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Detrés D, Camacho-Badillo A, Calo E. A pH-Centric Model of Nucleolar Activity and Regulation. J Mol Biol 2025; 437:169136. [PMID: 40216015 DOI: 10.1016/j.jmb.2025.169136] [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: 11/17/2024] [Revised: 04/05/2025] [Accepted: 04/07/2025] [Indexed: 04/27/2025]
Abstract
The nucleolus is essential for the efficient and accurate production of ribosomal subunits, which are crucial for assembling ribosomes-the cellular machinery responsible for protein synthesis. Emerging insights into its liquid-like nature have shed new light on the role of its unique biophysical properties in the activity and regulation of this organelle. In this perspective, we examine recent insights into nucleolar biophysical homeostasis, with a focus on its regulation as an acidic biomolecular condensate. We review current evidence on how nucleolar composition and biochemical activities could generate and maintain a proton gradient. Additionally, we propose an integrative model explaining how nucleolar acidity contributes to homeostasis at a molecular level, providing a unified framework for its role in health and disease.
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Affiliation(s)
- Diego Detrés
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, United States; David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Adriana Camacho-Badillo
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Eliezer Calo
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, United States; David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, United States.
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2
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Howard GC, Tansey WP. Ribosome-directed cancer therapies: the tip of the iceberg? Trends Pharmacol Sci 2025; 46:303-310. [PMID: 40044536 PMCID: PMC11972149 DOI: 10.1016/j.tips.2025.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2025] [Revised: 02/03/2025] [Accepted: 02/10/2025] [Indexed: 03/09/2025]
Abstract
Ribosomes and ribosome biogenesis (RiBi) are universally corrupted in cancer, fueling the high rates of translation that sustain malignancy and creating opportunities for discriminating therapeutic intervention. Despite longstanding recognition of the promise of ribosome-directed cancer therapies, only a handful of such agents have been used in the clinic, and with limited success, and the true potential of this approach is unknown. In the past few years, however, understanding of cancer ribosome specialization and the intricacies of RiBi have advanced dramatically, opening opportunities that could not be imagined when existing agents were discovered. Here, we discuss the rationale for targeting ribosomes to treat cancer, review the limitations of current agents, and highlight an important set of recent discoveries we propose could be exploited to discover molecularly-targeted ribosome-directed cancer therapeutics.
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Affiliation(s)
- Gregory C Howard
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - William P Tansey
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA.
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Zhang X, Gao Y, Zhang S, Wang Y, Du Y, Hao S, Ni T. The Regulation of Cellular Senescence in Cancer. Biomolecules 2025; 15:448. [PMID: 40149983 PMCID: PMC11940315 DOI: 10.3390/biom15030448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2025] [Revised: 03/10/2025] [Accepted: 03/18/2025] [Indexed: 03/29/2025] Open
Abstract
Cellular senescence is a stable state of cell cycle arrest caused by telomere shortening or various stresses. After senescence, cells cease dividing and exhibit many age-related characteristics. Unlike the halted proliferation of senescence cells, cancer cells are considered to have unlimited growth potential. When cells display senescence-related features, such as telomere loss or stem cell failure, they can inhibit tumor development. Therefore, inducing cells to enter a senescence state can serve as a barrier to tumor cell development. However, many recent studies have found that sustained senescence of tumor cells or normal cells under certain circumstances can exert environment-dependent effects of tumor promotion and inhibition by producing various cytokines. In this review, we first introduce the causes and characteristics of induced cellular senescence, analyze the senescence process of immune cells and cancer cells, and then discuss the dual regulatory role of cell senescence on tumor growth and senescence-induced therapies targeting cancer cells. Finally, we discuss the role of senescence in tumor progression and treatment opportunities, and propose further studies on cellular senescence and cancer therapy.
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Affiliation(s)
- Xianhong Zhang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China; (X.Z.); (Y.G.); (Y.W.); (Y.D.)
| | - Yue Gao
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China; (X.Z.); (Y.G.); (Y.W.); (Y.D.)
| | - Siyu Zhang
- Key Lab of Ministry of Education for Protection and Utilization of Special Biological Resources in Western China, School of Life Sciences, Ningxia University, Yinchuan 750021, China;
| | - Yixiong Wang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China; (X.Z.); (Y.G.); (Y.W.); (Y.D.)
| | - Yitian Du
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China; (X.Z.); (Y.G.); (Y.W.); (Y.D.)
| | - Shuailin Hao
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China; (X.Z.); (Y.G.); (Y.W.); (Y.D.)
| | - Ting Ni
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China; (X.Z.); (Y.G.); (Y.W.); (Y.D.)
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Koyano F, Yamano K, Hoshina T, Kosako H, Fujiki Y, Tanaka K, Matsuda N. AAA+ ATPase chaperone p97/VCP FAF2 governs basal pexophagy. Nat Commun 2024; 15:9347. [PMID: 39472561 PMCID: PMC11522385 DOI: 10.1038/s41467-024-53558-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 10/14/2024] [Indexed: 11/02/2024] Open
Abstract
Peroxisomes are organelles that are central to lipid metabolism and chemical detoxification. Despite advances in our understanding of peroxisome biogenesis, the mechanisms maintaining peroxisomal membrane proteins remain to be fully elucidated. We show here that mammalian FAF2/UBXD8, a membrane-associated cofactor of p97/VCP, maintains peroxisomal homeostasis by modulating the turnover of peroxisomal membrane proteins such as PMP70. In FAF2-deficient cells, PMP70 accumulation recruits the autophagy adaptor OPTN (Optineurin) to peroxisomes and promotes their autophagic clearance (pexophagy). Pexophagy is also induced by p97/VCP inhibition. FAF2 functions together with p97/VCP to negatively regulate pexophagy rather than as a factor for peroxisome biogenesis. Our results strongly suggest that p97/VCPFAF2-mediated extraction of ubiquitylated peroxisomal membrane proteins (e.g., PMP70) prevents peroxisomes from inducing nonessential autophagy under steady state conditions. These findings provide insight into molecular mechanisms underlying the regulation of peroxisomal integrity by p97/VCP and its associated cofactors.
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Affiliation(s)
- Fumika Koyano
- Department of Biomolecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University (TMDU) (Medical Research Laboratory, Institute of Integrated Research, Institute of Science Tokyo), 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan.
| | - Koji Yamano
- Department of Biomolecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University (TMDU) (Medical Research Laboratory, Institute of Integrated Research, Institute of Science Tokyo), 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Tomoyuki Hoshina
- Department of Biomolecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University (TMDU) (Medical Research Laboratory, Institute of Integrated Research, Institute of Science Tokyo), 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Hidetaka Kosako
- Division of Cell Signaling, Fujii Memorial Institute of Medical Sciences, Institute of Advanced Medical Sciences, Tokushima University, 3-18-15 Kuramoto-cho, Tokushima, 770-8503, Japan
| | - Yukio Fujiki
- Medical Institute of Bioregulation, Institute of Rheological Functions of Food-Kyushu University Collaboration Program, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
- Institute for Advanced Study, Kyushu University, Fukuoka, 816-8580, Japan
| | - Keiji Tanaka
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya, Tokyo, 156-8506, Japan
| | - Noriyuki Matsuda
- Department of Biomolecular Pathogenesis, Medical Research Institute, Tokyo Medical and Dental University (TMDU) (Medical Research Laboratory, Institute of Integrated Research, Institute of Science Tokyo), 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan.
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Francés R, Mata-Garrido J, Lafarga M, Hurlé MA, Tramullas M. miR-30c-5p Gain and Loss of Function Modulate Sciatic Nerve Injury-Induced Nucleolar Stress Response in Dorsal Root Ganglia Neurons. Int J Mol Sci 2024; 25:11427. [PMID: 39518978 PMCID: PMC11547303 DOI: 10.3390/ijms252111427] [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] [Subscribe] [Scholar Register] [Received: 09/17/2024] [Revised: 10/17/2024] [Accepted: 10/22/2024] [Indexed: 11/16/2024] Open
Abstract
Neuropathic pain is a prevalent and debilitating chronic syndrome that is often resistant to treatment. It frequently arises as a consequence of damage to first-order nociceptive neurons in the lumbar dorsal root ganglia (DRG), with chromatolysis being the primary neuropathological response following sciatic nerve injury (SNI). Nevertheless, the function of miRNAs in modulating this chromatolytic response in the context of neuropathic pain remains unexplored. Our previous research demonstrated that the intracisternal administration of a miR-30c mimic accelerates the development of neuropathic pain, whereas the inhibition of miR-30c prevents pain onset and reverses established allodynia. In the present study, we sought to elucidate the role of miR-30c-5p in the pathogenesis of neuropathic pain, with a particular focus on its impact on DRG neurons following SNI. The organisation and ultrastructural changes in DRG neurons, particularly in the protein synthesis machinery, nucleolus, and Cajal bodies (CBs), were analysed. The results demonstrated that the administration of a miR-30c-5p mimic exacerbates chromatolytic damage and nucleolar stress and induces CB depletion in DRG neurons following SNI, whereas the administration of a miR-30c-5p inhibitor alleviates these effects. We proposed that three essential cellular responses-nucleolar stress, CB depletion, and chromatolysis-are the pathological mechanisms in stressed DRG neurons underlying neuropathic pain. Moreover, miR-30c-5p inhibition has a neuroprotective effect by reducing the stress response in DRG neurons, which supports its potential as a therapeutic target for neuropathic pain management. This study emphasises the importance of miR-30c-5p in neuropathic pain pathogenesis and supports further exploration of miRNA-based treatments.
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Affiliation(s)
- Raquel Francés
- Departamento de Fisiología y Farmacología, Facultad de Medicina, Universidad de Cantabria, 39011 Santander, Spain; (R.F.); (M.A.H.)
- Instituto Marqués de Valdecilla (IDIVAL), 39011 Santander, Spain; (J.M.-G.); (M.L.)
| | - Jorge Mata-Garrido
- Instituto Marqués de Valdecilla (IDIVAL), 39011 Santander, Spain; (J.M.-G.); (M.L.)
- Departamento de Anatomía y Biología Celular, Universidad de Cantabria, 39011 Santander, Spain
- Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), 28029 Madrid, Spain
| | - Miguel Lafarga
- Instituto Marqués de Valdecilla (IDIVAL), 39011 Santander, Spain; (J.M.-G.); (M.L.)
- Departamento de Anatomía y Biología Celular, Universidad de Cantabria, 39011 Santander, Spain
- Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), 28029 Madrid, Spain
| | - María A. Hurlé
- Departamento de Fisiología y Farmacología, Facultad de Medicina, Universidad de Cantabria, 39011 Santander, Spain; (R.F.); (M.A.H.)
- Instituto Marqués de Valdecilla (IDIVAL), 39011 Santander, Spain; (J.M.-G.); (M.L.)
| | - Mónica Tramullas
- Departamento de Fisiología y Farmacología, Facultad de Medicina, Universidad de Cantabria, 39011 Santander, Spain; (R.F.); (M.A.H.)
- Instituto Marqués de Valdecilla (IDIVAL), 39011 Santander, Spain; (J.M.-G.); (M.L.)
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Ramalho S, Dopler A, Faller W. Ribosome specialization in cancer: a spotlight on ribosomal proteins. NAR Cancer 2024; 6:zcae029. [PMID: 38989007 PMCID: PMC11231584 DOI: 10.1093/narcan/zcae029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 06/11/2024] [Accepted: 06/19/2024] [Indexed: 07/12/2024] Open
Abstract
In the past few decades, our view of ribosomes has changed substantially. Rather than passive machines without significant variability, it is now acknowledged that they are heterogeneous, and have direct regulatory capacity. This 'ribosome heterogeneity' comes in many flavors, including in both the RNA and protein components of ribosomes, so there are many paths through which ribosome specialization could arise. It is easy to imagine that specialized ribosomes could have wide physiological roles, through the translation of specific mRNA populations, and there is now evidence for this in several contexts. Translation is highly dysregulated in cancer, needed to support oncogenic phenotypes and to overcome cellular stress. However, the role of ribosome specialization in this is not clear. In this review we focus on specialized ribosomes in cancer. Specifically, we assess the impact that post-translational modifications and differential ribosome incorporation of ribosomal proteins (RPs) have in this disease. We focus on studies that have shown a ribosome-mediated change in translation of specific mRNA populations, and hypothesize how such a process could be driving other phenotypes. We review the impact of RP-mediated heterogeneity in both intrinsic and extrinsic oncogenic processes, and consider how this knowledge could be leveraged to benefit patients.
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Affiliation(s)
- Sofia Ramalho
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Anna Dopler
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - William James Faller
- Division of Oncogenomics, The Netherlands Cancer Institute, Amsterdam, Netherlands
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Huppertz I. Free ribosomal proteins as culprits for nucleolar stress. Mol Cell 2024; 84:1400-1402. [PMID: 38640892 DOI: 10.1016/j.molcel.2024.03.026] [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: 03/26/2024] [Revised: 03/26/2024] [Accepted: 03/26/2024] [Indexed: 04/21/2024]
Abstract
Nucleolar stress has been consistently linked to age-related diseases. In this issue, Sirozh et al.1 find that the common molecular signature of nucleolar stress is the accumulation of free ribosomal proteins, which leads to premature aging in mice; however, it can be reversed by mTOR inhibition.
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Affiliation(s)
- Ina Huppertz
- Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9b, 50931 Cologne, Germany; University of Cologne, Faculty of Medicine and University Hospital Cologne, Cluster of Excellence Cellular Stress Responses in Aging-associated Diseases (CECAD), Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany.
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