Research

Circulating Cell-Free DNA

A large number of small fragments of cell-free DNA circulate in blood and urine. In healthy individuals, cfDNA is predominantly derived from apoptosis of normal cells of the hematopoietic lineage, with additional contributions from other tissues. 1,000 to 10,000 genome equivalents of cell-free DNA can be isolated from just one mL of plasma, including small fragments of chromosomal DNA and mitochondrial DNA, as well as fragments of viral, bacterial and fungal genomes. Cell-free DNA offers an information-rich window into human physiology, with rapidly expanding applications in prenatal testing, cancer diagnosis, and the monitoring of infection, rejection, and immunosuppression after solid-organ transplantation.

The lab develops assays to interrogate cell-free DNA via sequencing. This work requires innovation in both molecular biology and computational biology. We have recently developed an assay to sequence ultrashort molecules of cell-free DNA and we have described an algorithm to estimate donor cell-free DNA in absence of a donor genotype. We furthermore pursue new applications in medical diagnostics, in particular new approaches to the monitoring of solid organ transplant patients and blood and marrow transplant patients. 

 

 
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.