An attempt to understand glioma stem cell biology through centrality analysis of a protein interaction network

2018 ◽  
Vol 438 ◽  
pp. 78-91 ◽  
Author(s):  
Mrinmay Kumar Mallik
2009 ◽  
Vol 3 ◽  
pp. CMO.S1008 ◽  
Author(s):  
Okezie O. Kanu ◽  
Betsy Hughes ◽  
Chunhui Di ◽  
Ningjing Lin ◽  
Jinrong Fu ◽  
...  

In the adult population, glioblastoma multiforme is one of the most common primary brain tumors encountered. Unfortunately, this highly malignant tumor represents over 50% of all types of primary central nervous system gliomas. The vast majority of GBMs develops quite rapidly without clinical, radiological, or morphologic evidence of a less malignant precursor lesion (primary or de novo GBMs), as compared to secondary GBMs that develop slowly by progression from diffuse low-grade astrocytomas. These GBM subtypes must be kept in mind because they may constitute distinct disease entities. Even though they look histologically quite similar, they likely involve different genetic alterations and signaling pathways. Decades of surgical therapy, radiotherapy, and chemotherapy have failed to drastically change survival. Clearly, we do not fully understand this tumor; however, the exciting genetic revolution in glioma research over the past decade is providing a promising outlook for exploring this tumor at the genetic level. Science has begun to elucidate the numerous genetic alterations and critical signaling pathways, and it has opened new exciting areas of research such as glioma stem cell biology and neoangiogenesis. This work has already begun to improve our understanding of GBM cell proliferation, migration, and invasion. Indeed, exciting novel targeted therapies are making their way to clinical trials based on this increased knowledge. This review provides the current understanding of GBM oncogenomics, signaling pathways, and glioma stem cell biology and discusses the potential new therapeutic targets on the horizon.


2016 ◽  
Author(s):  
T Li ◽  
R Wernersson ◽  
RB Hansen ◽  
H Horn ◽  
JM Mercer ◽  
...  

Human protein-protein interaction networks are critical to understanding cell biology and interpreting genetic and genomic data, but are challenging to produce in individual large-scale experiments. We describe a general computational framework that through data integration and quality control provides a scored human protein-protein interaction network (InWeb_IM). Juxtaposed with five comparable resources, InWeb_IM has 2.8 times more interactions (~585K) and a superior functional signal showing that the added interactions reflect real cellular biology. InWeb_IM is a versatile resource for accurate and cost-efficient functional interpretation of massive genomic datasets illustrated by annotating candidate genes from >4,700 cancer genomes and genes involved in neuropsychiatric diseases.


2011 ◽  
Vol 2 (1-2) ◽  
pp. 13-25 ◽  
Author(s):  
Patricia Miang-Lon Ng ◽  
Thomas Lufkin

AbstractEmbryonic stem cells have the ability to differentiate into nearly all cell types. However, the molecular mechanism of its pluripotency is still unclear. Oct3/4, Sox2 and Nanog are important factors of pluripotency. Oct3/4 (hereafter referred to as Oct4), in particular, has been an irreplaceable factor in the induction of pluripotency in adult cells. Proteins interacting with Oct4 and Nanog have been identified via affinity purification and mass spectrometry. These data, together with iterative purifications of interacting proteins allowed a protein interaction network to be constructed. The network currently includes 77 transcription factors, all of which are interconnected in one network. In-depth studies of some of these transcription factors show that they all recruit the NuRD complex. Hence, transcription factor clustering and chromosomal remodeling are key mechanism used by embryonic stem cells. Studies using RNA interference suggest that more pluripotency genes are yet to be discovered via protein-protein interactions. More work is required to complete and curate the embryonic stem cell protein interaction network. Analysis of a saturated protein interaction network by system biology tools can greatly aid in the understanding of the embryonic stem cell pluripotency network.


Science ◽  
2013 ◽  
Vol 340 (6137) ◽  
pp. 1211-1214 ◽  
Author(s):  
Benjamin D. Ross ◽  
Leah Rosin ◽  
Andreas W. Thomae ◽  
Mary Alice Hiatt ◽  
Danielle Vermaak ◽  
...  

Evolutionarily young genes that serve essential functions represent a paradox; they must perform a function that either was not required until after their birth or was redundant with another gene. How young genes rapidly acquire essential function is largely unknown. We traced the evolutionary steps by which the Drosophila gene Umbrea acquired an essential role in chromosome segregation in D. melanogaster since the gene's origin less than 15 million years ago. Umbrea neofunctionalization occurred via loss of an ancestral heterochromatin-localizing domain, followed by alterations that rewired its protein interaction network and led to species-specific centromere localization. Our evolutionary cell biology approach provides temporal and mechanistic detail about how young genes gain essential function. Such innovations may constantly alter the repertoire of centromeric proteins in eukaryotes.


2010 ◽  
Vol 6 (4) ◽  
pp. 382-395 ◽  
Author(s):  
Mercedes Pardo ◽  
Benjamin Lang ◽  
Lu Yu ◽  
Haydn Prosser ◽  
Allan Bradley ◽  
...  

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