# next-generation sequencing approaches to identify genotype-phenotype relationships during miRNA tuning of neural crest osteogenesis

> **NIH NIH K18** · UNIVERSITY OF CALIFORNIA RIVERSIDE · 2023 · $126,958

## Abstract

PROJECT SUMMARY
Research: Every 4 ½ minutes, a baby is born with a birth defect, including such that affect the craniofacial
skeleton. These facial malformations cause disfigurement leading to long-term psychological impact and are
often associated with physical dysfunction imposing tremendous burden on the affected individuals and their
families. Although the causes for most of these severe developmental pathologies are still unknown, it is clear
that the inappropriate formation and differentiation of neural crest (NC) cells, the cells that normally give rise to
the osteoblasts in the affected craniofacial skeleton, plays a large part. Given the causality between miscontrolled
osteoblast differentiation from the NC and the tissue malformations arising from it, an understanding of the
molecular networks underlying NC development is crucial for the potential treatment or prevention of craniofacial
defects, yet far from complete. For instance, the contribution of epigenetic regulators, such as microRNAs to the
formation of craniofacial bones remains understudied, despite their potential as diagnostic markers.
For this K18 application it is proposed to use data sets generated already under 5R01DE025330 to examine the
epigenetic regulation of NC development by a specific microRNA, miR361, which is pro-osteogenic in vitro and
expressed in the developing NC in vivo. Assessment of skeletal phenotypes when miR361 is knocked out
together with single cell RNA-sequencing using an innovative and effective in vitro differentiation model based
on human pluripotent stem cells will validate the impact of miR361 on NC-osteogenesis. Bulk RNA sequencing
and ChIP sequencing will identify NC-specific loci that are transcriptionally regulated downstream of miR361.
Together, these data will define the relationship between this miRNA, transcriptional activation in NC cells and
their subsequent propensity for osteoblast differentiation.
Goals/Training plan/environment: The goals for this K18 application are two-fold: 1) to train in the design,
execution and specifically the analysis of next-generation sequencing data sets, and 2) to acquire hands-on
experience with imaging-modality-assisted analysis of skeletal phenotypes. The attainment of such skills, in
addition to attending several workshops focused on bioinformatics throughout the year of support will prepare
the applicant for future funding and mentoring opportunities. The applicant has assembled a strong team of local
mentors and regional collaborators who have extensive experience in the area of the proposed work and a strong
record of training scientists to become successful independent investigators. In summary, the proposed project
will allow the applicant to enrich her long-standing track record in stem cell biology with bioinformatics and
phenotypic skeletal analysis, which will foster the perspectives and augment the skills necessary to be a
successful craniofacial biologist.

## Key facts

- **NIH application ID:** 10579800
- **Project number:** 1K18DE032513-01
- **Recipient organization:** UNIVERSITY OF CALIFORNIA RIVERSIDE
- **Principal Investigator:** Nicole Isolde zur Nieden
- **Activity code:** K18 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2023
- **Award amount:** $126,958
- **Award type:** 1
- **Project period:** 2023-05-01 → 2026-04-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10579800

## Citation

> US National Institutes of Health, RePORTER application 10579800, next-generation sequencing approaches to identify genotype-phenotype relationships during miRNA tuning of neural crest osteogenesis (1K18DE032513-01). Retrieved via AI Analytics 2026-07-19 from https://api.ai-analytics.org/grant/nih/10579800. Licensed CC0.

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