucose. On days 1 and 14, RNA was extracted and expression microarray performed. Then, differentially expressed genes (DEGs) were selected for further validation using the reverse transcription quantitative polymerase chain reaction (RT-qPCR) method. Cells were fixed and stained with alizarin red on day 21 to detect the formation of mineralized nodules, which was further quantified by acetic acid extraction. Results Comparisons between high-glucose and low-glucose conditions showed that on day 1, there were 72 significantly up-regulated and 75 down-regulated genes in the high-glucose condition. Moreover, 115 significantly up- and 292 down-regulated genes were identified in the high-glucose condition on day 14. DEGs were enriched in different GO terms and pathways, such as biological and cellular processes, metabolic pathways, cytokine-cytokine receptor interaction and AGE-RAGE signaling pathways. RT-qPCR results confirmed the significant expression of pyruvate dehydrogenase kinase 3 (PDK3), cyclin-dependent kinase 8 (CDK8), activating transcription factor 3 (ATF3), fibulin-7 (Fbln-7), hyaluronan synthase 1 (HAS1), interleukin 4 receptor (IL-4R) and apolipoprotein C1 (ApoC1). Conclusions The high-glucose condition significantly inhibited the mineralization of hDPCs. DEGs were identified, and interestingly, HAS1 and Fbln-7 genes may be involved in the glucose inhibitory effect on hDPC mineralization.


Subject(s)
Humans , Dental Pulp , Transcriptome , Cell Differentiation , Cells, Cultured , Microarray Analysis , Cell Proliferation , Glucose
14.
Rev. chil. obstet. ginecol. (En línea) ; 85(1): 68-73, feb. 2020. graf
Article in Spanish | LILACS | ID: biblio-1092777

ABSTRACT

INTRODUCCIÓN: La hipoplasia de timo es una entidad que puede asociarse a múltiples patologías fetales de ahí la importancia de su diagnóstico y su manejo. OBJETIVO: Utilidad y métodos de evaluación del timo en la ecografía morfológica y valor de la interpretación del análisis genético de los microarrays. CASO CLÍNICO: Se presenta el caso clínico de una gestante en la que se detecta una glándula tímica hipoplásica utilizando para su medición el índice timo-torácico en un plano de tres vasos. Ante estos hallazgos se realiza una amniocentesis para análisis genético usando la QF-PCR y un análisis ARRAY-CGH. RESULTADOS: En el análisis de ARRAY-CGH se observa una duplicación patológica en mosaico compatible con una trisomía del cromosoma 10, alteración genética infrecuente de la que se han reportado unos 50 casos en recién nacidos vivos. Esta alteración presenta un rango muy amplio de alteraciones, desde malformaciones graves a niños completamente normales. En los controles posteriores la gestación es normoevolutiva y finaliza en la semana 40 mediante un parto eutócico de inicio espontáneo naciendo un bebé fenotípicamente normal con un timo de menor tamaño del habitual siendo pronto para saber las consecuencias de esta alteración en su inmunidad. CONCLUSIONES: Por un lado, el timo es una estructura fácil de visualizar en la ecografía morfológica de la semana 20 y su medición mediante el índice timo-torácico nos aporta información útil acerca de posibles patologías fetales. Por otro, tener en cuenta que debemos ser muy cautelosos con la interpretación de resultados de pruebas genéticas cuando éstas no tienen un significado clínico claro.


INTRODUCTION : Thymus hypoplasia can associate many different pathologies so is highly important the diagnosis and the management. OBJECTIVE: Utility and methods in the evaluation of the fetal thymus in the morphological ultrasound and interpretation of microarray results. CLINICAL CASE: We present a case of fetal hypoplastic thymus gland in a pregnant woman. We measure it using the thymus-torax index in a three vessel view. A genetical analysis was made using QF-PCR and Array-CGH. RESULTS: In the ARRAY-CGH analysis it is found a pathological mosaicism that match with chromosome 10 trisomy, a very uncommon genetical alteration with only 50 reported cases. This trisomy can traduce from serious malformations to complete normal children. The parents decide to continue with the pregnancy and in week 40 it finishes with an uncomplicated delivery of a healthy child. In the newborn pediatrics remark a thymus gland smaller than expected but it is early to say if it will have or not consequences in its immunity. CONCLUSION: On one hand the thymus is a structure that we can easily display in the morphological ultrasound in the 20 week of pregnancy and its measure, using the thymus-torax index, can be very helpful in the detection of fetal pathologies. On the other hand, is important being careful when we interpret a genetical alteration without a clear clinical significance.


Subject(s)
Humans , Female , Pregnancy , Infant, Newborn , Thymus Gland/abnormalities , Thymus Gland/diagnostic imaging , Trisomy/genetics , Trisomy/diagnosis , Chromosomes, Human, Pair 10 , Polymerase Chain Reaction/methods , Ultrasonography, Prenatal , Chromosome Aberrations , Microarray Analysis , Amniocentesis
15.
Braz. j. med. biol. res ; 53(5): e9021, 2020. graf
Article in English | LILACS | ID: biblio-1098108

ABSTRACT

Lung cancer is the most common malignancy worldwide and is characterized by rapid progression, aggressive behavior, frequent recurrence, and poor prognosis. The TCGA database indicates that chondroitin polymerizing factor (CHPF) is overexpressed in human lung cancer tissues compared with normal tissues and this overexpression corresponds to shorter overall survival in lung cancer patients. In this study, to investigate the function of CHPF in lung cancer, lentiviral vectors expressing CHPF shRNA were stably transduced into A549 and H1299 cells. Compared to shCtrl cells, CHPF knockdown cells had significantly reduced proliferation. Furthermore, the silencing of CHPF in A549 and H1299 cells resulted in apoptotic induction, which led to decreased colony formation. Wound healing and transwell invasion assays revealed that CHPF could positively regulate the migration of lung cancer cells. The tumorigenic role of CHPF was also validated in nude mouse xenograft models. Affymetrix gene chip analysis indicated that CHPF regulated the proliferation and invasion of lung cancer cells through CDH1, RRM2, MKI67, and TNFRSF10B. We thus highlight CHPF as a novel target for lung cancer treatment.


Subject(s)
Humans , Animals , Female , Rabbits , Gene Expression Regulation, Neoplastic , N-Acetylgalactosaminyltransferases/metabolism , Lung Neoplasms/metabolism , Blotting, Western , N-Acetylgalactosaminyltransferases/genetics , Cell Line, Tumor , Microarray Analysis , Cell Proliferation , Real-Time Polymerase Chain Reaction , Lung Neoplasms/genetics , Mice, Inbred BALB C
16.
Biol. Res ; 53: 32, 2020. tab, graf
Article in English | LILACS | ID: biblio-1131880

ABSTRACT

BACKGROUND: Circulating RNA (circRNA) regulates various bioactivities in cells. A better understanding of the exosomal circRNA can provide novel insights into the pathogenesis and treatment of Graves' disease (GD). We aimed to profile the differentially expressed circRNAs (DEcRs) in plasma exosomes of patients with GD and speculate and probe the functions of the DEcR by comprehensive bioinformatics analyses. METHODS: Serum exosomes were isolated from five primary GD patients and five healthy controls via ultracentrifugation. After verification with transmission electron microscopy, exosome samples were subjected to microarray profiling using human circRNA microarrays. Two up-regulated and two down-regulated DEcRs were selected for validation in plasma exosomes from 20 GD and 20 healthy control participants using reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR). The circRNA/microRNA/mRNA interaction network was then assembled and the analysis of the Gene Ontology and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways was utilized to predict the potential functions of the DEcR associated genes. RESULTS: There were 15 DEcRs revealed in primary GD cases. The intronic circRNA hsa_circRNA_000102 was confirmed as an up-regulated component in plasma exosomes from patients with GD. The circRNA/microRNA/mRNA interaction network unveiled the most potential targeting microRNAs of hsa_circRNA_000102 and its associated genes. The functional analyses predicted involvement of hsa_circRNA_000102 associated genes in pathways of immune system activation, such as viral infection and interferon-beta signaling. CONCLUSIONS: hsa_circRNA_000102 is a differentially up-regulated plasma exosomal circRNA in patients with GD. Our study highlights multiple pathways, particularly virus infection and interferon-beta signaling, for mediating immune activation in Graves' disease.


Subject(s)
Humans , Male , Female , Graves Disease/genetics , Graves Disease/blood , Microarray Analysis , RNA, Circular/blood , RNA, Messenger , MicroRNAs , Exosomes
17.
Article in English | WPRIM | ID: wpr-785547

ABSTRACT

We present a 33-year-old male patient with cerebellar ataxia. He was first considered to have a psychiatric conversion disorder but finally found to have chromosomal deletion in 7q31.2-31.32 involving Ca2⁺-dependent activator protein for secretion (CADPS) gene. When a targeted gene sequencing using next-generation sequencing panel and chromosomal microarray analysis were performed, an 8.6 Mb deletion within chromosome 7q31.2-31.32 was discovered. Deletion of CADPS gene in the 7q31.2-31.32 was suggested as the causative factor of cerebellar ataxia. Functional levels evaluated by Berg balance scale and modified Barthel index were improved via comprehensive rehabilitation including balance training and a dopamine agonist medication. To the best of our knowledge, this is the first report of chromosomal deletion in 7q31.2-31.32 including CADPS gene detected in patients with cerebellar ataxia.


Subject(s)
Adult , Cerebellar Ataxia , Chromosome Disorders , Conversion Disorder , Dopamine Agonists , Humans , Male , Microarray Analysis , Rehabilitation
18.
Article in Chinese | WPRIM | ID: wpr-826552

ABSTRACT

OBJECTIVE@#To explore the genetic basis for a fetus with cleft lip and palate.@*METHODS@#Copy number variations (CNVs) in the fetus and his parents were detected with chromosomal microarray analysis (CMA).@*RESULTS@#As revealed by the CMA assay, the fetus has carried a 228 kb deletion in Xp11.22 region and a 721 kb duplication in 9p21.1. Both CNVs were inherited from the parents. The CNV in Xp11.22 was predicted to be pathogenic by involving the PHF8 gene, whilst the CNV in 9p21.1 was predicted to be benign.@*CONCLUSION@#Deletion of the Xp11.22 region probably underlies the cleft lip and palate in this fetus.


Subject(s)
Chromosome Deletion , Chromosomes, Human, X , Genetics , Cleft Lip , Diagnosis , Genetics , Cleft Palate , Diagnosis , Genetics , DNA Copy Number Variations , Female , Fetus , Histone Demethylases , Humans , Microarray Analysis , Methods , Pregnancy , Prenatal Diagnosis , Transcription Factors
19.
Article in Chinese | WPRIM | ID: wpr-781291

ABSTRACT

OBJECTIVE@#To assess the application value of chromosomal microarray analysis (CMA) for prenatal diagnosis of fetus with ultrasound abnormalities.@*METHODS@#For 293 fetuses with ultrasound abnormalities (including 168 with structural abnormalities and 125 with non-structured abnormalities) but no common chromosomal abnormalities, CMA assay was performed.@*RESULTS@#Sixteen pathogenic copy number variants (pCNVs) were detected by CMA with a detection rate of 5.46%. The detection rates were 5.95% (10/168) for those with structural abnormalities and 4.80% (6/125) for those with non-structural abnormalities.@*CONCLUSION@#Compared with conventional karyotyping analysis, CMA can improve the detection of fetal chromosomal abnormality and provide an effective means for prenatal diagnosis.


Subject(s)
Chromosome Aberrations , Chromosome Disorders , DNA Copy Number Variations , Female , Fetus , Congenital Abnormalities , Humans , Microarray Analysis , Reference Standards , Pregnancy , Prenatal Diagnosis , Methods , Ultrasonography, Prenatal
20.
Article in English | WPRIM | ID: wpr-811221

ABSTRACT

OBJECTIVE: With the emerging significance of genetic profiles in the management of endometrial cancer, the identification of tumor-driving genes with prognostic value is a pressing need. The LAMC1 gene, encoding the laminin subunit gamma 1 (LAMC1) protein, has been reported to be involved in the progression of various malignant tumors. In this study, we aimed to investigate the role of LAMC1 in endometrial cancer and elucidate the underlying mechanism.METHODS: We evaluated the immunohistochemical expression of LAMC1 in atypical endometrial hyperplasia and endometrial cancer. Within the endometrial cancer cases, we analyzed the association of LAMC1 overexpression with clinicopathological factors and prognosis. Furthermore, to indentify genes influenced by LAMC1 overexpression, we transfected HEC50B and SPAC-S cells with siRNA targeting LAMC1 and conducted microarray gene expression assays.RESULTS: While none of the atypical endometrial hyperplasia specimens exhibited LAMC1 overexpression, endometrial cancer possessed a significantly higher LAMC1 overexpression rate. LAMC1 overexpression was strongly associated with histological type, lymphovascular space invasion, lymph node metastasis, advanced International Federation of Gynecology and Obstetrics stage, and poor overall survival in endometrial cancer. Gene expression microarray analysis identified 8 genes correlated with tumor progression (LZTFL1, TAPT1, SEL1L, PAQR6, NME7, TMEM109, CCDC58, and ANKRD40) that were commonly influenced in HEC50B and SPAC-S by LAMC1 silencing.CONCLUSION: LAMC1 overexpression is a potent biomarker for identifying endometrial cancer patients needing aggressive adjuvant therapy. We elucidated 8 candidate genes that may mediate progression of LAMC1 overexpressing cancer. Further investigation of the underlying mechanism should lead to the discovery of new therapeutic targets.


Subject(s)
Endometrial Hyperplasia , Endometrial Neoplasms , Female , Gene Expression , Gene Expression Profiling , Gynecology , Humans , Laminin , Lymph Nodes , Microarray Analysis , Neoplasm Metastasis , Obstetrics , Prognosis , RNA, Small Interfering
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