Search

Single-cell mass cytometry (SCMC) combines features of traditional flow cytometry (i.e., fluorescence-activated cell sorting) with mass spectrometry, making it possible to measure several parameters at the single-cell level for a complex analysis of biological regulatory mechanisms. In this study, we optimized SCMC to analyze hemocytes of the Drosophila innate immune system. We used metal-conjugated antibodies (against cell surface antigens H2, H3, H18, L1, L4, and P1, and intracellular antigens 3A5 and L2) and anti-IgM (against cell surface antigen L6) to detect the levels of antigens, while anti-GFP was used to detect crystal cells in the immune-induced samples. We investigated the antigen expression profile of single cells and hemocyte populations in naive states, in immune-induced states, in tumorous mutants bearing a driver mutation in the Drosophila homologue of Janus kinase (hopTum) and carrying a deficiency of the tumor suppressor gene lethal(3)malignant blood neoplasm-1 [l(3)mbn1], as well as in stem cell maintenance-defective hdcΔ84 mutant larvae. Multidimensional analysis enabled the discrimination of the functionally different major hemocyte subsets for lamellocytes, plasmatocytes, and crystal cells, and delineated the unique immunophenotype of Drosophila mutants. We have identified subpopulations of L2+/P1+ and L2+/L4+/P1+ transitional phenotype cells in the tumorous strains l(3)mbn1 and hopTum, respectively, and a subpopulation of L4+/P1+ cells upon immune induction. Our results demonstrated for the first time that SCMC, combined with multidimensional bioinformatic analysis, represents a versatile and powerful tool to deeply analyze the regulation of cell-mediated immunity of Drosophila.

Background & Aims Defining the genetic heterogeneity of intrahepatic biliary epithelial cells (BECs) is challenging, and tools for identifying BEC subpopulations are limited. Here, we characterize the expression of a Sox9EGFP transgene in the liver and demonstrate that green fluorescent protein (GFP) expression levels are associated with distinct cell types. Methods Sox9EGFP BAC transgenic mice were assayed by immunofluorescence, flow cytometry, and gene expression profiling to characterize in vivo characteristics of GFP populations. Single BECs from distinct GFP populations were isolated by fluorescence-activated cell sorting, and functional analysis was conducted in organoid forming assays. Intrahepatic ductal epithelium was grown as organoids and treated with a Yes-associated protein (Yap) inhibitor or bile acids to determine upstream regulation of Sox9 in BECs. Sox9EGFP mice were subjected to bile duct ligation, and GFP expression was assessed by immunofluorescence. Results BECs express low or high levels of GFP, whereas periportal hepatocytes express sublow GFP. Sox9EGFP+ BECs are differentially distributed by duct size and demonstrate distinct gene expression signatures, with enrichment of Cyr61 and Hes1 in GFPhigh BECs. Single Sox9EGFP+ cells form organoids that exhibit heterogeneous survival, growth, and HNF4A activation dependent on culture conditions, suggesting that exogenous signaling impacts BEC heterogeneity. Yap is required to maintain Sox9 expression in biliary organoids, but bile acids are insufficient to induce BEC Yap activity or Sox9 in vivo and in vitro. Sox9EGFP remains restricted to BECs and periportal hepatocytes after bile duct ligation. Conclusions Our data demonstrate that Sox9EGFP levels provide readout of Yap activity and delineate BEC heterogeneity, providing a tool for assaying subpopulation-specific cellular function in the liver.

Purpose Inhibition of p53 by amplification of MDM2 is one of the key contributors in the oncogenesis of a subset of soft tissue sarcoma (STS) known as well-/dedifferentiated liposarcoma. A small molecule MDM2 antagonist, nutlin-3, induces the p53 pathway by disrupting the interaction between MDM2 and p53. Radiation therapy is an integral component for treating liposarcoma and induces p53. Based on wild-type TP53 status in liposarcoma, it was investigated whether MDM2 inhibition with irradiation led to enhanced reactivation of p53 and subsequent p53-mediated effects in liposarcoma. Methods and Materials Clonogenic assays, immunoblotting, flow cytometry/fluorescence-activated cell sorting, and senescence assays were employed in liposarcoma cell lines after co-treatment with nutlin-3 and radiation. Results Upon treatment with nutlin-3, 2 of the well-/dedifferentiated liposarcoma (MDM2Amp/TP53WT) cell lines displayed radiosensitivity with sensitization enhancement ratio values of >1. In contrast, the cell line with mutant TP53 showed sensitization enhancement ratio values of ∼1. Immunoblotting revealed induced reactivation of the p53-MDM2-p21 signaling axis in response to combination therapy in all cell lines with wild-type TP53. Removal of MDM2 inhibitor (with or without radiation therapy) led to the emergence of ploidy-based heterogeneous subpopulations (4N and >4N) in TP53 wild-type cells and not in TP53 mutant cells. Immunoblotting of cell cycle markers (G1, G2/M) revealed the generation of 4N G1 cells. Sorting and long-term fate analysis of different populations (2N, 4N, and >4N) by colony assay displayed attenuated colony-forming potential and augmented senescence of the 4N and >4N cells contributing to the radiosensitization effect. Conclusions Nutlin-3 increases the vulnerability of liposarcoma cell lines to radiation by augmented activation of p53. The cells underwent senescence. Presence and activation of p53 are required for exertion of the radiosensitizing effect by nutlin-3, but this is not the sole determinant of the effect. This study opens avenues for the clinical translation in a stratified group of patients with liposarcoma.

Human amniotic mesenchymal stem cells (hAMSCs) were previously shown to effectively rescue ovarian function in a premature ovarian insufficiency (POI) mouse model. The therapeutic mechanism of hAMSC-derived exosomes (hAMSC-Exos) is not fully understood. In this study, the therapeutic mechanism involved in exosomal microRNA-320a (miR-320a) and Sirtuin 4 (SIRT4) was investigated in POI mouse ovaries oocytes and human granulosa cells (hGCs) by fluorescence-activated cell sorting (FACS), hematoxylin and eosin (H&E) staining, enzyme-linked immunosorbent assay (ELISA), and immunofluorescence experiments. hAMSC-Exos improved proliferation, inhibited apoptosis, and decreased the expression of SIRT4 and relative genes in POI hGCs and ovaries. hAMSC-Exos elevated ovarian function and prohibited SIRT4 expression in oogenesis. The therapeutic effects were attenuated when miR-320a was knocked down. hAMSC-Exos decreased the ROS levels in POI hGCs and oocytes and improved ovarian weight and litter size, except for the Exosanti-miR-320a/POI group. Finally, hAMSC-Exos reduced the SIRT4 and ROS levels in POI ovaries and hGCs. The downstream protein expression (ANT2, AMP-dependent kinase [AMPK], and L-OPA1) was downregulated in the hGCs-SIRT4KD group but disappeared in the Exosanti-miR-320a/POI group. Our study is the first to illustrate the therapeutic potential of hAMSC-Exos in POI. Exosomal miR-320 plays a key role in the hAMSC-Exos-mediated effects on ovarian function via SIRT4 signaling., Graphical Abstract, Ding et al. elucidate the therapeutic potential of hAMSC-Exos in POI disease. Furthermore, exosomal miR-320 derived from hAMSCs plays a key role in reducing of the ROS levels by regulating SIRT4 signaling in the POI oocytes, hGCs, and ovaries.

Summary Current single-cell RNA sequencing (scRNA-seq) protocols are limited by the number of cells that can be simultaneously sequenced, restricting the ability to resolve heterogeneity of rare cell types. We describe here a protocol for rapid isolation of myeloid cells from tumor-harboring mouse cerebellum without cell sorting to minimize cell damage for scRNA-seq. This protocol includes the procedures for further enrichment of myeloid cells using CD11b+ magnetic beads, followed by the generation of scRNA library and sequencing analysis. For complete details on the use and execution of this protocol, please refer to Dang et al. (2021)., Graphical abstract, Highlights • Isolation of myeloid cells from tumor-bearing mouse cerebellum • Single-cell RNA sequencing (scRNA-seq) of murine cerebellar myeloid cells • Identification of the major myeloid subsets using scRNA-seq data, Current single-cell RNA sequencing (scRNA-seq) protocols are limited by the number of cells that can be simultaneously sequenced, restricting the ability to resolve heterogeneity of rare cell types. We describe here a protocol for rapid isolation of myeloid cells from tumor-harboring mouse cerebellum without cell sorting to minimize cell damage for scRNA-Seq. This protocol includes the procedures for further enrichment of myeloid cells using CD11b+ magnetic beads, followed by the generation of scRNA library and sequencing analysis.

Summary: Accumulation of visceral (VIS) is a predictor of metabolic disorders and insulin resistance. This is due in part to the limited capacity of VIS fat to buffer lipids allowing them to deposit in insulin-sensitive tissues. Mechanisms underlying selective hypertrophic growth and tissue remodeling properties of VIS fat are not well understood. We identified subsets of adipose progenitors (APs) unique to VIS fat with differential Cd34 expression and adipogenic capacity. VIS low (Cd34 low) APs are adipogenic, whereas VIS high (Cd34 high) APs are not. Furthermore, VIS high APs inhibit adipogenic differentiation of SUB and VIS low APs in vitro through the secretion of soluble inhibitory factor(s). The number of VIS high APs increased with adipose tissue expansion, and their abundance in vivo caused hypertrophic growth, fibrosis, inflammation, and metabolic dysfunction. This study unveils the presence of APs unique to VIS fat involved in the paracrine regulation of adipogenesis and tissue remodeling. : Buffolo et al. show that the visceral fat of mice contains subsets of Cd34 positive stromal cells with distinct adipogenic potential. Stromal cells with high Cd34 expression inhibit adipogenic conversion of cells with low Cd34 expression. When implanted in vivo, Cd34 high stromal cells cause visceral adipose tissue remodeling and inflammation and impair insulin sensitivity. Keywords: adipose progenitors, fat expansion, cell sorting, transplantation, visceral fat

Isolating active mesenchymal stem cells from a heterogeneous population is an essential step that determines the efficacy of stem cell therapy such as for osteoarthritis. Nowadays, the gold standard of cell sorting, fluorescence-activated cell sorting, relies on labelling surface markers via antibody–antigen reaction. However, sorting stem cells with high stemness usually requires the labelling of multiple biomarkers. Moreover, the labelling process is costly, and the high operating pressure is harmful to cell functionality and viability. Although label-free cell sorting, based on physical characteristics, has gained increasing interest in the past decades, it has not shown the ability to eliminate stem cells with low stemness. Cell motility, as a novel sorting marker, is hence proposed for label-free sorting active stem cells. Accumulating evidence has demonstrated the feasibility in manipulating directional cell migration through patterning the biophysical, biochemical or both gradients of the extracellular matrix. However, applying those findings to label-free cell sorting has not been well discussed and studied. This review thus first provides a brief overview about the effect of biophysical and biochemical gradients of the extracellular matrix on cell migration. State-of-the-art fabrication techniques for generating such gradients of hydrogels are then introduced. Among current research, the authors suggest that hydrogels with dual-gradients of biochemistry and biophysics are potential tools for accurate label-free cell sorting with satisfactory selectivity and efficiency. Translational potential of this article: The reviewed label-free cell sorting approaches enable us to isolate active cell for cytotherapy. The proposed system can be further modified for single-cell analysis and drug screening. Keywords: Gradients, Cell sorting, Hydrogels, Stem cells

Summary Endothelial cells (ECs) harbor distinct phenotypical and functional characteristics depending on their tissue localization and contribute to brain, eye, lung, and muscle diseases such as dementia, macular degeneration, pulmonary hypertension, and sarcopenia. To study their function, isolation of pure ECs in high quantities is crucial. Here, we describe protocols for rapid and reproducible blood vessel EC purification established for scRNA sequencing from murine tissues using mechanical and enzymatic digestion followed by magnetic and fluorescence-activated cell sorting. For complete details on the use and execution of these protocol, please refer to Kalucka et al. (2020), Rohlenova et al. (2020), and Goveia et al. (2020)., Graphical Abstract, Highlights • Protocols for isolation of murine endothelial cells designed for scRNA-seq • Rapid and efficient isolation of ECs from brain, choroid, lung, and muscle • Combination of magnetic and fluorescent activated cell sorting • High purity and quality of isolated murine endothelial cells evident from scRNA-seq, Endothelial cells (ECs) harbor distinct phenotypical and functional characteristics depending on their tissue localization and contribute to brain, eye, lung, and muscle diseases such as dementia, macular degeneration, pulmonary hypertension, and sarcopenia. To study their function, isolation of pure ECs in high quantities is crucial. Here, we describe protocols for rapid and reproducible blood vessel EC purification established for scRNA sequencing from murine tissues using mechanical and enzymatic digestion followed by magnetic and fluorescence-activated cell sorting.

Summary Endothelial cells (ECs) exhibit phenotypic and functional tissue specificities, critical for studies in the vascular field and beyond. Thus, tissue-specific methods for isolation of highly purified ECs are necessary. Kidney, spleen, and testis ECs are relevant players in health and diseases such as chronic kidney disease, acute kidney injury, myelofibrosis, and cancer. Here, we provide tailored protocols for rapid and reproducible EC purification established for scRNA sequencing from these adult murine tissues using the combination of magnetic- and fluorescence-activated cell sorting. For complete details on the use and execution of these protocols, please refer to Kalucka et al. (2020) and Dumas et al. (2020)., Graphical abstract, Highlights • Protocols for isolation of murine endothelial cells applicable for scRNA-seq • Efficient isolation of ECs from the kidney, spleen, and testis • Combination of magnetic- and fluorescence-activated cell sorting • High purity and quality of isolated murine endothelial cells evident from scRNA-seq, Endothelial cells (ECs) exhibit phenotypic and functional tissue specificities, critical for studies in the vascular field and beyond. Thus, tissue-specific methods for isolation of highly purified ECs are necessary. Kidney, spleen, and testis ECs are relevant players in health and diseases such as chronic kidney disease, acute kidney injury, myelofibrosis, and cancer. Here, we provide tailored protocols for rapid and reproducible EC purification established for scRNA sequencing from these adult murine tissues using the combination of magnetic- and fluorescence-activated cell sorting.

Summary Neonatal mouse cochlear duct cells can proliferate and grow in vitro into inner ear organoids. Distinctive cochlear duct cell types have different organoid formation capacities. Here, we provide a flow cytometric cell-sorting method that allows the subsequent culture of individual cochlear cell populations. For the efficient culture of the sorted cells, we provide protocols for growing free-floating inner ear organoids, the adherence of organoids to a substrate, and the expansion of organoid-derived inner ear colonies. For complete details on the use and execution of this protocol, please refer to Kubota et al. (2021)., Graphical Abstract, Highlights • Flow cytometric sorting of mouse cochlear cells • Culture of sorted cochlear cell populations and growth of inner ear organoids • Adherent growth of inner ear organoid-derived colonies, Neonatal mouse cochlear duct cells can proliferate and grow in vitro into inner ear organoids. Distinctive cochlear duct cell types have different organoid formation capacities. Here, we provide a flow cytometric cell-sorting method that allows the subsequent culture of individual cochlear cell populations. For the efficient culture of the sorted cells, we provide protocols for growing free-floating inner ear organoids, the adherence of organoids to a substrate, and the expansion of organoid-derived inner ear colonies.

Highlights • Interception of CD47-SIRPα signaling is an elusive yet intriguing goal for anti-tumor immunotherapy since unbiased CD47 blockade by its antibody cannot avoid erythrocyte destruction. • We previously reported that isoQC, a Golgi-resident enzyme lacking in mature erythrocyte, disrupts the binding of CD47 to SIRPα by downregulating pGlu-CD47 and its interaction with SIRPα (Cell research 2019. 29:502–505). • In this study, we explored the possibility of utilizing isoQC inhibition to address the challenge of CD47 antibody treatment induced anemia. • We discovered a new lead compound of isoQC inhibitor, Luteolin, and revealed that posttranslational modification may work as an immunotherapeutic target by abolishing immune checkpoint signaling., ‘Don't eat me’ signal of CD47 is activated via its interaction with SIRPα protein on myeloid cells, especially phagocytic cells, and prevents malignant cells from anti-tumor immunity in which pyroglutamate modification of CD47 by glutaminyl-peptide cyclotransferase-like protein (isoQC) takes an important part evidenced by our previous report that isoQC is an essential regulator for CD47-SIRPα axis with a strong inhibition on macrophage-mediated phagoctyosis. Therefore, we screened for potential isoQC inhibitors by fluorescence-activated cell sorting assay and identified luteolin as a potent compound that blocked the pyroglutamation of CD47 by isoQC. We further demonstrated that luteolin directly bound to isoQC using pull-down assay and isothermal calorimetric (ITC) assay. In consistency, we showed that luteolin markedly abrogated the cell-surface interaction between CD47 and SIRPα in multiple myeloma H929 cells and consequently promoted the macrophage-mediated phagocytosis. Collectively, our study discovered a promising lead compound targeting isoQC, luteolin, which functions distinctly from current CD47 antibody-based drugs and therefore may potentially overcome the clinical side effects associated with CD47 antibody treatment-induced anemia.

Summary Isolation of leukemia stem cells presents a challenge due to the heterogeneity of the immunophenotypic markers commonly used to identify blood stem cells. Several studies have reported that relative levels of reactive oxygen species (ROS) can be used to enrich for stem cell populations, suggesting a potential alternative to surface antigen-based methods. Here, we describe a protocol to enrich for stem cells from human acute myeloid leukemia specimens using relative levels of ROS. This protocol provides consistent enrichment of leukemia stem cells. For complete details on the use and execution of this protocol, please refer to Lagadinou et al. (2013) and Pei et al. (2018)., Graphical abstract, Highlights • Low levels of reactive oxygen species are a hallmark of stem cells • Relative levels of reactive oxygen species allow for enrichment of leukemia stem cells • This protocol is an alternative to surface antigen-based methods, Isolation of leukemia stem cells presents a challenge due to the heterogeneity of the immunophenotypic markers commonly used to identify blood stem cells. Several studies have reported that relative levels of reactive oxygen species (ROS) can be used to enrich for stem cell populations, suggesting a potential alternative to surface antigen-based methods. Here, we describe a protocol to enrich for stem cells from human acute myeloid leukemia specimens using relative levels of ROS. This protocol provides consistent enrichment of leukemia stem cells.

Understanding microbial adhesion and retention is crucial for controlling many processes, including biofilm formation, antimicrobial therapy as well as cell sorting and cell detection platforms. Cell detachment is inextricably linked to cell adhesion and retention and plays an important part in the mechanisms involved in these processes. Physico-chemical and biological forces play a crucial role in microbial adhesion interactions and altering the medium ionic strength offers a potential means for modulating these interactions. Real-time studies on the effect of ionic strength on microbial adhesion are often limited to short-term bacterial adhesion. Therefore, there is a need, not only for long-term bacterial adhesion studies, but also for similar studies focusing on eukaryotic microbes, such as yeast. Hereby, we monitored, in real-time, S. cerevisiae adhesion on gold and silica as examples of surfaces with different surface charge properties to disclose long-term adhesion, retention and detachment as a function of ionic strength using quartz crystal microbalance with dissipation monitoring. Our results show that short- and long-term cell adhesion levels in terms of mass-loading increase with increasing ionic strength, while cells dispersed in a medium of higher ionic strength experience longer retention and detachment times. The positive correlation between the cell zeta potential and ionic strength suggests that zeta potential plays a role on cell retention and detachment. These trends are similar for measurements on silica and gold, with shorter retention and detachment times for silica due to strong short-range repulsions originating from a high electron-donicity. Furthermore, the results are comparable with measurements in standard yeast culture medium, implying that the overall effect of ionic strength applies for cells in nutrient-rich and nutrient-deficient media., SCOPUS: ar.j, info:eu-repo/semantics/published

Summary In order to process samples by fluorescence-activated cell sorting (FACS), it is essential to obtain a single-cell suspension of dissociated cells. Numerous protocols and commercial reagents are available; however, each requires optimization for specific tissue types. Here, we describe an optimized protocol for dissociating dissected chick embryos across a broad span of developmental stages. We also provide protocols for processing targeted cell populations isolated using FACS for ATAC-seq, RNA-seq, and chromatin immunoprecipitation. For complete details on the use and execution of this protocol, please refer to Ling and Sauka-Spengler (2019) and Williams et al. (2019)., Graphical abstract, Highlights • Combined enzymatic digestion and physical homogenization for tissue dissociation • Dissociate single-tissue dissections as well as large tissue collections • Preparation of FACS-isolated cells for numerous downstream experiments, In order to process samples by fluorescence-activated cell sorting (FACS), it is essential to obtain a single-cell suspension of dissociated cells. Numerous protocols and commercial reagents are available; however, each requires optimization for specific tissue types. Here, we describe an optimized protocol for dissociating dissected chick embryos across a broad span of developmental stages. We also provide protocols for processing targeted cell populations isolated using FACS for ATAC-seq, RNA-seq, and chromatin immunoprecipitation.

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.

Summary The combination of population and single-cell RNA sequencing analysis using human embryonic stem cell (hESC) differentiation and developmental tissues is a powerful approach to elucidate an organ-specific cellular and molecular atlas in human embryogenesis. This protocol describes (1) cardiac-directed differentiation and isolation of hESC-derived cardiac derivatives with fluorescence-activated cell sorting, (2) isolation of human embryonic heart-derived single cardiac cells, and (3) construction of cDNA libraries with Smart-seq2. These allow for the preparation of human developmental samples for comprehensive transcriptional analysis. For complete details on the use and execution of this protocol, please refer to Sahara et al. (2019)., Graphical abstract, Highlights • Efficient cardiac-directed differentiation of hESCs • Isolation of hESC-derived cardiac derivatives with fluorescence-activated cell sorting • Isolation of human embryonic heart-derived single cardiac cells • Construction of cDNA libraries for both population and single-cell RNA sequencing, The combination of population and single-cell RNA sequencing analysis using human embryonic stem cell (hESC) differentiation and developmental tissues is a powerful approach to elucidate an organ-specific cellular and molecular atlas in human embryogenesis. This protocol describes (1) cardiac-directed differentiation and isolation of hESC-derived cardiac derivatives with fluorescence-activated cell sorting, (2) isolation of human embryonic heart-derived single cardiac cells, and (3) construction of cDNA libraries with Smart-seq2. These allow for the preparation of human developmental samples for comprehensive transcriptional analysis.

Research question Which are the early compartment-specific transcriptional responses of the trophoblast and the endometrial epithelium throughout early attachment during implantation? Design An endometrial epithelium proxy (cell line Ishikawa) was co-cultured with spheroids of a green fluorescent protein (GFP) expressing trophoblast cell line (JEG-3). After 0, 8 and 24 h of co-culture, the compartments were sorted by fluorescence-activated cell sorting; GFP+ (trophoblast), GFP– (epithelium) and non-co-cultured control populations were analysed (in triplicate) by RNA-seq and gene set enrichment analysis (GSEA). Results Trophoblast challenge induced a wave of transcriptional changes in the epithelium that resulted in 295 differentially regulated genes involving epithelial to mesenchymal transition (EMT), cell movement, apoptosis, hypoxia, inflammation, allograft rejection, myogenesis and cell signalling at 8 h. Interestingly, many of the enriched pathways were subsequently de-enriched by 24 h (i.e. EMT, cell movement, allograft rejection, myogenesis and cell signalling). In the trophoblast, the co-culture induced more transcriptional changes and regulation of a variety of pathways. A total of 1247 and 481 genes were differentially expressed after 8 h and from 8 to 24 h, respectively. Angiogenesis and hypoxia were over-represented at both stages, while EMT and cell signalling only were at 8 h; from 8 to 24 h, inflammation and oestrogen response were enriched, while proliferation was under-represented. Conclusions Successful attachment produced a series of dynamic changes in gene expression, characterized by an overall early and transient transcriptional up-regulation in the receptive epithelium, in contrast to a more dynamic transcriptional response in the trophoblast.

Self-organization is an all-important feature of living systems that provides the means to achieve specialization and functionality at distinct spatio-temporal scales. Herein, we review this concept by addressing the packing organization of cells, the sorting/compartmentalization phenomenon of cell populations, and the propagation of organizing cues at the tissue level through traveling waves. We elaborate on how different theoretical models and tools from Topology, Physics, and Dynamical Systems have improved the understanding of self-organization by shedding light on the role played by mechanics as a driver of morphogenesis. Altogether, by providing a historical perspective, we show how ideas and hypotheses in the field have been revisited, developed, and/or rejected and what are the open questions that need to be tackled by future research., L.M.E and P.G.-G. has been supported by the Ramón y Cajal program (PI13/01347); L.M.E and P.G.-G. work is funded by the Ministry of Economy, Industry and Competitiveness grant BFU2016-74975-P co-funded by FEDER funds, and by the Spanish Ministry of Science and Innovation Ministry of Science through grant PID2019-103900GB-I00. S.A. and J.B. have been supported by a Faculty Innovation Grant (FIG) by Lehigh University JB-FIG-2019. J.B. also acknowledges financial support from the Spanish Ministry of Science and Innovation through grant PID2019-105566GB-I00.

Summary It remains challenging to generate reproducible, high-quality cDNA libraries from RNA derived from rare cell populations. Here, we describe a protocol for high-throughput RNA-seq library preparation, including isolation of 200 skeletal muscle stem cells from mouse tibialis anterior muscle by fluorescence-activated cell sorting and cDNA preparation. We also describe RNA extraction and cDNA preparation from differentiating mouse embryonic stem cells. For complete details on the use and execution of this protocol, please refer to Juan et al. (2016) and Garcia-Prat et al. (2016)., Graphical abstract, Highlights • FACS isolation of 200 muscle stem cells (MuSCs) from one mouse tibialis anterior muscle • cDNA library construction for deep sequencing by direct lysis of 200 MuSCs • cDNA library construction for deep sequencing from 5,000–10,000 embryonic stem cells, It remains challenging to generate reproducible, high-quality cDNA libraries from RNA derived from rare cell populations. Here, we describe a protocol for high-throughput RNA-seq library preparation, including isolation of 200 skeletal muscle stem cells from mouse tibialis anterior muscle by fluorescence-activated cell sorting and cDNA preparation. We also describe RNA extraction and cDNA preparation from differentiating mouse embryonic stem cells.

This work aimed to select a Tisochrysis lutea phenotype with higher biomass and fucoxanthin productivities using fluorescence-activated cell sorting (FACS). A novel phenotype was obtained after 2 rounds of selection, based on high-fucoxanthin fluorescence. The resulting phenotype forms cell aggregates, has no flagella, and was stable after 15 months. Optimal temperature (30 ◦C) and light (300 μmol m􀀀 2 s􀀀 1) were obtained at laboratory scale, identical to the original strain. The biomass productivity was higher than the original strain: 1.9× at laboratory scale (0.4 L), and 4.5× under outdoor conditions (190 L). Moreover, compared to the original strain, the productivity of fucoxanthin increased 1.6–3.1× and docosahexaenoic acid 1.5–1.9×. These are the highest ever reported outdoor productivities, obtained with a robust new phenotype from a T. lutea monoculture isolated with FACS without genetic manipulation. The resulting phenotype shows high potential for industrial production.

Summary Basophils, the rarest granulocyte, play critical roles in parasite- and allergen-induced inflammation. We applied mass cytometry (CyTOF) to simultaneously asses 44 proteins to phenotype and functionally characterize neutrophils, eosinophils, and basophils from 19 healthy donors. There was minimal heterogeneity seen in eosinophils and neutrophils, but data-driven analyses revealed four unique subpopulations within phenotypically basophilic granulocytes (PBG; CD45+HLA-DR−CD123+). Through CyTOF and fluorescence-activated cell sorting (FACS), we classified these four PBG subpopulations as (I) CD16lowFcεRIhighCD244high (88.5 ± 1.2%), (II) CD16highFcεRIhighCD244high (9.1 ± 0.4%), (III) CD16lowFcεRIlowCD244low (2.3 ± 1.3), and (IV) CD16highFcεRIlowCD244low (0.4 ± 0.1%). Prospective isolation confirmed basophilic-morphology of PBG I–III, but neutrophilic-morphology of PBG IV. Functional interrogation via IgE-crosslinking or IL-3 stimulation demonstrated that PBG I–II had significant increases in CD203c expression, whereas PBG III–IV remained unchanged compared with media-alone conditions. Thus, PBG III–IV could serve roles in non-IgE-mediated immunity. Our findings offer new perspectives in human basophil heterogeneity and the varying functional potential of these new subsets in health and disease., Graphical Abstract, Highlights • Unsupervised clustering revealed 4 basophil populations, driven by CD16, CD244, and FcεRI • The rarest basophil subpopulation IV was morphologically neutrophils • Anti-IgE and IL-3 stimulation did not induce functional responses in III and IV • Basophil subpopulation heterogeneity was observed in healthy and CML samples, Immunology; Systems Biology

Mesenchymal stem cells (MSCs) are expected to be useful in bone regeneration treatment for various diseases and conditions, including cleft lip and palate, fracture, and bone absorption. However, to date, MSCs have failed to produce satisfactory results in clinical settings. This is primarily due to the low rate of induced osteogenic differentiation. To realize MSC potential, it is necessary to establish methods for the isolation of MSC-derived living osteoblasts. However, no osteoblast markers have been reported to date. In an attempt to develop a method for the assessment of osteoblast differentiation, we established reporter human immortalized MSC (hiMSC) lines for in vitro monitoring of bone gamma-carboxyglutamate protein (BGLAP, osteocalcin) expression. To this end, we successfully knocked-in an enhanced green fluorescent protein (EGFP) gene cassette immediately downstream of the first ATG of BGLAP via CRISPR-Cas9, and established hiMSC lines expressing EGFP to monitor osteogenic differentiation. On differentiation day 7, EGFP-positive cells were collected by flow cytometric cell sorting, and the expression of EGFP and endogenous BGLAP was analyzed. During osteogenic differentiation, EGFP upregulation was found to correlate with expression of endogenous BGLAP. Moreover, mineralization was confirmed using Alizarin red-S staining after two weeks of osteogenic differentiation of the modified hiMSC lines. The modified hiMSC lines, as well as the derived differentiated osteoblasts obtained herein, are valuable tools for the monitoring osteoblast gene and protein expression, and can be used to develop novel methods for isolating living osteoblasts., Cell Culture; Cell Differentiation; Stem Cell Research; Cell biology; Promoter; Regenerative Medicine; bone gamma-carboxyglutamate protein; CRISPR-Cas9; mesenchymal stem cells; osteogenic differentiation; reporter cells

Summary The invasion of Chlamydia trachomatis, an obligate intracellular bacterium, into epithelial cells is driven by a complex interplay of host and bacterial factors. To comprehensively define the host genes required for pathogen invasion, we undertook a fluorescence-activated cell sorting (FACS)-based CRISPR screen in human cells. A genome-wide loss-of-function library was infected with fluorescent C. trachomatis and then sorted to enrich for invasion-deficient mutants. The screen identified heparan sulfate, a known pathogen receptor, as well as coatomer complex I (COPI). We found that COPI, through a previously unappreciated role, promotes heparan sulfate cell surface presentation, thereby facilitating C. trachomatis attachment. The heparan sulfate defect does not fully account for the resistance of COPI mutants. COPI also promotes the activity of the pathogen's type III secretion system. Together, our findings establish the requirement for COPI in C. trachomatis invasion and the utility of FACS-based CRISPR screening for the elucidation of host factors required for pathogen invasion., Graphical Abstract, Highlights • FACS-based CRISPR screen to identify host factors required for C. trachomatis invasion • Candidate genes comprise heparan sulfate biosynthesis, actin remodeling, and COPI • COPI regulates heparan sulfate cell surface presentation and C. trachomatis attachment • COPI is also required for efficient C. trachomatis T3SS translocation, Molecular Mechanism of Behavior; Medical Microbiology; Methodology in Biological Sciences; Cell Biology; Host-pathogen Interactions; Molecular Microbiology; Genetic Engineering; Genetic Screens

Background: Korean Red Ginseng (KRG; Panax ginseng Meyer) is a widely used medicinal herb known to exert various immune modulatory functions. KRG and one of its purified components, ginsenoside Rg3, are known to possess anti-inflammatory activities. How they impact helper T cell-mediated responses is not fully explored. In this study, we attempted to evaluate the effect of KRG extract (KRGE) and ginsenoside Rg3 on Th1 cell responses. Methods: Using well-characterized T cell in vitro differentiation systems, we examined the effects of KRGE or enhanced Rg3 on the Th1-inducing cytokine production from dendritic cells (DC) and the naïve CD4+ T cells differentiation to Th1 cells. Furthermore, we examined the change of Th1 cell population in the intestine after treatment of enhanced Rg3. The influence of KRGE or enhanced Rg3 on Th1 cell differentiation was evaluated by fluorescence-activated cell sorting, enzyme-linked immunosorbent assay, and quantitative real-time polymerase chain reaction. Results: KRGE significantly inhibited the production level of IL-12 from DCs and subsequent Th1 cell differentiation. Similarly, enhanced Rg3 significantly suppressed the expression of interferon gamma (IFNγ) and T-bet in T cells under Th1-skewing condition. Consistent with these effects in vitro, oral administration of enhanced Rg3 suppressed the frequency of Th1 cells in the Peyer's patch and lamina propria cells in vivo. Conclusion: Enhanced Rg3 negatively regulates the differentiation of Th1 cell in vitro and Th1 cell responses in the gut in vivo, providing fundamental basis for the use of this agent to treat Th1-related diseases. Keywords: Enhanced Rg3, IFNγ, IL-12, Korean Red Ginseng extract, Th1

The most highly studied endocytic pathway, clathrin-dependent endocytosis, mediates a wide range of fundamental processes including nutrient internalization, receptor recycling, and signal transduction. In order to model tissue specific and developmental aspects of this process, CRISPR/Cas9 genomic editing was utilized to fluorescently label the C-terminus of clathrin light chain A (CLTA) within the phenotypically normal, parental CRMi001-A human induced pluripotent stem cell line. Successfully edited cells were isolated by fluorescently activated cell sorting, remained karyotypically normal, and maintained their differentiation potential. This cell line facilitates imaging of endogenous clathrin trafficking within varied cell types.

Background: Korean ginseng has been widely evaluated to treat human diseases; however, most studies on Korean ginseng have focused on its root. In this study, polysaccharides [acidic-polysaccharide-linked glycopeptide (APGP) extracted with 90% ethanol and hot water] were prepared from Korean ginseng berries, and their effect on immunosenescence was explored. Methods: The effect of APGP on thymic involution was evaluated by measuring the size of thymi dissected from aged mice. The effect of APGP on populations of immune cells, including natural killer (NK) cells, dendritic cells, age-correlated CD11c-positive B cells, and several subtypes of T cells [CD4-positive, CD8-positive, and regulatory (Treg) T cells] in the thymi and spleens of aged mice was analyzed by fluorescence-activated cell sorting analysis. Serum levels of interleukin (IL)-2 and IL-6 were evaluated by enzyme-linked immunosorbent assay analysis. Profiles of APGP components were evaluated by high-performance liquid chromatography (HPLC) analysis. Results: APGP suppressed thymic involution by increasing the weight and areas of thymi in aged mice. APGP increased the population of NK cells, but showed no effect on the population of dendritic cells in the thymi and spleens of aged mice. APGP decreased the population of age-correlated CD11c-positive B cells in the spleens of aged mice. APGP showed no effect on the populations of CD4- and CD8-positive T cells in the thymi of aged mice, whereas it increased the population of Treg cells in the spleens of aged mice. APGP further decreased the reduced serum levels of IL-2 in aged mice, but serum levels of IL-6 were not statistically changed by APGP in aged mice. Finally, HPLC analysis showed that APGP had one major peak at 15 min (a main type of polysaccharide) and a long tail up to 35 min (a mixture of a variety of types of polysaccharides). Conclusion: These results suggested that APGP exerted an anti-immunosenescent effect by suppressing thymic involution and modulating several types of immune cells. Keywords: APGP, ginseng berry, immunosenescence, NK cell, Treg cell

Summary Deciphering the mechanisms that regulate the quiescence of adult neural stem cells (NSCs) is crucial for the development of therapeutic strategies based on the stimulation of their endogenous regenerative potential in the damaged brain. We show that LeXbright cells sorted from the adult mouse subventricular zone exhibit all the characteristic features of quiescent NSCs. Indeed, they constitute a subpopulation of slowly dividing cells that is able to enter the cell cycle to regenerate the irradiated niche. Comparative transcriptomic analyses showed that they express hallmarks of NSCs but display a distinct molecular signature from activated NSCs (LeX+EGFR+ cells). Particularly, numerous membrane receptors are expressed on quiescent NSCs. We further revealed a different expression pattern of Syndecan-1 between quiescent and activated NSCs and demonstrated its role in the proliferation of activated NSCs. Our data highlight the central role of the stem cell microenvironment in the regulation of quiescence in adult neurogenic niches., Highlights • Transcriptome analysis reveals molecular hallmarks of activated and quiescent NSCs • Data resource of putative markers and/or regulators of NSC quiescence • Quiescent NSCs integrate various signals from the microenvironment • Syndecan-1 is involved in proliferation of NSCs, In this article, Boussin, Mouthon, and colleagues provide transcriptomic profiles of quiescent and activated neural stem cells. They report on the use of Syndecan-1 as a marker to purify long-term proliferating stem cells.

Summary Undifferentiated spermatogonia comprise a pool of stem cells and progenitor cells that show heterogeneous expression of markers, including the cell surface receptor GFRα1. Technical challenges in isolation of GFRα1+ versus GFRα1– undifferentiated spermatogonia have precluded the comparative molecular characterization of these subpopulations and their functional evaluation as stem cells. Here, we develop a method to purify these subpopulations by fluorescence-activated cell sorting and show that GFRα1+ and GFRα1– undifferentiated spermatogonia both demonstrate elevated transplantation activity, while differing principally in receptor tyrosine kinase signaling and cell cycle. We identify the cell surface molecule melanocyte cell adhesion molecule (MCAM) as differentially expressed in these populations and show that antibodies to MCAM allow isolation of highly enriched populations of GFRα1+ and GFRα1– spermatogonia from adult, wild-type mice. In germ cell culture, GFRα1– cells upregulate MCAM expression in response to glial cell line-derived neurotrophic factor (GDNF)/fibroblast growth factor (FGF) stimulation. In transplanted hosts, GFRα1– spermatogonia yield GFRα1+ spermatogonia and restore spermatogenesis, albeit at lower rates than their GFRα1+ counterparts. Together, these data provide support for a model of a stem cell pool in which the GFRα1+ and GFRα1– cells are closely related but show key cell-intrinsic differences and can interconvert between the two states based, in part, on access to niche factors., Highlights • A new method to purify GFRα1+ and GFRα1– undifferentiated spermatogonia by FACS • GFRα1+ and GFRα1– cells differ in receptor tyrosine kinase signaling • Differential surface MCAM expression can distinguish GFRα1+ and GFRα1– cells • GFRα1– cells have a third of the transplantation activity of GFRα1+ cells, In this article, Garbuzov and colleagues devise a new strategy for isolating pure populations of GFRα1+ and GFRα1– undifferentiated spermatogonia from adult testis of TertTomato reporter mice based on expression of telomerase and GFRα1. Transcriptional profiling showed a remarkable similarity between GFRα1+ and GFRα1– cells, and both populations showed elevated stem cell activity by transplantation.

Summary Genome-edited human pluripotent stem cells (hPSCs) have broad applications in disease modeling, drug discovery, and regenerative medicine. We present and characterize a robust method for rapid, scarless introduction or correction of disease-associated variants in hPSCs using CRISPR/Cas9. Utilizing non-integrated plasmid vectors that express a puromycin N-acetyl-transferase (PAC) gene, whose expression and translation is linked to that of Cas9, we transiently select for cells based on their early levels of Cas9 protein. Under optimized conditions, co-delivery with single-stranded donor DNA enabled isolation of clonal cell populations containing both heterozygous and homozygous precise genome edits in as little as 2 weeks without requiring cell sorting or high-throughput sequencing. Edited cells isolated using this method did not contain any detectable off-target mutations and displayed expected functional phenotypes after directed differentiation. We apply the approach to a variety of genomic loci in five hPSC lines cultured using both feeder and feeder-free conditions., Graphical Abstract, Highlights • Stringent transient puromycin selection enriches for hPSCs with scarless genome edits • Clonal hPSC cell populations were isolated in as little as 2 weeks • Workflow does not require cell sorting or high-throughput sequencing • Genome editing at three disease-associated genes in five unique hPSC lines, In this article, Saha and colleagues describe a workflow for isolation of hPSC clones containing scarless, HDR-mediated, genome edits without the use of FACS or high-throughput sequencing technologies. They demonstrate that transient expression of a puromycin-resistance gene, from a non-integrated CRISPR/Cas9 plasmid, enables stringent selection for clones precisely edited with a single-stranded donor DNA template.

Summary Adrenomedullary chromaffin cells are catecholamine (CA)-producing cells originating from trunk neural crest (NC) via sympathoadrenal progenitors (SAPs). We generated NC and SAPs from human embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) in vitro via BMP2/FGF2 exposure, ascertained by qPCR and immunoexpression of SOX10, ASCL1, TFAP2α, and PHOX2B, and by fluorescence-activated cell sorting selection for p75NTR and GD2, and confirmed their trunk-like HOX gene expression. We showed that continuing BMP4 and curtailing FGF2 in vitro, augmented with corticosteroid mimetic, induced these cells to upregulate the chromaffin cell-specific marker PNMT and other CA synthesis and storage markers, and we demonstrated noradrenaline and adrenaline by Faglu and high-performance liquid chromatography. We showed these human cells' SAP-like property of migration and differentiation into cells expressing chromaffin cell markers by implanting them into avian embryos in vivo and in chorio-allantoic membrane grafts. These cells have the potential for investigating differentiation of human chromaffin cells and for modeling diseases involving this cell type., Highlights • Human ESCs and iPSCs differentiated to chromaffin cells via sympathoadrenal stage • Chromaffin-like cells are identified by PNMT expression • Adrenaline and noradrenaline production is revealed by FAGLU and by HPLC • Selection of GD2+ sympathoadrenal cells improves chromaffin cell differentiation, In this article, Newgreen and colleagues show that human pluripotent cells can be induced to form chromaffin-like cells, which produce adrenaline and noradrenaline in vitro. The method uses the dual-inhibitor method to induce neural crest progenitor and sympathoadrenal-like cells then extended BMP4 and corticosteroid exposure for the chromaffin-like stage, with curtailed FGF2 exposure to limit sympathetic neuron induction.

Cells dissociated from various tissues of vertebrate embryos preferentially reaggregate with cells from the same tissue when they are mixed together. This tissue-specific recognition process in vertebrates is mainly mediated by a family of cell adhesion molecules because of their specific binding properties. Recent studies have revealed that two families of adhesion molecules, nectins and cadherins, are associated with each other, and these associations provide cells with the differential adhesive affinities required for cellular recognition and complex cellular pattern formations during development. This review provides an overview of recent findings regarding the cooperative functions of nectins and cadherins, as well as a discussion of the molecular basis underlying these functions.

Drosophila melanogaster oogenesis is a versatile model system to address many fundamental questions of cell and developmental biology, such as stem cell biology, mitosis, meiosis or cell polarity. Many mutagenesis and powerful genetic tools have contributed massively to identify and dissect in vivo gene functions in a stage and tissue specific manner. However, the small number of germ cells during the early steps of oogenesis have hampered a systematic description of RNA and protein contents at each stage. We describe here a protocol for isolating and comparing two small subpopulations of cells in the ovary for the purpose of RNA sequence profiling. The method is based on fluorescence-activated cell sorting (FACS) of GFP- and RFP-labeled proteins that are expressed in distinct and mostly non-overlapping regions of the germline. We used a transgene expressing a GFP-tagged Bam protein driven by its own promoter, labeling specifically the mitotic region of the germarium. We also took advantage of the short-lived Wicked protein tagged with RFP and expressed under the nanos promoter to label the meiotic region. We generated flies expressing both markers and were able to sort enough cells from each region to extract total RNAs and small RNAs. Total RNA or small RNA extracted from sorted cells were then used to generate deep-sequencing libraries that show specificity toward each compartment. This method of isolating a very small number of cells and the data generated from comparing distinct cell populations within the germline should further our understanding of these conserved steps of oogenesis.

Summary Metabolism is a key regulator of hematopoietic stem cell (HSC) functions. There is a lack of real-time, non-invasive approaches to evaluate metabolism in single HSCs. Using fluorescence lifetime imaging microscopy, we developed a set of metabolic optical biomarkers (MOBs) from the auto-fluorescent properties of metabolic coenzymes NAD(P)H and FAD. The MOBs revealed the enhanced glycolysis, low oxidative metabolism, and distinct mitochondrial localization of HSCs. Importantly, the fluorescence lifetime of enzyme-bound NAD(P)H (τbound) can non-invasively monitor the glycolytic/lactate dehydrogenase activity in single HSCs. As a proof of concept for metabolism-based cell sorting, we further identified HSCs within the Lineage-cKit+Sca1+ (KLS) hematopoietic stem/progenitor population using MOBs and a machine-learning algorithm. Moreover, we revealed the dynamic changes of MOBs, and the association of longer τbound with enhanced glycolysis under HSC stemness-maintaining conditions during HSC culture. Our work thus provides a new paradigm to identify and track the metabolism of single HSCs non-invasively and in real time., Graphical Abstract, Highlights • Metabolic optical biomarkers non-invasively distinguish HSCs from early progenitors • NAD(P)H τbound reflects lactate dehydrogenase activity in single fresh/cultured HSCs • pHi correlates with τbound in hematopoietic populations, with HSCs being the highest • Optical biomarkers track metabolic changes and response to drugs in cultured HSCs, Optical Imaging; Biological Sciences; Cellular Physiology; Stem Cells Research

Glioblastoma multiforme (GBM) is the most common primary tumor of the human brain. It is characterized by invasive growth and strong resistance to treatment, and the median survival time of patients is 15 months. The invasive growth of this tumor type is associated with tumor cells with an aggressive phenotype, while its treatment resistance is attributed to cancer stem cells (CSCs). It remains unclear if CSCs have a more invasive nature than differentiated glioblastoma cells (DGCs), and what contribution CSCs make to the aggressive phenotype of GBM. Interaction with the extracellular matrix (ECM) is a key factor in the development of invasion. The aim of the present study was to compare the expression levels of signaling pathway proteins involved in interaction of receptors with the ECM in CSCs and DGCs. The U-87MG GBM cell line was used in the present study CSCs were extracted from gliomaspheres through magnetic-activated cell sorting based on the expression of cluster of differentiation 133 (CD133); CD133-negative DCGs were used as a control. HPLC and mass spectrometry were also used, and biological and molecular functions, signaling pathways and protein-protein interactions were analyzed using publicly available databases. Increased expression levels of the following 10 proteins involved in interaction with the ECM were identified in CSCs, compared with expression levels in DGCs: COL6A1, COL6A3, FN1, ITGA2, ITGA5, ITGAV, ITGB1, ITGB3, LAMB1 and LAMC1. The proteome of CSCs was observed to have >2-fold higher expression of these key proteins, when compared with the DGC proteome. Increased expression levels of four proteins (FERMT2, LOXL2, HDAC2 and FBN1) involved in activating signaling in response to receptor interaction with the ECM was also observed, indicating that CSCs may have highly invasive nature. LOXL2 expression level was >9-fold higher in CSCs compared to DGCs, suggesting that this protein may have potential as an marker for CSCs and as a target for this cell type in GBM.

To develop an iPSC SOX9 reporter line for monitoring differentiation into SOX9 expressing cells such as chondrocytes, cranial neural crest and Sertoli cells, we used gene editing to introduce sequences encoding the tdTomato fluorescent protein into the SOX9 locus. The gene-edited line had a normal karyotype, expressed pluripotency markers and differentiated into cells representative of the three embryonic germ layers. Endogenous SOX9 expression was undisturbed and the tdTomato fluorescent reporter mirrored SOX9 mRNA expression. This iPSC line will be useful for assessing iPSC differentiation into SOX9-expressing cells and enrichment by cell sorting.

Understanding the roles that individual species or communities play within a microbiome is a significant challenge. The complexity and heterogeneity of microbiomes presents a challenge to researchers looking to unravel the function that microbiomes serve within larger environments. While identification of the species and proteins present in a microbiome can be accomplished through genomics approaches, strategies that report on enzyme activity are limited. In this chapter, we describe the application of small molecule chemical probes in the isolation and subsequent characterization of microbiome subpopulations based on enzymatic function. We will cover protocols for labeling microbes with appropriate probes, microbiome sample preparation, and using fluorescence-activated cell sorting to isolate subpopulations based on function. We hope that the strategies outlined here will serve as a resource for researchers studying the functional role that microbiomes play in the gut and soil.

The incidence of chronic, non-healing skin wounds is accelerating, largely due to the epidemic of obesity-related Type 2 diabetes. Abnormal inflammation in wounds contributes to delayed healing. During wound repair, blood monocytes are recruited into the wound bed where they differentiate into macrophages that secrete cytokines and regulate subsequent repair events. Because the study of wound macrophages via immunohistochemistry is often unsatisfactory due to nonspecific antibody staining, the ability to isolate and analyze single cells is important for determining the phenotypes of the wound macrophages. In this article, we have expanded upon a protocol originally described by Wilson et al, 2002 [1], and optimized it for isolation of large numbers of viable macrophages from murine skin wounds that are suitable for flow cytometric cell sorting or analysis. Several parameters were found to be critical for improved macrophage yields, including: (1) The proper amount of starting material (skin tissue); (2) The optimal time for addition of Brefeldin A during enzymatic digestion; (3) Revamped guidelines for centrifugation to maximize cell pellet recovery. This optimized protocol could be further modified to perform cell sorting and flow-based immunophenotyping of any cell type involved in wound healing and inflammation., Graphical abstract Image, graphical abstract

Since its conception in the 1950s by Waddington and others, the role of epigenetics in various processes such as cellular development, differentiation, metabolism, and disease has been extensively studied. Epigenetic regulation enables a select set of genes to be expressed within each cell during development and differentiation by covalently modifying DNA and histones while keeping the DNA sequence unchanged. Various technical advancements, such as high-speed cell sorting and high-throughput genome-wide analyses of gene expression profiles and occupancy profiles of chromatin-based factors, have led to unraveling of the epigenetic mechanisms regulating immune cell development. In this chapter, we explicate the influence of histone/DNA modifications on chromatin landscape and gene expression. Further, we discuss how spatiotemporal modulation of chromatin accessibility plays a key role toward development and differentiation of various immune cell types, and how only a handful of chromatin-based factors can specifically determine this outcome. We describe the epigenetic regulatory mechanisms orchestrating the development, differentiation, and effector functions of various innate cells including natural killer (NK) cells, macrophages, and dendritic cells (DC) from hematopoietic stem cells (HSCs), followed by B and T adaptive immune cells arising from common lymphoid progenitors (CLPs). We further elaborate how chromatin accessibility is altered during activation and memory formation in these lineages. We also discuss the effect of long-distance or transregulation of gene expression in the context of the immune cells, with focus on Special AT-rich binding protein 1 (SATB1) as the T lineage-enriched global chromatin organizer. Finally, using an example of the TH2 cytokine cluster, we demonstrate how SATB1 integrates higher-order chromatin organization and gene regulation. The ongoing developments in the analysis of epigenetic components and regulatory mechanisms at a single-cell resolution hold great promise in providing novel cues toward understanding the cell type-specific dynamic epigenetic landscape pertaining to each cell state.

Biomaterials and cells are essential components of almost every tissue-engineering approach for the repair or replacement of injured or missing tissue. Until recently, the host response to these materials and cells has been considered as a proinflammatory phenomenon to be suppressed to the extent possible. However, technological advances in immunolabeling, cell sorting, genomics, and proteomics among other laboratory techniques have revealed the essential roles of the immune system in tissue and organ development, homeostasis, and stem cell recruitment, proliferation, and differentiation; processes of interest and importance to tissue engineering (TE) and regenerative medicine. The present chapter reviews the role of individual immune cell in the context of TE and remodeling, specialized functions and signaling mechanisms of these immune cells, and current methods for manipulating immune cell activity to achieve better outcomes.

Human endothelial cells (ECs) are important tools in research and development of new therapies in the fields of angiogenesis, vasculogenesis, engineering organoids and multicellular tissues, drug discovery, and disease modeling. Efficient and robust induction of ECs from human pluripotent stem cells (hPSCs) serve as a renewable and indefinite cell sources. However, individual lines of embryonic stem cells (hESCs) and induced pluripotent stem cells (iPSCs) are distinct and can often respond very differently to the same microenvironmental cues. Therefore, we set out to develop a differentiation methodology specifically designed for robustness across multiple human iPSC lines. In general, the key soluble signals remain consistent across cell lines, but because the differentiation and proliferation kinetics can differ slightly in hESC and iPSC cell lines, the time point for KDR+ cell sorting must be pre-determined for each cell line. This three-stage induction method uses three different chemically defined medium formulations and generates highly purified populations of actively proliferating and functional VE-cadherin+ ECs within 30 days. Keywords: Cell fate, Differentiation, Stem cells, Vascular progenitor cells, Endothelial cells