Mucin-7 as a Potential Candidate Risk Allele for Cleft Lip and/or Palate

Abstract Cleft lip and/or palate (CL/P) occur in approximately 1 in 700 live births in the United States. High hereditary rates (50-80%) of CL/P indicate a strong genetic cause. The concept of strong genetic causes has been well-demonstrated in previous studies such as GWAS studies that identified IRF6 for Van der Woode syndrome. Since the risk for genetic factors is strongly associated with CL/P, we hypothesized that RNA sequencing (RNA-seq) from CL/P patients may reveal enriched genes. Differential expression analysis examined changes in gene expression in CL/P patients compared to healthy controls, and gene-enrichment in relevant pathways. To explore the relationship between variants driving the observed changes in gene expression, we performed variant analysis and reported all CL/P-specific single nucleotide polymorphisms (SNPs). Our findings demonstrate that the normally upregulated MUC7 gene is significantly downregulated in CL/P patients. Using our list of prioritized differentially expressed genes (DEGs), we observed significantly enriched pathways for biological processes related to cornification, skin and epidermis development, and keratinocyte and epidermal cell differentiation. By performing variant analyses, a single nucleotide polymorphism (SNP) in MUC7, and 47 SNPs in 20 additional genes (CLCA4, ETNK2, ERLNC1, HAL, HOPX, IVL, KLK11, LIPK, LY6D, MUC21, NCCRP1, NEBL, PHYH, SERPINB11, SERPINB4, SORD, SPINK5, SULT2B1, TMEM154, TMPRSS11A) were revealed. To our knowledge, this is the first report on the potential role of MUC7 in contributing to CL/P. Together, these findings provide further insight into the genetic causes of CL/P. Competing Interest Statement The authors have declared no competing interest. Funding Statement This research was supported by the National Institute of Health (NIH R01 DA046258), Sulie L. Chang. Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The data that support the findings of this study are available in Sequence Read Archive at https://www.ncbi.nlm.nih.gov/bioproject/PRJNA700692, reference number PRJNA700692, and accession numbers SRX10054254, SRX10054253, SRX10054252, SRX10054250, SRX10054249. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes Footnotes Page 1 - Removed "Title Page" "Author Names"; Include affiliation by superscript # Page 6, Paragraph 2 - Replaced "(Table 2)" with "(Supplemental Table 1)" Data Availability The data that support the findings of this study are available in Sequence Read Archive at https://www.ncbi.nlm.nih.gov/bioproject/PRJNA700692, reference number PRJNA700692, and accession numbers SRX10054254, SRX10054253, SRX10054252, SRX10054250, SRX10054249.