scholarly journals Characterization and expression analysis of four members genes of flavanone 3-hydroxylase families from Chamaemelum nobile

2020 ◽  
Vol 48 (1) ◽  
pp. 102-115
Author(s):  
Shuiyuan CHENG ◽  
Qiling SONG ◽  
Tian YU ◽  
Xiaomeng LIU ◽  
Lanlan WANG ◽  
...  
Keyword(s):  
Binding Sites ◽  
Bioinformatics Analysis ◽  
Expression Patterns ◽  
Secondary Structures ◽  
High Similarity ◽  
Expression Levels ◽  
Traditional Chinese Herbal Medicine ◽  
Chinese Herbal ◽  
Significant Difference ◽  
Chamaemelum Nobile

Chamaemelum nobile is a traditional Chinese herbal medicine, whose secondary metabolites used in the pharmacology of Chinese medicine. Among them, the flavonoids have great research value. Flavanone 3-hydroxylase (F3H) is one of the core enzymes in the early steps of flavonoid biosynthesis. This study aimed to elucidate the structures, functions, and expression levels of F3H families from C. nobile. Four members of the F3H family were screened from C. nobile transcriptome data and performed bioinformatics analysis. Results showed that CnF3H1~4 had a high similarity with the other F3H plants, and all genes contained two conserved isopenicillin N synthase-like and oxoglutarate/iron-dependent dioxygenase domains. Further analysis revealed that the four CnF3H proteins contained some differences in binding sites. The results of secondary and 3-D structures displayed that the composition and proportion of the four CnF3H secondary structures were basically the same, and their 3D structures were consistent with the secondary structures. The phylogenetic tree displayed that CnF3H2, CnF3H3, and CnF3H4 were grouped with Asteraceae. The expression patterns of CnF3Hs in the roots, stems, leaves, and flowers of C. nobile were evaluated using the value of RPKM. The results indicated that CnF3Hs had significant difference in the expression of different tissues. Especially, CnF3H1~3 and CnF3H4 had the highest expression levels in the flowers and roots, respectively. Hence, CnF3Hs played a significant role in the flavonoid metabolism.

scholarly journals Bioinformatics Analysis of Allele Frequencies and Expression Patterns of ACE2, TMPRSS2 and FURIN in Different Populations and Susceptibility to SARS-CoV-2

Genes ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 1041
Author(s):  
Mohammad Tarek ◽  
Hana Abdelzaher ◽  
Firas Kobeissy ◽  
Hassan A. N. El-Fawal ◽  
Mohammed M. Salama ◽  
...  
Keyword(s):  
Immune Response ◽  
Genetic Factors ◽  
Bioinformatics Analysis ◽  
Expression Patterns ◽  
Spike Protein ◽  
Target Cells ◽  
Health Crisis ◽  
Expression Levels ◽  
Different Populations ◽  
Shed Light

The virus responsible for the COVID-19 global health crisis, SARS-CoV-2, has been shown to utilize the ACE2 protein as an entry point to its target cells. The virus has been shown to rely on the actions of TMPRSS2 (a serine protease), as well as FURIN (a peptidase), for the critical priming of its spike protein. It has been postulated that variations in the sequence and expression of SARS-CoV-2’s receptor (ACE2) and the two priming proteases (TMPRSS2 and FURIN) may be critical in contributing to SARS-CoV-2 infectivity. This study aims to examine the different expression levels of FURIN in various tissues and age ranges in light of ACE2 and TMPRSS2 expression levels using the LungMAP database. Furthermore, we retrieved expression quantitative trait loci (eQTLs) of the three genes and their annotation. We analyzed the frequency of the retrieved variants in data from various populations and compared it to the Egyptian population. We highlight FURIN’s potential interplay with the immune response to SARS-CoV-2 and showcase a myriad of variants of the three genes that are differentially expressed across populations. Our findings provide insights into potential genetic factors that impact SARS-CoV-2 infectivity in different populations and shed light on the varying expression patterns of FURIN.

scholarly journals Evaluation of circulating miRNAs and mRNAs expression patterns in autism spectrum disorder

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Amany H. Abdelrahman ◽  
Ola M. Eid ◽  
Mona H. Ibrahim ◽  
Safa N. Abd El-Fattah ◽  
Maha M. Eid ◽  
...  
Keyword(s):  
Autism Spectrum Disorder ◽  
Gene Family ◽  
Complex Disease ◽  
Expression Patterns ◽  
Normal Volunteer ◽  
Disease Diagnosis ◽  
Autism Spectrum ◽  
Spectrum Disorder ◽  
Expression Levels ◽  
Significant Difference

Abstract Background Autism spectrum disorder is a condition related to brain development that affects a person’s perception and socialization, resulting in problems in social interaction and communication. It has no single known cause, yet several different genes appear to be involved in autism. As a genetically complex disease, dysregulation of miRNA expression and miRNA–mRNA interactions might be a feature of autism spectrum disorder. The aim of the current study was to investigate the expression profile of circulating miRNA-128, miRNA-7 and SHANK gene family in ASD patients and to assess the possible influence of miRNA-128 and miRNA-7 on SHANK genes, which might provide an insight into the pathogenic mechanisms of ASD and introduce noninvasive molecular biomarkers for the disease diagnosis and prognosis. Quantitative real-time PCR technique was employed to determine expression levels of miRNA-128, miRNA-7 and SHANK gene family in blood samples of 40 autistic cases along with 30 age- and sex-matched normal volunteer subjects. Results Our study revealed a statistical significant upregulation of miRNA-128 expression levels in ASD cases compared to controls (p value < 0.001). A statistical significant difference in SHANK-3 expression was encountered on comparing cases to controls (p value < 0.001). However, miRNA-7 expression showed no significant difference between the studied groups. Conclusions MiRNA-128 and SHANK-3 gene are emerging players in the field of ASD. They are promising candidates as noninvasive biomarkers in autism. Future studies are needed to emphasize their pivotal role.

scholarly journals Gujin Dan is A Chinese Medicine Formulation That Stimulates Cell Proliferation And Differentiation By Controlling Multiple Genes Involved In MC3T3-E1 Cells

2021 ◽  
Author(s):  
Yu Zhou ◽  
Chaozong Liu ◽  
Zhenwei Zhou ◽  
Xin Li ◽  
Songchuan Su ◽  
...  
Keyword(s):  
Cell Proliferation ◽  
Chinese Medicine ◽  
Expression Patterns ◽  
Osteoclast Formation ◽  
Alizarin Red ◽  
Gene Markers ◽  
Expression Levels ◽  
Chinese Herbal ◽  
Alkaline Phosphatase Staining ◽  
Proliferation And Differentiation

Abstract Background: The development of Chinese medicine has been practised in China over a long period of time, and China has long used single medicines in various forms of decoction to treat illnesses, and later learned to combine several medicines to form formulas to enhance the effects of the medicines. The use of Chinese herbal medicines and formulas has played a pivotal role in the prevention and treatment of diseases in China since ancient times. The application of Chinese herbal preparations in the field of osteoporosis treatment has received widespread attention, and Gujin Dan（GJD） is one of the representative herbal formulas, however, the exact minute mechanism of its treatment of osteoporosis remains to be elucidated.Methods: In the study, we prepared an aqueous extract of GJD and measured the effect of different administration concentrations of GJD on cell proliferation by CCK-8 assay, and the effect of GJD on cell differentiation ability by Alizarin Red S Staining, Alkaline Phosphatase Staining and quantitative assay. Changes in gene expression patterns of MC3T3-E1 cells under GJD treatment were investigated by RNA-seq analysis and validation methods.Results: We demonstrate that GJD promotes the proliferation and differentiation of Mc3t3-e1 cells through the regulation of multiple functional genes. This was mainly achieved by regulating the expression levels of four categories of genes that promote the proliferation of Mc3t3-e1 cells or osteoblasts, inhibit apoptosis and autophagy, inhibit osteoclast formation and differentiation, and promote osteoblast differentiation. In addition, GJD slightly increased the expression levels of gene markers in osteoblasts. Conclusions: Our findings suggest that GJD promotes proliferation and differentiation of MC3T3-E1 cells and inhibits osteoclastogenesis and differentiation, as well as apoptosis and autophagy, through the synergistic interaction of various herbs and their active components in GJD. This study has significantly improved the current understanding of the molecular effects of GJD on MC3T3-E1 cells. This study also provides new ideas for possible strategies to further prevent and treat bone metabolism-related diseases using traditional Chinese medicinal preparations.

Correlations of ΔNp73 and TAp73 Expression Pattern with Specific Genetic Rearrengents in AML.

Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 4501-4501
Author(s):  
Antonio Roberto L. Araújo ◽  
Ana Silvia G. Lima ◽  
Rodrigo A. Panepucci ◽  
Eduardo M. Rego
Keyword(s):  
Bone Marrow ◽  
De Novo ◽  
Expression Patterns ◽  
Reference Sample ◽  
Distinct Pattern ◽  
Dominant Negative ◽  
Leukemic Cells ◽  
Transactivation Domain ◽  
Expression Levels ◽  
Significant Difference

Abstract The p73 protein is a p53 homolog and acts on cell cycle and apoptosis regulation. Resistance to apoptosis is a common feature of Acute Myeloid Leukemia (AML), but mutations on the genes p53 and p73 are rare. It is translated in two distinct isoforms: TAp73 and ΔNp73. The later does not possess the N-terminal transactivation domain and exerts a dominant negative action over TAp73 and p53 functions. Theoretically an aberrant high expression of ΔNp73 may lead to a block of p53 and TAp73, thus conferring a proliferative advantage to the leukemic cells. In order to evaluate this issue, we proposed to: Compare the gene expression levels of TAp73 and ΔNp73 isoforms in the bone marrow from de novo AML patients and normal individuals; Correlate these expression patterns with the presence of the rearrangements PML-RARα, AML1-ETO and CBFβ-MHY11, (previously determined by RT-PCR according the BIOMED-1 protocol). From 137 AML patients whose samples were evaluated by Real Time PCR, 78 harbored the genetic rearrangements (referred to as RP group): PML-RARα (n = 30), AML1-ETO (n = 16) or CBFβ-MHY11 (n = 32), whereas in the 59 remaining samples these rearrangements were not detected (RN group). Additionally, CD34+ cell samples of 22 normal bone marrow donors were also evaluated. Sample input was normalized by GAPDH expression and the relative expression was calculated using the cell line k562 as reference sample. The mean expression of TAp73 and ΔNp73 was significantly lower on normal CD34+ cell compared to leukemic samples [(TAp73: mean (m) = 0.0162 ± standard deviation = 0.004 vs m = 0.623 ± 0.0845, p = 0,0047); (ΔNp73: m = 0.277 ± 0.09 vs m = 8.09 ± 1.34, p = 0,0215)]. A higher expression of TAp73 and ΔNp73 was observed on RN compared to RP samples [(TAp73: m = 0.992 ± 0.171 vs m = 0.344 ± 0.055, p &lt; 0,0001); (ΔNp73: m = 12.44 ± 2.434 vs m = 4.80 ± 1.382, p = 0,0046)]. There was no difference in the expression of TAp73 between PML-RARα positive samples (m = 0.391 ± 0.095) and the remaining leukemic samples (m = 0.688 ± 0.104, p = 0,1476). However, the expression levels of ΔNp73 were significantly lower in the PML-RARα positive samples (m = 2.656 ± 0.370 vs m = 9.62 ± 1.69, p = 0,0317). No significant difference was observed in ΔNp73 and TAp73 expression between PML-RARα positive samples and the remaining samples with gene rearrengements (TAp73: m = 0.391 ± 0.095 vs m = 0.3144 ± 0.0671, p = 0,4990; ΔNp73: m = 2.656 ± 0.37 vs m = 6.153 ± 2.221, p = 0,2205). When compared to AML1-ETO and CBFβ-MHY11, the RN samples had a higher expression level of TAp73 (m = 0.3144 ± 0.0672 vs m = 0.992 ± 0.1717, p = 0.001), while there was no significant difference on the expression levels of ΔNp73 (m = 6.15 ± 2.22 vs m = 12.44 ± 2.43, p = 0.0642). These findings suggest that both p73 isoforms pathways are involved in the leukemogenic process. Moreover, the lower expression of ΔNp73 in the group with gene rearrangements may contribute to its better prognosis. The distinct pattern of ΔNp73 isoforms expression in AML with PML-RARα rearrangements suggests that it may be associated to a distinct response to apoptotic stimuli and to treatment outcome.

scholarly journals Prolactin may serve as a regulator to promote vocal fold wound healing

2020 ◽  
Vol 40 (7) ◽  
Author(s):  
Haizhou Wang ◽  
Xueyan Li ◽  
Jieyu Lu ◽  
Paul Jones ◽  
Wen Xu
Keyword(s):  
Wound Healing ◽  
Signaling Pathways ◽  
Vocal Fold ◽  
Bioinformatics Analysis ◽  
Control Group ◽  
Treatment Target ◽  
Expression Levels ◽  
Significant Difference ◽  
Underlying Mechanisms

Abstract Reduced prolactin (PRL) has been shown to delay wound healing with a limited understanding of the underlying mechanisms. Here, we aim to explore the role of PRL in the repair of vocal fold (VF) injury. A microarray was used to detect the expressed levels of PRL in rat VF tissue at 1, 4, and 8 weeks after VF injury compared with normal uninjured rats. Then, a systematic bioinformatics analysis has been conducted to explore the literature-based biology network and signaling pathways involved in the repair of VF injury. The expression of PRL was significantly decreased in all VF injury groups (week 1, 4, and 8) compared with the control group (F stats = 280.34; P=4.88e-14), with no significant difference among the three VF injury groups (F stats = 1.97; P=0.18). Wounding has been shown to interfere with both PRL-promoting and inhibiting pathways that were involved in wound healing, including 11 PRL inhibitors and 6 PRL promoters. Our results reveal decreased PRL expression levels in VF injury, which is not in favor of the wound healing. The pathways identified may help in understanding the role of PRL as a treatment target for VF wound healing.

scholarly journals The correlation of fibrinogen-like protein-1 expression with the progression and prognosis of hepatocellular carcinoma

2021 ◽  
Author(s):  
Nanni Hua ◽  
Chen Yang ◽  
Anxian Chen ◽  
Yi Feng ◽  
Xianglei He ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Cell Lines ◽  
Bioinformatics Analysis ◽  
Prognostic Biomarker ◽  
Normal Liver ◽  
Online Data ◽  
Expression Levels ◽  
Immunohistochemistry Staining ◽  
Significant Difference ◽  
Edmondson Grade

Abstract Background ConclusionsFibrinogen-like protein-1 (FGL1), as the member of FREP superfamily, had been widely concerned as a major immune inhibitory ligand of LAG-3. Although FGL1 expression levels didn’t have significant difference in most of tumors via online data analysis, we found that it was down-regulated in liver cancer. Moreover, the correlation between FGL1 expression and the progression and prognosis of hepatocellular carcinoma (HCC) was still disputed. Methods In our study, firstly, we used bioinformatics analysis to define the expression profile and clinical significance of FGL1 in HCC. Then, we determined the FGL1 level in human HCC cell lines, tumor and normal liver tissues from HCC patients by western blot. Furthermore, tissue microassays were used to detect the expression of FGL1 through immunohistochemistry staining and verify whether FGL1 expression levels were associated with clinicopathological features of HCC patients. Results The results proved that FGL1 was down-regulated significantly in HCC cell lines and HCC tissues, corresponding with the results of our bioinformatics analysis. FGL1 expression levels in HCC were related to Edmondson grade and metastasis. Additionally, high FGL1 expression was related to better overall survival in HCC patients, indicating that the down-regulated FGL1 was correlated with poor prognosis and FGL1 might function as a tumor suppressor. Conclusions Taken together, expression levels of FGL1 may correlate with the progression and prognosis of HCC, and FGL1 could be a potential prognostic biomarker.

scholarly journals The correlation of fibrinogen-like protein-1 expression with the progression and prognosis of hepatocellular carcinoma

2021 ◽  
Author(s):  
Nanni Hua ◽  
Anxian Chen ◽  
Chen Yang ◽  
Hui Dong ◽  
Xianglei He ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Cell Lines ◽  
Bioinformatics Analysis ◽  
Prognostic Biomarker ◽  
Normal Liver ◽  
Online Data ◽  
Expression Levels ◽  
Immunohistochemistry Staining ◽  
Significant Difference ◽  
Edmondson Grade

Abstract Fibrinogen-like protein-1 (FGL1), as the member of FREP superfamily, had been widely concerned as a major immune inhibitory ligand of LAG-3. Although FGL1 expression levels didn’t have significant difference in most of tumors via online data analysis, we found that it was down-regulated in liver cancer. Moreover, the correlation between FGL1 expression and the progression and prognosis of hepatocellular carcinoma (HCC) was still disputed. In our study, firstly, we used bioinformatics analysis to define the expression profile and clinical significance of FGL1 in HCC. Then, we determined the FGL1 level in 9 human HCC cell lines and 11 pairs of tumor and normal liver tissues from HCC patients by western blot. Furthermore, tissue microassays were used to detect the expression of FGL1 through immunohistochemistry staining and verify whether FGL1 expression levels were associated with clinicopathological features of HCC patients or not. The results of the experiment proved that FGL1 was down-regulated significantly in HCC cell lines and HCC tissues, corresponding with the results of our bioinformatics analysis. FGL1 expression levels in HCC were related to Edmondson grade and metastasis. Additionally, high FGL1 expression was related to better overall survival in HCC patients, indicating that the down-regulated FGL1 was correlated with poor prognosis and FGL1 might function as a tumor suppressor. Taken together, expression levels of FGL1 may correlate with the progression and prognosis of HCC, and FGL1 could be a potential prognostic biomarker.

scholarly journals Expression Changes of the FOXE1 and Lncrna PTCSC2 Expression in Tumor Tissues Compared with Normal Tissues in Patients with Colorectal Cancer

2022 ◽  
Author(s):  
Marzieh Ghani Dehkordi ◽  
Maryam Peymani
Keyword(s):  
Colorectal Cancer ◽  
Tumor Tissue ◽  
Expression Patterns ◽  
Study Groups ◽  
Expression Level ◽  
P Value ◽  
Expression Levels ◽  
Normal Tissues ◽  
Tumor Tissues ◽  
Significant Difference

Introduction: In recent studies, methylation of FOXE1 in colorectal cancer has been reported as a diagnostic biomarker. In this study for the first time, the expression of FOXE1 and PTCSC2 in colorectal cancer was investigated and their expression patterns in two healthy and tumor tissues of patients were compared. Methods: In this study, 40 tumor tissues with colorectal cancer and 40 adjacent normal samples were collected. Total RNA was extracted and cDNA synthesis followed. Then, the specific genes for lncRNA PTCSC2 and FOXE1 were amplified. The results were statistically analyzed by Graph Pad Prism software and a T-test was used to compare the expression levels of lncRNA PTCSC2 and FOXE1 in the patients and healthy group; p-value less than 0.05 was considered significant difference criteria. Results: In this study, the FOXE1 expression level was significantly decreased in tumor tissue (p-value = 0.005), whereas the lncRNA PTCSC2 expression level in tumor tissue was not significantly changed (p-value = 0.65). In addition, the expression levels of FOXE1 and lncRNA PTCSC2 did not show a significant relation with disease progression and age of the patients. ROC curve for changes in FOXE1 and lncRNA PTCSC2 expression showed that theFOXE1 gene could be a relatively appropriate independent variable (p-value = 0.03) to differentiate between the two study groups. Conclusion: According to the results of this study, changes in FOXE1 gene expression were significantly reduced in tumor samples and can be used as a biomarker in tumor diagnosis in colorectal cancer.

Checkpoint expression pre and post chemoradiation in operable esophageal cancer.

2017 ◽  
Vol 35 (4_suppl) ◽  
pp. 139-139
Author(s):  
Ronan Joseph Kelly ◽  
Ali Hussainy Zaidi ◽  
Matthew Smith ◽  
Ashten N. Omstead ◽  
Juliann E. Kosovec ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Patterns ◽  
Immune Checkpoints ◽  
Tumor Control ◽  
P Value ◽  
Immune Modulators ◽  
Expression Levels ◽  
Significant Difference ◽  
Tonsil Tissue ◽  
Laser Capture

139 Background: PD-L1 expression has been reported in 40% of gastroesophageal cancers, but little data exists with regards to expression of other immune checkpoints. Here, we examined baseline expression levels for multiple immune modulators in 31 resected esophageal adenocarcinomas (EAC) and investigated the change in expression levels post-chemoradiation. Methods: Slides were stained on a Ventana BenchMark ULTRA automated stainer for CTLA-4 (Santa Cruz Clone F-8, dilutions 1:100) and PD-L1 (Dako clone 22C3 prediluted). Tonsil tissue was used as a control for lymphocytes, and a provided tumor control was used for PD-L1. Positivity was classified as > 1%, and the stained cell type was recorded (lymphocytes or tumor). Additionally, laser capture microdissection was performed, and RNA was isolated and pre-amplified to determine expression levels of TIM-3, GITR, IDO-1, LAG-3, CD-137, OX-40, and KIR-3 using RT-PCR. Gene expression was calculated using the ΔΔ -Ct method, and intergroup comparisons were performed and normalized against a cohort of 15 pathologically confirmed normal esophageal epithelium cases. Results: Post-chemoradiation cases demonstrated increased expression for PD-L1, when compared to matched pre-chemoradiation controls [p-value = 0.0098]. Similarly, all immune modulators profiled by gene expression were significantly upregulated in matched post vs. pre samples, except for CD-137. There was no significant difference in percentage of 4-fold or more upregulation based on PD-L1 status for IDO-1, OX-40, CD-137 and KIR-1, indicating that these markers may function independently of PD-L1 positivity. Conclusions: PD-1 inhibiton in both the neoadjuvant and adjuvant setting is currently being investigated in EAC, but future studies may look to select patients according to personalized checkpoint expression patterns. [Table: see text]

scholarly journals Down-Regulation of Laminin (LN)- α5 is Associated with Preeclampsia and Impairs Trophoblast Cell Viability and Invasiveness Through PI3K Signaling Pathway

2018 ◽  
Vol 51 (5) ◽  
pp. 2030-2040 ◽  
Author(s):  
Xue Mei Zhang ◽  
Xi Xiong ◽  
Chao Tong ◽  
Qin Li ◽  
Shuai Huang ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Expression Patterns ◽  
Causative Factor ◽  
Mortality And Morbidity ◽  
Expression Levels ◽  
Significant Difference ◽  
Proliferation And Apoptosis ◽  
Pi3k Signaling Pathway ◽  
Polymerase Chain ◽  
Bisulfite Sequencing Pcr

Background/Aims: Preeclampsia (PE) is a gestational disorder defined as hypertension and proteinuria, which is deemed a major cause of maternal and neonatal mortality and morbidity worldwide. The aim of this study was to investigate the expression patterns of placental laminin (LN)-α5 expression in normal and PE pregnancies, as well as evaluating the effects of LN-α5 on trophoblast proliferation, apoptosis, and invasion. Methods: LN-α5 expression levels were examined by reverse-transcriptase polymerase chain reaction (RT-PCR), and further confirmed by western blotting and immunofluorescence staining. Cell proliferation and apoptosis were measured by CCK-8 assay and flow cytometry. Cell invasion was assessed by matrigel-based transwell assay. LN-α5 DNA methylation in placentas was determined by bisulfite sequencing PCR (BSP). Results: LN-α5 expression levels in PE placentas were significantly lower than that of normal pregnancies. Deficiency in LN-α5 expression resulted in decreased trophoblast proliferation and invasion but increased cell apoptosis, meanwhile, PI3K/AKT/mTOR signaling pathway was impaired by LN-α5 silencing. LN-α5 promoter methylation didn’t show significant difference between PE and normal placentas. Conclusion: LN-α5 downregulation is associated with PE placenta and impairs trophoblast viability and invasiveness, which could be a causative factor of PE pathogenesis.

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