scholarly journals Sensitivity Assessment of Wilms tumor gene (WT1) expression in Glioblastoma Using qPCR and Immunohistochemistry and its association with IDH1 mutation, and recurrence interval 

2021 ◽  
Author(s):  
Maher Kurdi ◽  
Nadeem Shafique Butt ◽  
Saleh Baeesa ◽  
Abudukadeer Kuerban ◽  
Yazid Maghrabi ◽  
...  
Keyword(s):  
Gene Expression ◽  
Wilms Tumor ◽  
Quantitative Polymerase Chain Reaction ◽  
Idh1 Mutation ◽  
Biological Data ◽  
Recurrence Interval ◽  
Isocitrate Dehydrogenase 1 ◽  
Female Ratio ◽  
Sensitivity Assessment ◽  
Significant Difference

Abstract Background The Wilms tumor 1 (WT1) gene has recently been shown to play a role in gliomagenesis, making it a potential immunotherapy target in glioblastomas. We aimed to investigate the most sensitive method to detect WT1 expression in glioblastoma and explore relationship between WT1 expression and isocitrate dehydrogenase-1 (IDH1) mutation. Methods Clinical and biological data were collected from 44 patients with totally resected glioblastomas, treated with adjuvant therapies, in the period between 2015 and 2019. WT1 protein expression was assessed in all cases using IHC while its gene expression was assessed in 13 clustered samples using quantitative polymerase chain reaction (qPCR). IDH1 mutation was assessed using immunohistochemistry (IHC). McNemar test was used to compare the sensitivity between IHC and RT-qPCR for WT1 gene expression detection. Kaplan Meier curves were used to compare the distribution of recurrence-free interval (RFI) between IDH1 and WT1 expression groups. Results The mean age was 54-years, with a male to female ratio 1.45. IDH1-wildtype was found in 26 cases (59.1%) and the remining 18 cases (40.9%) were IDH1-mutant. Through IHC, WT1 was overexpressed in 32 cases (72.7%), partially expressed in 9 cases (20.5%) and not expressed in only three cases (6.8%). For the 13 cases tested by qPCR, 6 cases showed WT1 gene up-regulation and 7 cases showed WT1 down-regulation. There was no significant difference in WT1 expression among cases with different RNA concentrations regardless the testing method (P-value < 0.05). However, the difference between IHC and qPCR revealed 83% sensitivity, 28.5% specificity and 53% accuracy. IDH1-mutant cases with WT1 overexpression showed significant difference in recurrence interval (P-value < 0.048). This significance was not seen among IDH1-mutant cases with WT1 partial or no expression (P-value = 0.56). There was also no significant difference in recurrence interval among IDH1-wildtype cases with WT1 partial or overexpression (P-value = 0.83). Conclusions Parallel testing for WT1 expression using IHC and qPCR is not reliable. However, IHC provides more accurate results than does qPCR, which runs on fragmented tissue with indeterminant RNA concentrations. Moreover, IDH1-mutant glioblastomas with WT1 overexpression are associated with slow recurrence interval particularly if temozolomide with additional chemotherapies are used.

scholarly journals Sensitivity Assessment of Wilms Tumor Gene (WT1) Expression in Glioblastoma using qPCR and Immunohistochemistry and its Association with IDH1 Mutation and Recurrence Interval

2021 ◽  
Vol Volume 15 ◽  
pp. 289-297
Author(s):  
Maher Kurdi ◽  
Nadeem Shafique Butt ◽  
Saleh Baeesa ◽  
Abudukadeer Kuerban ◽  
Yazid Maghrabi ◽  
...  
Keyword(s):  
Wilms Tumor ◽  
Idh1 Mutation ◽  
Recurrence Interval ◽  
Wilms Tumor Gene ◽  
Sensitivity Assessment ◽  
Tumor Gene

scholarly journals The Impact of IDH1 Mutation and MGMT Promoter Methylation on Recurrence-Free Interval in Glioblastoma Patients Treated With Radiotherapy and Chemotherapeutic Agents

2021 ◽  
Vol 27 ◽  
Author(s):  
Maher Kurdi ◽  
Nadeem Shafique Butt ◽  
Saleh Baeesa ◽  
Badrah Alghamdi ◽  
Yazid Maghrabi ◽  
...  
Keyword(s):  
Promoter Methylation ◽  
Tumor Recurrence ◽  
Dna Methyltransferase ◽  
Chemotherapeutic Agents ◽  
Idh1 Mutation ◽  
Treatment Modalities ◽  
Isocitrate Dehydrogenase 1 ◽  
Free Interval ◽  
Significant Difference ◽  
The Impact

The aim of this study is to investigate the relationship between isocitrate dehydrogenase-1 (IDH1) mutation and O6-methylguanine-DNA methyltransferase (MGMT) promoter methylation with recurrence-free interval in glioblastoma patients treated with chemoradiotherapies. Clinical data were collected from 82 patients with totally resected glioblastoma and treated with adjuvant therapies from 2014 to 2019. IDH1 mutation was assessed by immunohistochemistry and MGMT promoter methylation was assessed by different sequencing methods. IDH1 mutation was present in 32 cases and 50 cases were IDH1 wildtype; 54 and 28 patients had unmethylated and methylated MGMT promoter, respectively, Of the 82 patients, 62 patients received chemoradiotherapy while 20 patients only received radiation. Approximately, 61% of patients had a tumor recurrence after 1 year, and 39% showed a recurrence before 1 year of treatment. There was no significant relationship between IDH1 mutation and MGMT promoter methylation (p-value = 0.972). Patients with IDH1 mutation and their age &lt;50 years showed a significant difference in recurrence-free interval (p-value = 0.014). Difference in recurrence-free interval was also statistically observed in patients with unmethylated MGMT promoter and treated with chemoradiotherapies (p-value = 0.031), by which they showed a late tumor recurrence (p-value = 0.016). This revealed that IDH1 mutation and MGMT methylation are independent prognostic factors in glioblastoma. Although IDH1-mutant glioblastomas showed late tumor recurrence in patients less than 50 years old, the type of treatment modalities may not show additional beneficial outcome. Patients with unmethylated MGMT and IDH1 mutation, treated with different chemoradiotherapies, showed a late tumor recurrence.

scholarly journals Spatial regulation of gene expression in nonsyndromic sagittal craniosynostosis

2018 ◽  
Vol 22 (6) ◽  
pp. 620-626 ◽  
Author(s):  
Garrett N. Cyprus ◽  
Jefferson W. Overlin ◽  
Rafael A. Vega ◽  
Ann M. Ritter ◽  
René Olivares-Navarrete
Keyword(s):  
Gene Expression ◽  
Wnt Signaling ◽  
Transforming Growth Factor ◽  
Quantitative Polymerase Chain Reaction ◽  
Regulation Of Gene Expression ◽  
Micro Ct ◽  
Sagittal Suture ◽  
Sagittal Craniosynostosis ◽  
Significant Difference ◽  
Suture Fusion

OBJECTIVECranial suture patterning and development are highly regulated processes that are not entirely understood. While studies have investigated the differential gene expression for different sutures, little is known about gene expression changes during suture fusion. The aim of this study was to examine gene expression in patent, fusing, and fused regions along sagittal suture specimens in nonsyndromic craniosynostosis patients.METHODSSagittal sutures were collected from 7 patients (average age 4.5 months) who underwent minimally invasive craniotomies at the Children’s Hospital of Richmond at VCU under IRB approval. The sutures were analyzed using micro-CT to evaluate patency. The areas were classified as open, fusing, or fused and were harvested, and mRNA was isolated. Gene expression for bone-related proteins, osteogenic and angiogenic factors, transforming growth factor–β (TGF-β) superfamily, and Wnt signaling was analyzed using quantitative polymerase chain reaction and compared with normal sutures collected from fetal demise tissue (control).RESULTSMicro-CT demonstrated that there are variable areas of closure along the length of the sagittal suture. When comparing control samples to surgical samples, there was a significant difference in genes for Wnt signaling, TGF-β, angiogenic and osteogenic factors, bone remodeling, and nuclear rigidity in mRNA isolated from the fusing and fused areas of the sagittal suture compared with patent areas (p < 0.05).CONCLUSIONSIn nonsyndromic sagittal craniosynostosis, the affected suture has variable areas of being open, fusing, and fused. These specific areas have different mRNA expression. The results suggest that BMP-2, FGFR3, and several other signaling pathways play a significant role in the regulation of suture fusion as well as in the maintenance of patency in the normal suture.

scholarly journals The Potential Effect of the IDH1 Mutation and MGMT Gene Promotor Methylation on the Control of Glioblastoma-Associated Epilepsy in Patients Receiving Anti-Epileptic Agents and Chemotherapies

2021 ◽  
Author(s):  
Maher Kurdi ◽  
Nadeem Shafique Butt ◽  
Saleh Baeesa ◽  
Badrah Alghamdi ◽  
Yazid Maghrabi ◽  
...  
Keyword(s):  
Tumor Recurrence ◽  
Dna Methyltransferase ◽  
Seizure Control ◽  
Potential Effect ◽  
Idh1 Mutation ◽  
Recurrence Interval ◽  
Effective Control ◽  
Isocitrate Dehydrogenase 1 ◽  
Methylguanine Dna Methyltransferase ◽  
Anti Epileptic Drug

Abstract Objective: (a) To assess the control of glioblastoma-associated seizure in patients receiving different anti-epileptic drugs and chemotherapies after total resection and its association with O-methylguanine-DNA methyltransferase (MGMT) promotor methylation and the isocitrate dehydrogenase 1 (IDH1) mutation; (b) to determine which anti-epileptic drug exerts the best effective control on glioblastoma-associated epilepsy; (c) to identify the relationship between seizure control and different anti-epileptic drugs and recurrence interval. Methods: This was a retrospective cohort study of patients with postoperative glioblastoma-associated epilepsy in the period between 2014 and 2019. The correlations between the IDH1 mutation and MGMT promotor methylation with anti-epileptic drugs, chemotherapy type, seizure control, and recurrence interval were analyzed using different statistical methods. Results: This study included 53 adult patients with glioblastoma-associated epilepsy. The IDH1 mutation was present in 20 patients, and MGMT promotor methylation was present in 13 patients. Out of 53 patients, 37 cases received chemoradiotherapy while 16 cases receive only radiotherapy. Levetiracetam was the most prescribed anti-epileptic drug (n= 36, 60%), and 36 and 16 patients had controlled and uncontrolled seizures, respectively. The IDH1 mutation and unmethylated MGMT promotor were significantly present in cases with controlled epilepsy (P < 0.05). Among the anti-epileptic drugs, levetiracetam showed significantly better seizure control in cases with the IDH1 mutation and unmethylated MGMT promotor (P < 0.05). Patients did not show significant differences in either seizure control or the tumor recurrence interval (P > 0.05).Conclusion: (a) Glioblastoma-associated epilepsy can be better controlled in patients with the IDH1 mutation and unmethylated MGMT promotor compared with patients with the methylated MGMT promotor, (b) Levetiracetam is considered the first-line anti-epileptic drug for controlling seizures but may not enhance the sensitivity of glioblastomas to chemotherapies, (c) Lack of seizure control in glioblastoma patients may not be related to tumor recurrence despite one-year treatment with anti-epileptic drugs, (d) Better understanding of the risk factors and mechanisms associated with glioma-associated epilepsy are needed to improve patient quality of life.

scholarly journals Digital Droplet PCR is a Specific and Sensitive Tool for Detecting IDH2 Mutations in Acute Myeloid LeuKemia Patients

Cancers ◽  
2020 ◽  
Vol 12 (7) ◽  
pp. 1738 ◽  
Author(s):  
Susanna Grassi ◽  
Francesca Guerrini ◽  
Elena Ciabatti ◽  
Riccardo Puccetti ◽  
Serena Salehzadeh ◽  
...  
Keyword(s):  
Residual Disease ◽  
Quantitative Polymerase Chain Reaction ◽  
Progression Free Survival ◽  
Rapid Screening ◽  
Amplification Refractory Mutation System ◽  
Isocitrate Dehydrogenase 1 ◽  
Digital Droplet Pcr ◽  
Significant Difference ◽  
Droplet Pcr ◽  
Acute Myeloid

Isocitrate dehydrogenase 1 and 2 (IDH1 and IDH2) interfere with cellular metabolism contributing to oncogenesis. Mutations of IDH2 at R140 and R172 residues are observed in 20% of acute myeloid leukemias (AML), and the availability of the IDH2 inhibitor Enasidenib made IDH2 mutational screening a clinical need. The aim of this study was to set a new quantitative polymerase chain reaction (PCR) technique, the drop-off digital droplet PCR (drop-off ddPCR), as a sensitive and accurate tool for detecting IDH2 mutations. With this technique we tested 60 AML patients. Sanger sequencing identified 8/60 (13.5%) mutated cases, while ddPCR and the amplification refractory mutation system (ARMS) PCR, used as a reference technique, identified mutations in 13/60 (21.6%) cases. When the outcome of IDH2-mutated was compared to that of wild-type patients, no significant difference in terms of quality of response, overall survival, or progression-free survival was observed. Finally, we monitored IDH2 mutations during follow-up in nine cases, finding that IDH2 can be considered a valid marker of minimal residual disease (MRD) in 2/3 of our patients. In conclusion, a rapid screening of IDH2 mutations is now a clinical need well satisfied by ddPCR, but the role of IDH2 as a marker for MRD still remains a matter of debate.

scholarly journals High expression of RRM2 promotes the pathogenesis of malignant ovarian endometriosis.

2021 ◽  
Author(s):  
Binkai Yang ◽  
Yuanjing Hu ◽  
Tian Wang ◽  
Na Li ◽  
Wenwen Zhang
Keyword(s):  
Gene Expression ◽  
Ovarian Cancer ◽  
Malignant Transformation ◽  
Expression Profiles ◽  
Quantitative Polymerase Chain Reaction ◽  
Gene Expression Profiles ◽  
High Expression ◽  
Ovarian Endometriosis ◽  
Ki 67 ◽  
Significant Difference

Abstract Objective: Our objective was to investigate the upregulated expression of ribonucleotide reductase M2 (RRM2) in the ectopic endometrium (EC) of ovarian endometriosis (OE) patients that may indicate malignant transformation. RRM2 may be used as a marker of OE, which contribute to the research of the mechanism of the malignant transformation of OE.Methods: The gene expression profiles of ovarian cancer and OE were downloaded from Gene Expression Omnibus (GEO), and a common hub gene, RRM2, was identified. The expression of RRM2 was low in OE and high in ovarian cancer. A total of 44 patients with endometriosis-associated ovarian cancers (EAOC) and 44 with OE were enrolled in this study. Immunohistochemistry (IHC) and real-time quantitative polymerase chain reaction (RT-qPCR) were used to detect the expression of RRM2, while the relationship between RRM2 and Ki-67 was analyzed by IHC co-localization. Results: There was no significant difference in the expression of RRM2 in the eutopic endometrium (EU), EC, and cancer tissues of EAOC patients. Compared with OE patients, the mRNA and protein expression levels of RRM2 were higher in the EC of EAOC patients (p＜0.01). Moreover, the high expression of RRM2 was consistent with the expression of Ki-67 in EC of EAOC patients.Conclusions: The upregulated expression of RRM2 in the EC of OE patients may indicate malignant transformation. RRM2 may be used as a marker of OE, which allows the investigation of the mechanism of the malignant transformation of OE.

scholarly journals MEASUREMENT OF DNA DAMAGE, OXIDATIVE STRESS, AND GENE EXPRESSION OF β-CATENIN AND P53 GENES IN LIVER AND BRAIN OF MALE MICE RECEIVING MONOSODIUM L-GLUTAMATE MONOHYDRATE

2020 ◽  
pp. 127-132
Author(s):  
NOHA IBRAHIM SAID SALEM ◽  
HANAN R.H. MOHAMED ◽  
AREEG MOHAMED ABD-ELRAZEK
Keyword(s):  
Oxidative Stress ◽  
Gene Expression ◽  
Dna Damage ◽  
Oxidative Dna Damage ◽  
Quantitative Polymerase Chain Reaction ◽  
Significant Decline ◽  
Control Group ◽  
Group I ◽  
Significant Difference ◽  
P53 Genes

Introduction: Monosodium L-glutamate (MSG) monohydrate is a widespread nutritional additive and flavoring agent frequently consumed all over the world. In this study, we investigate the action of daily oral intake of MSG monohydrate in vivo using mammalian systems. Methods: Mice divided as follows: Group I (normal control), Group II, and Group III treated with MSG for 2 and 4 weeks, respectively. Brain and liver dissected out for the detection of fragmented DNA, DNA damage, and assay of oxidative stress markers. Moreover, expression levels of ß-Cat and p53 genes were measured by a real-time quantitative polymerase chain reaction. Results: The results showed a significant difference in MSG-treated group at the 2-time intervals than the control one regarding parameters of oxidative stress, and these were accompanied by a significant decline in glutathione (GSH) and a ratio of oxidized and reduced GSH in both tissues. Significant elevation of laddered DNA and oxidative DNA damage was observed in groups treated with MSG. In addition, a significant decline in gene expression of ß-Catenin in liver and brain tissues with elevations in the gene expression of p53 in the brain. Furthermore, the p53 gene in liver tissue was significantly upregulated in mice administered MSG for 15 days and was downregulated after 30 days of MSG intake compared with the control. Conclusion: According to our results, oral consumption of MSG leads to oxidative stress-mediated DNA damage and apoptosis.

scholarly journals Reductive regulation of BECN1 gene in adult Egyptian patients with do novo AML

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Manal Fawzy Ghozlan ◽  
Botheina Ahmed Thabet Farweez ◽  
Nesma Ahmed Safwat ◽  
Noha Bassiouny Hassan ◽  
Walaa Ali Elsalakawy
Keyword(s):  
Gene Expression ◽  
Bone Marrow ◽  
Peripheral Blood ◽  
De Novo ◽  
Quantitative Polymerase Chain Reaction ◽  
Control Group ◽  
Significant Difference ◽  
Egyptian Patients ◽  
Blast Cells ◽  
De Novo Aml

Abstract Background Acute myeloid leukaemia (AML) is a clonal haematopoietic disease characterized by the proliferation of immature blast cells in the bone marrow and peripheral blood. Autophagy is an inherent cellular route by which waste macromolecules are engulfed within autophagosomes prior to their fusion with cytoplasmic lysosomes for degradation. The BECN1 gene encodes the Beclin-1 protein, which regulates autophagy. Few reports have investigated BECN1 gene expression and its value in AML patients. Results This randomized case-control study included 50 newly diagnosed AML patients, in addition to 20 subjects as a control group. BECN1 gene expression was assessed using real-time quantitative polymerase chain reaction (qRT-PCR). The median level of BECN1 gene expression in AML patients was 0.41 (IQR 0.29–1.03) in comparison to 1.12 (IQR 0.93–1.26) in the control group (P = 0.000). Seventy-two percent of AML patients showed reduced BECN1 gene expression, which was highly significantly associated with intermediate and adverse cytogenetic risk. Reduced BECN1 gene expression was associated with older age, higher total leukocyte counts, the presence of peripheral blood blast cells, a higher percentage of bone marrow blast cells, and higher expression of CD34 and CD117. FLT3-ITD mutation was detected in 14 patients (38.9%), all of whom showed reduced BECN1 gene expression (P = 0.006). BECN1 gene expression was also reduced in non-responder AML patients, with a highly statistically significant difference (P = 0.002). Conclusion A reduction in BECN1 gene expression might indicate a poor prognosis in adult Egyptian patients with de novo AML. Decreased BECN1 gene expression is associated with a higher risk of resistance to treatment. Targeting autophagy pathways may help in the treatment of AML patients.

scholarly journals Persistent homology analysis of brain transcriptome data in autism

2019 ◽  
Vol 16 (158) ◽  
pp. 20190531 ◽  
Author(s):  
Daniel Shnier ◽  
Mircea A. Voineagu ◽  
Irina Voineagu
Keyword(s):  
Gene Expression ◽  
Cerebral Cortex ◽  
Gene Expression Data ◽  
Persistent Homology ◽  
Point Clouds ◽  
Autism Spectrum ◽  
Biological Data ◽  
Expression Data ◽  
Complex Disorders ◽  
Significant Difference

Persistent homology methods have found applications in the analysis of multiple types of biological data, particularly imaging data or data with a spatial and/or temporal component. However, few studies have assessed the use of persistent homology for the analysis of gene expression data. Here we apply persistent homology methods to investigate the global properties of gene expression in post-mortem brain tissue (cerebral cortex) of individuals with autism spectrum disorders (ASD) and matched controls. We observe a significant difference in the geometry of inter-sample relationships between autism and healthy controls as measured by the sum of the death times of zero-dimensional components and the Euler characteristic. This observation is replicated across two distinct datasets, and we interpret it as evidence for an increased heterogeneity of gene expression in autism. We also assessed the topology of gene-level point clouds and did not observe significant differences between ASD and control transcriptomes, suggesting that the overall transcriptome organization is similar in ASD and healthy cerebral cortex. Overall, our study provides a novel framework for persistent homology analyses of gene expression data for genetically complex disorders.

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