scholarly journals Role of Spatial Averaging in the Precision of Gene Expression Patterns

2009 ◽  
Vol 103 (25) ◽  
Author(s):  
Thorsten Erdmann ◽  
Martin Howard ◽  
Pieter Rein ten Wolde
Blood ◽  
2013 ◽  
Vol 122 (21) ◽  
pp. 3805-3805
Author(s):  
Jorge Contreras ◽  
Jayanth Kumar Palanichamy ◽  
Tiffany Tran ◽  
Dinesh S. Rao

Abstract Diffuse large B cell lymphoma (DLBCL) is one of the most common Non-Hodgkin lymphomas among adults. It is a heterogeneous disease characterized by multiple mutations and translocations. Gene expression profiling studies have revealed several characteristic gene expression patterns, with two main patterns emerging, namely Germinal Center(GC) type, and Activated B Cell (ABC) type. ABC-type DLBCL shows gene expression patterns that resemble activated B-cells, with increased expression of anti-apoptotic, and pro-proliferative genes. Critically, upregulation of the NF-κB the pathway is a hallmark of ABC-type DLBCL and has been shown to be necessary for survival, and is caused by several different mutations at different levels within the pathway. Recent work has revealed the critical importance of a new class of small RNA molecules, namely microRNAs, in gene regulation. Of these, microRNA-146a (miR-146a) was discovered as an NF-κB induced microRNA that plays a role as a negative feedback regulator of this pathway by targeting adaptor proteins. To further characterize miR-146a, mice deficient for this miRNA were created, and were found to develop lymphadenopathy, splenomegaly, and myeloid proliferation. As expected, immune cells in these mice have an upregulated NF-κB pathway and many of the phenotypes can be ameliorated by inhibition of the NF-κB pathway. Importantly, a significant proportion of the animals develop B-cell lymphoma at older ages. In this study, we examined the role of miR-146a in the development of malignancy in B-cells. To accelerate the role of miR-146a in tumor formation we overlaid the miR-146a deficient allele onto the Eμ-Myc like mouse model. Eμ-Myc mice develop tumors on average by 14weeks of age. The transgenic status of animals was verified by genotyping, RNA and protein expression analyses. miR-146a sufficient and deficient animals on the Eμ-Myc background were followed for tumor latency by peripheral blood analysis and careful physical examination. Based on approved humane criteria for animal discomfort, animals were sacrificed and hematopoietic tissue was harvested for analysis. Mice deficient for miR-146a had a statistically reduced survival in comparison with miR-146a sufficient animals with a p-value of .0098 (Kaplan Meir survival analysis). Complete Blood Count of animals at time of death revealed an increase leukemia presentation in the miR-146a deficient background. FACS analysis of tumor tissue from both groups revealed an increase in the number of IgM positive tumors in the miR-146a-deficient background indicating skewing towards more mature B cell neoplasms when miR-146a is lacking. Lineage analysis of tumors verified them to be of B cell origin although a subset of miR-146a sufficient tumors had higher numbers of infiltrating myeloid cells compared to deficient animals. Furthermore, histologic analysis of hematopoietic organs showed that while infiltration remained similar in kidneys and liver, more spleens in the miR-146a deficient background tended to be less involved. Our extensive histopathologic and immunophenotypic analyses indicate that miR-146a deficiency drives a more aggressive malignant phenotype in the B-cell lineage. In keeping with this, our profiling studies of human DLBCL suggest that a subset of DLBCL show decreased expression of miR-146a. We are currently examining the status of NF-κB in the murine tumors and using high throughput sequencing approaches to delineate gene expression differences between miR-146a sufficient and deficient tumors. We anticipate the discovery of novel gene targets of miR-146a and expect that these studies will lead to improved diagnostic and therapeutic options for patients of B-cell malignancies. Disclosures: No relevant conflicts of interest to declare.


2007 ◽  
Vol 196 (1) ◽  
pp. 70.e1-70.e6 ◽  
Author(s):  
Cathal McCarthy ◽  
Finbarr E. Cotter ◽  
Suzanne McElwaine ◽  
Anne Twomey ◽  
Eoghan E. Mooney ◽  
...  

2019 ◽  
Author(s):  
Ciera C. Martinez ◽  
Siyu Li ◽  
Margaret R. Woodhouse ◽  
Keiko Sugimoto ◽  
Neelima R. Sinha

ABSTRACTLeaf morphogenesis involves cell division, expansion, and differentiation in the developing leaf, cells at different positions along the medio-lateral and proximal-distal leaf axes divide, expand, and differentiate at different rates. The gene expression changes that control cell fate along these axes remain elusive due to difficulties in precisely isolating tissues. Here, we combined rigorous early leaf characterization, laser capture microdissection, and transcriptomic sequencing to ask how gene expression patterns regulate early leaf morphogenesis in wild-type tomato (Solanum lycopersicum) and the leaf morphogenesis mutant trifoliate. We observed transcriptional regulation of cell differentiation along the proximal-distal axis and identified molecular signatures delineating the classically defined marginal meristem/blastozone region during early leaf development. We describe the importance of endoreduplication during leaf development, when and where leaf cells first achieve photosynthetic competency, and the regulation of auxin transport and signaling along the leaf axes. Knockout mutants of BLADE-ON-PETIOLE2 exhibited ectopic shoot apical meristem formation on leaves, highlighting the role of this gene in regulating margin tissue identity. We mapped gene expression signatures in specific leaf domains and evaluated the role of each domain in conferring indeterminacy and permitting blade outgrowth. Finally, we generated a global gene expression atlas of the early developing compound leaf.One-sentence summaryRigorous structural characterization, laser capture microdissection, and transcriptomic sequencing reveal how gene expression patterns regulate early morphogenesis of the compound tomato leaf.The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantcell.org) is Ciera C. Martinez ([email protected]).


2017 ◽  
Vol 11 (3) ◽  
pp. 947
Author(s):  
F.A. Ehiaghe ◽  
C.C. Onyenekwe ◽  
I.J. Ehiaghe ◽  
C.O. Akosile ◽  
D.E. Agbonlahor

2020 ◽  
Vol 87 (9) ◽  
pp. S453
Author(s):  
Devin Rocks ◽  
Ivana Jaric ◽  
Eduardo Gallo ◽  
John M. Greally ◽  
Masako Suzuki ◽  
...  

2020 ◽  
Author(s):  
Jianjian Yang ◽  
Xue Wang ◽  
Bing Huang ◽  
Rong Liu ◽  
Hui Xiong ◽  
...  

Abstract Background Active IFN-γ signaling is a common feature of tumors responding to PD-1 checkpoint blockade. IFN-γ exhibits both anti- and pro-tumor activities. Therefore, identifying the pro-tumor effects of IFN-γ and their underlying molecular mechanisms could be a critical step for developing therapeutic strategies to maximize the anti-tumor efficacy of immunotherapies. Methods Western blot, immunofluorescence, and quantitative real-time PCR assays were used to evaluate the expression of ZEB1 and EMT associated biomarkers. Trans-well assay was used to examine the role of IFN-γ on cancer cell migration in vitro. Murine tumor xenograft models were performed to examine the effect of IFN-γ on cancer cell metastasis in vivo. Colony formation assay was performed to detect the role of ZEB1 in cell proliferation. RNA-seq was performed to analyze the EMT-associated gene expression patterns in response to IFN-g treatment. Loss-of-function analysis and chromatin immunoprecipitation were used to reveal the mechanism underlying ZEB1 induction by IFN-γ. Results we demonstrate that the treatment of lung adenocarcinoma cells with IFN-γ leads to a rapid increase of ZEB1 expression and a significant change in epithelial-mesenchymal-transition (EMT)-associated gene expression patterns. Moreover, functional analysis shows that IFN-γ promotes cell migration in vitro and metastasis in vivo. Mechanistically, IFN-γ-induced JMJD3 significantly reduces H3K27 trimethylation in the promoter of the ZEB1 gene, thereby activating ZEB1 transcription. Inhibition of JMJD3 abrogates IFN-γ-induced ZEB1 expression. We previously demonstrated that IFN-γ-mediated anti-tumor response, including suppression of cell proliferation and induction of CXCL9 and CXCL10 expression, is STAT1-IRF1 dependent. The knockdown of ZEB1 diminishes IFN-γ-mediated cell migration and metastasis, but it does not affect STAT1 and IRF1 expression and has no effect on cell proliferation as well as the induction of CXCL9 and CXCL10 expression. Conclusion Inhibition or downregulation of ZEB1 may prevent the pro-tumor activity of IFN-γ while retaining its anti-tumor function. The study expands our understanding of IFN-γ-mediated signaling and helps to identify therapeutic targets to improve current immunotherapies.


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