bims-raghud Biomed News
on RagGTPases in human diseases
Issue of 2025–02–09
eleven papers selected by
Irene Sambri, TIGEM



  1. JCI Insight. 2025 Feb 06. pii: e183560. [Epub ahead of print]
      Tacrolimus-induced chronic nephrotoxicity (TICN) hinders its long-term use, but its mechanism remains unclear. Tacrolimus exerts its pharmacological effect by inhibiting calcineurin and its substrate NFAT. Whether the inhibition of other calcineurin substrates is related to TICN remains to be explored. Transcription factor EB (TFEB), a substrate of calcineurin, plays a crucial role in various homeostasis. Herein, we found that tacrolimus inhibited TFEB nuclear translocation and activity in mouse kidneys and HK-2 cells. Then, TFEB gain- and loss-of-function rescued the effect of tacrolimus in HK-2 cells. Furthermore, TFEB activation both by phosphorylation sites mutation and agonist rescued TICN in mice. To elucidate the mechanism of TFEB, we analyzed ChIP-seq data. Growth arrest and DNA damage-inducible 45α (GADD45α) was identified as a transcriptional target of TFEB via chromatin immunoprecipitation and dual luciferase reporter assays. And then we revealed that GADD45α overexpression rescued DNA damage and kidney injury caused by tacrolimus or TFEB knockdown in vitro, and vise versa. The protective effect of GADD45α against TICN and DNA damage was further demonstrated by overexpressing it in mice. In conclusion, the persistent inhibition of TFEB-GADD45α pathway by tacrolimus contributes to TICN. This study identifies a specific target for intervention of TICN.
    Keywords:  Nephrology; Therapeutics; Toxicology
    DOI:  https://doi.org/10.1172/jci.insight.183560
  2. Nat Metab. 2025 Feb 06.
      Translocation renal cell carcinoma (tRCC) is an aggressive subtype of kidney cancer driven by TFE3 gene fusions, which act via poorly characterized downstream mechanisms. Here we report that TFE3 fusions transcriptionally rewire tRCCs toward oxidative phosphorylation (OXPHOS), contrasting with the highly glycolytic nature of most other renal cancers. Reliance on this TFE3 fusion-driven OXPHOS programme renders tRCCs vulnerable to NADH reductive stress, a metabolic stress induced by an imbalance of reducing equivalents. Genome-scale CRISPR screening identifies tRCC-selective vulnerabilities linked to this metabolic state, including EGLN1, which hydroxylates HIF-1α and targets it for proteolysis. Inhibition of EGLN1 compromises tRCC cell growth by stabilizing HIF-1α and promoting metabolic reprogramming away from OXPHOS, thus representing a vulnerability for OXPHOS-dependent tRCC cells. Our study defines tRCC as being dependent on a mitochondria-centred metabolic programme driven by TFE3 fusions and nominates EGLN1 inhibition as a therapeutic strategy in this cancer.
    DOI:  https://doi.org/10.1038/s42255-025-01218-9
  3. Stem Cell Res Ther. 2025 Feb 04. 16(1): 38
       BACKGROUND: Tuberous sclerosis complex is a genetic disorder caused by mutations in the TSC1 or TSC2 genes, affecting multiple systems. These genes produce proteins that regulate mTORC1 activity, essential for cell function and metabolism. While mTOR inhibitors have advanced treatment, maintaining long-term therapeutic success is still challenging. For over 20 years, significant progress has linked TSC1 or TSC2 gene mutations in stem cells to tuberous sclerosis complex symptoms.
    METHODS: A comprehensive review was conducted using databases like Web of Science, Google Scholar, PubMed, and Science Direct, with search terms such as "tuberous sclerosis complex," "TSC1," "TSC2," "stem cell," "proliferation," and "differentiation." Relevant literature was thoroughly analyzed and summarized to present an updated analysis of the TSC1-TSC2 complex's role in stem cell fate determination and its implications for tuberous sclerosis complex.
    RESULTS: The TSC1-TSC2 complex plays a crucial role in various stem cells, such as neural, germline, nephron progenitor, intestinal, hematopoietic, and mesenchymal stem/stromal cells, primarily through the mTOR signaling pathway.
    CONCLUSIONS: This review aims shed light on the role of the TSC1-TSC2 complex in stem cell fate, its impact on health and disease, and potential new treatments for tuberous sclerosis complex.
    Keywords:  Mammalian target of rapamycin; Stem cell; Tuberous sclerosis complex
    DOI:  https://doi.org/10.1186/s13287-025-04170-3
  4. Am J Physiol Renal Physiol. 2025 Feb 07.
      Chronic kidney disease (CKD) affects 50% of patients with heart failure. The pathophysiology of CKD in heart failure is proposed to be driven by macrocirculatory hemodynamic changes, including reduced cardiac output and elevated central venous pressure. However, our understanding of the renal microcirculation in heart failure and CKD remains limited. This is largely due to the lack of non-invasive techniques to assess the renal microcirculation in patients. Moreover, there is a lack of clinically relevant animal models of heart failure and CKD to advance our understanding of the timing and magnitude of renal microcirculatory dysfunction. Patients with heart failure and CKD commonly require cardiac surgery with cardiopulmonary bypass (CPB) to improve their prognosis. However, acute kidney injury (AKI) is a frequent unresolved clinical complication in these patients. There is emerging evidence that renal microcirculatory dysfunction, characterized by renal medullary hypoperfusion and hypoxia, plays a critical role in the pathogenesis of cardiac surgery-associated AKI. In this review, we consolidate the preclinical and clinical evidence of renal macro- and microcirculatory perturbations in heart failure and cardiac surgery requiring CPB. We also examine emerging biomarkers and therapies that may improve health outcomes for this vulnerable patient population by targeting the renal microcirculation.
    Keywords:  acute kidney injury; cardiac surgery; chronic kidney disease; heart failure; microcirculation
    DOI:  https://doi.org/10.1152/ajprenal.00266.2024
  5. Nephrol Dial Transplant. 2025 Feb 05. 40(Supplement_1): i18-i28
      The kidneys produce daily about 180 liters of urine but only about 2 liters are excreted. The proximal tubule plays an important role in reabsorbing the majority of filtered urine and many metabolites such as sugars, amino acids, salts or phosphate that are contained in this large volume. Reabsorption of these important metabolites is mediated by a diverse group of highly specialized transport proteins. Another group of transport proteins in the proximal tubule is responsible for the active secretion of metabolic waste products or toxins and drugs into urine. All these transporters have in common that they are directly linked to kidney metabolism and indirectly to whole-body metabolism and functions. In recent years, it has become evident that modulation of these transporters may influence the onset, progression and consequences of kidney disease. This review summarizes recent developments in this field and discusses some examples of drugs already in clinical use or in development. The examples include inhibitors of sugar transporters (SGLT2 inhibitors) that are successfully used in patients with kidney disease, diabetes or heart failure. Likewise, indirect inhibitors (acetazolamide) of an transporter absorbing sodium in exchange for protons (NHE3) are used mostly in patients with heart failure or for prevention of high altitude disease, while direct inhibitors show promise in preclinical studies to reduce damage in episodes of acute kidney disease or high blood pressure. Modulators of transporters mediating the excretion of urate have been used in patients with gout and are also discussed to prevent kidney disease. Novel drugs in development target transporters for phosphate, amino acids, or toxin and drug excretion and may be helpful for specific conditions associated with kidney disease. The advantages and challenges associated with these (novel) drugs targeting proximal tubule transport are discussed.
    ABSTRACT: The proximal tubule is responsible for reabsorbing about 60% of filtered solutes and water and is critical for the secretion of metabolic waste products, drugs and toxins. A large number of highly specialized ion channels and transport proteins belonging to the SLC and ABC transporter families are involved. Their activity is directly or indirectly linked to ATP consumption and requires large quantities of energy and oxygen supply. Moreover, the activity of these transporters is often coupled to the movement of Na+ ions thus influencing also salt and water balance, as well as transport and regulatory processes in downstream segments. Because of their relevance for systemic ion balance, for renal metabolism or for affecting regulatory processes, proximal tubule transporters are attractive targets for existing drug and for novel strategies to reduce kidney disease progression or to alleviate the consequences of decreased kidney function. In this review, the relevance of some major proximal tubule transport systems as drug targets in individuals with chronic kidney disease (CKD) is discussed. Inhibitors of the sodium-glucose cotransporter 2, SGLT2, are now part of standard therapy in patients with CKD and/or heart failure. Also, indirect inhibition of Na+/H+-exchangers by carbonic anhydrase inhibitors and uricosuric drugs have been used for decades. Inhibition of phosphate and amino acid transporters have recently been proposed as novel principles to remove excess phosphate or to protect the proximal tubule metabolically, respectively. In addition, organic cation and anion transporters involved in drug and toxin excretion may serve as targets of new drugs. The advantages and challenges associated with (novel) drugs targeting proximal tubule transport are discussed.
    Keywords:  ABC transporter; SLC transporter; chronic kidney disease; drugs; proximal tubule
    DOI:  https://doi.org/10.1093/ndt/gfae211
  6. Nat Commun. 2025 Feb 04. 16(1): 1330
      Physiological adaptations to fasting enable humans to survive for prolonged periods without food and involve molecular pathways that may drive life-prolonging effects of dietary restriction in model organisms. Mobilization of fatty acids and glycerol from adipocyte lipid stores by canonical neutral lipases, including the rate limiting adipose triglyceride lipase (Pnpla2/ATGL), is critical to the adaptive fasting response. Here we discovered an alternative mechanism of lipolysis in adipocytes involving a lysosomal program. We functionally tested lysosomal lipolysis with pharmacological and genetic approaches in mice and in murine and human adipocyte and adipose tissue explant culture, establishing dependency on lysosomal acid lipase (LIPA/LAL) and the microphthalmia/transcription factor E (MiT/TFE) family. Our study establishes a model whereby the canonical pathway is critical for rapid lipolytic responses to adrenergic stimuli operative in the acute stage of fasting, while the alternative lysosomal pathway dominates with prolonged fasting.
    DOI:  https://doi.org/10.1038/s41467-025-56613-3
  7. J Cell Sci. 2025 Feb 06. pii: jcs.263408. [Epub ahead of print]
      The paradoxical exacerbation of cellular injury and death during reperfusion remains a problem in treatment of myocardial infarction. Mitochondrial dysfunction plays a key role in the pathogenesis of myocardial ischemia and reperfusion injury. Dysfunctional mitochondria can be removed by mitophagy, culminating in their degradation within acidic lysosomes. Mitophagy is pivotal in maintaining cardiac homeostasis and emerges as a potential therapeutic target. Here we employ beating human engineered heart tissue (EHT) to assess mitochondrial dysfunction and mitophagy during ischemia and reperfusion simulation. Our data indicate adverse ultrastructural changes in mitochondrial morphology and impairment of mitochondrial respiration. Furthermore, our pH-sensitive mitophagy reporter EHTs, generated by CRISPR/Cas9 endogenous knock-in strategy, reveal induced mitophagy flux in EHTs after ischemia and reperfusion simulation. The induced flux requires the activity of the protein kinase ULK1, a member of the core-autophagy machinery. Our results demonstrate the applicability of the reporter EHTs for mitophagy assessment in a clinically relevant setting. Deciphering mitophagy in the human heart will facilitate development of novel therapeutic strategies.
    Keywords:  Engineered heart tissue; HiPSC; Ischemia-reperfusion; Mitochondria; Mitophagy
    DOI:  https://doi.org/10.1242/jcs.263408
  8. Cancer Genet. 2025 Jan 31. pii: S2210-7762(25)00015-8. [Epub ahead of print]292-293 65-68
      Birt-Hogg-Dubé syndrome (BHDS) is characterized by autosomal dominant alterations in the Folliculin (FLCN) gene, resulting in cutaneous, pulmonary, and renal abnormalities. In particular, affected individuals are susceptible to the development of renal cell carcinoma (RCC), which most frequently present as chromophobe tumors or hybrid cancers with features of oncocytoma and chromophobe RCC. Type 1 and type 2 papillary neoplasms have rarely been described in the setting of BHDS, and we present two additional cases. Utilizing next-generation sequencing, the patients were found to harbor germline FLCN variants that are not well-documented in the medical literature. While RCCs associated with BHDS are thought to portend a better prognosis compared to their non-syndromic counterparts, the patients described here experienced variable clinical outcomes-one developed locally aggressive disease, distant metastases, and quickly succumbed to his disease.
    Keywords:  Birt-Hogg-Dubé syndrome; Folliculin (FLCN) gene variants; Papillary renal cell carcinoma
    DOI:  https://doi.org/10.1016/j.cancergen.2025.01.007
  9. Curr Opin Cell Biol. 2025 Feb 04. pii: S0955-0674(25)00014-6. [Epub ahead of print]93 102476
      The Hippo pathway is a highly conserved signaling network integrating diverse intracellular, intercellular and extracellular biological cues to regulate complex physiological processes such as organ size, tissue development, homeostasis and regeneration. These cues include cytoskeletal organization, mechanical force, cell-cell interaction, cell polarity, cell-extracellular matrix interaction to govern cell proliferation, differentiation, apoptosis, stem cell property and tissue microenvironment. In this review, we discuss how the emerging role of biomolecular condensates regulates the activity of the pathway components, and how dysregulation of the pathway leads to cancer. Lastly, we highlight the therapeutic modalities which target YAP/TAZ-TEAD interaction for cancer therapy.
    DOI:  https://doi.org/10.1016/j.ceb.2025.102476
  10. Int J Biol Sci. 2025 ;21(3): 1014-1031
      Alzheimer's disease (AD) is characterized by the accumulation of amyloid-beta (Aβ) plaques, neurofibrillary tangles (NFTs) formed from hyperphosphorylated Tau, and widespread neuronal loss. The autophagy-lysosomal pathway plays a crucial role in maintaining cellular homeostasis by degrading and recycling of damaged organelles and aggregate amyloid proteins implicated in AD. Lysosomes are key effectors of autophagic process, responsible for the breakdown of a variety of damaged organelles and aggregate or dysfunctional proteins. This review examines the role of lysosomal dysfunction in AD pathophysiology, focusing on genetic factors, acidification abnormalities, and other contributing factors. We also explore the involvement of lysosomal dysfunction of microglia in AD pathology, and cover the role of lysosomal stress response (LSR) in cellular response to neuronal injury associated with AD. Furthermore, we discuss potential therapeutic strategies targeting lysosomal proteolysis pathway and addressing lysosomal dysfunction for AD treatment, including the pharmacologically activating lysosomal activity, regulating TFEB, and considering other emerging approaches.
    Keywords:  Alzheimer's disease; Autophagy-lysosomal pathway; Lysosomal dysfunction; Lysosomal stress response
    DOI:  https://doi.org/10.7150/ijbs.103028
  11. Front Cardiovasc Med. 2024 ;11 1464933
       Background: Tuberous sclerosis complex (TSC) is a multisystem genetic disorder primarily characterized by the development of benign tumors in multiple organs. While cardiovascular involvement is less common than neurological or renal manifestations, it typically presents with cardiac rhabdomyomas (CRs). The co-occurrence of a bicuspid aortic valve (BAV) with TSC is exceedingly rare.
    Case summary: We report the case of a 26-year-old woman with genetically confirmed TSC, harboring a novel pathogenic variant in the TSC2 gene. Cardiovascular characteristics included a history of heart valve disease, a bicuspid aortic valve, and severe aortic regurgitation. multi-system characteristics of TSC were also presented, affecting skin, brain, lung, kidney, and bone. She underwent aortic valve replacement but experienced postoperative complications, including significant pleural and pericardial effusions requiring drainage and subsequent thoracic duct ligation.
    Conclusion: This case expands the clinical spectrum of TSC-associated cardiovascular abnormalities, highlighting the rare association of BAV with this disorder. Our finding emphasizes the importance of considering TSC in individuals presenting with these cardiac features, as well reinforce the critical role of molecular genetic testing in confirming the diagnosis of TSC.
    Keywords:  aortic regurgitation; bicuspid aortic valve; genetic diagnosis; imaging diagnosis; tuberous sclerosis complex
    DOI:  https://doi.org/10.3389/fcvm.2024.1464933