NPJ Systems Biology and Applications最新文献

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Detecting and understanding meaningful cancerous mutations based on computational models of mRNA splicing. 基于 mRNA 剪接计算模型检测和理解有意义的癌症突变。
IF 4 2区 生物学
NPJ Systems Biology and Applications Pub Date : 2024-03-07 DOI: 10.1038/s41540-024-00351-7
Nicolas Lynn, Tamir Tuller
{"title":"Detecting and understanding meaningful cancerous mutations based on computational models of mRNA splicing.","authors":"Nicolas Lynn, Tamir Tuller","doi":"10.1038/s41540-024-00351-7","DOIUrl":"10.1038/s41540-024-00351-7","url":null,"abstract":"<p><p>Cancer research has long relied on non-silent mutations. Yet, it has become overwhelmingly clear that silent mutations can affect gene expression and cancer cell fitness. One fundamental mechanism that apparently silent mutations can severely disrupt is alternative splicing. Here we introduce Oncosplice, a tool that scores mutations based on models of proteomes generated using aberrant splicing predictions. Oncosplice leverages a highly accurate neural network that predicts splice sites within arbitrary mRNA sequences, a greedy transcript constructor that considers alternate arrangements of splicing blueprints, and an algorithm that grades the functional divergence between proteins based on evolutionary conservation. By applying this tool to 12M somatic mutations we identify 8K deleterious variants that are significantly depleted within the healthy population; we demonstrate the tool's ability to identify clinically validated pathogenic variants with a positive predictive value of 94%; we show strong enrichment of predicted deleterious mutations across pan-cancer drivers. We also achieve improved patient survival estimation using a proposed set of novel cancer-involved genes. Ultimately, this pipeline enables accelerated insight-gathering of sequence-specific consequences for a class of understudied mutations and provides an efficient way of filtering through massive variant datasets - functionalities with immediate experimental and clinical applications.</p>","PeriodicalId":19345,"journal":{"name":"NPJ Systems Biology and Applications","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10920900/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140060057","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Morphological entropy encodes cellular migration strategies on multiple length scales. 形态熵编码多种长度尺度上的细胞迁移策略
IF 4 2区 生物学
NPJ Systems Biology and Applications Pub Date : 2024-03-07 DOI: 10.1038/s41540-024-00353-5
Yanping Liu, Yang Jiao, Qihui Fan, Xinwei Li, Zhichao Liu, Dui Qin, Jun Hu, Liyu Liu, Jianwei Shuai, Zhangyong Li
{"title":"Morphological entropy encodes cellular migration strategies on multiple length scales.","authors":"Yanping Liu, Yang Jiao, Qihui Fan, Xinwei Li, Zhichao Liu, Dui Qin, Jun Hu, Liyu Liu, Jianwei Shuai, Zhangyong Li","doi":"10.1038/s41540-024-00353-5","DOIUrl":"10.1038/s41540-024-00353-5","url":null,"abstract":"<p><p>Cell migration is crucial for numerous physiological and pathological processes. A cell adapts its morphology, including the overall and nuclear morphology, in response to various cues in complex microenvironments, such as topotaxis and chemotaxis during migration. Thus, the dynamics of cellular morphology can encode migration strategies, from which diverse migration mechanisms can be inferred. However, deciphering the mechanisms behind cell migration encoded in morphology dynamics remains a challenging problem. Here, we present a powerful universal metric, the Cell Morphological Entropy (CME), developed by combining parametric morphological analysis with Shannon entropy. The utility of CME, which accurately quantifies the complex cellular morphology at multiple length scales through the deviation from a perfectly circular shape, is illustrated using a variety of normal and tumor cell lines in different in vitro microenvironments. Our results show how geometric constraints affect the MDA-MB-231 cell nucleus, the emerging interactions of MCF-10A cells migrating on collagen gel, and the critical transition from proliferation to invasion in tumor spheroids. The analysis demonstrates that the CME-based approach provides an effective and physically interpretable tool to measure morphology in real-time across multiple length scales. It provides deeper insight into cell migration and contributes to the understanding of different behavioral modes and collective cell motility in more complex microenvironments.</p>","PeriodicalId":19345,"journal":{"name":"NPJ Systems Biology and Applications","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10920856/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140060058","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Integration of graph neural networks and genome-scale metabolic models for predicting gene essentiality 整合图神经网络和基因组尺度代谢模型预测基因本质
IF 4 2区 生物学
NPJ Systems Biology and Applications Pub Date : 2024-03-06 DOI: 10.1038/s41540-024-00348-2
Ramin Hasibi, Tom Michoel, Diego A. Oyarzún
{"title":"Integration of graph neural networks and genome-scale metabolic models for predicting gene essentiality","authors":"Ramin Hasibi, Tom Michoel, Diego A. Oyarzún","doi":"10.1038/s41540-024-00348-2","DOIUrl":"https://doi.org/10.1038/s41540-024-00348-2","url":null,"abstract":"<p>Genome-scale metabolic models are powerful tools for understanding cellular physiology. Flux balance analysis (FBA), in particular, is an optimization-based approach widely employed for predicting metabolic phenotypes. In model microbes such as <i>Escherichia coli</i>, FBA has been successful at predicting essential genes, i.e. those genes that impair survival when deleted. A central assumption in this approach is that both wild type and deletion strains optimize the same fitness objective. Although the optimality assumption may hold for the wild type metabolic network, deletion strains are not subject to the same evolutionary pressures and knock-out mutants may steer their metabolism to meet other objectives for survival. Here, we present FlowGAT, a hybrid FBA-machine learning strategy for predicting essentiality directly from wild type metabolic phenotypes. The approach is based on graph-structured representation of metabolic fluxes predicted by FBA, where nodes correspond to enzymatic reactions and edges quantify the propagation of metabolite mass flow between a reaction and its neighbours. We integrate this information into a graph neural network that can be trained on knock-out fitness assay data. Comparisons across different model architectures reveal that FlowGAT predictions for <i>E. coli</i> are close to those of FBA for several growth conditions. This suggests that essentiality of enzymatic genes can be predicted by exploiting the inherent network structure of metabolism. Our approach demonstrates the benefits of combining the mechanistic insights afforded by genome-scale models with the ability of deep learning to infer patterns from complex datasets.</p>","PeriodicalId":19345,"journal":{"name":"NPJ Systems Biology and Applications","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140046735","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Sunset Yellow protects against oxidative damage and exhibits chemoprevention in chemically induced skin cancer model. 日落黄可防止氧化损伤,并在化学诱导的皮肤癌模型中显示出化学预防作用。
IF 4 2区 生物学
NPJ Systems Biology and Applications Pub Date : 2024-03-02 DOI: 10.1038/s41540-024-00349-1
Saurabh Singh, Sarika Yadav, Celine Cavallo, Durgesh Mourya, Ishu Singh, Vijay Kumar, Sachin Shukla, Pallavi Shukla, Romil Chaudhary, Gyan Prakash Maurya, Ronja Lea Jennifer Müller, Lilly Rohde, Aradhana Mishra, Olaf Wolkenhauer, Shailendra Gupta, Anurag Tripathi
{"title":"Sunset Yellow protects against oxidative damage and exhibits chemoprevention in chemically induced skin cancer model.","authors":"Saurabh Singh, Sarika Yadav, Celine Cavallo, Durgesh Mourya, Ishu Singh, Vijay Kumar, Sachin Shukla, Pallavi Shukla, Romil Chaudhary, Gyan Prakash Maurya, Ronja Lea Jennifer Müller, Lilly Rohde, Aradhana Mishra, Olaf Wolkenhauer, Shailendra Gupta, Anurag Tripathi","doi":"10.1038/s41540-024-00349-1","DOIUrl":"10.1038/s41540-024-00349-1","url":null,"abstract":"<p><p>Skin cancer and other skin-related inflammatory pathologies are rising due to heightened exposure to environmental pollutants and carcinogens. In this context, natural products and repurposed compounds hold promise as novel therapeutic and preventive agents. Strengthening the skin's antioxidant defense mechanisms is pivotal in neutralizing reactive oxygen species (ROS) and mitigating oxidative stress. Sunset Yellow (SY) exhibits immunomodulatory characteristics, evidenced by its capacity to partially inhibit the secretion of proinflammatory cytokines, regulate immune cell populations, and modulate the activation of lymphocytes. This study aimed to investigate the antioxidant and anti-genotoxic properties of SY using in-silico, in vitro, and physiochemical test systems, and to further explore its potential role in 7,12-dimethylbenz(a) anthracene (DMBA)/ 12-o-tetradecanoylphorbol-13-acetate (TPA)-induced two-stage skin carcinogenesis. In vitro experiments showed that pre-treatment of SY significantly enhanced the cell viability of HaCaT cells when exposed to tertiary-Butyl Hydrogen Peroxide (tBHP). This increase was accompanied by reduced ROS levels, restoration of mitochondrial membrane potential, and notable reduction in DNA damage in (SY + tBHP) treated cells. Mechanistic investigations using DPPH chemical antioxidant activity test and potentiometric titrations confirmed SY's antioxidant properties, with a standard reduction potential ( <math> <msup><mrow><mi>E</mi></mrow> <mrow><mi>o</mi></mrow> </msup> </math> ) of 0.211 V. Remarkably, evaluating the effect of topical application of SY in DMBA/TPA-induced two-step skin carcinogenesis model revealed dose-dependent decreases in tumor latency, incidence, yield, and burden over 21-weeks. Furthermore, computational analysis and experimental validations identified GSK3β, KEAP1 and EGFR as putative molecular targets of SY. Collectively, our findings reveal that SY enhances cellular antioxidant defenses, exhibits anti-genotoxic effects, and functions as a promising chemopreventive agent.</p>","PeriodicalId":19345,"journal":{"name":"NPJ Systems Biology and Applications","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-03-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10908785/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140022282","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Do calcium channel blockers applied to cardiomyocytes cause increased channel expression resulting in reduced efficacy? 应用于心肌细胞的钙通道阻滞剂是否会导致通道表达增加,从而降低药效?
IF 4 2区 生物学
NPJ Systems Biology and Applications Pub Date : 2024-03-01 DOI: 10.1038/s41540-024-00347-3
Karoline Horgmo Jæger, Verena Charwat, Samuel Wall, Kevin E Healy, Aslak Tveito
{"title":"Do calcium channel blockers applied to cardiomyocytes cause increased channel expression resulting in reduced efficacy?","authors":"Karoline Horgmo Jæger, Verena Charwat, Samuel Wall, Kevin E Healy, Aslak Tveito","doi":"10.1038/s41540-024-00347-3","DOIUrl":"10.1038/s41540-024-00347-3","url":null,"abstract":"<p><p>In the initial hours following the application of the calcium channel blocker (CCB) nifedipine to microtissues consisting of human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs), we observe notable variations in the drug's efficacy. Here, we investigate the possibility that these temporal changes in CCB effects are associated with adaptations in the expression of calcium ion channels in cardiomyocyte membranes. To explore this, we employ a recently developed mathematical model that delineates the regulation of calcium ion channel expression by intracellular calcium concentrations. According to the model, a decline in intracellular calcium levels below a certain target level triggers an upregulation of calcium ion channels. Such an upregulation, if instigated by a CCB, would then counteract the drug's inhibitory effect on calcium currents. We assess this hypothesis using time-dependent measurements of hiPSC-CMs dynamics and by refining an existing mathematical model of myocyte action potentials incorporating the dynamic nature of the number of calcium ion channels. The revised model forecasts that the CCB-induced reduction in intracellular calcium concentrations leads to a subsequent increase in calcium ion channel expression, thereby attenuating the drug's overall efficacy. The data and fit models suggest that dynamic changes in cardiac cells in the presence of CCBs may be explainable by induced changes in protein expression, and that this may lead to challenges in understanding calcium based drug effects on the heart unless timings of applications are carefully considered.</p>","PeriodicalId":19345,"journal":{"name":"NPJ Systems Biology and Applications","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10907638/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140013052","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Integrative temporal multi-omics reveals uncoupling of transcriptome and proteome during human T cell activation. 综合时间多组学揭示了人类 T 细胞活化过程中转录组和蛋白质组的脱钩。
IF 4 2区 生物学
NPJ Systems Biology and Applications Pub Date : 2024-02-28 DOI: 10.1038/s41540-024-00346-4
Harshi Weerakoon, Ahmed Mohamed, Yide Wong, Jinjin Chen, Bhagya Senadheera, Oscar Haigh, Thomas S Watkins, Stephen Kazakoff, Pamela Mukhopadhyay, Jason Mulvenna, John J Miles, Michelle M Hill, Ailin Lepletier
{"title":"Integrative temporal multi-omics reveals uncoupling of transcriptome and proteome during human T cell activation.","authors":"Harshi Weerakoon, Ahmed Mohamed, Yide Wong, Jinjin Chen, Bhagya Senadheera, Oscar Haigh, Thomas S Watkins, Stephen Kazakoff, Pamela Mukhopadhyay, Jason Mulvenna, John J Miles, Michelle M Hill, Ailin Lepletier","doi":"10.1038/s41540-024-00346-4","DOIUrl":"10.1038/s41540-024-00346-4","url":null,"abstract":"<p><p>Engagement of the T cell receptor (TCR) triggers molecular reprogramming leading to the acquisition of specialized effector functions by CD4 helper and CD8 cytotoxic T cells. While transcription factors, chemokines, and cytokines are known drivers in this process, the temporal proteomic and transcriptomic changes that regulate different stages of human primary T cell activation remain to be elucidated. Here, we report an integrative temporal proteomic and transcriptomic analysis of primary human CD4 and CD8 T cells following ex vivo stimulation with anti-CD3/CD28 beads, which revealed major transcriptome-proteome uncoupling. The early activation phase in both CD4 and CD8 T cells was associated with transient downregulation of the mRNA transcripts and protein of the central glucose transport GLUT1. In the proliferation phase, CD4 and CD8 T cells became transcriptionally more divergent while their proteome became more similar. In addition to the kinetics of proteome-transcriptome correlation, this study unveils selective transcriptional and translational metabolic reprogramming governing CD4 and CD8 T cell responses to TCR stimulation. This temporal transcriptome/proteome map of human T cell activation provides a reference map exploitable for future discovery of biomarkers and candidates targeting T cell responses.</p>","PeriodicalId":19345,"journal":{"name":"NPJ Systems Biology and Applications","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10901835/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139990775","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Agent-based modeling of the prostate tumor microenvironment uncovers spatial tumor growth constraints and immunomodulatory properties 基于代理的前列腺肿瘤微环境建模揭示了肿瘤生长的空间限制和免疫调节特性
IF 4 2区 生物学
NPJ Systems Biology and Applications Pub Date : 2024-02-21 DOI: 10.1038/s41540-024-00344-6
Maisa N. G. van Genderen, Jeroen Kneppers, Anniek Zaalberg, Elise M. Bekers, Andries M. Bergman, Wilbert Zwart, Federica Eduati
{"title":"Agent-based modeling of the prostate tumor microenvironment uncovers spatial tumor growth constraints and immunomodulatory properties","authors":"Maisa N. G. van Genderen, Jeroen Kneppers, Anniek Zaalberg, Elise M. Bekers, Andries M. Bergman, Wilbert Zwart, Federica Eduati","doi":"10.1038/s41540-024-00344-6","DOIUrl":"https://doi.org/10.1038/s41540-024-00344-6","url":null,"abstract":"<p>Inhibiting androgen receptor (AR) signaling through androgen deprivation therapy (ADT) reduces prostate cancer (PCa) growth in virtually all patients, but response may be temporary, in which case resistance develops, ultimately leading to lethal castration-resistant prostate cancer (CRPC). The tumor microenvironment (TME) plays an important role in the development and progression of PCa. In addition to tumor cells, TME-resident macrophages and fibroblasts express AR and are therefore also affected by ADT. However, the interplay of different TME cell types in the development of CRPC remains largely unexplored. To understand the complex stochastic nature of cell-cell interactions, we created a PCa-specific agent-based model (PCABM) based on in vitro cell proliferation data. PCa cells, fibroblasts, “pro-inflammatory” M1-like and “pro-tumor” M2-like polarized macrophages are modeled as agents from a simple set of validated base assumptions. PCABM allows us to simulate the effect of ADT on the interplay between various prostate TME cell types. The resulting in vitro growth patterns mimic human PCa. Our PCABM can effectively model hormonal perturbations by ADT, in which PCABM suggests that CRPC arises in clusters of resistant cells, as is observed in multifocal PCa. In addition, fibroblasts compete for cellular space in the TME while simultaneously creating niches for tumor cells to proliferate in. Finally, PCABM predicts that ADT has immunomodulatory effects on macrophages that may enhance tumor survival. Taken together, these results suggest that AR plays a critical role in the cellular interplay and stochastic interactions in the TME that influence tumor cell behavior and CRPC development.</p>","PeriodicalId":19345,"journal":{"name":"NPJ Systems Biology and Applications","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139926800","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Transomics2cytoscape: an automated software for interpretable 2.5-dimensional visualization of trans-omic networks Transomics2cytoscape:可解释的跨组学网络 2.5 维可视化自动软件
IF 4 2区 生物学
NPJ Systems Biology and Applications Pub Date : 2024-02-19 DOI: 10.1038/s41540-024-00342-8
Kozo Nishida, Junichi Maruyama, Kazunari Kaizu, Koichi Takahashi, Katsuyuki Yugi
{"title":"Transomics2cytoscape: an automated software for interpretable 2.5-dimensional visualization of trans-omic networks","authors":"Kozo Nishida, Junichi Maruyama, Kazunari Kaizu, Koichi Takahashi, Katsuyuki Yugi","doi":"10.1038/s41540-024-00342-8","DOIUrl":"https://doi.org/10.1038/s41540-024-00342-8","url":null,"abstract":"<p>Biochemical network visualization is one of the essential technologies for mechanistic interpretation of omics data. In particular, recent advances in multi-omics measurement and analysis require the development of visualization methods that encompass multiple omics data. Visualization in 2.5 dimension (2.5D visualization), which is an isometric view of stacked X-Y planes, is a convenient way to interpret multi-omics/trans-omics data in the context of the conventional layouts of biochemical networks drawn on each of the stacked omics layers. However, 2.5D visualization of trans-omics networks is a state-of-the-art method that primarily relies on time-consuming human efforts involving manual drawing. Here, we present an R Bioconductor package ‘transomics2cytoscape’ for automated visualization of 2.5D trans-omics networks. We confirmed that transomics2cytoscape could be used for rapid visualization of trans-omics networks presented in published papers within a few minutes. Transomics2cytoscape allows for frequent update/redrawing of trans-omics networks in line with the progress in multi-omics/trans-omics data analysis, thereby enabling network-based interpretation of multi-omics data at each research step. The transomics2cytoscape source code is available at https://github.com/ecell/transomics2cytoscape.</p>","PeriodicalId":19345,"journal":{"name":"NPJ Systems Biology and Applications","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139902946","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Forum on immune digital twins: a meeting report. 免疫数字双胞胎论坛:会议报告。
IF 4 2区 生物学
NPJ Systems Biology and Applications Pub Date : 2024-02-16 DOI: 10.1038/s41540-024-00345-5
Reinhard Laubenbacher, Fred Adler, Gary An, Filippo Castiglione, Stephen Eubank, Luis L Fonseca, James Glazier, Tomas Helikar, Marti Jett-Tilton, Denise Kirschner, Paul Macklin, Borna Mehrad, Beth Moore, Virginia Pasour, Ilya Shmulevich, Amber Smith, Isabel Voigt, Thomas E Yankeelov, Tjalf Ziemssen
{"title":"Forum on immune digital twins: a meeting report.","authors":"Reinhard Laubenbacher, Fred Adler, Gary An, Filippo Castiglione, Stephen Eubank, Luis L Fonseca, James Glazier, Tomas Helikar, Marti Jett-Tilton, Denise Kirschner, Paul Macklin, Borna Mehrad, Beth Moore, Virginia Pasour, Ilya Shmulevich, Amber Smith, Isabel Voigt, Thomas E Yankeelov, Tjalf Ziemssen","doi":"10.1038/s41540-024-00345-5","DOIUrl":"10.1038/s41540-024-00345-5","url":null,"abstract":"<p><p>Medical digital twins are computational models of human biology relevant to a given medical condition, which are tailored to an individual patient, thereby predicting the course of disease and individualized treatments, an important goal of personalized medicine. The immune system, which has a central role in many diseases, is highly heterogeneous between individuals, and thus poses a major challenge for this technology. In February 2023, an international group of experts convened for two days to discuss these challenges related to immune digital twins. The group consisted of clinicians, immunologists, biologists, and mathematical modelers, representative of the interdisciplinary nature of medical digital twin development. A video recording of the entire event is available. This paper presents a synopsis of the discussions, brief descriptions of ongoing digital twin projects at different stages of progress. It also proposes a 5-year action plan for further developing this technology. The main recommendations are to identify and pursue a small number of promising use cases, to develop stimulation-specific assays of immune function in a clinical setting, and to develop a database of existing computational immune models, as well as advanced modeling technology and infrastructure.</p>","PeriodicalId":19345,"journal":{"name":"NPJ Systems Biology and Applications","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-02-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10873299/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139747160","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Evaluation of single-sample network inference methods for precision oncology. 评估精准肿瘤学的单样本网络推断方法。
IF 4 2区 生物学
NPJ Systems Biology and Applications Pub Date : 2024-02-15 DOI: 10.1038/s41540-024-00340-w
Joke Deschildre, Boris Vandemoortele, Jens Uwe Loers, Katleen De Preter, Vanessa Vermeirssen
{"title":"Evaluation of single-sample network inference methods for precision oncology.","authors":"Joke Deschildre, Boris Vandemoortele, Jens Uwe Loers, Katleen De Preter, Vanessa Vermeirssen","doi":"10.1038/s41540-024-00340-w","DOIUrl":"10.1038/s41540-024-00340-w","url":null,"abstract":"<p><p>A major challenge in precision oncology is to detect targetable cancer vulnerabilities in individual patients. Modeling high-throughput omics data in biological networks allows identifying key molecules and processes of tumorigenesis. Traditionally, network inference methods rely on many samples to contain sufficient information for learning, resulting in aggregate networks. However, to implement patient-tailored approaches in precision oncology, we need to interpret omics data at the level of individual patients. Several single-sample network inference methods have been developed that infer biological networks for an individual sample from bulk RNA-seq data. However, only a limited comparison of these methods has been made and many methods rely on 'normal tissue' samples as reference, which are not always available. Here, we conducted an evaluation of the single-sample network inference methods SSN, LIONESS, SWEET, iENA, CSN and SSPGI using transcriptomic profiles of lung and brain cancer cell lines from the CCLE database. The methods constructed functional gene networks with distinct network characteristics. Hub gene analyses revealed different degrees of subtype-specificity across methods. Single-sample networks were able to distinguish between tumor subtypes, as exemplified by node strength clustering, enrichment of known subtype-specific driver genes among hubs and differential node strength. We also showed that single-sample networks correlated better to other omics data from the same cell line as compared to aggregate networks. We conclude that single-sample network inference methods can reflect sample-specific biology when 'normal tissue' samples are absent and we point out peculiarities of each method.</p>","PeriodicalId":19345,"journal":{"name":"NPJ Systems Biology and Applications","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10869342/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139741539","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
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