The multi-cellular architecture of tissues has been studied and characterized using microscopy, imaging, and other visualization techniques. Similarly, the structure and conformation of genetic components like DNA, RNA, and the chromatin network within the cell have also been looked at extensively. All this information has been critical for assessing gene expression changes, cellular function, and homeostasis, and has been correlated to disease states and progression. However, one aspect that has been lacking is information about the spatial organization, differentiation, and localization that exists at the genomic and transcriptomic level within each cell, and in the tissue. This information has never been effectively captured using conventional tools and, hence, some important details about cellular machinery were lost in translation.
Spatial genomics and spatial transcriptomics are rapidly evolving areas of research that aim to fill this knowledge gap. Progress has been made possible largely due to technical advancements that now enable resolution down to the single-cell level. Over the past year, the field has exploded with the launch of multiplexed, high-throughput systems that can analyze tens of thousands of genes localized in a small section of the tissue. Spatial genomics has also immensely benefited from enhancements in fluorescence in situ hybridization (FISH), microscopy-based live DNA imaging, genome perturbation tools, massively parallel sequencing, and a few other biochemical techniques.
“Our Visium Spatial Gene Expression technology enables researchers to unravel the biological architecture in normal and diseased tissues by preserving the spatial relationships between cells to provide insights not only at the individual cell level, but at the tissue level as well,” says Michael Schnall-Levin, Ph.D., SVP R&D, Founding Scientist at 10x Genomics. “Researchers can now map whole transcriptome spatial gene expression across multiple cells for complex tissue samples.” The technique is highly sensitive and allows the survey of hundreds of thousands of cells in a tissue section simultaneously using total mRNA spatial gene expression analysis.
Small details reveal the big picture
Although a new entrant in the genomics arena, the applications of spatial genomics appear to be quite diverse and impactful. There have been studies done to show how spatial genomics can help both research and clinical development in areas like immuno-oncology, neurology, cardiovascular and infectious diseases, and more. “Since our technology is tissue and species agnostic, it is being used in numerous applications in both healthy and diseased tissues for looking at tumor heterogeneity, tissue morphology, mechanisms of tissue development, and response to therapeutic interventions,” says Schnall-Levin.
Differences in the spatial patterns of the genome have also been used as diagnostic biomarkers for identifying certain disease conditions. Recent studies published in Nature (Cabrita et al, 2020; Helmink et al, 2020) demonstrate the utility of spatial technology to investigate tumor-associated tertiary lymphoid structures, which are highly organized emergent immune compartments, to characterize molecular patterns associated with response to checkpoint inhibitors in advanced melanoma.
“Dissecting the interplay between the immune system and tumor biology to understand disease progression and therapeutic response to immuno-oncology agents has been the focus of much research,” reports Anna Berdine, VP of Marketing at Nanostring Technologies. “These and other studies are advancing our understanding of immune responses in patients to checkpoint therapies and to guide biomarker development.” Spatial technologies have been applied to better understand the influence of immune response in dementia disorders (Prokop et al, 2019). Neuroscientists are using single-cell genomics and transcriptomics to study and understand the neural tissue architecture. The National Institutes of Health (NIH) has also launched the BRAIN Initiative to leverage spatial transcriptomics for disease diagnosis. Most recently, researchers have applied spatial technology to understand the mechanisms by which the SARS CoV-2 virus infects patients and the resulting immune response in the lung, brain, and cardiac tissue. Several of these studies have recently been submitted for publication.
In situ sequencing (ISS) offers sequencing of hundreds of genes to be performed directly in the tissue allowing spatial information to be preserved. This is achieved by generating and sequencing clonally amplified barcode sequences that are introduced by ligation of gene-specific probes at their original location in the tissue. “Our newly developed in situ technology allows researchers to analyze either fresh/fixed frozen or formalin fixed paraffin embedded (FFPE) samples and rapidly create single-cell gene expression maps of hundreds of genes,” says Malte Kühnemund, Ph.D., Co-founder and Executive Vice President, Head of R&D at CARTANA. CARTANA has made ISS commercially available by providing sample-preparation kits with customizable gene panels and optimized decoding chemistry.
“The ability to access high-plex information from FFPE tissue is particularly significant as it provides access to millions of samples in biobanks around the world associated with clinical outcomes data,” explains Berdine. “The launch of the Cancer Transcriptome Atlas and Whole Transcriptome Atlas will provide researchers with an unbiased approach to access spatial changes in RNA transcription from both fresh and FFPE tissues.” NanoString’s GeoMx™ Digital Spatial Profiler is a spatial platform that provides reproducible, transcriptome-wide gene expression results from FFPE tissue and enables use of the largest library of validated protein assays, optimized for robust performance in multiplex mode.
Spatial challenges
While certainly promising, there do exist some challenges in the application of spatial genomics. For instance, identifying and validating the right biomarkers for a specific disease state, merging sequencing data with imaging readouts, visualizing the phenotype of a tissue section, and accurately capturing the cell state and identifying the role of that cell in the tissue microenvironment, all have some limitations that are being looked at. As new applications for spatial genomics and transcriptomics continue to emerge, the need to expand the number of assays and analysis tools and to make them more economical, efficient, and unbiased is also underway. Similarly, there is a need to increase the resolution, scale, and types of information that can be measured in a spatial context. “Robust, reproducible assays and standardized protocols designed for analysis of tissue will be needed to enable implementation of spatial genomics in a wide variety of laboratory settings and to facilitate cross comparison of datasets generated across different labs and timepoints,” adds Berdine.
In order to improve and accelerate workflows related to assessing the spatial cellular relationship in clinical translational research studies, 10x Genomics has established the Visium Clinical Translational Research Network (CTRN) with 45 global members including GSK, Johns Hopkins, and others who are working in oncology, immuno-oncology, neuroscience, infectious disease, inflammation, fibrosis, COVID-19, and more. The Visium Spatial Solution aids clinical translational research by identifying gene signatures for biomarker discovery; evaluating target antigen expression for engineered immune cell therapy; and improving stratification for companion diagnostics and clinical trials. “Single-cell and spatial analysis are two of the most important technologies to enable us to gain a better biological understanding of the complexity of the 40 trillion dynamic cells in the human body,” says Schnall-Levin.