New Insights Into Cleft Palate Unlocked With 10x Genomics' Single Cell and Spatial Technologies

PLEASANTON, Calif., June 27, 2024

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.