Apr 19, 2018

#AACR Day 4 - Advances of Single Cell Genomics in Cancer Research

Shauna Clark

AACR 2018 is officially over! It was a great conference and the last day was no exception. I started off with a couple of posters this morning.  I checked out "Facile generation of single-cell transcriptome and immune repertoire freshly isolated from clinical tumor specimens," presented by Junjie Zhu, Stanford University. The authors used the Chromium Single Cell Immune Profiling Solution to profile the transcriptomes and immune repertoires of thousands of cells from fresh, clinical tumor samples collected across a variety of tissue types. Their demonstrated approach could lead to the future discovery of possible prognostic indicators of clinical phenotypes in immunotherapy response.

My last poster of the conference was "Single cell RNA sequencing of pancreatic ductal adenocarcinoma reveals tumor heterogeneity," which was presented by Pawan Noel, TGen, and described research done with the Chromium Single Cell Gene Expression Solution to learn more about the cellular composition of individual pancreatic ductal adenocarcinoma (PDAC) tumors. Using scRNA-seq, the authors identified several distinct cell types, including epithelial, endothelial, and immune cells, as well as cancer associated fibroblasts. They found scRNA-seq to be a powerful approach for studying heterogeneity in solid tumors, such as PDAC.

Then, I took the opportunity to to attend a very interesting Symposium on "Recent Advances of Single-Cell Genomics in Cancer Research," chaired by Sohrab Shah, BC Cancer Agency Vancouver Center. The speakers had some really fascinating work to share (sadly, I had to miss the last speaker to head to airport).

  • "Single-cell epigenomics reveal the epigenetic evolution and lineage histories of chronic lymphocytic leukemia" by Daniel Landau, Weill Cornell Medicine
  • "Genomic and transcriptomic analysis reveals incremental disruption of key signaling pathways during melanoma evolution" by A. Hunter Shain, UCSF
    • Researchers performed matched DNA and single cell RNA-seq in 45 matched cases of melanoma/precursor lesion and were able to track the evolution of melanoma from early to metastatic stages. For example, the team found that the MAP-kinase pathway is activated early and strengthens with progression and that the cell cycle regulation is disrupted at the transition to invasive melanoma.
  • "Exploiting single cell approaches to define the evolving tumor microenvironment" by Jacqui Shields, University of Cambridge
    • CAF cells represent the most abundant stromal cell population int the tumor microenvironment, but there is not much known about their biology and contribution to tumor development. Using scRNA-seq (309 CAFs over 3 time points), the researchers were able to identify 3 populations of CAFs with unique functional signatures. They also saw that the cell populations are dynamic, emerging and receding as the tumor develops.
  • "Scalable single cell whole genome sequencing: Towards population genetics of cancer" by Sohrab Shah, BC Cancer Agency Vancouver Center

It's been a really exciting meeting and great to hear about all the advances in cancer research. We were pleased to announce the launch of the Chromium Single Cell CNV Solution and can't wait to see how it will be used for innovative research at AACR 2019.  See you next year!

And don't forget, we've got more exciting single cell products coming out later this year.