Distinct transcriptional profiles in plasma exosomes associated with recurrence of nasopharyngeal carcinoma patients with standard treatment.

2020 ◽  
Vol 38 (15_suppl) ◽  
pp. 6534-6534
Author(s):  
Yongjiang Li ◽  
Xue Zheng ◽  
Xiaoqi Xie ◽  
Yukai Hu ◽  
Jingbo Kang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Nasopharyngeal Carcinoma ◽  
Survival Data ◽  
Standard Treatment ◽  
Expression Profiles ◽  
Endoplasmic Reticulum Membrane ◽  
Rna Expression ◽  
Biological Processes ◽  
Cox Regression Analysis ◽  
Wide Range

6534 Background: Nasopharyngeal carcinoma (NPC) is endemic with a high prevalence in Southern China, Asia,cetuximab and North Africa. Exosomes are small vesicles containing a wide range of functional proteins, mRNA and miRNA. In the progression of NPC, the tumor cells constantly release exosomes into the surrounding environment and also into the circulating blood. The aim of this study was to explore the association between RNA expression in plasma exosomes and prognosis of NPC patients after standard treatment. Methods: In this retrospective study, a total of 25 eligible NPC patients were included: 12 patients in the recurrence (R) subgroup and 13 patients in the no recurrence (NR) subgroup. RNA was extracted from the exosomes of plasma specimens which were collected at West China Hospital, Sichuan University. Gene expression profiles were conducted by using the RNA-sequencing platform. The DESeq2 package was used to analyze the differentially expressed genes (DEGs) between R and NR subgroups. The gene set variance analysis (GSVA) was performed to explore C5 gene sets enrichment related to the recurrence after standard treatment. Results: We observed 332 DEGs between R and NR subgroups, which include 125 up-regulated and 207 down-regulated genes (R vs. NR,∣log2fold change∣>1, p<0.05). Moreover, hierarchical clustering analysis of the 332 DEGs revealed that all samples clustered into two subgroups, with cluster 1 containing 82% (9/11) recurrence patients and cluster 2 containing 79% (11/14) no recurrence patients. Further, univariate Cox regression analysis showed that 293 out of 332 DEGs were significantly correlated with DFS ( p<0.05), such as TRAM1, CAPN1, SAT1 and ACTB. GSVA and Log Rank test of survival data demonstrated that a total of 824 pathways/biological processes were significantly different between R andNR subgroups ( p<0.05). Specifically, the top 9 pathways/biological processes, such lipoxygenase pathway, rough endoplasmic reticulum membrane and low density lipoprotein particle clearance, was mainly enriched in the NR subgroup ( p <0.001). Conclusions: Profiling of plasma exosomes RNA in NPC patients reveals distinctive gene expression pattern between patients with or without recurrence. Further functional analysis revealed that top enriched 9 pathways/biological processes may correlate with a favorable prognosis and are worth investigating. Moreover, for the prognosis of patients with NPC, RNA expression of plasma exosomes may be a potentially valuable research object.

An International Multi-Center Microarray Study for the Molecular Classification of Leukemia Identifies Novel Sub-Groupings in MDS Overlapping with AML.

Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 852-852
Author(s):  
Ken I. Mills ◽  
Torsten Haferlach ◽  
Jesus M. Hernandez ◽  
Wolf-Karsten Hofmann ◽  
Alexander Kohlmann ◽  
...  
Keyword(s):  
Gene Expression ◽  
Survival Data ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Molecular Classification ◽  
Control Group ◽  
Wide Range ◽  
Gene Expression Signatures ◽  
Highly Correlated ◽  
Microarray Classification

Abstract Microarrays can identify robust gene expression signatures associated with distinct sub-classes of paediatric and adult leukemias. Recently, the MILE (Microarray Innovations in LEukemia) study has analysed 1901 expression profiles from retrospective samples in 11 centres (ELN: 7, USA: 3, Singapore: 1). MILE has compared the microarray classification accuracy of 16 acute and chronic leukaemia subclasses, MDS, and non-leukaemia as control group, to routine diagnostic workup. The achieved cross-validation accuracy was very high for the leukaemia subclasses: ~96%. Included in the study were 175 samples diagnosed as MDS, however, only 49.1% of these samples were correctly called as MDS from their underlying gene expression profiles. The remainder were approximately equally split between a call of “non-leukaemia” (24%) and “AML” (24.6%). A further sub-division of MDS samples called “AML”: 81% called as “AML with normal or other cytogenetics”; and the remainder as “AML with complex cytogenetics”. MDS is a heterogeneous group of disorders with a wide range in blast cell count, cytogenetics and number of cytopenias. Our analysis showed that neither study centre nor age were a factor in differentiating between “MDS”, “AML” or “non-leukaemia”. However, WHO classification was highly correlated with the microarray classification result; specifically RAEB(I or II) was associated with “AML” call (p &lt; 0.0001). RA/RARS was highly correlated with “MDS” or “non-leukaemia” calls. Furthermore, IPSS was significantly correlated with call (p&gt;0.0001): 65% of patients with an IPSS score of Int-2 or above were classified as “AML”. Examination of the individual components of the IPSS showed that two patients classified as “AML” had a blast count of &gt;20%, under the WHO definition these would be defined as AML and were excluded. Individually, the blast, karyotype and cytopenia contributions were highly significant (p&lt;0.0001, &lt;0.013 and &lt;0.0001 respectively) when comparing “AML”, “MDS” and “non-leukemia” calls. All the “non-leukemia” patients had &lt;10% blasts, with 85% (34/40) having a cytogenetic score of 0 (Normal or Good (1 of: -Y, del(5q), del(20q))) and 82.5% having only 0 or 1 cytopenias. In contrast, 45% of the “AML” samples had between 11 & 20% blasts, 32% with intermediate (0.5) or poor/complex (1) cytogenetic score and 79% had 2 or 3 cytopenias. Furthermore, survival data was available for 122 of the diagnosed MDS patients and showed that MDS patients called “AML” had a trend towards shorter survival (2P=0.2) than those called “MDS” or “non-leukaemia”. These analyses, in combination with gene expression signatures, may contribute to a redefinition of MDS classifications.

scholarly journals Analysis of the transcriptome of bovine endometrial cells isolated by laser micro-dissection (1): specific signatures of stromal, glandular and luminal epithelial cells

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Wiruntita Chankeaw ◽  
Sandra Lignier ◽  
Christophe Richard ◽  
Theodoros Ntallaris ◽  
Mariam Raliou ◽  
...  
Keyword(s):  
Gene Expression ◽  
Protein Localization ◽  
Expression Profiles ◽  
Cell Types ◽  
Molecular Signature ◽  
Receptor Protein ◽  
Specific Gene ◽  
Specific Cell ◽  
Biological Processes ◽  
Endometrial Cells

Abstract Background A number of studies have examined mRNA expression profiles of bovine endometrium at estrus and around the peri-implantation period of pregnancy. However, to date, these studies have been performed on the whole endometrium which is a complex tissue. Consequently, the knowledge of cell-specific gene expression, when analysis performed with whole endometrium, is still weak and obviously limits the relevance of the results of gene expression studies. Thus, the aim of this study was to characterize specific transcriptome of the three main cell-types of the bovine endometrium at day-15 of the estrus cycle. Results In the RNA-Seq analysis, the number of expressed genes detected over 10 transcripts per million was 6622, 7814 and 8242 for LE, GE and ST respectively. ST expressed exclusively 1236 genes while only 551 transcripts were specific to the GE and 330 specific to LE. For ST, over-represented biological processes included many regulation processes and response to stimulus, cell communication and cell adhesion, extracellular matrix organization as well as developmental process. For GE, cilium organization, cilium movement, protein localization to cilium and microtubule-based process were the only four main biological processes enriched. For LE, over-represented biological processes were enzyme linked receptor protein signaling pathway, cell-substrate adhesion and circulatory system process. Conclusion The data show that each endometrial cell-type has a distinct molecular signature and provide a significantly improved overview on the biological process supported by specific cell-types. The most interesting result is that stromal cells express more genes than the two epithelial types and are associated with a greater number of pathways and ontology terms.

scholarly journals Gene Expression Profiles at Moxibustioned Site (ST36): A Microarray Analysis

2013 ◽  
Vol 2013 ◽  
pp. 1-7 ◽  
Author(s):  
Hai-Yan Yin ◽  
Yong Tang ◽  
Sheng-Feng Lu ◽  
Ling Luo ◽  
Jia-Ping Wang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Microarray Analysis ◽  
Expression Profiles ◽  
Alternative Therapy ◽  
Gene Expression Profiles ◽  
Biological Processes ◽  
Physiological Conditions ◽  
Pathological Conditions ◽  
Molecular Events ◽  
Zusanli Acupoint

As a major alternative therapy in Traditional Chinese Medicine, it has been demonstrated that moxibustion could generate a series of molecular events in blood, spleen, and brain, and so forth. However, what would happen at the moxibustioned site remained unclear. To answer this question, we performed a microarray analysis with skin tissue taken from the moxibustioned site also Zusanli acupoint (ST36) where 15-minute moxibustion stimulation was administrated. The results exhibited 145 upregulated and 72 downregulated genes which responded immediately under physiological conditions, and 255 upregulated and 243 downregulated genes under pathological conditions. Interestingly, most of the pathways and biological processes of the differentially expressed genes (DEGs) under pathological conditions get involved in immunity, while those under physiological conditions are involved in metabolism.

scholarly journals Gene Expression in RET/PTC3 and E7 Transgenic Mouse Thyroids: RET/PTC3 But Not E7 Tumors Are Partial and Transient Models of Human Papillary Thyroid Cancers

Endocrinology ◽  
2008 ◽  
Vol 149 (10) ◽  
pp. 5107-5117 ◽  
Author(s):  
Agnès Burniat ◽  
Ling Jin ◽  
Vincent Detours ◽  
Natacha Driessens ◽  
Jean-Christophe Goffard ◽  
...  
Keyword(s):  
Gene Expression ◽  
Fusion Gene ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Human Thyroid ◽  
Matrix Remodeling ◽  
Biological Processes ◽  
Papillary Thyroid ◽  
Thyroid Cancers ◽  
Transient Models

We studied gene expression profiles in two mouse models of human thyroid carcinoma: the Tg-RET/PTC3 (RP3) and Tg-E7 mice. RP3 fusion gene is the most frequent mutation found in the first wave post-Chernobyl papillary thyroid cancers (PTCs). E7 is an oncoprotein derived from the human papillomavirus 16 responsible for most cervical carcinoma in women. Both transgenic mice develop thyroid hyperplasia followed by solid differentiated carcinoma in older animals. To understand the different steps leading to carcinoma, we analyzed thyroid gene expression in both strains at different ages by microarray technology. Important biological processes were differentially regulated in the two tumor types. In E7 thyroids, cell cycle was the most up-regulated process, an observation consistent with the huge size of these tumors. In RP3 thyroids, contrary to E7 tumors, several human PTC characteristics were observed: overexpression of many immune-related genes, regulation of human PTC markers, up-regulation of EGF-like growth factors and significant regulation of angiogenesis and extracellular matrix remodeling-related genes. However, similarities were incomplete; they did not concern the overall gene expression and were not conserved in old animals. Therefore, RP3 tumors are partial and transient models of human PTC. They constitute a good model, especially in young animals, to study the respective role of the biological processes shared with human PTC and will allow testing drugs targeting these validated variables.

scholarly journals Identification of Hub Prognosis-Associated Oxidative Stress Genes in Pancreatic Cancer Using Integrated Bioinformatics Analysis

2020 ◽  
Vol 11 ◽  
Author(s):  
Xin Qiu ◽  
Qin-Han Hou ◽  
Qiu-Yue Shi ◽  
Hai-Xing Jiang ◽  
Shan-Yu Qin
Keyword(s):  
Oxidative Stress ◽  
Gene Expression ◽  
Pancreatic Cancer ◽  
Cancer Progression ◽  
Risk Model ◽  
Cox Regression ◽  
Expression Profiles ◽  
The Cancer Genome Atlas ◽  
Differentially Expressed ◽  
Cox Regression Analysis

BackgroundIntratumoral oxidative stress (OS) has been associated with the progression of various tumors. However, OS has not been considered a candidate therapeutic target for pancreatic cancer (PC) owing to the lack of validated biomarkers.MethodsWe compared gene expression profiles of PC samples and the transcriptome data of normal pancreas tissues from The Cancer Genome Atlas (TCGA) and Genome Tissue Expression (GTEx) databases to identify differentially expressed OS genes in PC. PC patients’ gene profile from the Gene Expression Omnibus (GEO) database was used as a validation cohort.ResultsA total of 148 differentially expressed OS-related genes in PC were used to construct a protein-protein interaction network. Univariate Cox regression analysis, least absolute shrinkage, selection operator analysis revealed seven hub prognosis-associated OS genes that served to construct a prognostic risk model. Based on integrated bioinformatics analyses, our prognostic model, whose diagnostic accuracy was validated in both cohorts, reliably predicted the overall survival of patients with PC and cancer progression. Further analysis revealed significant associations between seven hub gene expression levels and patient outcomes, which were validated at the protein level using the Human Protein Atlas database. A nomogram based on the expression of these seven hub genes exhibited prognostic value in PC.ConclusionOur study provides novel insights into PC pathogenesis and provides new genetic markers for prognosis prediction and clinical treatment personalization for PC patients.

scholarly journals Characterization of Metabolites and Transcripts Involved in Flower Pigmentation in Primula vulgaris

2020 ◽  
Vol 11 ◽  
Author(s):  
Long Li ◽  
Jing Ye ◽  
Houhua Li ◽  
Qianqian Shi
Keyword(s):  
Gene Expression ◽  
Metabolic Networks ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Flower Color ◽  
Myb Transcription Factor ◽  
High Accumulation ◽  
Primula Vulgaris ◽  
Wide Range

Primula vulgaris exhibits a wide range of flower colors and is a valuable ornamental plant. The combination of flavonols/anthocyanins and carotenoids provides various colorations ranging from yellow to violet-blue. However, the complex metabolic networks and molecular mechanisms underlying the different flower colors of P. vulgaris remain unclear. Based on comprehensive analysis of morphological anatomy, metabolites, and gene expression in different-colored flowers of P. vulgaris, the mechanisms relating color-determining compounds to gene expression profiles were revealed. In the case of P. vulgaris flower color, hirsutin, rosinin, petunidin-, and cyanidin-type anthocyanins and the copigment herbacetin contributed to the blue coloration, whereas peonidin-, cyandin-, and delphinidin-type anthocyanins showed high accumulation levels in pink flowers. The color formation of blue and pink were mainly via the regulation of F3′5′H (c53168), AOMT (c47583, c44905), and 3GT (c50034). Yellow coloration was mainly due to gossypetin and carotenoid, which were regulated by F3H (c43100), F3 1 (c53714), 3GT (c53907) as well as many carotenoid biosynthetic pathway-related genes. Co-expression network and transient expression analysis suggested a potential direct link between flavonoid and carotenoid biosynthetic pathways through MYB transcription factor regulation. This work reveals that transcription changes influence physiological characteristics, and biochemistry characteristics, and subsequently results in flower coloration in P. vulgaris.

scholarly journals Circular RNA Expression Profiles in Nasopharyngeal Carcinoma by Sequence Analysis

2020 ◽  
Vol 10 ◽  
Author(s):  
Jing Yang ◽  
Yongqian Gong ◽  
Qingshan Jiang ◽  
Lijun Liu ◽  
Shuyan Li ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Nasopharyngeal Carcinoma ◽  
Expression Profiles ◽  
Circular Rna ◽  
Rna Expression

Human Platelet-Derived Factors Regulate Mesenchymal Stem Cell Gene Expression.

Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 4255-4255
Author(s):  
Christina Malischnik ◽  
Katharina Schallmoser ◽  
Eva Rohde ◽  
Andreas Reinisch ◽  
Christian Guelly ◽  
...  
Keyword(s):  
Gene Expression ◽  
Stem Cell ◽  
Growth Factors ◽  
Human Platelet ◽  
Ex Vivo ◽  
Expression Profiles ◽  
Cell Structure ◽  
Considerable Proportion ◽  
Biological Processes ◽  
Regulated Gene Expression

Abstract The use of animal-derived products during human stem cell processing bears the evident risk of xenogeneic prion, virus, or zoonose contamination. Human platelet lysate (HPL) has recently been recognized as a rich source of cytokines and growth factors with the potential to replace fetal bovine serum (FBS) during ex vivo stem cell manipulation. In this study we compared the gene expression profile of human multipotent mesenchymal stromal/stem cells (MSC) during ex vivo expansion for clinical applications under the aegis of either FBS or HPL. The Applied Biosystems 1700 Expression Array System was used for full genome expression profiling of MSC after a 12–14 day expansion period in a previously optimized low density expansion system. Data have been obtained from biological as well as technical replicates. A starting amount of 40μg total RNA was directly labeled and DIG-labeled cDNA was hybridized to Human Genome Survey Microarray V2.0. Attribution of regulated genes to biological processes and pathways was done using the PANTHER® db analysis software. We identified more than 300 genes that are differentially regulated upon culture of MSC in HPL compared to FBS. Biological processes specifically activated in HPL culture include mesoderm development, cell cycle control, hematopoiesis and angiogenesis which interestingly correspond to a considerable proportion of the regenerative function of MSC. In contrast, processes related to cell adhesion and adhesion-mediated signaling, cell structure, cell motility and cell communication are significantly upregulated in MSC after FBS in comparison to HPL culture. Replacing FBS with HPL not only avoids bovine prion, viral and zoonose contamination of MSC for clinical use. The tightly regulated gene expression profiles under the aegis of human growth factors and cytokines provided by HPL may even help to develop new stem cell therapy strategies.

scholarly journals Overlapping and Unique Roles for C-Terminal Binding Protein 1 (CtBP1) and CtBP2 during Mouse Development

2002 ◽  
Vol 22 (15) ◽  
pp. 5296-5307 ◽  
Author(s):  
Jeffrey D. Hildebrand ◽  
Philippe Soriano
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Genetic Interaction ◽  
Binding Protein ◽  
Biological Processes ◽  
Vertebrate Development ◽  
Mouse Development ◽  
Axial Patterning ◽  
Wide Range

ABSTRACT The C-terminal binding protein (CtBP) family of proteins has been linked to multiple biological processes through their association with numerous transcription factors. We generated mice harboring mutations in both Ctbp1 and Ctbp2 to address the in vivo function of CtBPs during vertebrate development. Ctbp1 mutant mice are small but viable and fertile, whereas Ctbp2-null mice show defects in axial patterning and die by E10.5 due to aberrant extraembryonic development. Mice harboring various combinations of Ctbp1 and Ctbp2 mutant alleles exhibit dosage-sensitive defects in a wide range of developmental processes. The strong genetic interaction, as well as transcription assays with CtBP-deficient cells, indicates that CtBPs have overlapping roles in regulating gene expression. We suggest that the observed phenotypes reflect the large number of transcription factors whose activities are compromised in the absence of CtBP.

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