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Preckwinkel P, Mir KUI, Otto FW, Elrewany H, Sinz A, Hüttelmaier S, Bley N, Gutschner T. Long Non-Coding RNAs and RNA-Binding Proteins in Pancreatic Cancer Development and Progression. Cancers (Basel) 2025; 17:1601. [PMID: 40427100 PMCID: PMC12110025 DOI: 10.3390/cancers17101601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2025] [Revised: 05/04/2025] [Accepted: 05/06/2025] [Indexed: 05/29/2025] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is the most common type of pancreatic cancer and is responsible for about 467,000 cancer deaths annually. An oftentimes asymptomatic early phase of this disease results in a delayed diagnosis, and patients often present with advanced disease. Current treatment options have limited survival benefits, and only a minor patient population carries actionable genomic alterations. Hence, innovative personalized treatment strategies that consider molecular, cellular and functional analyses are urgently needed for pancreatic cancer patients. However, the majority of the genetic alterations found in PDAC are currently undruggable, or patients' response is not as expected. Therefore, non-genomic biomarkers and alternative molecular targets should be considered in order to advance the clinical management of PDAC patients. In line with this, recent gene expression and single-cell transcriptome analyses have identified molecular subtypes and transcriptional cell states that affect disease progression and drug efficiency. In this review, we will introduce long non-coding RNAs (lncRNAs) as well as RNA-binding proteins (RBPs) that are able to modulate the transcriptome of a cell through diverse mechanisms, thereby contributing to disease progression. We will provide a brief overview about the general functions of lncRNAs and RBPs, respectively. Subsequently, we will highlight selected lncRNAs and RBPs that have been shown to play a role in PDAC development, progression and drug response. Finally, we will present strategies aiming to interfere with the expression and function of lncRNAs and RBPs.
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Affiliation(s)
- Pit Preckwinkel
- Section for RNA Biology and Pathogenesis, Institute of Molecular Medicine, Faculty of Medicine, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany;
| | - Khursheed Ul Islam Mir
- Section for Molecular Cell Biology, Institute of Molecular Medicine, Faculty of Medicine, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany; (K.U.I.M.); (H.E.); (S.H.)
| | - Florian W. Otto
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Faculty of Natural Sciences I, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany; (F.W.O.); (A.S.)
- Center for Structural Mass Spectrometry, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Hend Elrewany
- Section for Molecular Cell Biology, Institute of Molecular Medicine, Faculty of Medicine, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany; (K.U.I.M.); (H.E.); (S.H.)
| | - Andrea Sinz
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Faculty of Natural Sciences I, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany; (F.W.O.); (A.S.)
- Center for Structural Mass Spectrometry, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Stefan Hüttelmaier
- Section for Molecular Cell Biology, Institute of Molecular Medicine, Faculty of Medicine, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany; (K.U.I.M.); (H.E.); (S.H.)
| | - Nadine Bley
- Section for Molecular Cell Biology, Institute of Molecular Medicine, Faculty of Medicine, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany; (K.U.I.M.); (H.E.); (S.H.)
| | - Tony Gutschner
- Section for RNA Biology and Pathogenesis, Institute of Molecular Medicine, Faculty of Medicine, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany;
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Tran U, Streets AJ, Smith D, Decker E, Kirschfink A, Izem L, Hassey JM, Rutland B, Valluru MK, Bräsen JH, Ott E, Epting D, Eisenberger T, Ong AC, Bergmann C, Wessely O. BICC1 Interacts with PKD1 and PKD2 to Drive Cystogenesis in ADPKD. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2024.08.27.608867. [PMID: 39253489 PMCID: PMC11383298 DOI: 10.1101/2024.08.27.608867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/11/2024]
Abstract
Autosomal dominant polycystic kidney disease (ADPKD) is primarily of adult-onset and caused by pathogenic variants in PKD1 or PKD2 . Yet, disease expression is highly variable and includes very early-onset PKD presentations in utero or infancy. In animal models, the RNA-binding molecule Bicc1 has been shown to play a crucial role in the pathogenesis of PKD. To study the interaction between BICC1, PKD1 and PKD2 we combined biochemical approaches, knockout studies in mice and Xenopus, genetic engineered human kidney cells as well as genetic association studies in a large ADPKD cohort. We first demonstrated that BICC1 physically binds to the proteins Polycystin-1 and -2 encoded by PKD1 and PKD2 via distinct protein domains. Furthermore, PKD was aggravated in loss-of-function studies in Xenopus and mouse models resulting in more severe disease when Bicc1 was depleted in conjunction with Pkd1 or Pkd2 . Finally, in a large human patient cohort, we identified a sibling pair with a homozygous BICC1 variant and patients with very early onset PKD (VEO-PKD) that exhibited compound heterozygosity of BICC1 in conjunction with PKD1 and PKD2 variants. Genome editing demonstrated that these BICC1 variants were hypomorphic in nature and impacted disease-relevant signaling pathways. These findings support the hypothesis that BICC1 cooperates functionally with PKD1 and PKD2 , and that BICC1 variants may aggravate PKD severity highlighting RNA metabolism as an important new concept for disease modification in ADPKD.
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Hasan MK, Jeannine Brady L. Nucleic acid-binding KH domain proteins influence a spectrum of biological pathways including as part of membrane-localized complexes. J Struct Biol X 2024; 10:100106. [PMID: 39040530 PMCID: PMC11261784 DOI: 10.1016/j.yjsbx.2024.100106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 06/18/2024] [Accepted: 06/24/2024] [Indexed: 07/24/2024] Open
Abstract
K-Homology domain (KH domain) proteins bind single-stranded nucleic acids, influence protein-protein interactions of proteins that harbor them, and are found in all kingdoms of life. In concert with other functional protein domains KH domains contribute to a variety of critical biological activities, often within higher order machineries including membrane-localized protein complexes. Eukaryotic KH domain proteins are linked to developmental processes, morphogenesis, and growth regulation, and their aberrant expression is often associated with cancer. Prokaryotic KH domain proteins are involved in integral cellular activities including cell division and protein translocation. Eukaryotic and prokaryotic KH domains share structural features, but are differentiated based on their structural organizations. In this review, we explore the structure/function relationships of known examples of KH domain proteins, and highlight cases in which they function within or at membrane surfaces. We also summarize examples of KH domain proteins that influence bacterial virulence and pathogenesis. We conclude the article by discussing prospective research avenues that could be pursued to better investigate this largely understudied protein category.
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Affiliation(s)
- Md Kamrul Hasan
- Department of Oral Biology, University of Florida, Gainesville, FL 32610, USA
- Division of Biology, Kansas State University, Manhattan, KS 66506, USA
| | - L. Jeannine Brady
- Department of Oral Biology, University of Florida, Gainesville, FL 32610, USA
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