MOLECULAR CHARACTERIZATION OF RFX3 LOSS DURING HUMAN IPSC-DERIVED PANCREATIC ISLET DEVELOPMENT: INSIGHTS FROM CODING AND NON-CODING TRANSCRIPTOMIC PROFILING

Abstract

Regulatory factor X 3 (RFX3) was recently identified as essential regulator for human pancreatic endocrine development and β-cell function. While its role in gene regulation during pancreatic differentiation is established, its broader impact on non-coding RNA expression remains largely unexplored. In this study, we investigated the effects of RFX3 loss on coding and non-coding RNA profiles during human iPSC-derived pancreatic islet development. Using our established RFX3 knockout (KO) human induced pluripotent stem cell (hiPSC) model, we performed integrated transcriptomic profiling of mRNAs, microRNAs (miRNAs), and long non-coding RNAs (lncRNAs) across pancreatic differentiation stages known to express high levels of RFX3. Loss of RFX3 led to significant alterations in both coding and non-coding transcriptomes, including 122 differentially expressed miRNAs (DEmiRs) and 242 differentially expressed lncRNAs (DElncRNAs) in pancreatic progenitors, and 139 DEmiRs and 304 DElncRNAs in pancreatic islets. Integration of miRNA and mRNA data revealed that several upregulated DEmiRs were predicted to target key genes involved in pancreatic development and β-cell identity, including RFX6, NEUROD1, PTF1A, INS, ISL1, and SLC30A8. Furthermore, miRanda-based analyses identified potential interactions between miRNAs and lncRNAs, suggesting the existence of complex miRNA–lncRNA–mRNA networks affected by RFX3 deficiency. Together, these findings provide insight into the transcriptomic alterations resulting from RFX3 loss and highlight the potential involvement of non-coding RNAs in mediating the developmental defects observed during human iPSC-derived pancreatic islet formation.

Date of Award	2026
Original language	American English
Awarding Institution	HBKU College of Health & Life Sciences