scholarly journals Comparative Functional Genomics Analysis of NNK Tobacco-Carcinogen Induced Lung Adenocarcinoma Development in Gprc5a-Knockout Mice

PLoS ONE ◽  
2010 ◽  
Vol 5 (7) ◽  
pp. e11847 ◽  
Author(s):  
Junya Fujimoto ◽  
Humam Kadara ◽  
Taoyan Men ◽  
Carolyn van Pelt ◽  
Dafna Lotan ◽  
...  
2019 ◽  
Vol 41 (8) ◽  
pp. 1134-1144 ◽  
Author(s):  
Ioanna Giopanou ◽  
Nikolaos I Kanellakis ◽  
Anastasios D Giannou ◽  
Ioannis Lilis ◽  
Antonia Marazioti ◽  
...  

Abstract Increased expression of osteopontin (secreted phosphoprotein 1, SPP1) is associated with aggressive human lung adenocarcinoma (LADC), but its function remains unknown. Our aim was to determine the role of SPP1 in smoking-induced LADC. We combined mouse models of tobacco carcinogen-induced LADC, of deficiency of endogenous Spp1 alleles, and of adoptive pulmonary macrophage reconstitution to map the expression of SPP1 and its receptors and determine its impact during carcinogenesis. Co-expression of Spp1 and mutant KrasG12C in benign cells was employed to investigate SPP1/KRAS interactions in oncogenesis. Finally, intratracheal adenovirus encoding Cre recombinase was delivered to LSL.KRASG12D mice lacking endogenous or overexpressing transgenic Spp1 alleles. SPP1 was overexpressed in experimental and human LADC and portended poor survival. In response to two different smoke carcinogens, Spp1-deficient mice developed fewer and smaller LADC with decreased cellular survival and angiogenesis. Both lung epithelial- and macrophage-secreted SPP1 drove tumor-associated inflammation, while epithelial SPP1 promoted early tumorigenesis by fostering the survival of KRAS-mutated cells. Finally, loss and overexpression of Spp1 was, respectively, protective and deleterious for mice harboring KRASG12D-driven LADC. Our data support that SPP1 is functionally involved in early stages of airway epithelial carcinogenesis driven by smoking and mutant KRAS and may present an important therapeutic target.


2014 ◽  
Vol 23 (22) ◽  
pp. 5524-5537 ◽  
Author(s):  
Vadim B. Fedorov ◽  
Anna V. Goropashnaya ◽  
Nathan C. Stewart ◽  
Øivind Tøien ◽  
Celia Chang ◽  
...  

Science ◽  
2011 ◽  
Vol 332 (6032) ◽  
pp. 930-936 ◽  
Author(s):  
N. Rhind ◽  
Z. Chen ◽  
M. Yassour ◽  
D. A. Thompson ◽  
B. J. Haas ◽  
...  

2021 ◽  
Author(s):  
Leila Fattel ◽  
Dennis Psaroudakis ◽  
Colleen F. Yanarella ◽  
Kevin Chiteri ◽  
Haley A. Dostalik ◽  
...  

BackgroundGenome-wide gene function annotations are useful for hypothesis generation and for prioritizing candidate genes responsible for phenotypes of interest. We functionally annotated the genes of 18 crop plant genomes across 14 species using the GOMAP pipeline.ResultsBy comparison to existing GO annotation datasets available for a subset of these genomes, GOMAP-generated datasets cover more genes, assign more GO terms, and produce datasets similar in quality (based on precision and recall metrics using existing gold standards as the basis for comparison). From there, we sought to determine whether the datasets could be used in tandem to carry out comparative functional genomics analyses. As a test of the idea and a proof of concept, we created parsimony and distance-based dendrograms of relatedness based on functions for all 18 genomes. These dendrograms were compared to well-established species-level phylogenies to determine whether trees derived through the analysis of gene function agree with known evolutionary histories, which they largely do. Where discrepancies were observed, we determined branch support based on jack-knifing then removed individual annotation sets by genome to identify the annotation sets causing errant relationships.ConclusionsBased on the results of these analyses, it is clear that for genome assembly and annotation products of similar quality, GOMAP-derived functional annotations used together across species do retain sufficient biological signal to recover known phylogenetic relationships, indicating that comparative functional genomics across species based on GO data hold promise as a tool for generating novel hypotheses about gene function and traits.


Author(s):  
Magda Spella ◽  
Dimitra Zazara ◽  
Ioannis Lilis ◽  
Vasilis Aidinis ◽  
Georgios T. Stathopoulos

Genetics ◽  
2013 ◽  
Vol 195 (1) ◽  
pp. 275-287 ◽  
Author(s):  
Amy A. Caudy ◽  
Yuanfang Guan ◽  
Yue Jia ◽  
Christina Hansen ◽  
Chris DeSevo ◽  
...  

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