bims-raghud 2025-11-09 papers

Issue of 2025–11–09
seven papers selected by
Irene Sambri, TIGEM

J Pathol. 2025 Nov 02.

mTOR-mediated upregulation of B7-H3 in MiT/TFE translocation renal cell carcinoma.

Huili Li, Adrianna Amaral, Thiago Vidotto, Juhyung Woo, Hans B Liu, Lia D Oliveira, Oluwademilade Dairo, Kewen Feng, Eugene Shenderov, Pedram Argani, Laura S Schmidt, W Marston Linehan, Tamara L Lotan, Kaushal Asrani.

Clinical trials targeting B7-H3 (CD276), a membranous immunomodulatory molecule in the B7 superfamily, have shown promise in prostate cancer and may be expanded to additional tumor types with high expression, such as those with mTOR signaling activation. MiT/TFE-rearranged translocation renal cell carcinoma (tRCC) is a rare, aggressive subtype that is relatively immune-depleted, with high levels of mTOR activity. Thus, we assessed B7-H3 expression in preclinical tRCC models and human tRCC samples. As hypothesized, we found that induction of TFE3 fusion proteins, including SFPQ-TFE3, PRCC-TFE3, ASPSCR1-TFE3, and NONO-TFE3, is associated with upregulation of B7-H3 in multiple human preclinical tRCC cell line systems and transgenic mouse models. Pharmacologic or genetic inhibition of mTOR signaling is sufficient to downregulate B7-H3 expression in inducible and patient-derived, human cell line models of tRCC. In keeping with these preclinical results, human tRCC demonstrated significantly higher gene expression of CD276 than normal kidney, across five of the six fusions studied. At the protein level, tRCC had higher tumor cell B7-H3 intensity and proportion scores than normal kidney or clear cell RCC (ccRCC). B7-H3 expression in tumor vasculature was similar in tRCC and ccRCC, both of which showed significantly higher expression than normal kidney. Within tRCC cases, higher CD276 expression was observed in metastatic compared to localized tumors and was associated with lower tumoral CD4+ T-cell content by bulk RNAseq deconvolution. Taken together, tRCC fusion proteins upregulate B7-H3 expression via increased mTOR signaling, resulting in a higher tumoral B7-H3 expression compared to normal kidney or conventional RCC, suggesting that B7-H3 may be a promising therapeutic target in tRCC. © 2025 The Pathological Society of Great Britain and Ireland.

Keywords: B7‐H3; GPNMB; TFE3; TFEB; mTOR; renal cell carcinoma; translocation renal cell carcinoma (tRCC)

DOI: https://doi.org/10.1002/path.6490

EMBO Rep. 2025 Nov 06.

Loss of the lysosomal protein CLN3 triggers c-Abl-dependent YAP1 pro-apoptotic signaling.

Neuza Domingues, Alessia Calcagni', Sofia Freire, Joana Pires, Ricardo Casqueiro, Ivan L Salazar, Niculin Joachim Herz, Tuong Huynh, Katarzyna Wieciorek, Tiago Fleming Outeiro, Henrique Girão, Ira Milosevic, Andrea Ballabio, Nuno Raimundo.

Batten disease is characterized by early-onset blindness, juvenile dementia and death within the second decade of life. The most common genetic cause are mutations in CLN3, encoding a lysosomal protein. Currently, no therapies targeting disease progression are available, largely because its molecular mechanisms remain poorly understood. To understand how CLN3 loss affects cellular signaling, we generated human CLN3 knock-out cells (CLN3-KO) and performed RNA-seq analysis. Our multi-dimensional analysis reveals the transcriptional regulator YAP1 as a key factor in remodeling the transcriptome in CLN3-KO cells. YAP1-mediated pro-apoptotic signaling is also increased as a consequence of CLN3 functional loss in retinal pigment epithelia cells, and in the hippocampus and thalamus of Cln3Δ7/8 mice, an established model of Batten disease. Loss of CLN3 leads to DNA damage, activating the kinase c-Abl which phosphorylates YAP1, stimulating its pro-apoptotic signaling. This novel molecular mechanism underlying the loss of CLN3 in mammalian cells and tissues may pave a way for novel c-Abl-centric therapeutic strategies to target Batten disease.

Keywords: Batten Disease; DNA Damage; Lysosome-Nucleus Communication; Lysosomes; YAP1

DOI: https://doi.org/10.1038/s44319-025-00613-3

Cell Tissue Res. 2025 Nov 05.

Kidney organoids in translational research: disease modeling, drug discovery, and unresolved challenges.

Yue Xi, Wei Song.

Kidney organoids derived from human pluripotent stem cells (hPSCs) have emerged as powerful platforms for translational nephrology, enabling complex renal pathophysiology modeling in physiologically relevant three-dimensional contexts. This review synthesizes recent advances in kidney organoid applications for disease modeling and drug discovery, highlighting their translational potential beyond developmental biology. These organoids recapitulate key human kidney architectural features, including nephron-like structures with glomeruli and tubules, while exhibiting greater cellular heterogeneity than traditional two-dimensional cultures. They effectively model monogenic renal disorders including autosomal dominant polycystic kidney disease (ADPKD), congenital nephrotic syndrome, and Alport syndrome, as well as acquired conditions like acute kidney injury and drug-induced nephrotoxicity. Kidney organoids serve as predictive nephrotoxicity screening platforms, demonstrating dose- and time-dependent responses to cisplatin, tenofovir, and aristolochic acid. However, significant challenges persist, including insufficient vascularization, developmental immaturity, segmental bias, absent urinary drainage systems, and reproducibility variability. Emerging bioengineering strategies-including endothelial co-culture, microfluidic integration, and 3D bioprinting-aim to address these limitations. Integrating stem cell biology with engineering innovations and multi-omics technologies will be crucial for refining kidney organoids into scalable, reproducible models that faithfully recapitulate human kidney physiology and disease, ultimately enabling their translation into precision medicine applications.

Keywords: Disease model; Drug screening; Kidney organoid; Pluripotent stem cell; Regenerative medicine

DOI: https://doi.org/10.1007/s00441-025-04018-5

Nat Commun. 2025 Nov 07. 16(1): 9833

Lysosomal and mTORC1 signaling dysregulation underpin the pathology of spastic paraplegia type 80.

Yiqiang Zhi, Tongtong Zhang, Danping Lu, Shuhuai Lin, Huizhen Su, Yupei Wu, Qiyuan Chang, Shuyuan Wang, Chenning Lv, Honggao Fu, Li-Yu Chen, Wan-Jin Chen, Ning Wang, Zhifei Fu, Xiang Lin, Dan Xu.

Endosomal sorting complex required for transport (ESCRT) is the major membrane remodeling complex, closely associated with endolysosomal repair and hereditary spastic paraplegias (HSP) diseases. Loss of function mutations in the ESCRT-I component UBAP1 causes a rare type of HSP (spastic paraplegia 80, SPG80), while the underlying pathological mechanism is unclear. Here, we found that UBAP1 but not SPG80 causing mutant was efficiently recruited to damaged lysosomes and mediated lysosome recovery. Loss of UBAP1 results in dysfunction of lysosomes, disconnecting mTOR localization on lysosomes, leading to cytoplasmic mTORC1 activation and TFEB dephosphorylation, as confirmed in vitro and in vivo models. Administration of rapamycin, a specific inhibitor of mTORC1, enhances mTOR lysosomal localization and TFEB phosphorylation. This pharmacological intervention effectively attenuated disease progression and restored lysosomal homeostasis in Ubap1 deficiency mice. Our findings reveal UBAP1's role in lysosome regulation and suggest rapamycin may benefit patients with HSP and other motor neuron disorders.

DOI: https://doi.org/10.1038/s41467-025-64800-5

Mol Biol Cell. 2025 Nov 05. mbcE25100498

TORC1-dependent sorting of PI(3,5)P2 is required for vacuole membrane remodeling and signaling endosome formation.

Frederik Brinks, Annabel Arens, Rainer Kurre, Jacob Piehler, Lars Langemeyer, Christian Ungermann.

Lysosomes, as central organelles of the endolysosomal system, support cell growth by releasing nutrients derived from hydrolytic digestion of macromolecules. Additionally, they serve as storage organelles for ions and amino acids and must respond to changes in osmolarity by adjusting their membrane to maintain membrane integrity. The nutrient-sensing target of rapamycin complex 1 (TORC1) and the lipid kinase Fab1 (PIKfyve in mammals) are key regulators of these processes on yeast vacuoles. TORC1 phosphorylates Fab1, yet how their activities are functionally coupled is unknown. Here, we show that yeast TORC1 is essential for the sorting of Fab1-derived phosphatidylinositol-3,5-bisphosphate (PI(3,5)P₂) from vacuoles to signaling endosomes (SEs), whose formation depends on the CROP membrane remodeling complex. TORC1 phosphorylation activates Fab1, presumably to maintain elevated PI(3,5)P₂ levels on SEs toward cell growth. In mutants defective in endosome-vacuole fusion, PI(3,5)P₂ accumulates on endosomes adjacent to the vacuole, indicating that its hydrolysis primarily occurs on the vacuolar membrane. Our findings reveal that synthesis and spatial distribution of the vacuolar signaling lipid PI(3,5)P₂ are directly coordinated by TORC1, coupling nutrient sensing to membrane remodeling and endosomal signaling.

DOI: https://doi.org/10.1091/mbc.E25-10-0498

JAMA. 2025 Nov 07.

SGLT2 Inhibitors and Kidney Outcomes by Glomerular Filtration Rate and Albuminuria: A Meta-Analysis.

SGLT2 Inhibitor Meta-Analysis Cardio-Renal Trialists’ Consortium (SMART-C)

Importance: Sodium-glucose cotransporter 2 (SGLT2) inhibitors reduce chronic kidney disease (CKD) progression in individuals with type 2 diabetes, CKD, or heart failure. However, their effects in those with stage 4 CKD or little to no albuminuria remain uncertain.
Objective: To assess whether estimated glomerular filtration rate (eGFR) or degree of albuminuria, measured by urinary albumin to creatinine ratio (UACR), modifies the effects of SGLT2 inhibitors on kidney outcomes.
Data Sources: SGLT2 inhibitor trials participating in the SGLT2 Inhibitor Meta-Analysis Cardio-Renal Trialists' Consortium (SMART-C).
Study Selection: Randomized, double-blind, placebo-controlled trials within SMART-C evaluating an SGLT2 inhibitor with label indications for reducing CKD progression including at least 500 participants in each group with at least 6 months of follow-up.
Data Extraction and Synthesis: Treatment effects in individual trials were pooled using inverse variance-weighted meta-analysis.
Main Outcomes and Measures: CKD progression, defined as kidney failure, at least 50% reduction in eGFR, or death due to kidney failure. Other outcomes included annual rate of eGFR decline and kidney failure.
Results: Among 70 361 participants (mean [SD] age, 64.8 [8.7] years; 24 595 [35.0%] females) in 10 randomized trials, 2314 (3.3%) experienced CKD progression and 988 (1.4%) reached kidney failure. SGLT2 inhibitors reduced the risk of CKD progression (25.4 vs 40.3 events per 1000 patient-years; hazard ratio [HR], 0.62 [95% CI, 0.57-0.68]), irrespective of baseline eGFR (HR of 0.61 [95% CI, 0.52-0.71] for eGFR ≥60 mL/min/1.73 m2; 0.57 [95% CI, 0.47-0.70] for eGFR of 45 to <60 mL/min/1.73 m2; 0.64 [95% CI, 0.54-0.75] for eGFR of 30 to <45 mL/min/1.73 m2; and 0.71 [95% CI, 0.60-0.83] for eGFR <30 mL/min/1.73 m2; P for trend = .16) and baseline albuminuria (HR of 0.58 [95% CI, 0.44-0.76] for albuminuria ≤30 mg/g; 0.74 [95% CI, 0.57-0.96] for >30-300 mg/g; and 0.57 [95% CI, 0.52-0.64] for more than 300 mg/g; P for trend = .49). Although the magnitude of protection varied, SGLT2 inhibitors reduced the annual rate of eGFR decline across all eGFR and UACR subgroups, including when participants with and without diabetes were analyzed separately. SGLT2 inhibitors also reduced the risk of kidney failure alone (HR, 0.66 [95% CI, 0.58-0.75]).
Conclusions and Relevance: In this meta-analysis, SGLT2 inhibitors were found to lower the risk of CKD progression regardless of baseline eGFR or albuminuria, including in patients with stage 4 CKD or minimal albuminuria, supporting their routine use to improve kidney outcomes across the full spectrum of kidney function among patients with type 2 diabetes, CKD, or heart failure.

DOI: https://doi.org/10.1001/jama.2025.20834

Annu Rev Physiol. 2025 Nov 04.

Scarred by Fibrosis: The Heart-Kidney Disease Connection.

Juliana H Boukhaled, Emily M Martin, Nathalie Gayrard, Àngel Argilés, Morten A Karsdal, Federica Genovese.

Cardiorenal syndrome (CRS) represents a complex interplay of pathophysiological processes that create a self-perpetuating cycle of heart and kidney dysfunction. While it is clearly understood how hemodynamic changes connect pathogenesis in the two organs, other processes are also in play. Some are the structural changes involving both the cellular and extracellular compartments that precede functional alterations. Fibrosis, which is initiated by an inflammatory response triggering myofibroblast activation and excessive extracellular matrix production, is a common denominator of heart and kidney pathology in CRS. This review focuses on fibroblast activities as a crucial factor in disease onset and progression in CRS. We explore how fibrosis in one organ can trigger or worsen dysfunction in the other organ, and we describe the key pathological signaling pathways of cardiorenal fibrosis, the extracellular matrix-derived biomarkers that can aid clinical management and drug development, and the therapeutic opportunities that can be beneficial in CRS by targeting fibroblast activities.

DOI: https://doi.org/10.1146/annurev-physiol-043024-115512