Molnupiravir clinical trial simulation suggests that polymerase chain reaction underestimates antiviral potency against SARS-CoV-2

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Abstract

Molnupiravir is an antiviral medicine that induces lethal copying errors during SARS-CoV-2 RNA replication. Molnupiravir reduced hospitalization in one pivotal trial by 50% and had variable effects on reducing viral RNA levels in three separate trials. We used mathematical models to simulate these trials and closely recapitulated their virologic outcomes. Model simulations suggest lower antiviral potency against pre-omicron SARS-CoV-2 variants than against omicron. We estimate that in vitro assays underestimate in vivo potency 6-7 fold against omicron variants. Our model suggests that because polymerase chain reaction detects molnupiravir mutated variants, the true reduction in non-mutated viral RNA is underestimated by ~0.4 log10 in the two trials conducted while omicron variants dominated. Viral area under the curve estimates differ significantly between non-mutated and mutated viral RNA. Our results reinforce past work suggesting that in vitro assays are unreliable for estimating in vivo antiviral drug potency and suggest that virologic endpoints for respiratory virus clinical trials should be catered to the drug mechanism of action.

Authors

Shadisadat Esmaeili, Katherine Owens, Ugo Avila-Ponce de Leon, Joseph F. Standing, David M. Lowe, Shengyuan Zhang, James A. Watson, William H.K. Schilling, Jessica Wagoner, Stephen J. Polyak, Joshua T. Schiffer

Targeting peroxiredoxin 2 prevents hepatocarcinogenesis in metabolic liver disease

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Abstract

Treatment options for advanced liver disease and hepatocellular carcinoma (HCC) are limited and strategies to prevent HCC development are lacking. Aiming to discover novel therapeutic targets, we combined genome wide transcriptomic analysis of liver tissues from patients with advanced liver disease and HCC and a cell-based system predicting liver disease progression and HCC risk. Computational analysis predicted peroxiredoxin 2 (PRDX2) as a candidate gene mediating hepatocarcinogenesis and HCC risk. Analysis of HCC patient tissues confirmed a perturbed expression of PRDX2 in cancer. In vivo perturbation studies in mouse models for MASH driven hepatocarcinogenesis showed that specific Prdx2 knockout in hepatocytes significantly improved metabolic liver functions, restored AMPK activity and prevented HCC development by suppressing oncogenic signaling. Perturbations studies in HCC cell lines, a CDX mouse model and patient-derived HCC spheroids unraveled that PRDX2 also mediates cancer initiation, cancer cell proliferation and survival through its antioxidant activity. Targeting PRDX2 may therefore be a valuable strategy to prevent HCC development in metabolic liver disease.

Authors

Emilie Crouchet, Eugénie Schaeffer, Marine A. Oudot, Julien Moehlin, Cloé Gadenne, Frank Jühling, Hussein El Saghire, Naoto Fujiwara, Shijia Zhu, Fahmida Akter Rasha, Sarah C. Durand, Anouk Charlot, Clara Ponsolles, Romain Martin, Nicolas Brignon, Fabio Del Zompo, Laura Meiss Heydmann, Marie Parnot, Nourdine Hamdane, Danijela Heide, Jenny Hetzer, Mathias Heikenwälder, Emanuele Felli, Patrick Pessaux, Nathalie Pochet, Joffrey Zoll, Brian Cunniff, Yujin Hoshida, Laurent Mailly, Thomas F. Baumert, Catherine Schuster

ZEB1 promotes chemo-immune resistance in pancreatic cancer models by downregulating chromatin acetylation of CXCL16

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Abstract

Pancreatic cancer (PC) is notoriously resistant to both chemotherapy and immunotherapy, presenting a major therapeutic challenge. Epigenetic modifications play a critical role in PC progression, yet their contribution to chemoimmunotherapy resistance remains poorly understood. Here, we identified the transcription factor ZEB1 as a critical driver of chemoimmunotherapy resistance in PC. ZEB1 knockdown synergized with gemcitabine and anti-PD1 therapy, markedly suppressed PC growth, and prolonged survival in vivo. Single-cell and spatial transcriptomics revealed that ZEB1 ablation promoted tumor pyroptosis by recruiting and activating GZMA+CD8+ T cells in the tumor core through epigenetic upregulation of CXCL16. Meanwhile, ZEB1 blockade attenuates CD44+ neutrophil-induced CD8+ T cell exhaustion by reducing tumor-derived SPP1 secretion, which otherwise promotes exhaustion through activation of the PD-L1–PD-1 pathway. Clinically, high ZEB1 expression correlated with chemoresistance, immunosuppression, and diminished CXCL16 levels in PC patients. Importantly, the epigenetic inhibitor Mocetinostat (targeting ZEB1) potentiated chemoimmunotherapy efficacy, including anti-PD1 and CAR-T therapies, in patient-derived organoids, xenografts, and orthotopic models. Our study unveils ZEB1 as a master epigenetic regulator of chemoimmunotherapy resistance and proposes its targeting as a transformative strategy for PC treatment.

Authors

Shaobo Zhang, Yumeng Hu, Zhijun Zhou, Gaoyuan Lv, Chenze Zhang, Yuanyuan Guo, Fangxia Wang, Yuxin Ye, Haoran Qi, Hui Zhang, Wenming Wu, Min Li, Mingyang Liu

TFIIH-p52∆C defines a ninth xeroderma pigmentosum complementation-group XP-J and restores TFIIH stability to p8-defective trichothiodystrophy

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Abstract

Few drugs are available for rare diseases due to economic disincentives. However, tailored medications for extremely-rare disorders (N-of-1) offer a ray of hope. Artificial antisense oligonucleotides (ASOs) are now best known for their use in spinal muscular atrophy (SMA). The success of nusinersen/Spinraza for SMA indicates ASO-therapies' potential for other rare conditions. We propose a strategy to develop N-of-1 ASOs for treating one form of trichothiodystrophy (TTD), a rare condition with multisystem abnormalities and reduced life expectancy, associated with instability and greatly reduced amounts of the DNA-repair/transcription factor TFIIH. The therapeutic target carry mutations in GTF2H5, encoding the TFIIH-p8 subunit. This approach was inspired by the diagnosis and molecular dissection of a xeroderma pigmentosum (XP) case with mutations in GTF2H4, encoding the TFIIH-p52 subunit. This is newly classified as a ninth XP complementation-group, XP-J, identified five decades after the discovery of the other XP complementation-groups. The p8-p52 interaction is required to support the TFIIH-complex formation, and the patient's p52 C-terminal truncation results in the complete absence of p8 in TFIIH. However, intriguingly, TFIIH remained stable in vivo, and the XP-J patient did not exhibit any TTD-features. The aim of our ASO-design is to induce a C-terminal truncation of p52 and we have successfully stabilised TFIIH in p8-deficient TTD-A patient cells.

Authors

Yuka Nakazawa, Lin Ye, Yasuyoshi Oka, Hironobu Morinaga, Kana Kato, Mayuko Shimada, Kotaro Tsukada, Koyo Tsujikawa, Yosuke Nishio, Hiva Fassihi, Shehla Mohammed, Alan R. Lehmann, Tomoo Ogi

Recessive TMEM167A variants cause neonatal diabetes, microcephaly and epilepsy syndrome

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Abstract

Understanding the genetic causes of diseases affecting pancreatic β cells and neurons can give insights into pathways essential for both cell types. Microcephaly, epilepsy and diabetes syndrome (MEDS) is a congenital disorder with two known aetiological genes, IER3IP1 and YIPF5. Both genes encode proteins involved in endoplasmic reticulum (ER) to Golgi trafficking. We used genome sequencing to identify 6 individuals with MEDS caused by biallelic variants in the novel disease gene, TMEM167A. All had neonatal diabetes (diagnosed <6 months) and severe microcephaly, five also had epilepsy. TMEM167A is highly expressed in developing and adult human pancreas and brain. To gain insights into the mechanisms leading to diabetes, we silenced TMEM167A in EndoC-βH1 cells and knocked-in one patient’s variant, p.Val59Glu, in induced pluripotent stem cells (iPSCs). Both TMEM167A depletion in EndoC-βH1 cells and the p.Val59Glu variant in iPSC-derived β cells sensitized β cells to ER stress. The p.Val59Glu variant impaired proinsulin trafficking to the Golgi and induced iPSC-β cell dysfunction. The discovery of TMEM167A variants as a new genetic cause of MEDS highlights a critical role of TMEM167A in the ER to Golgi pathway in β cells and neurons.

Authors

Enrico Virgilio, Sylvia Tielens, Georgia Bonfield, Fang-Shin Nian, Toshiaki Sawatani, Chiara Vinci, Molly Govier, Hossam Montaser, Romane Lartigue, Anoop Arunagiri, Alexandrine Liboz, Flavia Natividade da Silva, Maria Lytrivi, Theodora Papadopoulou, Matthew N. Wakeling, James Russ-Silsby, Pamela Bowman, Matthew B. Johnson, Thomas W. Laver, Anthony Piron, Xiaoyan Yi, Federica Fantuzzi, Sirine Hendrickx, Mariana Igoillo-Esteve, Bruno J. Santacreu, Jananie Suntharesan, Radha Ghildiyal, Darshan G. Hegde, Nikhil Avnish Shah, Sezer Acar, Beyhan Özkaya Dönmez, Behzat Özkan, Fauzia Mohsin, Iman M. Talaat, Mohamed Tarek Abbas, Omar Saied Abbas, Hamed Ali Alghamdi, Nurgun Kandemir, Sarah E. Flanagan, Raphael Scharfmann, Peter Arvan, Matthieu Raoux, Laurent Nguyen, Andrew T. Hattersley, Miriam Cnop, Elisa De Franco

Multi-omic analysis reveals a key BCAT1 role in mTOR activation by B-cell receptor and TLR9

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Abstract

B-lymphocytes play major adaptive immune roles, producing antibody and driving T-cell responses. However, how immunometabolism networks support B-cell activation and differentiation in response to distinct receptor stimuli remains incompletely understood. To gain insights, we systematically investigated acute primary human B-cell transcriptional, translational and metabolomic responses to B-cell receptor (BCR), Toll-like receptor 9 (TLR9), CD40-ligand (CD40L), interleukin-4 (IL4) or combinations thereof. T-independent BCR/TLR9 co-stimulation, which drives malignant and autoimmune B-cell states highly induced the transaminase branched chain amino acid transaminase 1 (BCAT1), which localized to lysosomal membranes to support branched chain amino acid synthesis and mechanistic target of rapamycin complex 1 (mTORC1) activation. BCAT1 inhibition blunted BCR/TLR9, but not CD40L/IL4-triggered B-cell proliferation, IL10 expression and BCR/TLR pathway-driven lymphoma xenograft outgrowth. These results provide a valuable resource, reveal receptor-mediated immunometabolism remodeling to support key B-cell phenotypes and identify BCAT1 as an activated B-cell therapeutic target.

Authors

Rui Guo, Yizhe Sun, Matthew Y. Lim, Hardik Shah, Joao A. Paulo, Rahaman A. Ahmed, Weixing Li, Yuchen Zhang, Haopeng Yang, Liang Wei Wang, Daniel Strebinger, Nicholas A. Smith, Meng Li, Merrin Man Long Leong, Michael Lutchenkov, Jin-Hua Liang, Zhixuan Li, Yin Wang, Rishi Puri, Ari Melnick, Michael R. Green, John M. Asara, Adonia E. Papathanassiu, Duane R. Wesemann, Steven P. Gygi, Vamsi K. Mootha, Benjamin E. Gewurz

UBA1-depleted neutrophils disrupt immune homeostasis and induce VEXAS-like autoinflammatory disease in mice

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Abstract

VEXAS (Vacuoles, E1 enzyme, X-linked, Autoinflammatory, Somatic) syndrome is a haemato-rheumatoid disease caused by somatic UBA1 mutations in hematopoietic stem cells (HSCs). The pathogenic cell type(s) responsible for the syndrome are unknown and murine models recapitulating the disease are lacking. We report that loss of Uba1 in various mouse hematopoietic cell types resulted in pleiotropic consequences and demonstrate that murine mutants with about 70% loss of Uba1 in neutrophils induced non-lethal VEXAS-like symptoms. Depletion of Uba1 in HSCs induced extensive hematopoietic cell loss while depletion of Uba1 in B or T cells, or in megakaryocytes induced corresponsive cell death but these mutants appeared normal. Depletion of Uba1 in monocytes and neutrophils failed to induce cell death and the mutants were viable. Among the tested models, only depletion of Uba1 in neutrophils induced autoinflammatory symptoms including increased counts and percentage of neutrophils, increased proinflammatory cytokines, occurrence of vacuoles in myeloid cells, splenomegaly and dermatitis. Residual Uba1 was about 30% in the mutant neutrophils, which disrupted cellular hemostasis. Finally, genetic loss of the myeloid pro-survival regulator Morrbid partially mitigated the VEXAS-like symptoms. The established VEXAS-like murine model will assist understanding and treatment of the newly identified autoinflammatory syndrome prevalent among aged men.

Authors

Ge Dong, Jingjing Liu, Wenyan Jin, Hongxi Zhou, Yuchen Wen, Zhiqin Wang, Keyao Xia, Jianlin Zhang, Linxiang Ma, Yunxi Ma, Lorie Chen Cai, Qiufan Zhou, Huaquan Wang, Wei Wei, Ying Fu, Zhigang Cai

Intermittent ischemia-reperfusion as a potent insulin-sensitizing intervention via blood flow enhancement and muscle Decanoyl-L-carnitine suppression

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Abstract

A single bout of exercise improves muscle insulin sensitivity for up to 48 hours via the AMP-activated protein kinase (AMPK). Limb ischemia activates AMPK in muscle, and subsequent reperfusion enhances insulin-stimulated vasodilation, potentially eliciting a more pronounced exercise effect with reduced workload. Here, we investigated the combined effect of upper leg intermittent ischemia-reperfusion (IIR) and continuous knee-extension exercise on muscle insulin sensitivity regulation. We found that IIR-exercise potentiated AMPK activation and muscle insulin sensitivity. The potentiating effect of IIR-exercise on muscle insulin sensitivity was associated with increased insulin-stimulated blood flow in parallel with enhanced phosphorylation of endothelial nitric oxide synthase. Metabolomics analyses demonstrated a suppression of muscle medium-chain acylcarnitines during IIR-exercise, which correlated with insulin sensitivity and was consistent with findings in isolated rat muscle treated with Decanoyl-L-carnitine. Collectively, combining IIR with low-to-moderate intensity exercise may represent a promising intervention to effectively enhance muscle insulin sensitivity. This approach could offer potential for mitigating muscle insulin resistance in clinical settings and among individuals with lower physical activity levels.

Authors

Kohei Kido, Janne R. Hingst, Johan Onslev, Kim A. Sjøberg, Jesper B. Birk, Nicolas O. Eskesen, Tongzhu Zhou, Kentaro Kawanaka, Jesper F. Havelund, Nils J. Færgeman, Ylva Hellsten, Jørgen F.P. Wojtaszewski, Rasmus Kjøbsted

IGFBP6 orchestrates anti-infective immune collapse in murine sepsis via prohibitin-2-mediated immunosuppression

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Abstract

The persistent challenge of sepsis-related mortality underscores the necessity for deeper insights, with our multi-center cross-age cohort study identifying insulin-like growth factor binding protein 6 (IGFBP6) as a critical regulator in sepsis diagnosis, prognosis, and mortality risk evaluation. Mechanistically, IGFBP6 engages in IGF-independent binding to prohibitin2 (PHB2) on epithelial cells, driving PHB2 tyrosine phosphorylation during sepsis. This process disrupts STAT1 phosphorylation, nuclear translocation, and its recruitment to the CCL2 promoter, ultimately impairing CCL2 transcription and macrophage chemotaxis. Crucially, PHB2 silencing via siPHB2 and STAT1 activation using 2-NP restored CCL2 expression in vitro and in vivo, improving bacterial clearance and survival in septic mice. Concurrently, IGFBP6 compromises macrophage bactericidal activity by inhibiting Akt phosphorylation, reducing ROS/IL-1β production and phagocytic capacity – defects reversible by Akt agonist SC79. Collectively, IGFBP6 emerges as an endogenous driver of sepsis pathogenesis, positioning it as a dual diagnostic biomarker and therapeutic target. Intervention strategies targeting IGFBP6-mediated signaling may offer transformative approaches for sepsis management.

Authors

Kai Chen, Ying Hu, Xiaoyan Yu, Hong Tang, Yanting Ruan, Yue Li, Xun Gao, Qing Zhao, Hong Wang, Xuemei Zhang, David Paul Molloy, Yibing Yin, Dapeng Chen, Zhixin Song

MPO-anchored ENO1 mediates neutrophil extracellular trap DNA for enhancing Treg differentiation via IFITM2 during sepsis

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Abstract

Sepsis is a life-threatening disease caused by a dysfunctional host response to infection. During sepsis, inflammation-related immunosuppression is the critical factor causing secondary infection and multiple organ dysfunction syndrome. The regulatory mechanisms underlying regulatory T-cell (Treg) differentiation and function, which significantly contribute to septic immunosuppression, require further clarification. In this study, we found that neutrophil extracellular traps (NETs) participated in the development of sepsis-induced immunosuppression by enhancing Treg differentiation and function via direct interaction with CD4+ T cells. Briefly, NETs anchored enolase 1 (ENO1) on the membrane of CD4+ T cells through its key protein myeloperoxidase (MPO) and subsequently recruited interferon-induced transmembrane protein 2 (IFITM2). IFITM2 acted as a DNA receptor that sensed NETs-DNA and activated intracellular RAS-associated protein 1B (RAP1B) and its downstream extracellular signal-regulated kinase (ERK) signaling pathway to promote Treg differentiation and function. ENO1 inhibition significantly attenuated NETs-induced Treg differentiation and alleviated sepsis in mice. Overall, we demonstrated the role of NETs in sepsis-induced immunosuppression by enhancing Treg differentiation, identified ENO1 as an anchor of NETs-MPO, and elucidated the downstream molecular mechanism by which IFITM2-RAP1B-ERK regulated Treg differentiation. These findings improve our understanding of the immunopathogenesis of sepsis and provide potential therapeutic targets for sepsis-induced immunosuppression.

Authors

Yi Jiang, Shenjia Gao, Xiya Li, Hao Sun, Xinyi Wu, Jiahui Gu, Zhaoyuan Chen, Han Wu, Xiaoqiang Zhao, Tongtong Zhang, Ronen Ben-Ami, Yuan Le, Timothy R. Billiar, Changhong Miao, Jie Zhang, Jun Wang, Wankun Chen