Neuronal activity can be modeled as a nonlinear dynamical system to yield measures of neuronal state and dysfunction. The electrical recordings of stem cell-derived neurons from individuals with ...autism spectrum disorder (ASD) and controls were analyzed using minimum embedding dimension (MED) analysis to characterize their dynamical complexity. MED analysis revealed a significant reduction in dynamical complexity in ASD neurons during differentiation, which was correlated to bursting and spike interval measures. MED was associated with clinical endpoints, such as nonverbal intelligence, and was correlated with 53 differentially expressed genes, which were overrepresented with ASD risk genes related to neurodevelopment, cell morphology, and cell migration. Spatiotemporal analysis also showed a prenatal temporal enrichment in cortical and deep brain structures. Together, we present dynamical analysis as a paradigm that can be used to distinguish disease-associated cellular electrophysiological and transcriptional signatures, while taking into account patient variability in neuropsychiatric disorders.
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•Electrical recordings of iPSC-derived neurons can be modeled as a dynamical system•Dynamical complexity is characterized by minimum embedding dimension (MED)•MED is reduced in ASD neuronal lines during differentiation•MED is correlated to gene expression changes relevant to prenatal neurodevelopment
Marchetto, Kim, and colleagues describe the application of dynamical analysis to stem cell-derived neuronal recordings from patients with ASD. They find that dynamical complexity is reduced in ASD electrical activity, as measured by minimum embedding dimension (MED). They go on to describe the gene expression, biological pathway, and neurodevelopmental correlates of the MED signature, supporting findings in the literature.
Bipolar disorder (BD) is characterized by cyclical mood shifts. Studies indicate that BD patients have a peripheral pro-inflammatory state and alterations in glial populations in the brain. We ...utilized an in vitro model to study inflammation-related phenotypes of astrocytes derived from induced pluripotent stem cells (iPSCs) generated from BD patients and healthy controls. BD astrocytes showed changes in transcriptome and induced a reduction in neuronal activity when co-cultured with neurons. IL-1β-stimulated BD astrocytes displayed a unique inflammatory gene expression signature and increased secretion of IL-6. Conditioned medium from stimulated BD astrocytes reduced neuronal activity, and this effect was partially blocked by IL-6 inactivating antibody. Our results suggest that BD astrocytes are functionally less supportive of neuronal excitability and this effect is partially mediated by IL-6. We confirmed higher IL-6 in blood in a distinct cohort of BD patients, highlighting the potential role of astrocyte-mediated inflammatory signaling in BD neuropathology.
•Bipolar disorder astrocytes are functionally less supportive of neuronal activity•Bipolar disorder astrocytes response to IL-1β is transcriptionally distinct•IL-6 secretion in bipolar disorder astrocytes reduces neuronal activity•Bipolar disorder patients show higher circulating levels of IL-6 in blood
In this article, Gage and collaborators show that astrocytes differentiated from induced pluripotent stem cells generated from bipolar disorder patients are functionally less supportive of neuronal activity. Bipolar disorder astrocytes' response to pro-inflammatory cytokines is characterized by a unique transcriptional response and increased IL-6 secretion that directly and negatively impacted on neuronal activity. Increased peripheral IL-6 was confirmed in a distinct clinical cohort highlighting the potential role of astrocyte-mediated inflammatory signaling in the neuropathology of bipolar disorder.
Several approaches have been introduced to interpret, in terms of high-resolution structure, low-resolution structural data as obtained from cryo-EM. As conformational changes are often observed in ...biological molecules, these techniques need to take into account the flexibility of proteins. Flexibility has been described in terms of movement between rigid domains and between rigid secondary structure elements, which present some limitations for studying dynamical properties. Normal mode analysis has also been used, but is limited to medium resolution data. All-atom molecular dynamics fitting techniques are more appropriate to fit structures into higher-resolution data as full protein flexibility is considered, but are cumbersome in terms of computational time. Here, we introduce a coarse-grained approach; a Go-model was used to represent biological molecules, combined with biased molecular dynamics to reproduce accurately conformational transitions. Illustrative examples on simulated data are shown. Accurate fittings can be obtained for resolution ranging from 5 to 20
Å. The approach was also tested on experimental data of Elongation Factor G and
Escherichia coli RNA polymerase, where its validity is compared to previous models obtained from different techniques. This comparison demonstrates that quantitative flexible techniques, as opposed to manual docking, need to be considered to interpret low-resolution data.
Epigenetic aging clocks are computational models that predict age using DNA methylation information. Initially, first-generation clocks were developed to make predictions using CpGs that change with ...age. Over time, next-generation clocks were created using CpGs that relate to both age and health. Since existing next-generation clocks were constructed in blood, we sought to develop a next-generation clock optimized for prediction in cheek swabs, which are non-invasive and easy to collect. To do this, we collected MethylationEPIC data as well as lifestyle and health information from 8045 diverse adults. Using a novel simulated annealing approach that allowed us to incorporate lifestyle and health factors into training as well as a combination of CpG filtering, CpG clustering, and clock ensembling, we constructed CheekAge, an epigenetic aging clock that has a strong correlation with age, displays high test–retest reproducibility across replicates, and significantly associates with a plethora of lifestyle and health factors, such as BMI, smoking status, and alcohol intake. We validated CheekAge in an internal dataset and multiple publicly available datasets, including samples from patients with progeria or meningioma. In addition to exploring the underlying biology of the data and clock, we provide a free online tool that allows users to mine our methylomic data and predict epigenetic age.
Understanding the functions of multi‐cellular organs in terms of the molecular networks within each cell is an important step in the quest to predict phenotype from genotype. B‐lymphocyte population ...dynamics, which are predictive of immune response and vaccine effectiveness, are determined by individual cells undergoing division or death seemingly stochastically. Based on tracking single‐cell time‐lapse trajectories of hundreds of B cells, single‐cell transcriptome, and immunofluorescence analyses, we constructed an agent‐based multi‐modular computational model to simulate lymphocyte population dynamics in terms of the molecular networks that control NF‐κB signaling, the cell cycle, and apoptosis. Combining modeling and experimentation, we found that NF‐κB cRel enforces the execution of a cellular decision between mutually exclusive fates by promoting survival in growing cells. But as cRel deficiency causes growing B cells to die at similar rates to non‐growing cells, our analysis reveals that the phenomenological decision model of wild‐type cells is rooted in a biased race of cell fates. We show that a multi‐scale modeling approach allows for the prediction of dynamic organ‐level physiology in terms of intra‐cellular molecular networks.
Synopsis
A new multi‐scale model predicts B‐cell population dynamics in terms of intra‐cellular molecular networks. We predict and confirm that NF‐κB cRel enforces cellular fate decisions and characterize how molecular network noise determines robust cell population dynamics.
We present a multi‐scale model that accounts for robust B‐cell population dynamics in terms of noisy molecular network dynamics in each cell.
Live cell microscopy confirms that cells entering a growth phase constitute a fate decision toward division rather than death.
Modeling and experimentation reveal that NF‐κB cRel is critical for enforcing the fate decision—its absence results in a ‘fate race’.
The multi‐scale model can predict how molecular perturbations and extrinsic noise effect cell population dynamics.
A new multi‐scale model predicts B‐cell population dynamics in terms intra‐cellular molecular networks. We predict and confirm that NF‐κB cRel enforces cellular fate decisions and characterize how molecular network noise determines robust cell population dynamics.
When messenger RNA splicing occurs co-transcriptionally, the potential for kinetic control based on transcription dynamics is widely recognized. Indeed, perturbation studies have reported that when ...transcription kinetics are perturbed genetically or pharmacologically splice patterns may change. However, whether kinetic control is contributing to the control of splicing within the normal range of physiological conditions remains unknown. We examined if the kinetic determinants for co-transcriptional splicing (CTS) might be reflected in the structure and expression patterns of the genome and epigenome. To identify and then quantitatively relate multiple, simultaneous CTS determinants, we constructed a scalable mathematical model of the kinetic interplay of RNA synthesis and CTS and parameterized it with diverse next generation sequencing (NGS) data. We thus found a variety of CTS determinants encoded in vertebrate genomes and epigenomes, and that these combine variously for different groups of genes such as housekeeping versus regulated genes. Together, our findings indicate that the kinetic basis of splicing is functionally and physiologically relevant, and may meaningfully inform the analysis of genomic and epigenomic data to provide insights that are missed when relying on statistical approaches alone.
Abstract
The maintenance of tissue homeostasis in steady state or under stress is dependent on the proper communication between the stem cells and the supporting cells in their microenvironment or ...“niche”. In addition to promoting immune tolerance, regulatory T cells (Tregs) have recently emerged as a critical component of the stem cell niche in the hair follicle (HF), injured muscle, bone marrow, and small intestine to support stem cell differentiation or maintain their quiescence. How Treg cells sense the dynamic signals in the niche environment and communicate with stem cells during tissue regeneration is largely unknown. Here, by using HF as a model, we uncover a hitherto unrecognized function of steroid hormone glucocorticoid that instructs skin-resident Treg cells through glucocorticoid receptor (GR) to facilitate hair follicle stem cell (HFSC) activation and HF regeneration. Ablation of GR signaling in Tregs blocked depilation-induced hair regeneration and natural hair growth without affecting Treg’s immune suppressive function. Mechanistic study revealed that GR signaling induces skin-resident Tregs to produce TGF-b3, which directly activates Smad2/3 in HFSCs and facilitates HFSC activation and proliferation. Our study identifies a novel crosstalk between skin-resident Tregs and HFSCs mediated by the GR/TGF-b3 axis, highlighting a new avenue to manipulate Tregs to support tissue regeneration.
Supported by NIH R01-AI107027 NIH R01-AI1511123 NIH R21-AI154919 NIH S10-OD023689
ARID1A, a subunit of the SWI/SNF chromatin remodeling complex, is frequently mutated in cancer. Deficiency in its homolog ARID1B is synthetically lethal with ARID1A mutation. However, the functional ...relationship between these homologs has not been explored. Here, we use ATAC-seq, genome-wide histone modification mapping, and expression analysis to examine colorectal cancer cells lacking one or both ARID proteins. We find that ARID1A has a dominant role in maintaining chromatin accessibility at enhancers, while the contribution of ARID1B is evident only in the context of ARID1A mutation. Changes in accessibility are predictive of changes in expression and correlate with loss of H3K4me and H3K27ac marks, nucleosome spacing, and transcription factor binding, particularly at growth pathway genes including
. We find that ARID1B knockdown in ARID1A mutant ovarian cancer cells causes similar loss of enhancer architecture, suggesting that this is a conserved function underlying the synthetic lethality between ARID1A and ARID1B.
The D1A mutant of recombinant NP2 has been prepared and shown to have the expression−initiation methionine-0 cleaved during expression in E. coli, as is the case for recombinant NP4, where Ala is the ...first amino acid for the recombinant protein as well as for the mature native protein. The heme substituent 1H NMR chemical shifts of NP2-D1A and those of its imidazole, N-methylimidazole, and cyanide complexes are rather different from those of NP2-M0D1. This difference is likely due to the much smaller size of the N-terminal amino acid (A) of NP2-D1A, which allows the formation of the closed loop form of this protein, as it does for NP4 (Weichsel, A., Andersen, J. F., Roberts, S. A., and Montfort, W. R. (2000) Nature Struct. Biol. 7, 551−554). The ratio of the two hemin rotational isomers A and B is different for the two proteins, and the rate at which the A:B ratio reaches equilibrium is strikingly different (NP2-M0D1 t 1/2 for heme rotation ∼2 h, NP2-D1A t 1/2 ∼43 h). This difference is consistent with the high stability of the closed loop form of the NP2-D1A protein and infrequent opening of the loops that could allow heme to at least partially exit the binding pocket in order to rotate about its α,γ-meso axis. Consistent with this, the rates of histamine binding and release to/from NP2-D1A are significantly slower than those for NP2-M0D1 at pH 7.5. This work suggests that care must be taken in interpreting data obtained from proteins that carry the expression-initiation M0.
Nitrophorins (NPs) are a class of NO-transporting and histamine-sequestering heme b proteins that occur in the saliva of the bloodsucking insect Rhodnius prolixus. A detailed study of the newly ...described member, NP7, is presented herein. NO association constants for NP7 (NO) reveal a drastic change when the pH is varied from 5.5 (reflecting the insect's saliva) to slightly above plasma pH (7.5) (>109 M-1 → 4.0 × 106 M-1); thus, the protein promotes the storage of NO in the insect's saliva and its release inside the victim's tissues. In contrast to the other nitrophorins, NP1−4, histamine sequestering cannot be accomplished in vivo due to the low binding constant (histamine) of 105 M-1 compared to the histamine concentration of 1−10 × 10-9 M in the blood. A major part of this study deals with the N-terminus, 1Leu-Pro-Gly-Glu-Cys5 of NP7, which is not found in NP1−4. Since NP7 has not been isolated from the insects but was recognized in a cDNA library instead, the N-terminal site of signal peptidase cleavage upon protein secretion was predicted by the program SignalP Andersen, J. F., Gudderra, N. P., Francischetti, I. M. B., Valenzuela, J. G., and Ribeiro, J. M. C. (2004) Biochemistry 43, 6987−6994. In marked contrast to wild-type NP7, NP7(Δ1−3) exhibits a very high NO affinity at pH 7.5 (NO) ≈ 109 M-1, suggesting that the release of NO in the plasma cannot efficiently be accomplished by the truncated form. Comparison of the reduction potentials of both constructs by spectroelectrochemistry revealed an average increase of +85 mV for various distal ligands bound to the heme iron when the 1Leu-Pro-Gly3 peptide was removed. However, 1H NMR and EPR spectroscopy show that the electronic properties of the FeIII cofactor are similar in both wild-type NP7 and NP7(Δ1−3). Further, thermal denaturation that revealed a higher stability of wild-type NP7 compared to NP7(Δ1−3), in combination with a homology model based on the NP2 crystal structure (rmsd = 0.39 Å), suggests that interaction of the 1Leu-Pro-Gly3 peptide with the A−B and/or G−H loops is key for proper protein function.
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