Monitoring immunity and infection via cell-free DNA

Short fragments of cell-free DNA circulate in blood, urine and other biofluids and offer an information-rich window into human physiology, with rapidly expanding applications in prenatal testing, cancer screening, organ transplant monitoring and infectious disease testing.

Our research pursues technologies and applications of cell-free DNA in infectious and immune-related disease. The great promise of cfDNA in diagnostic medicine derives from i) its abundance: 10-100 billion molecules of cell-free DNA can be isolated from just 1 mL of plasma. The combined DNA sequence of these molecules is sufficient to cover the human genome 1,000 to 10,000 fold. ii) Its origin: cell-free DNA is derived from dead cells and comprises rich information about cells in the blood and any vascularized tissue that can be accessed noninvasively. iii) Its short lifetime: cell-free DNA is cleared from the blood within 60 minutes. cell-free DNA therefore provides a very dynamic window into health.

Our recent research in this area has led to i) novel molecular and bioinformatic technologies to obtain and mine sequence information from cell-free DNA, and ii) novel applications of cell-free DNA in diagnostic medicine:

  • We have demonstrated that a single-stranded DNA library preparation uncovers the diversity of ultrashort cfDNA in plasma.
  • We have reported that urinary cell-free DNA is a versatile analyte for the diagnosis of urinary tract infection
  • We have developed a cell-free DNA metagenomic sequencing assay that integrates the damage response to infection.
  • We have reported how cell-free DNA tissues-of-origin profiling can be used to predict Graft versus Host Disease and detect infection after hematopoietic cell transplantation
  • We have created a bioinformatics tool to screen for infection from low-biomass isolates of cell-free DNA


Single-cell Genomics

One of our goals is to understand gene expression in complex biological systems using single-cell RNA sequencing (scRNA-seq). While almost all of the cells in an organism share the same genome, transcriptomic activity in individual cells is very heterogeneous and determines the function of the cell. A powerful technique we developed and employ is DART-seq, a high-throughput and cost effective method for targeted transcriptomics.

Our lab has a number of collaborative projects with clinicians, biologists, and engineers. We develop wet- and dry-lab scRNA-seq approaches to study immunity and infection at single cell resolution and to:

  • enable the discovery and analysis of novel RNA transcripts in under-studied organisms with poor gene annotations
  • study time-dependent changes in transcriptional activity during development, injury, and infection.
  • understand immune cell development in germinal centres with spatial information.



Precision Monitoring of Solid-Organ and Hematopoietic Stem Cell Transplants

Transplant medicine offers an ideal test bed for precision and genomic medicine. A diverse range of complications that are of relevance for the general population arise with high frequency after transplantation, including malignancies, infections and immunological complications. Consequently, investigations of the utility of genomic medicine tools that target the transplant population require a much smaller sample size and follow-up time than those recruiting from the general population. Further, transplant recipients are followed very closely and frequently visit the hospital, which aids in designing and executing prospective studies and studies that require serial sampling. These factors provide significant opportunities for early success in precision medicine affecting not just transplant recipients, but development and optimization of precision medicine monitoring and treatment techniques for the general population.

For more info on recent advances and outstanding opportunities for precision medicine in solid organ and hematopoeitic trasnplantation, check out our recent review here.



Highly multiplexed spatial mapping of microbial communities

Microbial communities exhibit rich species diversity and exquisite spatial organization. While the species diversity of microbial populations is accessible by shotgun DNA sequencing; their spatial organization remains difficult to survey with existing tools.

To overcome this limitation, we have developed High Phylogenetic Resolution microbiome mapping by Fluorescence In-Situ Hybridization (HiPR-FISH), a versatile and cost-effective technology that uses binary encoding and spectral imaging and machine learning based decoding to create micron-scale maps of the locations and identities of hundreds of microbial species in complex communities. We demonstrated the ability of 10-bit HiPR-FISH to distinguish 1023 E. coli strains, each fluorescently labeled with a unique binary barcode. We used HiPR-FISH, in conjunction with custom algorithms for automated probe design and segmentation of single-cells in the native context of tissues, to reveal the intricate spatial architectures formed by bacteria in the human oral plaque microbiome and disruption of spatial networks in the mouse gut microbiome in response to antibiotic treatment. HiPR-FISH provides a framework for analyzing the spatial organization of microbial communities in tissues and the environment at single cell resolution.