Microgenomics2021: Profiling tissue microenvironment with laser-capture microdissection & Smart-3SEQ
Channel: The International Symposium on Microgenomics 2023
Date: 2021-11-04

Dr. Joseph Foley  is a research scientist at the Stanford University School of Medicine. In the laboratory of Prof. Robert B. West, he applies laser-capture microdissection and single-cell technologies to study the functional genomics of the tumor microenvironment in breast cancer. Dr. Foley has been pioneering molecular biology and bioinformatics techniques for next-generation sequencing since the early days of the technology. He carried out his dissertation research in with Prof. Arend Sidow at Stanford University, using a new approach in large-scale ChIP-seq analysis to map the behavior of dozens of transcription factors at high-occupancy target regions. At Stanford he also assisted in the development of 3SEQ, a streamlined gene-expression profiling method that is robust to RNA degradation. He expanded on this work in his postdoctoral research in neurogenomics with Prof. Michael Meaney at McGill University's Douglas Hospital Research Centre, where he combined 3SEQ with other recent innovations to create a much more efficient and sensitive method, Smart-3SEQ. He then returned to Stanford to adapt Smart-SEQ to tissue samples from laser-capture microdissection. Together these techniques unlock gene-expression profiling from very small samples of fixed archival tissue, including single cells, which enables new approaches in molecular pathology and histology-directed genomics.


In recent decades the biological sciences have applied a series of new techniques to quantify genome-wide gene activity as a molecular phenotype, and in recent years these phenotypes have been profiled at the level of individual cells within heterogeneous tissue. However, most techniques for single-cell genomics currently rely on homogenizing a large sample of cells from fresh tissue and retroactively categorizing them by molecular phenotype. Instead we have developed a complementary approach combining laser-capture microdissection (LCM) and Smart-3SEQ, a streamlined version of RNA-seq that is robust with small and degraded samples, which allows us to choose cells by their histological phenotype prior to molecular profiling. By identifying and profiling small regions within a complex tissue sample, we can compare the gene expression of distinct clusters of cells, such as different stages of tumor progression in clinical biopsies preserved as FFPE blocks, or even individual cells within a single heterogeneous lesion. The combination of LCM and Smart-3SEQ unlocks the vast archives of existing FFPE tissue samples and opens new directions in molecular histology and pathology.