Single-cell droplet microfluidics for metagenomics and cancer multiomics

Cellular heterogeneity is inherent to many biological systems, across both normal and disease states. For example, diverse ensembles of microbes in the natural environment fulfill distinct roles related to nutrient metabolism and gas fixation. In human cancers, genetic and phenotypic heterogeneity is observed among cells originating from a common oncogenic clone. Understanding biological heterogeneity, whether for metabolic engineering applications or the design of cancer therapeutics, begins at the fundamental unit of the organism: a single cell. Droplet microfluidics enables analyses of single cells at a biologically-relevant scale through rapid compartmentalization and manipulation of millions of parallel reactions. In this thesis, I describe the development and application of single-cell genomics platforms leveraging droplet microfluidics to interrogate many individual genomes. These technologies enable single-cell metagenomics and multiomic analysis of single cancer cells, providing new insights into the extent of cellular heterogeneity and its implications across biology

An Ultrahigh-throughput Microfluidic Platform for Single-cell Genome Sequencing.

Sequencing technologies have undergone a paradigm shift from bulk to single-cell resolution in response to an evolving understanding of the role of cellular heterogeneity in biological systems. However, single-cell sequencing of large populations has been hampered by limitations in processing genomes for sequencing. In this paper, we describe a method for single-cell genome sequencing (SiC-seq) which uses droplet microfluidics to isolate, amplify, and barcode the genomes of single cells. Cell encapsulation in microgels allows the compartmentalized purification and tagmentation of DNA, while a microfluidic merger efficiently pairs each genome with a unique single-cell oligonucleotide barcode, allowing >50,000 single cells to be sequenced per run. The sequencing data is demultiplexed by barcode, generating groups of reads originating from single cells. As a high-throughput and low-bias method of single-cell sequencing, SiC-seq will enable a broader range of genomic studies targeted at diverse cell populations

Single-cell genome sequencing at ultra-high-throughput with microfluidic droplet barcoding.

The application of single-cell genome sequencing to large cell populations has been hindered by technical challenges in isolating single cells during genome preparation. Here we present single-cell genomic sequencing (SiC-seq), which uses droplet microfluidics to isolate, fragment, and barcode the genomes of single cells, followed by Illumina sequencing of pooled DNA. We demonstrate ultra-high-throughput sequencing of >50,000 cells per run in a synthetic community of Gram-negative and Gram-positive bacteria and fungi. The sequenced genomes can be sorted in silico based on characteristic sequences. We use this approach to analyze the distributions of antibiotic-resistance genes, virulence factors, and phage sequences in microbial communities from an environmental sample. The ability to routinely sequence large populations of single cells will enable the de-convolution of genetic heterogeneity in diverse cell populations

Networks of High Aspect Ratio Particles to Direct Colloidal Assembly Dynamics and Cellular Interactions

Injectable colloids that self-assemble into three-dimensional networks are promising materials for applications in regenerative engineering, as they create open systems for cellular infiltration, interaction, and activation. However, most injectable colloids have spherical morphologies, which lack the high material-biology contact areas afforded by higher aspect ratio materials. To address this need, injectable high aspect ratio particles (HARPs) were developed that form three-dimensional networks to enhance scaffold assembly dynamics and cellular interactions. HARPs were functionalized for tunable surface charge through layer-by-layer electrostatic assembly. Positively charged Chitosan-HARPs had improved particle suspension dynamics when compared to spherical particles or negatively charged HARPs. Chit-HARPs were used to improve the suspension dynamics and viability of MIN6 cells in three-dimensional networks. When combined with negatively charged gelatin microsphere (GelMS) porogens, Chit-HARPs reduced GelMS sedimentation and increased overall network suspension, due to a combination of HARP network formation and electrostatic interactions. Lastly, HARPs were functionalized with fibroblast growth factor 2 (FGF2) to highlight their use for growth factor delivery. FGF2-HARPs increased fibroblast proliferation through a combination of 3D scaffold assembly and growth factor delivery. Taken together, these studies demonstrate the development and diverse uses of high aspect ratio particles as tunable injectable scaffolds for applications in regenerative engineering

Microfluidic automated plasmid library enrichment for biosynthetic gene cluster discovery.

Microbial biosynthetic gene clusters are a valuable source of bioactive molecules. However, because they typically represent a small fraction of genomic material in most metagenomic samples, it remains challenging to deeply sequence them. We present an approach to isolate and sequence gene clusters in metagenomic samples using microfluidic automated plasmid library enrichment. Our approach provides deep coverage of the target gene cluster, facilitating reassembly. We demonstrate the approach by isolating and sequencing type I polyketide synthase gene clusters from an Antarctic soil metagenome. Our method promotes the discovery of functional-related genes and biosynthetic pathways

Microfluidic automated plasmid library enrichment for biosynthetic gene cluster discovery.

Microbial biosynthetic gene clusters are a valuable source of bioactive molecules. However, because they typically represent a small fraction of genomic material in most metagenomic samples, it remains challenging to deeply sequence them. We present an approach to isolate and sequence gene clusters in metagenomic samples using microfluidic automated plasmid library enrichment. Our approach provides deep coverage of the target gene cluster, facilitating reassembly. We demonstrate the approach by isolating and sequencing type I polyketide synthase gene clusters from an Antarctic soil metagenome. Our method promotes the discovery of functional-related genes and biosynthetic pathways

Joint profiling of DNA and proteins in single cells to dissect genotype-phenotype associations in leukemia.

Studies of acute myeloid leukemia rely on DNA sequencing and immunophenotyping by flow cytometry as primary tools for disease characterization. However, leukemia tumor heterogeneity complicates integration of DNA variants and immunophenotypes from separate measurements. Here we introduce DAb-seq, a technology for simultaneous capture of DNA genotype and cell surface phenotype from single cells at high throughput, enabling direct profiling of proteogenomic states in tens of thousands of cells. To demonstrate the approach, we analyze the disease of three patients with leukemia over multiple treatment timepoints and disease recurrences. We observe complex genotype-phenotype dynamics that illustrate the subtlety of the disease process and the degree of incongruity between blast cell genotype and phenotype in different clinical scenarios. Our results highlight the importance of combined single-cell DNA and protein measurements to fully characterize the heterogeneity of leukemia