Cancer-associated fibroblasts maintain critical pancreatic cancer cell lipid homeostasis in the tumor microenvironment
Han X, Burrows M, Kim LC, Xu JP, Vostrejs W, Le TNV, Poltorack C, Jiang Y, Cukierman E, Stanger BZ, Reiss KA, Shaffer SM, Mesaros C, Keith B, Simon MC
Cell Reports, 2024 November. doi: https://doi.org/10.1016/j.celrep.2024.114972 PDF
Non-genetic differences underlie variability in proliferation among esophageal epithelial clones
Reyes Hueros RA, Gier RA, Shaffer SM
PLOS Computational Biology. 2024 October. doi: https://doi.org/10.1371/journal.pcbi.1012360 PDF
Development of a functional beige fat cell line uncovers independent subclasses of cells expressing UCP1 and the futile creatine cycle
Vargas-Castillo A, Sun Y, Smythers AL, Grauvogel L, Dumesic PA, Emont MP, Tasi LT, Rosen ED, Zammit NW, Shaffer SM, Ordonez M, Chouchani ET, Gygi SP, Wang T, Sharma AK, Balaz M, Wolfrum C, Spiegelman BM
Cell Metabolism. 2024 September. doi: 10.1016/j.cmet.2024.07.002
Clonal differences underlie variable responses to sequential and prolonged treatment
Schaff DL*, Fasse AJ*, White PE, Vander Velde R, Shaffer SM *equal contributions
Cell Systems. 2024 March. doi: https://doi.org/10.1016/j.cels.2024.01.011 PDF
Clonal cell states link Barrett’s esophagus and esophageal adenocarcinoma
Gier RA, Reyes Hueros RA, Rong J, DeMarshall M, Karakasheva TA, Muir AB, Falk GW, Zhang NR, Shaffer SM
BioRxiv. 2023 Jan. doi: https://doi.org/10.1101/2023.01.26.525564
Patterns of tumour transcriptional variability
Ng RWS, Shaffer SM
Nature, News and Views, 2023 May. https://www.nature.com/articles/d41586-023-01744-0
Integrating mutational and nonmutational mechanisms of acquired therapy resistance within the Darwinian paradigm
Vander Velde R, Shaffer SM, Marusyk A
Trends in Cancer. 2022 June. doi: https://doi.org/10.1016/j.trecan.2022.02.004
Subcellular Detection of SARS-CoV-2 RNA in Human Tissue Reveals Distinct Localization in Alveolar Type 2 Pneumocytes and Alveolar Macrophages.
Acheampong KK, Schaff DL, Emert BL, Lake J, Reffsin S, Shea EK, Comar CE, Litzky LA, Khurram NA, Linn RL, Feldman M, Weiss SR, Montone KT, Cherry S, Shaffer SM
mBio. 2022 February 8. doi: 10.1128/mbio.03751-21 PDF | pubmed
Memory sequencing reveals heritable single cell gene expression programs associated with distinct cellular behaviors.
Shaffer SM*, Emert B*, Reyes-Hueros RA, Cote C, Harmange G, Schaff G, Sizemore AE, Gupte R, Torre E, Singh A, Basset DS, Raj A *equal contributions
Cell. 2020 August 20. doi: 10.1016/j.cell.2020.07.003 PDF | pubmed
Validation of a next-generation sequencing oncology panel optimized for low input DNA.
Sussman RT*, Shaffer S*, Azzato EM*, DeSloover D, Farooqi MS, Meyer A, Lieberman DB, Bigdeli A, Paolillo C, Ganapathy K, Sukhadia S, Rosenbaum JN, Daber RD, Morrissette JJD. *equal contributions
Cancer Genetics. 2018 December. journal website
SAVER: Gene expression recovery for single-cell RNA sequencing.
Huang M, Wang J, Torre E, Dueck H, Shaffer S, Bonasio R, Murray JI, Raj A, Li M, and Zhang NR.
Nature Methods. 2018 June 25. pubmed
Rare cell variability and drug-induced reprogramming as a mode of cancer drug resistance.
Shaffer SM, Dunagin MC, Torborg SR, Torre EA, Emert B, Krepler C, Beqiri M, Sproesser K, Brafford PA, Xiao M, Eggan E, Anastopoulos IN, Vargas-Garcia CA, Singh A, Nathanson KL, Herlyn M, Raj A.
