Researchers used Chromium Single Cell products
and Xenium In Situ to profile how gene expression is spatially
regulated during secondary palate formation
PLEASANTON, Calif.,
June 27, 2024 /PRNewswire/ -- 10x
Genomics, Inc. (Nasdaq: TXG), a leader in single cell and
spatial biology, announced today that its Xenium In Situ platform
was used in a study published in the Journal of Dental
Research, offering novel insights into cellular mechanisms
regulating the formation of the secondary palate. The study was led
by researchers at the National Institutes of Health (NIH) in
collaboration with computational experts at the University of Connecticut's Schools of Medicine and
Dental Medicine.
Annually, clefts of the lip and/or palate occur in ~1 in every
700 live births. Despite its prevalence, there is still a very
limited understanding of how the bones forming these foundational
facial structures develop and pattern as an embryo develops. In
this study, "Spatial Multi-omics Reveals the Role of the Wnt
Modulator, Dkk2, in Palatogenesis,"
the researchers set out to clearly define how the Pax9 protein
functions as a transcription factor in the context of Wnt
signaling, a crucial pathway known to regulate many elements of
embryonic development.
The study's first author, Jeremie Oliver Piña, PhD, MS, MBA, a
Postdoctoral Fellow in Dr. Rena
D'Souza's lab (Eunice Kennedy
Shriver National Institute of Child Health and Human
Development, NIH), said, "The higher spatial resolution of
compartment-specific gene enrichment using Xenium allowed us to
extend our understanding of these molecules at greater depth and
breadth than prior studies could using traditional in situ
hybridization approaches. With this more detailed understanding of
signaling pathway target genes in the developing palate, we will be
able to more effectively pave the way toward innovative diagnostic
and therapeutic strategies for cleft palate anomalies.
"Xenium In Situ's workflow and analysis pipeline allowed us to
optimize the assay conditions for our target tissue, run the whole
protocol and analyze all replicates in-house in less than one
month. The intuitive design of the bench workflow and post-run
analysis software may be the most valuable aspects of this
high-throughput in situ technology to accelerate science."
As part of their initial assessment, the researchers performed
an integrated assessment of the transcriptomic and epigenomic
profiles of wild-type and Pax9-deficient mice using the
Chromium Single Cell Multiome ATAC + Gene
Expression (Multiome) assay. Paired with 3D-micro-computerized
tomography (micro-CT) bone imaging analysis showing disrupted
patterning of the palate in Pax9-deficient mice, the authors
hypothesized that loss of Pax9 expression disrupts Wnt
signaling dynamics in a way that influences the process of proper
bone formation.
To further investigate the relationship between Pax9 and Wnt
signaling, the researchers created a fully custom gene expression
panel to profile 350 genes at single cell spatial resolution with
the Xenium In Situ platform. The researchers customized their gene
panel to focus on cell-type specific markers, genes involved in
signaling interactions and other genes of interest uncovered in the
Multiome data.
The Xenium analysis revealed significant spatial gene expression
differences between wild-type and Pax9-deficient mice,
indicating a role for Pax9 in regulating the differentiation and
maturation of a specific subset of progenitor cells. Of particular
note, Xenium revealed that disrupting Wnt signals blocks the
extension of the palate to the midline in this cleft palate model,
a process that could be targeted for discovery of potential in
utero and early postnatal treatments to correct cleft palate
anomalies.
Ben Hindson, Co-Founder and Chief
Scientific Officer, said, "This paper by Piña et. al is a strong
demonstration of the power of single cell multiomics coupled with
targeted in-situ sequencing. The detailed spatial analysis of cleft
palate dynamics also shows how researchers can take advantage of
the fully custom gene panel options on Xenium to answer their
specific research questions."
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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