Systematic analysis of noncoding somatic mutations and gene expression alterations across 14 tumor types

2014 ◽  
Vol 46 (12) ◽  
pp. 1258-1263 ◽  
Author(s):  
Nils J Fredriksson ◽  
Lars Ny ◽  
Jonas A Nilsson ◽  
Erik Larsson
2015 ◽  
Vol 6 (1) ◽  
Author(s):  
Jiarui Ding ◽  
Melissa K. McConechy ◽  
Hugo M. Horlings ◽  
Gavin Ha ◽  
Fong Chun Chan ◽  
...  

PLoS ONE ◽  
2016 ◽  
Vol 11 (5) ◽  
pp. e0155660 ◽  
Author(s):  
Wei-Ching Chen ◽  
Chih-Yang Wang ◽  
Yu-Hsuan Hung ◽  
Tzu-Yang Weng ◽  
Meng-Chi Yen ◽  
...  

Oncotarget ◽  
2017 ◽  
Vol 9 (3) ◽  
pp. 3198-3213 ◽  
Author(s):  
Xiangrong Cui ◽  
Xuan Jing ◽  
Qin Yi ◽  
Chunlan Long ◽  
Bin Tan ◽  
...  

Oncotarget ◽  
2017 ◽  
Vol 8 (16) ◽  
pp. 27216-27239 ◽  
Author(s):  
Shuanshuan Xie ◽  
Changxing Shen ◽  
Min Tan ◽  
Ming Li ◽  
Xiaolian Song ◽  
...  

2017 ◽  
Vol 63 (5) ◽  
pp. 695-702
Author(s):  
Oleg Kit ◽  
Dmitriy Vodolazhskiy ◽  
Yelena Frantsiyants ◽  
Svetlana Panina ◽  
E. Rastorguev ◽  
...  

Glioblastoma multiforme (GBM) is the most common and invasive poorly differentiated brain tumor with nearly 100 % rate of recurrence and unfavorable prognosis. The aim of the present review is to analyze recent studies and experimental results (Scopus, Web of Science, PubMed) concerning somatic mutations in glioblastoma, aberrant regulation of gene expression of signal pathways including EGFR, TGFß, etc. and markers for GBM progression. Particularly the molecular subtypes of glioblastoma and NGS results are considered in this review.


2004 ◽  
Vol 20 (1) ◽  
pp. 131-142 ◽  
Author(s):  
M. Kidd ◽  
T. Hinoue ◽  
G. Eick ◽  
K. D. Lye ◽  
S. M. Mane ◽  
...  

Enterochromaffin-like (ECL) cell hyperplasia and then irreversible neoplasia can be generated in the African rodent Mastomys natalensis using the H2 receptor blocker, loxtidine, for 8–16 wk. We used a GeneChip approach complemented by standard technologies to identify gene expression alterations in the gastric mucosa during gastrin-mediated ECL cell transformation. Gastric mucosa (mucosal scrapping) and ECL cell-enriched fractions were obtained from untreated Mastomys (controls) and from animals treated with loxtidine for 8 wk (hyperplasia). Tumor ECL cells were obtained by hand-dissection of gastric ECL cell nodules from animals treated with loxtidine for >16 wk and from a spontaneously developed ECL cell tumor. RNA was isolated, examined on rat U34A GeneChips, and comparison analysis was performed to identify altered gene expression. Alterations in gene expressions were examined further by immunohistochemistry, quantitative RT-PCR (Q-RT-PCR), sequencing and Western blot. GeneSpring analysis demonstrated alterations in few genes (<20) in hyperplastic and tumor mucosa. The histamine H1 receptor was consistently increased in proliferating mucosa. This gene change was confirmed by Q-RT-PCR. Other genes showing alterations included neural-(chromogranin A and somatostatin), cell-cycle-, and AP-1-associated genes. Immunostaining confirmed alterations in neural markers. Cluster analysis of ECL cell-enriched samples demonstrated that c- fos and junD were differently regulated. Q-RT-PCR and Western blot in prospectively collected gastric mucosal samples confirmed the differential expression of Fos and Jun. The negative regulators of AP-1, JunD, and Menin were decreased in tumor mucosa. A missense of unknown function was noted in the menin gene. Hypergastrinemia in an animal model of gastric carcinoids differentially altered the histamine type 1 receptor and gene expression and protein composition of AP-1. These results suggest that expression of this receptor and an altered composition of AP-1 with a loss of inhibition play a role in ECL cell transformation.


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