Tumors are complex ecosystems containing cells with different functions, which interact to maintain the cancerous environment. Profiling tumors has been severely limited by their cellular diversity, because the methods used for molecular analysis of whole tumor samples might not reflect any single tumor cell accurately. Measuring the RNA composition of 10,000s of individual cells from a tumor could turn this heterogeneity into a benefit, by revealing druggable vulnerabilities in immune and stromal cells, as well as potentially dangerous tumor-initiating transcriptomes in rare cancer cells. To address this opportunity, we propose to adapt a powerful microfluidic platform that we have developed, known as inDrops, for low-cost high-throughput single- cell profiling in cancer biology and specifically for biopsy samples. Relatively little additional technology development is required to make this method practical for analysis of individual tumors for basic research or in a clinical setting. This project focuses on solidifying the advantages of this transformative novel platform through achievable steps. Currently, inDrops is the only single-cell transcriptomics platform with the scale and cell recovery rate required to make it a practical tool for biopsy analysis.
Our specific aims focus on demonstrating the method on tumor samples, optimizing microfluidic engineering for robust work with biopsies, adapting the method to work with pre-fixed cells, adapting the method for screening with targeted gene panels, and integrating the resulting data with histological analysis so as to maximally facilitate diagnostically and prognostically relevant discoveries. Together, these advances will transform inDrops into a powerful method for wide use in cancer biology.

Public Health Relevance

Tumors contain cells with different propensities to contribute to tumor growth, or to affect treatment response. In order to develop patient-specific, ?precision? cancer therapies, it is critical to be able to identify which cells reside in each tumor. We propose to adapt a powerful new platform that we have developed, known as inDrops, for low-cost high-throughput single-cell profiling in cancer biology, and specifically for profiling thousands of cells from biopsy samples, thus taking a large step closer to the era of precision medicine. 1

Agency
National Institute of Health (NIH)
Institute
National Cancer Institute (NCI)
Type
Exploratory/Developmental Grants Phase II (R33)
Project #
1R33CA212697-01
Application #
9231545
Study Section
Special Emphasis Panel (ZCA1-TCRB-D (O1))
Program Officer
Ossandon, Miguel
Project Start
2017-02-16
Project End
2020-01-31
Budget Start
2017-02-16
Budget End
2018-01-31
Support Year
1
Fiscal Year
2017
Total Cost
$411,954
Indirect Cost
$162,953
Name
Harvard Medical School
Department
Biology
Type
Schools of Medicine
DUNS #
047006379
City
Boston
State
MA
Country
United States
Zip Code
02115
Engblom, Camilla; Pfirschke, Christina; Zilionis, Rapolas et al. (2017) Osteoblasts remotely supply lung tumors with cancer-promoting SiglecFhigh neutrophils. Science 358:
Weinreb, Caleb; Wolock, Samuel; Klein, Allon (2017) SPRING: a kinetic interface for visualizing high dimensional single-cell expression data. Bioinformatics :