1
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Solovev YV, Evpak AS, Kudriaeva AA, Gabibov AG, Belogurov AA. Evaluation of Clinically Significant miRNAs Level by Machine Learning Approaches Utilizing Total Transcriptome Data. DOKL BIOCHEM BIOPHYS 2024; 516:98-106. [PMID: 38539010 DOI: 10.1134/s1607672924700790] [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] [Received: 12/28/2023] [Revised: 01/25/2024] [Accepted: 02/03/2024] [Indexed: 05/26/2024]
Abstract
Analysis of the mechanisms underlying the occurrence and progression of cancer represents a key objective in contemporary clinical bioinformatics and molecular biology. Utilizing omics data, particularly transcriptomes, enables a detailed characterization of expression patterns and post-transcriptional regulation across various RNA types relative to the entire transcriptome. Here, we assembled a dataset comprising transcriptomic data from approximately 16 000 patients encompassing over 160 types of cancer. We employed state-of-the-art gradient boosting algorithms to discern intricate correlations in the expression levels of four clinically significant microRNAs, specifically, hsa-mir-21, hsa-let-7a-1, hsa-let-7b, and hsa-let-7i, with the expression levels of the remaining 60 660 unique RNAs. Our analysis revealed a dependence of the expression levels of the studied microRNAs on the concentrations of several small nucleolar RNAs and regulatory long noncoding RNAs. Notably, the roles of these RNAs in the development of specific cancer types had been previously established through experimental evidence. Subsequent evaluation of the created database will facilitate the identification of a broader spectrum of overarching dependencies related to changes in the expression levels of various RNA classes in diverse cancers. In future, it will make possible to discover unique alterations specific to certain types of malignant transformations.
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Affiliation(s)
- Ya V Solovev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.
| | - A S Evpak
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.
| | - A A Kudriaeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - A G Gabibov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Moscow State University, Moscow, Russia
| | - A A Belogurov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Moscow State University of Medicine and Dentistry, 127473, Moscow, Russia
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2
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Agabekian IA, Abdulkina LR, Lushnenko AY, Young PG, Valeeva LR, Boskovic O, Lilly EG, Sharipova MR, Shippen DE, Juenger TE, Shakirov EV. Arabidopsis AN3 and OLIGOCELLULA genes link telomere maintenance mechanisms with cell division and expansion control. PLANT MOLECULAR BIOLOGY 2024; 114:65. [PMID: 38816532 DOI: 10.1007/s11103-024-01457-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 04/23/2024] [Indexed: 06/01/2024]
Abstract
Telomeres are conserved chromosomal structures necessary for continued cell division and proliferation. In addition to the classical telomerase pathway, multiple other genes including those involved in ribosome metabolism and chromatin modification contribute to telomere length maintenance. We previously reported that Arabidopsis thaliana ribosome biogenesis genes OLI2/NOP2A, OLI5/RPL5A and OLI7/RPL5B have critical roles in telomere length regulation. These three OLIGOCELLULA genes were also shown to function in cell proliferation and expansion control and to genetically interact with the transcriptional co-activator ANGUSTIFOLIA3 (AN3). Here we show that AN3-deficient plants progressively lose telomeric DNA in early homozygous mutant generations, but ultimately establish a new shorter telomere length setpoint by the fifth mutant generation with a telomere length similar to oli2/nop2a -deficient plants. Analysis of double an3 oli2 mutants indicates that the two genes are epistatic for telomere length control. Telomere shortening in an3 and oli mutants is not caused by telomerase inhibition; wild type levels of telomerase activity are detected in all analyzed mutants in vitro. Late generations of an3 and oli mutants are prone to stem cell damage in the root apical meristem, implying that genes regulating telomere length may have conserved functional roles in stem cell maintenance mechanisms. Multiple instances of anaphase fusions in late generations of oli5 and oli7 mutants were observed, highlighting an unexpected effect of ribosome biogenesis factors on chromosome integrity. Overall, our data implicate AN3 transcription coactivator and OLIGOCELLULA proteins in the establishment of telomere length set point in plants and further suggest that multiple regulators with pleiotropic functions can connect telomere biology with cell proliferation and cell expansion pathways.
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Affiliation(s)
- Inna A Agabekian
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Republic of Tatarstan, Kazan, 420008, Russia
| | - Liliia R Abdulkina
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Republic of Tatarstan, Kazan, 420008, Russia
| | - Alina Y Lushnenko
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Republic of Tatarstan, Kazan, 420008, Russia
| | - Pierce G Young
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, Texas, 77843-2128, USA
| | - Lia R Valeeva
- Department of Biological Sciences, College of Science, Marshall University, Huntington, West Virginia, 25701, USA
| | - Olivia Boskovic
- Department of Biological Sciences, College of Science, Marshall University, Huntington, West Virginia, 25701, USA
| | - Ethan G Lilly
- Department of Biological Sciences, College of Science, Marshall University, Huntington, West Virginia, 25701, USA
| | - Margarita R Sharipova
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Republic of Tatarstan, Kazan, 420008, Russia
| | - Dorothy E Shippen
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, Texas, 77843-2128, USA.
| | - Thomas E Juenger
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas, 78712, USA.
| | - Eugene V Shakirov
- Department of Biological Sciences, College of Science, Marshall University, Huntington, West Virginia, 25701, USA.
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, West Virginia, 25755, USA.
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3
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Surya A, Bolton BM, Rothe R, Mejia-Trujillo R, Zhao Q, Leonita A, Liu Y, Rangan R, Gorusu Y, Nguyen P, Cenik C, Cenik ES. Cytosolic Ribosomal Protein Haploinsufficiency affects Mitochondrial Morphology and Respiration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.16.589775. [PMID: 38659761 PMCID: PMC11042305 DOI: 10.1101/2024.04.16.589775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
The interplay between ribosomal protein composition and mitochondrial function is essential for sustaining energy homeostasis. Precise stoichiometric production of ribosomal proteins is crucial to maximize protein synthesis efficiency while reducing the energy costs to the cell. However, the impact of this balance on mitochondrial ATP generation, morphology and function remains unclear. Particularly, the loss of a single copy ribosomal protein gene is observed in Mendelian disorders like Diamond Blackfan Anemia and is common in somatic tumors, yet the implications of this imbalance on mitochondrial function and energy dynamics are still unclear. In this study, we investigated the impact of haploinsufficiency for four ribosomal protein genes implicated in ribosomopathy disorders (rps-10, rpl-5, rpl-33, rps-23) in Caenorhabditis elegans and corresponding reductions in human lymphoblast cells. Our findings uncover significant, albeit variably penetrant, mitochondrial morphological differences across these mutants, alongside an upregulation of glutathione transferases, and SKN-1 dependent increase in oxidative stress resistance, indicative of increased ROS production. Specifically, loss of a single copy of rps-10 in C. elegans led to decreased mitochondrial activity, characterized by lower energy levels and reduced oxygen consumption. A similar reduction in mitochondrial activity and energy levels was observed in human leukemia cells with a 50% reduction in RPS10 transcript levels. Importantly, we also observed alterations in the translation efficiency of nuclear and mitochondrial electron transport chain components in response to reductions in ribosomal protein genes' expression in both C. elegans and human cells. This suggests a conserved mechanism whereby the synthesis of components vital for mitochondrial function are adjusted in the face of compromised ribosomal machinery. Finally, mitochondrial membrane and cytosolic ribosomal components exhibited significant covariation at the RNA and translation efficiency level in lymphoblastoid cells across a diverse group of individuals, emphasizing the interplay between the protein synthesis machinery and mitochondrial energy production. By uncovering the impact of ribosomal protein haploinsufficiency on the translation efficiency of electron transport chain components, mitochondrial physiology, and the adaptive stress responses, we provide evidence for an evolutionarily conserved strategy to safeguard cellular functionality under genetic stress.
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Affiliation(s)
- Agustian Surya
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Blythe Marie Bolton
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Reed Rothe
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Raquel Mejia-Trujillo
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Qiuxia Zhao
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Amanda Leonita
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Yue Liu
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Rekha Rangan
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Yasash Gorusu
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Pamela Nguyen
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Can Cenik
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Elif Sarinay Cenik
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
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4
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Gelfo V, Venturi G, Zacchini F, Montanaro L. Decoding Ribosome Heterogeneity: A New Horizon in Cancer Therapy. Biomedicines 2024; 12:155. [PMID: 38255260 PMCID: PMC10813612 DOI: 10.3390/biomedicines12010155] [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: 12/19/2023] [Revised: 01/05/2024] [Accepted: 01/08/2024] [Indexed: 01/24/2024] Open
Abstract
The traditional perception of ribosomes as uniform molecular machines has been revolutionized by recent discoveries, revealing a complex landscape of ribosomal heterogeneity. Opposing the conventional belief in interchangeable ribosomal entities, emerging studies underscore the existence of specialized ribosomes, each possessing unique compositions and functions. Factors such as cellular and tissue specificity, developmental and physiological states, and external stimuli, including circadian rhythms, significantly influence ribosome compositions. For instance, muscle cells and neurons are characterized by distinct ribosomal protein sets and dynamic behaviors, respectively. Furthermore, alternative forms of ribosomal RNA (rRNAs) and their post-transcriptional modifications add another dimension to this heterogeneity. These variations, orchestrated by spatial, temporal, and conditional factors, enable the manifestation of a broad spectrum of specialized ribosomes, each tailored for potentially distinct functions. Such specialization not only impacts mRNA translation and gene expression but also holds significant implications for broader biological contexts, notably in the realm of cancer research. As the understanding of ribosomal diversity deepens, it also paves the way for exploring novel avenues in cellular function and offers a fresh perspective on the molecular intricacies of translation.
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Affiliation(s)
- Valerio Gelfo
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy; (V.G.); (G.V.)
- Centre for Applied Biomedical Research (CRBA), Bologna University Hospital Authority St. Orsola-Malpighi Polyclinic, 40138 Bologna, Italy
| | - Giulia Venturi
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy; (V.G.); (G.V.)
- Centre for Applied Biomedical Research (CRBA), Bologna University Hospital Authority St. Orsola-Malpighi Polyclinic, 40138 Bologna, Italy
| | - Federico Zacchini
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy;
| | - Lorenzo Montanaro
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy; (V.G.); (G.V.)
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy;
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5
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Gaikani HK, Stolar M, Kriti D, Nislow C, Giaever G. From beer to breadboards: yeast as a force for biological innovation. Genome Biol 2024; 25:10. [PMID: 38178179 PMCID: PMC10768129 DOI: 10.1186/s13059-023-03156-9] [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: 02/14/2023] [Accepted: 12/21/2023] [Indexed: 01/06/2024] Open
Abstract
The history of yeast Saccharomyces cerevisiae, aka brewer's or baker's yeast, is intertwined with our own. Initially domesticated 8,000 years ago to provide sustenance to our ancestors, for the past 150 years, yeast has served as a model research subject and a platform for technology. In this review, we highlight many ways in which yeast has served to catalyze the fields of functional genomics, genome editing, gene-environment interaction investigation, proteomics, and bioinformatics-emphasizing how yeast has served as a catalyst for innovation. Several possible futures for this model organism in synthetic biology, drug personalization, and multi-omics research are also presented.
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Affiliation(s)
- Hamid Kian Gaikani
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
- Department of Chemistry, University of British Columbia, Vancouver, BC, Canada
| | - Monika Stolar
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Divya Kriti
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Corey Nislow
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada.
| | - Guri Giaever
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
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6
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Sherwood DR, Kenny-Ganzert IW, Balachandar Thendral S. Translational regulation of cell invasion through extracellular matrix-an emerging role for ribosomes. F1000Res 2023; 12:1528. [PMID: 38628976 PMCID: PMC11019292 DOI: 10.12688/f1000research.143519.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/22/2023] [Indexed: 04/19/2024] Open
Abstract
Many developmental and physiological processes require cells to invade and migrate through extracellular matrix barriers. This specialized cellular behavior is also misregulated in many diseases, such as immune disorders and cancer. Cell invasive activity is driven by pro-invasive transcriptional networks that activate the expression of genes encoding numerous different proteins that expand and regulate the cytoskeleton, endomembrane system, cell adhesion, signaling pathways, and metabolic networks. While detailed mechanistic studies have uncovered crucial insights into pro-invasive transcriptional networks and the distinct cell biological attributes of invasive cells, less is known about how invasive cells modulate mRNA translation to meet the robust, dynamic, and unique protein production needs of cell invasion. In this review we outline known modes of translation regulation promoting cell invasion and focus on recent studies revealing elegant mechanisms that expand ribosome biogenesis within invasive cells to meet the increased protein production requirements to invade and migrate through extracellular matrix barriers.
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7
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Clark IC, Fontanez KM, Meltzer RH, Xue Y, Hayford C, May-Zhang A, D'Amato C, Osman A, Zhang JQ, Hettige P, Ishibashi JSA, Delley CL, Weisgerber DW, Replogle JM, Jost M, Phong KT, Kennedy VE, Peretz CAC, Kim EA, Song S, Karlon W, Weissman JS, Smith CC, Gartner ZJ, Abate AR. Microfluidics-free single-cell genomics with templated emulsification. Nat Biotechnol 2023; 41:1557-1566. [PMID: 36879006 PMCID: PMC10635830 DOI: 10.1038/s41587-023-01685-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 01/20/2023] [Indexed: 03/08/2023]
Abstract
Current single-cell RNA-sequencing approaches have limitations that stem from the microfluidic devices or fluid handling steps required for sample processing. We develop a method that does not require specialized microfluidic devices, expertise or hardware. Our approach is based on particle-templated emulsification, which allows single-cell encapsulation and barcoding of cDNA in uniform droplet emulsions with only a vortexer. Particle-templated instant partition sequencing (PIP-seq) accommodates a wide range of emulsification formats, including microwell plates and large-volume conical tubes, enabling thousands of samples or millions of cells to be processed in minutes. We demonstrate that PIP-seq produces high-purity transcriptomes in mouse-human mixing studies, is compatible with multiomics measurements and can accurately characterize cell types in human breast tissue compared to a commercial microfluidic platform. Single-cell transcriptional profiling of mixed phenotype acute leukemia using PIP-seq reveals the emergence of heterogeneity within chemotherapy-resistant cell subsets that were hidden by standard immunophenotyping. PIP-seq is a simple, flexible and scalable next-generation workflow that extends single-cell sequencing to new applications.
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Affiliation(s)
- Iain C Clark
- Department of Bioengineering, University of California, Berkeley, California Institute for Quantitative Biosciences, Berkeley, CA, USA
| | | | | | - Yi Xue
- Fluent Biosciences, Watertown, MA, USA
| | | | | | | | | | | | | | | | - Cyrille L Delley
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Daniel W Weisgerber
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Joseph M Replogle
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Marco Jost
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Kiet T Phong
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Vanessa E Kennedy
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Cheryl A C Peretz
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Esther A Kim
- Division of Plastic and Reconstructive Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Siyou Song
- Division of Plastic and Reconstructive Surgery, University of California San Francisco, San Francisco, CA, USA
| | - William Karlon
- Departments of Pathology and Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Jonathan S Weissman
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Catherine C Smith
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Zev J Gartner
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Adam R Abate
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.
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8
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Lu Y, Wang S, Jiao Y. The Effects of Deregulated Ribosomal Biogenesis in Cancer. Biomolecules 2023; 13:1593. [PMID: 38002277 PMCID: PMC10669593 DOI: 10.3390/biom13111593] [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] [Received: 09/13/2023] [Revised: 10/04/2023] [Accepted: 10/22/2023] [Indexed: 11/26/2023] Open
Abstract
Ribosomes are macromolecular ribonucleoprotein complexes assembled from RNA and proteins. Functional ribosomes arise from the nucleolus, require ribosomal RNA processing and the coordinated assembly of ribosomal proteins (RPs), and are frequently hyperactivated to support the requirement for protein synthesis during the self-biosynthetic and metabolic activities of cancer cells. Studies have provided relevant information on targeted anticancer molecules involved in ribosome biogenesis (RiBi), as increased RiBi is characteristic of many types of cancer. The association between unlimited cell proliferation and alterations in specific steps of RiBi has been highlighted as a possible critical driver of tumorigenesis and metastasis. Thus, alterations in numerous regulators and actors involved in RiBi, particularly in cancer, significantly affect the rate and quality of protein synthesis and, ultimately, the transcriptome to generate the associated proteome. Alterations in RiBi in cancer cells activate nucleolar stress response-related pathways that play important roles in cancer-targeted interventions and immunotherapies. In this review, we focus on the association between alterations in RiBi and cancer. Emphasis is placed on RiBi deregulation and its secondary consequences, including changes in protein synthesis, loss of RPs, adaptive transcription and translation, nucleolar stress regulation, metabolic changes, and the impaired ribosome biogenesis checkpoint.
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Affiliation(s)
| | - Shizhuo Wang
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang 110055, China;
| | - Yisheng Jiao
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang 110055, China;
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9
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Agabekian IA, Abdulkina LR, Lushnenko AY, Young PG, Valeeva LR, Boskovic O, Lilly EG, Sharipova MR, Shippen DE, Juenger TE, Shakirov EV. Arabidopsis AN3 and OLIGOCELLULA genes link telomere maintenance mechanisms with cell division and expansion control. RESEARCH SQUARE 2023:rs.3.rs-3438810. [PMID: 37961382 PMCID: PMC10635316 DOI: 10.21203/rs.3.rs-3438810/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Telomeres are conserved chromosomal structures necessary for continued cell division and proliferation. In addition to the classical telomerase pathway, multiple other genes including those involved in ribosome metabolism and chromatin modification contribute to telomere length maintenance. We previously reported that Arabidopsis thaliana ribosome biogenesis genes OLI2/NOP2A, OLI5/RPL5A and OLI7/RPL5B have critical roles in telomere length regulation. These three OLIGOCELLULA genes were also shown to function in cell proliferation and expansion control and to genetically interact with the transcriptional co-activator ANGUSTIFOLIA3 (AN3). Here we show that AN3-deficient plants progressively lose telomeric DNA in early homozygous mutant generations, but ultimately establish a new shorter telomere length setpoint by the fifth mutant generation with a telomere length similar to oli2/nop2a - deficient plants. Analysis of double an3 oli2 mutants indicates that the two genes are epistatic for telomere length control. Telomere shortening in an3 and oli mutants is not caused by telomerase inhibition; wild type levels of telomerase activity are detected in all analyzed mutants in vitro. Late generations of an3 and oli mutants are prone to stem cell damage in the root apical meristem, implying that genes regulating telomere length may have conserved functional roles in stem cell maintenance mechanisms. Multiple instances of anaphase fusions in late generations of oli5 and oli7 mutants were observed, highlighting an unexpected effect of ribosome biogenesis factors on chromosome integrity. Overall, our data implicate AN3 transcription coactivator and OLIGOCELLULA proteins in the establishment of telomere length set point in plants and further suggest that multiple regulators with pleiotropic functions can connect telomere biology with cell proliferation and cell expansion pathways.
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Affiliation(s)
- Inna A Agabekian
- Kazan Federal University: Kazanskij Privolzskij federal'nyj universitet
| | | | - Alina Y Lushnenko
- Kazan Federal University: Kazanskij Privolzskij federal'nyj universitet
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10
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Valeeva LR, Abdulkina LR, Agabekian IA, Shakirov EV. Telomere biology and ribosome biogenesis: structural and functional interconnections. Biochem Cell Biol 2023; 101:394-409. [PMID: 36989538 DOI: 10.1139/bcb-2022-0383] [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] [Indexed: 03/31/2023] Open
Abstract
Telomeres are nucleoprotein structures that play a pivotal role in the protection and maintenance of eukaryotic chromosomes. Telomeres and the enzyme telomerase, which replenishes telomeric DNA lost during replication, are important factors necessary to ensure continued cell proliferation. Cell proliferation is also dependent on proper and efficient protein synthesis, which is carried out by ribosomes. Mutations in genes involved in either ribosome biogenesis or telomere biology result in cellular abnormalities and can cause human genetic diseases, defined as ribosomopathies and telomeropathies, respectively. Interestingly, recent discoveries indicate that many of the ribosome assembly and rRNA maturation factors have additional noncanonical functions in telomere biology. Similarly, several key proteins and enzymes involved in telomere biology, including telomerase, have unexpected roles in rRNA transcription and maturation. These observations point to an intriguing cross-talk mechanism potentially explaining the multiple pleiotropic symptoms of mutations in many causal genes identified in various telomeropathy and ribosomopathy diseases. In this review, we provide a brief summary of eukaryotic telomere and rDNA loci structures, highlight several universal features of rRNA and telomerase biogenesis, evaluate intriguing interconnections between telomere biology and ribosome assembly, and conclude with an assessment of overlapping features of human diseases of telomeropathies and ribosomopathies.
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Affiliation(s)
- Liia R Valeeva
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420008, Republic of Tatarstan, Russia
- Department of Biological Sciences, College of Science, Marshall University, Huntington, WV 25701, USA
| | - Liliia R Abdulkina
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420008, Republic of Tatarstan, Russia
| | - Inna A Agabekian
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan 420008, Republic of Tatarstan, Russia
| | - Eugene V Shakirov
- Department of Biological Sciences, College of Science, Marshall University, Huntington, WV 25701, USA
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, Huntington, WV 25755, USA
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11
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Eastham M, Pelava A, Wells G, Lee J, Lawrence I, Stewart J, Deichner M, Hertle R, Watkins N, Schneider C. The induction of p53 correlates with defects in the production, but not the levels, of the small ribosomal subunit and stalled large ribosomal subunit biogenesis. Nucleic Acids Res 2023; 51:9397-9414. [PMID: 37526268 PMCID: PMC10516649 DOI: 10.1093/nar/gkad637] [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: 12/20/2022] [Revised: 07/12/2023] [Accepted: 07/20/2023] [Indexed: 08/02/2023] Open
Abstract
Ribosome biogenesis is one of the biggest consumers of cellular energy. More than 20 genetic diseases (ribosomopathies) and multiple cancers arise from defects in the production of the 40S (SSU) and 60S (LSU) ribosomal subunits. Defects in the production of either the SSU or LSU result in p53 induction through the accumulation of the 5S RNP, an LSU assembly intermediate. While the mechanism is understood for the LSU, it is still unclear how SSU production defects induce p53 through the 5S RNP since the production of the two subunits is believed to be uncoupled. Here, we examined the response to SSU production defects to understand how this leads to the activation of p53 via the 5S RNP. We found that p53 activation occurs rapidly after SSU production is blocked, prior to changes in mature ribosomal RNA (rRNA) levels but correlated with early, middle and late SSU pre-rRNA processing defects. Furthermore, both nucleolar/nuclear LSU maturation, in particular late stages in 5.8S rRNA processing, and pre-LSU export were affected by SSU production defects. We have therefore uncovered a novel connection between the SSU and LSU production pathways in human cells, which explains how p53 is induced in response to SSU production defects.
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Affiliation(s)
- Matthew John Eastham
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Andria Pelava
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Graeme Raymond Wells
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Justine Katherine Lee
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Isabella Rachel Lawrence
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Joshua Stewart
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Maria Deichner
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Regina Hertle
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Nicholas James Watkins
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Claudia Schneider
- Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
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12
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Quddusi DM, Bajcinca N. Identification of genomic biomarkers and their pathway crosstalks for deciphering mechanistic links in glioblastoma. IET Syst Biol 2023; 17:143-161. [PMID: 37277696 PMCID: PMC10439498 DOI: 10.1049/syb2.12066] [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] [Received: 08/21/2022] [Revised: 04/22/2023] [Accepted: 05/03/2023] [Indexed: 06/07/2023] Open
Abstract
Glioblastoma is a grade IV pernicious neoplasm occurring in the supratentorial region of brain. As its causes are largely unknown, it is essential to understand its dynamics at the molecular level. This necessitates the identification of better diagnostic and prognostic molecular candidates. Blood-based liquid biopsies are emerging as a novel tool for cancer biomarker discovery, guiding the treatment and improving its early detection based on their tumour origin. There exist previous studies focusing on the identification of tumour-based biomarkers for glioblastoma. However, these biomarkers inadequately represent the underlying pathological state and incompletely illustrate the tumour because of non-recursive nature of this approach to monitor the disease. Also, contrary to the tumour biopsies, liquid biopsies are non-invasive and can be performed at any interval during the disease span to surveil the disease. Therefore, in this study, a unique dataset of blood-based liquid biopsies obtained primarily from tumour-educated blood platelets (TEP) is utilised. This RNA-seq data from ArrayExpress is acquired comprising human cohort with 39 glioblastoma subjects and 43 healthy subjects. Canonical and machine learning approaches are applied for identification of the genomic biomarkers for glioblastoma and their crosstalks. In our study, 97 genes appeared enriched in 7 oncogenic pathways (RAF-MAPK, P53, PRC2-EZH2, YAP conserved, MEK-MAPK, ErbB2 and STK33 signalling pathways) using GSEA, out of which 17 have been identified participating actively in crosstalks. Using PCA, 42 genes are found enriched in 7 pathways (cytoplasmic ribosomal proteins, translation factors, electron transport chain, ribosome, Huntington's disease, primary immunodeficiency pathways, and interferon type I signalling pathway) harbouring tumour when altered, out of which 25 actively participate in crosstalks. All the 14 pathways foster well-known cancer hallmarks and the identified DEGs can serve as genomic biomarkers, not only for the diagnosis and prognosis of Glioblastoma but also in providing a molecular foothold for oncogenic decision making in order to fathom the disease dynamics. Moreover, SNP analysis for the identified DEGs is performed to investigate their roles in disease dynamics in an elaborated manner. These results suggest that TEPs are capable of providing disease insights just like tumour cells with an advantage of being extracted anytime during the course of disease in order to monitor it.
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Affiliation(s)
- Darrak Moin Quddusi
- Chair of Mechatronics in the Faculty of Mechanical and Process EngineeringRheinland‐Pfälzische Technische Universität Kaiserslautern‐LandauKaiserslauternGermany
| | - Naim Bajcinca
- Chair of Mechatronics in the Faculty of Mechanical and Process EngineeringRheinland‐Pfälzische Technische Universität Kaiserslautern‐LandauKaiserslauternGermany
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13
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Ochkasova A, Arbuzov G, Malygin A, Graifer D. Two "Edges" in Our Knowledge on the Functions of Ribosomal Proteins: The Revealed Contributions of Their Regions to Translation Mechanisms and the Issues of Their Extracellular Transport by Exosomes. Int J Mol Sci 2023; 24:11458. [PMID: 37511213 PMCID: PMC10380927 DOI: 10.3390/ijms241411458] [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: 06/23/2023] [Revised: 07/10/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023] Open
Abstract
Ribosomal proteins (RPs), the constituents of the ribosome, belong to the most abundant proteins in the cell. A highly coordinated network of interactions implicating RPs and ribosomal RNAs (rRNAs) forms the functionally competent structure of the ribosome, enabling it to perform translation, the synthesis of polypeptide chain on the messenger RNA (mRNA) template. Several RPs contact ribosomal ligands, namely, those with transfer RNAs (tRNAs), mRNA or translation factors in the course of translation, and the contribution of a number of these particular contacts to the translation process has recently been established. Many ribosomal proteins also have various extra-ribosomal functions unrelated to translation. The least-understood and -discussed functions of RPs are those related to their participation in the intercellular communication via extracellular vesicles including exosomes, etc., which often carry RPs as passengers. Recently reported data show that such a kind of communication can reprogram a receptor cell and change its phenotype, which is associated with cancer progression and metastasis. Here, we review the state-of-art ideas on the implications of specific amino acid residues of RPs in the particular stages of the translation process in higher eukaryotes and currently available data on the transport of RPs by extracellular vesicles and its biological effects.
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Affiliation(s)
- Anastasia Ochkasova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Grigory Arbuzov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Alexey Malygin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Dmitri Graifer
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
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14
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Montiel-Dávalos A, Ayala Y, Hernández G. The dark side of mRNA translation and the translation machinery in glioblastoma. Front Cell Dev Biol 2023; 11:1086964. [PMID: 36994107 PMCID: PMC10042294 DOI: 10.3389/fcell.2023.1086964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 03/03/2023] [Indexed: 03/14/2023] Open
Abstract
Among the different types of cancer affecting the central nervous system (CNS), glioblastoma (GB) is classified by the World Health Organization (WHO) as the most common and aggressive CNS cancer in adults. GB incidence is more frequent among persons aged 45–55 years old. GB treatments are based on tumor resection, radiation, and chemotherapies. The current development of novel molecular biomarkers (MB) has led to a more accurate prediction of GB progression. Moreover, clinical, epidemiological, and experimental studies have established genetic variants consistently associated with the risk of suffering GB. However, despite the advances in these fields, the survival expectancy of GB patients is still shorter than 2 years. Thus, fundamental processes inducing tumor onset and progression remain to be elucidated. In recent years, mRNA translation has been in the spotlight, as its dysregulation is emerging as a key cause of GB. In particular, the initiation phase of translation is most involved in this process. Among the crucial events, the machinery performing this phase undergoes a reconfiguration under the hypoxic conditions in the tumor microenvironment. In addition, ribosomal proteins (RPs) have been reported to play translation-independent roles in GB development. This review focuses on the research elucidating the tight relationship between translation initiation, the translation machinery, and GB. We also summarize the state-of-the-art drugs targeting the translation machinery to improve patients’ survival. Overall, the recent advances in this field are shedding new light on the dark side of translation in GB.
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15
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Wu W, Wang J, Jiang Y, Hu X, Tian Y, Chen L, Sun H, Li Y, Liu S, Lv Y, Guo J, Xu H, Xing D, Zhai Y, Tian L, Li C, He X, Luo K, Pan Y, Zhao Z. Prognostic Significance of Ribosome-related Genes Signature in Diffuse Large B Cell Lymphoma. J Cancer 2023; 14:403-416. [PMID: 36860924 PMCID: PMC9969582 DOI: 10.7150/jca.80926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 01/17/2023] [Indexed: 02/04/2023] Open
Abstract
Background: The diffuse large B-cell lymphoma (DLBCL) is a heterogeneous lymphoma with a dismal outcome, due to approximately 40% patients will be relapsed or refractory to the standard therapy of rituximab plus cyclophosphamide, doxorubicin, vincristine and prednisone (R-CHOP). Therefore, we need urgently to explore the approach to classify the risk of DLBCL patients accurately and accurately targeting therapy. The ribosome is a vital cellular organelle that is mainly responsible for translation mRNA into protein, moreover, more and more reports revealed that ribosome was associated with cellular proliferation and tumorigenesis. Therefore, our study aimed to construct a prognostic model of DLBCL patients using ribosome-related genes (RibGs). Method: We screened differentially expressed RibGs between healthy donors' B cells and DLBCL patients' malignant B cells in GSE56315 dataset. Next, we performed analyses of univariate Cox regression, the least absolute shrinkage and selection operator (LASSO) regression and multivariate Cox regression analyses to establish the prognostic model consisting of 15 RibGs in GSE10846 training set. Then, we validated the model by a range of analyses including Cox regression, Kaplan-Meier survival, ROC curve, and nomogram in training and validation cohorts. Results: The RibGs model showed a reliably predictive capability. We found the upregulated pathways in high-risk group most associated with innate immune reaction such as interferon response, complement and inflammatory responses. In addition, a nomogram including age, gender, IPI score and risk score was constructed to help explain the prognostic model. We also discovered the high-risk patients were more sensitive to some certain drugs. Finally, knocking out the NLE1 could inhibit the proliferation of DLBCL cell lines. Conclusion: As far as we know, it is the first time to predict the prognosis of DLBCL using the RibGs and give a new sight for DLBCL treatment. Importantly, the RibGs model could be acted as a supplementary to the IPI in classifying the risk of DLBCL patients.
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Affiliation(s)
- Wenqi Wu
- Department of Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Jinhuan Wang
- Department of Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Yanan Jiang
- Department of Medical Oncology, Tianjin First Central Hospital, School of Medicine. Nankai University, Tianjin, 300192, China
| | - Xin Hu
- Department of Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Ye Tian
- Department of Senior Ward, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Long Chen
- Tianjin Sino-US Diagnostics, Tianjin, 300380, China
| | - Huimeng Sun
- Department of Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Yuhang Li
- Department of Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Su Liu
- Department of Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Yangyang Lv
- Department of Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Jing Guo
- Department of Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Hong Xu
- Department of Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Donghui Xing
- Department of Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Yixin Zhai
- Department of Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Linyan Tian
- Department of Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Cheng Li
- Department of Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Xiang He
- Department of Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Kaiping Luo
- Department of Oncology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China
| | - Yuan Pan
- Department of Senior Ward, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin, 300060, China,✉ Corresponding authors: Zhigang Zhao, ; Yuan Pan,
| | - Zhigang Zhao
- Department of Medical Oncology, Tianjin First Central Hospital, School of Medicine. Nankai University, Tianjin, 300192, China,✉ Corresponding authors: Zhigang Zhao, ; Yuan Pan,
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16
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Zhang W, Liu B, Wu S, Zhao L. TMT-based comprehensive proteomic profiling identifies serum prognostic signatures of acute myeloid leukemia. Open Med (Wars) 2023; 18:20220602. [PMID: 37016705 PMCID: PMC10066874 DOI: 10.1515/med-2022-0602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 09/19/2022] [Accepted: 10/16/2022] [Indexed: 04/06/2023] Open
Abstract
Acute myeloid leukemia (AML) is classified into favorable-risk, intermediate-risk, and poor-risk subtypes. This study aimed to compare the serum proteomic signatures of the three AML subtypes and identify prognostic biomarkers for AML. Serum samples from patients with favorable-risk (n = 14), intermediate-risk (n = 19), and poor-risk AMLs (n = 18) were used for the analysis of tandem mass tag (TMT) labeling-based quantitative proteomics. Comparative analysis was performed to identify differentially expressed proteins (DEPs) between groups. Prognostic proteins were screened using binary logistics regression analysis. TMT-MS/MS proteomics analysis identified 138 DEPs. Fumarate hydratase (FH), isocitrate dehydrogenase 2 (IDH2), and enolase 1 (ENO1) were significantly upregulated in poor-risk patients compared with favorable-risk patients. ELISA assay confirmed that patients with poor-risk AMLs had higher levels of IDH2, ENO1, and FH compared with intermediate-risk AML patients. Logistics analysis identified that proteins 3-hydroxyacyl-CoA dehydrogenase type-2 (HADH, odds ratio (OR) = 1.035, p = 0.010), glutamine synthetase (GLUL, OR = 1.022, p = 0.039), and lactotransferrin (LTF, OR = 1.1224, p = 0.016) were associated with poor prognosis, and proteins ENO1 (OR = 1.154, p = 0.053), FH (OR = 1.043, p = 0.059), and IDH2 (OR = 3.350, p = 0.055) were associated with AML prognosis. This study showed that AML patients had elevated levels of FH, IDH2, ENO1, LTF, and GLUL proteins and might be at high risk of poor prognosis.
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Affiliation(s)
- Wei Zhang
- Department of Central Laboratory, The First Hospital of Lanzhou University, Lanzhou 730000, Gansu Province, China
| | - Bei Liu
- Department of Hematology, The First Hospital of Lanzhou University, Lanzhou 730000, China
| | - Shiwen Wu
- Department of Laboratory Medicine, The First Hospital of Lanzhou University, Lanzhou 730000, China
| | - Li Zhao
- Department of Central Laboratory, The First Hospital of Lanzhou University, #1 Donggang West Road, Lanzhou 730000, Gansu Province, China
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17
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Standing S, Tran S, Murguia-Favela L, Kovalchuk O, Bose P, Narendran A. Identification of Altered Primary Immunodeficiency-Associated Genes and Their Implications in Pediatric Cancers. Cancers (Basel) 2022; 14:cancers14235942. [PMID: 36497424 PMCID: PMC9741011 DOI: 10.3390/cancers14235942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 11/25/2022] [Accepted: 11/28/2022] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Cancer is the leading cause of disease-related mortality in children and malignancies are more frequently observed in individuals with primary immunodeficiencies (PIDs). This study aimed to identify and highlight the molecular mechanisms, such as oncogenesis and immune evasion, by which PID-related genes may lead to the development of pediatric cancers. METHOD We implemented a novel bioinformatics framework using patient data from the TARGET database and performed a comparative transcriptome analysis of PID-related genes in pediatric cancers between normal and cancer tissues, gene ontology enrichment, and protein-protein interaction analyses, and determined the prognostic impacts of commonly mutated and differentially expressed PID-related genes. RESULTS From the Fulgent Genetics Comprehensive Primary Immunodeficiency panel of 472 PID-related genes, 89 genes were significantly differentially expressed between normal and cancer tissues, and 20 genes were mutated in two or more patients. Enrichment analysis highlighted many immune system processes as well as additional pathways in the mutated PID-related genes related to oncogenesis. Survival outcomes for patients with altered PID-related genes were significantly different for 75 of the 89 DEGs, often resulting in a poorer prognosis. CONCLUSIONS Overall, multiple PID-related genes demonstrated the connection between PIDs and cancer development and should be studied further, with hopes of identifying new therapeutic targets.
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Affiliation(s)
- Shaelene Standing
- Section of Pediatric Oncology and Blood and Marrow Transplantation, Division of Pediatrics, Alberta Children’s Hospital and University of Calgary, Calgary, AB T3B 6A8, Canada
| | - Son Tran
- Section of Pediatric Oncology and Blood and Marrow Transplantation, Division of Pediatrics, Alberta Children’s Hospital and University of Calgary, Calgary, AB T3B 6A8, Canada
| | - Luis Murguia-Favela
- Section of Pediatric Hematology and Immunology, Division of Pediatrics, Alberta Children’s Hospital and University of Calgary, Calgary, AB T3B 6A8, Canada
| | - Olga Kovalchuk
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
| | - Pinaki Bose
- Departments of Oncology, Biochemistry and Molecular Biology, University of Calgary, Calgary, AB T2N 1N4, Canada
- Correspondence: (P.B.); (A.N.)
| | - Aru Narendran
- Section of Pediatric Oncology and Blood and Marrow Transplantation, Division of Pediatrics, Alberta Children’s Hospital and University of Calgary, Calgary, AB T3B 6A8, Canada
- Correspondence: (P.B.); (A.N.)
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18
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Ilott NE, Neyazi M, Arancibia-Cárcamo CV, Powrie F, Geremia A. Tissue-dependent transcriptional and bacterial associations in primary sclerosing cholangitis-associated inflammatory bowel disease. Wellcome Open Res 2022; 6:199. [DOI: 10.12688/wellcomeopenres.16901.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/21/2022] [Indexed: 11/06/2022] Open
Abstract
Background: Patients with primary sclerosing cholangitis (PSC) frequently have co-ocurring ulcerative colitis (UC) and develop colorectal cancer. Colorectal cancer risk in patients with PSC-associated ulcerative colitis (PSC/UC) is elevated relative to patients with ulcerative colitis (UC) alone, reasons for which remain obscure. Understanding the molecular and microbial basis for differences between these two patient groups and how these vary across intestinal sites is important for the development of therapies to prevent colorectal cancer development in at-risk individuals. Methods: We employed ribonucleic acid sequencing (RNA-seq) analysis of biopsy samples across three intestinal tissue locations (ileum, caecum and rectum) in patients with PSC/UC (ileum n = 7, caecum n = 7, rectum n = 7), UC (ileum n = 9, caecum n = 10, rectum n = 10) and healthy controls (ileum n = 11, caecum n = 9, rectum n = 12) to determine tissue-dependent transcriptional alterations in PSC/UC. We also performed 16S ribosomal RNA (rRNA) amplicon sequencing to determine bacterial associations with PSC/UC. Results: Tissue-defining transcriptional signatures revealed that the ileum was enriched for genes involved in lipid and drug metabolism, the caecum for activated immune cells and the rectum for enteric neurogenesis. Transcriptional alterations relative to healthy control samples were largely shared between patients with PSC/UC or UC although were distinct across tissue locations. Nevertheless, we observed reduced expression of gamma-glutamyl transferase 1 (GGT1) specifically in the ileum and caecum of patients with PSC/UC. Analysis of the bacterial component of the microbiome revealed high inter-individual variability of microbiome composition and little evidence for tissue-dependency. We observed a reduction in Parabacteroides relative abundance in the rectum of patients with PSC/UC. Conclusions: The role of gamma-glutamyl transferase in maintaining the redox environment through the glutathione salvage pathway makes our observed alterations a potential pathway to PSC-associated colorectal cancer.
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Hannan KM, Soo P, Wong MS, Lee JK, Hein N, Poh P, Wysoke KD, Williams TD, Montellese C, Smith LK, Al-Obaidi SJ, Núñez-Villacís L, Pavy M, He JS, Parsons KM, Loring KE, Morrison T, Diesch J, Burgio G, Ferreira R, Feng ZP, Gould CM, Madhamshettiwar PB, Flygare J, Gonda TJ, Simpson KJ, Kutay U, Pearson RB, Engel C, Watkins NJ, Hannan RD, George AJ. Nuclear stabilization of p53 requires a functional nucleolar surveillance pathway. Cell Rep 2022; 41:111571. [DOI: 10.1016/j.celrep.2022.111571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/06/2022] [Accepted: 10/06/2022] [Indexed: 11/06/2022] Open
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20
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Lüchtenborg AM, Metzger P, Cosenza Contreras M, Oria V, Biniossek ML, Lindner F, Fröhlich K, Malyi A, Erbes T, Gensch N, Maurer J, Thomsen A, Boerries M, Schilling O, Werner M, Bronsert P. Krüppel-like factor 7 influences translation and pathways involved in ribosomal biogenesis in breast cancer. BREAST CANCER RESEARCH : BCR 2022; 24:65. [PMID: 36192788 PMCID: PMC9531505 DOI: 10.1186/s13058-022-01562-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 09/19/2022] [Indexed: 11/27/2022]
Abstract
Background Ribosomal biogenesis and ribosomal proteins have attracted attention in the context of tumor biology in recent years. Instead of being mere translational machineries, ribosomes might play an active role in tumor initiation and progression. Despite its importance, regulation of ribosomal biogenesis is still not completely understood.
Methods Using Gene Set Enrichment Analysis of RNA sequencing and proteomical mass spectrometry data in breast cancer cells expressing Krüppel-like factor 7 (KLF7), we identified processes altered by this transcription factor. In silico analyses of a cohort of breast cancer patients in The Cancer Genome Atlas confirmed our finding. We further verified the role of KLF7 the identified ribosomal processes in in vitro assays of mammary carcinoma cell lines and analyses of breast cancer patients’ tissue slices.
Results We identified the transcription factor Krüppel-like factor 7 (KLF7) as a regulator of ribosomal biogenesis and translation in breast cancer cells and tissue. Highly significant overlapping processes related to ribosomal biogenesis were identified in proteomics and transcriptomics data and confirmed in patients’ breast cancer RNA Seq data. Further, nucleoli, the sites of ribosomal biogenesis, were morphologically altered and quantitatively increased in KLF7-expressing cells. Pre-rRNA processing was identified as one potential process affected by KLF7. In addition, an increase in global translation independent from proliferation and transcription was observed upon exogenous KLF7 expression in vitro. Importantly, in a cohort of breast cancer patients, KLF7-expression levels correlated with aggressiveness of the intrinsic breast cancer subtype and tumor grading. Moreover, KLF7 correlated with nucleolar characteristics in human breast tumor tissue, indicating a role for KLF7 in ribosomal biogenesis. Conclusion In mammary carcinoma, KLF7 is involved in ribosomal biogenesis. Alterations of ribosomal biogenesis has far reaching quantitative and qualitative implications for the proteome of the cancer cells. This might influence the aggressiveness of cancer cells. Supplementary Information The online version contains supplementary material available at 10.1186/s13058-022-01562-8.
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Affiliation(s)
- Anne-Marie Lüchtenborg
- Institute for Surgical Pathology, Medical Center - University of Freiburg, Breisacher Straße 115A, 79106, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany.,German Cancer Consortium (DKTK) Partner Site Freiburg and Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Patrick Metzger
- Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Institute of Medical Bioinformatics and Systems Medicine, Medical Center - University of Freiburg, Freiburg, Germany.,Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Miguel Cosenza Contreras
- Institute for Surgical Pathology, Medical Center - University of Freiburg, Breisacher Straße 115A, 79106, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Victor Oria
- Faculty of Biology, University of Freiburg, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine, Faculty of Biology, University of Freiburg, Freiburg, Germany.,Biotech Research and Innovation Center (BRIC), University of Copenhagen, Copenhagen, Denmark
| | - Martin L Biniossek
- Institute of Molecular Medicine and Cell Research, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Franziska Lindner
- Institute for Surgical Pathology, Medical Center - University of Freiburg, Breisacher Straße 115A, 79106, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Klemens Fröhlich
- Institute for Surgical Pathology, Medical Center - University of Freiburg, Breisacher Straße 115A, 79106, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany.,Faculty of Biology, University of Freiburg, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Ambrus Malyi
- 2Nd Department of Pathology, Semmelweis University, Budapest, Hungary
| | - Thalia Erbes
- Department of Obstetrics and Gynecology, Medical Center - University of Freiburg, Freiburg, Germany
| | - Nicole Gensch
- Core Facility Signaling Factory, BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany
| | - Jochen Maurer
- Department of Obstetrics and Gynecology, University Hospital Aachen (UKA), Aachen, Germany
| | - Andreas Thomsen
- Department of Radiation Oncology, Medical Center - University of Freiburg, Freiburg, Germany
| | - Melanie Boerries
- Faculty of Medicine, University of Freiburg, Freiburg, Germany.,German Cancer Consortium (DKTK) Partner Site Freiburg and Cancer Research Center (DKFZ), Heidelberg, Germany.,Institute of Medical Bioinformatics and Systems Medicine, Medical Center - University of Freiburg, Freiburg, Germany
| | - Oliver Schilling
- Institute for Surgical Pathology, Medical Center - University of Freiburg, Breisacher Straße 115A, 79106, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany.,German Cancer Consortium (DKTK) Partner Site Freiburg and Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martin Werner
- Institute for Surgical Pathology, Medical Center - University of Freiburg, Breisacher Straße 115A, 79106, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany.,German Cancer Consortium (DKTK) Partner Site Freiburg and Cancer Research Center (DKFZ), Heidelberg, Germany.,Tumorbank Comprehensive Cancer Center Freiburg, Medical Center - University of Freiburg, Freiburg, Germany.,Core Facility for Histopathology and Digital Pathology, Medical Center - University of Freiburg, Freiburg, Germany
| | - Peter Bronsert
- Institute for Surgical Pathology, Medical Center - University of Freiburg, Breisacher Straße 115A, 79106, Freiburg, Germany. .,Faculty of Medicine, University of Freiburg, Freiburg, Germany. .,German Cancer Consortium (DKTK) Partner Site Freiburg and Cancer Research Center (DKFZ), Heidelberg, Germany. .,Core Facility for Histopathology and Digital Pathology, Medical Center - University of Freiburg, Freiburg, Germany.
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21
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Li P, Shi Y, Guo M, Xu H, Zhan M, Wang Z, Chen Y. MAFG-AS1 is a prognostic biomarker and facilitates prostate cancer progression. Front Oncol 2022; 12:856580. [PMID: 35992831 PMCID: PMC9389335 DOI: 10.3389/fonc.2022.856580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 07/08/2022] [Indexed: 12/02/2022] Open
Abstract
Long Noncoding RNAs (LncRNAs) have recently been identified as key regulator in tumor progression. The LncRNA MAFG-AS1 has been reported to facilitate the progression of multiple cancers, however, its role in prostate cancer is still unknown. Here, we reported that MAFG-AS1 was upregulated in prostate cancer. Importantly, high expression of MAFG-AS1 indicated advanced stage prostate cancer. Univariate and Multivariate Cox regression analyses showed that high MAFG-AS1 expression was independently correlated with poor progression-free interval (PFI). According to the result of The Cancer Genome Atlas (TCGA) database and tissue microarray, high MAFG-AS1 expression indicated a poor prognosis in prostate cancer patients. In addition, gene functional enrichment analysis revealed that MAFG-AS1 may be involved in ribosome biogenesis, ribonucleoprotein complex subunit organization, ribonucleoprotein complex assembly, rRNA metabolic process, structural constituent of ribosome, and ribonucleoprotein complex binding. Furthermore, MAFG-AS1 knockdown by siRNA markedly impaired prostate cancer cell proliferation, migration, and invasion.
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Affiliation(s)
- Peizhang Li
- Department of Urology, Shanghai Ninth People’s Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yuanping Shi
- Department of Endocrinology and Metabolism, Peking University People's Hospital, Beijing, China
| | - Miaomiao Guo
- The Core Laboratory in Medical Center of Clinical Research, Department of Molecular Diagnostics and Endocrinology, Shanghai Ninth People’s Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
- Department of Molecular Diagnostics, Shanghai Ninth People’s Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Huan Xu
- Department of Urology, Shanghai Ninth People’s Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Ming Zhan
- Department of Urology, Shanghai Ninth People’s Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Zhong Wang
- Department of Urology, Shanghai Ninth People’s Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
- *Correspondence: Yanbo Chen, ; Zhong Wang,
| | - Yanbo Chen
- Department of Urology, Shanghai Ninth People’s Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, China
- *Correspondence: Yanbo Chen, ; Zhong Wang,
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22
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Knockdown of Lamin B1 and the Corresponding Lamin B Receptor Leads to Changes in Heterochromatin State and Senescence Induction in Malignant Melanoma. Cells 2022; 11:cells11142154. [PMID: 35883595 PMCID: PMC9321645 DOI: 10.3390/cells11142154] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/02/2022] [Accepted: 07/05/2022] [Indexed: 11/17/2022] Open
Abstract
Modifications in nuclear structures of cells are implicated in several diseases including cancer. They result in changes in nuclear activity, structural dynamics and cell signalling. However, the role of the nuclear lamina and related proteins in malignant melanoma is still unknown. Its molecular characterisation might lead to a deeper understanding and the development of new therapy approaches. In this study, we analysed the functional effects of dysregulated nuclear lamin B1 (LMNB1) and its nuclear receptor (LBR). According to their cellular localisation and function, we revealed that these genes are crucially involved in nuclear processes like chromatin organisation. RNA sequencing and differential gene expression analysis after knockdown of LMNB1 and LBR revealed their implication in important cellular processes driving ER stress leading to senescence and changes in chromatin state, which were also experimentally validated. We determined that melanoma cells need both molecules independently to prevent senescence. Hence, downregulation of both molecules in a BRAFV600E melanocytic senescence model as well as in etoposide-treated melanoma cells indicates both as potential senescence markers in melanoma. Our findings suggest that LMNB1 and LBR influence senescence and affect nuclear processes like chromatin condensation and thus are functionally relevant for melanoma progression.
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23
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Ribosomes and Ribosomal Proteins Promote Plasticity and Stemness Induction in Glioma Cells via Reprogramming. Cells 2022; 11:cells11142142. [PMID: 35883585 PMCID: PMC9323835 DOI: 10.3390/cells11142142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 07/01/2022] [Accepted: 07/05/2022] [Indexed: 02/04/2023] Open
Abstract
Glioblastoma multiforme (GBM) is a lethal tumor that develops in the adult brain. Despite advances in therapeutic strategies related to surgical resection and chemo-radiotherapy, the overall survival of patients with GBM remains unsatisfactory. Genetic research on mutation, amplification, and deletion in GBM cells is important for understanding the biological aggressiveness, diagnosis, and prognosis of GBM. However, the efficacy of drugs targeting the genetic abnormalities in GBM cells is limited. Investigating special microenvironments that induce chemo-radioresistance in GBM cells is critical to improving the survival and quality of life of patients with GBM. GBM cells acquire and maintain stem-cell-like characteristics via their intrinsic potential and extrinsic factors from their special microenvironments. The acquisition of stem-cell-like phenotypes and aggressiveness may be referred to as a reprogramming of GBM cells. In addition to protein synthesis, deregulation of ribosome biogenesis is linked to several diseases including cancer. Ribosomal proteins possess both tumor-promotive and -suppressive functions as extra-ribosomal functions. Incorporation of ribosomes and overexpression of ribosomal protein S6 reprogram and induce stem-cell-like phenotypes in GBM cells. Herein, we review recent literature and our published data on the acquisition of aggressiveness by GBM and discuss therapeutic options through reprogramming.
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24
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The Transcriptional Landscape of BRAF Wild Type Metastatic Melanoma: A Pilot Study. Int J Mol Sci 2022; 23:ijms23136898. [PMID: 35805902 PMCID: PMC9266837 DOI: 10.3390/ijms23136898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 06/13/2022] [Accepted: 06/17/2022] [Indexed: 11/18/2022] Open
Abstract
Melanoma is a relatively rare disease worldwide; nevertheless, it has a great relevance in some countries, such as in Europe. In order to shed some light upon the transcriptional profile of skin melanoma, we compared the gene expression of six independent tumours (all progressed towards metastatic disease and with wild type BRAF) to the expression profile of non-dysplastic melanocytes (considered as a healthy control) in a pilot study. Paraffin-embedded samples were manually micro-dissected to obtain enriched samples, and then, RNA was extracted and analysed through a microarray-based approach. An exhaustive bioinformatics analysis was performed to identify differentially expressed transcripts between the two groups, as well as enriched functional terms. Overall, 50 up- and 19 downregulated transcripts were found to be significantly changed in the tumour compared to the control tissue. Among the upregulated transcripts, the majority belonged to the immune response group and to the proteasome, while most of the downregulated genes were related to cytosolic ribosomes. A Gene Set Enrichment Analysis (GSEA), along with the RNA-Seq data retrieved from the TCGA/GTEx databases, confirmed the general trend of downregulation affecting cytoribosome proteins. In contrast, transcripts coding for mitoribosome proteins showed the opposite trend.
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25
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Wang G, Lin X, Han H, Zhang H, Li X, Feng M, Jiang C. lncRNA H19 promotes glioblastoma multiforme development by activating autophagy by sponging miR-491-5p. Bioengineered 2022; 13:11440-11455. [PMID: 35506168 PMCID: PMC9275997 DOI: 10.1080/21655979.2022.2065947] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Glioblastoma multiforme (GBM) is a malignant cancer with severely poor survival, and the cells continue to thrive during hypoxia and toxic stress through autophagy. To validate the oncogenic role of long noncoding RNA H19 in GBM progression and examine whether autophagy and/or miR-491-5p participate in the process. The expression of H19 and autophagy-related genes in GBM and healthy control tissues was assessed via quantitative polymerase chain reaction. In addition, cell viability, proliferation, apoptosis and autophagy were respectively determined via cell counting kit-8 assay, clone formation assay, flow cytometry, western blotting and green fluorescent protein–microtubule-associated protein 1 light chain 3 alpha fluorescence analysis in vitro. Furthermore, a rescue assay was performed using rapamycin or miR-491-5p antagomir to examine the role of autophagy or miR-491-5p in H19-mediated regulation of proliferation and apoptosis. RNA pull-down and dual-luciferase reporter assays were employed to analyze the interaction between H19 and miR-491-5p. Additionally, tumor growth in a xenograft-bearing mouse model and autophagy in tumor mass were analyzed in vivo. The expression H19 was increased in GBM and was positively correlated with LC3 or Beclin-1. Silencing H19 inhibited growth and promoted apoptosis in GBM cells both in vitro and in vivo, and miR-491-5p was identified as one of the important mediators. H19 regulated the autophagy signaling pathway at least partly via miR-491-5p. Increased H19 expression in GBM exerts oncogenic effects by sponging miR-491-5p and enhancing autophagy. Therefore, H19 may be explored as a target for GBM therapy.
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Affiliation(s)
- Guo Wang
- Department of Pediatrics, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou Zhejiang, P.R. China.,Department of Pediatrics, Affiliated Hangzhou Hospital of Nanjing Medical University, Hangzhou First People's Hospital, Hangzhou Zhejiang, P.R. China
| | - Xiaoyan Lin
- Department of Pediatrics, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou Zhejiang, P.R. China.,Department of Pediatrics, Affiliated Hangzhou Hospital of Nanjing Medical University, Hangzhou First People's Hospital, Hangzhou Zhejiang, P.R. China
| | - Han Han
- Department of Pediatrics, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou Zhejiang, P.R. China.,Department of Pediatrics, Affiliated Hangzhou Hospital of Nanjing Medical University, Hangzhou First People's Hospital, Hangzhou Zhejiang, P.R. China
| | - Hongxu Zhang
- Department of Ophthalmology, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou Zhejiang, P.R. China.,Department of Ophthalmology, Affiliated Hangzhou Hospital of Nanjing Medical University, Hangzhou First People's Hospital, Hangzhou Zhejiang, P.R. China
| | - Xiaoli Li
- Department of Pediatrics, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou Zhejiang, P.R. China.,Department of Pediatrics, Affiliated Hangzhou Hospital of Nanjing Medical University, Hangzhou First People's Hospital, Hangzhou Zhejiang, P.R. China
| | - Mei Feng
- Department of Pediatrics, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou Zhejiang, P.R. China.,Department of Pediatrics, Affiliated Hangzhou Hospital of Nanjing Medical University, Hangzhou First People's Hospital, Hangzhou Zhejiang, P.R. China
| | - Chunming Jiang
- Department of Pediatrics, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou Zhejiang, P.R. China.,Department of Pediatrics, Affiliated Hangzhou Hospital of Nanjing Medical University, Hangzhou First People's Hospital, Hangzhou Zhejiang, P.R. China
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26
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Piao XM, Kim YU, Byun YJ, Zheng CM, Moon SM, Kim K, Lee HY, Jeong P, Kang HW, Kim WT, Lee SC, Kim WJ, Yun SJ. Expression of RPL9 predicts the recurrence of non-muscle invasive bladder cancer with BCG therapy. Urol Oncol 2022; 40:197.e1-197.e9. [PMID: 35382986 DOI: 10.1016/j.urolonc.2021.12.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/09/2021] [Accepted: 12/14/2021] [Indexed: 01/01/2023]
Abstract
Numerous biomarkers and risk tables can be used to predict recurrence or progression of patients with primary or recurrent non-muscle invasive bladder cancer (NMIBC) receiving Bacillus Calmette-Guerin (BCG). However, few are suitable for BCG-unresponsive disease (i.e., recurrence or progression after BCG treatment). Therefore, identification of a novel marker that allows accurate prediction of prognosis, particularly risk of recurrence, is critically important in clinical practice. In the current study, gene ontology and gene set enrichment analyses of microarray datasets (GSE13507, n = 47) revealed that differentially expressed genes in recurred NMIBC patients after BCG treatment were associated with virus and ribosomal pathways. Among the core-enrichment genes, the expression of RPL9, a putative tumor suppressor, was lower in recurred NMIBC patients after BCG therapy than in patients without recurrence (P = 0.033) from the E-MTAT-4321 European cohort (n = 84). Data from The Cancer Genome Atlas (n = 406) showed that bladder cancer patients with higher RPL9 expression had a longer overall survival probability than patients with lower RPL9 expression (P = 0.011). Moreover, we used the latest digital PCR platform to examine 59 NMIBC patients and identified downregulation of RPL9 in patients with recurrence after BCG therapy (P = 0.031). The Kaplan-Meier survival estimator showed that NMIBC patients with higher expression of RPL9 had longer recurrence-free survival (log-rank test, P = 0.015). Therefore, we conclude that RPL9 expression is a prospective predictor of recurrence after BCG therapy in NMIBC patients.
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Affiliation(s)
- Xuan-Mei Piao
- Department of Urology, College of Medicine, Chungbuk National University, Cheongju, 28644, South Korea
| | - Yeong Uk Kim
- Department of Urology, College of medicine, Yeungnam University, Daegu, 42415, Korea
| | - Young Joon Byun
- Department of Urology, College of Medicine, Chungbuk National University, Cheongju, 28644, South Korea
| | - Chuang-Ming Zheng
- Department of Urology, College of Medicine, Chungbuk National University, Cheongju, 28644, South Korea
| | - Sung Min Moon
- Department of Urology, Chungbuk National University Hospital, Cheongju, 28644, South Korea
| | - Kyeong Kim
- Department of Urology, Chungbuk National University Hospital, Cheongju, 28644, South Korea
| | - Hee Youn Lee
- Department of Urology, Chungbuk National University Hospital, Cheongju, 28644, South Korea
| | | | - Ho Won Kang
- Department of Urology, College of Medicine, Chungbuk National University, Cheongju, 28644, South Korea; Department of Urology, Chungbuk National University Hospital, Cheongju, 28644, South Korea
| | - Won Tae Kim
- Department of Urology, College of Medicine, Chungbuk National University, Cheongju, 28644, South Korea; Department of Urology, Chungbuk National University Hospital, Cheongju, 28644, South Korea
| | - Sang-Cheol Lee
- Department of Urology, College of Medicine, Chungbuk National University, Cheongju, 28644, South Korea; Department of Urology, Chungbuk National University Hospital, Cheongju, 28644, South Korea
| | - Wun-Jae Kim
- Department of Urology, College of Medicine, Chungbuk National University, Cheongju, 28644, South Korea; Institute of Urotech, Cheongju 28120, Korea
| | - Seok Joong Yun
- Department of Urology, College of Medicine, Chungbuk National University, Cheongju, 28644, South Korea; Department of Urology, Chungbuk National University Hospital, Cheongju, 28644, South Korea.
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27
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p53 at the crossroad of DNA replication and ribosome biogenesis stress pathways. Cell Death Differ 2022; 29:972-982. [PMID: 35444234 PMCID: PMC9090812 DOI: 10.1038/s41418-022-00999-w] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/28/2022] [Accepted: 03/30/2022] [Indexed: 01/05/2023] Open
Abstract
Despite several decades of intense research focused on understanding function(s) and disease-associated malfunction of p53, there is no sign of any “mid-life crisis” in this rapidly advancing area of biomedicine. Firmly established as the hub of cellular stress responses and tumor suppressor targeted in most malignancies, p53’s many talents continue to surprise us, providing not only fresh insights into cell and organismal biology, but also new avenues to cancer treatment. Among the most fruitful lines of p53 research in recent years have been the discoveries revealing the multifaceted roles of p53-centered pathways in the fundamental processes of DNA replication and ribosome biogenesis (RiBi), along with cellular responses to replication and RiBi stresses, two intertwined areas of cell (patho)physiology that we discuss in this review. Here, we first provide concise introductory notes on the canonical roles of p53, the key interacting proteins, downstream targets and post-translational modifications involved in p53 regulation. We then highlight the emerging involvement of p53 as a key component of the DNA replication Fork Speed Regulatory Network and the mechanistic links of p53 with cellular checkpoint responses to replication stress (RS), the driving force of cancer-associated genomic instability. Next, the tantalizing, yet still rather foggy functional crosstalk between replication and RiBi (nucleolar) stresses is considered, followed by the more defined involvement of p53-mediated monitoring of the multistep process of RiBi, including the latest updates on the RPL5/RPL11/5 S rRNA-MDM2-p53-mediated Impaired Ribosome Biogenesis Checkpoint (IRBC) pathway and its involvement in tumorigenesis. The diverse defects of RiBi and IRBC that predispose and/or contribute to severe human pathologies including developmental syndromes and cancer are then outlined, along with examples of promising small-molecule-based strategies to therapeutically target the RS- and particularly RiBi- stress-tolerance mechanisms to which cancer cells are addicted due to their aberrant DNA replication, repair, and proteo-synthesis demands. ![]()
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28
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Targeting Ribosome Biogenesis in Cancer: Lessons Learned and Way Forward. Cancers (Basel) 2022; 14:cancers14092126. [PMID: 35565259 PMCID: PMC9100539 DOI: 10.3390/cancers14092126] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/18/2022] [Accepted: 04/22/2022] [Indexed: 01/05/2023] Open
Abstract
Simple Summary Cells need to produce ribosomes to sustain continuous proliferation and expand in numbers, a feature that is even more prominent in uncontrollably proliferating cancer cells. Certain cancer cell types are expected to depend more on ribosome biogenesis based on their genetic background, and this potential vulnerability can be exploited in designing effective, targeted cancer therapies. This review provides information on anti-cancer molecules that target the ribosome biogenesis machinery and indicates avenues for future research. Abstract Rapid growth and unrestrained proliferation is a hallmark of many cancers. To accomplish this, cancer cells re-wire and increase their biosynthetic and metabolic activities, including ribosome biogenesis (RiBi), a complex, highly energy-consuming process. Several chemotherapeutic agents used in the clinic impair this process by interfering with the transcription of ribosomal RNA (rRNA) in the nucleolus through the blockade of RNA polymerase I or by limiting the nucleotide building blocks of RNA, thereby ultimately preventing the synthesis of new ribosomes. Perturbations in RiBi activate nucleolar stress response pathways, including those controlled by p53. While compounds such as actinomycin D and oxaliplatin effectively disrupt RiBi, there is an ongoing effort to improve the specificity further and find new potent RiBi-targeting compounds with improved pharmacological characteristics. A few recently identified inhibitors have also become popular as research tools, facilitating our advances in understanding RiBi. Here we provide a comprehensive overview of the various compounds targeting RiBi, their mechanism of action, and potential use in cancer therapy. We discuss screening strategies, drug repurposing, and common problems with compound specificity and mechanisms of action. Finally, emerging paths to discovery and avenues for the development of potential biomarkers predictive of therapeutic outcomes across cancer subtypes are also presented.
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29
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Ma X, Li Y, Zhao B. Ribosomal protein L5 (RPL5)/ E2F transcription factor 1 (E2F1) signaling suppresses breast cancer progression via regulating endoplasmic reticulum stress and autophagy. Bioengineered 2022; 13:8076-8086. [PMID: 35293275 PMCID: PMC9161874 DOI: 10.1080/21655979.2022.2052672] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 03/08/2022] [Accepted: 03/09/2022] [Indexed: 02/08/2023] Open
Abstract
Endoplasmic reticulum stress (ERS) is associated with breast cancer progression. However, the potential role of ribosomal protein L5 (RPL5) on ERS in breast cancer remains unclear. This study aimed to determine the role of RPL5/E2F transcription factor 1 (E2F1) in breast cancer. It was found that RPL5 was downregulated in breast cancer cells and tissues. Additionally, overexpression of RPL5 inhibited cell proliferation. Moreover, the levels of ERS and autophagy markers were estimated using western blotting. Overexpression of RPL5 induced ERS and suppressed autophagy. Additionally, RPL5 downregulated E2F1, which was overexpressed in breast cancer cells. However, E2F1 knockdown promoted the transcriptional activation of glucose regulated protein 78 (GRP78), suppressed ERS response, and promoted autophagy. Rescue assays indicated that the effects of RPL5 on ERS and autophagy were abolished by E2F1. Taken together, RPL5 inhibited the growth of breast cancer cells by modulating ERS and autophagy via the regulation of E2F1. These findings suggest that RPL5 has a tumor-suppressive effect in breast cancer.
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Affiliation(s)
- Xiaoping Ma
- Breast Internal Medicine Department, The 3rd Affiliated Teaching Hospital of XinJiang Medical University(Affiliated Tumor Hospital), Urumqi, China
| | - Yan Li
- Breast Internal Medicine Department, The 3rd Affiliated Teaching Hospital of XinJiang Medical University(Affiliated Tumor Hospital), Urumqi, China
| | - Bing Zhao
- Breast Internal Medicine Department, The 3rd Affiliated Teaching Hospital of XinJiang Medical University(Affiliated Tumor Hospital), Urumqi, China
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30
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van Dooijeweert B, Kia SK, Dahl N, Fenneteau O, Leguit R, Nieuwenhuis E, van Solinge W, van Wijk R, Da Costa L, Bartels M. GATA-1 Defects in Diamond-Blackfan Anemia: Phenotypic Characterization Points to a Specific Subset of Disease. Genes (Basel) 2022; 13:genes13030447. [PMID: 35328001 PMCID: PMC8949872 DOI: 10.3390/genes13030447] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/13/2022] [Accepted: 02/24/2022] [Indexed: 02/01/2023] Open
Abstract
Diamond−Blackfan anemia (DBA) is one of the inherited bone marrow failure syndromes marked by erythroid hypoplasia. Underlying variants in ribosomal protein (RP) genes account for 80% of cases, thereby classifying DBA as a ribosomopathy. In addition to RP genes, extremely rare variants in non-RP genes, including GATA1, the master transcription factor in erythropoiesis, have been reported in recent years in patients with a DBA-like phenotype. Subsequently, a pivotal role for GATA-1 in DBA pathophysiology was established by studies showing the impaired translation of GATA1 mRNA downstream of the RP haploinsufficiency. Here, we report on a patient from the Dutch DBA registry, in which we found a novel hemizygous variant in GATA1 (c.220+2T>C), and an Iranian patient with a previously reported variant in the initiation codon of GATA1 (c.2T>C). Although clinical features were concordant with DBA, the bone marrow morphology in both patients was not typical for DBA, showing moderate erythropoietic activity with signs of dyserythropoiesis and dysmegakaryopoiesis. This motivated us to re-evaluate the clinical characteristics of previously reported cases, which resulted in the comprehensive characterization of 18 patients with an inherited GATA-1 defect in exon 2 that is presented in this case-series. In addition, we re-investigated the bone marrow aspirate of one of the previously published cases. Altogether, our observations suggest that DBA caused by GATA1 defects is characterized by distinct phenotypic characteristics, including dyserythropoiesis and dysmegakaryopoiesis, and therefore represents a distinct phenotype within the DBA disease spectrum, which might need specific clinical management.
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Affiliation(s)
- Birgit van Dooijeweert
- Central Diagnostic Laboratory Research, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands; (B.v.D.); (W.v.S.); (R.v.W.)
- Department of Pediatric Hematology, van Creveldkliniek, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
| | - Sima Kheradmand Kia
- Laboratory for Red Blood Cell Diagnostics, Sanquin, 1006 AD Amsterdam, The Netherlands;
- Peyvand Lab Complex, Shiraz 7363871347, Iran
| | - Niklas Dahl
- Department of Immunology, Genetics and Pathology, Uppsala University and Children’s Hospital, 751 85 Uppsala, Sweden;
| | - Odile Fenneteau
- AP-HP, Service d’Hématologie Biologique, Hôpital Robert Debré, University of Paris Cité, Hematim EA 4666, UPJV, F-75019 Paris, France; (O.F.); (L.D.C.)
| | - Roos Leguit
- Department of Pathology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands;
| | - Edward Nieuwenhuis
- Department of Pediatrics, University Medical Center Utrecht, 3508 AB Utrecht, The Netherlands;
| | - Wouter van Solinge
- Central Diagnostic Laboratory Research, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands; (B.v.D.); (W.v.S.); (R.v.W.)
| | - Richard van Wijk
- Central Diagnostic Laboratory Research, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands; (B.v.D.); (W.v.S.); (R.v.W.)
| | - Lydie Da Costa
- AP-HP, Service d’Hématologie Biologique, Hôpital Robert Debré, University of Paris Cité, Hematim EA 4666, UPJV, F-75019 Paris, France; (O.F.); (L.D.C.)
| | - Marije Bartels
- Department of Pediatric Hematology, van Creveldkliniek, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
- Department of Pediatrics, University Medical Center Utrecht, 3508 AB Utrecht, The Netherlands;
- Correspondence:
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HEATR3 variants impair nuclear import of uL18 (RPL5) and drive Diamond-Blackfan anemia. Blood 2022; 139:3111-3126. [PMID: 35213692 PMCID: PMC9136880 DOI: 10.1182/blood.2021011846] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 02/03/2022] [Indexed: 11/21/2022] Open
Abstract
Biallelic variants in HEATR3 are associated with DBA and other clinical features in humans. HEATR3 variants destabilize the protein, resulting in a reduction of nuclear uL18 and impaired ribosome biogenesis.
The congenital bone marrow failure syndrome Diamond-Blackfan anemia (DBA) is typically associated with variants in ribosomal protein (RP) genes impairing erythroid cell development. Here we report multiple individuals with biallelic HEATR3 variants exhibiting bone marrow failure, short stature, facial and acromelic dysmorphic features, and intellectual disability. These variants destabilize a protein whose yeast homolog is known to synchronize the nuclear import of RPs uL5 (RPL11) and uL18 (RPL5), which are both critical for producing ribosomal subunits and for stabilizing the p53 tumor suppressor when ribosome biogenesis is compromised. Expression of HEATR3 variants or repression of HEATR3 expression in primary cells, cell lines of various origins, and yeast models impairs growth, differentiation, pre–ribosomal RNA processing, and ribosomal subunit formation reminiscent of DBA models of large subunit RP gene variants. Consistent with a role of HEATR3 in RP import, HEATR3-depleted cells or patient-derived fibroblasts display reduced nuclear accumulation of uL18. Hematopoietic progenitor cells expressing HEATR3 variants or small-hairpin RNAs knocking down HEATR3 synthesis reveal abnormal acceleration of erythrocyte maturation coupled to severe proliferation defects that are independent of p53 activation. Our study uncovers a new pathophysiological mechanism leading to DBA driven by biallelic HEATR3 variants and the destabilization of a nuclear import protein important for ribosome biogenesis.
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32
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Deregulation of ribosomal proteins in human cancers. Biosci Rep 2021; 41:230380. [PMID: 34873618 PMCID: PMC8685657 DOI: 10.1042/bsr20211577] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 10/28/2021] [Accepted: 11/22/2021] [Indexed: 12/26/2022] Open
Abstract
The ribosome, the site for protein synthesis, is composed of ribosomal RNAs (rRNAs) and ribosomal proteins (RPs). The latter have been shown to have many ribosomal and extraribosomal functions. RPs are implicated in a variety of pathological processes, especially tumorigenesis and cell transformation. In this review, we will focus on the recent advances that shed light on the effects of RPs deregulation in different types of cancer and their roles in regulating the tumor cell fate.
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Cruz J, Lemos B. Post-transcriptional diversity in riboproteins and RNAs in aging and cancer. Semin Cancer Biol 2021; 76:292-300. [PMID: 34474152 PMCID: PMC8627441 DOI: 10.1016/j.semcancer.2021.08.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 08/28/2021] [Accepted: 08/29/2021] [Indexed: 12/19/2022]
Abstract
Post-transcriptional (PtscM) and post-translational (PtrnM) modifications of nucleotides and amino acids are covalent modifications able to change physio-chemical properties of RNAs and proteins. In the ribosome, the adequate assembly of rRNAs and ribosomal protein subunits in the nucleolus ensures suitable translational activity, with protein synthesis tuned according to intracellular demands of energy production, replication, proliferation, and growth. Disruption in the regulatory control of PtscM and PtrnM can impair ribosome biogenesis and ribosome function. Ribosomal impairment may, in turn, impact the synthesis of proteins engaged in functions as varied as telomere maintenance, apoptosis, and DNA repair, as well as intersect with mitochondria and telomerase activity. These cellular processes often malfunction in carcinogenesis and senescence. Here we discuss regulatory mechanisms of PtscMs and PtrnMs on ribosomal function. We also address chemical modification in rRNAs and their impacts on cellular metabolism, replication control, and senescence. Further, we highlight similarities and differences of PtscMs and PtrnMs in ribosomal intermediates during aging and carcinogenesis. Understanding these regulatory mechanisms may uncover critical steps for the development of more efficient oncologic and anti-aging therapies.
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Affiliation(s)
- Jurandir Cruz
- Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA; Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP 01246, Brazil
| | - Bernardo Lemos
- Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
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Clarke LE, Cook A, Mathavarajah S, Bera A, Salsman J, Habib E, Van Iderstine C, Bydoun M, Lewis SM, Dellaire G. Haploinsufficient tumor suppressor PRP4K is negatively regulated during epithelial-to-mesenchymal transition. FASEB J 2021; 35:e22001. [PMID: 34674320 PMCID: PMC9298446 DOI: 10.1096/fj.202001063r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 09/23/2021] [Accepted: 10/05/2021] [Indexed: 01/28/2023]
Abstract
The pre‐mRNA processing factor 4 kinase (PRP4K, also known as PRPF4B) is an essential gene. However, reduced PRP4K expression is associated with aggressive breast and ovarian cancer phenotypes including taxane therapy resistance, increased cell migration and invasion in vitro, and cancer metastasis in mice. These results are consistent with PRP4K being a haploinsufficient tumor suppressor. Increased cell migration and invasion is associated with epithelial‐to‐mesenchymal transition (EMT), but how reduced PRP4K levels affect normal epithelial cell migration or EMT has not been studied. Depletion of PRP4K by small hairpin RNA (shRNA) in non‐transformed mammary epithelial cell lines (MCF10A, HMLE) reduced or had no effect on 2D migration in the scratch assay but resulted in greater invasive potential in 3D transwell assays. Depletion of PRP4K in mesenchymal triple‐negative breast cancer cells (MDA‐MB‐231) resulted in both enhanced 2D migration and 3D invasion, with 3D invasion correlated with higher fibronectin levels in both MDA‐MB‐231 and MCF10A cells and without changes in E‐cadherin. Induction of EMT in MCF10A cells, by treatment with WNT‐5a and TGF‐β1, or depletion of eukaryotic translation initiation factor 3e (eIF3e) by shRNA, resulted in significantly reduced PRP4K expression. Mechanistically, induction of EMT by WNT‐5a/TGF‐β1 reduced PRP4K transcript levels, whereas eIF3e depletion led to reduced PRP4K translation. Finally, reduced PRP4K levels after eIF3e depletion correlated with increased YAP activity and nuclear localization, both of which are reversed by overexpression of exogenous PRP4K. Thus, PRP4K is a haploinsufficient tumor suppressor negatively regulated by EMT, that when depleted in normal mammary cells can increase cell invasion without inducing full EMT.
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Affiliation(s)
- Livia E Clarke
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Allyson Cook
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada
| | | | - Amit Bera
- Atlantic Cancer Research Institute, Moncton, New Brunswick, Canada
| | - Jayme Salsman
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Elias Habib
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada
| | | | - Moamen Bydoun
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Stephen M Lewis
- Atlantic Cancer Research Institute, Moncton, New Brunswick, Canada.,Department of Chemistry & Biochemistry, Université de Moncton, Moncton, New Brunswick, Canada.,Beatrice Hunter Cancer Research Institute, Halifax, Nova Scotia, Canada
| | - Graham Dellaire
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada.,Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada.,Beatrice Hunter Cancer Research Institute, Halifax, Nova Scotia, Canada
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35
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A new murine Rpl5 (uL18) mutation provides a unique model of variably penetrant Diamond-Blackfan anemia. Blood Adv 2021; 5:4167-4178. [PMID: 34464976 PMCID: PMC8945612 DOI: 10.1182/bloodadvances.2021004658] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 05/04/2021] [Indexed: 01/28/2023] Open
Abstract
Ribosome dysfunction is implicated in multiple abnormal developmental and disease states in humans. Heterozygous germline mutations in genes encoding ribosomal proteins are found in most individuals with Diamond-Blackfan anemia (DBA), whereas somatic mutations have been implicated in a variety of cancers and other disorders. Ribosomal protein-deficient animal models show variable phenotypes and penetrance, similar to human patients with DBA. In this study, we characterized a novel ENU mouse mutant (Skax23m1Jus) with growth and skeletal defects, cardiac malformations, and increased mortality. After genetic mapping and whole-exome sequencing, we identified an intronic Rpl5 mutation, which segregated with all affected mice. This mutation was associated with decreased ribosome generation, consistent with Rpl5 haploinsufficiency. Rpl5Skax23-Jus/+ animals had a profound delay in erythroid maturation and increased mortality at embryonic day (E) 12.5, which improved by E14.5. Surviving mutant animals had macrocytic anemia at birth, as well as evidence of ventricular septal defect (VSD). Surviving adult and aged mice exhibited no hematopoietic defect or VSD. We propose that this novel Rpl5Skax23-Jus/+ mutant mouse will be useful in studying the factors influencing the variable penetrance that is observed in DBA.
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36
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Zhao W, Li X, Nian W, Wang J, Wang X, Sun L, Zhu Y, Tong Z. Ribosome Proteins Represented by RPL27A Mark the Development and Metastasis of Triple-Negative Breast Cancer in Mouse and Human. Front Cell Dev Biol 2021; 9:716730. [PMID: 34497807 PMCID: PMC8419227 DOI: 10.3389/fcell.2021.716730] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 07/28/2021] [Indexed: 12/14/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is known to have a poor prognosis and limited treatment options. The lack of targeted therapies and poor prognosis of patients with TNBC have made it urgent to discover novel critical diagnosis and therapeutic targets in the TNBC field. Here, in the current study, we integrated the single-cell RNA-sequencing (scRNA-seq) data from four normal mouse mammary tissues and four mouse breast tumors. Comparative analysis was conducted to identify the gene profiles of normal epithelial cells and cancer cells at different models. Surprisingly, two ribosomal protein genes, Rpl27a and Rpl15, were significantly upregulated in the cancer cells in all the TNBC models. Next, we accessed the scRNA-seq data from human primary and metastatic TNBC tissues, and comparative analysis revealed gene profiles of human primary and metastatic TNBC cancer cells. Ribosomal protein genes, represented by RPL27A and RPL15, showed significantly upregulated expression in metastatic TNBC cancer cells. Pathway analysis on the upregulated genes of the metastatic TNBC cancer cells identified the key regulators and signaling pathways that were driving the metastasis of the TNBC cancer cells. Specifically, EIF2 signaling was significantly activated, and major member genes of this signaling pathway were upregulated. In vitro study revealed that targeting RPL27A or EIF2 signaling in a TNBC cell line, MDA-MB-231, significantly reduced cell migration and invasion. Altogether, these data suggested that the RPL27A gene is conducting critical functions in TNBC cancer development and metastasis and is a potential therapeutic target for TNBC.
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Affiliation(s)
- Weipeng Zhao
- Key Laboratory of Cancer Prevention and Therapy, Department of Breast Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
| | - Xichuan Li
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Sciences, Tianjin Normal University, Tianjin, China
| | - Weiqi Nian
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing, China
| | - Jun Wang
- Department of Oncology, The First Affiliated Hospital of Shandong First Medical University, Jinan, China
| | - Xiaorui Wang
- Key Laboratory of Cancer Prevention and Therapy, Department of Breast Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
| | - Linlin Sun
- Key Laboratory of Cancer Prevention and Therapy, Department of Breast Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
| | - Ye Zhu
- Key Laboratory of Cancer Prevention and Therapy, Department of Breast Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
| | - Zhongsheng Tong
- Key Laboratory of Cancer Prevention and Therapy, Department of Breast Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin, China
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37
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Kang J, Brajanovski N, Chan KT, Xuan J, Pearson RB, Sanij E. Ribosomal proteins and human diseases: molecular mechanisms and targeted therapy. Signal Transduct Target Ther 2021; 6:323. [PMID: 34462428 PMCID: PMC8405630 DOI: 10.1038/s41392-021-00728-8] [Citation(s) in RCA: 112] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 07/12/2021] [Accepted: 07/30/2021] [Indexed: 02/07/2023] Open
Abstract
Ribosome biogenesis and protein synthesis are fundamental rate-limiting steps for cell growth and proliferation. The ribosomal proteins (RPs), comprising the structural parts of the ribosome, are essential for ribosome assembly and function. In addition to their canonical ribosomal functions, multiple RPs have extra-ribosomal functions including activation of p53-dependent or p53-independent pathways in response to stress, resulting in cell cycle arrest and apoptosis. Defects in ribosome biogenesis, translation, and the functions of individual RPs, including mutations in RPs have been linked to a diverse range of human congenital disorders termed ribosomopathies. Ribosomopathies are characterized by tissue-specific phenotypic abnormalities and higher cancer risk later in life. Recent discoveries of somatic mutations in RPs in multiple tumor types reinforce the connections between ribosomal defects and cancer. In this article, we review the most recent advances in understanding the molecular consequences of RP mutations and ribosomal defects in ribosomopathies and cancer. We particularly discuss the molecular basis of the transition from hypo- to hyper-proliferation in ribosomopathies with elevated cancer risk, a paradox termed "Dameshek's riddle." Furthermore, we review the current treatments for ribosomopathies and prospective therapies targeting ribosomal defects. We also highlight recent advances in ribosome stress-based cancer therapeutics. Importantly, insights into the mechanisms of resistance to therapies targeting ribosome biogenesis bring new perspectives into the molecular basis of cancer susceptibility in ribosomopathies and new clinical implications for cancer therapy.
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Affiliation(s)
- Jian Kang
- grid.1055.10000000403978434Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XSir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC Australia
| | - Natalie Brajanovski
- grid.1055.10000000403978434Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC Australia
| | - Keefe T. Chan
- grid.1055.10000000403978434Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XSir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC Australia
| | - Jiachen Xuan
- grid.1055.10000000403978434Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XSir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC Australia
| | - Richard B. Pearson
- grid.1055.10000000403978434Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XSir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC Australia ,grid.1002.30000 0004 1936 7857Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Biochemistry and Molecular Biology, University of Melbourne, Melbourne, VIC Australia
| | - Elaine Sanij
- grid.1055.10000000403978434Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XSir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Clinical Pathology, University of Melbourne, Melbourne, VIC Australia ,grid.1073.50000 0004 0626 201XSt. Vincent’s Institute of Medical Research, Fitzroy, VIC Australia
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38
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Ilott NE, Neyazi M, Arancibia-Cárcamo CV, Powrie F, Geremia A. Tissue-dependent transcriptional and bacterial associations in primary sclerosing cholangitis-associated inflammatory bowel disease. Wellcome Open Res 2021; 6:199. [DOI: 10.12688/wellcomeopenres.16901.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/20/2021] [Indexed: 11/20/2022] Open
Abstract
Background: Primary sclerosing cholangitis (PSC) is a disease of the bile duct and liver. However, patients frequently have co-morbidities including inflammatory bowel disease (IBD) and colorectal cancer. Colorectal cancer risk in patients with PSC-associated ulcerative colitis (PSC/UC) is elevated relative to patients with ulcerative colitis (UC) alone, reasons for which remain obscure. Further, clinical and immunological features, and involved intestinal sites differ between PSC/UC and UC. Understanding the molecular and microbial basis for differences in cancer risk between these two patient groups and how these differ across intestinal sites is important for the development of therapies to prevent colorectal cancer development in at-risk individuals. Methods: We employed ribonucleic acid sequencing (RNA-seq) analysis of biopsy samples across three intestinal tissue locations (ileum, caecum and rectum) in patients with PSC/UC (n = 8), UC (n = 10) and healthy controls (n = 12) to determine tissue-dependent transcriptional alterations in PSC/UC. We also performed 16S ribosomal RNA (rRNA) amplicon sequencing to determine bacterial associations with PSC/UC and host-microbiome associations. Results: Tissue-defining transcriptional signatures revealed that the ileum was enriched for genes involved in lipid and drug metabolism, the caecum for activated immune cells and the rectum for enteric neurogenesis. Transcriptional alterations relative to healthy control samples were largely shared between patients with PSC/UC or UC although were distinct across tissue locations. Nevertheless, we observed reduced expression of gamma-glutamyl transferase 1 (GGT1) specifically in the ileum and caecum of patients with PSC/UC. Analysis of the bacterial component of the microbiome revealed high inter-individual variability of microbiome composition and little evidence for tissue-dependency. We observed a reduction in Parabacteroides relative abundance in the rectum of patients with PSC/UC. Conclusions: The role of gamma-glutamyl transferase in maintaining the redox environment through the glutathione salvage pathway makes our observed alterations a potential pathway to PSC-associated colorectal cancer.
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39
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Panici B, Nakajima H, Carlston CM, Ozadam H, Cenik C, Cenik ES. Loss of coordinated expression between ribosomal and mitochondrial genes revealed by comprehensive characterization of a large family with a rare Mendelian disorder. Genomics 2021; 113:1895-1905. [PMID: 33862179 PMCID: PMC8266734 DOI: 10.1016/j.ygeno.2021.04.020] [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: 01/11/2021] [Revised: 03/30/2021] [Accepted: 04/11/2021] [Indexed: 10/21/2022]
Abstract
Non-canonical intronic variants are a poorly characterized yet highly prevalent class of alterations associated with Mendelian disorders. Here, we report the first RNA expression and splicing analysis from a family whose members carry a non-canonical splice variant in an intron of RPL11 (c.396 +3A>G). This mutation is causative for Diamond Blackfan Anemia (DBA) in this family despite incomplete penetrance and variable expressivity. Our analyses revealed a complex pattern of disruptions with many novel junctions of RPL11. These include an RPL11 transcript that is translated with a late stop codon in the 3' untranslated region (3'UTR) of the main isoform. We observed that RPL11 transcript abundance is comparable among carriers regardless of symptom severity. Interestingly, both the small and large ribosomal subunit transcripts were significantly overexpressed in individuals with a history of anemia in addition to congenital abnormalities. Finally, we discovered that coordinated expression between mitochondrial components and RPL11 was lost in all carriers, which may lead to variable expressivity. Overall, this study highlights the importance of RNA splicing and expression analyses in families for molecular characterization of Mendelian diseases.
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Affiliation(s)
- Brendan Panici
- Department of Molecular Biosciences, University of Texas at Austin, Austin, USA.
| | - Hosei Nakajima
- Department of Molecular Biosciences, University of Texas at Austin, Austin, USA
| | | | - Hakan Ozadam
- Department of Molecular Biosciences, University of Texas at Austin, Austin, USA.
| | - Can Cenik
- Department of Molecular Biosciences, University of Texas at Austin, Austin, USA.
| | - Elif Sarinay Cenik
- Department of Molecular Biosciences, University of Texas at Austin, Austin, USA.
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40
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García-Cortés D, Hernández-Lemus E, Espinal-Enríquez J. Luminal A Breast Cancer Co-expression Network: Structural and Functional Alterations. Front Genet 2021; 12:629475. [PMID: 33959148 PMCID: PMC8096206 DOI: 10.3389/fgene.2021.629475] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Accepted: 03/17/2021] [Indexed: 12/20/2022] Open
Abstract
Luminal A is the most common breast cancer molecular subtype in women worldwide. These tumors have characteristic yet heterogeneous alterations at the genomic and transcriptomic level. Gene co-expression networks (GCNs) have contributed to better characterize the cancerous phenotype. We have previously shown an imbalance in the proportion of intra-chromosomal (cis-) over inter-chromosomal (trans-) interactions when comparing cancer and healthy tissue GCNs. In particular, for breast cancer molecular subtypes (Luminal A included), the majority of high co-expression interactions connect gene-pairs in the same chromosome, a phenomenon that we have called loss of trans- co-expression. Despite this phenomenon has been described, the functional implication of this specific network topology has not been studied yet. To understand the biological role that communities of co-expressed genes may have, we constructed GCNs for healthy and Luminal A phenotypes. Network modules were obtained based on their connectivity patterns and they were classified according to their chromosomal homophily (proportion of cis-/trans- interactions). A functional overrepresentation analysis was performed on communities in both networks to observe the significantly enriched processes for each community. We also investigated possible mechanisms for which the loss of trans- co-expression emerges in cancer GCN. To this end we evaluated transcription factor binding sites, CTCF binding sites, differential gene expression and copy number alterations (CNAs) in the cancer GCN. We found that trans- communities in Luminal A present more significantly enriched categories than cis- ones. Processes, such as angiogenesis, cell proliferation, or cell adhesion were found in trans- modules. The differential expression analysis showed that FOXM1, CENPA, and CIITA transcription factors, exert a major regulatory role on their communities by regulating expression of their target genes in other chromosomes. Finally, identification of CNAs, displayed a high enrichment of deletion peaks in cis- communities. With this approach, we demonstrate that network topology determine, to at certain extent, the function in Luminal A breast cancer network. Furthermore, several mechanisms seem to be acting together to avoid trans- co-expression. Since this phenomenon has been observed in other cancer tissues, a remaining question is whether the loss of long distance co-expression is a novel hallmark of cancer.
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Affiliation(s)
- Diana García-Cortés
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico.,Programa de Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Enrique Hernández-Lemus
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico.,Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Jesús Espinal-Enríquez
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico.,Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
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41
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The role of RNA-binding and ribosomal proteins as specific RNA translation regulators in cellular differentiation and carcinogenesis. Biochim Biophys Acta Mol Basis Dis 2020; 1867:166046. [PMID: 33383105 DOI: 10.1016/j.bbadis.2020.166046] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 12/03/2020] [Accepted: 12/10/2020] [Indexed: 02/07/2023]
Abstract
Tight control of mRNA expression is required for cell differentiation; imbalanced regulation may lead to developmental disorders and cancer. The activity of the translational machinery (including ribosomes and translation factors) regulates the rate (slow or fast) of translation of encoded proteins, and the quality of these proteins highly depends on which mRNAs are available for translation. Specific RNA-binding and ribosomal proteins seem to play a key role in controlling gene expression to determine the differentiation fate of the cell. This demonstrates the important role of RNA-binding proteins, specific ribosome-binding proteins and microRNAs as key molecules in controlling the specific proteins required for the differentiation or dedifferentiation of cells. This delicate balance between specific proteins (in terms of quality and availability) and post-translational modifications occurring in the cytoplasm is crucial for cell differentiation, dedifferentiation and oncogenic potential. In this review, we report how defects in the regulation of mRNA translation can be dependent on specific proteins and can induce an imbalance between differentiation and dedifferentiation in cell fate determination.
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42
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A forward selection algorithm to identify mutually exclusive alterations in cancer studies. J Hum Genet 2020; 66:509-518. [PMID: 33177701 DOI: 10.1038/s10038-020-00870-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 08/11/2020] [Accepted: 10/23/2020] [Indexed: 01/18/2023]
Abstract
Mutual exclusivity analyses provide an effective tool to identify driver genes from passenger genes for cancer studies. Various algorithms have been developed for the detection of mutual exclusivity, but controlling false positive and improving accuracy remain challenging. We propose a forward selection algorithm for identification of mutually exclusive gene sets (FSME) in this paper. The method includes an initial search of seed pair of mutually exclusive (ME) genes and subsequently including more genes into the current ME set. Simulations demonstrated that, compared to recently published approaches (i.e., CoMEt, WExT, and MEGSA), FSME could provide higher precision or recall rate to identify ME gene sets, and had superior control of false positive rates. With application to TCGA real data sets for AML, BRCA, and GBM, we confirmed that FSME can be utilized to discover cancer driver genes.
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43
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Duică F, Condrat CE, Dănila CA, Boboc AE, Radu MR, Xiao J, Li X, Creţoiu SM, Suciu N, Creţoiu D, Predescu DV. MiRNAs: A Powerful Tool in Deciphering Gynecological Malignancies. Front Oncol 2020; 10:591181. [PMID: 33194751 PMCID: PMC7646292 DOI: 10.3389/fonc.2020.591181] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 10/01/2020] [Indexed: 12/14/2022] Open
Abstract
Accumulated evidence on the clinical roles of microRNAs (miRNAs) in cancer prevention and control has revealed the emergence of new genetic techniques that have improved the understanding of the mechanisms essential for pathology induction and progression. Comprehension of the modifications and individual differences of miRNAs and their interactions in the pathogenesis of gynecological malignancies, together with an understanding of the phenotypic variations have considerably improved the management of the diagnosis and personalized treatment for different forms of cancer. In recent years, miRNAs have emerged as signaling molecules in biological pathways involved in different categories of cancer and it has been demonstrated that these molecules could regulate cancer-relevant processes, our focus being on malignancies of the gynecologic tract. The aim of this paper is to summarize novel research findings in the literature regarding the parts that miRNAs play in cancer-relevant processes, specifically regarding gynecological malignancy, while emphasizing their pivotal role in the disruption of cancer-related signaling pathways.
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Affiliation(s)
- Florentina Duică
- Fetal Medicine Excellence Research Center, Alessandrescu-Rusescu National Institute for Mother and Child Health, Bucharest, Romania
| | - Carmen Elena Condrat
- Fetal Medicine Excellence Research Center, Alessandrescu-Rusescu National Institute for Mother and Child Health, Bucharest, Romania
| | - Cezara Alina Dănila
- Fetal Medicine Excellence Research Center, Alessandrescu-Rusescu National Institute for Mother and Child Health, Bucharest, Romania
| | - Andreea Elena Boboc
- Fetal Medicine Excellence Research Center, Alessandrescu-Rusescu National Institute for Mother and Child Health, Bucharest, Romania
| | - Mihaela Raluca Radu
- Fetal Medicine Excellence Research Center, Alessandrescu-Rusescu National Institute for Mother and Child Health, Bucharest, Romania
| | - Junjie Xiao
- Institute of Cardiovascular Sciences, Shanghai University, Shanghai, China
| | - Xinli Li
- Department of Cardiology, Jiangsu Province Hospital and Nanjing Medical University First Affiliated Hospital, Nanjing, China
| | - Sanda Maria Creţoiu
- Cellular and Molecular Biology and Histology Department, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
| | - Nicolae Suciu
- Fetal Medicine Excellence Research Center, Alessandrescu-Rusescu National Institute for Mother and Child Health, Bucharest, Romania.,Department of Obstetrics and Gynecology, Polizu Clinical Hospital, Alessandrescu-Rusescu National Institute for Mother and Child Health, Bucharest, Romania.,Obstetrics, Gynecology and Neonatology Department, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
| | - Dragoş Creţoiu
- Fetal Medicine Excellence Research Center, Alessandrescu-Rusescu National Institute for Mother and Child Health, Bucharest, Romania.,Cellular and Molecular Biology and Histology Department, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
| | - Dragoş-Valentin Predescu
- Department of General Surgery, Sf. Maria Clinical Hospital, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
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44
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Bursać S, Prodan Y, Pullen N, Bartek J, Volarević S. Dysregulated Ribosome Biogenesis Reveals Therapeutic Liabilities in Cancer. Trends Cancer 2020; 7:57-76. [PMID: 32948502 DOI: 10.1016/j.trecan.2020.08.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/30/2020] [Accepted: 08/17/2020] [Indexed: 12/24/2022]
Abstract
Ribosome biogenesis (RiBi) is one of the most complex and energy demanding processes in human cells, critical for cell growth and proliferation. Strong causal links between inherited and acquired impairment in RiBi with cancer pathogenesis are emerging, pointing to RiBi as an attractive therapeutic target for cancer. Here, we will highlight new knowledge about causes of excessive or impaired RiBi and the impact of these changes on protein synthesis. We will also discuss how new knowledge about secondary consequences of dysregulated RiBi and protein synthesis, including proteotoxic stress, metabolic alterations, adaptive transcriptional and translational programs, and the impaired ribosome biogenesis checkpoint (IRBC) provide a foundation for the development of new anticancer therapies.
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Affiliation(s)
- Slađana Bursać
- Department of Molecular Medicine and Biotechnology, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia
| | - Ylenia Prodan
- Department of Molecular Medicine and Biotechnology, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia
| | - Nick Pullen
- Bristol Myers Squibb, 200 Cambridge Park Drive, Cambridge, MA 02140, USA
| | - Jiri Bartek
- Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, 171 76, Stockholm, Sweden; The Danish Cancer Society Research Center, DK-2100 Copenhagen, Denmark.
| | - Siniša Volarević
- Department of Molecular Medicine and Biotechnology, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia.
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45
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Bhar S, Zhou F, Reineke LC, Morris DK, Khincha PP, Giri N, Mirabello L, Bergstrom K, Lemon LD, Williams CL, Toh Y, Elghetany MT, Lloyd RE, Alter BP, Savage SA, Bertuch AA. Expansion of germline RPS20 mutation phenotype to include Diamond-Blackfan anemia. Hum Mutat 2020; 41:1918-1930. [PMID: 32790018 DOI: 10.1002/humu.24092] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 07/18/2020] [Accepted: 08/08/2020] [Indexed: 11/10/2022]
Abstract
Diamond-Blackfan anemia (DBA) is a ribosomopathy of variable expressivity and penetrance characterized by red cell aplasia, congenital anomalies, and predisposition to certain cancers, including early-onset colorectal cancer (CRC). DBA is primarily caused by a dominant mutation of a ribosomal protein (RP) gene, although approximately 20% of patients remain genetically uncharacterized despite exome sequencing and copy number analysis. Although somatic loss-of-function mutations in RP genes have been reported in sporadic cancers, with the exceptions of 5q-myelodysplastic syndrome (RPS14) and microsatellite unstable CRC (RPL22), these cancers are not enriched in DBA. Conversely, pathogenic variants in RPS20 were previously implicated in familial CRC; however, none of the reported individuals had classical DBA features. We describe two unrelated children with DBA lacking variants in known DBA genes who were found by exome sequencing to have de novo novel missense variants in RPS20. The variants affect the same amino acid but result in different substitutions and reduce the RPS20 protein level. Yeast models with mutation of the cognate residue resulted in defects in growth, ribosome biogenesis, and polysome formation. These findings expand the phenotypic spectrum of RPS20 mutation beyond familial CRC to include DBA, which itself is associated with increased risk of CRC.
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Affiliation(s)
- Saleh Bhar
- Department of Pediatrics, Section of Hematology/Oncology, Baylor College of Medicine, Texas Children's Hospital, Houston, Texas
| | - Fujun Zhou
- Laboratory on the Mechanism and Regulation of Protein Synthesis, Eunice Kennedy Shriver National Institute of Child Health and Development, Bethesda, Maryland
| | - Lucas C Reineke
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Danna K Morris
- Department of Pediatrics, Section of Hematology/Oncology, Baylor College of Medicine, Texas Children's Hospital, Houston, Texas
| | - Payal P Khincha
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Neelam Giri
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Lisa Mirabello
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Katie Bergstrom
- Department of Pediatrics, Section of Hematology/Oncology, Baylor College of Medicine, Texas Children's Hospital, Houston, Texas
| | - Laramie D Lemon
- Integrative Molecular and Biomedical Sciences Graduate Program, Baylor College of Medicine, Houston, Texas
| | - Christopher L Williams
- Department of Pediatrics, Section of Hematology/Oncology, Baylor College of Medicine, Texas Children's Hospital, Houston, Texas
| | - Yukimatsu Toh
- Department of Pediatrics, Section of Hematology/Oncology, Baylor College of Medicine, Texas Children's Hospital, Houston, Texas
| | - M Tarek Elghetany
- Department of Pathology, Baylor College of Medicine, Texas Children's Hospital, Houston, Texas
| | - Richard E Lloyd
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas
| | - Blanche P Alter
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Sharon A Savage
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Alison A Bertuch
- Department of Pediatrics, Section of Hematology/Oncology, Baylor College of Medicine, Texas Children's Hospital, Houston, Texas
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46
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Johansson PA, Brooks K, Newell F, Palmer JM, Wilmott JS, Pritchard AL, Broit N, Wood S, Carlino MS, Leonard C, Koufariotis LT, Nathan V, Beasley AB, Howlie M, Dawson R, Rizos H, Schmidt CW, Long GV, Hamilton H, Kiilgaard JF, Isaacs T, Gray ES, Rolfe OJ, Park JJ, Stark A, Mann GJ, Scolyer RA, Pearson JV, van Baren N, Waddell N, Wadt KW, McGrath LA, Warrier SK, Glasson W, Hayward NK. Whole genome landscapes of uveal melanoma show an ultraviolet radiation signature in iris tumours. Nat Commun 2020; 11:2408. [PMID: 32415113 PMCID: PMC7229209 DOI: 10.1038/s41467-020-16276-8] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 04/22/2020] [Indexed: 01/04/2023] Open
Abstract
Uveal melanoma (UM) is the most common intraocular tumour in adults and despite surgical or radiation treatment of primary tumours, ~50% of patients progress to metastatic disease. Therapeutic options for metastatic UM are limited, with clinical trials having little impact. Here we perform whole-genome sequencing (WGS) of 103 UM from all sites of the uveal tract (choroid, ciliary body, iris). While most UM have low tumour mutation burden (TMB), two subsets with high TMB are seen; one driven by germline MBD4 mutation, and another by ultraviolet radiation (UVR) exposure, which is restricted to iris UM. All but one tumour have a known UM driver gene mutation (GNAQ, GNA11, BAP1, PLCB4, CYSLTR2, SF3B1, EIF1AX). We identify three other significantly mutated genes (TP53, RPL5 and CENPE). Uveal melanoma has a propensity to metastasise. Here, the authors report the whole genome sequence of 103 uveal melanomas and find that the tumour mutational burden is variable and that two subsets of tumours are characterised by MBD4 mutations and a UV exposure signature.
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Affiliation(s)
| | - Kelly Brooks
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Felicity Newell
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Jane M Palmer
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - James S Wilmott
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia.,Sydney Medical School, The University of Sydney, Sydney, NSW, Australia
| | - Antonia L Pritchard
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.,University of the Highlands and Island, Inverness, UK
| | - Natasa Broit
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.,University of Queensland, Brisbane, QLD, Australia
| | - Scott Wood
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Matteo S Carlino
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
| | - Conrad Leonard
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | | | - Vaishnavi Nathan
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.,University of Queensland, Brisbane, QLD, Australia
| | - Aaron B Beasley
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
| | - Madeleine Howlie
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Rebecca Dawson
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Helen Rizos
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia.,Department of Biomedical Science, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia
| | - Chris W Schmidt
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.,Mater Research, Woolloongabba, QLD, Australia
| | - Georgina V Long
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia.,Department of Medical Oncology, Royal North Shore Hospital, St Leonards, Sydney, NSW, Australia
| | - Hayley Hamilton
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.,Queensland Ocular Oncology Service, The Terrace Eye Centre, Brisbane, QLD, Australia
| | - Jens F Kiilgaard
- Department of Ophthalmology, Rigshospitalet-Glostrup Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Timothy Isaacs
- Perth Retina, Perth, WA, Australia.,Centre for Ophthalmology and Visual Science, University of Western Australia, Crawley, WA, Australia.,Department of Ophthalmology, Royal Perth Hospital, Perth, WA, Australia
| | - Elin S Gray
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia.,Centre for Ophthalmology and Visual Science, University of Western Australia, Crawley, WA, Australia
| | - Olivia J Rolfe
- Queensland Ocular Oncology Service, The Terrace Eye Centre, Brisbane, QLD, Australia
| | - John J Park
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia
| | - Andrew Stark
- Queensland Ocular Oncology Service, The Terrace Eye Centre, Brisbane, QLD, Australia
| | - Graham J Mann
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia.,Centre for Cancer Research, Westmead Institute for Medical Research, The University of Sydney, Westmead, Sydney, NSW, Australia.,John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - Richard A Scolyer
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia.,Sydney Medical School, The University of Sydney, Sydney, NSW, Australia.,Royal Prince Alfred Hospital and New South Wales Health Pathology, Sydney, Australia
| | - John V Pearson
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | | | - Nicola Waddell
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Karin W Wadt
- Department of Clinical Genetics, Rigshospitalet, Copenhagen, Denmark
| | - Lindsay A McGrath
- Queensland Ocular Oncology Service, The Terrace Eye Centre, Brisbane, QLD, Australia
| | - Sunil K Warrier
- Queensland Ocular Oncology Service, The Terrace Eye Centre, Brisbane, QLD, Australia
| | - William Glasson
- Queensland Ocular Oncology Service, The Terrace Eye Centre, Brisbane, QLD, Australia
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47
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Kampen KR, Sulima SO, Vereecke S, De Keersmaecker K. Hallmarks of ribosomopathies. Nucleic Acids Res 2020; 48:1013-1028. [PMID: 31350888 PMCID: PMC7026650 DOI: 10.1093/nar/gkz637] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 07/09/2019] [Accepted: 07/12/2019] [Indexed: 12/11/2022] Open
Abstract
Ribosomopathies are diseases caused by defects in ribosomal constituents or in factors with a role in ribosome assembly. Intriguingly, congenital ribosomopathies display a paradoxical transition from early symptoms due to cellular hypo-proliferation to an elevated cancer risk later in life. Another association between ribosome defects and cancer came into view after the recent discovery of somatic mutations in ribosomal proteins and rDNA copy number changes in a variety of tumor types, giving rise to somatic ribosomopathies. Despite these clear connections between ribosome defects and cancer, the molecular mechanisms by which defects in this essential cellular machinery are oncogenic only start to emerge. In this review, the impact of ribosomal defects on the cellular function and their mechanisms of promoting oncogenesis are described. In particular, we discuss the emerging hallmarks of ribosomopathies such as the appearance of ‘onco-ribosomes’ that are specialized in translating oncoproteins, dysregulation of translation-independent extra-ribosomal functions of ribosomal proteins, rewired cellular protein and energy metabolism, and extensive oxidative stress leading to DNA damage. We end by integrating these findings in a model that can provide an explanation how ribosomopathies could lead to the transition from hypo- to hyper-proliferation in bone marrow failure syndromes with elevated cancer risk.
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Affiliation(s)
- Kim R Kampen
- Department of Oncology, KU Leuven, LKI - Leuven Cancer Institute, 3000 Leuven, Belgium
| | - Sergey O Sulima
- Department of Oncology, KU Leuven, LKI - Leuven Cancer Institute, 3000 Leuven, Belgium
| | - Stijn Vereecke
- Department of Oncology, KU Leuven, LKI - Leuven Cancer Institute, 3000 Leuven, Belgium
| | - Kim De Keersmaecker
- Department of Oncology, KU Leuven, LKI - Leuven Cancer Institute, 3000 Leuven, Belgium
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48
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Lezzerini M, Penzo M, O'Donohue MF, Marques Dos Santos Vieira C, Saby M, Elfrink HL, Diets IJ, Hesse AM, Couté Y, Gastou M, Nin-Velez A, Nikkels PGJ, Olson AN, Zonneveld-Huijssoon E, Jongmans MCJ, Zhang G, van Weeghel M, Houtkooper RH, Wlodarski MW, Kuiper RP, Bierings MB, van der Werff Ten Bosch J, Leblanc T, Montanaro L, Dinman JD, Da Costa L, Gleizes PE, MacInnes AW. Ribosomal protein gene RPL9 variants can differentially impair ribosome function and cellular metabolism. Nucleic Acids Res 2020; 48:770-787. [PMID: 31799629 PMCID: PMC6954397 DOI: 10.1093/nar/gkz1042] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 10/17/2019] [Accepted: 11/19/2019] [Indexed: 12/20/2022] Open
Abstract
Variants in ribosomal protein (RP) genes drive Diamond-Blackfan anemia (DBA), a bone marrow failure syndrome that can also predispose individuals to cancer. Inherited and sporadic RP gene variants are also linked to a variety of phenotypes, including malignancy, in individuals with no anemia. Here we report an individual diagnosed with DBA carrying a variant in the 5′UTR of RPL9 (uL6). Additionally, we report two individuals from a family with multiple cancer incidences carrying a RPL9 missense variant. Analysis of cells from these individuals reveals that despite the variants both driving pre-rRNA processing defects and 80S monosome reduction, the downstream effects are remarkably different. Cells carrying the 5′UTR variant stabilize TP53 and impair the growth and differentiation of erythroid cells. In contrast, ribosomes incorporating the missense variant erroneously read through UAG and UGA stop codons of mRNAs. Metabolic profiles of cells carrying the 5′UTR variant reveal an increased metabolism of amino acids and a switch from glycolysis to gluconeogenesis while those of cells carrying the missense variant reveal a depletion of nucleotide pools. These findings indicate that variants in the same RP gene can drive similar ribosome biogenesis defects yet still have markedly different downstream consequences and clinical impacts.
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Affiliation(s)
- Marco Lezzerini
- Amsterdam UMC, University of Amsterdam, Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology and Metabolism, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Marianna Penzo
- Laboratorio di Patologia Clinica, Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale and Centro di Ricerca Biomedica Applicata (CRBA), Policlinico Universitario di S. Orsola, Università di Bologna,Via Massarenti 9, 40138 Bologna, Italy
| | - Marie-Françoise O'Donohue
- LBME, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France
| | | | - Manon Saby
- INSERM UMR S1134, F-75015, Paris, France
| | - Hyung L Elfrink
- Amsterdam UMC, University of Amsterdam, Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology and Metabolism, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands.,Amsterdam UMC, University of Amsterdam, Laboratory Genetic Metabolic Diseases, Core Facility Metabolomics, Amsterdam Gastroenterology and Metabolism, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Illja J Diets
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Anne-Marie Hesse
- University Grenoble Alpes, CEA, INSERM, IRIG, BGE, F-38000 Grenoble, France
| | - Yohann Couté
- University Grenoble Alpes, CEA, INSERM, IRIG, BGE, F-38000 Grenoble, France
| | - Marc Gastou
- Paris University, Paris, France.,Laboratory of Excellence for Red Cell, LABEX GR-Ex, F-75015, Paris, France.,Institute Gustave Roussy, Inserm unit U1170, F-94800 Villejuif, France
| | - Alexandra Nin-Velez
- Department of Comparative Biology and Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Peter G J Nikkels
- Department of Pathology, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
| | - Alexandra N Olson
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA
| | - Evelien Zonneveld-Huijssoon
- Department of Genetics, University Medical Center Utrecht, 3508 AB Utrecht, The Netherlands.,Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Marjolijn C J Jongmans
- Department of Genetics, University Medical Center Utrecht, 3508 AB Utrecht, The Netherlands.,Princess Maxima Center for Pediatric Oncology and Utrecht University Children's Hospital, Utrecht, The Netherlands
| | - GuangJun Zhang
- Department of Comparative Biology and Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Michel van Weeghel
- Amsterdam UMC, University of Amsterdam, Laboratory Genetic Metabolic Diseases, Core Facility Metabolomics, Amsterdam Gastroenterology and Metabolism, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Riekelt H Houtkooper
- Amsterdam UMC, University of Amsterdam, Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology and Metabolism, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
| | - Marcin W Wlodarski
- Department of Pediatrics and Adolescent Medicine, Division of Pediatric Hematology and Oncology, Medical Center, Faculty of Medicine, University of Freiburg, D-79106 Freiburg, Germany.,St. Jude's Children Research Hospital, Memphis, TN, USA
| | - Roland P Kuiper
- Department of Genetics, University Medical Center Utrecht, 3508 AB Utrecht, The Netherlands
| | - Marc B Bierings
- Princess Maxima Center for Pediatric Oncology and Utrecht University Children's Hospital, Utrecht, The Netherlands
| | | | - Thierry Leblanc
- Pediatric Hematology/Oncology Service, Robert Debré Hospital, F-75019 Paris, France
| | - Lorenzo Montanaro
- Laboratorio di Patologia Clinica, Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale and Centro di Ricerca Biomedica Applicata (CRBA), Policlinico Universitario di S. Orsola, Università di Bologna,Via Massarenti 9, 40138 Bologna, Italy
| | - Jonathan D Dinman
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA
| | - Lydie Da Costa
- INSERM UMR S1134, F-75015, Paris, France.,Paris University, Paris, France.,Laboratory of Excellence for Red Cell, LABEX GR-Ex, F-75015, Paris, France.,Hematology Lab, Robert Debré Hospital, F-75019 Paris, France
| | - Pierre-Emmanuel Gleizes
- LBME, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France
| | - Alyson W MacInnes
- Amsterdam UMC, University of Amsterdam, Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology and Metabolism, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands
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49
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Cancer-associated mutations in the ribosomal protein L5 gene dysregulate the HDM2/p53-mediated ribosome biogenesis checkpoint. Oncogene 2020; 39:3443-3457. [PMID: 32108164 DOI: 10.1038/s41388-020-1231-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 02/14/2020] [Accepted: 02/17/2020] [Indexed: 01/05/2023]
Abstract
Perturbations in ribosome biogenesis have been associated with cancer. Such aberrations activate p53 through the RPL5/RPL11/5S rRNA complex-mediated inhibition of HDM2. Studies using animal models have suggested that this signaling pathway might constitute an important anticancer barrier. To gain a deeper insight into this issue in humans, here we analyze somatic mutations in RPL5 and RPL11 coding regions, reported in The Cancer Genome Atlas and International Cancer Genome Consortium databases. Using a combined computational and statistical approach, complemented by a range of biochemical and functional analyses in human cancer cell models, we demonstrate the existence of several mechanisms by which RPL5 mutations may impair wild-type p53 upregulation and ribosome biogenesis. Unexpectedly, the same approach provides only modest evidence for a similar role of RPL11, suggesting that RPL5 represents a preferred target during human tumorigenesis in cancers with wild-type p53. Furthermore, we find that several functional cancer-associated RPL5 somatic mutations occur as rare germline variants in general population. Our results shed light on the so-far enigmatic role of cancer-associated mutations in genes encoding ribosomal proteins, with implications for our understanding of the tumor suppressive role of the RPL5/RPL11/5S rRNA complex in human malignancies.
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50
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Rahman N, Shamsuzzaman M, Lindahl L. Interaction between the assembly of the ribosomal subunits: Disruption of 40S ribosomal assembly causes accumulation of extra-ribosomal 60S ribosomal protein uL18/L5. PLoS One 2020; 15:e0222479. [PMID: 31986150 PMCID: PMC6984702 DOI: 10.1371/journal.pone.0222479] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 01/07/2020] [Indexed: 12/22/2022] Open
Abstract
Inhibition of the synthesis of an essential ribosomal protein (r-protein) abrogates the assembly of its cognate subunit, while assembly of the other subunit continues. Ribosomal components that are not stably incorporated into ribosomal particles due to the disrupted assembly are rapidly degraded. The 60S protein uL18/L5 is an exception and this protein accumulates extra-ribosomally during inhibition of 60S assembly. Since the r-proteins in each ribosomal subunit are essential only for the formation of their cognate subunit, it would be predicted that accumulation of extra-ribosomal uL18/L5 is specific to restriction of 60S assembly and does not occur abolition of 40S assembly. Contrary to this prediction, we report here that repression of 40S r-protein genes does lead to accumulation of uL18/L5 outside of the ribosome. Furthermore, the effect varies depending on which 40S ribosomal protein is repressed. Our results also show extra-ribosomal uL18/L5 is formed during 60S assembly, not during degradation of mature cytoplasmic 60S subunits. Finally, we propose a model for the accumulation of extra-ribosomal uL18 in response to the abolition of 40S r-proteins.
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Affiliation(s)
- Nusrat Rahman
- Department of Biological Sciences, University of Maryland, Baltimore County (UMBC), Baltimore, Maryland, United States of America
| | - Md Shamsuzzaman
- Department of Biological Sciences, University of Maryland, Baltimore County (UMBC), Baltimore, Maryland, United States of America
| | - Lasse Lindahl
- Department of Biological Sciences, University of Maryland, Baltimore County (UMBC), Baltimore, Maryland, United States of America
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