A Novel Adaptive Penalized Logistic Regression for Uncovering Biomarker Associated with Anti-Cancer Drug Sensitivity

Author(s):  
Heewon Park ◽  
Yuichi Shiraishi ◽  
Seiya Imoto ◽  
Satoru Miyano
Micromachines ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 624
Author(s):  
Qiang Liu ◽  
Tian Zhao ◽  
Xianning Wang ◽  
Zhongyao Chen ◽  
Yawei Hu ◽  
...  

Three-dimensional cultured patient-derived cancer organoids (PDOs) represent a powerful tool for anti-cancer drug development due to their similarity to the in vivo tumor tissues. However, the culture and manipulation of PDOs is more difficult than 2D cultured cell lines due to the presence of the culture matrix and the 3D feature of the organoids. In our other study, we established a method for lung cancer organoid (LCO)-based drug sensitivity tests on the superhydrophobic microwell array chip (SMAR-chip). Here, we describe a novel in situ cryopreservation technology on the SMAR-chip to preserve the viability of the organoids for future drug sensitivity tests. We compared two cryopreservation approaches (slow freezing and vitrification) and demonstrated that vitrification performed better at preserving the viability of LCOs. Next, we developed a simple procedure for in situ cryopreservation and thawing of the LCOs on the SMAR-chip. We proved that the on-chip cryopreserved organoids can be recovered successfully and, more importantly, showing similar responses to anti-cancer drugs as the unfrozen controls. This in situ vitrification technology eliminated the harvesting and centrifugation steps in conventional cryopreservation, making the whole freeze–thaw process easier to perform and the preserved LCOs ready to be used for the subsequent drug sensitivity test.


2019 ◽  
Author(s):  
Chan Hee Park ◽  
Seung Wook Ham ◽  
HyeKyoung Shin ◽  
Kyung Soo Oh

Molecules ◽  
2018 ◽  
Vol 23 (11) ◽  
pp. 2903 ◽  
Author(s):  
Yong Zhang ◽  
Jingjing Xu ◽  
Yuezhou Yu ◽  
Wenhao Shang ◽  
Anpei Ye

A novel anti-cancer drug sensitivity testing (DST) approach was developed based on in vitro single-cell Raman spectrum intensity (RSI). Generally, the intensity of Raman spectra (RS) for a single living cell treated with drugs positively relates to the sensitivity of the cells to the drugs. In this study, five cancer cell lines (BGC 823, SGC 7901, MGC 803, AGS, and NCI-N87) were exposed to three cytotoxic compounds or to combinations of these compounds, and then they were evaluated for their responses with RSI. The results of RSI were consistent with conventional DST methods. The parametric correlation coefficient for the RSI and Methylthiazolyl tetrazolium assay (MTT) was 0.8558 ± 0.0850, and the coefficient of determination was calculated as R2 = 0.9529 ± 0.0355 for fitting the dose–response curve. Moreover, RSI data for NCI-N87 cells treated by trastuzumab, everolimus (cytostatic), and these drugs in combination demonstrated that the RSI method was suitable for testing the sensitivity of cytostatic drugs. Furthermore, a heterogeneity coefficient H was introduced for quantitative characterization of the heterogeneity of cancer cells treated by drugs. The largest possible variance between RSs of cancer cells were quantitatively obtained using eigenvalues of principal component analysis (PCA). The ratio of H between resistant cells and sensitive cells was greater than 1.5, which suggested the H-value was effective to describe the heterogeneity of cancer cells. Briefly, the RSI method might be a powerful tool for simple and rapid detection of the sensitivity of tumor cells to anti-cancer drugs and the heterogeneity of their responses to these drugs.


PLoS ONE ◽  
2014 ◽  
Vol 9 (10) ◽  
pp. e108990 ◽  
Author(s):  
Heewon Park ◽  
Teppei Shimamura ◽  
Satoru Miyano ◽  
Seiya Imoto

2018 ◽  
Author(s):  
Shiki Fujino ◽  
Norikatsu Miyoshi ◽  
Masayuki Ohue ◽  
Kazuhiro Saso ◽  
Tsunekazu Mizushima ◽  
...  

Gene ◽  
2016 ◽  
Vol 594 (2) ◽  
pp. 190-196 ◽  
Author(s):  
Hui Wang ◽  
Weiying Li ◽  
Baitang Lai ◽  
Xuehui Yang ◽  
Chunyan Zhang ◽  
...  

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