Research Article
Abstract
Cancers reprogram their metabolism to provide anabolic needs without driving excessive oxidative stress. Attention has focused on glucose metabolism, yet amino acid synthesis and degradation also promote tumor cell states and growth. Here, we assessed amino acids that maintain cancer stem cells in glioblastoma and found increased proline levels relative to differentiated tumor progeny through increased proline synthesis. Cancer stem cells preferentially expressed the signaling molecule FAM3C induced by the stem cell transcription factor SOX2 to drive expression of proline synthesis enzymes. FAM3C classically mediated cellular responses as a secreted protein but gained intracellular functions in cancer stem cells through binding the histone reader spindlin 1 (SPIN1), thereby preventing its lysosomal degradation, assisting its nuclear localization, and promoting epigenetic regulation of proline synthesis. Proline synthesis depleted ROS, and genetic targeting of FAM3C attenuated ROS scavenging, whereas SPIN1 OE restored ROS levels. Molecular docking identified tucatinib as a brain-penetrant pharmacologic disruptor of FAM3C-SPIN1 interactions, promoting SPIN1 degradation and reducing intracellular proline levels. Thus, cancer stem cells induced a favorable metabolic state through proline synthesis and ROS depletion, revealing potential therapeutic dependencies.
Authors
Weichi Wu, Po Zhang, Donghai Wang, Xujia Wu, Qiulian Wu, Daqi Li, Tengfei Huang, Rui Wang, Huan Li, Hailong Mi, Suchet Taori, Fanen Yuan, Tingting Duan, Zhiye Chen, Huairui Yuan, Jeremy N. Rich
Abstract
The role of the epigenome in age-related neurodegenerative disorders remains understudied. Here, we analyzed circulating cell-free DNA (cfDNA) from blood to detect methylation changes as a liquid biopsy for Amyotrophic Lateral Sclerosis (ALS). Our study included 20 patients with sporadic ALS, 10 patients with C9orf72-associated ALS, 10 asymptomatic carriers of the C9orf72 repeat expansion mutation, and 21 nondisease control individuals. Following targeted enzymatic methyl-sequencing (EM-seq) of approximately 4 million CpG sites, we detected numerous differentially methylated genes, including several implicated in ALS disease risk and pathogenesis. By integrating multiple epigenetic features, we delineated a distinct epigenetic signature, which achieved an average area under the curve (AUC) of 0.91 ± 0.10 upon receiver operator characteristic (ROC) analysis, which enabled detection of approximately 70% of patients with ALS with close to 100% specificity. Furthermore, we also identified a set of genes whose methylation status significantly correlated with clinical disease progression and cerebrospinal fluid (CSF) neurofilament levels. Our results reveal the potential of cfDNA-based biomarkers to accurately diagnose ALS and potentially predict disease progression.
Authors
Sebastian Michels, Chaorong Chen, Wolfgang P. Ruf, M. Madhy Garcia Garcia, Frederick J. Arnold, Zhuoxing Wu, Craig L. Bennett, Daniel Shams, Leslie M. Thompson, Alyssa C. Walker, Dennis W. Dickson, Leonard Petrucelli, Johannes Dorst, Mercedes Prudencio, Wei Li, Albert R. La Spada
Abstract
The cyclic dinucleotide 2′3′–cyclic guanosine monophosphate–adenosine monophosphate (2′3′-cGAMP) serves as a central immunotransmitter that propagates stimulator of interferon gene–dependent (STING-dependent) innate immunity across tissues; however, how microenvironmental metabolites regulate its spatiotemporal dynamics remains unknown. Here, we identified polyamines (spermine and spermidine) as critical rheostats controlling 2′3′-cGAMP functionality. Mechanistically, polyamines sequestered 2′3′-cGAMP into polymer-like aggregates, blocking intercellular propagation and suppressing intracellular STING activation by reducing ligand-receptor binding affinity. Deficiency of spermidine and spermine N1-acetyltransferase 1 (SAT1), the rate-limiting enzyme in polyamine catabolism, elevated polyamine levels to entrap extracellular 2′3′-cGAMP and inhibit STING activation. Synergistic administration of endogenous 2′3′-cGAMP with SAT1 stabilizer N1,N11-diethylnorspermine restored 2′3′-cGAMP bioavailability and STING signaling, facilitated type I interferon responses to reprogram immunologically suppressive tumors into immunologically active states and enhanced tumor clearance. Our study established polyamine–cGAMP interactions as a critical spatiotemporal regulatory mechanism for tissue-level immunity, providing a unified model for metabolite-mediated cyclic GMP-AMP synthase–STING (cGAS-STING) regulation across diseases.
Authors
Yunjin Ma, Chunyuan Zhao, Jiacheng Guo, Yue Fu, Wei Wang, Jiangong Zhang, Kun Zhao, Xiangbo Meng, Zhongshang Yuan, Chengjiang Gao, Mutian Jia, Ying Qin, Hui Song, Wei Zhao
Abstract
Dilated cardiomyopathy (DCM) is a genetically heterogeneous disorder, characterized by ventricular dilatation and impaired systolic function, leading to heart failure and sudden cardiac death. Despite advances in genomic technologies, the genetic cause of DCM remains unidentified in more than half of the cases. Here, we performed an integrative analysis of genomic and transcriptomic data from patient-derived cardiac tissue to identify causative variants in genetically undiagnosed DCM. This approach enabled us to identify a homozygous splice-site variant (c.243+6T>A) in the sarcoglycan gene SGCB, which results in exon 2 skipping. This variant was significantly enriched in patients with DCM compared with the general population, with consistent genotype–phenotype correlations observed across multiple families. Protein-level analysis of cardiac tissue from homozygous individuals revealed loss of β-sarcoglycan, the protein product of SGCB, and destabilization of the sarcoglycan complex. Although SGCB has been previously associated with limb-girdle muscular dystrophy, these homozygous individuals showed no biochemical or clinical signs of skeletal muscle involvement, indicating an absence of myopathy. Compared with variant-negative patients with DCM, homozygous individuals also had a higher risk of early-onset adverse cardiac events. Together, these findings identify c.243+6T>A in SGCB as a cause of isolated DCM associated with unfavorable clinical outcomes.
Authors
Fangfang Li, Haruki Shinomiya, Yuki Kuramoto, Koshiro Kanaoka, Yuji Sakahashi, Yasuki Ishihara, Hidetaka Kioka, Seiko Ide, Yumi Yamaguchi-Kabata, Shu Tadaka, Ikuko N. Motoike, Kengo Kinoshita, Kinuko Ohneda, Hidetoshi Sakurai, Takahiro Okumura, Yohei Miyashita, Kota Jojima, Hisakazu Kato, Ken Matsuoka, Kazuya Tanabe, Shunsuke Nishimura, Seiji Takashima, Yoshihiro Asano, Yasushi Sakata
Abstract
Alveolar type 2 cells (AT2s) are critical to lung regeneration, and the absence of large-scale methods to expand AT2s has hindered regenerative medicine efforts. We report a microcarrier-based, large-scale expansion method that was used to generate hundreds of billions of human AT2s. Through our process, expanded AT2s largely retained their phenotype. Furthermore, we showed that culture medium, substrate composition, and stiffness are all critical to the maintenance of AT2s. Finally, we showed that expanded AT2s can differentiate into alveolar type 1–like cells, both in vitro and in a decellularized porcine lung, demonstrating the utility of these cells for lung tissue engineering.
Authors
Lauren K. Rochelle, Rachael S. Van, Richard J. Ottman, Daren F. Robinson, Ashley R. Dockham, Amy K. Smith, Daniel P. Keeley, Jia C. Wang, Darell W. McCoy, Tyler R. Zimmerman, Bryan A. Fioret, Ryan W. Bonvillain, Thomas H. Petersen, Sarah S. Hogan, Laila C. Roudsari
Abstract
Resistance to HIF-2α inhibitors such as belzutifan underscores the need to better understand how HIF-2α is transcriptionally regulated in clear cell renal cell carcinoma (ccRCC). Here, we uncover a cytokine-driven enhancer mechanism that sustains HIF-2α expression through the JAK1/STAT3 signaling pathway. Using a genome-wide CRISPR screen in von Hippel–Lindau–deficient (VHL-deficient) ccRCC cells, we identified SOCS3 as a key negative regulator of HIF-2α. Mechanistically, loss of SOCS3 activates JAK1/STAT3 signaling, leading to the recruitment of STAT3 to distal enhancers upstream of endothelial PAS domain-containing protein (EPAS1) that physically loop to its promoter to drive HIF-2α transcription. This cytokine-enhancer circuit was recapitulated in samples from patients with ccRCC and functionally validated using CRISPR interference (CRISPRi), which disrupted enhancer-promoter looping and reduced tumor growth in HIF-2α–dependent models. SOCS3 overexpression or pharmacologic inhibition of JAK1/STAT3 markedly suppressed HIF-2α expression and tumor progression both in vitro and in vivo. Unlike prior studies focusing on VHL/HIF occupancy–driven enhancer activation, this work defines a trans-acting cytokine–JAK1/STAT3 pathway that transcriptionally controls EPAS1. Together, these findings reveal a targetable enhancer mechanism that sustains HIF-2α expression and suggest that combined inhibition of JAK1/STAT3 and HIF-2α may overcome therapeutic resistance in kidney cancer.
Authors
Jun Fang, Jeremy M. Simon, Tao Wang, Yunpeng Gao, Xianju Bi, Lianxin Hu, Chengheng Liao, Cheng Zhang, Yayoi Adachi, Jin Zhou, Hongyi Liu, Qian Liang, James A. Nathan, Ram Mani, James Brugarolas, Qing Zhang
Abstract
Glioblastoma (GBM) is a highly aggressive brain tumor characterized by extensive crosstalk between glioblastoma stem cells (GSCs) and immunosuppressive microglia, with our previous work identifying CLOCK and TFPI2 as key regulators of this interaction. Here, we uncover a ‘symbiotic exclusivity’ pattern between CLOCK and TFPI2, showing that, despite mutually exclusive amplifications, they sustain symbiotic regulatory interactions in GBM. The CLOCK-BMAL1 complex transcriptionally upregulates TFPI2, while TFPI2-driven hypoxia inducible factor 1 α (HIF-1α) signaling activates nuclear factor k B (NF-kB) P65 to upregulate the CLOCK-BMAL1 complex, creating a positive feedback loop to promote stemness, immunosuppression, and tumor progression. Disrupting the CLOCK-TFPI2 interplay through dual inhibition of their downstream effectors reduces GSC stemness and immunosuppressive microglia, activates antitumor immunity, and synergizes with anti-PD1 therapy to achieve complete tumor regression in 50%–62.5% of tumor-bearing mice. This study uncovers a promising therapeutic strategy for a broader subset of patients with GBM with high expression of either CLOCK or TFPI2, and provides a framework for identifying ‘symbiotic exclusivity’ genes in cancer.
Authors
Fei Zhou, Lizhi Pang, Yang Liu, Fatima Khan, Peiwen Chen
Abstract
Airway mucus clearance from the lungs occurs by 2 widely recognized mechanisms: cilia-mediated clearance and high-velocity airflow-mediated cough clearance. However, a potentially important third mechanism of mucus clearance, referred to as cilia-independent gas–liquid transport (GLT), was proposed based on in vitro model systems to occur during normal tidal breathing but has largely been overlooked. We conducted in vitro and in vivo studies to investigate the role of tidal breathing airflow rates in mucus clearance. An in vitro airway culture bead-tracking model demonstrated airflow-dependent mucus transport at tidal breathing flow rates. As with other modes of mucus clearance, GLT was critically dependent on mucus concentration. In vivo studies in cilial beat-deficient mice demonstrated that GLT-mediated mucus clearance occurs during tidal breathing in the absence of cough, and the rate of GLT mucus clearance was dependent on breathing frequency and body orientation. These studies demonstrated that GLT is a third mechanism of mucus clearance and likely represents a significant mode of clearance in persons with cilial dysfunction. These findings indicate that increasing breathing rates through exercise, using mucus rehydrating agents or mucolytics, or combining these approaches may restore clinically and physiologically meaningful airway clearance in these patients.
Authors
Siddharth K. Shenoy, Mark Gutay, Ian Brown, Troy D. Rogers, Kane Banner, Nico Olegario, Nicholas Griffin, Henry P. Goodell, Bryan Yoder, David S. Lalush, David A. Edwards, Richard C. Boucher, Barbara R. Grubb, Brian Button
Abstract
Cilia are cellular organelles that extrude from the surface of various cell types, serving either sensory or motile functions. Retinitis pigmentosa GTPase regulator (RPGR) variants affect both photoreceptor sensory cilia and airway motile cilia, leading to retinitis pigmentosa (RP) and primary ciliary dyskinesia (PCD), respectively. Not all patients develop PCD, and it remains unclear which RPGR variants predispose patients to PCD. Here, we leverage 2D organoids, super-resolution microscopy, and live-cell imaging to characterize the multiciliated cells (MCCs) from patients with different RPGR variants and CRISPR-modified RPGR KO MCCs. We demonstrate that MCCs with RPGR variants have reduced ciliation, shorter cilia, impaired cilia beat, or cilia beat incoordination, potentially resulting in compromised mucociliary clearance and lung diseases. Moreover, we show that RPGR regulates motile cilia through interfering with F-actin dynamics, evidenced by the undissolved F-actin meshwork in RPGR-deficient MCCs, and the defects can be ameliorated with either latrunculin A or Y27632 treatment. Though PCD was observed only in patients with variants that affect both isoforms, patients with RPGRORF15 variants also had cilia and airway anomalies. All RPGR variants affected motile cilia in some way, and the mechanisms involved the accumulation of apical F-actin.
Authors
Yang Wu, Erika Tavares, Binrun Liang, Wallace B. Wee, Vito Mennella, Han-Chao Feng, Jiaying Cao, Pui Yee Wong, Jiayi Zheng, Mu He, Kirk AJ Stephenson, Liran Hanan Hochma, Janice Min Li, Nan-Peng Chen, Sharon D. Dell, Elise Heon, Zhen Liu
Abstract
Stimulant medications are widely prescribed for attention deficit hyperactivity disorder (ADHD) and have significant abuse liability. Here, we show that, consistent with clinical data, female mice exhibited enhanced behavioral sensitivity to stimulants, and we define sex- and hormone-dependent adaptations in the dopamine system that contributed to these effects. Single-nucleus RNA-seq of ventral tegmental area dopamine neurons revealed that projections to the nucleus accumbens (NAc) core, compared with other projection populations, were a hub of sexually dimorphic gene expression, including transcripts regulating dopamine synthesis, and transport. These molecular differences coincided with enhanced dopamine release and clearance in female mice, particularly during phases of the estrous cycle when estradiol levels were high. The stimulants amphetamine (a releaser) and methylphenidate (a reuptake inhibitor) more effectively increased dopamine levels in female mice under certain conditions. However, amphetamine showed more robust hormone-sensitive regulation, with potency reduced by ovariectomy and restored by direct estradiol replacement in the NAc core. Together, the findings indicate that even within a drug class, drugs with different mechanisms of action can leverage different aspects of sexually dimorphic dopamine function. This distinction highlights the notion that sex differences are not uniform but can be differentially sensitive to drug pharmacology.
Authors
Brooke A. Christensen, Jennifer Tat, Michael Z. Leonard, Soren D. Emerson, Shemuel Roberts, Eleanor B. Holmgren, Ainoa Konomi-Pilkati, Hannah B. Reiley, Devan M. Gomez, Lin Zheng, Hye Jean Yoon, Sofia H. Lago, Abigail L. Carr, Lillian J. Brady, Maxime Chevée, Erin S. Calipari
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Copyright © 2026 American Society for Clinical Investigation
ISSN: 0021-9738 (print), 1558-8238 (online)