scholarly journals Unpuréeing the Tomato: Layers of Information Revealed by Microdissection and High-Throughput Transcriptome Sequencing

2011 ◽  
Vol 23 (11) ◽  
pp. 3868-3868 ◽  
Author(s):  
Jennifer Mach
2019 ◽  
Vol 3 (1) ◽  
pp. 223-234 ◽  
Author(s):  
Hans Clevers ◽  
David A. Tuveson

Organoid cultures have emerged as powerful model systems accelerating discoveries in cellular and cancer biology. These three-dimensional cultures are amenable to diverse techniques, including high-throughput genome and transcriptome sequencing, as well as genetic and biochemical perturbation, making these models well suited to answer a variety of questions. Recently, organoids have been generated from diverse human cancers, including breast, colon, pancreas, prostate, bladder, and liver cancers, and studies involving these models are expanding our knowledge of the etiology and characteristics of these malignancies. Co-cultures of cancer organoids with non-neoplastic stromal cells enable investigation of the tumor microenvironment. In addition, recent studies have established that organoids have a place in personalized medicine approaches. Here, we describe the application of organoid technology to cancer discovery and treatment.


2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Yue Him Wong ◽  
Jin Sun ◽  
Li Sheng He ◽  
Lian Guo Chen ◽  
Jian-Wen Qiu ◽  
...  

2014 ◽  
Vol 13 ◽  
pp. CIN.S19435 ◽  
Author(s):  
Daryanaz Dargahi ◽  
Richard D. Swayze ◽  
Leanna Yee ◽  
Peter J. Bergqvist ◽  
Bradley J. Hedberg ◽  
...  

High-throughput transcriptome sequencing allows identification of cancer-related changes that occur at the stages of transcription, pre-messenger RNA (mRNA), and splicing. In the current study, we devised a pipeline to predict novel alternative splicing (AS) variants from high-throughput transcriptome sequencing data and applied it to large sets of tumor transcriptomes from The Cancer Genome Atlas (TCGA). We identified two novel tumor-associated splice variants of matriptase, a known cancer-associated gene, in the transcriptome data from epithelial-derived tumors but not normal tissue. Most notably, these variants were found in 69% of lung squamous cell carcinoma (LUSC) samples studied. We confirmed the expression of matriptase AS transcripts using quantitative reverse transcription PCR (qRT-PCR) in an orthogonal panel of tumor tissues and cell lines. Furthermore, flow cytometric analysis confirmed surface expression of matriptase splice variants in chinese hamster ovary (CHO) cells transiently transfected with cDNA encoding the novel transcripts. Our findings further implicate matriptase in contributing to oncogenic processes and suggest potential novel therapeutic uses for matriptase splice variants.


BMC Genomics ◽  
2013 ◽  
Vol 14 (1) ◽  
pp. 358 ◽  
Author(s):  
Jianjun Qi ◽  
Na Zheng ◽  
Bing Zhang ◽  
Peng Sun ◽  
Songnian Hu ◽  
...  

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