Existing preclinical methods for acquiring dissemination kinetics of rare circulating tumor cells (CTCs) en route to forming metastases have not been capable of providing a direct measure of CTC intravasation rate and subsequent half-life in the circulation. Here, we demonstrate an approach for measuring endogenous CTC kinetics by continuously exchanging CTC-containing blood over several hours between un-anesthetized, tumor-bearing mice and healthy, tumor-free counterparts. By tracking CTC transfer rates, we extrapolated half-life times in the circulation of between 40 and 260 s and intravasation rates between 60 and 107,000 CTCs/hour in mouse models of small-cell lung cancer (SCLC), pancreatic ductal adenocarcinoma (PDAC), and non-small cell lung cancer (NSCLC). Additionally, direct transfer of only 1−2% of daily-shed CTCs using our blood-exchange technique from late-stage, SCLC-bearing mice generated macrometastases in healthy recipient mice. We envision that our technique will help further elucidate the role of CTCs and the rate-limiting steps in metastasis.

Mass and growth rate are highly integrative measures of cell physiology not discernable via genomic measurements. Here, we introduce a microfluidic platform enabling direct measurement of single-cell mass and growth rate upstream of highly multiplexed single-cell profiling such as single-cell RNA sequencing. We resolve transcriptional signatures associated with single-cell mass and growth rate in L1210 and FL5.12 cell lines and activated CD8+ T cells. Further, we demonstrate a framework using these linked measurements to characterize biophysical heterogeneity in a patient-derived glioblastoma cell line with and without drug treatment. Our results highlight the value of coupled phenotypic metrics in guiding single-cell genomics.

We develop single-cell transcriptomic approaches to comprehensively profile human tissues and model systems. Previously, we focused on establishingvalidating, scaling, and simplifying single-cell RNA-seq, often through the development of microdevices, to enable genome-wide identification of the cell types/states contained within complex biological samples. More recently, we helped both enhance the detection of phenotype-defining transcripts using these methods and simplify their on-site processing for clinical applications. In parallel, we have also worked to democratize these techniques, providing open access to resources and protocols, training thousands locally and abroad, and establishing infrastructure and on-site collaborations spanning across 6 continents and 26+ countries.

As many factors define cellular phenotype and influence disease beyond mRNA, we develop complementary methods for co-assaying other cellular attributes to enrich our understanding of the drivers of cellular behaviors. Examples including the abundance of additional ‘-omes’, the sequence and amount of important transcripts, cellular history, biophysical properties, spatial position, and functional output. Recently, we have worked to: 1. detect pathogens in cells and potentially actionable associated host factors; 2. query for specific mutations to identify cancer cells; and, 3. extract T cell receptor sequences to examine clonality. We have also formulated computational methods to derive deeper insights from these data (e.g., to examine viral dynamic in infected cells, reproducible features hidden by inter-individual variability, multicellular immune dynamics, intercellular communication, or alteration in cellular ecosystems associated with pathology).

We explore how the extracellular milieu influences cellular decision-making. Here, we have employed controlled culture conditions with cells and organoids, chemical and genetic perturbations, and constant microfluidic perfusion. We also have leveraged natural microenvironmental variation within and across tissues via microdissection and by using photoactivatable probes that retain spatial information through dissociation. In each instance, we aim to understand the degree to which extracellular environments modulate, and can be used to rationally control, the responses of individual cells or the overall distribution thereof, with an eye toward engineering tissue responses.

We examine the impact of intercellular interactions on cellular function. We have used coculture, imaging and perturbation strategies, as well as matched computational methods, to reinforce findings from dissociated samples, validate inferred cell-cell communication in vivo (e.g., between sensory neurons and lymph node resident cells), and manipulate multicellular systems (e.g., organoids). We are currently working on building arrayed, synthetically-designed cellular ensembles to examine how ‘tissue’ structure impacts functional response. Our overall goal is to understand cellular co-dependencies that influence niche- and tissue-level response dynamics.

A generalized platform for introducing a diverse range of biomolecules into living cells in high-throughput could transform how complex cellular processes are probed and analyzed. Here, we demonstrate spatially localized, efficient, and universal delivery of biomolecules into immortalized and primary mammalian cells using surface-modified vertical silicon nanowires. The method relies on the ability of the silicon nanowires to penetrate a cell’s membrane and subsequently release surface-bound molecules directly into the cell’s cytosol, thus allowing highly efficient delivery of biomolecules without chemical modification or viral packaging. This modality enables one to assess the phenotypic consequences of introducing a broad range of biological effectors (DNAs, RNAs, peptides, proteins, and small molecules) into almost any cell type. We show that this platform can be used to guide neuronal progenitor growth with small molecules, knock down transcript levels by delivering siRNAs, inhibit apoptosis using peptides, and introduce targeted proteins to specific organelles. We further demonstrate codelivery of siRNAs and proteins on a single substrate in a microarray format, highlighting this technology’s potential as a robust, monolithic platform for high-throughput, miniaturized bioassays.


Electrostatic force microscopy shows that the electric field gradients above pentacene monolayer islands on 2-nm SiO2/Si substrates, in a dark, dry nitrogen environment, display a wide distribution of signs and magnitude that is dependent on sample history. Under 12 mW/cm2 green (532 nm) illumination, pentacene islands accumulate positive charge because of photoexcited electron transfer across the oxide to the Si substrate. At a strong illumination of 60 mW/cm2, pentacene islands reform into small spherical particles, apparently because the positive charge Coulomb repulsion energy becomes comparable to the cohesive energy of the pentacene monolayer.