Why study single cells?

As a preview to Single-Cell Sequencing: Diagnosing and Dissecting Cancer as a Disease of the Genome, Cambridge Healthtech Institute challenged conference faculty members to detail the benefits and opportunities in single-cell analysis.

Cambridge Healthtech Institute: Single-cell sequencing is a time-consuming, expensive and difficult process. What do we hope to learn from a single cell’s contribution to disease that makes this all worthwhile?

Yong WangYong Wang, Ph.D., Research Scientist, Nicholas E. Navin Laboratory, Genetics, Bioinformatics, MD Anderson Cancer Center

  • To study scarce clinical samples. Bulk sequencing, though less expensive and a routine process, requires DNA of millions of cells, hence not suitable to study the genome of scarce clinical samples, such as circulating tumor cells, therapy resistant cells, or cancer stem cells.
  • To investigate intratumor heterogeneity. Tumor includes a complex population of normal and tumor cells that each may carry unique mutations. Reconstructing genetic lineage of the tumor by single cell sequencing hundreds of cells can help us understand the clonal evolution of the tumor. Bulk sequencing is limited to reporting average genetic signals thus cannot resolve the clonal structure.

John F. ZhongJohn F. Zhong, Ph.D., Associate Professor, Pathology, University of Southern California School of Medicine

The major reason we want to study single-cell is that gene regulation happens within a cell. Cell fate is determined by genes interacting with other genes within a cell. If we want to infer gene regulation by expression levels or timing, we must measure relative expression levels of all genes within a cell, not the average level in cell lysate.

Michael Masterman-SmithMichael Masterman-Smith, Ph.D., Entrepreneurial Scientist, UCLA California NanoSystems Institute

In 1959, Nobel laureate Richard Feynman gave a prophetic lecture entitled “There's Plenty of Room at the Bottom”, which stimulated thinking about the development of smaller tools which could directly manipulate individual atoms. This approach towards technology development fueled advances across the physical sciences and provided the substrate for both space and digital ages. Half a century later, this conceptual framework is being deployed for biological analyses at the resolution of the single cell to understand, diagnose and treat human disease. Though the expense and efficiency of single-cell sequencing and analysis may complicate widespread adoption at present, data emerging from some single-cell analysis technologies are compelling and may ultimately prove useful in improving diagnostic and treatment guidance for complex, cellularly heterogeneous disease states such as cancer. Furthermore, as improvements in technology design, function and throughput continue, single-cell sequencing and analysis tools and methods may become cost effective for routine use in the life and medical sciences.

Parveen KumarParveen Kumar, Research Scientist, Thierry Voet Laboratory, Human Genetics, University of Leuven

The genomic composition and mutations private to individual cells are lost in conventional sequencing studies, which analyse DNA extracted from large populations of cells. Clear insights into many biological processes—from normal development to tumour evolution—will thus only be gained from a detailed understanding of genomic and epigenomic variation at the single-cell level.1 Furthermore, some cell types which are present rarely and in low concentrations make single-cell approaches of paramount importance for their identification and characterisation. The cells shed from primary solid tumours into blood stream, i.e., circulating tumour cells (CTCs) or cells disseminated to distant organs, i.e., disseminated tumour cells (DTCs) are important to investigate not only to unravel tumour evolution and progression but also as liquid biopsies of a solid tumour for diagnosis, prognosis and treatment.2 Advances in techniques for the isolation of single cells, whole-genome amplification (WGA) and genome-wide analysis platforms—primarily next-generation sequencing (NGS) devices—paved the way for high-resolution analysis of the genome from one cell, which is now revealing previously obscured biological complexity.

1Macaulay, I. C., and Voet, T. (2014). Single cell genomics: advances and future perspectives. PLoS Genet. 10:e1004126. doi: 10.1371/journal.pgen.1004126.2Van Loo P, Voet T: Single cell analysis of cancer genomes. Curr Opin Genet Dev 2014, 24C:82-91.

To learn more and connect with this faculty, make plans to attend Single-Cell Sequencing, taking place at the 2014 Next Generation Dx Summit, August 20-21 in Washington, DC.