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).
Contacts
Investors: investors@10xgenomics.com
Media: media@10xgenomics.com
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SOURCE 10x Genomics, Inc