bims-raghud Biomed News
on RagGTPases in human diseases
Issue of 2025–09–07
seven papers selected by
Irene Sambri, TIGEM



  1. J Cell Biol. 2025 Oct 06. pii: e202307079. [Epub ahead of print]224(10):
      TFEB, a master regulator of autophagy and lysosomal biogenesis, is activated by several cellular stresses including lysosomal damage, but its underlying mechanism is unclear. TFEB activation during lysosomal damage depends on the ATG conjugation system, which mediates lipidation of ATG8 proteins. Here, we newly identify ATG conjugation-independent TFEB regulation that precedes ATG conjugation-dependent regulation, designated Modes I and II, respectively. We reveal unique regulators of TFEB in each mode: APEX1 in Mode I and CCT7 and/or TRIP6 in Mode II. APEX1 interacts with TFEB independently of the ATG conjugation system, and is required for TFEB stability, while both CCT7 and TRIP6 accumulate on lysosomes during lysosomal damage, and interact with TFEB mainly in ATG conjugation system-deficient cells, presumably blocking TFEB activation. TFEB activation by several other stresses also involves either Mode I or Mode II. Our results pave the way for a unified understanding of TFEB regulatory mechanisms from the perspective of the ATG conjugation system under a variety of cellular stresses.
    DOI:  https://doi.org/10.1083/jcb.202307079
  2. Life Sci Alliance. 2025 Nov;pii: e202503206. [Epub ahead of print]8(11):
      The mammalian target of rapamycin complex 1 (mTORC1) signaling pathway, composed of amino acid (AA)-sensing (Ragulator/LAMTOR-Rag) and growth factor (GF)-sensing (AKT-TSC1/2-Rheb) axes, pivotally regulates intracellular anabolism and catabolism. mTORC1 deregulation is associated with various metabolic diseases, including cancer and diabetes. As a key regulator of nutrient signaling, mTORC1 integrates a variety of nutrient signals. However, signal integration and crosstalk in the mTORC1 pathway remain incompletely understood. Therefore, in this study, we aimed to understand the complex mTORC1 signaling cascade by constructing an integrated mathematical model of temporal mTORC1 regulation using two AA-sensing and GF-sensing axes. Mathematical simulations and experimental data revealed robust AKT phosphorylation (P-T308/P-S473) after insulin stimulation, regardless of the intracellular AA levels. Conversely, AKT-mediated inhibitory TSC2 phosphorylation (P-T1462) substantially diminished during AA deprivation compared with AA treatment. Furthermore, we highlighted PP2A-mediated TSC2 dephosphorylation during AA removal, ensuring complete mTORC1 activation only upon concurrent AA and GF sensing. Thus, we elucidated mTORC1 signaling dynamics, revealing the complex interplay between AAs and GFs and offering insights into metabolic regulation.
    DOI:  https://doi.org/10.26508/lsa.202503206
  3. PLoS One. 2025 ;20(9): e0330437
      In Npc1 deficient mice, postnatal developmental alterations in cerebellar microglia and Purkinje cells (PCs) are followed by early-onset neurodegeneration. Even in the absence of PC loss, microglia in Npc1nmf164 mice display hallmark features of activation during early postnatal development, including increased proliferation, enhanced phagocytic activity, and morphological changes indicative of an activated state. In this study, we investigated whether mammalian target of rapamycin complex 1 (mTORC1) drives postnatal activation of cerebellar microglia in Npc1nmf164 mice. We found that elevated CLEC7A (Dectin-1) expression and phosphorylation of S6 ribosomal protein (pS6R), a downstream target of mTORC1, co-occurred in microglial precursors within the developing white matter region (dWMR) of wild-type (WT) mice at postnatal day 7 (P7), as well as in neurodegeneration-associated microglia located in the molecular layer (ML) of Npc1nmf164 mice at P60. In contrast, microglia in the WMR of Npc1nmf164 mice at P60 did not show evidence of CLEC7A expression or increased mTORC1 activation. Interestingly, microglial precursors in the dWMR of Npc1nmf164 mice did not exhibit increased mTORC1 activation at P7 but instead showed delayed increased activation at P10. Inhibiting mTORC1 signaling with rapamycin from P10 to P21 reduced both microglial proliferation and soma size in Npc1nmf164 mice. Additionally, rapamycin treatment preserved VGLUT2⁺ presynaptic terminals/axons that innervate PC dendrites and decreased the total volume of CD68⁺ phagosomes per microglial cell, suggesting a reduction in phagocytic activity. However, the volume of VGLUT2⁺ synaptic material per phagosome remained unchanged between vehicle- and rapamycin-treated groups. While rapamycin enhanced myelination in Npc1nmf164 mice, it did not alter microglial phenotypes in the cerebellar WMR, suggesting that mTORC1 signaling does not mediate WMR microglial activation in this model. Together, our findings demonstrate that mTORC1 activation contributes to the aberrant activation of postnatal ML microglia and to early cerebellar pathology in Npc1nmf164 mice.
    DOI:  https://doi.org/10.1371/journal.pone.0330437
  4. Nephrol Dial Transplant. 2025 Sep 01. pii: gfaf179. [Epub ahead of print]
       BACKGROUND: Renal fibrosis is a common pathological feature of chronic kidney disease (CKD), but its underlying mechanisms remain incompletely understood. Our previous study demonstrated that insulin-like growth factor-binding protein 5 (IGFBP-5) promotes glycolytic reprogramming in vascular endothelial cells (ECs) and exacerbates renal inflammation in diabetic kidney disease (DKD).
    METHODS: Human renal proximal tubular epithelial cells (HK-2) and human umbilical vein endothelial cells (HUVECs) were used. A co-culture system was employed to investigate endothelial cell-tubular epithelial cell (EC-TEC) crosstalk. Unilateral ureteral obstruction (UUO) and aristolochic acid nephropathy (ANN) models were established in wild-type (WT), global IGFBP-5-/-, and endothelial-specific Tie-2 Cre; IGFBP-5-/- mice. Expression levels of IGFBP-5, TGF-β1, and fibrosis markers were assessed to to investigate the role of IGFBP-5 in renal fibrogenesis.
    RESULTS: Serum IGFBP-5 levels were significantly elevated in patients with chronic kidney disease (CKD). Genetic ablation of IGFBP-5 attenuated renal fibrosis in murine models, demonstrating its critical role in fibrogenesis. IGFBP-5 was predominantly expressed in endothelial cells (ECs), and endothelial-specific deletion delayed renal fibrosis progression via suppression of the TGF-β1/Smad3 pathway. In vitro, endothelial-derived IGFBP-5 promoted a profibrotic phenotypic transformation in TECs through AKT-mediated phosphorylation of the TGF-β1/Smad3 axis. Conversely, TGF-β1 stimulated IGFBP-5 biosynthesis and secretion in ECs via the ERK signaling pathway, establishing a self-amplifying feedback loop. This reciprocal IGFBP-5/TGF-β1 crosstalk between ECs and TECs was confirmed in co-culture experiments.
    CONCLUSION: Our findings reveal a novel endothelial cell-tubular epithelial cell (EC-TEC) crosstalk axis mediated by reciprocal IGFBP-5/TGF-β1 signaling, which is a critical driver of renal fibrosis. IGFBP-5 emerges as a promising therapeutic target for inhibiting renal fibrogenesis in CKD.
    Keywords:  IGFBP-5; TGF-β1; chronic kidney disease; crosstalk; fibrosis
    DOI:  https://doi.org/10.1093/ndt/gfaf179
  5. Science. 2025 Sep 04. 389(6764): 1016-1023
      The global burden of kidney disease displays marked sexual dimorphism. Lineage tracing and single-cell RNA-sequencing revealed that starting from puberty, estrogen signaling in female mice supports self-renewal and differentiation of renal progenitors to increase filtration capacity, reducing sensitivity to glomerular injury compared with that of males. This phenomenon accelerated as female kidneys adapted to the workload of pregnancy. Deletion of estrogen receptor α in renal progenitors disrupted this adaptation, leading to preeclampsia, fetal growth restriction, and increased maternal risk of hypertension and chronic kidney disease. Offspring from affected mothers had fewer nephrons, resulting in early-life hypertension and greater susceptibility to kidney disease. These results highlight the fundamental role of kidney fitness and renal progenitors for pregnancy and preeclampsia and as a determinant of sexual dimorphism in kidney disease.
    DOI:  https://doi.org/10.1126/science.adp4629
  6. Sci Rep. 2025 Aug 31. 15(1): 32013
      YAP1 gene fusions are found in a multitude of human tumors and are the likely tumor-initiating events in these tumors. We have previously shown that YAP1 fusion proteins exert TEAD-dependent oncogenic YAP1 activity. However, the contributions of the C-terminal fusion partners to the oncogenic functions of YAP1 fusion proteins are understudied. Here, we expressed eight different YAP1 gene fusions in vivo. Tumors induced by YAP1::TFE3 displayed a significantly different histomorphology compared to tumors induced by other YAP1 fusions or activated non-fusion YAP1. To assess the extent to which TFE3 activity and the functional TFE3 domains (DNA binding: leucine zipper (LZ) and basic-helix-loop-helix (bHLH); activation domain (AD)) contribute to the oncogenic functions of YAP1::TFE3, we generated several mutant variants and performed functional in vitro and in vivo assays. In vitro, mutation or deletion of the TFE3 DNA binding domains (LZ, bHLH) resulted in reduced TFE3 activity but increased YAP1 activity of YAP1::TFE3. In vivo, deletion of the LZ and bHLH domains did not result in a decrease in tumor incidence but induced the formation of more YAP1-like tumors that lacked prominent features of YAP1::TFE3-driven tumors. By contrast, loss of the TFE3 AD almost completely abrogated tumor formation. Our results suggest that the TFE3 domains significantly contribute to the oncogenic activity of YAP1::TFE3.
    DOI:  https://doi.org/10.1038/s41598-025-17409-z
  7. Eur Heart J. 2025 Sep 04. pii: ehaf591. [Epub ahead of print]
      Chronic kidney disease (CKD) and cardiovascular disease are tightly interconnected, with common mechanisms that underlie the development and progression of both diseases, recently articulated into the framework of the cardiovascular-kidney-metabolic syndrome. CKD and heart failure commonly coexist in the same individual, with increasing evidence for common therapies in both disease states. It is valuable for patients, clinicians, and regulatory agencies to understand how to best assess CKD progression in patients with heart failure for evaluation of individual patients and as part of an endpoint for outcome trials. Given the relatively short duration of most heart failure outcome trials, early measures of CKD progression prior to the occurrence of clinical events of kidney replacement therapy would be desirable. Such surrogate measures include slowing of the decline in glomerular filtration rate (GFR) decline either computed as annualized mean change in GFR (GFR slope) or time to substantial declines in GFR by specified threshold percentages (40% or 50% GFR decline). Regulatory agencies accept these endpoints for full drug approval which has enabled progress in design and conduct of trials for CKD progression. Application of these endpoints in heart failure outcome trials has the potential for similar progress. However, an immediate reduction in GFR is common following initiation of several of the guideline directed therapy for heart failure. Understanding how to best interpret an immediate GFR reduction vs long term kidney benefit is critical to optimal assessment of endpoint in an outcome trial and in the use of these medications for management of patients with heart failure. Here, the intersection of heart failure and CKD is described, how GFR and its change over time are assessed in both individual patients and in interventional trials, the evidence supporting use of GFR changes as endpoints in CKD progression trials, and the challenges and possible solutions for the use of GFR as endpoint in heart failure outcome trials and for care of individual patients, guided by case studies to inform the discussion.
    Keywords:  Chronic kidney disease; GFR slope; Glomerular filtration rate; Heart failure; Randomized control trials
    DOI:  https://doi.org/10.1093/eurheartj/ehaf591