bims-raghud 2025-02-16 papers

bims-raghud

Biomed News

on RagGTPases in human diseases

Issue of 2025–02–16
eight papers selected by
Irene Sambri, TIGEM

Hyperosmotic Stress Promotes the Nuclear Translocation of TFEB in Tubular Epithelial Cells Depending on Intracellular Ca2+ Signals via TRPML Channels.
Ezrin defines TSC complex activation at endosomal compartments through EGFR-AKT signaling.
BBOX1 restrains TBK1-mTORC1 oncogenic signaling in clear cell renal cell carcinoma.
Transcriptional repression of autophagy and lysosome biogenesis.
Lysosome Functions in Atherosclerosis: A Potential Therapeutic Target.
Application progress of bio-manufacturing technology in kidney organoids.
Role of Hippo-YAP/TAZ signaling pathway in organ fibrosis.
Clear cell renal carcinoma essentially requires CDKL3 for oncogenesis.

Cell Mol Bioeng. 2025 Feb;18(1): 39-52

Hyperosmotic Stress Promotes the Nuclear Translocation of TFEB in Tubular Epithelial Cells Depending on Intracellular Ca2+ Signals via TRPML Channels.

Takashi Miyano, Atsushi Suzuki, Hisaaki Konta, Naoya Sakamoto.

   Purpose: We previously demonstrated that hyperosmotic stress, which acts as mechanical stress, induces autophagy of tubular epithelial cells. This study aims to elucidate the molecular mechanisms of hyperosmolarity-induced autophagy. The research question addresses how hyperosmotic stress activates autophagy through transcription factor EB (TFEB) and Ca2+ signaling pathways, contributing to understanding cellular responses to mechanical stress.
Methods: NRK-52E normal rat kidney cells were subjected to hyperosmotic stress using mannitol-containing medium. Fluorescence microscopy was utilized to observe TFEB nuclear translocation, a crucial event in autophagy regulation. An intracellular Ca2+ chelator, BAPTA-AM, and a calcineurin inhibitor were used to dissect the Ca2+ signaling pathway involved in TFEB translocation. The phosphorylation of p70S6K, a substrate of the mammalian target of rapamycin complex 1 kinase, was analyzed to explore its role in TFEB localization. Additionally, the function of transient receptor potential mucolipin 1 (TRPML1), an intracellular Ca2+ channel, was assessed using pharmacological inhibition to determine its impact on TFEB translocation and autophagy marker LC3-II levels.
Results: Mannitol-induced hyperosmotic stress promoted the nuclear translocation of TFEB, which was completely abolished by treatment with BAPTA-AM. Inhibition of calcineurin suppressed TFEB nuclear translocation under hyperosmolarity, indicating that a signaling pathway governed by intracellular Ca2+ is involved in TFEB's nuclear translocation. In contrast, hyperosmotic stress did not significantly alter p70S6K phosphorylation. Pharmacological inhibition of TRPML1 attenuated both TFEB nuclear translocation and LC3-II upregulation in response to hyperosmotic stress.
Conclusions: Hyperosmotic stress promotes TFEB nuclear localization, and TRPML1-induced activation of calcineurin is involved in the mechanism of hyperosmolarity-induced autophagy.
Supplementary Information: The online version contains supplementary material available at 10.1007/s12195-024-00839-6.

Keywords:  Calcineurin; Hyperosmolarity; TRPML1; Transcription factor EB (TFEB); Tubular epithelial cell

DOI:  https://doi.org/10.1007/s12195-024-00839-6
Elife. 2025 Feb 12. pii: RP98523. [Epub ahead of print]13

Ezrin defines TSC complex activation at endosomal compartments through EGFR-AKT signaling.

Giuliana Giamundo, Daniela Intartaglia, Eugenio Del Prete, Elena Polishchuk, Fabrizio Andreone, Marzia Ognibene, Sara Buonocore, Bruno Hay Mele, Francesco Giuseppe Salierno, Jlenia Monfregola, Dario Antonini, Paolo Grumati, Alessandra Eva, Rossella De Cegli, Ivan Conte.

  Endosomes have emerged as major signaling hubs where different internalized ligand-receptor complexes are integrated and the outcome of signaling pathways are organized to regulate the strength and specificity of signal transduction events. Ezrin, a major membrane-actin linker that assembles and coordinates macromolecular signaling complexes at membranes, has emerged recently as an important regulator of lysosomal function. Here, we report that endosomal-localized EGFR/Ezrin complex interacts with and triggers the inhibition of the Tuberous Sclerosis Complex (TSC complex) in response to EGF stimuli. This is regulated through activation of the AKT signaling pathway. Loss of Ezrin was not sufficient to repress TSC complex by EGF and culminated in translocation of TSC complex to lysosomes triggering suppression of mTORC1 signaling. Overexpression of constitutively active EZRINT567D is sufficient to relocalize TSC complex to the endosomes and reactivate mTORC1. Our findings identify EZRIN as a critical regulator of autophagy via TSC complex in response to EGF stimuli and establish the central role of early endosomal signaling in the regulation of mTORC1. Consistently, Medaka fish deficient for Ezrin exhibit defective endo-lysosomal pathway, attributable to the compromised EGFR/AKT signaling, ultimately leading to retinal degeneration. Our data identify a pivotal mechanism of endo-lysosomal signaling involving Ezrin and its associated EGFR/TSC complex, which are essential for retinal function.

Keywords:  EGFR; EZRIN; TSC complex; cell biology; endosome; lysosome; mTORC1

DOI:  https://doi.org/10.7554/eLife.98523
Nat Commun. 2025 Feb 11. 16(1): 1543

BBOX1 restrains TBK1-mTORC1 oncogenic signaling in clear cell renal cell carcinoma.

Chengheng Liao, Lianxin Hu, Liwei Jia, Jin Zhou, Tao Wang, Kangsan Kim, Hua Zhong, Hongwei Yao, Lei Dong, Lei Guo, Qian Liang, Cheng Zhang, Fangzhou Zhao, Jun Fang, Hongyi Liu, Shina Li, Lin Xu, Jeremy M Simon, Srinivas Malladi, Payal Kapur, James Brugarolas, Ralph J DeBerardinis, Qing Zhang.

Clear cell renal cell carcinoma (ccRCC), a metabolic disease originating from renal proximal convoluted tubule (PCT) epithelial cells, remains incompletely understood in terms of its initiating signaling events. Here, we identify γ-butyrobetaine hydroxylase 1 (BBOX1), a key enzyme in carnitine synthesis predominantly expressed in PCT cells, as a tumor suppressor in ccRCC. BBOX1 expression is lost during ccRCC malignant transformation, and its restoration reduces cell viability in physiological medium and inhibits xenograft tumor growth. Transcriptomic analyses reveal that BBOX1 suppresses critical metabolic pathways including mTORC1 signaling and glycolysis in ccRCC. Further, we identify TANK-binding kinase 1 (TBK1) as an essential mediator of mTORC1 and glycolysis activation and as a target of BBOX1-mediated tumor suppression. Mechanistically, BBOX1 disrupts TBK1 activation by preventing its interaction with the upstream activator doublecortin-like kinase 2 (DCLK2). This BBOX1-DCLK2-TBK1 axis unveils an important mechanism in ccRCC metabolic dysregulation and highlights potential therapeutic strategies.

DOI: https://doi.org/10.1038/s41467-025-56955-y
Autophagy. 2025 Feb 12.

Transcriptional repression of autophagy and lysosome biogenesis.

Jaebeom Kim, Young Suk Yu, Keun Il Kim, Sung Hee Baek.

  The microphthalmia/transcription factor E (MiT/TFE) family activates macroautophagy/autophagy and lysosomal genes during acute nutrient deficiency. However, the mechanisms that suppress transcription of these genes under steady-state, nutrient-rich conditions to prevent unnecessary expression remain unclear. In this study, we identified a previously unrecognized mechanism of transcriptional repression for autophagy and lysosomal genes. Under nutrient-rich conditions, USF2 (upstream transcription factor 2) binds to the coordinated lysosomal expression and regulation (CLEAR) motif, recruiting a repressive complex containing HDAC (histone deacetylase). In contrast, during nutrient deficiency, TFEB (transcription factor EB) displaces USF2 at the same motif, activating transcription. This switch is regulated by USF2 phosphorylation at serine 155 by GSK3B (glycogen synthase kinase 3 beta). Reduced phosphorylation under nutrient-deprived conditions weakens USF2's DNA binding affinity, allowing TFEB to competitively bind and activate target genes. Knockdown or knockout of Usf2 upregulates specific autophagy and lysosomal genes, leading to enhanced lysosomal functionality and increased autophagic flux. In USF2-deficient cells, the SERPINA1 Z variant/antitrypsin Z - an aggregation-prone mutant protein used as a model - is rapidly cleared via the autophagy-lysosome pathway. Therefore, modulation of USF2 activity may be a therapeutic strategy for managing diseases associated with autophagy and lysosomal dysfunction.

Keywords:  Autophagy; MiT/TFE; TFEB; USF2; lysosome; transcriptional repressor

DOI:  https://doi.org/10.1080/15548627.2025.2465404
Cells. 2025 Jan 24. pii: 183. [Epub ahead of print]14(3):

Lysosome Functions in Atherosclerosis: A Potential Therapeutic Target.

Zhengchao Wang, Xiang Li, Alexandra K Moura, Jenny Z Hu, Yun-Ting Wang, Yang Zhang.

  Lysosomes in mammalian cells are recognized as key digestive organelles, containing a variety of hydrolytic enzymes that enable the processing of both endogenous and exogenous substrates. These organelles digest various macromolecules and recycle them through the autophagy-lysosomal system. Recent research has expanded our understanding of lysosomes, identifying them not only as centers of degradation but also as crucial regulators of nutrient sensing, immunity, secretion, and other vital cellular functions. The lysosomal pathway plays a significant role in vascular regulation and is implicated in diseases such as atherosclerosis. During atherosclerotic plaque formation, macrophages initially engulf large quantities of lipoproteins, triggering pathogenic responses that include lysosomal dysfunction, foam cell formation, and subsequent atherosclerosis development. Lysosomal dysfunction, along with the inefficient degradation of apoptotic cells and the accumulation of modified low-density lipoproteins, negatively impacts atherosclerotic lesion progression. Recent studies have highlighted that lysosomal dysfunction contributes critically to atherosclerosis in a cell- and stage-specific manner. In this review, we discuss the mechanisms of lysosomal biogenesis and its regulatory role in atherosclerotic lesions. Based on these lysosomal functions, we propose that targeting lysosomes could offer a novel therapeutic approach for atherosclerosis, shedding light on the connection between lysosomal dysfunction and disease progression while offering new insights into potential anti-atherosclerotic strategies.

Keywords:  atherosclerosis; autophagy; endothelial cells; lysosomes; macrophages; smooth muscle cells

DOI:  https://doi.org/10.3390/cells14030183
Biofabrication. 2025 Feb 11.

Application progress of bio-manufacturing technology in kidney organoids.

Runqi Mao, Junming Zhang, Haoxiang Qin, Yuanyuan Liu, Yuxin Xing, Wen Zeng.

  Kidney transplantation remains a pivotal treatment modality for kidney disease, yet its progress is significantly hindered by the scarcity of donor kidneys and ethical dilemmas surrounding their procurement. As organoid technology evolves and matures, the creation of bionic human kidney organoids offers profound potential for advancing kidney disease research, drug nephrotoxicity screening, and regenerative medicine. Nevertheless, current kidney organoid models grapple with limitations such as constrained cellular differentiation, underdeveloped functional structures, and a crucial absence of vascularization. This deficiency in vascularization, in particular, stunts organoid development, restricts their size, diminishes filtration capabilities, and triggers immunoinflammatory responses. Hence, the achievement of vascularization within kidney organoids and the successful establishment of functional microvascular networks constitutes a paramount goal for their future progression. In this review, we provide an overview of recent advancements in biotechnology domains, encompassing organ-on-a-chip technology, biomimetic matrices, and bioprinting, with the aim of catalyzing technological breakthroughs that can enhance the vascularization of kidney organoids and broaden their applicability. These technologies hold the key to unlocking the full potential of kidney organoids as a transformative therapeutic option for kidney disease.

Keywords:  biomimetic extracellular matrix; endothelial cells; kidney organoid; organ-on-a-chip; three-dimensional printing; vascularization

DOI:  https://doi.org/10.1088/1758-5090/adb4a1
Zhong Nan Da Xue Xue Bao Yi Xue Ban. 2024 Sept 28;49(9):pii: 1672-7347(2024)09-1509-08. [Epub ahead of print]49(9): 1509-1516

Role of Hippo-YAP/TAZ signaling pathway in organ fibrosis.

Junqing Wang, Linsheng Huang, Huifan Yu, Jingyu Liu, Lu Yuan, Fei Li.

  Organ fibrosis is closely associated with inflammation, tissue injury, and abnormal repair processes, characterized primarily by the activation of myofibroblasts and excessive extracellular matrix deposition. While the clinical manifestations and pathogenesis of fibrosis vary across organs, the progression of fibrosis can disrupt normal organ function, leading to disability or even death. The Hippo signaling pathway, an evolutionarily conserved kinase cascade, plays a pivotal role in regulating cell proliferation, apoptosis, differentiation, and tissue regeneration. Its primary effectors, yes-associated protein (YAP) and transcriptional co-activator with PDZ-binding motif (TAZ), are critically implicated in fibrosis of organs such as the kidney, liver, lung, heart, and skin. Currently, effective and specific treatments for organ fibrosis are lacking. A comprehensive understanding of the relationship between Hippo-YAP/TAZ signaling and organ fibrosis may provide novel perspectives for the clinical management of these conditions.

Keywords:  Hippo-Yes-associated protein/transcriptional coactivator with PDZ-binding motif; dermatofibrosis; liver fibrosis; myocardial fibrosis; pulmonary fibrosis; renal fibrosis

DOI:  https://doi.org/10.11817/j.issn.1672-7347.2024.230577
Proc Natl Acad Sci U S A. 2025 Feb 18. 122(7): e2415244122

Clear cell renal carcinoma essentially requires CDKL3 for oncogenesis.

Lanjing Ma, Zhongqiu Pang, Haijiao Zhang, Xueling Yang, Shaoqin Zheng, Yi Chen, Weijie Ding, Qing Han, Xi Zhang, Liu Cao, Teng Fei, Qiang Wang, Daming Gao, Aina He, Ke-Bang Hu, Xuexin Li, Ren Sheng.

  Clear cell renal cell carcinoma (ccRCC) is the predominant human renal cancer with surging incidence and fatality lately. Hyperactivation of hypoxia-inducible factor (HIF) and mammalian target of rapamycin (mTOR) signaling are the common signatures in ccRCC. Herein, we employed spontaneous ccRCC model to demonstrate the indispensability of an underappreciated Ser/Thr kinase, CDKL3, in the initiation and progression of ccRCC. Ablation of CDKL3 does not affect normal kidney, but abrogates Akt-mTOR hyperactivity and thoroughly prevents the formation and growth of the HIF-agitated ccRCC in vivo. Remarkable clinical correlations also supported the oncogenic role of CDKL3. Mechanism-wise, cytosolic CDKL3 unexpectedly behaves as the adaptor to physically potentiate mTORC2-dependent Akt activation without functioning through kinase activity. And mTORC2 can phosphorylate and stabilize CDKL3 to form a positive feedback loop to sustain the cancer-favored Akt-mTOR overactivation. Together, we revealed the pathological importance and molecular mechanism of CDKL3-mediated Akt-mTOR axis in ccRCC initiation and progression.

Keywords:  Akt; CDKL3; ccRCC; mTOR; oncogene

DOI:  https://doi.org/10.1073/pnas.2415244122