Abstract：
:Network-based molecular modeling of physiological behaviors has proven invaluable in the study of complex diseases such as cancer, but these approaches remain largely untested in contexts involving interacting tissues such as autoimmunity. Here, using Alopecia Areata (AA) as a model, we have adapted regulatory network analysis to specifically isolate physiological behaviors in the skin that contribute to the recruitment of immune cells in autoimmune disease. We use context-specific regulatory networks to deconvolve and identify skin-specific regulatory modules with IKZF1 and DLX4 as master regulators (MRs). These MRs are sufficient to induce AA-like molecular states in vitro in three cultured cell lines, resulting in induced NKG2D-dependent cytotoxicity. This work demonstrates the feasibility of a network-based approach for compartmentalizing and targeting molecular behaviors contributing to interactions between tissues in autoimmune disease.
journal_name
Cell Systjournal_title
Cell systemsauthors
Chen JC,Cerise JE,Jabbari A,Clynes R,Christiano AMdoi
10.1016/j.cels.2015.11.001subject
Has Abstractpub_date
2015-11-25 00:00:00pages
326-337issue
5eissn
2405-4712issn
2405-4720pii
S2405-4712(15)00187-8journal_volume
1pub_type
杂志文章相关文献
Cell Systems文献大全abstract：:Escherichia coli gene expression knockdown using synthetic small RNA (sRNA) can be fine-tuned by altering sRNA sequences to modulate target mRNA-binding ability, but this requires thorough checking for off-target effects. Here, we present an sRNA gene expression knockdown system fine-tuned by using different promoters...
journal_title：Cell systems
pub_type： 杂志文章
doi：10.1016/j.cels.2017.08.016
更新日期：2017-10-25 00:00:00
abstract：:Although molecular mechanisms that prompt cell-cycle arrest in response to DNA damage have been elucidated, the systems-level properties of DNA damage checkpoints are not understood. Here, using time-lapse microscopy and simulations that model the cell cycle as a series of Poisson processes, we characterize DNA damage...
journal_title：Cell systems
pub_type： 杂志文章
doi：10.1016/j.cels.2017.09.015
更新日期：2017-11-22 00:00:00
abstract：:Advances in biological engineering headline this month's Cell Systems call (Cell Systems 1, 307), alongside intriguing applications of modeling from the Elf, Goentoro, and Wolf groups. Check out our recent blogpost: http://crosstalk.cell.com/blog/a-call-for-papers-on-biological-engineering-and-synthetic-biology. ...
journal_title：Cell systems
pub_type： 杂志文章
doi：10.1016/j.cels.2016.08.006
更新日期：2016-08-01 00:00:00
abstract：:Adenocarcinoma accounts for more than 40% of lung malignancy, and microscopic pathology evaluation is indispensable for its diagnosis. However, how histopathology findings relate to molecular abnormalities remains largely unknown. Here, we obtained H&E-stained whole-slide histopathology images, pathology reports, RNA ...
journal_title：Cell systems
pub_type： 杂志文章
doi：10.1016/j.cels.2017.10.014
更新日期：2017-12-27 00:00:00
abstract：:DNA shape adds specificity to sequence motifs but has not been explored systematically outside this context. We hypothesized that DNA-binding proteins (DBPs) preferentially occupy DNA with specific structures ("shape motifs") regardless of whether or not these correspond to high information content sequence motifs. We...
journal_title：Cell systems
pub_type： 杂志文章
doi：10.1016/j.cels.2018.12.001
更新日期：2019-01-23 00:00:00
abstract：:Alterations of circadian clock genes are associated with patient survival, tumor stage, and clinical subtype across various cancer types, highlighting the importance of timing in cancer treatment. ...
journal_title：Cell systems
pub_type： 评论
doi：10.1016/j.cels.2018.03.006
更新日期：2018-03-28 00:00:00
abstract：:How do rich biological behaviors arise from bi-molecular collisions? ...
journal_title：Cell systems
pub_type： 杂志文章
doi：10.1016/j.cels.2015.09.006
更新日期：2015-09-23 00:00:00
abstract：:Many data sets exhibit well-defined structure that can be exploited to design faster search tools, but it is not always clear when such acceleration is possible. Here we introduce a framework for similarity search based on characterizing a data set's entropy and fractal dimension. We prove that searching scales in tim...
journal_title：Cell systems
pub_type： 杂志文章
doi：10.1016/j.cels.2015.08.004
更新日期：2015-08-26 00:00:00
abstract：:Understanding the complex interactions that occur between heterologous and native biochemical pathways represents a major challenge in metabolic engineering and synthetic biology. We present a workflow that integrates metabolomics, proteomics, and genome-scale models of Escherichia coli metabolism to study the effects...
journal_title：Cell systems
pub_type： 杂志文章
doi：10.1016/j.cels.2016.04.004
更新日期：2016-05-25 00:00:00
abstract：:Recent mass spectrometry maps of the human interactome independently support the existence of a large multiprotein complex, dubbed "Commander." Broadly conserved across animals and ubiquitously expressed in nearly every human cell type examined thus far, Commander likely plays a fundamental cellular function, akin to ...
journal_title：Cell systems
pub_type： 杂志文章,评审
doi：10.1016/j.cels.2017.04.006
更新日期：2017-05-24 00:00:00
abstract：:Small RNA sequencing has been widely adopted to study the diversity of extracellular RNAs (exRNAs) in biofluids; however, the analysis of exRNA samples can be challenging: they are vulnerable to contamination and artifacts from different isolation techniques, present in lower concentrations than cellular RNA, and occa...
journal_title：Cell systems
pub_type： 杂志文章
doi：10.1016/j.cels.2019.03.004
更新日期：2019-04-24 00:00:00
abstract：:Gram-negative bacteria are intrinsically resistant to drugs because of their double-membrane envelope structure that acts as a permeability barrier and as an anchor for efflux pumps. Antibiotics are blocked and expelled from cells and cannot reach high-enough intracellular concentrations to exert a therapeutic effect....
journal_title：Cell systems
pub_type： 杂志文章
doi：10.1016/j.cels.2019.03.008
更新日期：2019-04-24 00:00:00
abstract：:The field of systems immunology has grown extensively over the last few years, spurred by the generation of large datasets, new analytical tools, and modeling approaches. In this piece and its counterpart in Trends in Immunology [http://www.cell.com/trends/immunology/fulltext/S1471-4906(18)30013-9], eight authors disc...
journal_title：Cell systems
pub_type： 社论,面试
doi：10.1016/j.cels.2018.02.005
更新日期：2018-02-28 00:00:00
abstract：:Translation of mRNA into protein is a fundamental yet complex biological process with multiple factors that can potentially affect its efficiency. Here, we study a stochastic model describing the traffic flow of ribosomes along the mRNA and identify the key parameters that govern the overall rate of protein synthesis,...
journal_title：Cell systems
pub_type： 杂志文章
doi：10.1016/j.cels.2019.12.003
更新日期：2020-02-26 00:00:00
abstract：:Ribosome profiling is a widespread tool for studying translational dynamics in human cells. Its central assumption is that ribosome footprint density on a transcript quantitatively reflects protein synthesis. Here, we test this assumption using pulsed-SILAC (pSILAC) high-accuracy targeted proteomics. We focus on multi...
journal_title：Cell systems
pub_type： 杂志文章
doi：10.1016/j.cels.2017.05.001
更新日期：2017-06-28 00:00:00
abstract：:One snapshot of the peer review process for "Cytoplasmic Amplification of Transcriptional Noise Generates Substantial Cell-to-Cell Variability" (Hansen et al., 2018). ...
journal_title：Cell systems
pub_type： 评论,杂志文章
doi：10.1016/j.cels.2018.10.003
更新日期：2018-10-24 00:00:00
abstract：:A number of sequencing-based transcriptase drop-off assays have recently been developed to probe post-transcriptional dynamics of RNA-protein interaction, RNA structure, and RNA modification. Although these assays survey a diverse set of epitranscriptomic marks, we use the term toeprinting assays since they share meth...
journal_title：Cell systems
pub_type： 杂志文章
doi：10.1016/j.cels.2017.04.007
更新日期：2017-05-24 00:00:00
abstract：:Isogenic cells in a common environment show substantial cell-to-cell variation in gene expression, often referred to as "expression noise." Here, we use multiple single-cell RNA-sequencing datasets to identify features associated with high or low expression noise in mouse embryonic stem cells. These include the core p...
journal_title：Cell systems
pub_type： 杂志文章
doi：10.1016/j.cels.2017.10.003
更新日期：2017-11-22 00:00:00
abstract：:This month: selected work from the 2018 RECOMB meeting, organized by Ecole Polytechnique and held last April in Paris. ...
journal_title：Cell systems
pub_type： 杂志文章
doi：10.1016/j.cels.2018.08.005
更新日期：2018-08-22 00:00:00
abstract：:Effective design of combination therapies requires understanding the changes in cell physiology that result from drug interactions. Here, we show that the genome-wide transcriptional response to combinations of two drugs, measured at a rigorously controlled growth rate, can predict higher-order antagonism with a third...
journal_title：Cell systems
pub_type： 杂志文章
doi：10.1016/j.cels.2019.10.004
更新日期：2019-11-27 00:00:00
abstract：:Machine learning can be used to predict compounds acting synergistically, and this could greatly expand the universe of available potential treatments for diseases that are currently hidden in the dark chemical matter. ...
journal_title：Cell systems
pub_type： 杂志文章
doi：10.1016/j.cels.2015.12.005
更新日期：2015-12-23 00:00:00
abstract：:An integrated approach unifies experimental observations and mathematical modeling to represent differentiation dynamics as discrete transition events underpinned by stochastic transitions between hidden states. ...
journal_title：Cell systems
pub_type： 评论,杂志文章
doi：10.1016/j.cels.2017.09.009
更新日期：2017-09-27 00:00:00
abstract：:Although genetic mutations that alter organisms' average lifespans have been identified in aging research, our understanding of the dynamic changes during aging remains limited. Here, we integrate single-cell imaging, microfluidics, and computational modeling to investigate phenotypic divergence and cellular heterogen...
journal_title：Cell systems
pub_type： 杂志文章
doi：10.1016/j.cels.2019.02.002
更新日期：2019-03-27 00:00:00
abstract：:One snapshot of the peer review process for "Critical Roles of the Pentose Phosphate Pathway and GLN3 in Isobutanol-Specific Tolerance in Yeast" (Kuroda et al., 2019). ...
journal_title：Cell systems
pub_type： 评论,杂志文章
doi：10.1016/j.cels.2020.01.005
更新日期：2020-02-26 00:00:00
abstract：:Two recent studies in Cell and Science demonstrate the reconstruction of global mechanistic networks and identification of regulatory principles from multi-omics data. ...
journal_title：Cell systems
pub_type： 评论,杂志文章
doi：10.1016/j.cels.2017.01.007
更新日期：2017-01-25 00:00:00
abstract：:Patterning of periodic stripes during development requires mechanisms to control both stripe spacing and orientation. A number of models can explain how stripe spacing is controlled, including molecular mechanisms, such as Turing's reaction-diffusion model, as well as cell-based and mechanical mechanisms. However, how...
journal_title：Cell systems
pub_type： 杂志文章
doi：10.1016/j.cels.2015.12.001
更新日期：2015-12-23 00:00:00
abstract：:Chinese hamster ovary (CHO) cells dominate biotherapeutic protein production and are widely used in mammalian cell line engineering research. To elucidate metabolic bottlenecks in protein production and to guide cell engineering and bioprocess optimization, we reconstructed the metabolic pathways in CHO and associated...
journal_title：Cell systems
pub_type： 杂志文章
doi：10.1016/j.cels.2016.10.020
更新日期：2016-11-23 00:00:00
abstract：:The recent increase of immunopeptidomics data, obtained by mass spectrometry or binding assays, opens up possibilities for investigating endogenous antigen presentation by the highly polymorphic human leukocyte antigen class I (HLA-I) protein. State-of-the-art methods predict with high accuracy presentation by HLA all...
journal_title：Cell systems
pub_type： 杂志文章
doi：10.1016/j.cels.2020.11.005
更新日期：2020-12-11 00:00:00
abstract：:Hemizygous deletion of a gene in tumor cells frequently causes reduced expression of its encoded mRNA and protein, as well as reduced protein-but not mRNA-expression of other members in the same protein complex. ...
journal_title：Cell systems
pub_type： 评论,杂志文章
doi：10.1016/j.cels.2017.10.005
更新日期：2017-10-25 00:00:00
abstract：:The construction of complex gene-regulatory networks requires both inhibitory and upregulatory modules. However, the vast majority of RNA-based regulatory "parts" are inhibitory. Using a synthetic biology approach combined with SHAPE-seq, we explored the regulatory effect of RNA-binding protein (RBP)-RNA interactions ...
journal_title：Cell systems
pub_type： 杂志文章
doi：10.1016/j.cels.2019.04.007
更新日期：2019-07-24 00:00:00
