NPJ Systems Biology and Applications最新文献_第8页

Metacell-based differential expression analysis identifies cell type specific temporal gene response programs in COVID-19 patient PBMCs 基于元细胞的差异表达分析确定了 COVID-19 患者 PBMC 中特定细胞类型的时间基因反应程序

IF 4 2区生物学

NPJ Systems Biology and Applications Pub Date : 2024-04-05 DOI: 10.1038/s41540-024-00364-2

Kevin O’Leary, Deyou Zheng

{"title":"Metacell-based differential expression analysis identifies cell type specific temporal gene response programs in COVID-19 patient PBMCs","authors":"Kevin O’Leary, Deyou Zheng","doi":"10.1038/s41540-024-00364-2","DOIUrl":"https://doi.org/10.1038/s41540-024-00364-2","url":null,"abstract":"By profiling gene expression in individual cells, single-cell RNA-sequencing (scRNA-seq) can resolve cellular heterogeneity and cell-type gene expression dynamics. Its application to time-series samples can identify temporal gene programs active in different cell types, for example, immune cells’ responses to viral infection. However, current scRNA-seq analysis has limitations. One is the low number of genes detected per cell. The second is insufficient replicates (often 1-2) due to high experimental cost. The third lies in the data analysis—treating individual cells as independent measurements leads to inflated statistics. To address these, we explore a new computational framework, specifically whether “metacells” constructed to maintain cellular heterogeneity within individual cell types (or clusters) can be used as “replicates” for increasing statistical rigor. Toward this, we applied SEACells to a time-series scRNA-seq dataset from peripheral blood mononuclear cells (PBMCs) after SARS-CoV-2 infection to construct metacells, and used them in maSigPro for quadratic regression to find significantly differentially expressed genes (DEGs) over time, followed by clustering expression velocity trends. We showed that such metacells retained greater expression variances and produced more biologically meaningful DEGs compared to either metacells generated randomly or from simple pseudobulk methods. More specifically, this approach correctly identified the known ISG15 interferon response program in almost all PBMC cell types and many DEGs enriched in the previously defined SARS-CoV-2 infection response pathway. It also uncovered additional and more cell type-specific temporal gene expression programs. Overall, our results demonstrate that the metacell-pseudoreplicate strategy could potentially overcome the limitation of 1-2 replicates.","PeriodicalId":19345,"journal":{"name":"NPJ Systems Biology and Applications","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140594485","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

Automatic design of gene regulatory mechanisms for spatial pattern formation 自动设计空间模式形成的基因调控机制

IF 4 2区生物学

NPJ Systems Biology and Applications Pub Date : 2024-04-02 DOI: 10.1038/s41540-024-00361-5

Reza Mousavi, Daniel Lobo

{"title":"Automatic design of gene regulatory mechanisms for spatial pattern formation","authors":"Reza Mousavi, Daniel Lobo","doi":"10.1038/s41540-024-00361-5","DOIUrl":"https://doi.org/10.1038/s41540-024-00361-5","url":null,"abstract":"Gene regulatory mechanisms (GRMs) control the formation of spatial and temporal expression patterns that can serve as regulatory signals for the development of complex shapes. Synthetic developmental biology aims to engineer such genetic circuits for understanding and producing desired multicellular spatial patterns. However, designing synthetic GRMs for complex, multi-dimensional spatial patterns is a current challenge due to the nonlinear interactions and feedback loops in genetic circuits. Here we present a methodology to automatically design GRMs that can produce any given two-dimensional spatial pattern. The proposed approach uses two orthogonal morphogen gradients acting as positional information signals in a multicellular tissue area or culture, which constitutes a continuous field of engineered cells implementing the same designed GRM. To efficiently design both the circuit network and the interaction mechanisms—including the number of genes necessary for the formation of the target spatial pattern—we developed an automated algorithm based on high-performance evolutionary computation. The tolerance of the algorithm can be configured to design GRMs that are either simple to produce approximate patterns or complex to produce precise patterns. We demonstrate the approach by automatically designing GRMs that can produce a diverse set of synthetic spatial expression patterns by interpreting just two orthogonal morphogen gradients. The proposed framework offers a versatile approach to systematically design and discover complex genetic circuits producing spatial patterns.","PeriodicalId":19345,"journal":{"name":"NPJ Systems Biology and Applications","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140569310","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

Logic programming-based Minimal Cut Sets reveal consortium-level therapeutic targets for chronic wound infections 基于逻辑编程的最小切割集揭示了慢性伤口感染的联盟级治疗目标

IF 4 2区生物学

NPJ Systems Biology and Applications Pub Date : 2024-04-02 DOI: 10.1038/s41540-024-00360-6

Maxime Mahout, Ross P. Carlson, Laurent Simon, Sabine Peres

{"title":"Logic programming-based Minimal Cut Sets reveal consortium-level therapeutic targets for chronic wound infections","authors":"Maxime Mahout, Ross P. Carlson, Laurent Simon, Sabine Peres","doi":"10.1038/s41540-024-00360-6","DOIUrl":"https://doi.org/10.1038/s41540-024-00360-6","url":null,"abstract":"Minimal Cut Sets (MCSs) identify sets of reactions which, when removed from a metabolic network, disable certain cellular functions. The traditional search for MCSs within genome-scale metabolic models (GSMMs) targets cellular growth, identifies reaction sets resulting in a lethal phenotype if disrupted, and retrieves a list of corresponding gene, mRNA, or enzyme targets. Using the dual link between MCSs and Elementary Flux Modes (EFMs), our logic programming-based tool aspefm was able to compute MCSs of any size from GSMMs in acceptable run times. The tool demonstrated better performance when computing large-sized MCSs than the mixed-integer linear programming methods. We applied the new MCSs methodology to a medically-relevant consortium model of two cross-feeding bacteria, Staphylococcus aureus and Pseudomonas aeruginosa. aspefm constraints were used to bias the computation of MCSs toward exchanged metabolites that could complement lethal phenotypes in individual species. We found that interspecies metabolite exchanges could play an essential role in rescuing single-species growth, for instance inosine could complement lethal reaction knock-outs in the purine synthesis, glycolysis, and pentose phosphate pathways of both bacteria. Finally, MCSs were used to derive a list of promising enzyme targets for consortium-level therapeutic applications that cannot be circumvented via interspecies metabolite exchange.","PeriodicalId":19345,"journal":{"name":"NPJ Systems Biology and Applications","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140594338","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

Quantifying in vitro B. anthracis growth and PA production and decay: a mathematical modelling approach. 量化体外炭疽杆菌的生长和 PA 的产生与衰变：一种数学建模方法。

IF 4 2区生物学

NPJ Systems Biology and Applications Pub Date : 2024-03-29 DOI: 10.1038/s41540-024-00357-1

Bevelynn Williams, Jamie Paterson, Helena J Rawsthorne-Manning, Polly-Anne Jeffrey, Joseph J Gillard, Grant Lythe, Thomas R Laws, Martín López-García

{"title":"Quantifying in vitro B. anthracis growth and PA production and decay: a mathematical modelling approach.","authors":"Bevelynn Williams, Jamie Paterson, Helena J Rawsthorne-Manning, Polly-Anne Jeffrey, Joseph J Gillard, Grant Lythe, Thomas R Laws, Martín López-García","doi":"10.1038/s41540-024-00357-1","DOIUrl":"10.1038/s41540-024-00357-1","url":null,"abstract":"Protective antigen (PA) is a protein produced by Bacillus anthracis. It forms part of the anthrax toxin and is a key immunogen in US and UK anthrax vaccines. In this study, we have conducted experiments to quantify PA in the supernatants of cultures of B. anthracis Sterne strain, which is the strain used in the manufacture of the UK anthrax vaccine. Then, for the first time, we quantify PA production and degradation via mathematical modelling and Bayesian statistical techniques, making use of this new experimental data as well as two other independent published data sets. We propose a single mathematical model, in terms of delay differential equations (DDEs), which can explain the in vitro dynamics of all three data sets. Since we did not heat activate the B. anthracis spores prior to inoculation, germination occurred much slower in our experiments, allowing us to calibrate two additional parameters with respect to the other data sets. Our model is able to distinguish between natural PA decay and that triggered by bacteria via proteases. There is promising consistency between the different independent data sets for most of the parameter estimates. The quantitative characterisation of B. anthracis PA production and degradation obtained here will contribute towards the ambition to include a realistic description of toxin dynamics, the host immune response, and anti-toxin treatments in future mechanistic models of anthrax infection.","PeriodicalId":19345,"journal":{"name":"NPJ Systems Biology and Applications","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-03-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10980772/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140326920","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

Transcriptome free energy can serve as a dynamic patient-specific biomarker in acute myeloid leukemia. 转录组自由能可作为急性髓性白血病患者的动态特异性生物标志物。

IF 4 2区生物学

NPJ Systems Biology and Applications Pub Date : 2024-03-25 DOI: 10.1038/s41540-024-00352-6

Lisa Uechi, Swetha Vasudevan, Daniela Vilenski, Sergio Branciamore, David Frankhouser, Denis O'Meally, Soheil Meshinchi, Guido Marcucci, Ya-Huei Kuo, Russell Rockne, Nataly Kravchenko-Balasha

{"title":"Transcriptome free energy can serve as a dynamic patient-specific biomarker in acute myeloid leukemia.","authors":"Lisa Uechi, Swetha Vasudevan, Daniela Vilenski, Sergio Branciamore, David Frankhouser, Denis O'Meally, Soheil Meshinchi, Guido Marcucci, Ya-Huei Kuo, Russell Rockne, Nataly Kravchenko-Balasha","doi":"10.1038/s41540-024-00352-6","DOIUrl":"10.1038/s41540-024-00352-6","url":null,"abstract":"Acute myeloid leukemia (AML) is prevalent in both adult and pediatric patients. Despite advances in patient categorization, the heterogeneity of AML remains a challenge. Recent studies have explored the use of gene expression data to enhance AML diagnosis and prognosis, however, alternative approaches rooted in physics and chemistry may provide another level of insight into AML transformation. Utilizing publicly available databases, we analyze 884 human and mouse blood and bone marrow samples. We employ a personalized medicine strategy, combining state-transition theory and surprisal analysis, to assess the RNA transcriptome of individual patients. The transcriptome is transformed into physical parameters that represent each sample's steady state and the free energy change (FEC) from that steady state, which is the state with the lowest free energy.We found the transcriptome steady state was invariant across normal and AML samples. FEC, representing active molecular processes, varied significantly between samples and was used to create patient-specific barcodes to characterize the biology of the disease. We discovered that AML samples that were in a transition state had the highest FEC. This disease state may be characterized as the most unstable and hence the most therapeutically targetable since a change in free energy is a thermodynamic requirement for disease progression. We also found that distinct sets of ongoing processes may be at the root of otherwise similar clinical phenotypes, implying that our integrated analysis of transcriptome profiles may facilitate a personalized medicine approach to cure AML and restore a steady state in each patient.","PeriodicalId":19345,"journal":{"name":"NPJ Systems Biology and Applications","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10963775/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140288679","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

Making drugs from T cells: The quantitative pharmacology of engineered T cell therapeutics 用 T 细胞制造药物：工程化 T 细胞疗法的定量药理学

IF 4 2区生物学

NPJ Systems Biology and Applications Pub Date : 2024-03-18 DOI: 10.1038/s41540-024-00355-3

Daniel C. Kirouac, Cole Zmurchok, Denise Morris

引用次数: 0

A robust ultrasensitive transcriptional switch in noisy cellular environments. 嘈杂细胞环境中的稳健超灵敏转录开关

IF 4 2区生物学

NPJ Systems Biology and Applications Pub Date : 2024-03-16 DOI: 10.1038/s41540-024-00356-2

Eui Min Jeong, Jae Kyoung Kim

{"title":"A robust ultrasensitive transcriptional switch in noisy cellular environments.","authors":"Eui Min Jeong, Jae Kyoung Kim","doi":"10.1038/s41540-024-00356-2","DOIUrl":"10.1038/s41540-024-00356-2","url":null,"abstract":"Ultrasensitive transcriptional switches enable sharp transitions between transcriptional on and off states and are essential for cells to respond to environmental cues with high fidelity. However, conventional switches, which rely on direct repressor-DNA binding, are extremely noise-sensitive, leading to unintended changes in gene expression. Here, through model simulations and analysis, we discovered that an alternative design combining three indirect transcriptional repression mechanisms, sequestration, blocking, and displacement, can generate a noise-resilient ultrasensitive switch. Although sequestration alone can generate an ultrasensitive switch, it remains sensitive to noise because the unintended transcriptional state induced by noise persists for long periods. However, by jointly utilizing blocking and displacement, these noise-induced transitions can be rapidly restored to the original transcriptional state. Because this transcriptional switch is effective in noisy cellular contexts, it goes beyond previous synthetic transcriptional switches, making it particularly valuable for robust synthetic system design. Our findings also provide insights into the evolution of robust ultrasensitive switches in cells. Specifically, the concurrent use of seemingly redundant indirect repression mechanisms in diverse biological systems appears to be a strategy to achieve noise-resilience of ultrasensitive switches.","PeriodicalId":19345,"journal":{"name":"NPJ Systems Biology and Applications","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10944533/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140140517","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

GO2Sum: generating human-readable functional summary of proteins from GO terms. GO2Sum：根据 GO 术语生成人类可读的蛋白质功能摘要。

IF 4 2区生物学

NPJ Systems Biology and Applications Pub Date : 2024-03-15 DOI: 10.1038/s41540-024-00358-0

Swagarika Jaharlal Giri, Nabil Ibtehaz, Daisuke Kihara

{"title":"GO2Sum: generating human-readable functional summary of proteins from GO terms.","authors":"Swagarika Jaharlal Giri, Nabil Ibtehaz, Daisuke Kihara","doi":"10.1038/s41540-024-00358-0","DOIUrl":"10.1038/s41540-024-00358-0","url":null,"abstract":"Understanding the biological functions of proteins is of fundamental importance in modern biology. To represent a function of proteins, Gene Ontology (GO), a controlled vocabulary, is frequently used, because it is easy to handle by computer programs avoiding open-ended text interpretation. Particularly, the majority of current protein function prediction methods rely on GO terms. However, the extensive list of GO terms that describe a protein function can pose challenges for biologists when it comes to interpretation. In response to this issue, we developed GO2Sum (Gene Ontology terms Summarizer), a model that takes a set of GO terms as input and generates a human-readable summary using the T5 large language model. GO2Sum was developed by fine-tuning T5 on GO term assignments and free-text function descriptions for UniProt entries, enabling it to recreate function descriptions by concatenating GO term descriptions. Our results demonstrated that GO2Sum significantly outperforms the original T5 model that was trained on the entire web corpus in generating Function, Subunit Structure, and Pathway paragraphs for UniProt entries.","PeriodicalId":19345,"journal":{"name":"NPJ Systems Biology and Applications","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10943200/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140140518","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

Multivariate canonical correlation analysis identifies additional genetic variants for chronic kidney disease. 多变量典型相关分析确定了慢性肾病的其他遗传变异。

IF 4 2区生物学

NPJ Systems Biology and Applications Pub Date : 2024-03-09 DOI: 10.1038/s41540-024-00350-8

Amy J Osborne, Agnieszka Bierzynska, Elizabeth Colby, Uwe Andag, Philip A Kalra, Olivier Radresa, Philipp Skroblin, Maarten W Taal, Gavin I Welsh, Moin A Saleem, Colin Campbell

{"title":"Multivariate canonical correlation analysis identifies additional genetic variants for chronic kidney disease.","authors":"Amy J Osborne, Agnieszka Bierzynska, Elizabeth Colby, Uwe Andag, Philip A Kalra, Olivier Radresa, Philipp Skroblin, Maarten W Taal, Gavin I Welsh, Moin A Saleem, Colin Campbell","doi":"10.1038/s41540-024-00350-8","DOIUrl":"10.1038/s41540-024-00350-8","url":null,"abstract":"Chronic kidney diseases (CKD) have genetic associations with kidney function. Univariate genome-wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) associated with estimated glomerular filtration rate (eGFR) and blood urea nitrogen (BUN), two complementary kidney function markers. However, it is unknown whether additional SNPs for kidney function can be identified by multivariate statistical analysis. To address this, we applied canonical correlation analysis (CCA), a multivariate method, to two individual-level CKD genotype datasets, and metaCCA to two published GWAS summary statistics datasets. We identified SNPs previously associated with kidney function by published univariate GWASs with high replication rates, validating the metaCCA method. We then extended discovery and identified previously unreported lead SNPs for both kidney function markers, jointly. These showed expression quantitative trait loci (eQTL) colocalisation with genes having significant differential expression between CKD and healthy individuals. Several of these identified lead missense SNPs were predicted to have a functional impact, including in SLC14A2. We also identified previously unreported lead SNPs that showed significant correlation with both kidney function markers, jointly, in the European ancestry CKDGen, National Unified Renal Translational Research Enterprise (NURTuRE)-CKD and Salford Kidney Study (SKS) datasets. Of these, rs3094060 colocalised with FLOT1 gene expression and was significantly more common in CKD cases in both NURTURE-CKD and SKS, than in the general population. Overall, by using multivariate analysis by CCA, we identified additional SNPs and genes for both kidney function and CKD, that can be prioritised for further CKD analyses.","PeriodicalId":19345,"journal":{"name":"NPJ Systems Biology and Applications","volume":null,"pages":null},"PeriodicalIF":4.0,"publicationDate":"2024-03-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10924093/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140065645","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

Data-driven energy landscape reveals critical genes in cancer progression. 数据驱动的能量图谱揭示了癌症进展过程中的关键基因。

IF 4 2区生物学

NPJ Systems Biology and Applications Pub Date : 2024-03-08 DOI: 10.1038/s41540-024-00354-4

Juntan Liu, Chunhe Li

引用次数: 0