A non-syndromic orofacial cleft risk locus links tRNA splicing defects to neural crest cell pathologies

Michaela Bartusel¹, Skylar X Kim², Rizwan Rehimi³, Alicia M Darnell⁴, Miloš Nikolić⁵, Julia Heggemann⁶, Petros Kolovos⁷, Wilfred F J van Ijcken⁸, Jade Varineau², Giuliano Crispatzu⁵, Elisabeth Mangold⁶, Samantha A Brugmann⁹, Matthew G Vander Heiden¹⁰, Magdalena Laugsch¹¹, Kerstin U Ludwig⁶, Alvaro Rada-Iglesias¹², Eliezer Calo¹³

Affiliations

¹ Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA; Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany. Electronic address: bartusel@mit.edu.
² Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
³ Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany; Institute for Pharmacology and Toxicology (IPT), University Hospital Bonn, Venusberg-Campus 1, Biomedical Center 1 (Building 13), 53127 Bonn, Germany.
⁴ Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
⁵ Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.
⁶ Institute of Human Genetics, University of Bonn, University Hospital Bonn, Medical Faculty, Venusberg-Campus 1, 53127 Bonn, Germany.
⁷ Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece.
⁸ Center for Biomics, Erasmus Medical Center, Rotterdam, the Netherlands.
⁹ Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, MLC 7007, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA.
¹⁰ Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA; Dana-Farber Cancer Institute, Boston, MA, USA.
¹¹ Institute of Human Genetics, Heidelberg University, Heidelberg, Germany.
¹² Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/University of Cantabria, Santander, Spain.
¹³ Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA. Electronic address: calo@mit.edu.

PMID: 40250422
PMCID: PMC12120183 (available on 2025-11-01)
DOI: 10.1016/j.ajhg.2025.03.017

A non-syndromic orofacial cleft risk locus links tRNA splicing defects to neural crest cell pathologies

Michaela Bartusel et al. Am J Hum Genet. 2025.

. 2025 May 1;112(5):1097-1116.

doi: 10.1016/j.ajhg.2025.03.017. Epub 2025 Apr 17.

Authors

Affiliations

¹ Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA; Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany. Electronic address: bartusel@mit.edu.
² Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
³ Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany; Institute for Pharmacology and Toxicology (IPT), University Hospital Bonn, Venusberg-Campus 1, Biomedical Center 1 (Building 13), 53127 Bonn, Germany.
⁴ Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
⁵ Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.
⁶ Institute of Human Genetics, University of Bonn, University Hospital Bonn, Medical Faculty, Venusberg-Campus 1, 53127 Bonn, Germany.
⁷ Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece.
⁸ Center for Biomics, Erasmus Medical Center, Rotterdam, the Netherlands.
⁹ Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, MLC 7007, Cincinnati, OH 45229, USA; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA.
¹⁰ Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA; Dana-Farber Cancer Institute, Boston, MA, USA.
¹¹ Institute of Human Genetics, Heidelberg University, Heidelberg, Germany.
¹² Institute of Biomedicine and Biotechnology of Cantabria (IBBTEC), CSIC/University of Cantabria, Santander, Spain.
¹³ Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA. Electronic address: calo@mit.edu.

PMID: 40250422
PMCID: PMC12120183 (available on 2025-11-01)
DOI: 10.1016/j.ajhg.2025.03.017

Abstract

Orofacial clefts are the most common form of congenital craniofacial malformation worldwide. The etiology of these birth defects is multifactorial, involving genetic and environmental factors. However, in most cases, the underlying causes remain unexplained, precluding a molecular understanding of disease mechanisms. Here, we integrated genome-wide association data, targeted resequencing of case and control cohorts, tissue- and cell-type-specific epigenomic profiling, and genome architecture analyses to molecularly dissect a genomic locus associated with an increased risk of non-syndromic orofacial cleft. We found that common and rare risk variants associated with orofacial cleft intersect with an enhancer (e2p24.2) that is active in human embryonic craniofacial tissue. We mapped e2p24.2 long-range interactions to a topologically associated domain harboring MYCN, DDX1, and CYRIA. We found that MYCN and DDX1, but not CYRIA, are required during craniofacial development in chicken embryos. We investigated the role of DDX1, a key component of the tRNA splicing complex, in cranial neural crest cells (cNCCs). The loss of DDX1 in cNCCs resulted in the accumulation of unspliced tRNA fragments, depletion of mature intron-containing tRNAs, and ribosome stalling at codons decoded by these tRNAs. This was accompanied by defects in both global protein synthesis and cNCC migration. We further showed that the induction of tRNA fragments is sufficient to disrupt craniofacial development. Together, these results uncovered a molecular mechanism in which impaired tRNA splicing affects cNCCs and craniofacial development and positioned MYCN, DDX1, and tRNA processing defects as risk factors in the pathogenesis of orofacial clefts.

Keywords: DDX1; MYCN; craniofacial development; epigenetics; neural crest cells; orofacial cleft; tRNA; tRNA fragments.

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Conflict of interest statement

Declaration of interests M.G.V.H. discloses that he is an advisor for Agios Pharmaceuticals, iTeos Therapeutics, Droia Ventures, MPM Capital, Pretzel Therapeutics, Lime Therapeutics, and Auron Therapeutics, although M.G.V.H. is not aware of any conflict with the material in this study.

References

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A non-syndromic orofacial cleft risk locus links tRNA splicing defects to neural crest cell pathologies

Affiliations

A non-syndromic orofacial cleft risk locus links tRNA splicing defects to neural crest cell pathologies

Authors

Affiliations

Abstract

Conflict of interest statement

References

MeSH terms

Substances

Supplementary concepts

Grants and funding

LinkOut - more resources

Full Text Sources

Medical

Miscellaneous