The annual conference of the American Society of Human Genomics (ASHG) was held virtually this year. One of the upsides of virtual conferences is the ability to pause, rewind, and review these fast-paced presentations. Definitely take advantage of this feature as there is a lot of information to unpack, particularly in two presentations that highlight NanoString’s GeoMx® Digital Spatial Profiler (DSP) technology and the new GeoMx® Whole Transcriptome Atlas.
To get up to speed with the latest technology, start with the CoLab presentation by Illumina and NanoString. Dr. Ashley van Zeeland, VP Development, Illumina, kicks off the showcase with “Accelerating Scientific Breakthroughs: Delivering Sample to insight Workflows” where she discusses how Illumina has streamlined next generation sequencing (NGS) workflows by reducing touchpoints and transfer steps to maximize data output. Illumina has made improvements in three areas: sample prep, sequencing technology, and data analysis. A PCR-free library prep reduces polymerase slippage, preserves clinical variant calling accuracy, decreases sample prep time, and can be used with DNA inputs as low as 25 ng. While every researcher can relate to the desire for faster results, Dr. van Zeeland shares an example where accelerated sequencing can save lives, particularly for children with rare diseases. Using Illumina’s NGS, the Rady Children’s Institute for Genomic Medicine has demonstrated the ability to perform rapid whole genome sequencing (rWGS) in just over 20 hours, a critical advancement in the understanding of rare diseases in seriously ill children.
From there, the microphone is passed to Dr. Joe Beechem, VP and Chief Scientific Officer, from NanoString for his talk “Whole Transcriptome RNA and High-plex Protein Detection Using the GeoMx Digital Spatial Profiler (DSP) with NGS Detection Readout”. Dr. Beechem’s early days were spent in the development of next generation sequencing machines before he turned his attention to solving the question of spatial distribution of those sequences. This portion clearly articulates how the high-plex spatial biology technology of the GeoMx DSP can be used with NGS technology to advance scientific discovery. Noteworthy is the announcement of the Human Whole Genome Atlas is now available through NanoString’s Technology Access Program (TAP)and (over 18,000 genes) now available for use with the GeoMx DSP, with the Mouse Whole Transcriptome Atlas (22,000 genes) available in early 2021These rapid advancements are due, in part, to leveraging Illumina’s NGS technology. Within approximately two years, NanoString DSP has gone from supporting 84 genes to over 18,000 spatially resolved mRNAs by integrating the reagent biochemistry to fit with Illumina’s NGS readout. The results are unprecedented.
As Dr. Beechem displays the results from a FFPE-fixed sample with over 9,000 spatially resolved genes using the Whole Transcriptome Atlas, get ready to pause and rewind. NanoString has developed the tools to gather and analyze massive amounts of data, and equally impressive is the way in which the data are displayed using circos plots. The data from each ROI are arrayed around the circumference, sorted by signaling pathways, such as cytokine signaling and cell cycle. Around the circle are the expression levels for both the whole transcriptome for the tumor and the whole transcriptome for the stromal immune cells. As Dr. Beechem notes, you can “watch the whole transcriptome change across a single FFPE slice”. For example, the cytokine profile of an adjacent normal ROI clearly changes as the DSP moves 1 mm across the sample to a hyper proliferative ROI. This holds true for the cell-cell interaction and cell cycle transcriptomes, begging the question “what next?”
Following is the presentation “Single-nucleus and Digital Spatial Profiling of Archival Pancreatic Adenocarcinoma” by Dr. William Hwang of Massachusetts General Hospital, putting this technology to the test using a precommercial version of the GeoMx Whole Transcriptome Atlas. One of the challenges of pancreatic cancer is that malignant cells frequently represent a very small fraction of the total cell population. Of that small population, single nucleus RNA (snRNA) has identified two subtypes: classical and a more aggressive basal-like subtype. The unique characteristics of these cells are often lost or overshadowed in the process of bulk sequencing, presenting an excellent opportunity for the GeoMx DSP. Dr. Hwang and his team queried samples from 26 patients with pancreatic cancer that underwent surgical resection; at the time of surgery 15 patients were untreated and the other 11 patients had received neoadjuvant therapy. Using the GeoMx DSP, they are able to identify three specific types of ROI: regions infiltrated by both immune cells and fibroblasts, regions only infiltrated by fibroblasts, and regions only infiltrated by immune cells. They compared the single snRNA data with the data collected from the GeoMx DSP and the 18,000 mRNA targets of the GeoMx Whole Transcriptome Atlas. This analysis revealed a relationship between malignant-intrinsic and fibroblast-intrinsic programs in pancreatic cancer. Moreover, they discerned distinct immune micro niches that could be used in generating subtype-specific immunotherapies, targeted to either the classical or basal-like malignant cells.
The GeoMx DSP technology combined with NGS is groundbreaking and the possibilities for scientific discovery are staggering. As this technology becomes more widely available, expect the pace of rare cell disease research to accelerate by leaps and bounds. Links to the workshop and products are posted below.
CoLabs: ASHG page
Illumina workshop: https://youtu.be/3ARwqflvtNw
Cancer Transcriptome Atlas: https://www.nanostring.com/products/geomx-digital-spatial-profiler/geomx-cancer-transcriptome-atlas
FOR RESEARCH USE ONLY Not for use in diagnostic procedures.