The USF College of Public Health’s Genomics Program and the Center for Global Health and Infectious Diseases Research (GHIDR) recently hosted a Digital Spatial Genomics Symposium, in collaboration with biotech companies Nanostring and Illumina.

More than 100 attendees participated in the one-day symposium held in February, with a majority being USF faculty and students. Representatives from other institutions, such as Moffitt Cancer Center and Shriners Hospital for Children, also attended.

The symposium showcased the NanoString GeoMx Digital Spatial Profiler (DSP). This cutting-edge technology has numerous applications, including the ability to identify and analyze specific genes and proteins associated with diseases such as Alzheimer’s disease, infectious diseases and cancer.

By understanding how these markers are expressed and distributed within tissues, researchers can develop better diagnostic tools and therapies for patients. The GeoMx DSP instrument is housed in the Byrd Institute Spatial Biology Core, which provides researchers with access to the NanoString Digital Spatial Profiler as a shared resource.

According to Dr. John Adams, director of the USF Genomics Program and co-director of GHIDR, the NanoString GeoMx DSP is particularly noteworthy for its ability to perform whole transcriptome and protein assays, which provide a comprehensive view of gene expression and protein distribution in a given sample.

However, to fully utilize this technology, a follow-up sequencing step is required using the Illumina instrument. This additional step is necessary to identify the specific probe and map it to its corresponding gene. The USF Genomics Sequencing Core and Byrd Institute Spatial Biology Core work together to provide comprehensive service support, enabling researchers to take full advantage of this advanced technology.

Adams emphasized that the USF Genomics Program Core Facilities have all the necessary instrumentation for next-generation sequencing (NGS) applications, including the Illumina NextSeq2000 and 10x Genomics Chromium Controller for high-throughput sequencing and single-cell analysis. The availability of the GeoMx DSP and the associated sequencing capabilities represents a significant step forward in the university’s efforts to support innovative research in the field of genomics.

The symposium featured presentations from renowned researchers who have utilized digital spatial genomics profiling to analyze tissue and gain insights into the development of Alzheimer’s disease and cancer.

Dr. Gopal Thinakaran, CEO of the Byrd Alzheimer’s Center and Research Institute at USF, presented his research on Alzheimer’s tau pathogenesis. He emphasized the sensitivity and versatility of the GeoMx technology, which enables the detection of genes with varying levels of expression in different tissue types, including challenging samples.

 Dr. Kenneth Tsai, pathology research vice chair of Moffitt Cancer Center, presented his research on the tumor immune landscape of Merkel cell carcinoma and its relevance to immunotherapy. He showcased how digital spatial technology has enabled a breakthrough in visualizing cancer development, opening new treatment possibilities.

Representatives from Nanostring and Illumina also introduced the latest DSP technologies and key applications to discover more about accessing the full richness of spatial biological complexity.

The symposium included breakout sessions in the afternoon, covering sample preparation for the GeoMx Digital Spatial Profiler and its data analysis connection within the workflow to visualize tissue structures.

The USF researchers have been encouraged to utilize the GeoMx Digital Spatial Profiler and Next-Gen sequencing by Nanostring and Illumina. As part of this encouragement, they offered the GeoMx Whole Transcriptome Atlas Grants, which cover the cost of reagents, including four slides worth of Whole Transcriptome Reagents for GeoMx from Nanostring, which costs $10,000, and the initial sequencing cost of reagents from Illumina, which costs $5,000.

During the symposium, two grant winners were announced: Drs. Paula Bickford and Lianchun Wang.

Bickford’s project focuses on studying the role of aging in response to therapeutic stem cell-derived exosomes following traumatic brain injury. Wang’s project aims to investigate the roles of microglial heparan sulfate in brain homeostasis and Alzheimer’s disease. Both emphasized the importance of the NanoString GeoMx DSP, which allows for spatial profiling of gene expression in tissues, providing a high-resolution view of the molecular landscape of diseases such as Alzheimer’s.

The Genomics Program Sequencing and Computational Cores have supported 26 grant proposals with letters of support, and 11 of these proposals, amounting to $16 million in grant funding, have been successfully funded. These grants focus on various fields, including Alzheimer’s disease, infectious diseases, cancer and other areas utilizing digital spatial, single-cell multiomics and other next-generation sequencing technologies.

 Dr. Min Zhang, the USF Genomics Program sequencing core director and one of the organizers of the event, highlighted the importance of genomics cores in providing hands-on training, consultation and assistance to USF researchers. This support includes help with grant proposals, experimental design and data analysis to achieve research goals. In fact, demonstrating the in-house capability of cutting-edge technologies is crucial for success in grant proposals.

Overall, the NanoString DSP and single-cell technologies represent a significant step forward in understanding complex diseases, such as cancer and Alzheimer’s disease. By providing a detailed view of the molecular landscape of cells within tissues, researchers can develop more effective diagnostic tools and therapies. As such, this technology is an important area of research with the potential to improve public health outcomes.

Story by Desiree Lara Norat and Min Zhang, USF College of Public Health