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Dix-Peek T, Dickens C, Valcárcel J, Duarte RAB. Lower FGFR2 mRNA Expression and Higher Levels of FGFR2 IIIc in HER2-Positive Breast Cancer. BIOLOGY 2024; 13:920. [PMID: 39596875 PMCID: PMC11591975 DOI: 10.3390/biology13110920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2024] [Revised: 10/25/2024] [Accepted: 10/28/2024] [Indexed: 11/29/2024]
Abstract
Fibroblast growth factor receptor 2 (FGFR2) has been associated with breast cancer. We performed in silico analyses to investigate the FGFR2 mRNA expression and splice variants associated with breast cancer subtypes. Online databases, including cBioPortal and TCGA SpliceSeq, were used to examine the association between the FGFR2 expression and splice variants with breast cancer subtypes. A higher FGFR2 mRNA was significantly associated with luminal, oestrogen receptor (ER)-positive breast cancers, and invasive lobular carcinomas, whereas a lower FGFR2 was associated with human epidermal growth factor receptor 2 (HER2)-positive breast cancer and invasive ductal carcinomas. The epithelial alternatively spliced FGFR2 IIIb isoform was significantly enriched in ER+ breast cancer, while the mesenchymal FGFR2 IIIc isoform was significantly prevalent in HER2+ cancer. Increased levels of FGFR2 and IIIb splice isoforms are associated with less aggressive breast cancer phenotypes, while decreased levels of FGFR2 and increased IIIc splice isoform are associated with more aggressive phenotypes.
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Affiliation(s)
- Thérèse Dix-Peek
- Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, 07 York Road, Parktown, Johannesburg 2193, South Africa;
| | - Caroline Dickens
- Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, 07 York Road, Parktown, Johannesburg 2193, South Africa;
| | - Juan Valcárcel
- ICREA and Center for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain;
| | - Raquel A. B. Duarte
- Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, 07 York Road, Parktown, Johannesburg 2193, South Africa;
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Zheng W, Guo J, Ma S, Sun R, Song Y, Chen Y, Mao R, Fan Y. The NEDD4-binding protein N4BP1 degrades mRNA substrates through the coding sequence independent of nonsense-mediated decay. J Biol Chem 2024; 300:107954. [PMID: 39491646 DOI: 10.1016/j.jbc.2024.107954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2024] [Revised: 10/17/2024] [Accepted: 10/21/2024] [Indexed: 11/05/2024] Open
Abstract
3'UTRs are recognized for their role in regulating mRNA turnover while the turnover of a specific group of mRNAs mediated by coding sequences (CDSs) remains poorly understood. N4BP1 is a critical inflammatory regulator in vivo with a molecular mechanism that is not yet clearly defined. Our study reveals that N4BP1 efficiently degrades its mRNA targets via CDS rather than the 3'-UTR. This CDS-dependent mRNA turnover mechanism appears to be a general feature of N4BP1, as evidenced by testing multiple mRNA substrates, such as Fos-C, Fos-B, Jun-B, and C-X-C motif chemokine ligand 1. Detailed mapping of the motif identified a crucial 33-nt (289-322) sequence near the 5'-end of Fos-C-CDS, where the presence of polyC is necessary for N4BP1-mediated degradation. Functional studies involving domain deletion and point mutations showed that both the K homology and N4BP1, YacP-like nuclease domains are essential for N4BP1 to restrict mRNA substrates. The function of N4BP1 in mRNA turnover is not dependent on nonsense-mediated decay as it efficiently restricts mRNA substrates even in cells deficient in UPF1, UPF3A, and UPF3B. Additionally, the function of N4BP1 is not reliant on LUC7L3 despite its known association with this protein. Our findings suggest that N4BP1 acts as an endoribonuclease to degrade mRNA substrates primarily through CDSs containing a C-rich motif.
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Affiliation(s)
- Wen Zheng
- Department of Pathogenic Biology, School of Medicine, Nantong University, Nantong, China; Laboratory of Medical Science, School of Medicine, Nantong University, Nantong, China
| | - Jinjing Guo
- Department of Pathogenic Biology, School of Medicine, Nantong University, Nantong, China; Laboratory of Medical Science, School of Medicine, Nantong University, Nantong, China
| | - Shuyan Ma
- Department of Pathogenic Biology, School of Medicine, Nantong University, Nantong, China; Laboratory of Medical Science, School of Medicine, Nantong University, Nantong, China
| | - Rong Sun
- Laboratory of Medical Science, School of Medicine, Nantong University, Nantong, China
| | - Yihua Song
- Department of Stomatology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, China
| | - Yuanmeng Chen
- Department of Pathogenic Biology, School of Medicine, Nantong University, Nantong, China; Laboratory of Medical Science, School of Medicine, Nantong University, Nantong, China
| | - Renfang Mao
- Department of Pathophysiology, School of Medicine, Nantong University, Nantong, China.
| | - Yihui Fan
- Department of Pathogenic Biology, School of Medicine, Nantong University, Nantong, China; Laboratory of Medical Science, School of Medicine, Nantong University, Nantong, China.
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Burnett SB, Culver AM, Simon TA, Rowson T, Frederick K, Palmer K, Murray SA, Davis SW, Patel RC. Mutation in Prkra results in cerebellar abnormality and reduced eIF2α phosphorylation in a model of DYT-PRKRA. Dis Model Mech 2024; 17:dmm050929. [PMID: 39512178 PMCID: PMC11625895 DOI: 10.1242/dmm.050929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Accepted: 10/19/2024] [Indexed: 11/15/2024] Open
Abstract
Variants in the PRKRA gene, which encodes PACT, cause the early-onset primary dystonia DYT-PRKRA, a movement disorder associated with disruption of coordinated muscle movements. PACT and its murine homolog RAX activate protein kinase R (PKR; also known as EIF2AK2) by a direct interaction in response to cellular stressors to mediate phosphorylation of the α subunit of eukaryotic translation initiation factor 2 (eIF2α). Mice homozygous for a naturally arisen, recessively inherited frameshift mutation, Prkralear-5J, exhibit progressive dystonia. In the present study, we investigated the biochemical and developmental consequences of the Prkralear-5J mutation. Our results indicated that the truncated PACT/RAX protein retains its ability to interact with PKR but inhibits PKR activation. Mice homozygous for the mutation showed abnormalities in cerebellar development as well as a severe lack of dendritic arborization of Purkinje neurons. Additionally, reduced eIF2α phosphorylation was noted in the cerebellum and Purkinje neurons of the homozygous Prkralear-5J mice. These findings indicate that PACT/RAX-mediated regulation of PKR activity and eIF2α phosphorylation plays a role in cerebellar development and contributes to the dystonia phenotype resulting from the Prkralear-5J mutation.
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Affiliation(s)
- Samuel B. Burnett
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Allison M. Culver
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Tricia A. Simon
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Taylor Rowson
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Kenneth Frederick
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Kristina Palmer
- Genetic Resource Center, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Stephen A. Murray
- Genetic Resource Center, The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Shannon W. Davis
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Rekha C. Patel
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
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Behera A, Panigrahi GK, Sahoo A. Nonsense-Mediated mRNA Decay in Human Health and Diseases: Current Understanding, Regulatory Mechanisms and Future Perspectives. Mol Biotechnol 2024:10.1007/s12033-024-01267-7. [PMID: 39264527 DOI: 10.1007/s12033-024-01267-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 08/24/2024] [Indexed: 09/13/2024]
Abstract
Nonsense-mediated mRNA decay (NMD) is a surveillance mechanism that is conserved across all eukaryotes ensuring the quality of transcripts by targeting messenger RNA (mRNA) harbouring premature stop codons. It regulates the gene expression by targeting aberrant mRNA carrying pre-termination codons (PTCs) and eliminates C-terminal truncated proteins. NMD distinguishes aberrant and non-aberrant transcript by looking after long 3' UTRs and exon-junction complex (EJC) downstream of stop codon that indicate the presence of PTC. Therefore, NMD modulates cellular surveillance and eliminates the truncated proteins but if the PTC escapes the surveillance pathway it can lead to potential negative phenotype resulting in genetic diseases. The alternative splicing also contributes in formation of NMD-sensitive isoforms by introducing PTC. NMD plays a complex role in cancer, it can either aggravate or downregulates the tumour. Some tumours agitate NMD to deteriorate mRNAs encoding tumour suppressor proteins, stress response proteins and neoantigens. In other case, tumours suppress the NMD to encourage the expression of oncoproteins for tumour growth and survival. This mechanism augmented in the development of new therapeutics by PTC read-through mechanism and personalized medicine. Detailed studies on NMD surveillance will possibly lead towards development of strategies for improving human health aligning with United Nations sustainable development goals (SDG 3: Good health and well-being). The potential therapeutic applications of NMD pose a challenge in terms of safe and effective modulation. Understanding the complexities of NMD regulation and its interaction with other cellular processes can lead to the development of new interventions for various diseases.
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Affiliation(s)
- Amrita Behera
- Department of Zoology, School of Applied Sciences, Centurion University of Technology and Management, Jatni, Khordha, Odisha, India
| | - Gagan Kumar Panigrahi
- Department of Zoology, School of Applied Sciences, Centurion University of Technology and Management, Jatni, Khordha, Odisha, India.
| | - Annapurna Sahoo
- Department of Zoology, School of Applied Sciences, Centurion University of Technology and Management, Jatni, Khordha, Odisha, India.
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Burnett SB, Culver AM, Simon TA, Rowson T, Frederick K, Palmer K, Murray SA, Davis SW, Patel RC. A frameshift mutation in the murine Prkra gene causes dystonia and exhibits abnormal cerebellar development and reduced eIF2α phosphorylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.04.597421. [PMID: 38895245 PMCID: PMC11185611 DOI: 10.1101/2024.06.04.597421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Mutations in Prkra gene, which encodes PACT/RAX cause early onset primary dystonia DYT-PRKRA, a movement disorder that disrupts coordinated muscle movements. PACT/RAX activates protein kinase R (PKR, aka EIF2AK2) by a direct interaction in response to cellular stressors to mediate phosphorylation of the α subunit of the eukaryotic translation initiation factor 2 (eIF2α). Mice homozygous for a naturally arisen, recessively inherited frameshift mutation, Prkra lear-5J exhibit progressive dystonia. In the present study, we investigate the biochemical and developmental consequences of the Prkra lear-5J mutation. Our results indicate that the truncated PACT/RAX protein retains its ability to interact with PKR, however, it inhibits PKR activation. Furthermore, mice homozygous for the mutation have abnormalities in the cerebellar development as well as a severe lack of dendritic arborization of Purkinje neurons. Additionally, reduced eIF2α phosphorylation is noted in the cerebellums and Purkinje neurons of the homozygous Prkra lear-5J mice. These results indicate that PACT/RAX mediated regulation of PKR activity and eIF2α phosphorylation plays a role in cerebellar development and contributes to the dystonia phenotype resulting from this mutation.
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Affiliation(s)
| | | | | | | | | | - Kristina Palmer
- The Jackson Laboratory, 600 Main St., Bar Harbor, ME 04609, USA
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Miskin RP, DiPersio CM. Roles for epithelial integrin α3β1 in regulation of the microenvironment during normal and pathological tissue remodeling. Am J Physiol Cell Physiol 2024; 326:C1308-C1319. [PMID: 38497112 PMCID: PMC11371326 DOI: 10.1152/ajpcell.00128.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 03/08/2024] [Accepted: 03/08/2024] [Indexed: 03/19/2024]
Abstract
Integrin receptors for the extracellular matrix activate intracellular signaling pathways that are critical for tissue development, homeostasis, and regeneration/repair, and their loss or dysregulation contributes to many developmental defects and tissue pathologies. This review will focus on tissue remodeling roles for integrin α3β1, a receptor for laminins found in the basement membranes (BMs) that underlie epithelial cell layers. As a paradigm, we will discuss literature that supports a role for α3β1 in promoting ability of epidermal keratinocytes to modify their tissue microenvironment during skin development, wound healing, or tumorigenesis. Preclinical and clinical studies have shown that this role depends largely on ability of α3β1 to govern the keratinocyte's repertoire of secreted proteins, or the "secretome," including 1) matrix proteins and proteases involved in matrix remodeling and 2) paracrine-acting growth factors/cytokines that stimulate other cells with important tissue remodeling functions (e.g., endothelial cells, fibroblasts, inflammatory cells). Moreover, α3β1 signaling controls gene expression that helps epithelial cells carry out these functions, including genes that encode secreted matrix proteins, proteases, growth factors, or cytokines. We will review what is known about α3β1-dependent gene regulation through both transcription and posttranscriptional mRNA stability. Regarding the latter, we will discuss examples of α3β1-dependent alternative splicing (AS) or alternative polyadenylation (APA) that prevents inclusion of cis-acting mRNA sequences that would otherwise target the transcript for degradation via nonsense-mediated decay or destabilizing AU-rich elements (AREs) in the 3'-untranslated region (3'-UTR). Finally, we will discuss prospects and anticipated challenges of exploiting α3β1 as a clinical target for the treatment of cancer or wound healing.
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Affiliation(s)
| | - C Michael DiPersio
- Department of Surgery, Albany Medical College, Albany, New York, United States
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, New York, United States
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Das R, Panigrahi GK. Messenger RNA Surveillance: Current Understanding, Regulatory Mechanisms, and Future Implications. Mol Biotechnol 2024:10.1007/s12033-024-01062-4. [PMID: 38411790 DOI: 10.1007/s12033-024-01062-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 01/02/2024] [Indexed: 02/28/2024]
Abstract
Nonsense-mediated mRNA decay (NMD) is an evolutionarily conserved surveillance mechanism in eukaryotes primarily deployed to ensure RNA quality control by eliminating aberrant transcripts and also involved in modulating the expression of several physiological transcripts. NMD, the mRNA surveillance pathway, is a major form of gene regulation in eukaryotes. NMD serves as one of the most significant quality control mechanisms as it primarily scans the newly synthesized transcripts and differentiates the aberrant and non-aberrant transcripts. The synthesis of truncated proteins is restricted, which would otherwise lead to cellular dysfunctions. The up-frameshift factors (UPFs) play a central role in executing the NMD event, largely by recognizing and recruiting multiple protein factors that result in the decay of non-physiological mRNAs. NMD exhibits astounding variability in its ability across eukaryotes in an array of pathological and physiological contexts. The detailed understanding of NMD and the underlying molecular mechanisms remains blurred. This review outlines our current understanding of NMD, in regulating multifaceted cellular events during development and disease. It also attempts to identify unanswered questions that deserve further investigation.
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Affiliation(s)
- Rutupurna Das
- Department of Zoology, School of Applied Sciences, Centurion University of Technology and Management, Jatni, Khordha, Odisha, India
| | - Gagan Kumar Panigrahi
- Department of Zoology, School of Applied Sciences, Centurion University of Technology and Management, Jatni, Khordha, Odisha, India.
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