scholarly journals Reliable Clinical MLH1 Promoter Hypermethylation Assessment Using a High-Throughput Genome-Wide Methylation Array Platform

2020 ◽  
Vol 22 (3) ◽  
pp. 368-375 ◽  
Author(s):  
Jamal K. Benhamida ◽  
Jaclyn F. Hechtman ◽  
Khedoudja Nafa ◽  
Liliana Villafania ◽  
Justyna Sadowska ◽  
...  
Endoscopy ◽  
2005 ◽  
Vol 37 (05) ◽  
Author(s):  
EJ Fox ◽  
DT Leahy ◽  
R Geraghty ◽  
AM Lennon ◽  
D Keegan ◽  
...  

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Sarah E. Pierce ◽  
Jeffrey M. Granja ◽  
William J. Greenleaf

AbstractChromatin accessibility profiling can identify putative regulatory regions genome wide; however, pooled single-cell methods for assessing the effects of regulatory perturbations on accessibility are limited. Here, we report a modified droplet-based single-cell ATAC-seq protocol for perturbing and evaluating dynamic single-cell epigenetic states. This method (Spear-ATAC) enables simultaneous read-out of chromatin accessibility profiles and integrated sgRNA spacer sequences from thousands of individual cells at once. Spear-ATAC profiling of 104,592 cells representing 414 sgRNA knock-down populations reveals the temporal dynamics of epigenetic responses to regulatory perturbations in cancer cells and the associations between transcription factor binding profiles.


Cell Reports ◽  
2021 ◽  
Vol 35 (6) ◽  
pp. 109125
Author(s):  
Nikki M. McCormack ◽  
Mahlet B. Abera ◽  
Eveline S. Arnold ◽  
Rebecca M. Gibbs ◽  
Scott E. Martin ◽  
...  

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Jovana Maksimovic ◽  
Alicia Oshlack ◽  
Belinda Phipson

AbstractDNA methylation is one of the most commonly studied epigenetic marks, due to its role in disease and development. Illumina methylation arrays have been extensively used to measure methylation across the human genome. Methylation array analysis has primarily focused on preprocessing, normalization, and identification of differentially methylated CpGs and regions. GOmeth and GOregion are new methods for performing unbiased gene set testing following differential methylation analysis. Benchmarking analyses demonstrate GOmeth outperforms other approaches, and GOregion is the first method for gene set testing of differentially methylated regions. Both methods are publicly available in the missMethyl Bioconductor R package.


2011 ◽  
Vol 59 (1) ◽  
pp. 206-224 ◽  
Author(s):  
Dorothy A. Steane ◽  
Dean Nicolle ◽  
Carolina P. Sansaloni ◽  
César D. Petroli ◽  
Jason Carling ◽  
...  

Methods ◽  
2009 ◽  
Vol 47 (3) ◽  
pp. 142-150 ◽  
Author(s):  
Kyle R. Pomraning ◽  
Kristina M. Smith ◽  
Michael Freitag

2018 ◽  
Vol 15 (8) ◽  
pp. 598-600 ◽  
Author(s):  
Matthias Meurer ◽  
Yuanqiang Duan ◽  
Ehud Sass ◽  
Ilia Kats ◽  
Konrad Herbst ◽  
...  

Genomics ◽  
2011 ◽  
Vol 98 (2) ◽  
pp. 79-89 ◽  
Author(s):  
Thomas J. Hoffmann ◽  
Mark N. Kvale ◽  
Stephanie E. Hesselson ◽  
Yiping Zhan ◽  
Christine Aquino ◽  
...  

2022 ◽  
Vol 23 (2) ◽  
pp. 587
Author(s):  
Dong Woo Lee ◽  
Jung Eun Kim ◽  
Ga-Haeng Lee ◽  
Arang Son ◽  
Hee Chul Park ◽  
...  

Proton beam therapy (PBT) is a critical treatment modality for head and neck squamous cell carcinoma (HNSCC). However, not much is known about drug combinations that may improve the efficacy of PBT. This study aimed to test the feasibility of a three-dimensional (3D) tumor-spheroid-based high-throughput screening platform that could assess cellular sensitivity against PBT. Spheroids of two HNSCC cell lines—Fadu and Cal27—cultured with a mixture of Matrigel were arrayed on a 384-pillar/well plate, followed by exposure to graded doses of protons or targeted drugs including olaparib at various concentrations. Calcein staining of HNSCC spheroids revealed a dose-dependent decrease in cell viability for proton irradiation or multiple targeted drugs, and provided quantitative data that discriminated the sensitivity between the two HNSCC cell lines. The combined effect of protons and olaparib was assessed by calculating the combination index from the survival rates of 4 × 4 matrices, showing that Cal27 spheroids had greater synergy with olaparib than Fadu spheroids. In contrast, adavosertib did not synergize with protons in both spheroids. Taken together, we demonstrated that the 3D pillar/well array platform was a useful tool that provided rapid, quantitative data for evaluating sensitivity to PBT and drug combinations. Our results further supported that administration of the combination of PBT and olaparib may be an effective treatment strategy for HNSCC patients.


Sign in / Sign up

Export Citation Format

Share Document