Cell Sorting Research Articles

Defining an Optimized Workflow for Enriching and Analyzing Residual Tumor Populations Using Intracellular Markers

Tumor relapse is well-recognized to arise from treatment-resistant residual populations. Strategies enriching such populations for in-depth downstream analyses focus on tumor-specific surface markers; however, enrichment using intracellular biomarkers remains challenging. Using B-cell lymphoma as an exemplar, we demonstrate feasibility to enrich BCL2high populations, a surrogate marker for t(14;18)+ lymphomas, for use in downstream applications. Different fixation protocols were assessed for impact on antibody expression and RNA integrity; glyoxal fixation demonstrated superior results regarding minimal effects on surface and intracellular expression, and RNA quality, compared to alternative fixatives evaluated. Furthermore, t(14;18)+ B-cells were effectively detected using intracellular BCL2 over-expression to facilitate tumor cell enrichment. Tumor cell populations were enriched using the cellenONE F1.4 single cell sorting platform, which detected and dispensed BCL2high-expressing cells directly into library preparation reagents for transcriptome analyses. Sorted glyoxal-fixed cells generated good quality sequencing libraries, with high concordance between live and fixed single cell transcriptomic profiles, discriminating cell populations predominantly on B-cell biology. Overall, we successfully develop a proof-of-concept workflow employing a robust cell preparation protocol for intracellular markers combined with cell enrichment using the cellenONE platform, providing an alternative to droplet-based technologies when cellular input is low or requires prior enrichment to detect rare populations. This workflow has wider prognostic and therapeutic potential to study residual cells in a pan-cancer setting.

Numerical and experimental characterization of a piezoelectric actuator for microfluidic cell sorting

Piezoelectric actuators offer great opportunities for precise and low-cost control of fluids at the microscale. Microfluidic systems with integrated piezoelectric actuators find application as droplet generators, micropumps, and microsorters. To accelerate device design and optimization, modeling and simulation approaches represent an attractive tool, but there are challenges arising from the multiphysics nature of the problem. Simple, potentially real-time approaches to experimentally characterize the fluid response to piezoelectric actuation are also highly desirable. In this work, we propose a strategy for the numerical and experimental characterization of a piezoelectric microfluidic cell sorter. Specifically, we present a 3D coupled multiphysics finite-element model of the system and an easy image-based approach for flow monitoring. Sinusoidal and pulse actuation are considered as case studies to test the proposed methodology. The results demonstrate the validity of the approach as well as the suitability of the system for cell sorting applications.

In Vivo Studies and Flow Cytometric Investigation on Anticancer Potential of Selenium Nanoparticles Synthesized via Aqueous Extract of Clerodendron phlomidis

Nowadays, doctors and nutritionists recommend individuals incorporate selenium-rich foods such as nuts, cereals, and mushrooms into their regular diet to maintain fitness and overall health. Selenium nanoparticles (SeNPs) exhibit strong chemopreventive capabilities. The anticipations for SeNPs with enhanced and tunable bioactive activities have led to a keen interest in phytofabrication. In this study, the aqueous extract of Clerodendron phlomidis plant leaves was utilized for the synthesis of SeNPs. In traditional Indian medicine, this plant extract is recognized as a significant anti-diabetic agent. The flavonoids tetrahydroxylflavone, 7-hydroxyflavanone, and 6,4’-dimethyl-7-acetoxy-scutellarein present in this plant leaf extract demonstrate excellent anticancer activity. These secondary metabolites exhibit the ability to reduce sodium selenite into SeNPs. At a concentration of 13 µg/mL, the synthesized SeNPs effectively inhibited the proliferation of the HepG2 cell line. The results suggest that the SeNPs possess promising anti-cancer potential against liver cancer and can be considered as a therapeutic agent for liver cancer treatment. Additionally, the cell cycle arrest induced by SeNPs was further confirmed by the fluorescence-activated cell sorting (FACS) method, indicating that SeNPs could efficiently differentiate cancer cells from normal cells. Notably, it showed a significant improvement in diethylnitrosamine (DEN)-induced Swiss Wistar rat groups. This scientific investigation highlights the high anti-cancer potential of SeNPs, positioning them as a promising therapeutic agent for liver cancer treatment.

Screening of astaxanthin-overproducing Xanthophyllomyces dendrorhous strains via iterative ARTP mutagenesis and cell sorting by flow cytometry.

The astaxanthin-producing yeast Xanthophyllomyces dendrorhous is widely used in aquaculture. Due to the production of carotenoid, this yeast shows visible color; however, high-throughput approaches for identification of astaxanthin-overproducing strains remain rare. This study verified an effective approach to identify astaxanthin-overproducing mutants of X. dendrorhous by flow cytometry (FCM) and cell sorting. First, the mutant libraries were generated by atmospheric and room-temperature plasma (ARTP) mutagenesis. Second, a highly direct correlation between the concentrations of intracellular astaxanthin and the levels of emitting fluorescence was constructed by testing a variety of astaxanthin-contained populations via FCM and cell sorting. Third, iterative cell sorting efficiently improves the identification of astaxanthin-overproducing strains. Finally, two mutants producing 4.96mg astaxanthin g-1 DCW (dry cell weight) and 5.30mg astaxanthin g-1 DCW were obtained, which were 25.3% and 33.8% higher than that of the original strain, respectively. This study demonstrated that iterative ARTP mutagenesis along with cell sorting by FCM is effective for identifying astaxanthin-overproduction strains.

Anti-Inflammatory Effect of Synaptamide in Ischemic Acute Kidney Injury and the Role of G-Protein-Coupled Receptor 110.

The development of drugs for the treatment of acute kidney injury (AKI) that could suppress the excessive inflammatory response in damaged kidneys is an important clinical challenge. Recently, synaptamide (N-docosahexaenoylethanolamine) has been shown to exert anti-inflammatory and neurogenic properties. The aim of this study was to investigate the anti-inflammatory effect of synaptamide in ischemic AKI. For this purpose, we analyzed the expression of inflammatory mediators and the infiltration of different leukocyte populations into the kidney after injury, evaluated the expression of the putative synaptamide receptor G-protein-coupled receptor 110 (GPR110), and isolated a population of CD11b/c+ cells mainly representing neutrophils and macrophages using cell sorting. We also evaluated the severity of AKI during synaptamide therapy and the serum metabolic profile. We demonstrated that synaptamide reduced the level of pro-inflammatory interleukins and the expression of integrin CD11a in kidney tissue after injury. We found that the administration of synaptamide increased the expression of its receptor GPR110 in both total kidney tissue and renal CD11b/c+ cells that was associated with the reduced production of pro-inflammatory interleukins in these cells. Thus, we demonstrated that synaptamide therapy mitigates the inflammatory response in kidney tissue during ischemic AKI, which can be achieved through GPR110 signaling in neutrophils and a reduction in these cells' pro-inflammatory interleukin production.

Cold dispase digestion of murine lungs improves recovery and culture of airway epithelial cells.

Airway epithelial cells (AECs) play a key role in maintaining lung homeostasis, epithelium regeneration and the initiation of pulmonary immune responses. To isolate and study murine AECs investigators have classically used short and hot (1h 37°C) digestion protocols. Here, we present a workflow for efficient AECs isolation and culture, utilizing long and cold (20h 4°C) dispase II digestion of murine lungs. This protocol yields a greater number of viable AECs compared to an established 1h 37°C dispase II digestion. Using a combination of flow cytometry and immunofluorescent microscopy, we demonstrate that compared to the established method, the cold digestion allows for recovery of a 3-fold higher number of CD45-CD31-EpCAM+ cells from murine lungs. Their viability is increased compared to established protocols, they can be isolated in larger numbers by magnetic-activated cell sorting (MACS), and they result in greater numbers of distal airway stem cell (DASC) KRT5+p63+ colonies in vitro. Our findings demonstrate that temperature and duration of murine lung enzymatic digestion have a considerable impact on AEC yield, viability, and ability to form colonies in vitro. We believe this workflow will be helpful for studying lung AECs and their role in the biology of lung.

OP04 Endoscopic healing in paediatric IBD perpetuates a persistent signature characterized by pathogenic Th17 cells and tissue-associated molecular and microbial drivers of disease

Abstract Background Endoscopic healing (EH) is the major long-term treatment target for inflammatory bowel diseases (IBD) in adults and paediatric patients. However, EH may not represent disease clearance. Hence, risk of relapse remains high and treatment discontinuation after reaching EH often results in disease exacerbation. We aimed to identify persistent cellular, molecular and microbial drivers of IBD under EH and longitudinally collected endoscopic biopsies from paediatric patients for analysis of single T-cell and bulk transcriptomics as well as mucosa-associated microbiota. Methods We followed disease trajectories of paediatric IBD patients treated according to international guidelines and collected mucosal biopsies from the terminal ileum (TI) and sigmoid colon (SC) at baseline (T1) and after approximately 3-12 months (T2) to assess EH. Non-IBD controls showed no macroscopic or histologic signs of inflammation. Host RNA and bacterial DNA were simultaneously extracted from single biopsies for bulk RNA-seq, and 16S rRNA seq. A second biopsy was used for isolation of lamina propria mononuclear cells (LPMCs), followed by CD45+, CD3+ cell sorting and single T-cell analysis (10X Genomics). Data were quality controlled and integrated. Results 217 biopsies (135 simultaneous extraction of host RNA and bacterial DNA; 82 single T-cell analysis) from 32 paediatric IBD patients (mean age 13 ± 3.5 years, 21 Crohn’s disease [CD], 11 ulcerative colitis [UC]; T1 = 32, T2 = 32, T > 2 = 6) and 5 non-IBD controls were analysed. Time between T1 and T2 averages 40 ± 22 weeks. At baseline, 15 patients (14 CD, 1 UC) were newly diagnosed and 31/32 patients had active mucosal inflammation. Twenty-two patients (71%) achieved EH at T2 (SES-CED ≤2 and absence of ulcerations), mostly on anti-TNF therapy. One patient (EH at T1) experienced relapsing disease within 10 weeks after discontinuing medication. In the bulk RNA-seq, we identified 299 differential expressed genes (DEGs; corrected p-value <0.05, FC >2.0), such as DUOX2, SAA2-SAA4, FCGR3B and NOS2, that are associated with active IBD and remained upregulated in EH in contrast to non-IBD controls. In addition single cell analysis revealed an IBD-specific pathogenic Th17 cluster that continued to exist in EH and showed high correlation with top DEGs after data integration. 16S rRNA gene seq highlighted highly individual mucosa-associated bacterial profiles and a reduced α-diversity in active and EH compared to non-IBD controls. Conclusion A persisting IBD signature in EH reflects ongoing cellular, molecular and microbial activity in comparison to non-IBD controls despite EH and mucosal regeneration. These markers may provide targets for future or sequential therapies.

P061 The macrophage-specific role of PTPN23 in Acute and Chronic Colitis

Abstract Background Single nucleotide polymorphisms within the gene locus encoding PTPN2, are associated with Crohn’s disease and ulcerative colitis. We have previously shown that, deletion of PTPN2 results in PTPN23 upregulation in intestinal epithelial cells (IEC) in vivo. PTPN23 is known to be involved in endosomal sorting and responsible for epidermal growth factor receptor (EGFR) internalization from the cell surface and thus negatively controls EGFR signalling in epithelial cells. Though PTPN23 is highly expressed in IEC and intestinal macrophages, nothing is known about its function in myeloid cells and its role in intestinal inflammation. Methods Experimental colitis was induced in PTPN23fl/flLysMCre+/- (KO) and PTPN23fl/flLysMCre-/- (WT) littermates by administration of 2% DSS in drinking water for 7 days (acute colitis) or for 4 cycles of 1.5% DSS for 7 days followed by 10 days recovery, each (chronic colitis). Immune cells were isolated from spleen and colon lamina propria from KO and WT mice and PTPN23 expression was detected by qPCR of RNA isolated after cell sorting with flow cytometry. Results The mRNA expression of PTPN23 in untreated WT mice was significantly higher in macrophages isolated from the lamina propria of the colon than in those isolated from spleen (p=0.0279). PTPN23fl/flLysMCre+/- (KO) mice were protected from DSS-induced acute colitis when compared to their WT littermates. This was apparent by a lack of DSS-induced weight loss (p=0.02); longer colon length (p=0.01), reduced endoscopic colitis scores (p=0.0016) and lower spleen weights (p=0.0063) in KO mice. In HE staining of colon tissue, the loss of crypts was less pronounced in KO mice. On mRNA level a lower expression of the pro-inflammatory cytokines interleukin 6 (IL-6) (p=0.0117) and tumour necrosis factor α (TNFα) (p=0.0024) was observed in KO compared to WT mice, supporting a reduced inflammatory response. In chronic colitis the same trends was observed, however the effects were less pronounced. WT mice lost more weight during the DSS cycles compared to KO mice, whereas no difference in weight development was detected between the genotypes in water control groups. Higher MEICSs scores were observed in WT compared to KO mice (p<0.0001) and loss of colonic crypts was more pronounced in HE stained colon samples in WT mice than KO mice. Conclusion PTPN23 deletion in myeloid cells results in protection from DSS-induced acute and chronic colitis. Additionally, a higher expression in intestinal macrophages compared to macrophages isolated from the spleen suggest a specific role in the intestinal immune system.

Microfluidics-assisted Tumor Cell Separation Approaches for Clinical Applications: An Overview on Emerging Devices.

Recent advances in science and technology have led to revolutions in many different scientific and industrial fields. The term lab on a chip, or in other word, performing a variety of complex analyzes in just a short time and in a very small space, is a term that has become very common in recent years, and what used to be a dream has now come to life in practice. In this paper, we has been tried to investigate a specific type of lab technology on a chip, which is of course one of the most common, namely the knowledge and technology of cell separation by using microfluidic technique that can be separated based on size and deformation, adhesion and electrical properties. The tissue of the human body is degraded due to injury or aging, which is often tried to treat this tissue disorder by using drugs, but they are not always enough. Stem cell-based medicine is a novel form of medicine which promises the restoration or regeneration of tissues and functioning organs. Although many models of microfluidic systems have been designed for cell separation, the choice of appropriate device to achieve a reliable result is presented as a challenge. So, in this study, Fluorescence Activated Cell Sorting (FACS), Dielectrophoresis (DEP), Magnetic Activated Cell Sorting (MACS) and Acoustic microfluidic system are four distinct categories of active microfluidic systems explored. Also, the advantages, disadvantages and the current status of the mentioned devices in these methods, are reviewed.

P031 Microbiota-driven appendiceal B lymphocytes aggravate DSS-induced murine colitis through facilitating colonic CD4+ T cells polarization

Abstract Background The appendix is an immunological organ sustaining a microbiome inoculum that plays a vital role in intestinal mucosal immunity and colonic microbiome stability. Previous studies have proposed the appendix exerts effects on ulcerative colitis (UC)’s pathogenesis, but the nature and basis underlying this connection remain unclear. B lymphocytes account for the largest proportion of appendiceal immunocytes and activate in the experimental colitis model, we systematically investigated how appendiceal B lymphocytes (appB) participate in UC’s pathogenesis and provided rational evidence for appendectomy and B cell immunotherapy being used in UC treatments. Methods The chronic colitis model was established in C57BL/6J mice by three cycles of 2% dextran sodium sulfate (DSS) treatment. Bulk RNA sequencing and 16S rRNA sequencing were used to explore appB’s characteristics and the potential causes of appB activation in DSS-induced colitis. Adoptive appB transfer and intravital imaging were used to evaluate appB’s homing and functional features in DSS-induced chronic colitis. Magnetic microbead-based cell sorting and cells experiments in vitro were used to investigate the underlying mechanisms of appB’s activation and effects on DSS-induced chronic colitis. Flow cytometry was used to assess the colonic mucosal adaptive immunity alterations in colitis mice adopted appB. Results Firmicutes and Bacteroidetes are the dominant phylum in the normal appendix, while Firmicutes, Verrucomicrobia, and Proteobacteria are prominent in the colitis appendix. The appendiceal IgG+ B cells expended in colitis mice compared with the normal mice; and the DSS colitis appB (DSS_appB), compared with the normal control appB (NC_appB), had much more potential to migrate to the colon and fired the gut flare, accompanied by the increment of CD19+ IgG+ cells, CD4+ IFN-γ+ cells and CD4+ IL-17+ cells in the colonic lamina propria in colitis mice. In vitro, DSS_appB secreted more inflammatory cytokines (IFN-γ, IL-6) than NC_appB under the stimulation of Toll-like receptor agonist analogs (Pam3CSK4, LPS, and ODN1826); DSS_appB facilitated colonic CD4+ T cells to secrete IFN-γ and IL-17 by up-regulating surface marker (CD80/86) and secreting IFN-γ and IL-6. Conclusion In DSS-induced chronic colitis mice, appB activated, driven by appendiceal microbiota,migrated to the colonic lamina propria and aggravated colitis through facilitating CD4+ Tcells polarize to Th1 and Th17 by up-regulating CD80/86 and secreting IFN-γ and IL-6 (Figure 1). Our research provides evidence for the connection between the appendix and UC, and we propose that appendectomy or B cell immunotherapy is promising to treat UC.

P009 IL-17 mediates visceral hypersensitivity by sensitising colonic nociceptors

Abstract Background Comparison of cytokine expression in colitic tissue with respective cytokine receptor expression in pain sensing neurons highlights a likely contribution of IL-17 to the production of abdominal pain during flare. To explore this pro-nociceptive potential of IL-17 in colitis we examined the ability of IL-17 to stimulate sensory neurons and the colonic afferent response to noxious distension. Methods IL-17 mediated sensory neuron activation: changes in the intracellular [Ca2+]i within thoracolumbar (T12-L5 spinal segments) dorsal root ganglia sensory neurons were examined in cells cultured overnight and loaded with Fluo-4-AM (30min) prior to imaging. Responses were measured to IL-17 (10-300 ng/mL) alone and following pre-treatment with either TRPV1 or TRPA1 inhibitors. Afterwards cells were exposed to capsaicin (1 µM) followed by 50 mM KCl, to confirm the presence of nociceptors and neurons respectively by positive response. In a separate set of experiments the effect of IL-17 was also examine on a neuron pure cell culture in which non-neuronal cells were removes by magnet assisted cell sorting. IL-17 mediated colonic nociceptor activation: electrophysiological recordings were made of lumbar splanchnic nerve activity and the response to noxious luminal distension of the isolated colorectum (ex-vivo), perfused with carbogenated Krebs solution, examined following pre-treatment with IL-17 (50 ng/mL) alone or in the presence of respective inhibitors. All experiments were performed using tissue from male C57BL/6J mice euthanaised by rising concentration of CO2followed by exsanguination in accordance with Schedule 1 of the UK Animals Scientific Procedures act (1986). Results Consistent with the ability of IL-17 to stimulate sensory neurons including those classified as nociceptors by their co-sensitivity to capsaicin, pre-treatment with IL-17 also produced a significant sensitisation of the colonic afferent response to luminal distension at noxious distending pressures. The increase in [Ca2+]i produced by IL-17 in sensory neurons was blocked by pre-treament with a TRPV1 antagonist but not a TRPA1 antagonist. Furthermore, the proportion of neurons stimulated by IL-17 was comparable between standard DRG cell cultures and neuron pure cell cultures demonstrating a direct effect of IL-17 on sensory neurons. Finally, IL-17 mediated mechanosensitisation of colonic nociceptors was unaffected by TRPV1 inhibition. Conclusion Our findings demonstrate that IL-17 stimulates capsaicin-sensitive nociceptors and mediates visceral hypersensitivity in colonic nociceptors consistent with a causative role for IL-17 is the generation of abdominal pain in people with colitis.

P057 Caudovirales may trigger molecular mimicry mechanisms in Crohn’s Disease

Abstract Background The gut virome is known to play a role in the development of Crohn's disease (CD), a type of Inflammatory Bowel Disease (IBD). Several years ago, Norman and colleagues observed an expansion of Caudovirales linked to CD pathogenesis, alongside a reduction in bacterial diversity. To delve deeper, we exploited the IBD TaMMA framework and observed a significantly higher abundance of Caudovirales in the CD individuals compared to healthy controls, confirming earlier findings. Methods To further examine the involvement of this viral species in various mucosal cell compartments, we conducted flow cytometry cell sorting (FACS) on intestinal biopsies from CD and healthy individuals. Isolated immune and non-immune cells based on population-specific markers, including CD8 and CD4 T cells, B cells, macrophages, dendritic cells, epithelium, endothelium, and fibroblasts underwent transcriptomics and metatranscriptomics. Results We identified higher abundance of the Proteus virus Isfahan, belonging to Caudovirales viral order, in CD dendritic cells and CD macrophages compared to their healthy counterparts. Notably, gene ontology (GO) analysis indicated that only CD dendritic cells, fibroblasts, and epithelial cells exhibited compromised biological responses to viral insults compared to their healthy counterparts. In contrast, CD macrophages displayed upregulation of molecular pathways regulating viral processes. This suggests that virome dysbiosis in these cells may contribute to CD pathogenesis by altering their biological functions. We thus wondered whether Proteus virus Isfahan encoded proteins had similarities with the human ones, somehow establishing molecular mimicry justifying the likelihood of the autoimmune nature of CD. We observed sequence homology in the Proteus virus Isfahan and the human thymidylate synthase, RECQ-like DNA helicase, and dCMP deaminase. These viral proteins are likely to be recognized by the immune system by sharing similarities with the human homologs, thus activating autoreactive immune response and establishing the persistent chronic inflammatory environment within CD mucosa. Experiments employing T helper cells in coculture with Proteus virus Isfahan proteins-overexpressing innate immune cells are ongoing to prove the autoreactive activation of the host’s immunity. Conclusion Given the growing evidence of viral entities as triggers for IBD, these data could pave the way for discovering viruses directly involved in CD pathogenesis and serving as the booster for molecular mimicry mechanisms, finally providing potential targets for novel intervention strategies that may improve CD management.

Predicting Anaerobic Membrane Bioreactor Performance Using Flow-Cytometry-Derived High and Low Nucleic Acid Content Cells.

Having a tool to monitor the microbial abundances rapidly and to utilize the data to predict the reactor performance would facilitate the operation of an anaerobic membrane bioreactor (AnMBR). This study aims to achieve the aforementioned scenario by developing a linear regression model that incorporates a time-lagging mode. The model uses low nucleic acid (LNA) cell numbers and the ratio of high nucleic acid (HNA) to LNA cells as an input data set. First, the model was trained using data sets obtained from a 35 L pilot-scale AnMBR. The model was able to predict the chemical oxygen demand (COD) removal efficiency and methane production 3.5 days in advance. Subsequent validation of the model using flow cytometry (FCM)-derived data (at time t - 3.5 days) obtained from another biologically independent reactor did not exhibit any substantial difference between predicted and actual measurements of reactor performance at time t. Further cell sorting, 16S rRNA gene sequencing, and correlation analysis partly attributed this accurate prediction to HNA genera (e.g., Anaerovibrio and unclassified Bacteroidales) and LNA genera (e.g., Achromobacter, Ochrobactrum, and unclassified Anaerolineae). In summary, our findings suggest that HNA and LNA cell routine enumeration, along with the trained model, can derive a fast approach to predict the AnMBR performance.

Interleukin 21 Drives a Hypermetabolic State and CD4+ T-Cell–Associated Pathogenicity in Chronic Intestinal Inflammation

Incapacitated regulatory T cells (Tregs) contribute to immune-mediated diseases. Inflammatory Tregs are evident during human inflammatory bowel disease; however, mechanisms driving the development of these cells and their function are not well understood. Therefore, we investigated the role of cellular metabolism in Tregs relevant to gut homeostasis. Using human Tregs, we performed mitochondrial ultrastructural studies via electron microscopy and confocal imaging, biochemical and protein analyses using proximity ligation assay, immunoblotting, mass cytometry and fluorescence-activated cell sorting, metabolomics, gene expression analysis, and real-time metabolic profiling utilizing the Seahorse XF analyzer. We used a Crohn's disease single-cell RNA sequencing dataset to infer the therapeutic relevance of targeting metabolic pathways in inflammatory Tregs. We examined the superior functionality of genetically modified Tregs in CD4+ T-cell-induced murine colitis models. Mitochondria-endoplasmic reticulum appositions, known to mediate pyruvate entry into mitochondria via voltage-dependent anion channel 1 (VDAC1), are abundant in Tregs. VDAC1 inhibition perturbed pyruvate metabolism, eliciting sensitization to other inflammatory signals reversible by membrane-permeable methyl pyruvate supplementation. Notably, interleukin (IL) 21 diminished mitochondria-endoplasmic reticulum appositions, resulting in enhanced enzymatic function of glycogen synthase kinase 3 β, a putative negative regulator of VDAC1, and a hypermetabolic state that amplified Treg inflammatory response. Methyl pyruvate and glycogen synthase kinase 3 β pharmacologic inhibitor (LY2090314) reversed IL21-induced metabolic rewiring and inflammatory state. Moreover, IL21-induced metabolic genes in Tregs invitro were enriched in human Crohn's disease intestinal Tregs. Adoptively transferred Il21r-/- Tregs efficiently rescued murine colitis in contrast to wild-type Tregs. IL21 triggers metabolic dysfunction associated with Treg inflammatory response. Inhibiting IL21-induced metabolism in Tregs may mitigate CD4+ T-cell-driven chronic intestinal inflammation.

Enriching new transplantable RGC-like cells from retinal organoids for RGC replacement therapy

Optic neuropathies, such as glaucoma, are due to progressive retinal ganglion cells (RGCs) degeneration, result in irreversible vision loss. The promising RGCs replacement therapy for restoring vision are impeded by insufficient RGC-like cells sources. The present work was enriched one new type RGC-like cells using two surface markers CD184 and CD171 from human induced pluripotent stem cells (hiPSCs) by FACS sorting firstly. These new kind cells have well proliferation ability and possessed passage tolerance in vitro 2D or 3D spheroids culture, which kept expressing Pax6, Brn3b and βIII-Tubulin and so on. The transplanted CD184+CD171+ RGC-like cells could survive and integrate into the normal and optic nerve crush (ONC) mice retina, especially they were more inclined to across the optic nerve head and extend to the damaged optic nerve. These data support the feasible application for cell replacement therapy in RGC degenerative diseases, as well as help to develop new commercial cells sorting reagents and establish good manufacturing practice (GMP) grade RGC-like donor cells for further clinical application.

Combination Screening of a Naïve Antibody Library Using E. coli Display and Single-Step Colony Assay

The use of single-domain camelid antibodies, termed VHHs or nanobodies, has found increasing application in diagnosis, pharmaceutical development, and research because of their superior properties, such as small size, elevated stability, high water solubility, and excellent affinity for the antigen. Antigen-specific VHHs are generated by screening VHH display libraries via bio-panning. However, the bio-panning step needs to be repeated multiple times, which is time-consuming and laborious. Here, we developed a simple and rapid screening method that combined Escherichia coli display and a single-step colony assay to successfully identify positive clones from a naïve VHH library. The library was constructed from peripheral blood mononuclear cells of alpaca, and VHHs were displayed on the surface of E. coli using the inverse autotransporter intimin. Libraries enriched by magnetic cell sorting were screened directly using a single-step colony assay. Colonies formed on the hydrophilic filter and antigen-coated membrane. The expression of VHHs was induced, and those bound to the antigen on the membrane were detected as positive clones. Screening and identification of positive clones required only two days, which saves considerable time and resources compared to existing protocols.

DNA methylation and chromatin accessibility predict age in the domestic dog.

Across mammals, the epigenome is highly predictive of chronological age. These "epigenetic clocks," most of which have been built using DNA methylation (DNAm) profiles, have gained traction as biomarkers of aging and organismal health. While the ability of DNAm to predict chronological age has been repeatedly demonstrated, the ability of other epigenetic features to predict age remains unclear. Here, we use two types of epigenetic information-DNAm, and chromatin accessibility as measured by ATAC-seq-to develop age predictors in peripheral blood mononuclear cells sampled from a population of domesticated dogs. We measured DNAm and ATAC-seq profiles for 71 dogs, building separate predictive clocks from each, as well as the combined dataset. We also use fluorescence-assisted cell sorting to quantify major lymphoid populations for each sample. We found that chromatin accessibility can accurately predict chronological age (R2 ATAC = 26%), though less accurately than the DNAm clock (R2 DNAm = 33%), and the clock built from the combined datasets was comparable to both (R2 combined = 29%). We also observed various populations of CD62L+ T cells significantly correlated with dog age. Finally, we found that all three clocks selected features that were in or near at least two protein-coding genes: BAIAP2 and SCARF2, both previously implicated in processes related to cognitive or neurological impairment. Taken together, these results highlight the potential of chromatin accessibility as a complementary epigenetic resource for modeling and investigating biologic age.

Ultrahigh-throughput screening-assisted in vivo directed evolution for enzyme engineering.

Classical directed evolution is a powerful approach for engineering biomolecules with improved or novel functions. However, it traditionally relies on labour- and time-intensive iterative cycles, due in part to the need for multiple molecular biology steps, including DNA transformation, and limited screening throughput. In this study, we present an ultrahigh throughput in vivo continuous directed evolution system with thermosensitive inducible tunability, which is based on error-prone DNA polymerase expression modulated by engineered thermal-responsive repressor cI857, and genomic MutS mutant with temperature-sensitive defect for fixation of mutations in Escherichia coli. We demonstrated the success of the in vivo evolution platform with β-lactamase as a model, with an approximately 600-fold increase in the targeted mutation rate. Furthermore, the platform was combined with ultrahigh-throughput screening methods and employed to evolve α-amylase and the resveratrol biosynthetic pathway. After iterative rounds of enrichment, a mutant with a 48.3% improvement in α-amylase activity was identified via microfluidic droplet screening. In addition, when coupled with an in vivo biosensor in the resveratrol biosynthetic pathway, a variant with 1.7-fold higher resveratrol production was selected by fluorescence-activated cell sorting. In this study, thermal-responsive targeted mutagenesis coupled with ultrahigh-throughput screening was developed for the rapid evolution of enzymes and biosynthetic pathways.

IMN041 is an immunotherapeutic and an effective treatment in mouse xenograft models of pancreatic cancer, renal cancer and triple negative breast cancer

BackgroundiMN013 (5-aza-2',2'-difluorodeoxycytidine), a DNA methyl transferase inhibitor and ribonucleotide reductase inhibitor, and its prodrug iMN041 (3',5'-di-trimethylsilyl-2',2'-difluro-5- azadeoxycytidine), have been shown to be active in mouse xenograft models of hematogenous and solid tumors. In a xenograft of non-small cell lung cancer (NCI-H460), iMN041 treated mice demonstrated a marked inflammatory response upon analysis of tumor histology, which was hypothesized to be mediated by upregulation of natural killer (NK) cells. This study aimed to characterize the antitumor immune responses generated by iMN041 and test the efficacy iMN041 in solid tumors with poor prognosis.MethodsIn the Renca syngeneic mouse model, tumors were harvested following two doses of iMN041 or vehicle control, and analyzed by fluorescent-activated cell sorting for an antitumor immune response. iMN041 was also tested for tumor growth inhibition and animal survival for up to 42 days in xenograft models of pancreatic, renal, and triple negative breast cancer.ResultsTumors from mice implanted with the Renca cell line and treated with iMN041 demonstrated an increase in granzyme B in NK (p = 0.024) and NKT cells (p = 0.004), an increase in the ratios of CD8-T to regulatory T cells (Treg) (p = 0.0026) and CD4-T to Treg cells (p = 0.022) and a decrease in myeloid-derived suppressor cells (p = 0.040), compared to vehicle controls. A significant decrease in MAGE-A positive tumor cells in treated mice, concordant with a proportional decrease in all live tumor cells, suggests that these cells are one of the main targets of the activated immune system. Xenograft models of the triple negative breast cancer cell line DU4475, renal cancer cell lines 786-O and Caki-1, and pancreatic cancer cell lines CFPAC-1 and SW1990, demonstrated significantly lower tumor volumes, and, where there were a sufficient number of events, significantly improved survival in treated mice compared to vehicle control mice.ConclusionsIn mouse cancer models, iMN041 is an effective treatment for solid tumors mediated in part through a unique antitumor immune response.

Genome-Wide CRISPR/Cas9 Screening Unveils a Novel Target ATF7IP-SETDB1 Complex for Enhancing Difficult-to-Express Protein Production.

With the emerging novel biotherapeutics that are typically difficult-to-express (DTE), improvement is required for high-yield production. To identify novel targets that can enhance DTE protein production, we performed genome-wide fluorescence-activated cell sorting (FACS)-based clustered regularly interspaced short palindromic repeats (CRISPR) knockout screening in bispecific antibody (bsAb)-producing Chinese hamster ovary (CHO) cells. The screen identified the two highest-scoring genes, Atf7ip and Setdb1, which are the binding partners for H3K9me3-mediated transcriptional repression. The ATF7IP-SETDB1 complex knockout in bsAb-producing CHO cells suppressed cell growth but enhanced productivity by up to 2.7-fold. Decreased H3K9me3 levels and an increased transcriptional expression level of the transgene were also observed. Furthermore, perturbation of the ATF7IP-SETDB1 complex in monoclonal antibody (mAb)-producing CHO cells led to substantial improvements in mAb production, increasing the productivity by up to 3.9-fold without affecting the product quality. Taken together, the genome-wide FACS-based CRISPR screen identified promising targets associated with histone methylation, whose perturbation enhanced the productivity by unlocking the transgene expression.