Spatial transcriptomics of tumor microenvironment in formalin-fixed paraffin-embedded breast cancer
作者： Lou Romanens , Prasad Chaskar , Jean-Christophe Tille , Stephan Ryser , Nicolas Liaudet
DOI: 10.1101/2020.01.31.928143
关键词:
摘要: Abstract Tumor samples are conserved in clinical practice formalin-fixed paraffin-embedded (FFPE) blocks. Formalin fixation chemically alters nucleic acids, rendering transcriptomic analysis challenging. RNA-sequencing is usually performed on tumor bulk, without distinction of cell subtypes or location. Here we describe the development a robust method for RNA extraction and exome-capture laser-capture microdissected cells (TC) stromal immune (TIL) based their morphology. We applied this 7 (surgical core needle biopsy) triple-negative breast cancer (TNBC) stored FFPE blocks over 3-10 years. Unsupervised clustering principal component showed clear separation between gene-expression profile TIL TC. were enriched markers B (CD79B, PAX5 BLNK) T (CD2, CD3D CD8B) whereas expressed epithelial (EPCAM, MUC1 KRT8). Microenvironment populations-counter (MCP)-counter deconvolution an enrichment adaptive signatures TIL. Transcripts checkpoints differentially further validated our results by qRT-PCR multispectral immunohistochemistry. In conclusion, that combining microdissection archived feasible allows spatial transcriptional characterization microenvironment.
sci-hub.st 参考文章(48)
Jose Russo, Fathima Sheriff, Ricardo Lopez de Cicco, Thomas J. Pogash, Theresa Nguyen, Irma H. Russo, Methodology for Studying the Compartments of the Human Breast Springer, New York, NY. pp. 75- 102 ,(2014) , 10.1007/978-1-4939-0718-2_3
Jo Vandesompele, Katleen De Preter, Filip Pattyn, Bruce Poppe, Nadine Van Roy, Anne De Paepe, Frank Speleman, Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes Genome Biology. ,vol. 3, pp. 1- 12 ,(2002) , 10.1186/GB-2002-3-7-RESEARCH0034
Hadley Wickham, ggplot2: Elegant Graphics for Data Analysis ,(2009)
Shabnam Shalapour, Michael Karin, Immunity, inflammation, and cancer: an eternal fight between good and evil Journal of Clinical Investigation. ,vol. 125, pp. 3347- 3355 ,(2015) , 10.1172/JCI80007
F. R. Balkwill, M. Capasso, T. Hagemann, The tumor microenvironment at a glance Journal of Cell Science. ,vol. 125, pp. 5591- 5596 ,(2012) , 10.1242/JCS.116392
Vladimir Vincek, Mehdi Nassiri, Jennean Knowles, Mehrdad Nadji, Azorides R Morales, Preservation of Tissue RNA in Normal Saline Laboratory Investigation. ,vol. 83, pp. 137- 138 ,(2003) , 10.1097/01.LAB.0000047490.26282.CF
Aaron M Newman, Chih Long Liu, Michael R Green, Andrew J Gentles, Weiguo Feng, Yue Xu, Chuong D Hoang, Maximilian Diehn, Ash A Alizadeh, Robust enumeration of cell subsets from tissue expression profiles Nature Methods. ,vol. 12, pp. 453- 457 ,(2015) , 10.1038/NMETH.3337
ROBERT TIBSHIRANI, Variance stabilization and the bootstrap Biometrika. ,vol. 75, pp. 433- 444 ,(1988) , 10.1093/BIOMET/75.3.433
Michael S. Rooney, Sachet A. Shukla, Catherine J. Wu, Gad Getz, Nir Hacohen, Molecular and genetic properties of tumors associated with local immune cytolytic activity. Cell. ,vol. 160, pp. 48- 61 ,(2015) , 10.1016/J.CELL.2014.12.033
Donald W Kufe, None, MUC1-C oncoprotein as a target in breast cancer: activation of signaling pathways and therapeutic approaches Oncogene. ,vol. 32, pp. 1073- 1081 ,(2013) , 10.1038/ONC.2012.158