Stephen R. Quake, D.Phil., Professor, Departments of Bioengineering, Applied Physics and (by courtesy) Physics, Stanford University Schools of Medicine, Engineering, and Humanities & Sciences; Co-President, Chan Zuckerberg Biohub
Research Description: Dr. Quake’s research program has made important contributions to multiple biomedical fields. His innovative technologies have been capitalized in research and clinical applications. His work on single cell RNA sequencing has resulted in the understanding and identification of cell physiologies in various tissues. One such project, in collaboration with Seung Kim and colleagues, is aimed at understanding the lineage, gene expression and epigenetic characteristics of normal somatic stem cells and premalignant or malignant cells from the human pancreas to define markers to identify and remove these cells from contaminated cell cultures intended for regenerative medicine. This work will build an openly accessible database for pancreas with lists of gene expression and epigenetic signatures that identify subpopulations. Quake’s group has also collaborated with Seung Kim to assess conversion of primary islet alpha-cells to beta-cells in a project supported by the NIH Beta-cell biology consortium (BCBC), Human Islet Resource Network (HIRN), and JDRF. Finally, Dr. Quake’s single cell RNA-profiling methods have been widely adopted by collaborating investigators in the SDRC (listed below) and others at Stanford, and in collaborations worldwide.
Selected relevant publications (Stanford DRC Members in BOLD):
1. Zambon A, Zoso A, Gagliano O, Magrofuoco E, Fadini GP, Avogaro A, Foletto M, Quake S, Elvassore N. High Temporal Resolution Detection of Patient-Specific Glucose Uptake from Human ex Vivo Adipose Tissue On-Chip. Anal Chem. 87: 6535-43, 2015.
2. Martin L, Meier M, Lyons SM, Sit RV, Marzluff WF, Quake SR, Chang HY. Systematic reconstruction of RNA functional motifs with high-throughput microfluidics. Nat Methods 9:1192-4, 2012.
3. Dalerba P, Kalisky T, Sahoo D, Rajendran PS, Rothenberg ME, Leyrat AA, Sim S, Okamoto J, Johnston DM, Qian DL, Zabala M, Bueno J, Neff NF, Wang JB, Shelton AA, Visser B, Hisamori S, Shimono Y, van de Wetering M, Clevers H, Clarke MF, and Quake SR. Single-cell dissection of transcriptional heterogeneity in human colon tumors. Nature Biotechnology 29: 1120-U11, 2011.
4. Fan HC, Wang JB, Potanina A, and Quake SR. Whole-genome molecular haplotyping of single cells. Nature Biotechnology. 29: 51-57, 2011.
5. Chakravarthy H, Gu X, Enge M, Dai X, Wang Y, Damond N, Downie C, Liu K, Wang J, Xing Y, Chera S, Thorel F, Quake S, Oberholzer J, MacDonald PE, Herrera PL, and Kim SK. 2017. Converting adult pancreatic α-cells into β-cells by targeting both Dnmt1 and Arx. 2017. Cell Metabolism 25:622-634.
6. Enge, M, Arda, HE, Mignardi, M, Beausang, J, Bottino, R, Kim, SK, and Quake, SR. (2017). Single cell transcriptome analysis of human pancreas reveals transcriptional signatures of aging and somatic mutation patterns. bioRxiv 108043; doi: https://doi.org/10.1101/108043.