scholarly journals miRNA expression profiling and zeatin dynamic changes in a new model system of in vivo indirect regeneration of tomato

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0237690
Author(s):  
Huiying Cao ◽  
Xinyue Zhang ◽  
Yanye Ruan ◽  
Lijun Zhang ◽  
Zhenhai Cui ◽  
...  
Keyword(s):  
Mirna Expression ◽  
Target Genes ◽  
Higher Plants ◽  
Callus Formation ◽  
Expression Patterns ◽  
Adventitious Shoot ◽  
Model System ◽  
Indirect Regeneration ◽  
Mirna Expression Profiling

Callus formation and adventitious shoot differentiation could be observed on the cut surface of completely decapitated tomato plants. We propose that this process can be used as a model system to investigate the mechanisms that regulate indirect regeneration of higher plants without the addition of exogenous hormones. This study analyzed the patterns of trans-zeatin and miRNA expression during in vivo regeneration of tomato. Analysis of trans-zeatin revealed that the hormone cytokinin played an important role in in vivo regeneration of tomato. Among 183 miRNAs and 1168 predicted target genes sequences identified, 93 miRNAs and 505 potential targets were selected based on differential expression levels for further characterization. Expression patterns of six miRNAs, including sly-miR166, sly-miR167, sly-miR396, sly-miR397, novel 156, and novel 128, were further validated by qRT-PCR. We speculate that sly-miR156, sly-miR160, sly-miR166, and sly-miR397 play major roles in callus formation of tomato during in vivo regeneration by regulating cytokinin, IAA, and laccase levels. Overall, our microRNA sequence and target analyses of callus formation during in vivo regeneration of tomato provide novel insights into the regulation of regeneration in higher plants.

scholarly journals MiRNA expression profiling and zeatin dynamic changes in a new model system of in vivo indirect regeneration of tomato

2020 ◽  
Author(s):  
Huiying Cao ◽  
Xinyue Zhang ◽  
Yanye Ruan ◽  
Lijun Zhang ◽  
Zhenhai Cui ◽  
...  
Keyword(s):  
Mirna Expression ◽  
Target Genes ◽  
Higher Plants ◽  
Callus Formation ◽  
Expression Patterns ◽  
Adventitious Shoot ◽  
Model System ◽  
Indirect Regeneration ◽  
Mirna Expression Profiling

AbstractCallus formation and adventitious shoot differentiation could be observed on the cut surface of completely decapitated tomato plants. We propose that this process can be used as a model system to investigate the mechanisms that regulate indirect regeneration of higher plants without the addition of exogenous hormones. This study analyzed the patterns of trans-zeatin and miRNA expression during in vivo regeneration of tomato. Analysis of trans-zeatin revealed that the hormone cytokinin played an important role in in vivo regeneration of tomato. Among 183 miRNAs and 1168 predicted target genes sequences identified, 93 miRNAs and 505 potential targets were selected based on differential expression levels for further characterization. Expression patterns of six miRNAs, including sly-miR166, sly-miR167, sly-miR396, sly-miR397, novel 156, and novel 128, were further validated by qRT-PCR. We speculate that sly-miR156, sly-miR160, sly-miR166, and sly-miR397 play major roles in callus formation of tomato during in vivo regeneration by regulating cytokinin, IAA, and laccase levels. Overall, our microRNA sequence and target analyses of callus formation during in vivo regeneration of tomato provide novel insights into the regulation of regeneration in higher plants.

scholarly journals Circular RNA circSDHC serves as a sponge for miR-127-3p to promote the proliferation and metastasis of renal cell carcinoma via the CDKN3/E2F1 axis

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Junjie Cen ◽  
Yanping Liang ◽  
Yong Huang ◽  
Yihui Pan ◽  
Guannan Shu ◽  
...  
Keyword(s):  
Renal Cell Carcinoma ◽  
Cell Carcinoma ◽  
Renal Cell ◽  
Target Genes ◽  
Expression Patterns ◽  
Luciferase Reporter ◽  
Circular Rnas ◽  
Proliferation And Metastasis

Abstract Background There is increasing evidence that circular RNAs (circRNAs) have significant regulatory roles in cancer development and progression; however, the expression patterns and biological functions of circRNAs in renal cell carcinoma (RCC) remain largely elusive. Method Bioinformatics methods were applied to screen for circRNAs differentially expressed in RCC. Analysis of online circRNAs microarray datasets and our own patient cohort indicated that circSDHC (hsa_circ_0015004) had a potential oncogenic role in RCC. Subsequently, circSDHC expression was measured in RCC tissues and cell lines by qPCR assay, and the prognostic value of circSDHC evaluated. Further, a series of functional in vitro and in vivo experiments were conducted to assess the effects of circSDHC on RCC proliferation and metastasis. RNA pull-down assay, luciferase reporter and fluorescent in situ hybridization assays were used to confirm the interactions between circSDHC, miR-127-3p and its target genes. Results Clinically, high circSDHC expression was correlated with advanced TNM stage and poor survival in patients with RCC. Further, circSDHC promoted tumor cell proliferation and invasion, both in vivo and in vitro. Analysis of the mechanism underlying the effects of circSDHC in RCC demonstrated that it binds competitively to miR-127-3p and prevents its suppression of a downstream gene, CDKN3, and the E2F1 pathway, thereby leading to RCC malignant progression. Furthermore, knockdown of circSDHC caused decreased CDKN3 expression and E2F1 pathway inhibition, which could be rescued by treatment with an miR-127-3p inhibitor. Conclusion Our data indicates, for the first time, an essential role for the circSDHC/miR-127-3p/CDKN3/E2F1 axis in RCC progression. Thus, circSDHC has potential to be a new therapeutic target in patients with RCC.

scholarly journals xMD-miRNA-seq to generate near in vivo miRNA expression estimates in colon epithelial cells

2018 ◽  
Author(s):  
Avi Z. Rosenberg ◽  
Carrie Wright ◽  
Karen Fox-Talbot ◽  
Anandita Rajpurohit ◽  
Courtney Williams ◽  
...  
Keyword(s):  
Epithelial Cells ◽  
Small Rna ◽  
Mirna Expression ◽  
Low Cost ◽  
Expression Patterns ◽  
Small Rna Sequencing ◽  
Rna Seq ◽  
Cell Type

AbstractAccurate, RNA-seq based, microRNA (miRNA) expression estimates from primary cells have recently been described. However, this in vitro data is mainly obtained from cell culture, which is known to alter cell maturity/differentiation status, significantly changing miRNA levels. What is needed is a robust method to obtain in vivo miRNA expression values directly from cells. We introduce expression microdissection miRNA small RNA sequencing (xMD-miRNA-seq), a method to isolate cells directly from formalin fixed paraffin-embedded (FFPE) tissues. xMD-miRNA-seq is a low-cost, high-throughput, immunohistochemistry-based method to capture any cell type of interest. As a proof-of-concept, we isolated colon epithelial cells from two specimens and performed low-input small RNA-seq. We generated up to 600,000 miRNA reads from the samples. Isolated epithelial cells, had abundant epithelial-enriched miRNA expression (miR-192; miR-194; miR-200b; miR-200c; miR-215; miR-375) and overall similar miRNA expression patterns to other epithelial cell populations (colonic enteroids and flow-isolated colon epithelium). xMD-derived epithelial cells were generally not contaminated by other adjacent cells of the colon as noted by t-SNE analysis. xMD-miRNA-seq allows for simple, economical, and efficient identification of cell-specific miRNA expression estimates. Further development will enhance rapid identification of cell-specific miRNA expression estimates in health and disease for nearly any cell type using archival FFPE material.

scholarly journals Left-Sided Colorectal Cancer Distinct in Indigenous African Patients Compared to Other Ethnic Groups in South Africa.

2021 ◽  
Author(s):  
M. McCabe ◽  
C. Penny ◽  
P. Magangane ◽  
S. Mirza ◽  
Y. Perner
Keyword(s):  
Colorectal Cancer ◽  
South Africa ◽  
Ethnic Groups ◽  
Mirna Expression ◽  
Expression Profiling ◽  
Expression Patterns ◽  
Molecular Characteristics ◽  
Anatomical Site ◽  
Molecular Features ◽  
Mirna Expression Profiling

Abstract Introduction: A large proportion of indigenous African (IA) colorectal cancer (CRC) patients in South Africa are young (<50years), with no unique histopathological or molecular characteristics. Anatomical site as well as microsatellite instability (MSI) status have shown to be associated with different clinicopathological and molecular features. This study aimed to ascertain key histopathological and miRNA expression patterns in microsatellite stable (MSS) and low-frequency MSI (MSI-L) patients, to provide insight into the mechanism of the disease. Methods: A retrospective cohort (2011-2015) of MSS/MSI-L CRC patient samples diagnosed at Charlotte Maxeke Johannesburg Academic Hospital was analyzed. Samples were categorized by site [Right colon cancer (RCC) versus left (LCC)], ethnicity [IA versus other ethnic groups (OEG)] and MSI status (MSI-L vs MSS). T-test, Fischer’s exact and Chi-square tests were conducted. Additional miRNA expression profiling was performed on IA patient samples. Results: IA patients with LCC demonstrated an increased prevalence in males, sigmoid colon, signet-ring-cell morphology, MSI-L with BAT25/26 marker instability and advanced disease association. MiRNA expression profiling revealed unique clustering, with dysregulation of let-7 and miRNA-125. Conclusion: This study revealed distinct histopathological features for LCC, and suggests BAT25/26, miRNAs let-7a-5p and miRNA-125a/b-5p as negative prognostic markers in African CRC patients. Larger confirmatory studies are recommended.

Analysis of Predictive Value and Target Gene Prediction of Serum Micro-RNA-205 in Diagnosis and Prognosis of Prostate Cancer

2020 ◽  
Vol 12 (2) ◽  
pp. 196-201
Author(s):  
Xiangnan Hu ◽  
Xiaoliang Dou ◽  
He Wang ◽  
Jinbo Sun ◽  
Bo Zhang ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Mirna Expression ◽  
Predictive Value ◽  
Expression Profiling ◽  
Target Genes ◽  
Micro Rna ◽  
Serum Samples ◽  
Serum Mirna ◽  
Diagnosis And Prognosis ◽  
Mirna Expression Profiling

The aim of this study was to explore the predictive value of serum micro-RNA (miRNA)-205 in the diagnosis and prognosis of prostate cancer, and analyze miRNA-205 target genes and functions. Eight patients diagnosed with prostate cancer or benign prostatic hyperplasia (BPH) that were treated in January 2011 were selected. The serum samples between the two groups were analyzed for miRNA expression profiling, and the differentially expressed miRNA-205 was selected for further analysis. The serum samples of 64 patients with prostate cancer and 20 patients with BPH from March 2011 to March 2013 were collected for qPCR verification. We evaluated the correlation between miRNA-205 expression level and clinicopathological data of 64 patients with prostate cancer and its prognostic value. Finally, through bioinformatic analysis, target genes of miRNA-205 were predicted, and gene ontology (GO) analysis and signal pathway analysis were performed. A total of 657 differential miRNAs were screened from miRNA expression profiling. Compared with patients with BPH, miRNA-205 showed lower expression in the serum of patients with prostate cancer. Serum miRNA-205 + PSA combined had the strongest predictive ability, 0.805. The expression level of miRNA-205 in the patients with a Gleason score ≥7 was lower than that in patients with a Gleason score <7, Low miRNA-205 expression was associated with bone metastasis and higher T stage ratings, and the 5-year overall survival rate of the low miRNA-205 expression group was lower than the high miRNA-205 expression group. A total of 27 miRNA-205 target genes were predicted. The target genes of miRNA-205 are mainly enriched in biological functions such as cell adhesion and GTP kinase activity. The target genes of miRNA-205 are mainly enriched in Axon guidance and signal transduction by L1 and other signal pathways. In this study, serum miRNA-205 was successfully identified as a potential noninvasive serum marker for diagnosis and prognosis of prostate cancer, which will be helpful for future clinical research and prostate cancer drug target design.

Engineering of clinical glioma treatment: Prediction of pro-invasive molecular events in treated gliomas

2008 ◽  
Vol 222 (7) ◽  
pp. 1149-1160 ◽  
Author(s):  
D Trog ◽  
K Yeghiazaryan ◽  
H H Schild ◽  
O Golubnitschaja
Keyword(s):  
Malignant Glioma ◽  
Target Genes ◽  
Expression Patterns ◽  
Malignant Gliomas ◽  
Treatment Algorithm ◽  
Poor Response ◽  
Response To Therapy ◽  
Molecular Events ◽  
Therapeutic Algorithms

The diffusely infiltrative nature of malignant gliomas is the main obstacle to successful treatment approaches. Advanced simulation models of the in vivo response to therapy conditions are expected to improve malignant glioma treatment substantially. In parallel experiments, human malignant glioma cells underwent either radiation or chemotherapy treatment (chemotreatment) with temozolomide alone, or combined chemoradiation. Cells were treated according to diverse, clinically relevant, therapeutic algorithms. Quantitative ‘real-time’ polymerase chain reaction (PCR) measurements were performed for target genes, namely vascular endothelial growth factor, p53, and cyclooxygenase-2, which allow a comparative evaluation of pro-invasive molecular events in treated gliomas. The proof-of-principle study simulated variable intratumoural regional conditions. Pro-invasive molecular patterns were strongly dependent on the treatment algorithm, cellular density, and drug delivery. The highest pro-invasive potential was demonstrated for simulated peripheral regions under continued chemoradiation. This result strongly supports the clinical observations of increased aggressiveness and relatively poor response to second-line therapies in post-operatively chemoradiation-treated malignant gliomas at the time of relapse. Individualized and potentially the most effective treatment algorithms can be designed using established gene expression patterns applied on primary cell cultures obtained from individual patients. Individual drug toxicity and response to anti-cancer therapy can be predicted.

scholarly journals Recapitulation of Transcriptomic Characteristics of Primary Breast Tumours in Patient-Derived 3D Cultures in Vitro

2021 ◽  
Vol 75 (1) ◽  
pp. 20-24
Author(s):  
Dina Nitiša ◽  
Nityanand Jain ◽  
Arvīds Irmejs ◽  
Valdis Pirsko ◽  
Inese Čakstiņa
Keyword(s):  
Gene Expression ◽  
Quantitative Polymerase Chain Reaction ◽  
Expression Patterns ◽  
3D Cell Culture ◽  
Model System ◽  
Gene Expression Patterns ◽  
3D Cultures ◽  
Culture Development

AbstractBreast cancer (BC) is the most common cause of cancer-related deaths among women in Europe and worldwide. Adherent (2D) cell cultures have been the routine in vitro model system employed in preclinical BC research for the last half-century. Over the past decade, new protocols have been developed allowing patient-derived three-dimensional organoid (3D) cell culture development from a range of solid tumours, including BC. These 3D models offer a promise of closer resemblance to the native tumour than the 2D cultures. To test the assumption that an in vitro 3D BC model system provides increased faithfulness to the molecular processes happening in vivo, as compared to 2D BC cultures, post-operational material from three BC patients was used to simultaneously develop 2D and 3D cultures in vitro. When analysed by quantitative polymerase chain reaction (PCR), the gene expression patterns of the cells from 3D cultures resembled the original tissues, while the gene expression patterns of the conventional 2D cultures were more distant.

The Transcriptional Program of Terminal Granulocytic Differentiation in Man.

Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 1469-1469
Author(s):  
Niels Borregaard ◽  
Lars C. Jacobsen ◽  
Rehanah Borup ◽  
Thomas Rasmussen ◽  
Malene D. Bjerregaard ◽  
...  
Keyword(s):  
Host Defense ◽  
Target Genes ◽  
Major Gene ◽  
Expression Patterns ◽  
Correlation Coefficients ◽  
Quantitative Measure ◽  
Effector Proteins ◽  
Transcriptional Program ◽  
Granulocytic Differentiation

Abstract To characterize the transcriptional program that governs terminal granulocytic differentiation in vivo, we performed comprehensive microarray analyses of human bone marrow (BM) populations highly enriched in promyelocytes (PMs), myelocytes/metamyelocytes (MYs), and neutrophils (bm-PMNs). These analyses identified 11,310 genes involved in differentiation, of which 6,700 were differentially regulated including granule proteins and surface receptors previously not identified in neutrophils. Functional clustering demonstrated that differentially expressed genes were assigened to all of the major gene categories including apoptosis, cell cycle, chaperones, enzymes, immunity proteins, kinases, motor proteins, signal transducers, structural proteins, and transcription factors. In an attempt to define the developmental distance between PM, MY, and bm-PMN populations, we assessed the Pearsons correlation coefficient (γ) by correlating the transcriptomes (=all 44.760 probe sets, Affymetrix) of BM populations. The correlation coefficients among replicates of BM populations were in the range of 0.97–0.99. On the other hand the correlation coefficients between BM populations were 0.81 (γPM - MY), 0.79 (γMY - bm-PMN), and 0.52 (γPM - bm-PMN), and thus, provided a useful quantitative measure reflecting the hierarchical relationship between the three BM populations. Additional correlation of bm-PMN and peripheral blood-PMN transcriptomes revealed a high similarity of both populations (γbm-PMN - pb-PMN=0.95) indicating a termination of granulocytic differentiation in the BM microenvironment during steady state hematopoesis. Differentiation of PMs towards MYs was accompanied by a marked decline of proliferative and general cellular activity as defined by downregulation of E2F target genes, cyclin dependent kinases 2/4/6, and various metabolic, proteasomal, and mitochondrial genes. Expression patterns of apoptosis genes indicated death control by the p53-pathway in PMs and by death receptor pathways in bm-PMNs. Effector proteins critical for host defense were expressed successively throughout granulocytic differentiation, whereas receptors and receptor ligands essential for the activation of the host defense program were terminally upregulated in bm-PMNs. The upregulation of ligand-receptor pairs, which are defined inducers as well as target genes of NF-kB, suggests a constitutive activation of NF-kB in bm-PMNs by autocrine loops. Overall, these results define a granulocytic differentiation model governed by a highly coordinated fail-safe program, which promotes completion of differentiation before cells gain responsiveness towards activating stimuli that accompany infections.

scholarly journals MicroRNA Profiling: From Dark Matter to White Matter, or Identifying New Players in Neurobiology

2007 ◽  
Vol 7 ◽  
pp. 155-166 ◽  
Author(s):  
Anna M. Krichevsky
Keyword(s):  
Dark Matter ◽  
Mirna Expression ◽  
Regulatory Networks ◽  
Expression Patterns ◽  
Basic Principles ◽  
Protein Coding ◽  
Rna Molecules ◽  
Coding Regions ◽  
Small Regulatory Rna ◽  
Mirna Expression Profiling

Contemporary biology has been revolutionized by a recently discovered class of small regulatory RNA molecules, microRNAs (miRNAs). Missed by researchers for decades due to their tiny size, usually mapping to non-protein-coding regions of genomes, miRNAs and miRNA-mediated regulatory networks have been the “dark matter” of molecular biology. Deciphering miRNA pathways and functions in the CNS of complex organisms is tightly linked to understanding miRNA expression patterns. To facilitate these emerging studies, I here review the basic principles of medium- and high-throughput technologies available for miRNA expression profiling.

scholarly journals Probe into the Target and Mechanism of Jianpi Xiaoke Prescription for Treating Type 2 Diabetes Mellitus through miRNA Expression Profiling

2020 ◽  
Vol 2020 ◽  
pp. 1-12
Author(s):  
Qiuyue Guo ◽  
Yunsheng Xu ◽  
Jie Li ◽  
Dan Luo ◽  
Jun Li ◽  
...  
Keyword(s):  
Type 2 Diabetes ◽  
Signaling Pathways ◽  
Mirna Expression ◽  
Expression Profiling ◽  
Target Genes ◽  
Cell Function ◽  
Control Group ◽  
Sequencing Data ◽  
Mirna Expression Profiling

Object. To probe into the target and molecular mechanism of Jianpi Xiaoke (JPXK) prescription in the treatment of type 2 diabetes through high-throughput microRNA (miRNA) sequencing. Methods. Ten of the 31 SPF male Wistar rats were randomly taken as the control group; the remaining rats were fed a high-sugar and high-fat diet, combined with Streptozotocin (STZ, 35 mg/kg) that induced a type 2 diabetes model. The model rats were randomly divided into model groups (n = 11) and the JPXK group (n = 10). After 8 weeks of JPXK intervention, we detected the function of islet cells through HE staining and ELISA. High-pass sequencing technology was adopted to identify the differential expression of miRNA to explore the target of JPXK treatment, assess the relevant target genes, conduct functional analysis, and lastly verify the sequencing data by qRT-PCR. Results. After treatment, FPG, FINS, and HOMA-IR levels of the treatment group improved significantly compared with those of the control group ( P < 0.05 ). Among the miRNAs differentially expressed between the model group and the control group, there were 7 reversals after JPXK treatment, including miR-1-3p, miR-135a-5p, miR-181d-5p, miR-206-3p, miR-215, miR-3473, and miR-547-3p (log2FC ≥ 1 or ≤ −1, P < 0.05 ). Besides, the 1810 target genes associated with these 7 miRNAs were assessed by multiMiR. According to the results of the GO and KEGG analyses, they were associated with biological processes (e.g., glucose transport and fat cell formation), and it covered multiple signaling pathways, capable of regulating islet cell function (e.g., MAPK, PI3K-Akt, Ras, AMPK, and HIF-1 signaling pathways). The PCR verification results were consistent with the sequencing results. Conclusion. This discovery interpreted the potential therapeutic targets and signaling pathways of JPXK prescription against T2DM based on miRNA expression profiling. In conclusion, our research provided novel research insights into traditional Chinese medicine (TCM) treatment of diabetes.

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