Integrative Study Conducted by 10x Genomics Combines Single Cell, Spatial and In Situ Analyses to Investigate Tumor Invasiveness

A team of 10x Genomics scientists conducted a comprehensive analysis of human breast tumor microenvironments using all three of its industry-leading platforms

PLEASANTON, Calif., Dec. 19, 2023 /PRNewswire/ -- 10x Genomics, Inc. (Nasdaq: TXG), a leader in single cell and spatial biology, announced today that Nature Communications has published a 10x-conducted study using the Chromium Single Cell, Visium Spatial and Xenium In Situ platforms as part of an integrative approach to understand how tumor microenvironment differences influence invasiveness. 

In this study, "High resolution mapping of the tumor microenvironment using integrated single-cell, spatial and in situ analysis," the 10x scientists sought to untangle the complex heterogeneity of the tumor microenvironment of a formalin-fixed paraffin-embedded (FFPE) breast cancer block using independent but complementary technologies. The peer-reviewed publication, which is now available in Nature Communications, refines and builds on work previously posted in bioRxiv in late 2022. 

The researchers first defined the cellular composition of the sample using Chromium Single Cell Gene Expression Flex (Chromium scFFPE-seq), which yields highly sensitive whole transcriptome data. Since this profiling is performed on FFPE sections from the same block assessed via pathology and spatial profiling, the Chromium Flex data is a more precise representation of the tissue biology observed with those methods than dissociated tumor cells from the same patient. To determine where the various cell types in the sample reside in the tumor microenvironment, the team performed whole transcriptome Visium CytAssist Spatial Gene Expression profiling on an adjacent tissue section. Visium analysis was able to identify three spatially distinct tumor regions. Lastly, the team used the single cell spatial resolution of Xenium In Situ to more precisely map complex regions of the tumor where multiple cell types were present in very close proximity. Importantly, this high-resolution spatial view of the sample identified a tiny region expressing three receptors commonly used for diagnosis of a breast cancer subtype, which otherwise would have gone unnoticed.

In addition to this groundbreaking approach demonstrating the strengths of each platform, it also showcases the power of integrating the findings. For example, integration of the Chromium and Visium data enabled the three spatially distinct tumor domains to be correlated with specific clusters and differentially expressed genes, while Xenium provided the cell-type composition of the domains. Furthermore, after pinpointing the triple-positive receptor region in the sample in the Xenium data, the team was able to reexamine this region within the Visium data to assess differences in cellular composition and gene expression.  

Sarah Taylor, Senior Director of Applications at 10x Genomics, said, "This study was only possible due to the complementarity that exists between our platforms. The shared sample compatibility allowed us to process sections from the same FFPE sample with all three workflows, while the synergies of the technologies and software solutions made the data integration simple. Critically, it was the integration of this data that allowed us to understand the unique cancer biology occurring in the sample with more rigor and refinement than using any single technology alone." 

"This study also illuminates the value of supplementing traditional pathological analysis with the more detailed molecular profiling capabilities of spatial profiling techniques," said Amanda Janesick, first author and a Senior Scientist on the 10x Genomics Applications Team. "For example, the three spatially distinct tumor regions identified by Visium and the small triple-positive receptor region detected by Xenium were not initially noted via pathological assessment. In a second breast cancer sample assessed by Xenium, the data picked up tumor cell markers in regions pathologically annotated as having normal duct morphology. These findings highlight that spatial profiling methods may provide valuable clues into disease biology and progression before any notable morphological changes could be detected by current methods and tools for pathology."

To learn more about this study, read the full article.

About 10x Genomics

10x Genomics is a life science technology company building products to accelerate the mastery of biology and advance human health. Our integrated solutions include instruments, consumables and software for single cell and spatial biology, which help academic and translational researchers and biopharmaceutical companies understand biological systems at a resolution and scale that matches the complexity of biology. Our products are behind breakthroughs in oncology, immunology, neuroscience and more, fueling powerful discoveries that are transforming the world's understanding of health and disease. To learn more, visit 10xgenomics.com or connect with us on LinkedIn or X (Twitter).

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