1
|
Jones M, Norman M, Tiet AM, Lee J, Lee MH. C. elegans Germline as Three Distinct Tumor Models. BIOLOGY 2024; 13:425. [PMID: 38927305 DOI: 10.3390/biology13060425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Revised: 06/04/2024] [Accepted: 06/07/2024] [Indexed: 06/28/2024]
Abstract
Tumor cells display abnormal growth and division, avoiding the natural process of cell death. These cells can be benign (non-cancerous growth) or malignant (cancerous growth). Over the past few decades, numerous in vitro or in vivo tumor models have been employed to understand the molecular mechanisms associated with tumorigenesis in diverse regards. However, our comprehension of how non-tumor cells transform into tumor cells at molecular and cellular levels remains incomplete. The nematode C. elegans has emerged as an excellent model organism for exploring various phenomena, including tumorigenesis. Although C. elegans does not naturally develop cancer, it serves as a valuable platform for identifying oncogenes and the underlying mechanisms within a live organism. In this review, we describe three distinct germline tumor models in C. elegans, highlighting their associated mechanisms and related regulators: (1) ectopic proliferation due to aberrant activation of GLP-1/Notch signaling, (2) meiotic entry failure resulting from the loss of GLD-1/STAR RNA-binding protein, (3) spermatogenic dedifferentiation caused by the loss of PUF-8/PUF RNA-binding protein. Each model requires the mutations of specific genes (glp-1, gld-1, and puf-8) and operates through distinct molecular mechanisms. Despite these differences in the origins of tumorigenesis, the internal regulatory networks within each tumor model display shared features. Given the conservation of many of the regulators implicated in C. elegans tumorigenesis, it is proposed that these unique models hold significant potential for enhancing our comprehension of the broader control mechanisms governing tumorigenesis.
Collapse
Affiliation(s)
- Mariah Jones
- Division of Hematology/Oncology, Department of Internal Medicine, Brody School of Medicine at East Carolina University, Greenville, NC 27834, USA
| | - Mina Norman
- Division of Hematology/Oncology, Department of Internal Medicine, Brody School of Medicine at East Carolina University, Greenville, NC 27834, USA
| | - Alex Minh Tiet
- Neuroscience Program, East Carolina University, Greenville, NC 27858, USA
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
| | - Jiwoo Lee
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
| | - Myon Hee Lee
- Division of Hematology/Oncology, Department of Internal Medicine, Brody School of Medicine at East Carolina University, Greenville, NC 27834, USA
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
| |
Collapse
|
2
|
Gujjala VA, Klimek I, Abyadeh M, Tyshkovskiy A, Oz N, Castro JP, Gladyshev VN, Newton J, Kaya A. A disease similarity approach identifies short-lived Niemann-Pick type C disease mice with accelerated brain aging as a novel mouse model for Alzheimer's disease and aging research. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.19.590328. [PMID: 38712089 PMCID: PMC11071364 DOI: 10.1101/2024.04.19.590328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Since its first description in 1906 by Dr. Alois Alzheimer, Alzheimer's disease (AD) has been the most common type of dementia. Initially thought to be caused by age-associated accumulation of plaques, in recent years, research has increasingly associated AD with lysosomal storage and metabolic disorders, and the explanation of its pathogenesis has shifted from amyloid and tau accumulation to oxidative stress and impaired lipid and glucose metabolism aggravated by hypoxic conditions. However, the underlying mechanisms linking those cellular processes and conditions to disease progression have yet to be defined. Here, we applied a disease similarity approach to identify unknown molecular targets of AD by using transcriptomic data from congenital diseases known to increase AD risk, namely Down Syndrome, Niemann Pick Disease Type C (NPC), and Mucopolysaccharidoses I. We uncovered common pathways, hub genes, and miRNAs across in vitro and in vivo models of these diseases as potential molecular targets for neuroprotection and amelioration of AD pathology, many of which have never been associated with AD. We then investigated common molecular alterations in brain samples from an NPC disease mouse model by juxtaposing them with brain samples of both human and mouse models of AD. Detailed phenotypic and molecular analyses revealed that the NPC mut mouse model can serve as a potential short-lived in vivo model for AD research and for understanding molecular factors affecting brain aging. This research represents the first comprehensive approach to congenital disease association with neurodegeneration and a new perspective on AD research while highlighting shortcomings and lack of correlation in diverse in vitro models. Considering the lack of an AD mouse model that recapitulates the physiological hallmarks of brain aging, the characterization of a short-lived NPC mouse model will further accelerate the research in these fields and offer a unique model for understanding the molecular mechanisms of AD from a perspective of accelerated brain aging.
Collapse
|
3
|
Neumann DP, Phillips CA, Lumb R, Palethorpe HM, Ramani Y, Hollier BG, Selth LA, Bracken CP, Goodall GJ, Gregory PA. Quaking isoforms cooperate to promote the mesenchymal phenotype. Mol Biol Cell 2024; 35:ar17. [PMID: 38019605 PMCID: PMC10881146 DOI: 10.1091/mbc.e23-08-0316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 10/18/2023] [Accepted: 11/20/2023] [Indexed: 12/01/2023] Open
Abstract
The RNA-binding protein Quaking (QKI) has widespread effects on mRNA regulation including alternative splicing, stability, translation, and localization of target mRNAs. Recently, QKI was found to be induced during epithelial-mesenchymal transition (EMT), where it promotes a mesenchymal alternative splicing signature that contributes to the mesenchymal phenotype. QKI is itself alternatively spliced to produce three major isoforms, QKI-5, QKI-6, and QKI-7. While QKI-5 is primarily localized to the nucleus where it controls mesenchymal splicing during EMT, the functions of the two predominantly cytoplasmic isoforms, QKI-6 and QKI-7, in this context remain uncharacterized. Here we used CRISPR-mediated depletion of QKI in a human mammary epithelial cell model of EMT and studied the effects of expressing the QKI isoforms in isolation and in combination. QKI-5 was required to induce mesenchymal morphology, while combined expression of QKI-5 with either QKI-6 or QKI-7 further enhanced mesenchymal morphology and cell migration. In addition, we found that QKI-6 and QKI-7 can partially localize to the nucleus and contribute to alternative splicing of QKI target genes. These findings indicate that the QKI isoforms function in a dynamic and cooperative manner to promote the mesenchymal phenotype.
Collapse
Affiliation(s)
- Daniel P. Neumann
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, South Australia 5000, Australia
| | - Caroline A. Phillips
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, South Australia 5000, Australia
| | - Rachael Lumb
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, South Australia 5000, Australia
| | - Helen M. Palethorpe
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, South Australia 5000, Australia
| | - Yesha Ramani
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, South Australia 5000, Australia
| | - Brett G. Hollier
- Australian Prostate Cancer Research Centre - Queensland, Centre for Genomics and Personalised Health, Faculty of Health, School of Biomedical Sciences, Queensland University of Technology, Translational Research Institute, Brisbane, Queensland 4102, Australia
| | - Luke A. Selth
- Flinders Health and Medical Research Institute and Freemasons Centre for Male Health and Wellbeing, Flinders University, Bedford Park, South Australia 5042, Australia
- Faculty of Health and Medical Sciences, and
| | - Cameron P. Bracken
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, South Australia 5000, Australia
- Faculty of Health and Medical Sciences, and
- School of Biological Sciences, Faculty of Sciences, Engineering and Technology, The University of Adelaide, Adelaide, South Australia 5000, Australia
| | - Gregory J. Goodall
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, South Australia 5000, Australia
- Faculty of Health and Medical Sciences, and
- School of Biological Sciences, Faculty of Sciences, Engineering and Technology, The University of Adelaide, Adelaide, South Australia 5000, Australia
| | - Philip A. Gregory
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, South Australia 5000, Australia
- Faculty of Health and Medical Sciences, and
| |
Collapse
|
4
|
Neumann DP, Pillman KA, Dredge BK, Bert AG, Phillips CA, Lumb R, Ramani Y, Bracken CP, Hollier BG, Selth LA, Beilharz TH, Goodall GJ, Gregory PA. The landscape of alternative polyadenylation during EMT and its regulation by the RNA-binding protein Quaking. RNA Biol 2024; 21:1-11. [PMID: 38112323 PMCID: PMC10732628 DOI: 10.1080/15476286.2023.2294222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/05/2023] [Indexed: 12/21/2023] Open
Abstract
Epithelial-mesenchymal transition (EMT) plays important roles in tumour progression and is orchestrated by dynamic changes in gene expression. While it is well established that post-transcriptional regulation plays a significant role in EMT, the extent of alternative polyadenylation (APA) during EMT has not yet been explored. Using 3' end anchored RNA sequencing, we mapped the alternative polyadenylation (APA) landscape following Transforming Growth Factor (TGF)-β-mediated induction of EMT in human mammary epithelial cells and found APA generally causes 3'UTR lengthening during this cell state transition. Investigation of potential mediators of APA indicated the RNA-binding protein Quaking (QKI), a splicing factor induced during EMT, regulates a subset of events including the length of its own transcript. Analysis of QKI crosslinked immunoprecipitation (CLIP)-sequencing data identified the binding of QKI within 3' untranslated regions (UTRs) was enriched near cleavage and polyadenylation sites. Following QKI knockdown, APA of many transcripts is altered to produce predominantly shorter 3'UTRs associated with reduced gene expression. These findings reveal the changes in APA that occur during EMT and identify a potential role for QKI in this process.
Collapse
Affiliation(s)
- Daniel P. Neumann
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
| | - Katherine A. Pillman
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
| | - B. Kate Dredge
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
| | - Andrew G. Bert
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
| | - Caroline A. Phillips
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
| | - Rachael Lumb
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
| | - Yesha Ramani
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
| | - Cameron P. Bracken
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
- Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - Brett G. Hollier
- Australian Prostate Cancer Research Centre - Queensland, Centre for Genomics and Personalised Health, Faculty of Health, School of Biomedical Sciences, Queensland University of Technology, Brisbane, QLD, Australia
| | - Luke A. Selth
- Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, Australia
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA, Australia
| | - Traude H. Beilharz
- Development and Stem Cells Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
| | - Gregory J. Goodall
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
- Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - Philip A. Gregory
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
- Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, Australia
| |
Collapse
|
5
|
Baldwin KT, Murai KK, Khakh BS. Astrocyte morphology. Trends Cell Biol 2023:S0962-8924(23)00204-0. [PMID: 38180380 DOI: 10.1016/j.tcb.2023.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 09/18/2023] [Accepted: 09/29/2023] [Indexed: 01/06/2024]
Abstract
Astrocytes are predominant glial cells that tile the central nervous system (CNS). A cardinal feature of astrocytes is their complex and visually enchanting morphology, referred to as bushy, spongy, and star-like. A central precept of this review is that such complex morphological shapes evolved to allow astrocytes to contact and signal with diverse cells at a range of distances in order to sample, regulate, and contribute to the extracellular milieu, and thus participate widely in cell-cell signaling during physiology and disease. The recent use of improved imaging methods and cell-specific molecular evaluations has revealed new information on the structural organization and molecular underpinnings of astrocyte morphology, the mechanisms of astrocyte morphogenesis, and the contributions to disease states of reduced morphology. These insights have reignited interest in astrocyte morphological complexity as a cornerstone of fundamental glial biology and as a critical substrate for multicellular spatial and physiological interactions in the CNS.
Collapse
Affiliation(s)
- Katherine T Baldwin
- Neuroscience Center, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Cell Biology and Physiology, University of North Carolina, Chapel Hill, NC 27599, USA.
| | - Keith K Murai
- Centre for Research in Neuroscience, Department of Neurology and Neurosurgery, Brain Repair and Integrative Neuroscience Program, The Research Institute of the McGill University Health Centre, Montreal General Hospital, 1650 Cedar Avenue, Montreal, QC H3G 1A4, Canada.
| | - Baljit S Khakh
- Department of Physiology, David Geffen School of Medicine, University of California Los Angeles, 10833 Le Conte Avenue, Los Angeles, CA 90034, USA; Department of Neurobiology, David Geffen School of Medicine, University of California Los Angeles, 10833 Le Conte Avenue, Los Angeles, CA 90034, USA.
| |
Collapse
|
6
|
Frazel PW, Labib D, Fisher T, Brosh R, Pirjanian N, Marchildon A, Boeke JD, Fossati V, Liddelow SA. Longitudinal scRNA-seq analysis in mouse and human informs optimization of rapid mouse astrocyte differentiation protocols. Nat Neurosci 2023; 26:1726-1738. [PMID: 37697111 PMCID: PMC10763608 DOI: 10.1038/s41593-023-01424-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 08/08/2023] [Indexed: 09/13/2023]
Abstract
Macroglia (astrocytes and oligodendrocytes) are required for normal development and function of the central nervous system, yet many questions remain about their emergence during the development of the brain and spinal cord. Here we used single-cell/single-nucleus RNA sequencing (scRNA-seq/snRNA-seq) to analyze over 298,000 cells and nuclei during macroglia differentiation from mouse embryonic and human-induced pluripotent stem cells. We computationally identify candidate genes involved in the fate specification of glia in both species and report heterogeneous expression of astrocyte surface markers across differentiating cells. We then used our transcriptomic data to optimize a previous mouse astrocyte differentiation protocol, decreasing the overall protocol length and complexity. Finally, we used multi-omic, dual single-nuclei (sn)RNA-seq/snATAC-seq analysis to uncover potential genomic regulatory sites mediating glial differentiation. These datasets will enable future optimization of glial differentiation protocols and provide insight into human glial differentiation.
Collapse
Affiliation(s)
- Paul W Frazel
- Neuroscience Institute, NYU Grossman School of Medicine, New York City, NY, USA.
| | - David Labib
- The New York Stem Cell Foundation Research Institute, New York City, NY, USA
| | - Theodore Fisher
- Neuroscience Institute, NYU Grossman School of Medicine, New York City, NY, USA
| | - Ran Brosh
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York City, NY, USA
| | - Nicolette Pirjanian
- The New York Stem Cell Foundation Research Institute, New York City, NY, USA
| | - Anne Marchildon
- Neuroscience Institute, NYU Grossman School of Medicine, New York City, NY, USA
| | - Jef D Boeke
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York City, NY, USA
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York City, NY, USA
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY, USA
| | - Valentina Fossati
- The New York Stem Cell Foundation Research Institute, New York City, NY, USA
| | - Shane A Liddelow
- Neuroscience Institute, NYU Grossman School of Medicine, New York City, NY, USA.
- Department of Neuroscience and Physiology, NYU Grossman School of Medicine, New York City, NY, USA.
- Department of Ophthalmology, NYU Grossman School of Medicine, New York City, NY, USA.
- Parekh Center for Interdisciplinary Neurology, NYU Grossman School of Medicine, New York City, NY, USA.
| |
Collapse
|
7
|
Martinez-Lozada Z, Todd FW, Schober AL, Krizman E, Robinson MB, Murai KK. Cooperative and competitive regulation of the astrocytic transcriptome by neurons and endothelial cells: Impact on astrocyte maturation. J Neurochem 2023; 167:52-75. [PMID: 37525469 PMCID: PMC10543513 DOI: 10.1111/jnc.15908] [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: 03/01/2023] [Revised: 06/19/2023] [Accepted: 06/20/2023] [Indexed: 08/02/2023]
Abstract
Astrocytes have essential roles in central nervous system (CNS) health and disease. During development, immature astrocytes show complex interactions with neurons, endothelial cells, and other glial cell types. Our work and that of others have shown that these interactions are important for astrocytic maturation. However, whether and how these cells work together to control this process remains poorly understood. Here, we test the hypothesis that cooperative interactions of astrocytes with neurons and endothelial cells promote astrocytic maturation. Astrocytes were cultured alone, with neurons, endothelial cells, or a combination of both. This was followed by astrocyte sorting, RNA sequencing, and bioinformatic analysis to detect transcriptional changes. Across culture configurations, 7302 genes were differentially expressed by 4 or more fold and organized into 8 groups that demonstrate cooperative and antagonist effects of neurons and endothelia on astrocytes. We also discovered that neurons and endothelial cells caused splicing of 200 and 781 mRNAs, respectively. Changes in gene expression were validated using quantitative PCR, western blot (WB), and immunofluorescence analysis. We found that the transcriptomic data from the three-culture configurations correlated with protein expression of three representative targets (FAM107A, GAT3, and GLT1) in vivo. Alternative splicing results also correlated with cortical tissue isoform representation of a target (Fibronectin 1) at different developmental stages. By comparing our results to published transcriptomes of immature and mature astrocytes, we found that neurons or endothelia shift the astrocytic transcriptome toward a mature state and that the presence of both cell types has a greater effect on maturation than either cell alone. These results increase our understanding of cellular interactions/pathways that contribute to astrocytic maturation. They also provide insight into how alterations to neurons and/or endothelial cells may alter astrocytes with implications for astrocytic changes in CNS disorders and diseases.
Collapse
Affiliation(s)
- Zila Martinez-Lozada
- Departments of Pediatrics and Systems Pharmacology & Translational Therapeutics, The Children’s Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, USA, 19104-4318
| | - Farmer W. Todd
- Centre for Research in Neuroscience, Department of Neurology & Neurosurgery, Brain Repair and Integrative Neuroscience Program, The Research Institute of the McGill University Health Centre, Montreal General Hospital, Montreal, Quebec, Canada H3G 1A4
| | - Alexandra L. Schober
- Centre for Research in Neuroscience, Department of Neurology & Neurosurgery, Brain Repair and Integrative Neuroscience Program, The Research Institute of the McGill University Health Centre, Montreal General Hospital, Montreal, Quebec, Canada H3G 1A4
| | - Elizabeth Krizman
- Departments of Pediatrics and Systems Pharmacology & Translational Therapeutics, The Children’s Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, USA, 19104-4318
| | - Michael B. Robinson
- Departments of Pediatrics and Systems Pharmacology & Translational Therapeutics, The Children’s Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, USA, 19104-4318
| | - Keith K. Murai
- Centre for Research in Neuroscience, Department of Neurology & Neurosurgery, Brain Repair and Integrative Neuroscience Program, The Research Institute of the McGill University Health Centre, Montreal General Hospital, Montreal, Quebec, Canada H3G 1A4
| |
Collapse
|
8
|
Kong Y, Luo Y, Zheng S, Yang J, Zhang D, Zhao Y, Zheng H, An M, Lin Y, Ai L, Diao X, Lin Q, Chen C, Chen R. Mutant KRAS Mediates circARFGEF2 Biogenesis to Promote Lymphatic Metastasis of Pancreatic Ductal Adenocarcinoma. Cancer Res 2023; 83:3077-3094. [PMID: 37363990 PMCID: PMC10502454 DOI: 10.1158/0008-5472.can-22-3997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 04/05/2023] [Accepted: 06/21/2023] [Indexed: 06/28/2023]
Abstract
Circular RNAs (circRNA) contribute to cancer stemness, proliferation, and metastasis. The biogenesis of circRNAs can be impacted by the genetic landscape of tumors. Herein, we identified a novel circRNA, circARFGEF2 (hsa_circ_0060665), which was upregulated in KRASG12D pancreatic ductal adenocarcinoma (PDAC) and positively associated with KRASG12D PDAC lymph node (LN) metastasis. CircARFGEF2 overexpression significantly facilitated KRASG12D PDAC LN metastasis in vitro and in vivo. Mechanistically, circARFGEF2 biogenesis in KRASG12D PDAC was significantly activated by the alternative splicing factor QKI-5, which recruited U2AF35 to facilitate spliceosome assembly. QKI-5 bound the QKI binding motifs and neighboring reverse complement sequence in intron 3 and 6 of ARFGEF2 pre-mRNA to facilitate circARFGEF2 biogenesis. CircARFGEF2 sponged miR-1205 and promoted the activation of JAK2, which phosphorylated STAT3 to trigger KRASG12D PDAC lymphangiogenesis and LN metastasis. Importantly, circARFGEF2 silencing significantly inhibited LN metastasis in the KrasG12D/+Trp53R172H/+Pdx-1-Cre (KPC) mouse PDAC model. These findings provide insight into the mechanism and metastasis-promoting function of mutant KRAS-mediated circRNA biogenesis. SIGNIFICANCE Increased splicing-mediated biogenesis of circARFGEF2 in KRAS-mutant pancreatic ductal adenocarcinoma activates JAK2-STAT3 signaling and triggers lymph node metastasis, suggesting circARFGEF2 could be a therapeutic target to inhibit pancreatic cancer progression.
Collapse
Affiliation(s)
- Yao Kong
- Department of Pancreas Center, Department of General Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, P.R. China
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, P.R. China
| | - Yuming Luo
- Department of Pancreas Center, Department of General Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, P.R. China
| | - Shangyou Zheng
- Department of Pancreas Center, Department of General Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, P.R. China
| | - Jiabin Yang
- Department of Pancreas Center, Department of General Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, P.R. China
- School of Medicine, South China University of Technology, Guangzhou, Guangdong, P.R. China
| | - Dingwen Zhang
- Department of Pancreas Center, Department of General Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, P.R. China
- School of Medicine, South China University of Technology, Guangzhou, Guangdong, P.R. China
| | - Yue Zhao
- Department of Tumor Intervention, Sun Yat-sen University First Affiliated Hospital, Guangzhou, Guangdong, P.R. China
| | - Hanhao Zheng
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, State Key Laboratory of Oncology in South China, Guangzhou, Guangdong, P.R. China
| | - Mingjie An
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, State Key Laboratory of Oncology in South China, Guangzhou, Guangdong, P.R. China
| | - Yan Lin
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, State Key Laboratory of Oncology in South China, Guangzhou, Guangdong, P.R. China
| | - Le Ai
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, State Key Laboratory of Oncology in South China, Guangzhou, Guangdong, P.R. China
- Department of Oncology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
| | - Xiayao Diao
- Department of Thoracic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P.R. China
| | - Qing Lin
- Department of Pancreas Center, Department of General Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, P.R. China
| | - Changhao Chen
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, P.R. China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, State Key Laboratory of Oncology in South China, Guangzhou, Guangdong, P.R. China
| | - Rufu Chen
- Department of Pancreas Center, Department of General Surgery, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong, P.R. China
- School of Medicine, South China University of Technology, Guangzhou, Guangdong, P.R. China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong, P.R. China
| |
Collapse
|
9
|
Bartelt LC, Switonski PM, Adamek G, Carvalho J, Duvick LA, Jarrah SI, McLoughlin HS, Scoles DR, Pulst SM, Orr HT, Hull C, Lowe CB, La Spada AR. Purkinje-Enriched snRNA-seq in SCA7 Cerebellum Reveals Zebrin Identity Loss as a Central Feature of Polyglutamine Ataxias. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.19.533345. [PMID: 37214832 PMCID: PMC10197555 DOI: 10.1101/2023.03.19.533345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Spinocerebellar ataxia type 7 (SCA7) is an inherited neurodegenerative disorder caused by a CAG-polyglutamine repeat expansion. SCA7 patients display a striking loss of Purkinje cell (PC) neurons with disease progression; however, PCs are rare, making them difficult to characterize. We developed a PC nuclei enrichment protocol and applied it to single-nucleus RNA-seq of a SCA7 knock-in mouse model. Our results unify prior observations into a central mechanism of cell identity loss, impacting both glia and PCs, driving accumulation of inhibitory synapses and altered PC spiking. Zebrin-II subtype dysregulation is the predominant signal in PCs, leading to complete loss of zebrin-II striping at motor symptom onset in SCA7 mice. We show this zebrin-II subtype degradation is shared across Polyglutamine Ataxia mouse models and SCA7 patients. It has been speculated that PC subtype organization is critical for cerebellar function, and our results suggest that a breakdown of zebrin-II parasagittal striping is pathological.
Collapse
Affiliation(s)
- Luke C. Bartelt
- University Program in Genetics & Genomics, Duke University Medical Center, Durham, NC 27710, USA
- Departments of Pathology & Laboratory Medicine, Neurology, Biological Chemistry, and Neurobiology & Behavior, University of California, Irvine; Irvine, CA 92697, USA
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Pawel M. Switonski
- Department of Medical Biotechnology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Grażyna Adamek
- Department of Medical Biotechnology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Juliana Carvalho
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Lisa A. Duvick
- Institute for Translational Neuroscience, and Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Sabrina I. Jarrah
- Department of Neurology, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Daniel R. Scoles
- Department of Neurology, University of Utah, Salt Lake City, UT 84132, USA
| | - Stefan M. Pulst
- Department of Neurology, University of Utah, Salt Lake City, UT 84132, USA
| | - Harry T. Orr
- Institute for Translational Neuroscience, and Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Court Hull
- Department of Neurobiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Craig B. Lowe
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Albert R. La Spada
- Departments of Pathology & Laboratory Medicine, Neurology, Biological Chemistry, and Neurobiology & Behavior, University of California, Irvine; Irvine, CA 92697, USA
- Department of Neurology, Duke University School of Medicine, Durham, NC 27710, USA
- UCI Center for Neurotherapeutics, University of California, Irvine; Irvine, CA 92697, USA
| |
Collapse
|
10
|
Oudart M, Avila-Gutierrez K, Moch C, Dossi E, Milior G, Boulay AC, Gaudey M, Moulard J, Lombard B, Loew D, Bemelmans AP, Rouach N, Chapat C, Cohen-Salmon M. The ribosome-associated protein RACK1 represses Kir4.1 translation in astrocytes and influences neuronal activity. Cell Rep 2023; 42:112456. [PMID: 37126448 DOI: 10.1016/j.celrep.2023.112456] [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: 07/07/2022] [Revised: 02/10/2023] [Accepted: 04/16/2023] [Indexed: 05/02/2023] Open
Abstract
The regulation of translation in astrocytes, the main glial cells in the brain, remains poorly characterized. We developed a high-throughput proteomics screen for polysome-associated proteins in astrocytes and focused on ribosomal protein receptor of activated protein C kinase 1 (RACK1), a critical factor in translational regulation. In astrocyte somata and perisynaptic astrocytic processes (PAPs), RACK1 preferentially binds to a number of mRNAs, including Kcnj10, encoding the inward-rectifying potassium (K+) channel Kir4.1. By developing an astrocyte-specific, conditional RACK1 knockout mouse model, we show that RACK1 represses production of Kir4.1 in hippocampal astrocytes and PAPs. Upregulation of Kir4.1 in the absence of RACK1 increases astrocytic Kir4.1-mediated K+ currents and volume. It also modifies neuronal activity attenuating burst frequency and duration. Reporter-based assays reveal that RACK1 controls Kcnj10 translation through the transcript's 5' untranslated region. Hence, translational regulation by RACK1 in astrocytes represses Kir4.1 expression and influences neuronal activity.
Collapse
Affiliation(s)
- Marc Oudart
- Center for Interdisciplinary Research in Biology, College de France, CNRS, INSERM, Université PSL, Labex Memolife, Paris, France
| | - Katia Avila-Gutierrez
- Center for Interdisciplinary Research in Biology, College de France, CNRS, INSERM, Université PSL, Labex Memolife, Paris, France
| | - Clara Moch
- Laboratoire de Biochimie, Ecole Polytechnique, CNRS, Université Paris-Saclay, Palaiseau, France
| | - Elena Dossi
- Center for Interdisciplinary Research in Biology, College de France, CNRS, INSERM, Université PSL, Labex Memolife, Paris, France
| | - Giampaolo Milior
- Center for Interdisciplinary Research in Biology, College de France, CNRS, INSERM, Université PSL, Labex Memolife, Paris, France
| | - Anne-Cécile Boulay
- Center for Interdisciplinary Research in Biology, College de France, CNRS, INSERM, Université PSL, Labex Memolife, Paris, France
| | - Mathis Gaudey
- Center for Interdisciplinary Research in Biology, College de France, CNRS, INSERM, Université PSL, Labex Memolife, Paris, France
| | - Julien Moulard
- Center for Interdisciplinary Research in Biology, College de France, CNRS, INSERM, Université PSL, Labex Memolife, Paris, France
| | - Bérangère Lombard
- CurieCoreTech Spectrométrie de Masse Protéomique, Institut Curie, University PSL, Paris, France
| | - Damarys Loew
- CurieCoreTech Spectrométrie de Masse Protéomique, Institut Curie, University PSL, Paris, France
| | - Alexis-Pierre Bemelmans
- CEA, Institut de Biologie François Jacob, Molecular Imaging Research Center (MIRCen), CNRS, Université Paris-Sud, Université Paris-Saclay, Fontenay-aux-Roses, France
| | - Nathalie Rouach
- Center for Interdisciplinary Research in Biology, College de France, CNRS, INSERM, Université PSL, Labex Memolife, Paris, France
| | - Clément Chapat
- Laboratoire de Biochimie, Ecole Polytechnique, CNRS, Université Paris-Saclay, Palaiseau, France
| | - Martine Cohen-Salmon
- Center for Interdisciplinary Research in Biology, College de France, CNRS, INSERM, Université PSL, Labex Memolife, Paris, France.
| |
Collapse
|
11
|
Bartsch D, Kalamkar K, Ahuja G, Lackmann JW, Hescheler J, Weber T, Bazzi H, Clamer M, Mendjan S, Papantonis A, Kurian L. mRNA translational specialization by RBPMS presets the competence for cardiac commitment in hESCs. SCIENCE ADVANCES 2023; 9:eade1792. [PMID: 36989351 PMCID: PMC10058251 DOI: 10.1126/sciadv.ade1792] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 02/01/2023] [Indexed: 06/19/2023]
Abstract
The blueprints of developing organs are preset at the early stages of embryogenesis. Transcriptional and epigenetic mechanisms are proposed to preset developmental trajectories. However, we reveal that the competence for the future cardiac fate of human embryonic stem cells (hESCs) is preset in pluripotency by a specialized mRNA translation circuit controlled by RBPMS. RBPMS is recruited to active ribosomes in hESCs to control the translation of essential factors needed for cardiac commitment program, including Wingless/Integrated (WNT) signaling. Consequently, RBPMS loss specifically and severely impedes cardiac mesoderm specification, leading to patterning and morphogenetic defects in human cardiac organoids. Mechanistically, RBPMS specializes mRNA translation, selectively via 3'UTR binding and globally by promoting translation initiation. Accordingly, RBPMS loss causes translation initiation defects highlighted by aberrant retention of the EIF3 complex and depletion of EIF5A from mRNAs, thereby abrogating ribosome recruitment. We demonstrate how future fate trajectories are programmed during embryogenesis by specialized mRNA translation.
Collapse
Affiliation(s)
- Deniz Bartsch
- Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine, University of Cologne, Cologne 50931, Germany
- Institute for Neurophysiology, Faculty of Medicine, University of Cologne, Cologne 50931, Germany
- Cologne Cluster of Excellence in Cellular Stress Responses in Ageing-associated Diseases (CECAD), University of Cologne, Cologne 50931, Germany
| | - Kaustubh Kalamkar
- Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine, University of Cologne, Cologne 50931, Germany
- Institute for Neurophysiology, Faculty of Medicine, University of Cologne, Cologne 50931, Germany
- Cologne Cluster of Excellence in Cellular Stress Responses in Ageing-associated Diseases (CECAD), University of Cologne, Cologne 50931, Germany
| | - Gaurav Ahuja
- Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine, University of Cologne, Cologne 50931, Germany
- Institute for Neurophysiology, Faculty of Medicine, University of Cologne, Cologne 50931, Germany
- Cologne Cluster of Excellence in Cellular Stress Responses in Ageing-associated Diseases (CECAD), University of Cologne, Cologne 50931, Germany
| | - Jan-Wilm Lackmann
- Cologne Cluster of Excellence in Cellular Stress Responses in Ageing-associated Diseases (CECAD), University of Cologne, Cologne 50931, Germany
| | - Jürgen Hescheler
- Institute for Neurophysiology, Faculty of Medicine, University of Cologne, Cologne 50931, Germany
| | - Timm Weber
- Laboratory of Experimental Immunology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne 50931, Germany
| | - Hisham Bazzi
- Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine, University of Cologne, Cologne 50931, Germany
- Cologne Cluster of Excellence in Cellular Stress Responses in Ageing-associated Diseases (CECAD), University of Cologne, Cologne 50931, Germany
- Department of Dermatology and Venereology, Medical Faculty, University of Cologne, Cologne 50931, Germany
| | | | - Sasha Mendjan
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter, Dr. Bohr Gasse 3, Vienna 1030, Austria
| | - Argyris Papantonis
- Institute of Pathology, University Medical Center Göttingen, Göttingen 37075, Germany
| | - Leo Kurian
- Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine, University of Cologne, Cologne 50931, Germany
- Institute for Neurophysiology, Faculty of Medicine, University of Cologne, Cologne 50931, Germany
- Cologne Cluster of Excellence in Cellular Stress Responses in Ageing-associated Diseases (CECAD), University of Cologne, Cologne 50931, Germany
| |
Collapse
|
12
|
Gala DS, Titlow JS, Teodoro RO, Davis I. Far from home: the role of glial mRNA localization in synaptic plasticity. RNA (NEW YORK, N.Y.) 2023; 29:153-169. [PMID: 36442969 PMCID: PMC9891262 DOI: 10.1261/rna.079422.122] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Neurons and glia are highly polarized cells, whose distal cytoplasmic functional subdomains require specific proteins. Neurons have axonal and dendritic cytoplasmic extensions containing synapses whose plasticity is regulated efficiently by mRNA transport and localized translation. The principles behind these mechanisms are equally attractive for explaining rapid local regulation of distal glial cytoplasmic projections, independent of their cell nucleus. However, in contrast to neurons, mRNA localization has received little experimental attention in glia. Nevertheless, there are many functionally diverse glial subtypes containing extensive networks of long cytoplasmic projections with likely localized regulation that influence neurons and their synapses. Moreover, glia have many other neuron-like properties, including electrical activity, secretion of gliotransmitters and calcium signaling, influencing, for example, synaptic transmission, plasticity and axon pruning. Here, we review previous studies concerning glial transcripts with important roles in influencing synaptic plasticity, focusing on a few cases involving localized translation. We discuss a variety of important questions about mRNA transport and localized translation in glia that remain to be addressed, using cutting-edge tools already available for neurons.
Collapse
Affiliation(s)
- Dalia S Gala
- Department of Biochemistry, The University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Joshua S Titlow
- Department of Biochemistry, The University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Rita O Teodoro
- iNOVA4Health, NOVA Medical School-Faculdade de Ciências Médicas, Universidade Nova de Lisboa, Lisboa 1169-056, Portugal
| | - Ilan Davis
- Department of Biochemistry, The University of Oxford, Oxford OX1 3QU, United Kingdom
| |
Collapse
|
13
|
Nishanth MJ, Jha S. Genome-wide landscape of RNA-binding protein (RBP) networks as potential molecular regulators of psychiatric co-morbidities: a computational analysis. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2023. [DOI: 10.1186/s43042-022-00382-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Abstract
Background
Psychiatric disorders are a major burden on global health. These illnesses manifest as co-morbid conditions, further complicating the treatment. There is a limited understanding of the molecular and regulatory basis of psychiatric co-morbidities. The existing research in this regard has largely focused on epigenetic modulators, non-coding RNAs, and transcription factors. RNA-binding proteins (RBPs) functioning as multi-protein complexes are now known to be predominant controllers of multiple gene regulatory processes. However, their involvement in gene expression dysregulation in psychiatric co-morbidities is yet to be understood.
Results
Ten RBPs (QKI, ELAVL2, EIF2S1, SRSF3, IGF2BP2, EIF4B, SNRNP70, FMR1, DAZAP1, and MBNL1) were identified to be associated with psychiatric disorders such as schizophrenia, major depression, and bipolar disorders. Analysis of transcriptomic changes in response to individual depletion of these RBPs showed the potential influence of a large number of RBPs driving differential gene expression, suggesting functional cross-talk giving rise to multi-protein networks. Subsequent transcriptome analysis of post-mortem human brain samples from diseased and control individuals also suggested the involvement of ~ 100 RBPs influencing gene expression changes. These RBPs were found to regulate various processes including transcript splicing, mRNA transport, localization, stability, and translation. They were also found to form an extensive interactive network. Further, hnRNP, SRSF, and PCBP family RBPs, Matrin3, U2AF2, KHDRBS1, PTBP1, and also PABPN1 were found to be the hub proteins of the RBP network.
Conclusions
Extensive RBP networks involving a few hub proteins could result in transcriptome-wide dysregulation of post-transcriptional modifications, potentially driving multiple psychiatric disorders. Understanding the functional involvement of RBP networks in psychiatric disorders would provide insights into the molecular basis of psychiatric co-morbidities.
Collapse
|
14
|
Borgenheimer E, Hamel K, Sheeler C, Moncada FL, Sbrocco K, Zhang Y, Cvetanovic M. Single nuclei RNA sequencing investigation of the Purkinje cell and glial changes in the cerebellum of transgenic Spinocerebellar ataxia type 1 mice. Front Cell Neurosci 2022; 16:998408. [PMID: 36457352 PMCID: PMC9706545 DOI: 10.3389/fncel.2022.998408] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 10/27/2022] [Indexed: 11/16/2022] Open
Abstract
Glial cells constitute half the population of the human brain and are essential for normal brain function. Most, if not all, brain diseases are characterized by reactive gliosis, a process by which glial cells respond and contribute to neuronal pathology. Spinocerebellar ataxia type 1 (SCA1) is a progressive neurodegenerative disease characterized by a severe degeneration of cerebellar Purkinje cells (PCs) and cerebellar gliosis. SCA1 is caused by an abnormal expansion of CAG repeats in the gene Ataxin1 (ATXN1). While several studies reported the effects of mutant ATXN1 in Purkinje cells, it remains unclear how cerebellar glia respond to dysfunctional Purkinje cells in SCA1. To address this question, we performed single nuclei RNA sequencing (snRNA seq) on cerebella of early stage Pcp2-ATXN1[82Q] mice, a transgenic SCA1 mouse model expressing mutant ATXN1 only in Purkinje cells. We found no changes in neuronal and glial proportions in the SCA1 cerebellum at this early disease stage compared to wild-type controls. Importantly, we observed profound non-cell autonomous and potentially neuroprotective reactive gene and pathway alterations in Bergmann glia, velate astrocytes, and oligodendrocytes in response to Purkinje cell dysfunction.
Collapse
|
15
|
Emerging Roles of RNA-Binding Proteins in Neurodevelopment. J Dev Biol 2022; 10:jdb10020023. [PMID: 35735914 PMCID: PMC9224834 DOI: 10.3390/jdb10020023] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/02/2022] [Accepted: 06/08/2022] [Indexed: 02/06/2023] Open
Abstract
Diverse cell types in the central nervous system (CNS) are generated by a relatively small pool of neural stem cells during early development. Spatial and temporal regulation of stem cell behavior relies on precise coordination of gene expression. Well-studied mechanisms include hormone signaling, transcription factor activity, and chromatin remodeling processes. Much less is known about downstream RNA-dependent mechanisms including posttranscriptional regulation, nuclear export, alternative splicing, and transcript stability. These important functions are carried out by RNA-binding proteins (RBPs). Recent work has begun to explore how RBPs contribute to stem cell function and homeostasis, including their role in metabolism, transport, epigenetic regulation, and turnover of target transcripts. Additional layers of complexity are provided by the different target recognition mechanisms of each RBP as well as the posttranslational modifications of the RBPs themselves that alter function. Altogether, these functions allow RBPs to influence various aspects of RNA metabolism to regulate numerous cellular processes. Here we compile advances in RNA biology that have added to our still limited understanding of the role of RBPs in neurodevelopment.
Collapse
|
16
|
A Proposed Role for Interactions between Argonautes, miRISC, and RNA Binding Proteins in the Regulation of Local Translation in Neurons and Glia. J Neurosci 2022; 42:3291-3301. [PMID: 35444007 PMCID: PMC9034781 DOI: 10.1523/jneurosci.2391-21.2022] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 03/04/2022] [Accepted: 03/08/2022] [Indexed: 11/21/2022] Open
Abstract
The first evidence of local translation in the CNS appeared nearly 40 years ago, when electron microscopic studies showed polyribosomes localized to the base of dendritic spines. Since then, local translation has been established as an important regulatory mechanism for gene expression in polarized or functionally compartmentalized cells. While much attention has been placed on characterizing the local transcriptome and regulatory "grammar" directing mRNA localization in neurons and glia, less is understood about how these cells subsequently de-repress mRNA translation in their peripheral processes to produce a rapid translational response to stimuli. MicroRNA-mediated translation regulation offers a possible solution to this question. Not only do miRNAs provide the specificity needed for targeted gene regulation, but association and dynamic interactions between Argonaute (AGO) with sequence-specific RNA-binding proteins may provide a molecular switch to allow for de-repression of target mRNAs. Here, we review the expression and activity of different AGO proteins in miRNA-induced silencing complexes in neurons and glia and discuss known pathways of miRNA-mediated regulation, including activity-dependent pre-miRNA maturation in dendrites. We further detail work on AGO and RNA-binding protein interactions that allow for the reversal of miRNA-mediated translational silencing, and we propose a model for how intercellular communication may play a role in the regulation of local translation.
Collapse
|
17
|
Salamon I, Rasin MR. Evolution of the Neocortex Through RNA-Binding Proteins and Post-transcriptional Regulation. Front Neurosci 2022; 15:803107. [PMID: 35082597 PMCID: PMC8784817 DOI: 10.3389/fnins.2021.803107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 12/16/2021] [Indexed: 12/24/2022] Open
Abstract
The human neocortex is undoubtedly considered a supreme accomplishment in mammalian evolution. It features a prenatally established six-layered structure which remains plastic to the myriad of changes throughout an organism’s lifetime. A fundamental feature of neocortical evolution and development is the abundance and diversity of the progenitor cell population and their neuronal and glial progeny. These evolutionary upgrades are partially enabled due to the progenitors’ higher proliferative capacity, compartmentalization of proliferative regions, and specification of neuronal temporal identities. The driving force of these processes may be explained by temporal molecular patterning, by which progenitors have intrinsic capacity to change their competence as neocortical neurogenesis proceeds. Thus, neurogenesis can be conceptualized along two timescales of progenitors’ capacity to (1) self-renew or differentiate into basal progenitors (BPs) or neurons or (2) specify their fate into distinct neuronal and glial subtypes which participate in the formation of six-layers. Neocortical development then proceeds through sequential phases of proliferation, differentiation, neuronal migration, and maturation. Temporal molecular patterning, therefore, relies on the precise regulation of spatiotemporal gene expression. An extensive transcriptional regulatory network is accompanied by post-transcriptional regulation that is frequently mediated by the regulatory interplay between RNA-binding proteins (RBPs). RBPs exhibit important roles in every step of mRNA life cycle in any system, from splicing, polyadenylation, editing, transport, stability, localization, to translation (protein synthesis). Here, we underscore the importance of RBP functions at multiple time-restricted steps of early neurogenesis, starting from the cell fate transition of transcriptionally primed cortical progenitors. A particular emphasis will be placed on RBPs with mostly conserved but also divergent evolutionary functions in neural progenitors across different species. RBPs, when considered in the context of the fascinating process of neocortical development, deserve to be main protagonists in the story of the evolution and development of the neocortex.
Collapse
|
18
|
Neumann DP, Goodall GJ, Gregory PA. The Quaking RNA-binding proteins as regulators of cell differentiation. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1724. [PMID: 35298877 PMCID: PMC9786888 DOI: 10.1002/wrna.1724] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/18/2022] [Accepted: 02/21/2022] [Indexed: 12/30/2022]
Abstract
The RNA-binding protein Quaking (QKI) has emerged as a potent regulator of cellular differentiation in developmental and pathological processes. The QKI gene is itself alternatively spliced to produce three major isoforms, QKI-5, QKI-6, and QKI-7, that possess very distinct functions. Here, we highlight roles of the different QKI isoforms in neuronal, vascular, muscle, and monocyte cell differentiation, and during epithelial-mesenchymal transition in cancer progression. QKI isoforms control cell differentiation through regulating alternative splicing, mRNA stability and translation, with activities in gene transcription now also becoming evident. These diverse functions of the QKI isoforms contribute to their broad influences on RNA metabolism and cellular differentiation. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA Processing > Splicing Regulation/Alternative Splicing RNA in Disease and Development > RNA in Development.
Collapse
Affiliation(s)
- Daniel P. Neumann
- Centre for Cancer BiologyUniversity of South Australia and SA PathologyAdelaideSouth Australia
| | - Gregory J. Goodall
- Centre for Cancer BiologyUniversity of South Australia and SA PathologyAdelaideSouth Australia,Faculty of Health and Medical SciencesThe University of AdelaideAdelaideSouth Australia
| | - Philip A. Gregory
- Centre for Cancer BiologyUniversity of South Australia and SA PathologyAdelaideSouth Australia,Faculty of Health and Medical SciencesThe University of AdelaideAdelaideSouth Australia
| |
Collapse
|