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Background: Fibroblasts in the skin are highly heterogeneous, both in vivo and in vitro. One intriguing difference between follicular and interfollicular fibroblasts in vitro is their ability to differentiate in response to osteogenic media, or mechanical stimulation. In this study, we asked whether differences in the ability to respond to differentiation stimuli are due to baseline differences in chromatin accessibility. Results: We performed chromatin accessibility and transcriptional profiling of two fibroblast subtypes found in human skin, which arise from a common progenitor during development yet display distinct characteristics in adult tissue and in vitro. We found that when cells were grown in regular growth media (GM) in culture they had unique chromatin accessibility profiles, however, these profiles control similar functional networks. When we introduced a chemical perturbation and grew cells in osteogenic media (OM) to promote differentiation, we observed a divergence not only in the accessible chromatin signatures but also in the functional networks controlled by these signatures. The biggest divergence was observed when we applied two perturbations to cells; growth in OM combined with mechanical stimulation in the form of a shock wave (OMSW). Here, in one of the fibroblast subtypes we found a number of uniquely accessible promoters which controlled osteogenic interaction networks associated with bone and differentiation functions. This fibroblast subtype also readily differentiates into bone in OMSW conditions, while the other fibroblast subtype under analysis lacks differentiation capability in vitro. Conclusions: Using ATAC-seq and RNA-seq we found that a combination of two stimuli could result significant and specific changes in chromatin accessibility associated with osteogenic differentiation, but only within the fibroblast sub-type capable of osteogenic differentiation. Our results suggest that these two stimuli elicit this cell specific response by modifying chromatin accessibility of osteogenic related gene promoters.

Frontiers in immunology 12, 1-7 (2021). doi:10.3389/fimmu.2021.633845 special issue: "Focusing on T-cells for Novel Treatments of Systemic Lupus Erythematosus", Published by Frontiers Media, Lausanne

Nanoparticle-based delivery systems have shown great promise for theranostics and bioimaging on the laboratory scale due to favorable pharmacokinetics and biodistribution. In this study, we examine the utility of a cage-forming variant of the protein lumazine synthase, which was previously designed and evolved to encapsulate biomacromolecular cargo. Linking antibody-binding domains to the exterior of the cage enabled binding of targeting immunoglobulins and cell-specific uptake of encapsulated cargo. Protein nanocages displaying antibody-binding domains appear to be less immunogenic than their unmodified counterparts, but they also recruit serum antibodies that can mask the efficacy of the targeting antibody. Our study highlights the strengths and limitations of a common targeting strategy for practical nanoparticle-based delivery applications. ISSN:1554-8929 ISSN:1554-8937

Background: Cerebral palsy (CP) is a permanent neurodevelopmental disorder with considerable global disability. Various rehabilitation strategies are currently available. However, none represents a convincing curative result. Cellular therapy recently holds much promise as an alternative strategy to repair neurologic defects. Method: In this narrative review, a comprehensive search of the MEDLINE and ClinicalTrials.gov was made, using the terms: “cell therapy” and “cerebral palsy”, including published and registered clinical studies, respectively. Results: The early effects of these studies demonstrated that using cell therapy in CP patients is safe and improves the deficits for a variable duration. Despite such hopeful early bird results, the long-term outcomes are not conclusive. Conclusions: Due to the heterogeneous nature of CP, personal factors seem essential to consider. Cell dosage, routes of administration, and repeated dosing are pivotal to establish optimal personalized treatments. Future clinical trials should consider employing other cell types, specific cell modifications before administration, and cell-free platforms.

The complexity of brain circuitry is manifested by numerous cell types based on genetic marker, location and neural connectivity. Cell-type specific recording and manipulation is essential to disentangle causal neural mechanisms in physiology and behavior; however, many current approaches are largely limited by number of intersectional features, incompatibility of common effectors and insufficient gene expression. To tackle these limitations, we devise an intein-based intersectional synthesis of transactivator (IBIST) to selectively control gene expression of common effectors in specific cell types defined by a combination of multiple features. We validate the specificity and sufficiency of IBIST to control common effectors including fluorophores, optogenetic opsins and Ca2+ indicators in various intersectional conditions in vivo. Using IBIST-based Ca2+ imaging, we show that the IBIST can intersect up to five features, and that hippocampal cells tune differently to distinct emotional valences depending on the pattern of projection targets. Collectively, the IBIST multiplexes the capability to intersect cell-type features and is compatible with common effectors to effectively control gene expression, monitor and manipulate neural activities.

Many specific cell afferent signalling pathways like the insulin/IGF-1-like or the mechanistic target of rapamycin (mTOR) pathways contribute to modify longevity by modulating the nuclear aging program (AP) [1,2] target gene expression, which modulates the activity of its various aging effectors [2].

SUMMARY The γ-chain receptor dimerizes with complexes of the cytokines interleukin-2 (IL-2), IL-4, IL-7, IL-9, IL-15, and IL-21 and their corresponding “private” receptors. These cytokines have existing uses and future potential as immune therapies because of their ability to regulate the abundance and function of specific immune cell populations. Here, we build a binding reaction model for the ligand-receptor interactions of common γ-chain cytokines, which includes receptor trafficking dynamics, enabling quantitative predictions of cell-type-specific response to natural and engineered cytokines. We then show that tensor factorization is a powerful tool to visualize changes in the input-output behavior of the family across time, cell types, ligands, and concentrations. These results present a more accurate model of ligand response validated across a panel of immune cell types as well as a general approach for generating interpretable guidelines for manipulation of cell-type-specific targeting of engineered ligands., Graphical Abstract, In brief Farhat et al. develop a mechanistic model of the common γ-chain receptor cytokines incorporating the structure of receptor-ligand interaction and trafficking. This model can predict the response to these cytokines, alone and in combination, and changes in binding affinity, enabling more rational cytokine engineering.

Neuromuscular disorders (NMDs) represent an important subset of rare diseases associated with elevated morbidity and mortality whose diagnosis can take years. Here we present a novel approach using systems biology to produce functionally-coherent phenotype clusters that provide insight into the cellular functions and phenotypic patterns underlying NMDs, using the Human Phenotype Ontology as a common framework. Gene and phenotype information was obtained for 424 NMDs in OMIM and 126 NMDs in Orphanet, and 335 and 216 phenotypes were identified as typical for NMDs, respectively. ‘Elevated serum creatine kinase’ was the most specific to NMDs, in agreement with the clinical test of elevated serum creatinine kinase that is conducted on NMD patients. The approach to obtain co-occurring NMD phenotypes was validated based on co-mention in PubMed abstracts. A total of 231 (OMIM) and 150 (Orphanet) clusters of highly connected co-occurrent NMD phenotypes were obtained. In parallel, a tripartite network based on phenotypes, diseases and genes was used to associate NMD phenotypes with functions, an approach also validated by literature co-mention, with KEGG pathways showing proportionally higher overlap than Gene Ontology and Reactome. Phenotype-function pairs were crossed with the co-occurrent NMD phenotype clusters to obtain 40 (OMIM) and 72 (Orphanet) functionally coherent phenotype clusters. As expected, many of these overlapped with known diseases and confirmed existing knowledge. Other clusters revealed interesting new findings, indicating informative phenotypes for differential diagnosis, providing deeper knowledge of NMDs, and pointing towards specific cell dysfunction caused by pleiotropic genes. This work is an example of reproducible research that i) can help better understand NMDs and support their diagnosis by providing a new tool that exploits existing information to obtain novel clusters of functionally-related phenotypes, and ii) takes us another step towards personalised medicine for NMDs.

Diffusion-weighted imaging is a non-invasive functional imaging modality for breast tumor characterization through apparent diffusion coefficients. Yet, it has so far been unable to intuitively inform on tissue microstructure. In this IRB-approved prospective study, we applied novel multidimensional diffusion (MDD) encoding across 16 patients with suspected breast cancer to evaluate its potential for tissue characterization in the clinical setting. Data acquired via custom MDD sequences was processed using an algorithm estimating non-parametric diffusion tensor distributions. The statistical descriptors of these distributions allow us to quantify tissue composition in terms of metrics informing on cell densities, shapes, and orientations. Additionally, signal fractions from specific cell types, such as elongated cells (bin1), isotropic cells (bin2), and free water (bin3), were teased apart. Histogram analysis in cancers and healthy breast tissue showed that cancers exhibited lower mean values of “size” (1.43 ± 0.54 × 10−3 mm2/s) and higher mean values of “shape” (0.47 ± 0.15) corresponding to bin1, while FGT (fibroglandular breast tissue) presented higher mean values of “size” (2.33 ± 0.22 × 10−3 mm2/s) and lower mean values of “shape” (0.27 ± 0.11) corresponding to bin3 (p &lt, 0.001). Invasive carcinomas showed significant differences in mean signal fractions from bin1 (0.64 ± 0.13 vs. 0.4 ± 0.25) and bin3 (0.18 ± 0.08 vs. 0.42 ± 0.21) compared to ductal carcinomas in situ (DCIS) and invasive carcinomas with associated DCIS (p = 0.03). MDD enabled qualitative and quantitative evaluation of the composition of breast cancers and healthy glands.

Background Calpains are a family of calcium-dependent thiol proteases that participate in a wide variety of biological activities. In our recent study, calpain is increased in the sera of scleroderma or systemic sclerosis (SSc). However, the role of calpain in interstitial lung disease (ILD) has not been reported. ILD is a severe complication of SSc, which is the leading cause of death in SSc. The pathogenesis of SSc-related ILD remains incompletely understood. This study investigated the role of myeloid cell calpain in SSc-related ILD. Methods A novel line of mice with myeloid cell-specific deletion of Capns1 (Capns1-ko) was created. SSc-related ILD was induced in Capns1-ko mice and their wild-type littermates by injection 0.l mL of bleomycin (0.4 mg/mL) for 4 weeks. In a separate experiment, a pharmacological inhibitor of calpain PD150606 (Biomol, USA, 3 mg/kg/day, i.p.) daily for 30 days was given to mice after bleomycin injection on daily basis. At the end of the experiment, the animals were killed, skin and lung tissues were collected for the following analysis. Inflammation, fibrosis and calpain activity and cytokines were assessed by histological examinations and ELISA, and immunohistochemical analyses, western blot analysis and Flow cytometry analysis. Results Calpain activities increased in SSc-mouse lungs. Both deletion of Capns1 and administration of PD150606 attenuated dermal sclerosis as evidenced by a reduction of skin thickness and reduced interstitial fibrosis and inflammation in SSc mice. These effects of reduced calpain expression or activity were associated with prevention of macrophage polarization toward M1 phenotype and consequent reduced production of pro-inflammatory cytokines including TNF-α, IL-12 and IL-23 in lung tissues of Capns1-ko mice with SSc. Furthermore, inhibition of calpain correlated with an increase in the protein levels of PI3K and phosphorylated AKT1 in lung tissues of SSc mice. Conclusions This study for the first time demonstrates that the role of myeloid cell calpain may be promotion of macrophage M1 polarization and pro-inflammatory responses related PI3K/AKT1 signaling. Thus, myeloid cell calpain may be a potential therapeutic target for SSc-related ILD.

The development of nanomedical devices has led to a considerable number of clinically applied nanotherapeutics. Yet, the overall poor translation of nanoparticular concepts into marketable systems has not met the initial expectations and led to increasing criticism in recent years. Most novel nano approaches thereby use highly refined formulations including a plethora of active targeting sequences, but ultimately fail to reach their target due to a generally high off-target deposition in organs such as the liver or kidney. In this context, we argue that initial nanoparticle (NP) development should not entirely become set on conventional formulation aspects. In contrast, we propose a change of focus towards a prior analysis of general sites of NP in vivo deposition and an assessment of how accumulation in these organs or tissues can be harnessed to develop therapies for site-related pathologies. We therefore give a comprehensive overview of existing nanotherapeutic targeting strategies for specific cell types within three of the usual suspects, i.e. the liver, kidney and the vascular system. We discuss the physiological surroundings and relevant pathologies of described tissues as well as the implications for NP-mediated drug delivery. Additionally, successful cell-selective NP concepts using active targeting strategies are assessed. By bringing together both (patho)physiological aspects and concepts for cell-selective NP formulations, we hope to show a novel opportunity for the development of more promising nanotherapeutic devices.

Chronic Obstructive Pulmonary Disease (COPD) is a leading cause of death worldwide. To identify cell-specific mechanisms underlying COPD pathobiology, we analysed single-cell RNA sequencing (scRNAseq) profiles of explanted lung tissue from subjects with advanced COPD or control lungs. Findings were validated with scRNAseq of lungs from mice exposed to 10 months of cigarette smoke (CS), isolated human alveolar epithelial cells, and immunostaining of human lung tissue samples. We identified a subpopulation of alveolar epithelial type II cells with transcriptional evidence for aberrant cellular metabolism and reduced cellular stress tolerance, exemplified by decreased expression of the stress-response gene NUPR1. Network analyses identified an important role for inflamed capillary endothelial cells in COPD, particularly through CXCL-motif chemokine signalling. Finally, we detected a metallothionein expressing macrophage subpopulation unique to COPD. Collectively, these findings highlight cell-specific mechanisms involved in the pathobiology of advanced COPD.

Nucleic acid nanodevices present great potential as agents for logic-based therapeutic intervention as well as in basic biology. Often, however, the disease targets that need corrective action are localized in specific organs and thus realizing the full potential of DNA nanodevices also requires ways to target them to specific cell-typesin vivo. Here we show that by exploiting either endogenous or synthetic receptor-ligand interactions and by leveraging the biological barriers presented by the organism, we can target extraneously introduced DNA nanodevices to specific cell types inC. elegans, with sub-cellular precision. The amenability of DNA nanostructures to tissue-specific targetingin vivosignificantly expands their utility in biomedical applications and discovery biology.

The integration-free iPSC lines TISSUi006-A and TISSUi007-A were generated by reprogramming blood cells with episomal vectors. The male human donors belong to a Caucasian family in which four additional family members donated and iPSC lines were generated. All iPSC lines within this family are approved for commercial use by donor consent. Those iPSC lines offer the opportunity to study the influence of affiliation within one family. In future, more iPSCs lines of many more family members can be created to understand the effects of relatives with different ages on the reprogramming into iPSCs and differentiation into specific cell types.

The development and progression of cardiovascular disease (CVD) can mainly be attributed to the narrowing of blood vessels caused by atherosclerosis and thrombosis, which induces organ damage that will result in end-organ dysfunction characterized by events such as myocardial infarction or stroke. It is also essential to consider other contributory factors to CVD, including cardiac remodelling caused by cardiomyopathies and co-morbidities with other diseases such as chronic kidney disease. Besides, there is a growing amount of evidence linking the gut microbiota to CVD through several metabolic pathways. Hence, it is of utmost importance to decipher the underlying molecular mechanisms associated with these disease states to elucidate the development and progression of CVD. A wide array of systems biology approaches incorporating multi-omics data have emerged as an invaluable tool in establishing alterations in specific cell types and identifying modifications in signalling events that promote disease development. Here, we review recent studies that apply multi-omics approaches to further understand the underlying causes of CVD and provide possible treatment strategies by identifying novel drug targets and biomarkers. We also discuss very recent advances in gut microbiota research with an emphasis on how diet and microbial composition can impact the development of CVD. Finally, we present various biological network analyses and other independent studies that have been employed for providing mechanistic explanation and developing treatment strategies for end-stage CVD, namely myocardial infarction and stroke.

Summary The mammalian brain has over 10,000 types of neurons. Therefore, studying gene regulation in the brain requires effective strategies for targeting specific cell types, especially those in low abundance. Cell isolation may alter gene expression and is disruptive to mature neurons with extensive processes. This protocol describes cell-type-specific expression of tagged ribosome and the use of ribosome tagging followed by RNA-seq to identify translatome of low number and sparse cells in mouse brains without disruptive cell isolation. For complete details on the use and execution of this protocol, please refer to Gao et al. (2020), Graphical Abstract, Highlights • The protocol is optimized to identify translating mRNAs in low abundance cell types • Useful in cell types that normally require pooling tissue from multiple animals • Tissue processing and immunoprecipitation are optimized for low-abundance cell types • RNA purification and library synthesis are modified for small amount of RNA, The mammalian brain has over 10,000 types of neurons. Therefore, studying gene regulation in the brain requires effective strategies for targeting specific cell types, especially those in low abundance. Cell isolation may alter gene expression and is disruptive to mature neurons with extensive processes. This protocol describes cell-type-specific expression of tagged ribosome and the use of ribosome tagging followed by RNA-seq to identify translatome of low number and sparse cells in mouse brains without disruptive cell isolation.

Summary Addressing bioenergetics is key to evaluate the impact of metabolism on the regulation of biological processes and its alteration in disease. Organoids are in vitro grown self-organizing structures derived from healthy and diseased tissue that recapitulate with high fidelity the tissue of origin. Bioenergetics is commonly analyzed by Seahorse XF analysis. However, its application to organoid studies is technically challenging. Here, we share our in-house optimized protocols to examine organoid bioenergetics in response to drugs, gene knockdown, or to characterize the metabolism of specific cell types. For complete details on the use and execution of this protocol, please refer to Ludikhuize et al. (2020)., Graphical abstract, Highlights • Analysis of bioenergetics in organoids is technically challenging • We share a detailed protocol to overcome the pitfalls of Seahorse analysis in organoids • Accurate timing of organoid re-plating improves the robustness of Seahorse analysis • DNA-based normalization overcomes organoid-related limitations for normalization, Addressing bioenergetics is key to evaluate the impact of metabolism on the regulation of biological processes and its alteration in disease. Organoids are self-organizing structures derived from healthy and diseased tissue that closely recapitulate the tissue of origin. Bioenergetics is commonly analyzed by Seahorse XF analysis. However, its application to organoid studies is technically challenging. Here, we share our in-house optimized protocols to examine organoid bioenergetics in response to drugs, gene knockdown, or to characterize the metabolism of specific cell types.

Summary Cell sorting can be used to purify cell populations for cell type-specific molecular probing. Fluorescence-activated cell sorting (FACS) coupled with high-throughput sequencing affords molecular signature identification for specific cell types. FACS has many challenges that limit comprehensive cell purification from the brain, leading to incomplete molecular characterization. Here, we present the intranuclear immunostaining-based FACS protocol with several modified steps, which allows optimized nuclei/cell sorting from mouse or human embryonic cortical tissue for distinct downstream molecular investigation of basal intermediate progenitors., Graphical Abstract, Highlights • The FACS technique allows effective nuclei and cell sorting for molecular profiling • The protocol is optimized for nuclei and cell purification from embryonic cortical tissue • Modified steps ensured isolation of TBR2+ cells for mass spectroscopy analysis • The protocol was used to generate extensive RNA-seq and epigenome data for TBR2+ nuclei, Cell sorting can be used to purify cell populations for cell type-specific molecular probing. Fluorescence-activated cell sorting (FACS) coupled with high-throughput sequencing affords molecular signature identification for specific cell types. FACS has many challenges that limit comprehensive cell purification from the brain, leading to incomplete molecular characterization. Here, we present the intranuclear immunostaining-based FACS protocol with several modified steps, which allows optimized nuclei/cell sorting from mouse or human embryonic cortical tissue for distinct downstream molecular investigation of basal intermediate progenitors.

Precise exchange of information and resources among cells is essential for multicellular organisms. Intercellular communication among diverse cell types requires differential mechanisms to achieve the specific regulation. Despite the significance of intercellular communication, it is largely unknown how the communication between different cells is regulated. Here, we report that two members of plasmodesmata-located proteins modulate plasmodesmata at two distinct cell-cell interfaces.

A polka-dotted fruit fly,Drosophila guttifera,has a unique pigmentation pattern on its wings and is used as a model for evo-devo studies exploring the mechanism of evolutionary gain of novel traits. In this species, a morphogen-encoding gene,wingless, is expressed in species-specific positions and induces a unique pigmentation pattern. To produce some of the pigmentation spots on wing veins,winglessis thought to be expressed in developing campaniform sensilla cells, but it was unknown which of the four cell types there express(es)wingless. Here we show that two of the cell types, dome cells and socket cells, expresswingless, as indicated byin situhybridization together with immunohistochemistry. This is a unique case in which non-neuronal SOP (sensory organ precursor) progeny cells produce Wingless as an inducer of pigmentation pattern formation. Our finding opens a path to clarifying the mechanism of evolutionary gain of a uniquewinglessexpression pattern by analyzing gene regulation in dome cells and socket cells.

The skin is made up of a plethora of cells arranged in multiple layers with complex and intricate vascular networks, creating a dynamic microenvironment of cells-to-matrix interactions. With limited donor sites, engineered skin substitute has been in high demand for many therapeutic purposes. Over the years, remarkable progress has occurred in the skin tissue-engineering field to develop skin grafts highly similar to native tissue. However, the major hurdle to successful engraftment is the incorporation of functional vasculature to provide essential nutrients and oxygen supply to the embedded cells. Limitations of traditional tissue engineering have driven the rapid development of vascularized skin tissue production, leading to new technologies such as 3D bioprinting, nano-fabrication and micro-patterning using hydrogel based-scaffold. In particular, the key hope to bioprinting would be the generation of interconnected functional vessels, coupled with the addition of specific cell types to mimic the biological and architectural complexity of the native skin environment. Additionally, stem cells have been gaining interest due to their highly regenerative potential and participation in wound healing. This review briefly summarizes the current cell therapies used in skin regeneration with a focus on the importance of vascularization and recent progress in 3D fabrication approaches to generate vascularized network in the skin tissue graft.

Intravital microscopy (IVM) study approach offers several advantages over in vitro, ex vivo, and 3D models. IVM provides real-time imaging of cellular events, which provides us a comprehensive picture of dynamic processes. Rapid improvement in microscopy techniques has permitted deep tissue imaging at a higher resolution. Advances in fluorescence tagging methods enable tracking of specific cell types. Moreover, IVM can serve as an important tool to study different stages of tissue regeneration processes. Furthermore, the compatibility of different tissue engineered constructs can be analyzed. IVM is also a promising approach to investigate host reactions on implanted biomaterials. IVM can provide instant feedback for improvising tissue engineering strategies. In this review, we aim to provide an overview of the requirements and applications of different IVM approaches. First, we will discuss the history of IVM development, and then we will provide an overview of available optical modalities including the pros and cons. Later, we will summarize different fluorescence labeling methods. In the final section, we will discuss well-established chronic and acute IVM models for different organs.

Mesoscale molecular assemblies on the cell surface, such as cilia and filopodia, integrate information, control transport and amplify signals. Synthetic devices mimicking these structures could sensitively monitor these cellular functions and direct new ones. The challenges in creating such devices, however are that they must be integrated with cells in a precise kinetically controlled process and a device's structure and its precisely structured cell interface must then be maintained during active cellular function. Here we report the ability to integrate synthetic micro-scale filaments, DNA nanotubes, into a cell's architecture by anchoring them by their ends to specific receptors on the surfaces of mammalian cells. These filaments can act as shear stress meters: how anchored nanotubes bend at the cell surface quantitatively indicates the magnitude of shear stresses between 0-2 dyn per cm2, a regime important for cell signaling. Nanotubes can also grow while anchored to cells, thus acting as dynamic components of cells. This approach to cell surface engineering, in which synthetic biomolecular assemblies are organized within existing cellular architecture, could make it possible to build new types of sensors, machines and scaffolds that can interface with, control and measure properties of cells., 20 pages, 5 figures

Biomaterials engineered with specific cell binding sites, tunable mechanical properties, and complex architectures are essential to control cell adhesion and proliferation. The influence of the local properties, such as the local hardness and stability on the interaction with cells, has not been yet fully understood and exploited. This is particularly relevant for hydrogels, very promising materials with, unfortunately, poor cell adhesion properties, attributed mostly to their softness. Here, we propose a new approach for producing hybrid hydrogels by functionalizing them with particles and performing a thermal treatment. Exploring the interaction of cells with these materials we introduce a new concept, cells-grabbing-onto-particles, a facilitation of the cell adhesion through modulation of local properties. The approach is implemented on alginate hydrogels typically unsuitable for cell growth by turning them into a very effective cell culture growth platform. Specifically, alginate hydrogels are bio-mineralized with calcium carbonate (CaCO

Statistical methods that allow for cell type specific DNA methylation (DNAm) analyses based on bulk-tissue methylation data have great potential to improve our understanding of human disease and have created unprecedented opportunities for new insights using the wealth of publicly available bulk-tissue methylation data. These methodologies involve incorporating interaction terms formed between the phenotypes/exposures of interest and proportions of the cell types underlying the bulk-tissue sample used for DNAm profiling. Despite growing interest in such “interaction-based” methods, there has been no comprehensive assessment how variability in the cellular landscape across study samples affects their performance. To answer this question, we used numerous publicly available whole-blood DNAm data sets along with extensive simulation studies and evaluated the performance of interaction-based approaches in detecting cell-specific methylation effects. Our results show that low cell proportion variability results in large estimation error and low statistical power for detecting cell-specific effects of DNAm. Further, we identified that many studies targeting methylation profiling in whole-blood may be at risk to be underpowered due to low variability in the cellular landscape across study samples. Finally, we discuss guidelines for researchers seeking to conduct studies utilizing interaction-based approaches to help ensure that their studies are adequately powered.

Roots are the anchorage organs of plants, responsible for water and nutrient uptake, exhibiting high plasticity. Root architecture is driven by the interactions of biomolecules, including transcription factors and hormones that are crucial players regulating root plasticity. Multiple transcription factor families are involved in root development; some, such as ARFs and LBDs, have been well characterized, whereas others remain less well investigated. In this review, we synthesize the current knowledge about the involvement of the large family of homeodomain-leucine zipper (HD-Zip) transcription factors in root development. This family is divided into four subfamilies (I–IV), mainly according to structural features, such as additional motifs aside from HD-Zip, as well as their size, gene structure, and expression patterns. We explored and analyzed public databases and the scientific literature regarding HD-Zip transcription factors in Arabidopsis and other species. Most members of the four HD-Zip subfamilies are expressed in specific cell types and several individuals from each group have assigned functions in root development. Notably, a high proportion of the studied proteins are part of intricate regulation pathways involved in primary and lateral root growth and development.

There are two types of cell death-apoptosis and necrosis. Apoptosis is cell death regulated by cell signaling pathways, while necrosis has until recently been considered a passive mechanism of cell death caused by environmental pressures. However, recent studies show that necrosis can also be regulated by specific cell signaling pathways. This mode of death, termed necroptosis, has been found to be related to the occurrence and development of many diseases. We used bibliometrics to analyze the global output of literature on necroptosis in the field of neuroscience published in the period 2007-2019 to identify research hotspots and prospects. We included 145 necroptosis-related publications and 2239 references published in the Web of Science during 2007-2019. Visualization analysis revealed that the number of publications related to necroptosis has increased year by year, reaching a peak in 2019. China is the country with the largest number of publications. Key word and literature analyses demonstrated that mitochondrial function change, stroke, ischemia/reperfusion and neuroinflammation are likely the research hotspots and future directions of necroptosis research in the nervous system. The relationship between immune response-related factors, damage-associated molecular patterns, pathogen-associated molecular patterns and necroptosis may become a potential research hotspot in the future. Taken together, our findings suggest that although the inherent limitations of bibliometrics may affect the accuracy of the literature-based prediction of research hotspots, the results obtained from the included publications can provide a reference for the study of necroptosis in the field of neuroscience.

© 2021 by the authors., Nanomaterials are currently being developed for the specific cell/tissue/organ delivery of genetic material. Nanomaterials are considered as non-viral vectors for gene therapy use. However, there are several requirements for developing a device small enough to become an efficient genedelivery tool. Considering that the non-viral vectors tested so far show very low efficiency of gene delivery, there is a need to develop nanotechnology-based strategies to overcome current barriers in gene delivery. Selected nanostructures can incorporate several genetic materials, such as plasmid DNA, mRNA, and siRNA. In the field of nanotechnologies, there are still some limitations yet to be resolved for their use as gene delivery systems, such as potential toxicity and low transfection efficiency. Undeniably, novel properties at the nanoscale are essential to overcome these limitations. In this paper, we will explore the latest advances in nanotechnology in the gene delivery field., ST and SBM were supported by EBT CSIC 14102020

This chapter addresses how the immune system adapts to and influences individual responses to exercise and physical activity by focusing on epigenetic regulation. The role of inflammation, specific cell populations of the immune system, and cytokine production including IL-6, TNF-alpha, and IL-10 are discussed. Where possible we demonstrate how exercise, epigenetics, and immunity are intrinsically linked and emphasize how “Exercise as Medicine” may have implications for cancer prevention and healthy aging.

The heart is a complex multicellular organ comprising both cardiomyocytes (CM), which make up the majority of the cardiac volume, and non-myocytes (NM), which represent the majority of cardiac cells. CM drive the pumping action of the heart, triggered via rhythmic electrical activity. NM, on the other hand, have many essential functions including generating extracellular matrix, regulating CM activity, and aiding in repair following injury. NM include neurons and interstitial, immune, and endothelial cells. Understanding the role of specific cell types and their interactions with one another may be key to developing new therapies with minimal side effects to treat cardiac disease. However, assessing cell-type-specific behavior in situ using standard techniques is challenging. Optogenetics enables population-specific observation and control, facilitating studies into the role of specific cell types and subtypes. Optogenetic models targeting the most important cardiac cell types have been generated and used to investigate non-canonical roles of those cell populations, e.g., to better understand how cardiac pacing occurs and to assess potential translational possibilities of optogenetics. So far, cardiac optogenetic studies have primarily focused on validating models and tools in the healthy heart. The field is now in a position where animal models and tools should be utilized to improve our understanding of the complex heterocellular nature of the heart, how this changes in disease, and from there to enable the development of cell-specific therapies and improved treatments.

Optogenetic approaches combine the power to allocate optogenetic tools (proteins) to specific cell populations (defined genetically or functionally) and the use of light-based interfaces between biological wetware (cells and tissues) and hardware (controllers and recorders). The optogenetic toolbox contains two main compartments: tools to interfere with cellular processes and tools to monitor cellular events. Among the latter are genetically encoded voltage indicators (GEVIs). This chapter outlines the development, current state of the art and prospects of emerging optical GEVI imaging technologies.

The blood-brain barrier (BBB) is important to maintain brain homeostasis, which is crucial for the functionality of neuronal networks. BBB dysfunction is observed in several neurological diseases, including epilepsy. Prolonged BBB dysfunction and subsequent perivascular inflammation as well as alterations in the extracellular matrix (ECM) play an important role in epileptogenesis. In this chapter we aim to give an overview of the processes involved in BBB dysfunction and epileptogenesis and provide evidence from animal as well as from human studies. We will focus on modulators of BBB function including specific cell types, inflammatory mediators as well as ECM molecules. Furthermore, we will discuss new therapeutic targets and the results of intervention studies that are important for the development of novel therapeutic approaches in epilepsy.

Flow cytometry enables the simultaneous detection of multiple surface and intracellular antigens for proteomic profiling of cells. This allows characterization and identification of specific cell subtypes within a heterogeneous population and is usually called immunophenotyping. Antigen-specific antibodies, conjugated to various fluorophores, are incubated with the sample to identify each marker. Fluorescent light of various wavelengths can be separated, detected, and converted into a digital signal in a flow cytometer. Here we describe an eight-color experiment to identify key peripheral blood cell types; however, this technique can be expanded to detect more than 30 parameters simultaneously.

Current CHO cell production processes require an optimized space-time-yield. Process intensification can support achieving this by enhancing the productivity and improving facility utilization. The use of perfusion at the last stage of the seed train (N-1) for high cell density inoculation of the fed-batch N-stage production culture is a relatively new approach with few industry applicable examples. Within this work, the impact of the cell-specific perfusion rate (CSPR) of the N-1 perfusion and the relevance of its control for the quality of generated inoculation cells was evaluated using an automated perfusion rate (PR) control based on online biomass measurements. Precise correlations (R² = 0.99) between permittivity and viable cell counts were found up to the high densities of 100⋅106 c·mL−1. Cells from N-1 perfusion were cultivated at a high and low CSPR with 50 and 20 pL·(c·d)−1, respectively. Lowered cell growth and an increased apoptotic reaction was found as a consequence of the latter due to nutrient limitations and reduced uptake rates. Subsequently, batch cultivations (N-stage) from the different N-1 sources were inoculated to evaluate the physiological state of the inoculum. Successive responses resulting from the respective N-1 condition were uncovered. While cell growth and productivity of approaches inoculated from high CSPR and a conventional seed were comparable, low CSPR inoculation suffered significantly in terms of reduced initial cell growth and impaired viability. This study underlines the importance to determine the CSPR for the design and implementation of an N-1 perfusion process in order to achieve the desired performance at the crucial production stage.

Cardiovascular disease is the leading cause of death worldwide. The societal health burden it represents can be reduced by taking preventive measures and developing more effective therapies. Reaching these goals, however, requires a better understanding of the pathophysiological processes leading to and occurring in the diseased heart. In the last 5 years, several biological advances applying single-cell technologies have enabled researchers to study cardiovascular diseases with unprecedented resolution. This has produced many new insights into how specific cell types change their gene expression level, activation status and potential cellular interactions with the development of cardiovascular disease, but a comprehensive overview of the clinical implications of these findings is lacking. In this review, we summarize and discuss these recent advances and the promise of single-cell technologies from a translational perspective across the cardiovascular disease continuum, covering both animal and human studies, and explore the future directions of the field.

RNA molecules start assembling into ribonucleoprotein (RNP) complexes during transcription. Dynamic RNP assembly, largely directed by cis-acting elements on the RNA, coordinates all processes in which the RNA is involved. To identify the sites bound by a specific RNA-binding protein on endogenous RNAs, cross-linking and immunoprecipitation (CLIP) and complementary, proximity-based methods have been developed. In this Primer, we discuss the main variants of these protein-centric methods and the strategies for their optimization and quality assessment, as well as RNA-centric methods that identify the protein partners of a specific RNA. We summarize the main challenges of computational CLIP data analysis, how to handle various sources of background and how to identify functionally relevant binding regions. We outline the various applications of CLIP and available databases for data sharing. We discuss the prospect of integrating data obtained by CLIP with complementary methods to gain a comprehensive view of RNP assembly and remodelling, unravel the spatial and temporal dynamics of RNPs in specific cell types and subcellular compartments and understand how defects in RNPs can lead to disease. Finally, we present open questions in the field and give directions for further development and applications. Ule and colleagues discuss cross-linking and immunoprecipitation (CLIP) methods for characterizing the RNA binding partners of RNA-binding proteins and explore the data analysis workflows, best practices and applications for these techniques. The Primer also considers methods for characterizing the protein binding partners of specific RNAs and discusses how data from these complementary methods can be integrated into CLIP workflows.

CD56\(^{+}\) T cells are a group of pro‐inflammatory CD3\(^{+}\) lymphocytes with characteristics of natural killer cells, being involved in antimicrobial immune defense. Here, we performed deep phenotypic profiling of CD3\(^{+}\)CD56\(^{+}\) cells in peripheral blood of normal human donors and individuals sensitized to birch‐pollen or/and house dust mite by high‐dimensional mass cytometry combined with manual and computational data analysis. A co‐regulation between major conventional T‐cell subsets and their respective CD3\(^{+}\)CD56\(^{+}\) cell counterparts appeared restricted to CD8\(^{+}\), MAIT, and TCRγδ\(^{+}\) T‐cell compartments. Interestingly, we find a co‐regulation of several CD3\(^{+}\)CD56\(^{+}\) cell subsets in allergic but not in healthy individuals. Moreover, using FlowSOM, we distinguished a variety of CD56\(^{+}\) T‐cell phenotypes demonstrating a hitherto underestimated heterogeneity among these cells. The novel CD3\(^{+}\)CD56\(^{+}\) subset description comprises phenotypes superimposed with naive, memory, type 1, 2, and 17 differentiation stages, in part represented by a phenotypical continuum. Frequencies of two out of 19 CD3\(^{+}\)CD56\(^{+}\) FlowSOM clusters were significantly diminished in allergic individuals, demonstrating less frequent presence of cells with cytolytic, presumably protective, capacity in these donors consistent with defective expansion or their recruitment to the affected tissue. Our results contribute to defining specific cell populations to be targeted during therapy for allergic conditions.

The term, optical imaging, is currently used to indicate a number of procedures allowing the noninvasive monitoring of specific physiologic, pathologic, and molecular processes as well as specific cell population behavior. These procedures are based on the detection of photons in the visible range, up to the near-infrared (400–1700 nm), produced by different physical phenomena including luminescence, fluorescence, and Cerenkov effect, emitted by optical probes, that is, fluorescent and bio/chemoluminescent molecules. Such agents have been developed to noninvasively assess both gross physiological processes, such as vascularization and permeability, cell population behavior, as well as molecular processes including the expression and activity of specific proteins. There are several classes of optical agents, including nonspecific molecules (both intravascular and diffusible), target-specific agents (subdivided into small molecules, peptides or antibodies, that specifically bind to a defined target), and target-specific activatable agents (that are made detectable following their priming in relation to a specific molecular process or enzymatic activity). This chapter focuses on the classification of available optical imaging agents, their features, the processes and molecular targets that can be noninvasively monitored by their use, their labeling, and their translational potential and clinical use.

Graphdiyne oxide (GDYO) is a carbon-based nanomaterial possessing sp(2) and sp-hybridized carbon atoms with many promising applications. However, its biocompatibility and potential biodegradability remain poorly understood. Using human primary monocyte-derived macrophages as a model we show here that GDYO elicited little or no cytotoxicity toward classically activated (M1) and alternatively activated (M2) macrophages. Moreover, GDYO reprogrammed M2 macrophages towards M1 macrophages, as evidenced by the elevation of specific cell surface markers and cytokines and the induction of NOS2 expression. We could also show inducible nitric oxide synthase (iNOS)-dependent biodegradation of GDYO in M1 macrophages, and this was corroborated in an acellular system using the peroxynitrite donor, SIN-1. Furthermore, GDYO elicited the production of pro-inflammatory cytokines in a biodegradation-dependent manner. Our findings shed new light on the reciprocal interactions between GDYO and human macrophages. This is relevant for biomedical applications of GDYO such as the re-education of tumor-associated macrophages or TAMs.

Histochemistry is an essential analytical tool interfacing extensively with plant science. The literature is indeed constellated with examples showing its use to decipher specific physiological and developmental processes, as well as to study plant cell structures. Plant cell structures are translucent unless they are stained. Histochemistry allows the identification and localization, at the cellular level, of biomolecules and organelles in different types of cells and tissues, based on the use of specific staining reactions and imaging. Histochemical techniques are also widely used for the in vivo localization of promoters in specific tissues, as well as to identify specific cell wall components such as lignin and polysaccharides. Histochemistry also enables the study of plant reactions to environmental constraints, e.g. the production of reactive oxygen species (ROS) can be traced by applying histochemical staining techniques. The possibility of detecting ROS and localizing them at the cellular level is vital in establishing the mechanisms involved in the sensitivity and tolerance to different stress conditions in plants. This review comprehensively highlights the additional value of histochemistry as a complementary technique to high-throughput approaches for the study of the plant response to environmental constraints. Moreover, here we have provided an extensive survey of the available plant histochemical staining methods used for the localization of metals, minerals, secondary metabolites, cell wall components, and the detection of ROS production in plant cells. The use of recent technological advances like CRISPR/Cas9-based genome-editing for histological application is also addressed. This review also surveys the available literature data on histochemical techniques used to study the response of plants to abiotic stresses and to identify the effects at the tissue and cell levels., The authors would like to thank Head of the Department, University of Allahabad, Allahabad, India, for providing the necessary facilities to carry out the work.

Biodegradable nanoparticles are highly versatile and adaptable delivery systems for pharmaceutical drugs. The nanoparticles can be targeted to specific cell types and tissues, modified to overcome biological barriers the contained drugs cannot overcome on their own and at the same time mask the undesirable side effects of pharmacological substances. The nanoparticle characteristics can be tailored to specific targets by modifications such as the addition of antibodies to the particle surface or coating them in substances altering their circulation behaviour. Different approaches and examples for targeted drug delivery with biodegradable nanoparticles are discussed, as well as model systems for the advanced evaluation of the used formulations shown.

Summary Isolation of nuclei tagged in specific cell types (INTACT) allows for stress-free and high-throughput analyses of cellular subpopulations. Here, we present an improved protocol for isolation of pure and high-quality GFP-labeled nuclei from frozen livers of INTACT mice, as well as protocols for downstream sequencing analyses. The adaptation to frozen tissue provides a pause point that allows sampling at multiple time points and/or phenotypic characterization of livers prior to nuclei isolation and downstream analyses. For complete details on the use of this protocol, please refer to Loft et al. (2021)., Graphical abstract, Highlights • Optimized protocol for isolation of nuclei from frozen livers • Protocol for immunopurification of nuclei tagged in specific cell types (INTACT) • Preparation of nuclear RNA- and ATAC-seq libraries • Nuclei from frozen and fresh livers perform equally in downstream assays, Isolation of nuclei tagged in specific cell types (INTACT) allows for stress-free and high-throughput analyses of cellular subpopulations. Here, we present an improved protocol for isolation of pure and high-quality GFP-labeled nuclei from frozen livers of INTACT mice, as well as protocols for downstream sequencing analyses. The adaptation to frozen tissue provides a pause point that allows sampling at multiple time points and/or phenotypic characterization of livers prior to nuclei isolation and downstream analyses.