scholarly journals A gene-signature progression approach to identifying candidate small-molecule cancer therapeutics with connectivity mapping

2016 ◽  
Vol 17 (1) ◽  
Author(s):  
Qing Wen ◽  
Chang-Sik Kim ◽  
Peter W. Hamilton ◽  
Shu-Dong Zhang
The Analyst ◽  
2015 ◽  
Vol 140 (4) ◽  
pp. 1260-1264 ◽  
Author(s):  
Yanhong Zhu ◽  
Guangfeng Wang ◽  
Liang Sha ◽  
Yuwei Qiu ◽  
Hong Jiang ◽  
...  

Development of strategies for the sensitive and selective detection of the folate receptor (FR) that are simple and low cost is of great importance for assessing cancer therapeutics due to its crucial role in physiological, pharmacological and pathological processes.


2019 ◽  
Vol 383 ◽  
pp. 114771
Author(s):  
Ognian C. Ikonomov ◽  
Diego Sbrissa ◽  
Assia Shisheva

2011 ◽  
Vol 18 (6) ◽  
pp. 759-771 ◽  
Author(s):  
Zhihong Chen ◽  
Lora W Forman ◽  
Kenneth A Miller ◽  
Brandon English ◽  
Asami Takashima ◽  
...  

The concept of targeting cancer therapeutics toward specific mutations or abnormalities in tumor cells, which are not found in normal tissues, has the potential advantages of high selectivity for the tumor and correspondingly low secondary toxicities. Many human malignancies display activating mutations in the Ras family of signal-transducing genes or over-activity of p21Ras-signaling pathways. Carcinoid and other neuroendocrine tumors have been similarly demonstrated to have activation of Ras signaling directly by mutations in Ras, indirectly by loss of Ras-regulatory proteins, or via constitutive activation of upstream or downstream effector pathways of Ras, such as growth factor receptors or PI3-kinase and Raf/mitogen-activated protein kinases. We previously reported that aberrant activation of Ras signaling sensitizes cells to apoptosis when the activity of the PKCδ isozyme is suppressed and that PKCδ suppression is not toxic to cells with normal levels of p21Rassignaling. We demonstrate here that inhibition of PKCδ by a number of independent means, including genetic mechanisms (shRNA) or small-molecule inhibitors, is able to efficiently and selectively repress the growth of human neuroendocrine cell lines derived from bronchopulmonary, foregut, or hindgut tumors. PKCδ inhibition in these tumors also efficiently induced apoptosis. Exposure to small-molecule inhibitors of PKCδ over a period of 24 h is sufficient to significantly suppress cell growth and clonogenic capacity of these tumor cell lines. Neuroendocrine tumors are typically refractory to conventional therapeutic approaches. This Ras-targeted therapeutic approach, mediated through PKCδ suppression, which selectively takes advantage of the very oncogenic mutations that contribute to the malignancy of the tumor, may hold potential as a novel therapeutic modality.


2015 ◽  
Vol 113 (8) ◽  
pp. 1158-1167 ◽  
Author(s):  
Yu-chi Shen ◽  
Ravi Upadhyayula ◽  
Stephanie Cevallos ◽  
Ryan J Messick ◽  
Tammy Hsia ◽  
...  

2018 ◽  
pp. 1-17 ◽  
Author(s):  
Alexey Stupnikov ◽  
Paul G. O’Reilly ◽  
Caitriona E. McInerney ◽  
Aideen C. Roddy ◽  
Philip D. Dunne ◽  
...  

Purpose Gene expression profiling can uncover biologic mechanisms underlying disease and is important in drug development. RNA sequencing (RNA-seq) is routinely used to assess gene expression, but costs remain high. Sample multiplexing reduces RNA-seq costs; however, multiplexed samples have lower cDNA sequencing depth, which can hinder accurate differential gene expression detection. The impact of sequencing depth alteration on RNA-seq–based downstream analyses such as gene expression connectivity mapping is not known, where this method is used to identify potential therapeutic compounds for repurposing. Methods In this study, published RNA-seq profiles from patients with brain tumor (glioma) were assembled into two disease progression gene signature contrasts for astrocytoma. Available treatments for glioma have limited effectiveness, rendering this a disease of poor clinical outcome. Gene signatures were subsampled to simulate sequencing alterations and analyzed in connectivity mapping to investigate target compound robustness. Results Data loss to gene signatures led to the loss, gain, and consistent identification of significant connections. The most accurate gene signature contrast with consistent patient gene expression profiles was more resilient to data loss and identified robust target compounds. Target compounds lost included candidate compounds of potential clinical utility in glioma (eg, suramin, dasatinib). Lost connections may have been linked to low-abundance genes in the gene signature that closely characterized the disease phenotype. Consistently identified connections may have been related to highly expressed abundant genes that were ever-present in gene signatures, despite data reductions. Potential noise surrounding findings included false-positive connections that were gained as a result of gene signature modification with data loss. Conclusion Findings highlight the necessity for gene signature accuracy for connectivity mapping, which should improve the clinical utility of future target compound discoveries.


2014 ◽  
Vol 144 (1) ◽  
pp. 82-95 ◽  
Author(s):  
Longchuan Bai ◽  
David C. Smith ◽  
Shaomeng Wang

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