The Advances in Genome Biology and Technology conference celebrated its 20th anniversary event this February, and what a dramatic range of advances have occurred in our field since the first meeting! Technical advances have enabled dramatic escalation in data generation and analysis capacity, while in parallel reducing sample input requirements and cost. Amongst diverse topics such as core sequencing approaches, exome capture improvements, liquid biopsy developments, single cell methodologies, and biological analyses, the central “buzz” at the meeting this year was about the new spatial genomics technologies and applications presented. A survey by Decibio confirmed this topic as the central highlight of the meeting, and furthermore indicated that attendees were impressed by the number of early access customer presentations utilizing our new GeoMx® Cancer Transcriptome Atlas and the still in development Whole Transcriptome Atlas.
Front and center, NanoString organized our 2nd annual Spatial Genomics Summit as an accessory meeting prior to the official start of AGBT 2020. The symposium was well attended, and many attendees later visited our booth to see the system and software demonstrations. There were also several early access customer presentations throughout the general AGBT sessions. All these presentations demonstrated the unique power of the GeoMx customized sample selection for spatially resolved transcriptome analysis from specific tissue compartments and cell types.
These were our speakers and their topics:
Spatial landscape of the immune microenvironment in
metastatic prostate cancer using GeoMx™ Digital Spatial Profiler
Pete Nelson, MD, et al., Fred Hutchinson Cancer Research Center, Seattle, WA USA
The team used GeoMx DSP Cancer Transcriptome Atlas to interrogate tissue microarrays of metastatic prostate cancer samples and characterize immune responses. Spatial analysis revealed intra-patient heterogeneity that would not have been readily apparent from bulk RNA profiling experiments.
Spatial proteomic characterization of the tumor and immune
microenvironment reveals features associated with response to neoadjuvant
Katherine McNamara et al., Stanford University, Palo Alto, CA, USA
They used spatial proteomic analysis of biopsies from on-treatment HER2+ breast cancer patients to stratify responders vs. non-responders early during a course of neoadjuvant HER2-targeted therapy. GeoMx analysis allowed unique segmentation of cell populations to provide insight into the effect of innate immune markers, ER status, and PAM50 subtype on treatment response.
Neural stem cell differentiation trajectories in the
developing human brain revealed by whole-transcriptome in situ spatial profiling
Kenny Roberts, MD, Ph.D., et al. et al., Sanger Institute, Cambridge, UK
GeoMx DSP Whole Transcriptome Atlas was used to distinguish the transcriptomic profiles of neural stem cells, intermediate progenitors and neurons in the fetal human cerebral cortex at 14 and 19 post-conception weeks. This study examined cell type specific gene expression programs throughout the cortical germinal zones, subplate and the maturing cortical plate and identified spatiotemporal gene expression correlated with neural stem cell self-renewal and differentiation.
Single Cell Programs of Immune Activation in Human MSI vs MSS
Jonathan Chen, MD, Ph.D., et al. et al., Broad Institute, Cambridge, MA, USA
GeoMx DSP Cancer Transcriptome Atlas and Whole Transcriptome Atlas were used to interrogate how tumor and microenvironment interactions vary spatially within colorectal cancers, allowing spatial mapping of signatures linked to single cell RNA sequencing. This study highlights the capacity of GeoMx to identify locations of specific cell populations distributed across tissues.
Mapping intratumoral heterogeneity of triple negative breast
cancer through integrated single cell RNA-Sequencing and whole transcriptome
Digital Spatial Profiling
Alex Swarbrick Ph.D. et al., Garvan Institute of Medical Research, Sydney, Australia
Primary, untreated, triple negative breast cancer (TNBC) was profiled using GeoMx DSP whole transcriptome. Segmentation was performed based on visual markers characterize immune and stromal cells in the invasive edge, tumor core, and distant stromal regions with the goal of discovering novel therapeutic targets in TNBC.
And don’t worry if you weren’t able to attend in person! We are organizing a webinar series to share these presentations soon, scheduled for the week of March 30th . You can pre-register below!