The interaction between genetics and tissue environment shapes how individual teeth form in different regions of the jaw. While most experimental studies have focused on mandibular (lower jaw) teeth, little was known about how human maxillary (upper jaw) and mandibular teeth diverge at the molecular level during early development.
In a new study published in Oral Science and Homeostatic Medicine, a collaborative team from Beijing Stomatological Hospital, Capital Medical University, and Peking University School and Hospital of Stomatology performed a RNA-sequencing analysis of human fetal tooth germs at the cap stage (11–12 post-conception weeks). They compared gene expression profiles between pooled maxillary and mandibular tooth germs and validated key findings with quantitative PCR and immunofluorescence staining.
Upper and lower tooth germs show distinct transcriptomic profiles at the cap stage
Morphologically, both upper and lower tooth germs displayed typical cap-stage features, but principal component analysis of the RNA-seq data revealed a clear separation between maxillary and mandibular samples, indicating distinct transcriptional signatures despite their similar morphology.
The team identified 14,267 genes that were highly expressed in both regions, enriched in pathways related to extracellular matrix organization, TGF-β, WNT, NOTCH and BMP signaling, reflecting a shared core program for epithelial–mesenchymal interactions and early odontogenesis.
Upper tooth germs are enriched for morphogenesis-related genes, whereas lower tooth germs are enriched for mineralization-related genes.
Beyond this common framework, 687 genes were differentially expressed between the two regions: 282 were upregulated in maxillary tooth germs and 405 in mandibular tooth germs.
Maxillary-enriched genes, including GATA3, SHOX2 and PAX3, were associated with embryonic organ morphogenesis, regulation of FGF and BMP signaling, and extracellular matrix remodeling. These genes have been previously implicated in craniofacial patterning, palatal development and upper jaw formation.
In contrast, mandibular-enriched genes such as HAND2, DLX6, NKX2-3, PHEX and DMP1 were linked to actin-based movement, calcium ion transport and homeostasis, dentinogenesis and cytokine secretion—processes that support mineralized tissue formation and mechanical function.
"Even though the tooth germs in the upper and lower jaws look very similar at the cap stage, their gene expression patterns are diverging," said Ran Zhang, corresponding author of the study.
Protein–protein interaction network analysis highlighted several hub regulators, including IHH, HAND2, PAX3 and SP7, that connect multiple signaling pathways and may orchestrate region-specific tooth germ differentiation.
Validation at RNA and protein levels
To confirm the RNA-seq results, the investigators selected 18 representative genes for RT-qPCR. Most showed significant and consistent regional differences, with SHOX2, CHRDL1, GATA3, SP7 and PAX3 higher in maxillary tooth germs, and DMP1, NKX2-3, PHEX, HAND2 and DLX6 higher in mandibular tooth germs.
Immunofluorescence staining additionally showed that DLX6 and PHEX were strongly expressed in mandibular tooth germs, whereas SHOX2 was predominantly expressed in the maxillary tooth germs, revealing both regional and compartment-specific expression across epithelium and mesenchyme.
"These region-specific regulatory programs likely contribute to the distinct eruption timing, crown morphology and functional specialization of maxillary and mandibular teeth," said corresponding author Songlin Wang.
Implications and next steps
Human embryonic samples at this stage are extremely rare, so the authors acknowledge the modest sample size as a limitation but emphasize the value of obtaining direct human data rather than extrapolating solely from animal models. They suggest that functional studies in model organisms, guided by the identified hub genes and pathways, will be needed to decode how these transcriptional programs translate into jaw-specific tooth morphology.
The RNA-seq data from this study have been deposited in the CNGB Sequence Archive (accession CNP0008028) to facilitate reuse by the dental research community.
About the Authors
Songlin Wang
Songlin Wang is an academician of the Chinese Academy of Sciences and a recipient of the Outstanding Performance Award for Members of the National Committee of the Chinese People's Political Consultative Conference. He serves as Dean of the School of Medicine at Southern University of Science and Technology, Director of the National Institute of Health Big Data at Capital Medical University, and Director of the Beijing Laboratory for Oral Health. He is President of the China Anti-aging Promotion Association, convener of the stomatology discipline of the Academic Degrees Committee of the State Council, and chair of the National Textbook Review Committee for Stomatology. Prof. Wang is Editor-in-Chief of Oral Science and Homeostatic Medicine, the Chinese Journal of Stomatology, Medical Education Management and Today's Stomatology.
Prof. Wang has published 349 scientific papers, including 197 English-language articles as the primary author. As first contributor, he has received two Second-Class National Science and Technology Progress Awards, as well as the William J. Gies Award, the Wu Jieping Medical Innovation Award, and the Ho Leung Ho Lee Science and Technology Award. He discovered the human cellular nitrate transport pathway and nitrate receptor, demonstrated their key roles in maintaining systemic homeostasis, and proposed the concept of "homeostasis medicine." He and his team developed the novel drug Naireite based on this concept, revealed new mechanisms of tooth development, and advanced dental pulp stem cell-based therapies that enable biological tooth regeneration.
Ran Zhang
Ran Zhang obtained her PhD in oral pathology from Peking University School and Hospital of Stomatology. She is currently an associate researcher, attending physician, and doctoral supervisor at Peking University School and Hospital of Stomatology, and serves as Deputy Secretary of the hospital's Youth League Committee. She is also a member of the Oral Pathology Committee of the Chinese Stomatological Association and holds several other academic appointments.
Dr. Zhang has led two projects funded by the National Natural Science Foundation of China. Her research focuses on oral and maxillofacial pathology and tooth development, and her work has been published in high-impact journals such as Nature Communications and Cell Reports.
