Guidelines for the use of flow cytometry and cell sorting in immunological studies (third edition)

Comprehensive single-cell profiling of T and B cell subsets in mice reveals impacts on memory immune responses in FMDV infection

The impact of Foot-and-Mouth Disease Virus (FMDV) on memory immune responses has not been thoroughly investigated due to limited availability of immunological research tools. Using single-cell RNA sequencing, we identified specific gene markers for the majority of T and B cell subsets in the spleens of mice. Our findings indicate that FMDV infection significantly reduces the proportions of memory cell populations (e.g., memory B cells, memory CD4+ T cells, and memory CD8+ T cells) relative to their respective lymphocyte subsets (total B cells, CD4+ T cells, and CD8+ T cells) in the short term, impacting their functions. These alterations largely reverse over the long term. Specifically, FMDV infection primarily exerts its impacts on the function of memory cells by enhancing key immunological functions such as activation, proliferation, differentiation, and polarization, while simultaneously suppressing essential cellular biological functions including proliferation and metabolism. These impacts were significantly associated with Fos-related genes. Our study provides new insights into the immune evasion mechanisms of FMDV, establishes adult mice as potential models for FMDV immunological research, and offers valuable tools for single-cell RNA sequencing in murine immunological studies.

Fluorescent Cell Barcoding of Peripheral Blood Mononuclear Cells for High-Throughput Assessment of Vaccine-Induced T Cell Responses in Low-Volume Research Samples

T cell responses are rarely measured in large-scale human vaccine studies due to the sample volumes required, as well as the logistical, technical, and financial challenges associated with available assays. Fluorescent cell barcoding has been proposed in other contexts to allow for more high-throughput flow cytometry-based assays. Here, we aimed to expand on existing barcoding approaches to develop a reagent and sample-sparing assay for in-depth assessment of T cell responses to vaccine antigens. By using various concentrations of two fixable viability dyes in a matrix format, up to 25 samples that were pooled and acquired together could be successfully deconvoluted based on their unique fluorescent signature. This fluorescent cell barcoding approach was then combined with extracellular and intracellular staining to identify functional (i.e., producing at least one cytokine) and polyfunctional (i.e., producing multiple cytokines) T cells in response to vaccine antigen stimulation. As a proof-of-concept, we plated just 200,000 peripheral blood mononuclear cells (PBMC) per condition, and by staining and acquiring only two pooled samples, we were able to detect rare antigen-specific T cell responses in eight donors to four stimulants each. The frequencies of antigen-induced cytokine-positive cells detected in barcoded samples with 200,000 input PBMC were strongly correlated with those detected in non-barcoded samples from the same donors with 1 million input PBMC, demonstrating the validity of this approach. In conclusion, by reducing the number of PBMC needed by five-fold, and the volume of staining reagents needed by 25-fold, this assay has widespread potential applications to human vaccine studies.

PLC and PAD2 Regulate Extracellular Calcium-Triggered Release of Macrophage Extracellular DNA Traps

Macrophages can respond to infection or cellular stress by forming inflammasomes or by releasing extracellular traps (ETs) of DNA through METosis. While ETs have been extensively studied in neutrophils, there are fewer studies on METosis. We show that extracellular calcium and LPS enable human monocyte-derived macrophages (hMDM) to release extracellular DNA decorated with myeloperoxidase (MPO) and citrullinated histone, alongside ASC aggregation and IL-1ß maturation, indicating NLRP3 inflammasome activation. Compared with m-CSF differentiated macrophages only gm-CSF differentiated macrophages expressed macrophage elastase (MMP12) and METs released by the latter had significantly more bactericidal activity toward E. coli. Mechanistically, phospholipase C and peptidyl arginine deiminase-2 inhibition attenuate MET release. Interestingly, NLRP3 inflammasome blockade by MCC950 had a significant effect on MET release. Finally, MET release was completely blocked by plasma membrane stabilization by punicalagin. Altogether, we demonstrate that extracellular calcium-activated hMDM extrude DNA, containing citrullinated histones, MPO, MMP12, and ASC specks and released METs kill bacteria independent of hMDM phagocytotic activity. We believe that calcium-activated hMDM adds a physiologically relevant condition to calcium ionophore induced cell death that may be important in autoimmunity.

Vaccine Hesitancy and Associated Factors Among Caregivers of Children With Special Health Care Needs in the COVID-19 Era in China: Cross-Sectional Study

Background

Immunization is a cost-effective way to prevent infectious diseases in children, but parental hesitancy leads to low vaccination rates, leaving children at risk. Caregivers of children with special health care needs are more hesitant about vaccines than those of healthy children.

Objective

The aim of the study is to investigate the changes in caregivers' vaccination hesitation of children with special health care needs before, during, and after the COVID-19 pandemic in China and to identify associated factors for caregivers' attitudes toward National Immunization Program (NIP) and non-NIP vaccines.

Methods

We included 7770 caregivers of children with special health care needs (median age 7.0, IQR 2.4-24.1 months) who visited the Vaccination Consultation Clinic at Children's Hospital, Zhejiang University School of Medicine (Hangzhou, China) from May 2017 to May 2023. General and clinical information was extracted from the immunization evaluation system for children with special health care needs and medical records. We compared the differences in caregivers' willingness and hesitation for vaccinating their children across the 3 stages of the COVID-19 pandemic using chi-square tests. Multinomial logistic regression models were used to identify independent variables that were associated with caregivers' willingness and hesitation toward NIP and non-NIP vaccines.

Results

There is a statistically significant difference in caregivers' vaccine hesitancy before, during, and after the COVID-19 pandemic (P<.05). During the COVID-19 pandemic, the percentages of choosing NIP, alternative non-NIP, and non-NIP vaccines are highest (n=1428, 26%, n=3148, 57.4%, and n=3442, 62.7%, respectively) than those at other 2 stages. In comparison, caregivers' hesitation toward NIP and non-NIP vaccines is lowest (n=911, 16.6% and n=2045, 37.3%, respectively). Despite the stages of the COVID-19 pandemic, multiple factors, including children's age and sex, parents' educational level, comorbidities, and history of allergy, were significantly associated with caregivers' attitude toward NIP and non-NIP vaccines (P<.05). The profiles of risk factors for hesitancy toward NIP and non-NIP vaccines are different, as indicated by the results from the logistic regression models.

Conclusions

This study demonstrated that caregivers' willingness to vaccinate their children with special health care needs with NIP and non-NIP vaccines was highest during the COVID-19 pandemic in China, and their hesitancy was lowest. Additionally, we have identified multiple factors associated with caregivers' willingness and hesitancy to vaccinate their children. These findings provide evidence-based support for developing personalized health education strategies.

Acsbg1 regulates differentiation and inflammatory properties of CD4+ T cells

Epigenetic modifications are critical for the regulation of CD4+ T cell differentiation and function. Previously, we identified Acyl-CoA Synthetase Bubble Gum 1 (Acsbg1), a gene involved in fatty acid metabolism, as part of an epigenetic signature that was selectively demethylated in ex vivo isolated T helper 17 (TH17) cells. However, its functional relevance for CD4+ T cells remains incompletely understood. Here, we used in vitro differentiation assays and the adoptive transfer colitis model to investigate the role of Acsbg1 in the differentiation and function of TH1, TH17, and regulatory T (Treg) cells. In vitro, Acsbg1 was expressed in both TH17 and in vitro-induced Treg (iTreg) cells, whereas TH1 cells lacked Acsbg1 expression. Accordingly, Acsbg1 deficiency resulted in impaired TH17 and iTreg differentiation, whereas TH1 differentiation was unaffected. In vivo, upon adoptive transfer of Acsbg1⁻/⁻ Tnaïve cells, immunodeficient recipient mice exhibited an exacerbated colitis, characterized by an altered balance of TH17 and Treg cells, indicating that Acsbg1 expression is essential for optimal TH17 and Treg cell differentiation and function. Our findings highlight the importance of fatty acid (FA) metabolism in maintaining immune homeostasis by regulating T cell differentiation and provide novel insights into the metabolic targeting of inflammatory diseases.

MIML: multiplex image machine learning for high precision cell classification via mechanical traits within microfluidic systems

Label-free cell classification is advantageous for supplying pristine cells for further use or examination, yet existing techniques frequently fall short in terms of specificity and speed. In this study, we address these limitations through the development of a novel machine learning framework, Multiplex Image Machine Learning (MIML). This architecture uniquely combines label-free cell images with biomechanical property data, harnessing the vast, often underutilized biophysical information intrinsic to each cell. By integrating both types of data, our model offers a holistic understanding of cellular properties, utilizing cell biomechanical information typically discarded in traditional machine learning models. This approach has led to a remarkable 98.3% accuracy in cell classification, a substantial improvement over models that rely solely on image data. MIML has been proven effective in classifying white blood cells and tumor cells, with potential for broader application due to its inherent flexibility and transfer learning capability. It is particularly effective for cells with similar morphology but distinct biomechanical properties. This innovative approach has significant implications across various fields, from advancing disease diagnostics to understanding cellular behavior.

Vaginal Prevotella timonensis Bacteria Enhance HIV-1 Uptake and Differentially Affect Transmission by Distinct Primary Dendritic Cell Subsets

Young females are at high risk of acquiring HIV-1 infections and an imbalance in the vaginal microbiome enhances susceptibility to HIV-1 infection. More insights into the underlying mechanisms could open up new strategies to prevent HIV-1 acquisition and dissemination. Here, we investigated the effect of anaerobic bacteria associated with bacterial vaginosis (BV) on HIV-1 transmission by two distinct dendritic cell (DC) subsets, that is, inflammatory monocyte-derived DCs (moDCs) and primary CD1c+ DCs. Notably, in contrast to other BV-associated microbiota, Prevotella timonensis enhanced uptake of HIV-1 by both moDCs and CD1c+ DCs and the increased uptake was independent of cellular HIV-1 (co-)receptors. Imaging flow cytometry analyses showed that HIV-1 did not co-localise with P. timonensis but was internalized into tetraspanin-positive compartments known to be involved in HIV-1 transmission. P. timonensis bacteria enhanced HIV-1 transmission by CD1c+ DCs, but not by moDCs, and the enhanced transmission was independent of viral infection. Our study strongly suggests that mucosal DC subsets have distinct functions in BV-associated HIV-1 susceptibility, and underscores the importance of early diagnosis and targeted treatment of vaginal dysbiosis to reduce the risk of HIV-1 acquisition.

Signaling events driving Aspergillus fumigatus-induced eosinophil activation

Allergic bronchopulmonary aspergillosis is an incurable disease caused by the environmental mold Aspergillus fumigatus. This hypersensitivity pneumonia is characterized by an inflammatory type 2 immune response, accompanied by influx of eosinophils into the lung. To investigate the mode of action of eosinophils and the signaling events triggered by A. fumigatus, we used an in vitro coculture system of murine bone marrow-derived eosinophils confronted with conidia. Using small-molecule inhibitors, we identified signaling modules of eosinophils in the course of A. fumigatus confrontation. Eosinophils reduced fungal metabolic activity, but inhibition of relevant signaling modules did not affect this phenomenon upon eosinophil confrontation. A. fumigatus-induced secretion of Th2 cytokines and chemokines by eosinophils engaged proto-oncogene tyrosine-protein kinase Src, phosphatidylinositol 3-kinase, p38 mitogen-activated protein kinase as well as calcium cations and to some extent serine/threonine-protein kinase Akt and protein arginine deiminase 4. Src and PI3K kinases were also involved in A. fumigatus-mediated ROS production and regulation of eosinophils surface receptors. Especially Src and PI3K inhibitors prevented A. fumigatus-induced eosinophil activation. Taken together, identification of signaling cascades of eosinophils during their interaction with A. fumigatus provides relevant insights into the host-pathogen interaction in the context of ABPA to yield therapeutic perspectives.

Age and Latent Cytomegalovirus Infection Do Not Affect the Magnitude of De Novo SARS-CoV-2-Specific CD8+ T Cell Responses

Immunosenescence, age-related immune dysregulation, reduces immunity upon vaccinations and infections. Cytomegalovirus (CMV) infection results in declining naïve (Tnaïve) and increasing terminally differentiated (Temra) T cell populations, further aggravating immune aging. Both immunosenescence and CMV have been speculated to hamper the formation of protective T-cell immunity against novel or emerging pathogens. The SARS-CoV-2 pandemic presented a unique opportunity to examine the impact of age and/or CMV on the generation of de novo SARS-CoV-2-specific CD8+ T cell responses in 40 younger (22-40 years) and 37 older (50-66 years) convalescent individuals. Heterotetramer combinatorial coding combined with phenotypic markers were used to study 35 SARS-CoV-2 epitope-specific CD8+ T cell populations directly ex vivo. Neither age nor CMV affected SARS-CoV-2-specific CD8+ T cell frequencies, despite reduced total CD8+ Tnaïve cells in older CMV- and CMV+ individuals. Robust SARS-CoV-2-specific central memory CD8+ T (Tcm) responses were detected in younger and older adults regardless of CMV status. Our data demonstrate that immune aging and CMV status did not impact the SARS-CoV-2-specific CD8+ T cell response. However, SARS-CoV-2-specific CD8+ T cells of older CMV- individuals displayed the lowest stem cell memory (Tscm), highest Temra and PD1+ populations, suggesting that age, not CMV, may impact long-term SARS-CoV-2 immunity.

Single-cell RNA sequencing in autoimmune diseases: New insights and challenges

Autoimmune diseases involve a variety of cell types, yet the intricacies of their individual roles within molecular mechanisms and therapeutic strategies remain poorly understood. Single-cell RNA sequencing (scRNA-seq) offers detailed insights into transcriptional diversity at the single-cell level, significantly advancing research in autoimmune diseases. This article explores how scRNA-seq enhances the understanding of cellular heterogeneity and its potential applications in the etiology, diagnosis, treatment, and prognosis of autoimmune diseases. By revealing a comprehensive cellular landscape, scRNA-seq illuminates the functional regulation of different cell subtypes during disease progression. It aids in identifying diagnostic and prognostic markers, and analyzing cell communication networks to uncover potential therapeutic targets. Despite its valuable contributions, addressing the limitations of scRNA-seq is essential for making further advancements.

Phenotypes of porcine blood CD8β T cells and their capacity for IFN gamma production in the context of PRV vaccination

CD8 T cells play a key role in elimination of intracellular pathogens. Here, we have carried out a detailed phenotypic and functional analysis of swine blood CD8β T cells, after vaccination with a live attenuated PRV vaccine. Based on the expression of six surface molecules (CD11a, CD27, CD45RA, CD95, CCR7 and SLA-DR), up to eight subsets can be identified within the circulating compartment of CD8β T cells of adult pigs; six of which correlate phenotypically with naïve, stem cell memory, central memory, transitional memory, effector memory, and terminal effector subsets described in humans. The remaining two subsets appear to correspond to intermediate stages between naïve and central memory cells, and between transitional memory and effector memory or terminal effector cells, respectively. Although CD45RA has been proposed as a marker to distinguish between porcine naïve and central memory CD8β T cells, we found that a substantial proportion of naïve T cells, which varies among animals, lack this marker and that the combination of CD95 and CD11a allows a more accurate discrimination of these subsets among CD27hi CCR7+ cells. The majority of virus-specific IFN-γ-producing CD8β T cells in the blood of PRV-vaccinated pigs, collected at 10-16-days postvaccination, showed a CD27+ CD11ahi CD45RA- phenotype, consistent with that of central, and/or transitional memory T cells.

Maximizing Insights, Minimizing Animal Testing: A Framework for Validating Multiparametric Single-Cell Cytokine Analysis Panels

Intracellular cytokine labeling combined with high-parametric flow cytometry offers substantial promise in elucidating the nuanced effector functions of cells. However, the establishment of complex multicolor panels is often laborious and the importance of validation processes may be underestimated in research practice. This raises the risk of prematurely translating multicolor panels into in vivo studies. Alternatively, researchers may resort to animal disease models to procure cytokine-producing cells. Both scenarios raise ethical concerns as they entail the potential for unnecessary animal suffering without yielding novel insights into immunobiology. Here, we perform multicolor panel optimization and validation without the need for stressful animal testing. We designed two spectral flow cytometry panels for cytokine expression analyses across mouse immune and joint cells. Animal testing was replaced by stimulated co-cultures of T cells, splenocytes, and fibroblast-like synoviocytes. These cultures were used for multicolor labeling experiments. Our method proved suitable for validating the two cytometry panels, as it provided a complex cellular environment in which a variety of cytokine-producing populations were identified. In summary, we here present a blueprint for the quality control of single-cell cytokine assays by cell culture and further introduce multicolor panels that can be employed for studies on inflammatory or infectious diseases.

Uncovering two neutrophil-committed progenitors that immediately precede promyelocytes during human neutropoiesis

Technological advances have greatly improved our knowledge of myelopoiesis, for example, with the discovery of granulocyte‒monocyte‒dendritic cell (DC) progenitors (GMDPs), monocyte‒DC progenitors (MDPs), common DC progenitors (CDPs) and common monocyte progenitors (cMoPs) on the basis of flow cytometry approaches. Concomitantly, some progress has been made in characterizing the very early phases of human neutropoiesis with the description of novel CD66b+ progenitors, including eNePs, PMs w/o eNePs, ProNeus, and PreNeus. More recently, we identified four SSCloLin-CD66b-CD45dimCD34+/CD34dim/-CD64dimCD115- cells as the earliest precursors specifically committed to the neutrophil lineage present in human bone marrow (BM), which we called neutrophil-committed progenitors (NCPs, from NCP1s to NCP4s). In this study, we report the isolation and characterization of two new SSChiCD66b-CD64dimCD115-NCPs that, by phenotypic, transcriptomic, maturation and immunohistochemistry properties, as well as by flow cytometric side-scattered light (SSC), stand after NCP4s but precede promyelocytes during the neutropoiesis cascade. Similar to SSCloCD45RA+NCP2s/NCP3s and SSCloCD45RA-NCP1s/NCP4s, these cells exhibit phenotypic differences in CD45RA expression levels and, therefore, were named SSChiCD45RA+NCP5s and SSChiCD45RA-NCP6s. Moreover, NCP5s were more immature than NCP6s, as determined by cell differentiation and proliferative potential, as well as by transcriptomic and phenotypical features. Finally, by examining whether NCPs and all other CD66b+ neutrophil precursors are altered in representative hematological malignancies, we found that, in patients with chronic-phase chronic myeloid leukemia (CP-CML), but not with systemic mastocytosis (SM), there is an increased frequency of BM NCP4s, NCP6s, and all downstream CD45RA-negative neutrophil progenitors, suggesting their expansion in CML pathogenesis. Taken together, our data advance our knowledge of human neutropoiesis.

PEPITEM, its tripeptide pharmacophores and their peptidomimetic analogues regulate the inflammatory response through parenteral and topical dosing in models of peritonitis and psoriasis

PEPITEM is an immune-modulatory peptide that effectively regulates inflammation and mitigates immune-mediated inflammatory diseases (IMIDs). Here, we identify two independently active tripeptide pharmacophores within PEPITEM and engineered peptidomimetics with enhanced pharmacodynamic properties. These peptidomimetics regulate T-cell trafficking in vitro and reduce T-cell, neutrophil and macrophage numbers in the inflamed peritoneal cavity in vivo. In a plaque psoriasis model, topical administration reduced disease severity, inflammation and immune cell infiltration, while regulating cytokine release in macrophages and fibroblasts, as well as keratinocyte proliferation. Th1 and Th17 cell abundance, along with their cytokines, was reduced in secondary lymphoid organs. This expanded functional repertoire of PEPITEM and its derivatives provides innovative tools for countering immune and stromal cell-induced pathology in IMIDs. Moreover, by identifying significantly smaller tripeptide pharmacophores of 14 amino acid PEPITEM, we may be able to deliver substantial financial advantages in synthesis and formulation. The order of magnitude increase in efficacy observed for some peptidomimetics may deliver agents with enhanced pharmacological characteristics compared to the parent PEPITEM sequence. Taken together with other reports on the efficacy of PEPITEM, this study paves the way for the development and translation of a novel class of anti-inflammatory agents which may have utility in a broad range of autoimmune and chronic inflammatory diseases.

Combining molecular characteristics and therapeutic analysis of PDOs predict clinical responses and guide PDAC personalized treatment

BACKGROUND

The emergence of targeted therapies and immunotherapy has broadened treatment options for patients with pancreatic ductal adenocarcinoma (PDAC). Despite this, traditional drug selection, predominantly relies on tumor markers and clinical staging, has underutilized these drugs due to ignoring patient genomic diversity. Patient-derived organoids (PDOs) and corresponding patient-derived organoid xenograft (PDOX) models offer a way to better understand and address this.

METHODS

In this study, we established PDOs and PDOX models from PDAC clinical samples. These models were analyzed using immunohistochemistry, H&E staining, and genomic profiling. Drug screening with 111 FDA-approved drugs was performed on PDOs, and drug responses in PDOs and PDOX models were compared to assess consistency with clinical treatment outcomes. Gene analysis was conducted to explore the molecular mechanisms underlying variations in drug responses. Additionally, by analyzing the sequencing results from various drug-sensitive groups, the identified differential gene-drug metabolism gene UGT1A10 were modulated in PDOs to evaluate its impact on drug efficacy. A co-culture system of PDOs with immune cells was developed to study the efficacy of immunotherapies.

RESULTS

PDOs and matched PDOX models retain the morphological, biological, and genomic characteristics of the primary tumor. Exome sequencing and RNA sequencing confirmed both the consistency and heterogeneity among the PDOs. High-throughput drug screening revealed significant variability in drug sensitivity across different organoids, yet PDOs and PDOX derived from the same patient exhibited a high degree of concordance in response to clinical chemotherapy agents. The gene expression analysis of PDOs with significant differences in drug sensitivity revealed UGT1A10 as a crucial regulator. The knockdown of UGT1A10 notably increased drug sensitivity. Furthermore, immune cells demonstrated specific cytotoxicity towards the organoids, underscoring the potential of the co-culture system for application in tumor immunotherapy.

CONCLUSION

Our results highlight the necessity for personalized treatment strategies that consider genomic diversity beyond tumor markers, thus validating the utility of PDOs and PDOX models in advancing PDAC research and personalized medicine.

Mechanistic insight into the induction of liver tissue-resident memory CD8+ T cells by glycolipid-peptide vaccination

We recently demonstrated that vaccines comprising antigenic peptides conjugated to a glycolipid agonist, termed glycolipid-peptide (GLP) vaccines, efficiently generate substantial numbers of long-lived CD8+ liver-resident memory T (Trm) cells that are crucial for protection against malaria liver-stage infection. To understand the underlying mechanism, we examined the prerequisites for priming, differentiation, and secondary boosting of liver Trm cells using these GLP vaccines. Our study revealed that generation of long-lived liver Trm cells relies on CD8+ T cell priming by type 1 conventional dendritic (cDC1) cells, followed by post-priming exposure to a combination of vaccine-derived inflammatory and antigenic signals. Boosting of liver Trm cells is feasible using the same GLP vaccine, but a substantial delay is required for optimal responses due to natural killer T (NKT) cell anergy. Overall, our study unveils key requirements for the development of long-lived liver Trm cells, offering valuable insights for future vaccine design.

MAIT cells protect against sterile lung injury

Mucosal-associated invariant T (MAIT) cells, the most abundant unconventional T cells in the lung, can exhibit a wide range of functional responses to different triggers via their T cell receptor (TCR) and/or cytokines. Their role, especially in sterile lung injury, is unknown. Using single-cell RNA sequencing (scRNA-seq), spectral analysis, and adoptive transfer in a bleomycin-induced sterile lung injury, we found that bleomycin activates murine pulmonary MAIT cells and is associated with a protective role against bleomycin-induced lung injury. MAIT cells drive the accumulation of type 1 conventional dendritic cells (cDC1s), limiting tissue damage in a DNGR-1-dependent manner. Human scRNA-seq data revealed that MAIT cells were activated, with increased cDC populations in idiopathic pulmonary fibrosis patients. Thus, MAIT cells enhance defense against sterile lung injury by fostering cDC1-driven anti-fibrotic pathways.

Dielectrophoretic Microfluidic Designs for Precision Cell Enrichments and Highly Viable Label-Free Bacteria Recovery from Blood

Conducting detailed cellular analysis of complex biological samples poses challenges in cell sorting and recovery for downstream analysis. Label-free microfluidics provide a promising solution for these complex applications. In this work, we investigate particle manipulation on two label-free microdevice designs using cDEP to enrich E. coli from whole human blood to mimic infection workflows. E. coli is still a growing source of bacteremia, sepsis, and other infections in modern countries, affecting millions of patients globally. The two microfluidic designs were evaluated for throughput, scaling, precision targeting, and high-viability recovery. While CytoChip D had the potential for higher throughput, given its continuous method of DEP-based sorting to accommodate larger clinical samples like a 10 mL blood draw, it could not effectively recover the bacteria. CytoChip B achieved a high-purity recovery of over 98% of bacteria from whole human blood, even in concentrations on the order of <100 CFU/mL, demonstrating the feasibility of processing and recovering ultra-low concentrations of bacteria for downstream analysis, culture, and drug testing. Future work will aim to scale CytoChip B for larger volume throughput while still achieving high bacteria recovery.

Cost-effective microfluidic flow cytometry for precise and gentle cell sorting

Microfluidic flow cytometry (MFCM) is considered to be an effective substitute for traditional flow cytometry, because of its advantages in terms of higher integration, smaller device size, lower cost, and higher cell sorting activity. However, MFCM still faces challenges in balancing parameters such as sorting throughput, viability, sorting efficiency, and cost. Here, we demonstrate a cost-effective and high-performance microfluidic cytometry cell sorting system, along with a customized microfluidic chip that integrates hydrodynamic focusing, droplet encapsulation, and sorting for precise cell manipulation. An innovative photon incremental counting-based fluorescence detection method is proposed, which requires only one-fiftieth of the data compared to traditional methods. This significantly simplifies the structure of the system and substantially reduces costs. The system exhibits detection recoveries exceeding 95% across sample solution flow rates ranging from 10 to 80 μL min-1. Moreover, it accurately achieves individual droplet deflections at a droplet generation frequency of 1600 Hz. Ultimately, our cell sorting system offers an impressive sorting efficiency of 90.7% and a high cell viability of 94.3% when operating at a droplet generation frequency of 1316 Hz, highlighting its accuracy and gentleness throughout the entire process. Our work will enhance advances in the life sciences, thereby creating a boom in great applications in single-cell cloning, single-cell analysis, drug screening, etc.

Exploring the dynamics of T-cell responses: a combined approach using EdU incorporation and proliferation dye dilution assay

Understanding antigen-specific T-cell responses is crucial for advancing immunotherapies and vaccine development. This study proposes a novel approach combining two complementary assays: the 5-ethynyl-2'-deoxyuridine (EdU) incorporation assay (tracking proliferation over 0-48 h) and the VPD450 dye dilution assay (tracking proliferation over 4-6 days). Integrating these techniques provides additional insights into T-cell proliferation kinetics. Both assays were independently optimized using anti-CD3 and anti-CD28 polyclonal T cell stimulation. 1 μM VPD450 is suitable for assessing T-cell proliferation. The EdU concentration should match the stimulation strength, requiring higher concentrations to efficiently track DNA replication detection during increased cellular division. Day 5 was the optimal read-out day for the EdU incorporation assay. We then combined the VPD450 dye dilution and EdU incorporation assays. As a proof of principle, we stimulated PBMCs from healthy donors with tetanus toxoid to assess antigen-specific T-cell responses. Additionally, we demonstrated the assay's application in drug research by evaluating proliferation in a mixed lymphocyte reaction with abatacept, an agonistic anti-CTLA-4 antibody. This combined approach offers qualitative insights into T-cell proliferation kinetics, beneficial for assessing novel vaccine efficiency or for designing new treatments targeting T cell proliferation, such as in autoimmune settings.

HCMV Variants Expressing ULBP2 Enhance the Function of Human NK Cells via its Receptor NKG2D

The immunosuppressed state of transplant patients allows opportunistic pathogens such as human cytomegalovirus (HCMV) to cause severe disease. Therefore, inducing and boosting immunity against HCMV in recipients prior to organ transplantation is highly desirable, and accordingly, the development of an HCMV vaccine has been identified as a clinically relevant priority. Such vaccines need to be highly attenuated while eliciting specific and protective immune responses. We tested the concept of expressing the NKG2D ligand (NKG2D-L) ULBP2 by HCMV vaccine candidates to achieve NK cell activation, and, thereby viral attenuation. ULBP2 expression was found on HCMV-infected cells, reflecting the promotor strengths used to drive ULBP2 transgene expression. Moreover, significantly increased shedding of soluble ULBP2 (sULBP2) was detected for these mutants mirroring the surface expression levels. No negative effect of sULBP2 on NK cell function was observed. NK cells efficiently controlled viral spread, which was further increased by additional triggering of the activating receptor NKG2D. Engagement of NKG2D was also confirmed by its downregulation depending on ULBP2 surface density. Finally, expression of ULBP2 significantly enhanced NK cell cytotoxicity, which was independent of KIR-ligand mismatch as well as the presence of T cells. This NKG2D-L-based approach represents a feasible and promising strategy for HCMV vaccine development.

Anti-PD-L1 blockade facilitates antitumor effects of radiofrequency ablation by improving tumor immune microenvironment in hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is a complex disease with advanced presentation that significantly affects survival rates. Therefore, novel therapeutic strategies are needed. In this study, we investigate the tumor microenvironment (TME) in HCC by analyzing 13 HCC samples at single cell level. We identified key cell populations, including CD8 + T cells, Tregs, M1/M2 macrophages, and CD4 + memory T cells, and explored their roles and interactions. Our research revealed an early enrichment of CD8 + T cells, which could potentially lead to their exhaustion and facilitate tumor progression. We also investigated the impact of percutaneous radiofrequency ablation (RFA) on the immune microenvironment. Using a dual tumor mouse model, we demonstrated that RFA induces necrosis, enhancing antigen presentation and altering immune responses. Our results indicate that RFA increases PD-L1 expression in residual liver tissue, suggesting potential immune escape mechanisms. Furthermore, the combination of RFA and anti-PD-L1 therapy in the mouse model resulted in significant improvements in immune modulation. This included increased CD8 + T cell efficacy and decreased Treg infiltration. This combination shows promise as an approach to counteract HCC progression by altering the immune landscape. This study highlights the critical interaction within the TME of HCC and suggests the possibility of improving patient outcomes by targeting immune evasion mechanisms through combined therapeutic strategies.

Dual Activation-Induced Marker Combinations Efficiently Identify and Discern Antigen-Specific and Bystander-Activated Human CD4+ T Cells

Identifying activated T lymphocytes and differentiating antigen-specific from bystander T cells is crucial for understanding adaptive immune responses. This study investigates the efficacy of activation-induced markers (AIMs) in distinguishing these cell populations. We measured the expression of commonly used AIMs (CD25, CD38, CD40L, CD69, CD137, HLA-DR, ICOS, and OX40) in an in vitro T-cell activation system and evaluated their sensitivity, specificity, and positive predictive value. We demonstrated that individual AIMs, while specific in detecting activated CD4+ T cells, poorly discriminate between antigen-specific and bystander activation, as assessed by a discriminative capacity (DC) score we developed. Our analysis revealed that dual AIM combinations significantly enhanced the ability to distinguish antigen-specific from bystander-activated T cells, achieving DC scores above 90%. These combinations also improved positive predictive value and specificity with a modest reduction in sensitivity. The CD25hi/ICOShi combination emerged as the most efficient, with an average sensitivity of 84.35%, specificity of 99.7%, and DC score of 90.12%. Validation through T-cell cloning and antigen re-stimulation confirmed the robustness of our predictions. This study provides a practical framework for researchers to optimize strategies for identifying and isolating antigen-specific human CD4+ T lymphocytes and studying their phenotype, function, and T-cell receptor repertoire.

Harnessing the biology of regulatory T cells to treat disease

Regulatory T (Treg) cells are a suppressive subset of CD4+ T cells that maintain immune homeostasis and restrain inflammation. Three decades after their discovery, the promise of strategies to harness Treg cells for therapy has never been stronger. Multiple clinical trials seeking to enhance endogenous Treg cells or deliver them as a cell-based therapy have been performed and hint at signs of success, as well as to important limitations and unanswered questions. Strategies to deplete Treg cells in cancer are also in active clinical testing. Furthermore, multi-dimensional methods to interrogate the biology of Treg cells are leading to a refined understanding of Treg cell biology and new approaches to harness tissue-specific functions for therapy. A new generation of Treg cell clinical trials is now being fuelled by advances in nanomedicine and synthetic biology, seeking more precise ways to tailor Treg cell function. This Review will discuss recent advances in our understanding of human Treg cell biology, with a focus on mechanisms of action and strategies to assess outcomes of Treg cell-targeted therapies. It highlights results from recent clinical trials aiming to enhance or inhibit Treg cell activity in a variety of diseases, including allergy, transplantation, autoimmunity and cancer, and discusses ongoing strategies to refine these approaches.

CytoNorm 2.0: A flexible normalization framework for cytometry data without requiring dedicated controls

Cytometry is a single cell, high-dimensional, high-throughput technique that is being applied across a range of disciplines. However, many elements alongside the data acquisition process might give rise to technical variation in the dataset, called batch effects. CytoNorm is a normalization algorithm for batch effect removal in cytometry data that was originally published in 2020 and has been applied on a variety of datasets since then. Here, we present CytoNorm 2.0, discussing new, illustrative use cases to increase the applicability of the algorithm and showcasing new visualizations that enable thorough quality control and understanding of the normalization process. We explain how CytoNorm can be used without the need for technical replicates or controls, show how the goal distribution can be tailored toward the experimental design and we elaborate on the choice of markers for CytoNorm's internal FlowSOM clustering step.

High-Throughput Single-Cell Analysis of Local Nascent Protein Deposition in 3D Microenvironments via Extracellular Protein Identification Cytometry (EPIC)

Extracellular matrix (ECM) guides cell behavior and tissue fate. Cell populations are notoriously heterogeneous leading to large variations in cell behavior at the single-cell level. Although insights into population heterogeneity are valuable for fundamental biology, regenerative medicine, and drug testing, current ECM analysis techniques only provide either averaged population-level data or single-cell data from a limited number of cells. Here, extracellular protein identification cytometry (EPIC) is presented as a novel platform technology that enables high-throughput measurements of local nascent protein deposition at single-cell level. Specifically, human primary chondrocytes are microfluidically encapsulated in enzymatically crosslinked microgels of 16 picoliter at kHz rates, forming large libraries of discrete 3D single-cell microniches in which ECM can be deposited. ECM proteins are labeled using fluorescence immunostaining to allow for nondestructive analysis via flow cytometry. This approach reveals population heterogeneity in matrix deposition at unprecedented throughput, allowing for the identification and fluorescent activated cell sorting-mediated isolation of cellular subpopulations. Additionally, it is demonstrated that inclusion of a second cell into microgels allows for studying the effect of cell-cell contact on matrix deposition. In summary, EPIC enables high-throughput single-cell analysis of nascent proteins in 3D microenvironments, which is anticipated to advance fundamental knowledge and tissue engineering applications.

Understanding the Dual Role of Macrophages in Tumor Growth and Therapy: A Mechanistic Review

Macrophages are heterogeneous cells that are the mediators of tissue homeostasis. These immune cells originated from monocytes and are classified into two basic categories, M1 and M2 macrophages. M1 macrophages exhibit anti-tumorous inflammatory reactions due to the behavior of phagocytosis. M2 macrophages or tumor-associated macrophages (TAMs) are the most abundant immune cells in the tumor microenvironment (TME) and have a basic role in tumor progression by interacting with other immune cells in TME. By the expression of various cytokines, chemokines, and growth factors, TAMs lead to strengthening tumor cell proliferation, angiogenesis, and suppression of the immune system which further support invasion and metastasis. This review discusses recent and updated mechanisms regarding tumor progression by M2 macrophages. Moreover, the current therapeutic approaches targeting TAMs, their advantages, and limitations are also summarized, and further treatment approaches are outlined along with an elaboration of the tumor regression role of macrophages. This comprehensive review article possibly helps to understand the mechanisms underlying the tumor progression and regression role of macrophages in a comparative way from a basic level to the advanced one.

Markers of immunosenescence in CMV seropositive healthy elderly adults

A significant increase in life expectancy has accompanied the growth of the world's population. Approximately 10% of the global population are adults over 60, and it is estimated that 2050 this figure will double. This increase in the proportion of older adults leads to a more significant burden of age-related diseases. Immunosenescence predisposes elderly individuals to a higher incidence of infectious and chronic non-communicable diseases with higher mortality rates. Despite advances in research, it is necessary to evaluate the cellular characteristics of the aging immune system in populations with a high incidence of latent viruses such as cytomegalovirus (CMV). In this sense, this work aimed to identify senescence markers in cells of the innate and adaptive immune system in healthy older adults with CMV infection. We observed that older adults present an increase in the population of CD14+CD16+ intermediate monocytes, an expansion of CD56neg NK cells with an increase in the expression of CD57, as well as a decrease in the naïve CD4+ and CD8+ T cells, accompanied by an increased expression of senescence markers CD57 and KLRG1 in effector CD8+ T cells.

Inflammatory Monocytes Are Rapidly Recruited to the Post-Ischaemic Liver in Patients Undergoing Liver Transplantation and Cytokines Associated with Their Activation Correlate with Graft Outcomes

Liver ischaemia-reperfusion (IR) injury remains a major cause of morbidity and mortality following liver transplantation and resection. CD4+ T cells have been shown to play a key role in murine models; however, there is currently a lack of data that support their role in human patients. Methods: Data on clinical outcomes and complications were documented prospectively in 28 patients undergoing first elective liver transplant surgery. Peripheral blood samples were collected at baseline (pre-op), 2 h post graft reperfusion, immediately post-op, and 24 h post-op. A post-reperfusion biopsy was analysed in all patients, and in five patients, a donor liver biopsy was available pre-implantation. Circulating cytokines were measured, and T cells were analysed for activation markers and cytokine production. Results: Circulating levels of cytokines associated with innate immune cell recruitment and activation were significantly elevated in the peri-transplant period. High circulating IL-10 levels corresponded with the development of graft-specific complications. The proportion of CD4+ T cells in the peripheral circulation fell throughout the peri-operative period, suggesting CD4+ T cell recruitment to the graft. Although TNFα was the predominant cytokine produced by CD4+ T cells in the intrahepatic environment, the production of IFNγ was significantly upregulated by circulating CD4+ T cells. Furthermore, we demonstrated clear recruitment of inflammatory monocytes in the peri-operative period. In donor-and-recipient pairs with a mismatch at the HLA-A2 or A3 allele, we demonstrated that inflammatory monocytes in the liver are recipient-derived. Discussion: This is the first study to our knowledge that tracks early immune cell responses in humans undergoing liver transplantation. The recruitment of inflammatory monocytes from the recipient and their cytokine release is associated with liver-specific complications. Inflammatory monocytes would be an attractive target to ameliorate ischaemia-reperfusion injury.

Transcription Factor Analysis to Investigate Immunosenescence in Rheumatoid Arthritis Patients

Rheumatoid arthritis (RA) is linked to various signs of advanced aging, such as premature immunosenescence which occurs due to decline in regenerative ability of T cells. RA T cells develop a unique aggressive inflammatory senescent phenotype with an imbalance of Th17/T regulatory (Treg) cell homeostasis and presence of CD28- T cells. The phenotypic analysis and characterization of T cell subsets become necessary to ascertain if any functional deficiencies exist within with the help of transcription factor (TF) analysis. These subset-specific TFs dictate the functional characteristics of T-cell populations, leading to the production of distinct effector cytokines and functions. Examining the expression, activity, regulation, and genetic sequence of TFs not only aids researchers in determining their importance in disease processes but also aids in immunological monitoring of patients enrolled in clinical trials, particularly in evaluating various T-cell subsets [Th17 (CD3+CD4+IL17+RORγt+) cells and T regulatory (Treg) (CD3+CD4+CD25+CD127-FOXP3+) cells], markers of T-cell aging [aged Th17 cells (CD3+CD4+IL17+RORγt+CD28-), and aged Treg cells (CD3+CD4+CD25+CD127-FOXP3+CD28-)]. In this context, we propose and outline the protocols for assessing the expression of TFs in aged Th17 and Treg cells, highlighting the crucial aspects of this cytometric approach.

The Anti-Human P2X7 Monoclonal Antibody (Clone L4) Can Mediate Complement-Dependent Cytotoxicity of Human Leukocytes

P2X7 is an extracellular adenosine 5'-triphosphate (ATP)-gated cation channel that plays various roles in inflammation and immunity. P2X7 is present on peripheral blood monocytes, dendritic cells (DCs), and innate and adaptive lymphocytes. The anti-human P2X7 monoclonal antibody (mAb; clone L4), used for immunolabelling P2X7 or blocking P2X7 activity, is a murine IgG2b antibody, but its ability to mediate complement-dependent cytotoxicity (CDC) is unknown. In this study the functionality of this mAb was confirmed by inhibition of ATP-induced Ca2+ responses in HEK-293 cells expressing P2X7 (HEK-P2X7). Spectrophotometric measurements of lactate dehydrogenase release demonstrated that the anti-P2X7 mAb mediated CDC in HEK-P2X7 but not HEK-293 cells. Further, flow cytometric measurements of the viability dye, 7-aminoactinomycin D, showed that this mAb mediated CDC in human RPMI 8226 but not mouse J774 cells. Immunolabelling with this mAb and flow cytometry revealed that relative amounts of cell surface P2X7 varied between human peripheral blood leukocytes. As such, the anti-P2X7 mAb preferentially mediated CDC of leukocytes that displayed relatively high cell surface P2X7, namely monocytes, DCs, natural killer T cells, myeloid-derived suppressor cells, and T helper 17 cells. Together, this data highlights a novel approach to target cellular P2X7 and to limit unwanted P2X7 functions.

Development of Simple and Rapid Bead-Based Cytometric Immunoassays Using Superparamagnetic Hybrid Core-Shell Microparticles

Flow cytometry-based immunoassays are valuable in biomedical research and clinical applications due to their high throughput and multianalyte capability, but their adoption in areas such as food safety and environmental monitoring is limited by long assay times and complex workflows. Rapid, simplified bead-based cytometric immunoassays are needed to make these methods viable for point-of-need applications, especially with the increasing accessibility of miniaturized cytometers. This work introduces superparamagnetic hybrid polystyrene-silica core-shell microparticles as promising alternatives to conventional polymer beads in competitive cytometric immunoassays. These beads, featuring high specificity, sensitivity, and excellent handling capabilities via magnetic separation, were evaluated with three different antibodies and binding methods, showing variations in signal intensity based on the antibody and its attachment method. The optimal performance was achieved through a secondary antibody binding approach, providing strong and consistent signals with minimal uncertainty. The optimized protocol made it possible to achieve a detection limit of 0.025 nM in a total assay time of only 15 min and was successfully used to detect ochratoxin A (OTA) in raw flour samples. This work highlights the potential of these beads as versatile tools for flow cytometry-based immunoassays, with significant implications for food safety, animal health, environmental monitoring, and clinical diagnostics.

Synergistic combinations of Angelica sinensis for myocardial infarction treatment: network pharmacology and quadratic optimization approach

Background and aim

Angelica sinensis (Oliv.) Diels (Danggui, DG), exhibits potential in myocardial infarction (MI) treatment. However, research on its synergistic combinations for cardioprotective effects has been limited owing to inadequate approaches.

Experimental procedure

We identified certain phenolic acids and phthalein compounds in DG. Network pharmacology analysis and experimental validation revealed the components that protected H9c2 cells and reduced lactate dehydrogenase levels. Subsequently, a combination of computational experimental strategies and a secondary phenotypic optimization platform was employed to identify effective component combinations with synergistic interactions. The Chou-Talalay and Zero Interaction Potency (ZIP) models were utilized to quantify the synergistic relationships. The optimal combination identified, Z-Ligustide and Chlorogenic acid (Z-LIG/CGA), was evaluated for its protective effects on cardiac function and cardiomyocytes apoptosis induced by inflammatory in a mouse model of induced by left anterior descending coronary artery ligation. Flow cytometry was further utilized to detect the polarization ratio of M1/M2 macrophages and the expression of inflammatory cytokines in serum was measured, assessing the inhibition of inflammatory responses and pro-inflammatory signaling factors by Z-LIG/CGA.

Key results

Quadratic surface analysis revealed that the Z-LIG/CGA combination displayed synergistic cardioprotective effects (combination index value <1; ZIP value >10). In vivo, Z-LIG/CGA significantly improved cardiac function and reduced the fibrotic area in mice post-MI, surpassing the results in groups treated with Z-LIG or CGA alone. Compared to the MI group, the Z-LIG/CGA group exhibited decreased ratios of the myocardial cell apoptosis-related proteins BAX/Bcl-2 and Cleaved Caspase-3/Caspase-3 in mice. Further research revealed that Z-LIG/CGA treatment significantly increased IL-1R2 levels, significantly decreased IL-17RA levels, and inhibited the activation of p-STAT1, thereby alleviating cell apoptosis after MI. Additionally, the Z-LIG/CGA combination significantly inhibited the ratio of M1/M2 macrophages and suppressed the expression levels of pro-inflammatory cytokines IL-1β, IL-6, IL-17, and TNF-α in the serum.

Conclusion and implications

We successfully identified a synergistic drug combination, Z-LIG/CGA, which improves MI outcomes by inhibiting cardiomyocyte apoptosis and inflammatory damage through modulating macrophage polarization and regulating the IL-1R2/IL-17RA/STAT1 signaling pathway. This study provides a charming paradigm to explore effective drug combinations in traditional Chinese medicine and a promising treatment for MI.

A20 intrinsically influences human effector T-cell survival and function by regulating both NF-κB and JNK signaling

A20 is a dual-function ubiquitin-editing enzyme that maintains immune homeostasis by restraining inflammation. Although A20 serves a similar negative feedback function for T-cell receptor (TCR) signaling, the molecular mechanisms utilized and their ultimate impact on human T-cell function remain unclear. TCR engagement triggers the assembly of the CARD11-BCL10-MALT1 (CBM) protein complex, a signaling platform that governs the activation of downstream transcription factors including NF-κB and c-Jun/AP-1. Utilizing WT and A20 knockout Jurkat T cells, we found that A20 is required to negatively regulate NF-κB and JNK. Utilizing a novel set of A20 mutants in NF-κB and AP-1-driven reporter systems, we discovered the ZnF7 domain is crucial for negative regulatory capacity, while deubiquitinase activity is dispensable. Successful inactivation of A20 in human primary effector T cells congruently conferred sustained NF-κB and JNK signaling, including enhanced upregulation of activation markers, and increased secretion of several cytokines including IL-9. Finally, loss of A20 in primary human T cells resulted in decreased sensitivity to restimulation-induced cell death and increased sensitivity to cytokine withdrawal-induced death. These findings demonstrate the importance of A20 in maintaining T-cell homeostasis via negative regulation of both NF-κB and JNK signaling.

The essential roles of memory B cells in the pathogenesis of systemic lupus erythematosus

Emerging evidence indicates that memory B cells are dysfunctional in systemic lupus erythematosus (SLE). They are hyporesponsive to signalling through the B cell receptor (BCR) but retain responsiveness to Toll-like receptor (TLR) and type I interferon signalling, as well as to T cell-mediated activation via CD40-CD154. Chronic exposure to immune complexes of ribonucleoprotein (RNP)-specific autoantibodies and TLR-engaging or BCR-engaging cargo is likely to contribute to this partially anergic phenotype. TLR7 or TLR8 signalling and the resulting production of type I interferon, as well as the sustained activation by bystander T cells, fuel a positive feedforward loop in memory B cells that can evade negative selection and permit preferential expansion of anti-RNP autoantibodies. Clinical trials of autologous stem cell transplantation or of B cell-targeted monoclonal antibodies and chimeric antigen receptor (CAR) T cells have correlated replenishment of the memory B cell population with relapse of SLE. Moreover, the BCR hyporesponsiveness of memory B cells might explain the failure of non-depleting B cell-targeting approaches in SLE, including BTK inhibitors and anti-CD22 monoclonal antibodies. Thus, targeting of dysfunctional memory B cells might prove effective in SLE, while also avoiding the adverse events of broad-spectrum targeting of B cell and plasma cell subsets that are not directly involved in disease pathogenesis.

Rise of a CD27- IgD- CD11c+ B cells population in kidney recipients achieving long-term graft stability under immunosuppression

The use of immunosuppressive treatment is required to prevent rejection events, even a long time after kidney transplantation despite rare recipients achieving long-term graft stability without the need for immunosuppressive treatment, called operationally tolerant patients (TOLs). We comprehensively investigate the immune system of long-term IS recipients (LTTs) and TOLs to highlight their shared and unique immune features. Blood immune cell phenotyping was performed by spectral cytometry. Samples from 34 individuals were analyzed, including 6 LTTs, 8 TOLs, 10 stable patients at 1 year posttransplantation (STAs), and 10 healthy volunteers. B cells differed between LTTs and TOLs with a decreased total B-cell frequency and the acquisition of a memory phenotype in LTTs whereas a naive phenotype is maintained in TOLs. The frequencies of IgD-CD27- B cells and CD11c+ memory B cells are increased in LTTs, with an exhausted phenotype, evoked by a significant decrease in CD25 expression. These CD11c+ B cells display an exhausted phenotype similar to those found in several chronic immune diseases in which they have been shown to participate in their pathophysiology, suggesting active chronic inflammation in LTTs. Altogether, these data indicate that precautions should be taken to minimize IS use.

Biological variability of human intraepithelial lymphocytes throughout the human gastrointestinal tract in health and coeliac disease

BACKGROUND

Intraepithelial lymphocytes are the first line of defence of the human intestinal immune system. Besides, their composition is altered on patients with coeliac disease (CD), so they are considered as biomarkers with utility on their diagnose and/or monitoring. Our aim is to address their variability through the human gastrointestinal tract in health and characterized them in further depth in the coeliac duodenum.

METHODS

Intraepithelial lymphocytes were isolated from human gastric, duodenal, ileal and colonic biopsies, then stained with specific antibodies and acquired by flow cytometry.

RESULTS

Our results confirmed that the profile of Intraepithelial lymphocytes change through the length of the human gastrointestinal tract. Besides and given the central role that Interleukin-15 (IL-15) elicits on CD pathogenesis; we also assessed the expression of its receptor revealing that there was virtually no functional IL-15 receptor on duodenal Intraepithelial lymphocytes. Nevertheless and contrary to our expectations, the active IL-15 receptor was not increased either on Intraepithelial lymphocytes from CD patients.

CONCLUSIONS

IL-15 might require additional stimulus to activate intraepithelial lymphocytes. These findings may provide novel tools to aid on a CD diagnosis and/or monitoring, at the time that provide the bases to perform functional studies in order of getting a deeper insight in the specific function that Intraepithelial lymphocytes elicit on CD pathogenesis.

Exploring the Unknown: How Can We Improve Single-cell RNAseq Cell Type Annotations in Non-model Organisms?

Single-cell RNA sequencing (scRNAseq) is a powerful tool to describe cell types in multicellular organisms across the animal kingdom. In standard scRNAseq analysis pipelines, clusters of cells with similar transcriptional signatures are given cell type labels based on marker genes that infer specialized known characteristics. Since these analyses are designed for model organisms, such as humans and mice, problems arise when attempting to label cell types of distantly related, non-model species that have unique or divergent cell types. Consequently, this leads to limited discovery of novel species-specific cell types and potential mis-annotation of cell types in non-model species while using scRNAseq. To address this problem, we discuss recently published approaches that help annotate scRNAseq clusters for any non-model organism. We first suggest that annotating with an evolutionary context of cell lineages will aid in the discovery of novel cell types and provide a marker-free approach to compare cell types across distantly related species. Secondly, machine learning has greatly improved bioinformatic analyses, so we highlight some open-source programs that use reference-free approaches to annotate cell clusters. Lastly, we propose the use of unannotated genes as potential cell markers for non-model organisms, as many do not have fully annotated genomes and these data are often disregarded. Improving single-cell annotations will aid the discovery of novel cell types and enhance our understanding of non-model organisms at a cellular level. By unifying approaches to annotate cell types in non-model organisms, we can increase the confidence of cell annotation label transfer and the flexibility to discover novel cell types.

Prevalence of hybrid TLR4+M2 monocytes/macrophages in peripheral blood and lung of systemic sclerosis patients with interstitial lung disease

Introduction

Systemic sclerosis (SSc) is a complex autoimmune connective tissue disease characterized by microvascular damage, immune system reactivity and progressive fibrosis of skin and internal organs. Interstitial lung disease is the leading cause of death for SSc patients (SSc-ILD), and the process of lung fibrosis involves also circulating monocytes and alveolar macrophages.

Methods

Current study aimed to identify monocyte/macrophage phenotypes in lung and peripheral blood of SSc-ILD patients by immunostaining and flow cytometry, respectively. Single immunostaining was performed using primary antibodies against CD68 (pan-macrophage marker), CD80, CD86, TLR4 (M1 markers), CD163, CD204, and CD206 (M2 markers). Flow cytometry analysis included the evaluation of CD45, CD14, CD16 (monocyte lineage), CD1c (dendritic lineage), together with M1 and M2 activation markers on circulating monocytes. Protein synthesis of TLR4 and M2 markers was also investigated in cultured monocytes-derived macrophages (MDMs) from SSc-ILD patients by Western Blotting.

Results

Lung samples were obtained from 9 SSc-ILD patients (50 ± 9 years old) and 5 control non-SSc patients without lung fibrosis (58 ± 23 years old). Alveolar macrophages (CD68+ cells) showed a significantly higher positivity of M1 and M2 markers in SSc-ILD lung samples than in controls (p<0.05 for CD80, p<0.01 for CD86, p<0.001 for CD68, p<0.0001 for TLR4, CD163, CD204 and CD206). In CD68 positive areas of SSc-ILD samples, a significantly higher percentage of TLR4, CD163, CD204, and CD206 positive cells was observed compared to CD80 and CD86 positive cells (p<0.001 in both cases), suggesting the possible presence of hybrid TLR4+M2 macrophages (CD68+CD80-CD86-TLR4+CD163+CD204+CD206+cells) in SSc-ILD samples. A second cohort of 26 SSc-ILD patients (63 ± 14 years old) and 14 SSc patients without ILD (63 ± 19 years old) was recruited for flow cytometry analysis of circulating monocytes. Again, a significantly higher percentage of hybrid TLR4+M2 monocytes (CD1c-CD80-TLR4+CD163+CD204+CD206+cells) was found in SSc-ILD positive than SSc-ILD negative patients (p<0.05). Moreover, the protein synthesis of TLR4 and M2 markers was also found higher in cultured MDMs obtained from SSc-ILD patients than in MDMs from SSc patients without ILD and this increase was significantly higher for CD163 (p<0.05) and CD206 (p<0.01).

Conclusions

The presence of hybrid TLR4+M2 markers on both circulating monocytes and resident lung macrophages in SSc-ILD patients, is reported for the first time. Therefore, the detection of circulating hybrid TLR4+M2 monocytes in SSc-ILD might represent a further potential biomarker of progressive organ fibrosis, to be searched in blood samples of SSc patients.

Biological characteristics and immune responses of NK Cells in commonly used experimental mouse models

The biology of natural killer (NK) cells in commonly used mouse models is discussed in this review, along with their crucial function in a variety of immunological responses. It has been demonstrated that the formation, maturation, subtype variety, and immunological recognition mechanisms of NK cells from various mice strains exhibit notable differences. These variations shed light on the intricacy of NK cell function and offer crucial information regarding their possible uses in treating human illnesses. The application of flow cytometry in mouse NK cell research is also covered in the article. Improved knowledge of the biology of NK cells across species may facilitate the development of new NK cell-based therapeutic approaches.

Cytokine profile, differential somatic cell count, and oxidative status of Italian Mediterranean buffalo milk affected by the temperature-humidity index

In the context of climate change, there has been an increased interest in improving management practices for animals genetically adapted to extreme environmental conditions, such as buffaloes. The temperature-humidity index (THI) is used to determine the severity of heat stress in livestock. This study aimed to evaluate the cytokine profile, oxidative staus, differential somatic cell count (DCC), and the surface expression and activity of myeloperoxidase (MPO) in the somatic cells (SCs) of buffalo. Milk samples (n = 216) were collected from the spring to summer season under three different THI classes (THI < 72; ≤72 THI < 76, and THI ≥ 76). The cytokine profile was determined using ELISA, and the expression of DSCC and MPO was determined by flow cytometry. MPO activity was performed on SC extracts using a specific ELISA kit. Oxidative status was determined by the antioxidant/oxidant balance combining the free radical scavenging activity levels, and reactive oxygen and nitrogenous species. The results on the cytokine profile showed that at the THI ≥ 76 the levels of both IL-10 and IFN-γ were highest. IL-1β secretion was lower at the THI < 72 than at the THI values ranging from ≤72 THI < 76. Higher levels of both TNF-α and IL-12 were registered in both THI < 72 and THI ≥ 76 classes. The level of IL-4 was higher in the THI ≥ 76 class than in the ≤72 to <76 range. Data on DCC showed a decrease in the percentage of macrophages and lymphocytes as the THI increased from the ≤72 to <76 range to THI ≥ 76. Furthermore, the highest percentage of polymorphonuclear leukocyte (PMNLs) was registered in both ≤72 to <76 and THI ≥ 76 classes. The MPO activity and surface expression on SC were lower at a THI above 76, which could be associated with an absence of inflammation. A condition of oxidative imbalance was registered as demonstrated by the lower levels of antioxidant/oxidant balance along with increasing THI. Present data demonstrated that buffaloes were able to modulate the alteration of immune response activated by heat stress throughout a series of cross-linked mechanisms involving cytokine networks, different somatic cell distribution, and oxidative status.

Mechanics-activated fibroblasts promote pulmonary group 2 innate lymphoid cell plasticity propelling silicosis progression

Crystalline silica (CS) particle exposure leads to silicosis which is characterized as progressive fibrosis. Fibroblasts are vital effector cells in fibrogenesis. Emerging studies have identified immune sentinel roles for fibroblasts in chronic disease, while their immune-modulatory roles in silicosis remain unclear. Herein, we show that group 2 innate lymphoid cell (ILC2) conversion to ILC1s is closely involved in silicosis progression, which is mediated by activated fibroblasts via interleukin (IL)-18. Mechanistically, Notch3 signaling in mechanics-activated fibroblasts modulates IL-18 production via caspase 1 activity. The mouse-specific Notch3 knockout in fibroblasts retards pulmonary fibrosis progression that is linked to attenuated ILC conversion. Our results indicate that activated fibroblasts in silicotic lungs are regulators of ILC2-ILC1 conversion, associated with silicosis progression via the Notch3-IL-18 signaling axis. This finding broadens our understanding of immune-modulatory mechanisms in silicosis, and indicates potential therapeutic targets for lung fibrotic diseases.

DLK1 Is Associated with Stemness Phenotype in Medullary Thyroid Carcinoma Cell Lines

Medullary thyroid carcinoma (MTC) is a rare and aggressive tumor, often requiring systemic treatment in advanced or metastatic stages, where drug resistance presents a significant challenge. Given the role of cancer stem cells (CSCs) in cancer recurrence and drug resistance, we aimed to identify CSC subpopulations within two MTC cell lines harboring pathogenic variants in the two most common MEN2-associated codons. We analyzed 15 stemness-associated markers, along with well-established thyroid stem cell markers (CD133, CD44, and ALDH1), a novel candidate (DLK1), and multidrug resistance proteins (MRP1 and MRP3). The ability to efflux the fluorescent dye Hoechst 3342 and form spheroids, representing CSC behavior, was also assessed. MZ-CRC-1 cells (p.M918T) displayed higher expressions of canonical markers, DLK1, and MRP proteins than TT cells (p.C634W). MZ-CRC-1 cells also formed more spheroids and showed less dye accumulation (p < 0.0001). Finally, we observed that DLK1+ cells (those expressing DLK1) in both cell lines exhibited significantly higher levels of stemness markers compared to DLK1- cells (those lacking DLK1 expression). These findings underscore DLK1's role in enhancing the stemness phenotype, providing valuable insights into MTC progression and resistance and suggesting potential therapeutic implications.

The lifespan and kinetics of human dendritic cell subsets and their precursors in health and inflammation

Dendritic cells (DC) are specialized mononuclear phagocytes that link innate and adaptive immunity. They comprise two principal subsets: plasmacytoid DC (pDC) and conventional DC (cDC). Understanding the generation, differentiation, and migration of cDC is critical for immune homeostasis. Through human in vivo deuterium-glucose labeling, we observed the rapid appearance of AXL+ Siglec6+ DC (ASDC) in the bloodstream. ASDC circulate for ∼2.16 days, while cDC1 and DC2 circulate for ∼1.32 and ∼2.20 days, respectively, upon release from the bone marrow. Interestingly, DC3, a cDC subset that shares several similarities with monocytes, exhibits a labeling profile closely resembling that of DC2. In a human in vivo model of cutaneous inflammation, ASDC were recruited to the inflammatory site, displaying a distinctive effector signature. Taken together, these results quantify the ephemeral circulating lifespan of human cDC and propose functions of cDC and their precursors that are rapidly recruited to sites of inflammation.

Evaluation of attenuated Salmonella Typhimurium (STMΔznuABC) anticancer activity on canine mammary cancer-associated fibroblasts

Bacteria-mediated treatments gained increasing attention as alternative therapies against tumors. An attenuated mutant strain of Salmonella enterica serovar Typhimurium (STMΔznuABC) has recently been considered as a potential new anti-cancer strategy. However, it is unclear whether this activity is tumor-induced or species-specific, and no data are available regarding STMΔznuABC on canine mammary tumors (CMTs). This study aimed to investigate the ability of STMΔznuABC in modulating the response of CMTs, focusing on cancer-associated fibroblasts. Four CMT cell lines (CF33, TM51, TM52 TM53) were treated with STMΔznuABC. Then, antiproliferative activity (MTT assay), bacterial invasion, and CMT cell lines gene expression analysis (RT-qPCR) of genes involved in immune response and cancer aggressiveness were evaluated. STMΔznuABC penetrated in TM51, TM52, TM53, and CF33 cell lines, causing a significant reduction of cell viability. Moreover, the expression of several genes was significantly modulated in all CMT cell lines: STMΔznuABC infection determined a significant up-regulation of CXCL8, IL18, IL10, TLR4 and RAD51, while CD14, IL6, CXCR4, P53, PTEN, STAT5, TLR5 and TGFB1 were downregulated in TM53. In CF33, CXCL8 and P53 were upregulated, while MYD88, MD2, IL18, TLR4,5, TGFB1 were downregulated. In TM52, CXCL8, CD44 and MD2 were upregulated and PTEN was downregulated, while in TM51 CXCL8, CD44 and ErbB2 were downregulated. We demonstrated the anti-proliferative and immuno-modulatory activity of STMΔznuABC in CMTs, paving the way for potential new anti-cancer treatments.

Brief guide to flow cytometry

Flow cytometry is a powerful analytical technique for measuring the physical and chemical properties of cells or particles as they flow through a beam of light in a fluid stream. It is widely used in several research fields for a wide variety of purposes. This article provides a concise guide to the principles and utilization of flow cytometry. Step-by-step instructions, from instrument setup to data analysis, are intended to help researchers successfully apply flow cytometry in their studies.

In vitro, the aging of stallion spermatozoa at 22 °C is linked to alteration in Ca2+ and redox homeostasis and may be slowed by regulating metabolism

BACKGROUND

Conservation of equine semen in the liquid state is a central procedure in horse breeding and constitutes the basis of associated reproductive technologies. The intense mitochondrial activity of the stallion spermatozoa increases oxidative stress along the storage period, leading to sperm demise within 24-48 h of storage, particularly when maintained at room temperature. Recently, the relationship between metabolism and oxidative stress has been revealed. The study aimed to extend the period of conservation of equine semen, at room temperature through modification of the metabolites present in the media.

MATERIAL AND METHODS

Processed ejaculates (n = 9) by single-layer colloid centrifugation were split in different aliquots and extended in Tyrode's basal media, or modified Tyrode's consisting of 1 mM glucose, 1 mM glucose 10 mM pyruvate, 40 mM glucose, 40 mM Glucose 10 mM pyruvate, 67 mM glucose and 67 mM glucose 10 mM pyruvate. At time 0h, and after 24 and 96 h of storage, motility was evaluated by CASA, while mitochondrial production of Reactive oxygen species (ROS), and intracellular Ca2+ concentrations were determined via flow cytometry using Mitosox Red and Fluo-4 respectively. ROS and Ca2+ were estimated as Relative Fluorescence Units (RFU) in compensated, arcsin-transformed data in the live sperm population.

RESULTS

After 48 h of incubation, motility was greater in all the 10 mM pyruvate-based media, with the poorest result in the 40 mM glucose (41 ± 1.1 %) while the highest motility was yielded in the 40 mM glucose 10 mM pyruvate aliquot (60.3 ± 3.5 %; P < 0.001); after 96 h of storage highest motility values were observed in the 40 mM glucose 10 mM pyruvate media (23.0 ± 6.2 %) while the lowest was observed in the 1 mM glucose media was 9.2 ± 2.0 % (P < 0.05). Mitochondrial ROS was lower in the 40 mM glucose 10 mM pyruvate group compared to the 40 mM glucose (P < 0.01). Over time Ca2+ increased in all treatment groups compared to time 0h.

DISCUSSION AND CONCLUSION

Viable spermatozoa may experience oxidative stress and alterations in Ca2+ homeostasis during prolonged storage, however, these effects can be reduced by regulating metabolism. The 40 mM glucose- 10 mM pyruvate group yielded the highest sperm quality parameters.

Single-Cell RNA Sequencing Reveals Monocyte-Derived Interstitial Macrophages with a Pro-Fibrotic Phenotype in Bleomycin-Induced Pulmonary Fibrosis

Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive lung disease with limited effective therapies. Interstitial macrophages (IMs), especially those derived from monocytes, play an unknown role in IPF pathogenesis. By using single-cell RNA sequencing (scRNA-seq), bleomycin (BLM)-induced pulmonary fibrosis mouse lungs were analyzed to characterize the cellular landscape and heterogeneity of macrophages in this model. scRNA-seq was used to identify distinct interstitial macrophage subpopulations in fibrotic lungs, with monocyte-derived macrophages exhibiting a pro-fibrotic gene expression profile enriched in wound healing, extracellular matrix (ECM) remodeling, and pro-fibrotic cytokine production functions. A pseudotime analysis revealed that IMs originated from monocytes and differentiated along a specific trajectory. A cell-cell communication analysis demonstrated strong interactions between monocyte-derived interstitial macrophages (Mo-IMs) and fibroblasts through the transforming growth factor beta (TGFβ), secreted phosphoprotein 1 (SPP1), and platelet-derived growth factor (PDGF) signaling pathways. Flow cytometry validated the presence and expansion of Mo-IMs subpopulations in BLM-treated mice. This study reveals the cellular heterogeneity and developmental trajectory of lung macrophages in early BLM-induced pulmonary fibrosis, highlighting the crucial role of Mo-IMs with a pro-fibrotic phenotype in IPF pathogenesis via interactions with fibroblasts. Targeting these specific macrophage subpopulations and associated signaling pathways may provide novel therapeutic strategies for IPF.

Perioperative sintilimab and neoadjuvant anlotinib plus chemotherapy for resectable non-small-cell lung cancer: a multicentre, open-label, single-arm, phase 2 trial (TD-NeoFOUR trial)

This open-label, single-arm, phase 2 trial evaluated the efficacy and safety of neoadjuvant sintilimab combined with anlotinib and chemotherapy, followed by adjuvant sintilimab, for resectable NSCLC. Forty-five patients received anlotinib (10 mg, QD, PO, days 1-14), sintilimab (200 mg, day 1), and platinum-based chemotherapy of each three-week cycle for 3 cycles, followed by surgery within 4-6 weeks. Adjuvant sintilimab (200 mg) was administered every 3 weeks. The primary endpoint was achieving a pathological complete response (pCR). From June 10, 2021 through October 10, 2023, 45 patients were enrolled and composed the intention-to-treat population. Twenty-six patients (57.8%) achieved pCR, and 30 (66.7%) achieved major pathological response (MPR). Forty-one patients underwent surgery. In the per-protocol set (PP set), 63.4% (26/41) achieved pCR, and 73.2% achieved MPR. The median event-free survival was not attained (95% CI, 25.1-NE). During the neoadjuvant treatment phase, grade 3 or 4 treatment-related adverse events were observed in 25 patients (55.6%), while immune-related adverse events were reported in 7 patients (15.6%). We assessed vascular normalization and infiltration of immune-related cells by detecting the expression of relevant cell markers in NSCLC tissues with mIHC. Significant tumor microenvironment changes were observed in pCR patients, including reduced VEGF+ cells and CD4+Foxp3+ Treg cells, and increased perivascular CD4+ T cells, CD39+CD8+ T cells, and M1 macrophages. In conclusion, perioperative sintilimab and neoadjuvant anlotinib plus chemotherapy achieved pCR in a notable proportion of patients with resectable NSCLC and were associated with profound changes in the tumour microenvironment (ClinicalTrials.gov NCT05400070).

Advancing Immunotherapy in Pancreatic Cancer

Pancreatic cancer remains one of the deadliest malignancies, with a consistently low five-year survival rate for the past several decades. This is in stark contrast to other cancers, which have seen significant improvement in survival and prognosis due to recent developments in therapeutic modalities. These modest improvements in pancreatic cancer outcomes have primarily resulted from minor advances in cytotoxic chemotherapeutics, with limited progress in other treatment approaches. A major focus of current therapeutic research is the further development of immunomodulatory therapies characterized by antibody-based approaches, cellular therapies, and vaccines. Although initial results utilizing immunotherapy in pancreatic cancer have been mixed, recent clinical trials have demonstrated significant improvements in patient outcomes. In this review, we detail these three approaches to immunomodulation, highlighting their common targets and distinct shortcomings, and we provide a narrative summary of completed and ongoing clinical trials that utilize these approaches to immunomodulation. Within this context, we aim to inform future research efforts by identifying promising areas that warrant further exploration.