Molecular Systems Biology最新文献

Pulsed stimuli enable p53 phase resetting to synchronize single cells and modulate cell fate.

IF 8.5 1区生物学

Molecular Systems Biology Pub Date : 2025-03-03 DOI: 10.1038/s44320-025-00091-8

Harish Venkatachalapathy, Samuel Dallon, Zhilin Yang, Samira M Azarin, Casim A Sarkar, Eric Batchelor

{"title":"Pulsed stimuli enable p53 phase resetting to synchronize single cells and modulate cell fate.","authors":"Harish Venkatachalapathy, Samuel Dallon, Zhilin Yang, Samira M Azarin, Casim A Sarkar, Eric Batchelor","doi":"10.1038/s44320-025-00091-8","DOIUrl":"10.1038/s44320-025-00091-8","url":null,"abstract":"Oscillatory p53 expression occurs in individual cells responding to DNA breaks. While the majority of cells exhibit the same qualitative response, quantitative features of the oscillations (e.g., amplitude or period) can be highly variable between cells, generating heterogeneity in downstream cell fate responses. Since heterogeneity can be detrimental to therapies based on DNA damage, methods to induce synchronization of p53 oscillations across cells in a population have the potential to generate more predictable responses to DNA-damaging treatments. Using mathematical modeling and time-lapse microscopy, we demonstrated that p53 oscillations can be synchronized through the phenomenon of phase resetting. Surprisingly, p53 oscillations were synchronized over a wider range of damage-induction frequencies than predicted computationally. Recapitulating the range of synchronizing frequencies required, non-intuitively, a less robust oscillator. We showed that p53 phase resetting altered the expression of downstream targets responsible for cell fate depending on target mRNA stability. This study demonstrates that p53 oscillations can be phase reset and highlights the potential of driving p53 dynamics to reduce cellular variability and synchronize cell fate responses to DNA damage.","PeriodicalId":18906,"journal":{"name":"Molecular Systems Biology","volume":" ","pages":""},"PeriodicalIF":8.5,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143542544","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Gemcitabine and ATR inhibitors synergize to kill PDAC cells by blocking DNA damage response. 吉西他滨和ATR抑制剂通过阻断DNA损伤反应协同杀死PDAC细胞。

IF 8.5 1区生物学

Molecular Systems Biology Pub Date : 2025-03-01 Epub Date: 2025-01-21 DOI: 10.1038/s44320-025-00085-6

Stefanie Höfer, Larissa Frasch, Sarah Brajkovic, Kerstin Putzker, Joe Lewis, Hendrik Schürmann, Valentina Leone, Amirhossein Sakhteman, Matthew The, Florian P Bayer, Julian Müller, Firas Hamood, Jens T Siveke, Maximilian Reichert, Bernhard Kuster

{"title":"Gemcitabine and ATR inhibitors synergize to kill PDAC cells by blocking DNA damage response.","authors":"Stefanie Höfer, Larissa Frasch, Sarah Brajkovic, Kerstin Putzker, Joe Lewis, Hendrik Schürmann, Valentina Leone, Amirhossein Sakhteman, Matthew The, Florian P Bayer, Julian Müller, Firas Hamood, Jens T Siveke, Maximilian Reichert, Bernhard Kuster","doi":"10.1038/s44320-025-00085-6","DOIUrl":"10.1038/s44320-025-00085-6","url":null,"abstract":"The DNA-damaging agent Gemcitabine (GEM) is a first-line treatment for pancreatic cancer, but chemoresistance is frequently observed. Several clinical trials investigate the efficacy of GEM in combination with targeted drugs, including kinase inhibitors, but the experimental evidence for such rationale is often unclear. Here, we phenotypically screened 13 human pancreatic adenocarcinoma (PDAC) cell lines against GEM in combination with 146 clinical inhibitors and observed strong synergy for the ATR kinase inhibitor Elimusertib in most cell lines. Dose-dependent phosphoproteome profiling of four ATR inhibitors following DNA damage induction by GEM revealed a strong block of the DNA damage response pathway, including phosphorylated pS468 of CHEK1, as the underlying mechanism of drug synergy. The current work provides a strong rationale for why the combination of GEM and ATR inhibition may be useful for the treatment of PDAC patients and constitutes a rich phenotypic and molecular resource for further investigating effective drug combinations.","PeriodicalId":18906,"journal":{"name":"Molecular Systems Biology","volume":" ","pages":"231-253"},"PeriodicalIF":8.5,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11876601/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143008697","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Leveraging prior knowledge to infer gene regulatory networks from single-cell RNA-sequencing data.

IF 8.5 1区生物学

Molecular Systems Biology Pub Date : 2025-03-01 Epub Date: 2025-02-12 DOI: 10.1038/s44320-025-00088-3

Marco Stock, Corinna Losert, Matteo Zambon, Niclas Popp, Gabriele Lubatti, Eva Hörmanseder, Matthias Heinig, Antonio Scialdone

{"title":"Leveraging prior knowledge to infer gene regulatory networks from single-cell RNA-sequencing data.","authors":"Marco Stock, Corinna Losert, Matteo Zambon, Niclas Popp, Gabriele Lubatti, Eva Hörmanseder, Matthias Heinig, Antonio Scialdone","doi":"10.1038/s44320-025-00088-3","DOIUrl":"10.1038/s44320-025-00088-3","url":null,"abstract":"Many studies have used single-cell RNA sequencing (scRNA-seq) to infer gene regulatory networks (GRNs), which are crucial for understanding complex cellular regulation. However, the inherent noise and sparsity of scRNA-seq data present significant challenges to accurate GRN inference. This review explores one promising approach that has been proposed to address these challenges: integrating prior knowledge into the inference process to enhance the reliability of the inferred networks. We categorize common types of prior knowledge, such as experimental data and curated databases, and discuss methods for representing priors, particularly through graph structures. In addition, we classify recent GRN inference algorithms based on their ability to incorporate these priors and assess their performance in different contexts. Finally, we propose a standardized benchmarking framework to evaluate algorithms more fairly, ensuring biologically meaningful comparisons. This review provides guidance for researchers selecting GRN inference methods and offers insights for developers looking to improve current approaches and foster innovation in the field.","PeriodicalId":18906,"journal":{"name":"Molecular Systems Biology","volume":" ","pages":"214-230"},"PeriodicalIF":8.5,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11876610/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143409153","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Refuse in order to resist: metabolic bottlenecks reduce antibiotic susceptibility.

IF 8.5 1区生物学

Molecular Systems Biology Pub Date : 2025-03-01 Epub Date: 2025-02-18 DOI: 10.1038/s44320-025-00089-2

Orestis Kanaris, Frank Schreiber

引用次数: 0

Metabolic mutations reduce antibiotic susceptibility of E. coli by pathway-specific bottlenecks. 代谢突变通过途径特异性瓶颈降低大肠杆菌的抗生素敏感性。

IF 8.5 1区生物学

Molecular Systems Biology Pub Date : 2025-03-01 Epub Date: 2025-01-02 DOI: 10.1038/s44320-024-00084-z

Paul Lubrano, Fabian Smollich, Thorben Schramm, Elisabeth Lorenz, Alejandra Alvarado, Seraina Carmen Eigenmann, Amelie Stadelmann, Sevvalli Thavapalan, Nils Waffenschmidt, Timo Glatter, Nadine Hoffmann, Jennifer Müller, Silke Peter, Knut Drescher, Hannes Link

{"title":"Metabolic mutations reduce antibiotic susceptibility of E. coli by pathway-specific bottlenecks.","authors":"Paul Lubrano, Fabian Smollich, Thorben Schramm, Elisabeth Lorenz, Alejandra Alvarado, Seraina Carmen Eigenmann, Amelie Stadelmann, Sevvalli Thavapalan, Nils Waffenschmidt, Timo Glatter, Nadine Hoffmann, Jennifer Müller, Silke Peter, Knut Drescher, Hannes Link","doi":"10.1038/s44320-024-00084-z","DOIUrl":"10.1038/s44320-024-00084-z","url":null,"abstract":"Metabolic variation across pathogenic bacterial strains can impact their susceptibility to antibiotics and promote the evolution of antimicrobial resistance (AMR). However, little is known about how metabolic mutations influence metabolism and which pathways contribute to antibiotic susceptibility. Here, we measured the antibiotic susceptibility of 15,120 Escherichia coli mutants, each with a single amino acid change in one of 346 essential proteins. Across all mutants, we observed modest increases of the minimal inhibitory concentration (twofold to tenfold) without any cases of major resistance. Most mutants that showed reduced susceptibility to either of the two tested antibiotics carried mutations in metabolic genes. The effect of metabolic mutations on antibiotic susceptibility was antibiotic- and pathway-specific: mutations that reduced susceptibility against the β-lactam antibiotic carbenicillin converged on purine nucleotide biosynthesis, those against the aminoglycoside gentamicin converged on the respiratory chain. In addition, metabolic mutations conferred tolerance to carbenicillin by reducing growth rates. These results, along with evidence that metabolic bottlenecks are common among clinical E. coli isolates, highlight the contribution of metabolic mutations for AMR.","PeriodicalId":18906,"journal":{"name":"Molecular Systems Biology","volume":" ","pages":"274-293"},"PeriodicalIF":8.5,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11876631/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142922180","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Hormone circuit explains why most HPA drugs fail for mood disorders and predicts the few that work.

IF 8.5 1区生物学

Molecular Systems Biology Pub Date : 2025-03-01 Epub Date: 2025-01-23 DOI: 10.1038/s44320-024-00083-0

Tomer Milo, Shiraz Nir Halber, Moriya Raz, Dor Danan, Avi Mayo, Uri Alon

{"title":"Hormone circuit explains why most HPA drugs fail for mood disorders and predicts the few that work.","authors":"Tomer Milo, Shiraz Nir Halber, Moriya Raz, Dor Danan, Avi Mayo, Uri Alon","doi":"10.1038/s44320-024-00083-0","DOIUrl":"10.1038/s44320-024-00083-0","url":null,"abstract":"Elevated cortisol in chronic stress and mood disorders causes morbidity including metabolic and cardiovascular diseases. There is therefore interest in developing drugs that lower cortisol by targeting its endocrine pathway, the hypothalamic-pituitary-adrenal (HPA) axis. However, several promising HPA-modulating drugs have failed to reduce long-term cortisol in mood disorders, despite effectiveness in other hypercortisolism conditions such as Cushing's syndrome. The reasons for these failures remain unclear. Here, we use a mathematical model of the HPA axis to demonstrate that the pituitary and adrenal glands compensate for drug effects by adjusting their functional mass, a feedback mechanism absent in Cushing tumors. Our systematic in silico analysis identifies two interventions targeting corticotropin-releasing hormone (CRH) as effective for lowering long-term cortisol. Other targets either fail due to gland mass compensation or harm other aspects of the HPA axis. We propose CRH-neutralizing antibodies and CRH-synthesis inhibitors as potential targets for reducing long-term cortisol in mood disorders and chronic stress. More generally, this study indicates that understanding the slow compensatory mechanisms in endocrine axes can be crucial to prioritize drug targets.","PeriodicalId":18906,"journal":{"name":"Molecular Systems Biology","volume":" ","pages":"254-273"},"PeriodicalIF":8.5,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11876312/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143029179","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Epigenetic modifications and metabolic gene mutations drive resistance evolution in response to stimulatory antibiotics. 表观遗传修饰和代谢基因突变驱动对刺激性抗生素的抗性进化。

IF 8.5 1区生物学

Molecular Systems Biology Pub Date : 2025-03-01 Epub Date: 2025-01-16 DOI: 10.1038/s44320-025-00087-4

Hui Lin, Donglin Wang, Qiaojuan Wang, Jie Mao, Lutong Yang, Yaohui Bai, Jiuhui Qu

{"title":"Epigenetic modifications and metabolic gene mutations drive resistance evolution in response to stimulatory antibiotics.","authors":"Hui Lin, Donglin Wang, Qiaojuan Wang, Jie Mao, Lutong Yang, Yaohui Bai, Jiuhui Qu","doi":"10.1038/s44320-025-00087-4","DOIUrl":"10.1038/s44320-025-00087-4","url":null,"abstract":"The antibiotic resistance crisis, fueled by misuse and bacterial evolution, is a major global health threat. Traditional perspectives tie resistance to drug target mechanisms, viewing antibiotics as mere growth inhibitors. New insights revealed that low-dose antibiotics may also serve as signals, unexpectedly promoting bacterial growth. Yet, the development of resistance under these conditions remains unknown. Our study investigated resistance evolution under stimulatory antibiotics and uncovered new genetic mechanisms of resistance linked to metabolic remodeling. We documented a shift from a fast, reversible mechanism driven by methylation in central metabolic pathways to a slower, stable mechanism involving mutations in key metabolic genes. Both mechanisms contribute to a metabolic profile transition from glycolysis to rapid gluconeogenesis. In addition, our findings demonstrated that rising environmental temperatures associated with metabolic evolution accelerated this process, increasing the prevalence of metabolic gene mutations, albeit with a trade-off in interspecific fitness. These findings expand beyond the conventional understanding of resistance mechanisms, proposing a broader metabolic mechanism within the selective window of stimulatory sub-MIC antibiotics, particularly in the context of climate change.","PeriodicalId":18906,"journal":{"name":"Molecular Systems Biology","volume":" ","pages":"294-314"},"PeriodicalIF":8.5,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11876630/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143008695","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Circadian clock features define novel subtypes among breast cancer cells and shape drug sensitivity.

IF 8.5 1区生物学

Molecular Systems Biology Pub Date : 2025-02-24 DOI: 10.1038/s44320-025-00092-7

Carolin Ector, Jeff Didier, Sébastien De Landtsheer, Malthe S Nordentoft, Christoph Schmal, Ulrich Keilholz, Hanspeter Herzel, Achim Kramer, Thomas Sauter, Adrián E Granada

{"title":"Circadian clock features define novel subtypes among breast cancer cells and shape drug sensitivity.","authors":"Carolin Ector, Jeff Didier, Sébastien De Landtsheer, Malthe S Nordentoft, Christoph Schmal, Ulrich Keilholz, Hanspeter Herzel, Achim Kramer, Thomas Sauter, Adrián E Granada","doi":"10.1038/s44320-025-00092-7","DOIUrl":"https://doi.org/10.1038/s44320-025-00092-7","url":null,"abstract":"The circadian clock regulates key physiological processes, including cellular responses to DNA damage. Circadian-based therapeutic strategies optimize treatment timing to enhance drug efficacy and minimize side effects, offering potential for precision cancer treatment. However, applying these strategies in cancer remains limited due to a lack of understanding of the clock's function across cancer types and incomplete insights into how the circadian clock affects drug responses. To address this, we conducted deep circadian phenotyping across a panel of breast cancer cell lines. Observing diverse circadian dynamics, we characterized metrics to assess circadian rhythm strength and stability in vitro. This led to the identification of four distinct circadian-based phenotypes among 14 breast cancer cell models: functional, weak, unstable, and dysfunctional clocks. Furthermore, we demonstrate that the circadian clock plays a critical role in shaping pharmacological responses to various anti-cancer drugs and we identify circadian features descriptive of drug sensitivity. Collectively, our findings establish a foundation for implementing circadian-based treatment strategies in breast cancer, leveraging clock phenotypes and drug sensitivity patterns to optimize therapeutic outcomes.","PeriodicalId":18906,"journal":{"name":"Molecular Systems Biology","volume":" ","pages":""},"PeriodicalIF":8.5,"publicationDate":"2025-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143492870","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Abundant clock proteins point to missing molecular regulation in the plant circadian clock. 丰富的时钟蛋白表明植物昼夜节律时钟中缺少分子调控。

IF 8.5 1区生物学

Molecular Systems Biology Pub Date : 2025-02-20 DOI: 10.1038/s44320-025-00086-5

Uriel Urquiza-García, Nacho Molina, Karen J Halliday, Andrew J Millar

{"title":"Abundant clock proteins point to missing molecular regulation in the plant circadian clock.","authors":"Uriel Urquiza-García, Nacho Molina, Karen J Halliday, Andrew J Millar","doi":"10.1038/s44320-025-00086-5","DOIUrl":"https://doi.org/10.1038/s44320-025-00086-5","url":null,"abstract":"Understanding the biochemistry behind whole-organism traits such as flowering time is a longstanding challenge, where mathematical models are critical. Very few models of plant gene circuits use the absolute units required for comparison to biochemical data. We refactor two detailed models of the plant circadian clock from relative to absolute units. Using absolute RNA quantification, a simple model predicted abundant clock protein levels in Arabidopsis thaliana, up to 100,000 proteins per cell. NanoLUC reporter protein fusions validated the predicted levels of clock proteins in vivo. Recalibrating the detailed models to these protein levels estimated their DNA-binding dissociation constants (Kd). We estimate the same Kd from multiple results in vitro, extending the method to any promoter sequence. The detailed models simulated the Kd range estimated from LUX DNA-binding in vitro but departed from the data for CCA1 binding, pointing to further circadian mechanisms. Our analytical and experimental methods should transfer to understand other plant gene regulatory networks, potentially including the natural sequence variation that contributes to evolutionary adaptation.","PeriodicalId":18906,"journal":{"name":"Molecular Systems Biology","volume":" ","pages":""},"PeriodicalIF":8.5,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143468614","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Enhanced flux potential analysis links changes in enzyme expression to metabolic flux.

IF 8.5 1区生物学

Molecular Systems Biology Pub Date : 2025-02-17 DOI: 10.1038/s44320-025-00090-9

Xuhang Li, Albertha J M Walhout, L Safak Yilmaz

{"title":"Enhanced flux potential analysis links changes in enzyme expression to metabolic flux.","authors":"Xuhang Li, Albertha J M Walhout, L Safak Yilmaz","doi":"10.1038/s44320-025-00090-9","DOIUrl":"https://doi.org/10.1038/s44320-025-00090-9","url":null,"abstract":"Algorithms that constrain metabolic network models with enzyme levels to predict metabolic activity assume that changes in enzyme levels are indicative of flux variations. However, metabolic flux can also be regulated by other mechanisms such as allostery and mass action. To systematically explore the relationship between fluctuations in enzyme expression and flux, we combine available yeast proteomic and fluxomic data to reveal that flux changes can be best predicted from changes in enzyme levels of pathways, rather than the whole network or only cognate reactions. We implement this principle in an 'enhanced flux potential analysis' (eFPA) algorithm that integrates enzyme expression data with metabolic network architecture to predict relative flux levels of reactions including those regulated by other mechanisms. Applied to human data, eFPA consistently predicts tissue metabolic function using either proteomic or transcriptomic data. Additionally, eFPA efficiently handles data sparsity and noisiness, generating robust flux predictions with single-cell gene expression data. Our approach outperforms alternatives by striking an optimal balance, evaluating enzyme expression at pathway level, rather than either single-reaction or whole-network levels.","PeriodicalId":18906,"journal":{"name":"Molecular Systems Biology","volume":" ","pages":""},"PeriodicalIF":8.5,"publicationDate":"2025-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143441542","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0