bims-raghud Biomed News
on RagGTPases in human diseases
Issue of 2025–08–03
eight papers selected by
Irene Sambri, TIGEM
  1. Structural basis for mTORC1 regulation by the CASTOR1-GATOR2 complex.
  2. FGF Signaling Promotes Lysosome Biogenesis in Chondrocytes via the Mannose Phosphate Receptor Pathway.
  3. Elevation of master autophagy regulator Tfeb in osteoblast lineage cells increases bone mass and strength.
  4. Dual Inhibition of CDK4/6 and mTORC1 Establishes a Preclinical Strategy for Translocation Renal Cell Carcinoma.
  5. Post-translational modifications orchestrate mTOR-driven cell death in cardiovascular disease.
  6. Long-Term Outcomes After Kidney Transplantation in a Recipient With Birt-Hogg-Dubé Syndrome.
  7. METTL3 Modulates Autophagy by Targeting TFEB in Myocardial Hypertrophy.
  8. Modeling heart rhythm using human engineered heart tissues.
  1. Nat Struct Mol Biol. 2025 Jul 25.
    Structural basis for mTORC1 regulation by the CASTOR1-GATOR2 complex.
    Rachel M Jansen, Clément Maghe, Karla Tapia, Selina Wu, Serim Yang, Xuefeng Ren, Roberto Zoncu, James H Hurley.
      Mechanistic target of rapamycin complex 1 (mTORC1) is a nutrient-responsive master regulator of metabolism. Amino acids control the recruitment and activation of mTORC1 at the lysosome through the nucleotide loading state of the heterodimeric Rag GTPases. Under low nutrients, including arginine, the GTPase-activating protein complex GATOR1 promotes GTP hydrolysis on RagA/B, inactivating mTORC1. GATOR1 is regulated by the cage-like GATOR2 complex and cytosolic amino acid sensors. To understand how the arginine sensor CASTOR1 binds to GATOR2 to disinhibit GATOR1 under low cytosolic arginine, we determined the cryo-electron microscopy structure of human GATOR2 bound to CASTOR1 in the absence of arginine. Two MIOS WD40 domain β-propellers of the GATOR2 cage engage with both subunits of a single CASTOR1 homodimer. Each propeller binds to a negatively charged MIOS-binding interface on CASTOR1 that is distal to the arginine pocket. The structure shows how arginine-triggered loop ordering in CASTOR1 blocks the MIOS-binding interface, switches off its binding to GATOR2 and, thus, communicates to downstream mTORC1 activation.
    DOI:  https://doi.org/10.1038/s41594-025-01635-0
  2. Traffic. 2025 Jul-Sep;26(7-9):26(7-9): e70013
    FGF Signaling Promotes Lysosome Biogenesis in Chondrocytes via the Mannose Phosphate Receptor Pathway.
    Laura Cinque, Maria Iavazzo, Gennaro Di Bonito, Elena Polishchuk, Rossella De Cegli, Carmine Settembre.
      The mannose 6-phosphate (M6P) pathway is critical for lysosome biogenesis, facilitating the trafficking of hydrolases to lysosomes to ensure cellular degradative capacity. Fibroblast Growth Factor (FGF) signaling, a key regulator of skeletogenesis, has been linked to the autophagy-lysosomal pathway in chondrocytes, but its role in lysosome biogenesis remains poorly characterized. Here, using mass spectrometry, lysosome immune-purification, and functional assays, we reveal that RCS (Swarm rat chondrosarcoma cells) lacking FGF receptors 3 and 4 exhibit dysregulations of the M6P pathway, resulting in hypersecretion of lysosomal enzymes and impaired lysosomal function. We found that FGF receptors control the expression of M6P receptor genes in response to FGF stimulation and during cell cycle via the activation of the transcription factors TFEB and TFE3. Notably, restoring M6P pathway-either through gene expression or activation of TFEB-significantly rescues lysosomal defects in FGFR3;4-deficient RCS. These findings uncover a novel mechanism by which FGF signaling regulates lysosomal function, offering insights into the control of chondrocyte catabolism and the understanding of FGF-related human diseases.
    Keywords:  FGF signaling; MPR trafficking pathway; TFEB; chondrocytes; lysosome; mannose phosphate receptors
    DOI:  https://doi.org/10.1111/tra.70013
  3. JCI Insight. 2025 Jul 29. pii: e191688. [Epub ahead of print]
    Elevation of master autophagy regulator Tfeb in osteoblast lineage cells increases bone mass and strength.
    Alicen James, James A Hendrixson, Ilham Kadhim, Adriana Marques-Carvalho, Jacob Laster, Julie Crawford, Jeff Thostenson, Visanu Wanchai, Amy Y Sato, Intawat Nookaew, Jinhu Xiong, Maria Almeida, Melda Onal.
      Autophagy is a recycling pathway in which damaged proteins, protein aggregates, and organelles are delivered to lysosomes for degradation. Autophagy insufficiency is thought to contribute to osteoporosis. Accordingly, autophagy elimination from the osteoblast lineage reduces bone formation and bone mass. However, whether increasing autophagy would benefit bone health is unknown. Here, we increased expression of endogenous transcription factor EB gene (Tfeb) in osteoblast lineage cells in vivo via CRISPR activation (TfebCRa mice). Elevated Tfeb stimulated autophagy and lysosomal biogenesis in osteoblasts. TfebCRa mice displayed a robust increase in femoral and vertebral cortical thickness at 4.5 months of age. Increases in cortical thickness was due to increased periosteal bone formation. Tfeb elevation also increased femoral trabecular bone volume. These changes increased bone strength of TfebCRa mice. Female TfebCRa mice displayed a progressive increase in bone mass and at 12 months of age had high cortical thickness and trabecular bone volume. Increased vertebral trabecular bone volume was due to elevated bone formation. Osteoblastic cultures showed that Tfeb elevation increased proliferation and mineral deposition. Overall, these results demonstrate TFEB-driven stimulation of autophagy in osteoblast lineage cells is associated with increased bone formation and strength and may represent an effective approach to combat osteoporosis.
    Keywords:  Autophagy; Bone biology; Cell biology; Osteoclast/osteoblast biology; Osteoporosis
    DOI:  https://doi.org/10.1172/jci.insight.191688
  4. bioRxiv. 2025 Jul 17. pii: 2025.07.11.663903. [Epub ahead of print]
    Dual Inhibition of CDK4/6 and mTORC1 Establishes a Preclinical Strategy for Translocation Renal Cell Carcinoma.
    Shikha Gupta, Prateek Khanna, Eddy Saad, Renee Maria Saliby, Shatha AbuHammad, Jiao Li, Bingchen Li, Prathyusha Konda, Usman Ali Ahmed, Ananthan Sadagopan, Qingru Xu, Ziad Bakouny, Wenxin Xu, Ramaprasad Srinivasan, Toni K Choueiri, Srinivas R Viswanathan.
       Purpose: Translocation renal cell carcinoma (tRCC) is a rare and aggressive subtype of kidney cancer driven by an oncogenic fusion involving a transcription factor in the MiT/TFE gene family, most commonly TFE3 . Treatment of tRCC currently lacks a clear standard of care, underscoring the pressing need to nominate new therapeutic targets with mechanistic rationale in this cancer.
    Experimental Design: In this study, we applied integrative genomic approaches to identify activation of the cyclin-dependent kinase 4/6 (CDK4/6) and mammalian target of rapamycin complex 1 (mTORC1) pathways in tRCC. We tested the activity of CDK4/6 inhibitors (CDK4/6i), alone or in combination with mTORC1-selective inhibition, using in vitro and in vivo models of tRCC.
    Results: tRCC tumors displayed multiple genomic and transcriptional features associated with activation of the CDK4/6 and mTORC1 signaling pathways. Genetic or pharmacologic inhibition of CDK4/6 suppressed tRCC cell growth and induced cell cycle arrest in vitro but was not cytotoxic, with rapid cell regrowth observed after drug withdrawal. The mTORC1-selective inhibitor, RMC-5552, potently reduced translation of Cyclin D1, which complexes with CDK4/6 proteins to regulate G1-S cell cycle progression. Combined treatment with the CDK4/6 inhibitor, palbociclib, and RMC-5552 resulted in synergistic suppression of tRCC cell viability and increased markers of apoptosis in vitro . The combination of palbociclib and RMC-5552 in a tRCC xenograft model showed greater eOicacy than either single agent while also being well-tolerated.
    Conclusions: Our study indicates the therapeutic potential of combined CDK4/6 and mTORC1 inhibition in tRCC, providing the rationale for further clinical evaluation of this strategy.
    Translational Relevance: Translocation renal cell carcinoma (tRCC) is a rare and aggressive form of kidney cancer that accounts for 2-5% of all RCCs in adults and around 50% of RCCs in children. tRCC lacks effective therapies and represents a significant unmet clinical need. Therapies approved for clear cell RCC (ccRCC), including VEGF/multikinase inhibitors and immune checkpoint blockade, typically show decreased efficacy in tRCC. Via an integrative genomic analysis, we nominate combined inhibition of the cyclin-dependent kinase 4/6 (CDK4/6) and mammalian target of rapamycin complex 1 (mTORC1) pathways in tRCC. We demonstrate that combining the CDK4/6 inhibitor palbociclib with the mTORC1-selective inhibitor RMC-5552 synergistically inhibits the growth of tRCC cells in vitro and of tRCC xenografts in vivo , where the combination is well-tolerated. This proof-of-concept study provides preclinical evidence supporting CDK4/6 inhibitor-based combination regimens tailored to tRCC biology, offering a foundation for future clinical studies in tRCC, which currently has no clear standard of care.
    DOI:  https://doi.org/10.1101/2025.07.11.663903
  5. Front Cardiovasc Med. 2025 ;12 1620669
    Post-translational modifications orchestrate mTOR-driven cell death in cardiovascular disease.
    Jiawei Guo, Yiting Wu, Zhengdong Wan, Zhaoshan Zhang.
      The mechanistic target of rapamycin (mTOR) signaling pathway is a central regulator of cellular physiology, modulating processes such as metabolism, protein synthesis, growth, and various forms of cell death. Increasing evidence has revealed that dysregulation of mTOR activity, often triggered or exacerbated by aberrant post-translational modifications (PTMs), contributes to the onset and progression of cardiovascular diseases (CVDs), including atherosclerosis, myocardial infarction, heart failure, and ischemia-reperfusion injury. PTMs such as phosphorylation, ubiquitination, SUMOylation, acetylation, and glycosylation alter mTOR's upstream regulators and downstream effectors, influencing the balance between apoptosis, autophagy, pyroptosis, and ferroptosis. These regulatory mechanisms provide a molecular basis for cell fate decisions during cardiovascular stress and injury. In this review, we systematically summarize recent advances in the understanding of PTM-mediated control of mTOR signaling, with a focus on cardiovascular pathophysiology. We also highlight emerging therapeutic strategies that target PTMs or the mTOR axis, including mTOR inhibitors, AMPK activators, proteasome blockers, and SUMOylation modulators, all of which show promise in preclinical or clinical settings. Understanding how PTMs fine-tune mTOR activity and cell death may pave the way for novel, targeted interventions in cardiovascular medicine and offer potential avenues for the development of precision therapies.
    Keywords:  MTOR signaling; cardiovascular diseases; cell death; protein modifications; therapeutic strategies
    DOI:  https://doi.org/10.3389/fcvm.2025.1620669
  6. Case Rep Transplant. 2025 ;2025 5889953
    Long-Term Outcomes After Kidney Transplantation in a Recipient With Birt-Hogg-Dubé Syndrome.
    Armando Salim Munoz Abraham, Adriana Medina, Rojin Esmail, Timothy Trestrail, Franco Cabeza Rivera.
      Introduction: Birt-Hogg-Dubé syndrome is a rare autosomal dominant disorder caused by folliculin germline mutations. Renal cell carcinoma is the most serious manifestation of this condition occurring at a rate of 30%, often requiring nephrectomy. Although preserving renal function remains the central goal of management, the risk of end-stage renal disease remains high. Patients with other inherited renal carcinomas have been successfully transplanted in the past, but there is scarce literature regarding Birt-Hogg-Dubé syndrome and kidney transplantation. Case Presentation: A 48-year-old male presented to our facility for evaluation of recurrent pneumothorax. Computed tomography of the chest revealed bilateral pulmonary cysts and multiple bilateral renal masses. Given the coexisting pulmonary cysts and renal masses, he was diagnosed with Birt-Hogg-Dubé syndrome. Bilateral radical nephrectomy was performed due to the presence of multifocal tumors measuring up to 5 cm. Tumor pathology was consistent with oncocytoma and renal cell carcinoma. After 2 years of hemodialysis and surveillance, the patient underwent kidney transplant. At 2-year follow-up after transplantation, renal function remains stable and has no evidence of recurrent renal disease, managed with belatacept and mTor inhibitors. Discussion: Tumor aggressiveness, metastasis risk, and time in remission are important factors when evaluating a patient with a history of Birt-Hogg-Dubé syndrome associated with renal cell carcinoma for kidney transplant. Therefore, these patients are suitable candidates for transplant after a minimum waiting period. Posttransplant immunosuppression with mTOR inhibitors can be considered since the mutation of the tumor suppressor folliculin germline in the mTOR pathway is central to Birt-Hogg-Dubé syndrome pathogenesis. Conclusion: In this case report, we demonstrated that kidney transplantation is a viable option for patients with Birt-Hogg-Dubé syndrome-related renal cell carcinoma.
    Keywords:  Birt–Hogg–Dubé syndrome; cancer; dialysis and transplantation; genetics; renal cell carcinoma
    DOI:  https://doi.org/10.1155/crit/5889953
  7. Int Heart J. 2025 ;66(4): 615-627
    METTL3 Modulates Autophagy by Targeting TFEB in Myocardial Hypertrophy.
    Yanan Xie, Wei Jiao, Hongchao Wang, Shaowei Kang, Jie Hao, Jinming Liu, Yongjun Li, Bingyan Guo.
      The aim of this study was to investigate the mechanism of m6A methylation in pathological myocardial hypertrophy (PMH), focusing on whether the methyltransferase METTL3 regulates the expression and nuclear translocation of the transcription factor EB (TFEB), thereby affecting autophagic activity and exacerbating the development of myocardial hypertrophy.An in vivo PMH model was established in mice via transverse aortic constriction (TAC), and an in vitro hypertrophy model was established using H9C2 cells stimulated with angiotensin II (AngII). HE staining, Western blotting, qRT-PCR, immunofluorescence, and dual-color autophagy flux analyses were employed to detect the expression of autophagy-related proteins (LC3, Beclin-1, P62, ATG5) and apoptosis levels. Changes in TFEB and key m6A-related enzymes (METTL3, ALKBH5, heterogeneous nuclear ribonucleoprotein D [HNRNPD]) were examined, and gene overexpression or knockdown experiments were performed to clarify their roles in regulating autophagy and myocardial hypertrophy. Finally, m6A MeRIP-qPCR and RIP-qPCR were conducted to explore the effect of METTL3 on m6A modification and the stability of TFEB transcripts, verifying the interplay between METTL3 and TFEB and its impact on autophagy.In both the in vivo and in vitro hypertrophy models, autophagy was significantly impaired and apoptosis was elevated, while TFEB mRNA and protein expression and its nuclear localization were clearly reduced. At the same time, global m6A methylation was markedly increased, accompanied by upregulation of METTL3 and HNRNPD, as well as downregulation of ALKBH5. Functional assays indicated that METTL3 overexpression further inhibited autophagy-related protein expression and autophagic flux, whereas METTL3 knockdown partially restored autophagy. Mechanistic studies revealed that METTL3 modulates TFEB pre-mRNA stability by influencing the binding efficiencies of ALKBH5 and HNRNPD, resulting in decreased TFEB expression. Conversely, overexpression of TFEB could partly counteract the autophagy impairment caused by METTL3 overexpression and reciprocally regulate the expression of METTL3, ALKBH5, and HNRNPD.METTL3 mediates the inhibition of TFEB via m6A modification, thereby impairing autophagy and aggravating myocardial hypertrophy. These findings suggest that the m6A-TFEB axis may serve as a novel therapeutic target for preventing and treating myocardial hypertrophy and heart failure, offering new insights into the intervention of cardiac remodeling-related diseases.
    Keywords:  Autophagic flux regulation; Cardiac remodeling; Epitranscriptomic regulation; Heart failure progression; m6A modification
    DOI:  https://doi.org/10.1536/ihj.24-683
  8. Nat Protoc. 2025 Aug 01.
    Modeling heart rhythm using human engineered heart tissues.
    Chengyi Tu, Arianne Caudal, Yu Liu, Sanjiv M Narayan, Joseph C Wu.
      Heart rate is both an indicator and modulator of cardiovascular health. Prolonged elevation in heart rate or irregular heart rhythm can trigger the onset of cardiac dysfunction, a condition termed 'tachycardia-induced cardiomyopathy'. While large animals have historically served as the primary model for studying this condition owing to their similar resting heart rates to humans, their use is limited by cost and throughput constraints. We recently developed the first engineered model of tachycardia-induced cardiomyopathy to overcome this technical bottleneck. Our model uses matured human engineered myocardium coupled with programmable electrical stimulation to emulate the pathophysiological changes in human heart rhythm. This in vitro model, capable of acutely and chronically modulating both beating rate and rhythm, recapitulated the clinical hallmarks of tachycardia-induced cardiomyopathy, and its utility was further validated via molecular comparisons against data from a canine model and human patients. Moreover, this model has improved the throughput and relevance to human genetics, enabling deep mechanistic explorations that were previously impossible. Here we present a comprehensive workflow detailing the fabrication and maturation of human engineered heart tissue, assembly of the electrical pacing system, functional analysis using open-source software and preparation for proteomic and transcriptomic analyses. This 5-week Protocol could be implemented by an experienced bench scientist with strong expertise in cell culture, ideally involving stem cell-derived cardiomyocytes. Given the broad implications of heart rhythm alterations in various cardiac conditions, this workflow can be employed with other biophysical and chemical cues to generate more complex and physiologically relevant cardiac models.
    DOI:  https://doi.org/10.1038/s41596-025-01217-w
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