bims-pideca 2025-02-23 papers

bims-pideca

Biomed News

on Class IA PI3K signalling in development and cancer

Issue of 2025–02–23
twenty-one papers selected by
Ralitsa Radostinova Madsen, MRC-PPU

CRISPuRe-seq: pooled screening of barcoded ribonucleoprotein reporters reveals regulation of RNA polymerase III transcription by the integrated stress response via mTOR.
Distinct requirements for PI3K isoforms p110α and p110δ for PIP3 synthesis in mouse oocytes and early embryos.
Genetically encoded biosensor for fluorescence lifetime imaging of PTEN dynamics in the intact brain.
Effects of alpelisib treatment on murine Pten-deficient lipomas.
Lysosomal NKG7 restrains mTORC1 activity to promote CD8+ T cell durability and tumor control.
Sex Differences in Cancer Functional Genomics: Gene Dependency and Drug Sensitivity.
Combined forces of hydrostatic pressure and actin polymerization drive endothelial tip cell migration and sprouting angiogenesis.
Activation of CAMK2 by pseudokinase PEAK1 represents a targetable pathway in triple negative breast cancer.
An efficient, non-viral arrayed CRISPR screening platform for iPSC-derived myeloid and microglia models.
Unveiling the Negative Synergistic Effect of Wall Shear Stress and Insulin on Endothelial NO Dynamics by Mathematical Modeling.
PI3Kα-specific inhibitor BYL-719 synergizes with cisplatin in vitro in PIK3CA-mutated ovarian cancer cells.
Solute carriers: The gatekeepers of metabolism.
Cell enlargement modulated by GATA4 and YAP instructs the senescence-associated secretory phenotype.
Contextual computation by competitive protein dimerization networks.
MYC in cancer: from undruggable target to clinical trials.
Stress-induced mitochondrial fragmentation in endothelial cells disrupts blood-retinal barrier integrity causing neurodegeneration.
Aberrant ERK signaling in astrocytes impairs learning and memory in RASopathy-associated BRAF mutant mouse models.
How to use mTOR inhibitors in children.
Super-enhancer-driven EFNA1 fuels tumor progression in cervical cancer via the FOSL2-Src/AKT/STAT3 axis.
ARHGEF18 is a flow-responsive exchange factor controlling endothelial tight junctions and vascular leakage.
EndoMAP.v1, a Structural Protein Complex Landscape of Human Endosomes.

Nucleic Acids Res. 2025 Feb 08. pii: gkaf062. [Epub ahead of print]53(4):

CRISPuRe-seq: pooled screening of barcoded ribonucleoprotein reporters reveals regulation of RNA polymerase III transcription by the integrated stress response via mTOR.

David T Harris, Calvin H Jan.

Genetic screens using CRISPR (Clustered Regularly Interspaced Palindromic Repeats) provide valuable information about gene function. Nearly all pooled screening technologies rely on the cell to link genotype to phenotype, making it challenging to assay mechanistically informative, biochemically defined phenotypes. Here, we present CRISPuRe-seq (CRISPR PuRification), a novel pooled screening strategy that expands the universe of accessible phenotypes through the purification of ribonucleoprotein complexes that link genotypes to expressed RNA barcodes. While screening for regulators of the integrated stress response (ISR), we serendipitously discovered that the ISR represses transfer RNA (tRNA) production under conditions of reduced protein synthesis. This regulation is mediated through inhibition of mTORC1 and corresponding activation of the RNA polymerase III inhibitor MAF1. These data demonstrate that coherent downregulation of tRNA expression and protein synthesis is achieved through cross-talk between the ISR and mTOR, two master integrators of cell state.

DOI: https://doi.org/10.1093/nar/gkaf062
Development. 2025 Feb 21. pii: dev.204398. [Epub ahead of print]

Distinct requirements for PI3K isoforms p110α and p110δ for PIP3 synthesis in mouse oocytes and early embryos.

Anne Bourdais, Patricia Viard, Jenny Bormann, Côme Sesboüé, Daniel Guerrier, Nicole Therville, Julie Guillermet-Guibert, John Carroll, Guillaume Halet.

  The PI3K/Akt pathway is thought to regulate key steps of mammalian oogenesis, such as dormant oocyte awakening during follicular activation, meiotic resumption and oocyte maturation. Supporting evidence is however indirect, as oocyte PI3K activation has never been formally demonstrated, and the PI3K isoforms involved have not been revealed. Here, we employed fluorescent PIP3 biosensors to characterize PI3K dynamics in mouse oocytes and we investigated the contribution of PI3K isoform p110α via conditional genetic ablation. Prophase oocytes showed baseline PI3K/Akt activation that could be further stimulated by adding Kit ligand (KitL). Contrary to previous reports, maternal PI3K proved dispensable for oocyte maturation in vitro, yet it was required for PIP3 synthesis in early embryos. We further show that oocyte p110α is not essential for oogenesis and female fertility. Accordingly, our data suggest that KitL activates isoform p110δ for PIP3 synthesis in oocytes. In contrast, constitutive PIP3 synthesis in early embryos is achieved by maternal p110α acting redundantly with p110δ. This study highlights the relevance of PIP3 biosensors in establishing the dynamics, mechanisms and roles of maternal PI3K signaling during mammalian oogenesis.

Keywords:  AKT; Kit; Mouse; Oocyte; PI3K; PIP3

DOI:  https://doi.org/10.1242/dev.204398
Nat Methods. 2025 Feb 20.

Genetically encoded biosensor for fluorescence lifetime imaging of PTEN dynamics in the intact brain.

Tomer Kagan, Matan Gabay, Aasha Meenakshisundaram, Yossi Levi, Sharbel Eid, Nikol Malchenko, Maya Maman, Anat Nitzan, Luca Ravotto, Ronen Zaidel-Bar, Britta Johanna Eickholt, Maayan Gal, Tal Laviv.

The phosphatase and tensin homolog (PTEN) is a vital protein that maintains an inhibitory brake for cellular proliferation and growth. Accordingly, PTEN loss-of-function mutations are associated with a broad spectrum of human pathologies. Despite its importance, there is currently no method to directly monitor PTEN activity with cellular specificity within intact biological systems. Here we describe the development of a FRET-based biosensor using PTEN conformation as a proxy for the PTEN activity state, for two-photon fluorescence lifetime imaging microscopy. We identify a point mutation that allows the monitoring of PTEN activity with minimal interference to endogenous PTEN signaling. We demonstrate imaging of PTEN activity in cell lines, intact Caenorhabditis elegans and in the mouse brain. Finally, we develop a red-shifted sensor variant that allows us to identify cell-type-specific PTEN activity in excitatory and inhibitory cortical cells. In summary, our approach enables dynamic imaging of PTEN activity in vivo with unprecedented spatial and temporal resolution.

DOI: https://doi.org/10.1038/s41592-025-02610-9
Adipocyte. 2025 Dec;14(1): 2468275

Effects of alpelisib treatment on murine Pten-deficient lipomas.

Lea M Merz, Karsten Winter, Sandy Richter, Sonja Kallendrusch, Andreas Horn, Sonja Grunewald, Nora Klöting, Kerstin Krause, Wieland Kiess, Diana Le Duc, Antje Garten.

   Phosphatase and tensin homolog (PTEN) hamartoma tumour syndrome (PHTS) is a rare disorder caused by germline mutations in the tumour suppressor gene PTEN, a key negative regulator of phosphatidylinositol 3-kinase (PI3K)/AKT signalling. Children with PHTS often develop lipomas, for which only surgical resection is available as treatment. We investigated the effects of the selective PI3K-inhibitor alpelisib on Pten-deficient lipomas. After incubation with alpelisib or the non-selective PI3K inhibitor wortmannin, we analysed histology, gene expression, and Pi3k pathway in lipoma and control epididymal adipose tissue (epiWAT). Alpelisib increased adipocyte area in lipomas compared to epiWAT. Baseline gene expression showed higher levels of markers for proliferation (Pcna), fibrosis (Tgfb1), and adipogenesis (Pparg) in lipomas, while hormone-sensitive lipase expression was lower than in epiWAT. Following alpelisib incubation, target genes of Pi3k signalling and extracellular matrix factors were reduced. We confirmed Pi3k inhibition through detecting decreased Akt levels compared to control treatment. Human lipoma samples treated with alpelisib showed variable lipolysis responses, suggesting variability in therapeutic outcomes. We established an ex vivo model to study alpelisib effects on Pten-deficient lipomas. These results underscore the therapeutic potential of targeted PI3K inhibition in the treatment of PHTS-associated lipomas, particularly in cases that are inoperable.

Keywords:  Adipose tissue; phosphatase and tensin homolog; phosphatidylinositol 3-kinase; tissue slice culture; wortmannin

DOI:  https://doi.org/10.1080/21623945.2025.2468275
Nat Commun. 2025 Feb 14. 16(1): 1628

Lysosomal NKG7 restrains mTORC1 activity to promote CD8+ T cell durability and tumor control.

Hyoungjun Ham, Jacob B Hirdler, Daniel T Bihnam, Zhiming Mao, Joanina K Gicobi, Bruna Gois Macedo, Maria F Rodriguez-Quevedo, Destiny F Schultz, Cristina Correia, Jun Zhong, Kodi E Martinez, Alma Banuelos, Dallin S Ashton, Anthony B Lagnado, Ruifeng Guo, Rodrigo Pessoa, Akhilesh Pandey, Hu Li, Fabrice Lucien, Henrique Borges da Silva, Haidong Dong, Daniel D Billadeau.

During infection and cancer, mTORC1-mediated metabolic regulation impacts CD8+ T cell effector expansion and memory development. However, the mechanisms by which CD8+ T cells regulate mTORC1 to support their unique metabolic requirements remain unknown. Here we show that NKG7, a lysosomal protein whose expression is restricted to cytotoxic lymphocytes, negatively regulates mTORC1 recruitment and activation by inhibiting assembly and function of the lysosomal proton pump, vacuolar ATPase (v-ATPase). Human and mouse CD8+ T cells lacking NKG7 show more acidic lysosomes and increased activation of mTORC1 signaling, which could be reversed by inhibition of v-ATPase activity. In mice responding to LCMV infection, NKG7-deleted effector CD8+ T cells are less durable and generate fewer memory precursors, whereas induced expression of NKG7 in CD8+ T cells results in increased presence of intra-tumoral T cells. Overall, our work identifies NKG7 as a CD8+ T cell-specific regulator of mTORC1 activity, required for optimal immune responses.

DOI: https://doi.org/10.1038/s41467-025-56931-6
bioRxiv. 2025 Feb 08. pii: 2025.02.05.636540. [Epub ahead of print]

Sex Differences in Cancer Functional Genomics: Gene Dependency and Drug Sensitivity.

Nicole Zeltser, Chenghao Zhu, Jieun Oh, Constance H Li, Paul C Boutros.

Patient sex influences a wide range of cancer phenotypes, including prevalence, response to therapy and survival endpoints. Molecular sex differences across the central dogma have been identified that may drive these phenotypic differences. Despite a growing catalog of specific genomic, transcriptomic and proteomic sex differences in a range of cancer types, their functional consequences remain unclear. To assess how patient sex impacts cancer cell function, we evaluated 1,209 cell lines subjected to CRISPR knockout, RNAi knockdown or drug exposures. Despite limited statistical power, we identified pan- and per-cancer sex differences in gene essentiality in six sex-linked and fourteen autosomal genes, and in drug sensitivity for two compounds. These data expand our understanding of the propagation of sex-differing molecular features to functional outcomes, and their role in influencing patient phenotypes. They highlight the importance of considering sex-specific effects in mechanistic and functional studies.

DOI: https://doi.org/10.1101/2025.02.05.636540
Elife. 2025 Feb 20. pii: RP98612. [Epub ahead of print]13

Combined forces of hydrostatic pressure and actin polymerization drive endothelial tip cell migration and sprouting angiogenesis.

Igor Kondrychyn, Liqun He, Haymar Wint, Christer Betsholtz, Li-Kun Phng.

  Cell migration is a key process in the shaping and formation of tissues. During sprouting angiogenesis, endothelial tip cells invade avascular tissues by generating actomyosin-dependent forces that drive cell migration and vascular expansion. Surprisingly, endothelial cells (ECs) can still invade if actin polymerization is inhibited. In this study, we show that endothelial tip cells employ an alternative mechanism of cell migration that is dependent on Aquaporin (Aqp)-mediated water inflow and increase in hydrostatic pressure. In the zebrafish, ECs express aqp1a.1 and aqp8a.1 in newly formed vascular sprouts in a VEGFR2-dependent manner. Aqp1a.1 and Aqp8a.1 loss-of-function studies show an impairment in intersegmental vessels formation because of a decreased capacity of tip cells to increase their cytoplasmic volume and generate membrane protrusions, leading to delayed tip cell emergence from the dorsal aorta and slower migration. Further inhibition of actin polymerization resulted in a greater decrease in sprouting angiogenesis, indicating that ECs employ two mechanisms for robust cell migration in vivo. Our study thus highlights an important role of hydrostatic pressure in tissue morphogenesis.

Keywords:  actin; angiogenesis; aquaporin; cell migration; developmental biology; hydrostatic pressure; water flow; zebrafish

DOI:  https://doi.org/10.7554/eLife.98612
Nat Commun. 2025 Feb 22. 16(1): 1871

Activation of CAMK2 by pseudokinase PEAK1 represents a targetable pathway in triple negative breast cancer.

Xue Yang, Xiuquan Ma, Tianyue Zhao, David R Croucher, Elizabeth V Nguyen, Kimberley C Clark, Changyuan Hu, Sharissa L Latham, Charles Bayly-Jones, Bao V Nguyen, Srikanth Budnar, Sung-Young Shin, Lan K Nguyen, Thomas R Cotton, Anderly C Chüeh, Terry C C Lim Kam Sian, Margaret M Stratton, Andrew M Ellisdon, Roger J Daly.

The PEAK family of pseudokinases, comprising PEAK1-3, play oncogenic roles in several poor prognosis human cancers, including triple negative breast cancer (TNBC). However, therapeutic targeting of pseudokinases is challenging due to their lack of catalytic activity. To address this, we screen for PEAK1 effectors and identify calcium/calmodulin-dependent protein kinase 2 (CAMK2)D and CAMK2G. PEAK1 promotes CAMK2 activation in TNBC cells via PLCγ1/Ca2+ signalling and direct binding to CAMK2. In turn, CAMK2 phosphorylates PEAK1 to enhance association with PEAK2, which is critical for PEAK1 oncogenic signalling. To achieve pharmacologic targeting of PEAK1/CAMK2, we repurpose RA306, a second generation CAMK2 inhibitor. RA306 inhibits PEAK1-enhanced migration and invasion of TNBC cells in vitro and significantly attenuates TNBC xenograft growth and metastasis in a manner mirrored by PEAK1 ablation. Overall, these studies establish PEAK1 as a critical cell signalling nexus that integrates Ca2+ and tyrosine kinase signals and identify CAMK2 as a therapeutically 'actionable' target downstream of PEAK1.

DOI: https://doi.org/10.1038/s41467-025-57046-8
Stem Cell Reports. 2025 Feb 11. pii: S2213-6711(25)00024-4. [Epub ahead of print] 102420

An efficient, non-viral arrayed CRISPR screening platform for iPSC-derived myeloid and microglia models.

Sonja Meier, Anne Sofie Gry Larsen, Florian Wanke, Nicolas Mercado, Arianna Mei, Livia Takacs, Eva Suszanna Mracsko, Ludovic Collin, Martin Kampmann, Filip Roudnicky, Ravi Jagasia.

  Here, we developed a CRISPR-Cas9 arrayed screen to investigate lipid handling pathways in human induced pluripotent stem cell (iPSC)-derived microglia. We established a robust method for the nucleofection of CRISPR-Cas9 ribonucleoprotein complexes into iPSC-derived myeloid cells, enabling genetic perturbations. Using this approach, we performed a targeted screen to identify key regulators of lipid droplet formation dependent on Apolipoprotein E (APOE). We identify the Mammalian Target of Rapamycin Complex 1 (mTORC1) signaling pathway as a critical modulator of lipid storage in both APOE3 and APOE knockout microglia. This study is a proof of concept underscoring the utility of CRISPR-Cas9 technology in elucidating the molecular pathways of lipid dysregulation associated with Alzheimer's disease and neuroinflammation.

Keywords:  APOE; CRISPR-Cas9 gene editing; arrayed genetic screening; iPSC-derived microglia; lipid accumulation; lipid droplet screen; lipid metabolism; lipid regulation; lysosome; mTORC1

DOI:  https://doi.org/10.1016/j.stemcr.2025.102420
Bull Math Biol. 2025 Feb 19. 87(4): 46

Unveiling the Negative Synergistic Effect of Wall Shear Stress and Insulin on Endothelial NO Dynamics by Mathematical Modeling.

Yu-Yuan Zhang, Yong-Jiang Li, Xu-Qu Hu, Chun-Dong Xue, Shen Li, Zheng-Nan Gao, Kai-Rong Qin.

  Diabetic vascular complications (DVCs) are diabetes-induced vascular dysfunction and pathologies, leading to the major causes of morbidity and mortality in millions of diabetic patients worldwide. DVCs are provoked by endothelial dysfunction which is closely coordinated with two important hallmarks: one is the insufficient insulin secretion or insulin resistance, and another is the decrease in intracellular nitric oxide (NO) influenced by dynamic wall shear stress (WSS). Although the intracellular NO dynamics in endothelial cells (ECs) is crucial for endothelial function, the regulation of NO production by dynamic WSS and insulin is still poorly understood. In this study, we have proposed a mathematical model of intracellular NO production in ECs under the stimulation of dynamic WSS combined with insulin. The model integrates simultaneously the biochemical signaling pathways of insulin and the mechanotransduction pathways induced by dynamic WSS. The accuracy and reliability of the model to quantitatively describe NO production in ECs were compared and validated with reported experimental data. According to the validated model, inhibition of protein kinase B (AKT) phosphorylation and Ca2+ influx by dynamic oscillatory WSS disrupts the dual nature of endothelial nitric oxide synthase (eNOS) enzyme activation. This disruption leads to the decrease in NO production and the bimodal disappearance of NO waveforms. Moreover, the results reveal that dynamic WSS combined with insulin promote endothelial NO production through negative synergistic effects, which is resulted from the temporal differences in mechanical and biochemical signaling. In brief, the proposed model elucidates the mechanism of NO generation activated by dynamic WSS combined with insulin, providing a potential target and theoretical framework for future treatment of DVCs.

Keywords:  Dynamic WSS; Endothelial cells; Insulin; Negative synergistic effect; Nitric oxide

DOI:  https://doi.org/10.1007/s11538-025-01424-2
Sci Rep. 2025 Feb 20. 15(1): 6265

PI3Kα-specific inhibitor BYL-719 synergizes with cisplatin in vitro in PIK3CA-mutated ovarian cancer cells.

Benoît Thibault, Adrien Thole, Romina D'Angelo, Céline Basset, Julie Guillermet-Guibert.

  Peritoneal carcinomatosis in ovarian cancer is often associated with ascites where cancer cells grow as aggregates. Given the emerging evidence that multicellular growth enhances resistance to conventional therapies, and that patients frequently develop resistance to platinum salts, we investigated the efficiency of PI3K/Akt signalling pathway targeting in multicellular growth and its importance as a potential therapeutic target in cells resistant to platinum salts. Due to its importance in many cancers and to the frequent mutations of its encoding gene PIK3CA, we focused on targeting PI3Kα using BYL-719 (Alpelisib), an isoform-specific inhibitor already used in clinics. We used a panel of 3 ovarian cancer cell lines, SKOV-3, EFO-21 and OVCAR-3, which come from different histological origins and bear different mutations. PI3K targeting drugs inhibit the activity of the PI3K/Akt pathway in all tested ovarian cancer cell lines with a drastic reduction of the phosphorylation of Akt on the serine 473, regardless the histology or the mutational profile. We showed that when cultured in 3D aggregates, ovarian cancer cells are more resistant to the PI3Kα-specific inhibitor BYL-719 and cisplatin compared to 2D monolayers. BYL-719 synergizes with cisplatin in 3D cultures only in PIK3CA-mutated SKOV-3 cells. This drug combination leads to a major cytotoxicity in 3D aggregates of this cell line. Finally, BYL-719 in combination with cisplatin remains active in 3D aggregates of SKOV-3 cells co-cultured with mesenchymal stem cells. We have identified a signalling pathway of interest for the treatment of advanced ovarian cancer in vitro, which could limit the progression of this disease. These data pave the road to investigate whether PI3Kα-specific inhibitor BYL-719 should be proposed in combination with cisplatin, in priority in patients bearing a PIK3CA mutation.

Keywords:  BYL-719/Alpelisib; Cisplatin; Combination therapy; Mesenchymal stem cells; PI3K signalling; Resistance to treatment; Signal-targeted therapies; Tumour cell aggregates

DOI:  https://doi.org/10.1038/s41598-025-90714-9
Cell. 2025 Feb 20. pii: S0092-8674(25)00044-3. [Epub ahead of print]188(4): 869-884

Solute carriers: The gatekeepers of metabolism.

Artem Khan, Yuyang Liu, Mark Gad, Timothy C Kenny, Kıvanç Birsoy.

  Solute carrier (SLC) proteins play critical roles in maintaining cellular and organismal homeostasis by transporting small molecules and ions. Despite a growing body of research over the past decade, physiological substrates and functions of many SLCs remain elusive. This perspective outlines key challenges in studying SLC biology and proposes an evidence-based framework for defining SLC substrates. To accelerate the deorphanization process, we explore systematic technologies, including human genetics, biochemistry, and computational and structural approaches. Finally, we suggest directions to better understand SLC functions beyond substrate identification in physiology and disease.

Keywords:  SLC; deorphanization; metabolism; solute carriers

DOI:  https://doi.org/10.1016/j.cell.2025.01.015
Nat Commun. 2025 Feb 17. 16(1): 1696

Cell enlargement modulated by GATA4 and YAP instructs the senescence-associated secretory phenotype.

Joae Joung, Yekang Heo, Yeonju Kim, Jaejin Kim, Haebeen Choi, Taerang Jeon, Yeji Jang, Eun-Jung Kim, Sang Heon Lee, Jae Myoung Suh, Stephen J Elledge, Mi-Sung Kim, Chanhee Kang.

Dynamic changes in cell size are associated with development and pathological conditions, including aging. Although cell enlargement is a prominent morphological feature of cellular senescence, its functional implications are unknown; moreover, how senescent cells maintain their enlargement state is less understood. Here we show that an extensive remodeling of actin cytoskeleton is necessary for establishing senescence-associated cell enlargement and pro-inflammatory senescence-associated secretory phenotype (SASP). This remodeling is attributed to a balancing act between the SASP regulator GATA4 and the mechanosensor YAP on the expression of the Rho family of GTPase RHOU. Genetic or pharmacological interventions that reduce cell enlargement attenuate SASP with minimal effect on senescence growth arrest. Mechanistically, actin cytoskeleton remodeling couples cell enlargement to the nuclear localization of GATA4 and NF-κB via the Linker of Nucleoskeleton and Cytoskeleton (LINC) complex. RhoU protein accumulates in mouse adipose tissue under senescence-inducing conditions. Furthermore, RHOU expression correlates with SASP expression in adipose tissue during human aging. Thus, our study highlights an unexpected instructive role of cell enlargement in modulating the SASP and reveals a mechanical branch in the senescence regulatory network.

DOI: https://doi.org/10.1038/s41467-025-56929-0
Cell. 2025 Feb 11. pii: S0092-8674(25)00105-9. [Epub ahead of print]

Contextual computation by competitive protein dimerization networks.

Jacob Parres-Gold, Matthew Levine, Benjamin Emert, Andrew Stuart, Michael B Elowitz.

  Many biological signaling pathways employ proteins that competitively dimerize in diverse combinations. These dimerization networks can perform biochemical computations in which the concentrations of monomer inputs determine the concentrations of dimer outputs. Despite their prevalence, little is known about the range of input-output computations that dimerization networks can perform and how it depends on network size and connectivity. Using a systematic computational approach, we demonstrate that even small dimerization networks of 3-6 monomers are expressive, performing diverse multi-input computations. Further, dimerization networks are versatile, performing different computations when their protein components are expressed at different levels, such as in different cell types. Remarkably, individual networks with random interaction affinities, when large enough, can perform nearly all potential one-input network computations merely by tuning their monomer expression levels. Thus, even the simple process of competitive dimerization provides a powerful architecture for multi-input, cell-type-specific signal processing.

Keywords:  biological computation; competitive dimerization; computational expressivity; computational modeling; protein-protein interaction networks

DOI:  https://doi.org/10.1016/j.cell.2025.01.036
Nat Rev Drug Discov. 2025 Feb 19.

MYC in cancer: from undruggable target to clinical trials.

Jonathan R Whitfield, Laura Soucek.

MYC is among the most infamous oncogenes in cancer. A notable feature that distinguishes it from other common oncogenes is that its deregulation is not usually due to direct mutation, but instead to its relentless activation by other oncogenic lesions. These signalling pathways funnel through MYC to execute the transcriptional programmes that eventually lead to the uncontrolled proliferation of cancer cells. Indeed, deregulated MYC activity may be linked to most - if not all - human cancers. Despite this unquestionable role of MYC in tumour development and maintenance, no MYC inhibitor has yet been approved for clinical use. The main reason is that MYC has long fallen into the category of 'undruggable' or 'difficult-to-drug' targets, mainly because of its intrinsically disordered structure, which is not amenable to traditional drug development strategies. However, in recent years, attempts to develop MYC inhibitors have multiplied, and the first clinical trials have been testing their efficacy in patients. We are finally reaching the point at which its inhibition seems clinically viable. This Review provides an overview of the various strategies to inhibit MYC, focusing on the most recently described inhibitors and those that have reached clinical trials.

DOI: https://doi.org/10.1038/s41573-025-01143-2
bioRxiv. 2025 Jan 31. pii: 2024.12.21.629919. [Epub ahead of print]

Stress-induced mitochondrial fragmentation in endothelial cells disrupts blood-retinal barrier integrity causing neurodegeneration.

Jorge L Cueva-Vargas, Nicolas Belforte, Isaac A Vidal-Paredes, Florence Dotigny, Christine Vande Velde, Heberto Quintero, Adriana Di Polo.

Increased vascular leakage and endothelial cell (EC) dysfunction are major features of neurodegenerative diseases. Here, we investigated the mechanisms leading to EC dysregulation and asked whether altered mitochondrial dynamics in ECs impinge on vascular barrier integrity and neurodegeneration. We show that ocular hypertension, a major risk factor to develop glaucoma, induced mitochondrial fragmentation in retinal capillary ECs accompanied by increased oxidative stress and ultrastructural defects. Analysis of EC mitochondrial components revealed overactivation of dynamin-related protein 1 (DRP1), a central regulator of mitochondrial fission, during glaucomatous damage. Pharmacological inhibition or EC-specific in vivo gene delivery of a dominant negative DRP1 mutant was sufficient to rescue mitochondrial volume, reduce vascular leakage, and increase expression of the tight junction claudin-5 (CLDN5). We further demonstrate that EC-targeted CLDN5 gene augmentation restored blood-retinal-barrier integrity, promoted neuronal survival, and improved light-evoked visual behaviors in glaucomatous mice. Our findings reveal that preserving mitochondrial homeostasis and EC function are valuable strategies to enhance neuroprotection and improve vision in glaucoma.

DOI: https://doi.org/10.1101/2024.12.21.629919
J Clin Invest. 2025 Feb 18. pii: e176631. [Epub ahead of print]

Aberrant ERK signaling in astrocytes impairs learning and memory in RASopathy-associated BRAF mutant mouse models.

Minkyung Kang, Jihye Choi, Jeongho Han, Toshiyuki Araki, Soo-Whee Kim, Hyun-Hee Ryu, Min-Gyun Kim, Seoyeon Kim, Hanbyul Jang, Sun Yong Kim, Kyoung-Doo Hwang, Soobin Kim, Myeongjong Yoo, Jaegeon Lee, Kitae Kim, Pojeong Park, Ja Eun Choi, Dae Hee Han, Yujin Kim, Jeongyeon Kim, Sunghoe Chang, Bong-Kiun Kaang, Jung Min Ko, Keun-Ah Cheon, Joon-Yong An, Sang Jeong Kim, Hyungju Park, Benjamin G Neel, Chul Hoon Kim, Yong-Seok Lee.

  RAS/MAPK pathway mutations often induce RASopathies with overlapping features, such as craniofacial dysmorphology, cardiovascular defects, dermatologic abnormalities, and intellectual disabilities. Although BRAF gene mutations are associated with cardio-facio-cutaneous (CFC) syndrome and Noonan syndrome, it remains unclear how these mutations impair cognition. Here, we investigated the underlying neural mechanisms using several mouse models harboring a gain-of-function BRAF mutation (K499E) discovered in RASopathy patients. We found expressing BRAF K499E (KE) in neural stem cells under the control of a Nestin-Cre promoter (Nestin;BRAFKE/+) induced hippocampal memory deficits, but expressing it in excitatory or inhibitory neurons did not. BRAF KE expression in neural stem cells led to aberrant reactive astrogliosis, increased astrocytic Ca2+ fluctuations, and reduced hippocampal long-term depression (LTD) in mice. Consistently, 3D human cortical spheroids expressing BRAF KE also showed reactive astrogliosis. Astrocyte-specific AAV-BRAF KE delivery induced memory deficits, reactive astrogliosis, and increased astrocytic Ca2+ fluctuations. Notably, reducing ERK activity in astrocytes rescued the memory deficits and altered astrocytic Ca2+ activity of Nestin;BRAFKE/+ mice. Furthermore, reducing astrocyte Ca2+ activity rescued the spatial memory impairments of BRAF KE-expressing mice. Our results demonstrate that ERK hyperactivity contributes to astrocyte dysfunction associated with Ca2+ dysregulation, leading to the memory deficits of BRAF-associated RASopathies.

Keywords:  Development; Genetic diseases; Intellectual disability; Neurodevelopment; Neuroscience

DOI:  https://doi.org/10.1172/JCI176631
Arch Dis Child Educ Pract Ed. 2025 Feb 16. pii: edpract-2024-327852. [Epub ahead of print]

How to use mTOR inhibitors in children.

Yincent Tse, Nicola Vasey, Rhys Thomas, Suzy Leech, Stephen Owens, John Sayer.

  Paediatricians across many specialities and pharmacists are increasingly being asked to prescribe, or jointly look after, children treated with mammalian target of rapamycin (mTOR) inhibitors (eg, sirolimus and everolimus). There is an expanding list of conditions including tuberous sclerosis and vascular malformations where treatment with mTOR inhibitors may help. This brief practice pointer summarises the practical steps before starting these treatments, what potential side effects to discuss with families and what monitoring arrangements should be put in place.

Keywords:  Paediatrics; Pharmacology; Therapeutics

DOI:  https://doi.org/10.1136/archdischild-2024-327852
J Clin Invest. 2025 Feb 18. pii: e177599. [Epub ahead of print]

Super-enhancer-driven EFNA1 fuels tumor progression in cervical cancer via the FOSL2-Src/AKT/STAT3 axis.

Shu-Qiang Liu, Xi-Xi Cheng, Shuai He, Tao Xia, Yi-Qi Li, Wan Peng, Ya-Qing Zhou, Zi-Hao Xu, Mi-Si He, Yang Liu, Pan-Pan Wei, Song-Hua Yuan, Chang Liu, Shu-Lan Sun, Dong-Ling Zou, Min Zheng, Chun-Yan Lan, Chun-Ling Luo, Jin-Xin Bei.

  Super-enhancers (SEs) are expansive cis-regulatory elements known for amplifying oncogene expression across various cancers. However, their role in cervical cancer (CC), a remarkable global malignancy affecting women, remains underexplored. Here we applied integrated epigenomic and transcriptomic profiling to delineate the distinct SE landscape in CC by analyzing paired tumor and normal tissues. Our study identifies a tumor-specific SE at the EFNA1 locus that drives EFNA1 expression in CC. Mechanically, the EFNA1 SE region contains consensus sequences for the transcription factor FOSL2, whose knockdown markedly suppressed luciferase activity and diminished H3K27ac enrichment within the SE region. Functional analyses further underlined EFNA1's oncogenic role in CC, linking its overexpression to poor patient outcomes. EFNA1 knockdown strikingly reduced CC cell proliferation, migration, and tumor growth. Moreover, EFNA1 cis-interacted with its receptor EphA2, leading to decreased EphA2 tyrosine phosphorylation and subsequent activation of the Src/AKT/STAT3 forward signaling pathway. Inhibition of this pathway with specific inhibitors substantially attenuated the tumorigenic capacity of EFNA1-overexpressing CC cells in both in vitro and in vivo models. Collectively, our study unveils the critical role of SEs in promoting tumor progression through the FOSL2-EFNA1-EphA2-Src/AKT/STAT3 axis, providing new prognostic and therapeutic avenues for CC patients.

Keywords:  Cell biology; Cervical cancer; Epigenetics; Oncology

DOI:  https://doi.org/10.1172/JCI177599
Cell Rep. 2025 Feb 19. pii: S2211-1247(25)00059-2. [Epub ahead of print]44(3): 115288

ARHGEF18 is a flow-responsive exchange factor controlling endothelial tight junctions and vascular leakage.

Surya Prakash Rao Batta, Marc Rio, Corentin Lebot, Céline Baron-Menguy, Maxence Bodet, Reda Moutaoukil, Robin Le Ruz, Ibtissam Babahnini, Gervaise Loirand, Anne-Clémence Vion.

  The shear stress resulting from blood flow is a major regulator of endothelial cell (EC) biology and morphology. Rho protein-mediated cytoskeleton remodeling is an early and essential step of EC responses to flow. However, how Rho protein signaling is controlled by shear stress remains unclear. Here we demonstrate that phosphorylation, activity, and expression of the Rho nucleotide exchange factor (RhoGEF) ARHGEF18 in ECs are modulated by the magnitude of shear stress. When phosphorylated, ARHGEF18 interacts with tight junctions; participates in EC elongation, alignment, and migration; and allows the maintenance of the endothelial barrier under physiological flow conditions. In mice, ARHGEF18 is involved in tight junction formation, flow response of ECs, and the control of vascular permeability. Together, our results identified ARHGEF18 as the first flow-sensitive RhoGEF in ECs, whose activity is essential for the maintenance of intercellular junctions and the control of vascular permeability in vivo.

Keywords:  CP: Cell biology; endothelial cell; guanine exchange factor; mechano-transduction; shear stress; vascular permeability

DOI:  https://doi.org/10.1016/j.celrep.2025.115288
bioRxiv. 2025 Feb 09. pii: 2025.02.07.636106. [Epub ahead of print]

EndoMAP.v1, a Structural Protein Complex Landscape of Human Endosomes.

Miguel A Gonzalez-Lozano, Ernst W Schmid, Enya Miguel Whelan, Yizhi Jiang, Joao A Paulo, Johannes C Walter, J Wade Harper.

Early/sorting endosomes are dynamic organelles that play key roles in proteome control by triaging plasma membrane proteins for either recycling or degradation in the lysosome 1,2,3 . These events are coordinated by numerous transiently-associated regulatory complexes and integral membrane components that contribute to organelle identity during endosome maturation 4 . While a subset of the several hundred protein components and cargoes known to associate with endosomes have been studied at the biochemical and/or structural level, interaction partners and higher order molecular assemblies for many endosomal components remain unknown. Here, we combine cross-linking and native gel mass spectrometry 5-8 of purified early endosomes with AlphaFold 9,10 and computational analysis to create a systematic human endosomal structural interactome. We present dozens of structural models for endosomal protein pairs and higher order assemblies supported by experimental cross-links from their native subcellular context, suggesting structural mechanisms for previously reported regulatory processes. Using induced neurons, we validate two candidate complexes whose interactions are supported by crosslinks and structural predictions: TMEM230 as a subunit of ATP8/11 lipid flippases 11 and TMEM9/9B as subunits of CLCN3/4/5 chloride-proton antiporters 12 . This resource and its accompanying structural network viewer provide an experimental framework for understanding organellar structural interactomes and large-scale validation of structural predictions.

DOI: https://doi.org/10.1101/2025.02.07.636106