HMGA2 Antisense Long Non-coding RNAs as New Players in the Regulation of HMGA2 Expression and Pancreatic Cancer Promotion

Abstract

Background: Natural antisense long non-coding RNAs (lncRNAs) are regulatory RNAs transcribed from the opposite strand of either protein coding or non-coding genes, able to modulate their own sense gene expression. Hence, their dysregulation can lead to pathologic processes. Cancer is a complex class of diseases determined by the aberrant expression of a variety of factors, among them, the oncofetal chromatin architectural proteins High Mobility Group A (HMGA) modulate several cancer hallmarks. Thus, we decided to investigate the presence of natural antisense lncRNAs in HMGA1 and HMGA2 loci, and their possible involvement in gene expression regulation. Methods: We used FANTOM5 data resources, FANTOM-CAT genome browser and Zenbu visualization tool, which employ 1,829 human CAGE and RNA-sequencing libraries, to determine expression, ontology enrichment, and dynamic regulation of natural antisense lncRNAs in HMGA1 and HMGA2 loci. We then performed qRT-PCR in different cancer cell lines to validate the existence of HMGA2-AS1 transcripts. We depleted HMGA2-AS1 transcripts with siRNAs and investigated HMGA2 expression by qRT-PCR and western blot analyses. Moreover, we evaluated cell viability and migration by MTS and transwell assays, and EMT markers by qRT-PCR and immunofluorescence. Furthermore, we used bioinformatics approaches to evaluate HMGA2 and HMGA2-AS1 correlation and overall survival in tumor patients. Results: We found the presence of a promoter-associated lncRNA (CATG00000088127.1) in the HMGA1 gene and three antisense genes (RPSAP52, HMGA2-AS1, and RP11-366L20.3) in the HMGA2 gene. We studied the uncharacterized HMGA2-AS1 transcripts, validating their existence in cancer cell lines and observing a positive correlation between HMGA2 and HMGA2-AS1 expression in a cancer-derived patient dataset. We showed that HMGA2-AS1 transcripts positively modulate HMGA2 expression and migration properties of PANC1 cells through HMGA2. In addition, Kaplan-Meier analysis showed that high level of HMGA2-AS1 is a negative prognostic factor in pancreatic cancer patients. Ros et al. HMGA2 Regulation by HMGA2-AS1 Conclusions: Our results describe novel antisense lncRNAs associated with HMGA1 and HMGA2 genes. In particular, we demonstrate that HMGA2-AS1 is involved in the regulation of its own sense gene expression, mediating tumorigenesis. Thus, we highlight a new layer of complexity in the regulation of HMGA2 expression, providing new potential targets for cancer therapy.

Prioritization of Osteoporosis‐Associated Genome‐wide Association Study (GWAS) Single‐Nucleotide Polymorphisms (SNPs) Using Epigenomics and Transcriptomics

“…The noncoding RNA (ncRNA) gene RPSAP52 can regulate HMGA2 both posttranscriptionally by blocking HMGA2 ‐targeted miRNA activity and transcriptionally. ( 40 )…”

The role of long noncoding RNA AL161431.1 in the development and progression of pancreatic cancer

“…A search using the key words of lncRNA and pancreatic cancer in PubMed on July 28, 2020 yielded 589 publications, with the most relevant one dating back in 2011 (19). Most lncRNAs have been reported to promote the proliferation of pancreatic cancer through different signaling pathways (20)(21)(22)(23). In the case of lncRNA AL161431.1, its identi ed targets include miR-1252-5p, and the pathways include MAPK signaling in endometrial carcinoma and a competing endogenous RNA network in lung squamous cell carcinoma (7,9; Table S2).…”

Prioritization of osteoporosis-associated GWAS SNPs using epigenomics and transcriptomics

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