Immunology

Nanoparticle vaccines can provide advantages over traditional vaccine methodologies, including adjuvant delivery to enhance the effectiveness of recombinant antigens. Many approaches exist to formulate different vaccine nanoparticles, which are designed for different biomolecular cargos, adjuvant compositions, and disease targets. Here, a protocol is described to produce nanoliposomes whose surface is decorated with recombinant protein influenza antigens with monophosphoryl lipid A and QS-21 adjuvants incorporated into the lipid bilayer for protection against influenza infection. This protocol includes methods for producing adjuvanted liposomes and coupling with His-tagged antigens for surface decoration of the particle. This allows for a rapid methodology of producing immunogenic antigen-presenting liposomes that can be tailored to display a combination of influenza surface antigens.

Obesity is a risk factor for many diseases. The 3T3-L1 cell line is often used to obtain mature adipocytes, but these lack the inflammatory phenotype observed in obesity. Using a cocktail of cytokines that mimics the secretome of macrophages found in the inflammatory adipose tissue, we developed a protocol for obtaining mature inflammatory adipocytes. This model was validated at gene (RT-qPCR) and protein levels (multiplex adipokine array) as we found a decrease of adipogenic markers (C/EBPα, PPARУ, adiponectin, and CD36) and an increase of pro-inflammatory cytokines (IL-6, IL-1β, CXCL1, CXCL10, TNF-α, ICAM-1, and lipocalin-2). We provide a relevant in vitro model for studying the impact of low-grade chronic inflammation caused by obesity and its downstream effects on metabolic disorders and tumor microenvironments.

Experimental autoimmune encephalomyelitis (EAE) is a widely used rodent model of multiple sclerosis (MS), typically induced with pertussis toxin (PTX) to achieve robust disease onset. However, PTX has been shown to exert broad immunomodulatory effects that include disruption of G protein-coupled receptor (GPCR) signaling, altered T-cell response, and exogenous suppression of regulatory T cells, all of which are not present in human MS pathophysiology. Moreover, PTX also obscures the sex differences observed in MS, limiting the translational value of EAE models that rely on it. Given EAE’s widespread use in preclinical therapeutic testing, there is a critical need for a model that better recapitulates both clinical and immunological features of MS without PTX-induced confounds. Here, we demonstrate a non-pertussis toxin (non-PTX) EAE model in C57BL/6 mice, using optimized concentrations of complete Freund’s adjuvant (CFA), Mycobacterium tuberculosis, and myelin oligodendrocyte glycoprotein (MOG_35-55) peptide. This model recapitulates hallmark features of MS that include demyelination, neuroinflammation, motor deficits, and neuropathic pain. Importantly, it retains sex-specific differences in disease onset and pathology, providing a more physiologically and clinically relevant platform for mechanistic and translational MS research.

It is common practice for laboratories to discard clotted blood or freeze it for future DNA extraction after extracting serum from a serum-separating tube. If freezing for DNA extraction, the blood clot is not usually cryopreserved, which leads to cell membrane fragility. In this protocol, we describe steps to isolate high-quality nuclei from leukocytes derived from whole blood samples frozen without a cryoprotective medium. Nuclei isolated from this protocol were able to undergo ATAC (assay for transposase-accessible chromatin) sequencing to obtain chromatin accessibility data. We successfully characterized and isolated B cells and T cells from leukocytes isolated from previously frozen blood clot using Miltenyi’s gentleMACS Octo Dissociator coupled with flow sorting. Nuclei showed round, intact nuclear envelopes suitable for downstream applications, including bulk sequencing of nuclei or single-cell nuclei sequencing. We validated this protocol by performing bulk ATAC-seq.

Congenital renal disorders, such as the Potter sequence, result from renal dysgenesis. To explore a prenatal therapeutic approach for fetuses with kidney insufficiency, we established an in utero transplantation protocol using donor fetal kidneys. Although numerous rodent studies have reported cellular injections into fetal recipients, no protocol to date has described whole-organ transplantation during gestation. Here, we present a step-by-step method for grafting donor fetal kidneys (embryonic day 14.0–16.5) into allogeneic rat fetuses at embryonic day 18.0–18.5, resulting in term neonates that retain the grafts postnatally. A 15–16 G needle preloaded with the donor kidney is inserted transuterinely, depositing the organ into the subcutaneous space of the fetus. Four days later, the term pups are delivered naturally and evaluated for graft development. This protocol enables organ-level transplantation and longitudinal assessment of graft maturation within the unique fetal environment, which differs markedly from adult settings in terms of growth factor availability and immune reactivity. To our knowledge, this is the first protocol to successfully achieve whole-organ transplantation directly into fetuses in utero. Therefore, the model provides a valuable platform for studying developmental organogenesis, fetal immunology, and regenerative strategies that leverage embryonic cues.

The tissue explant culture (histoculture) is a method that involves maintaining small pieces taken from an organ ex vivo or post mortem in a controlled laboratory setting. Such a technique has a number of advantages: unlike the 2D, organoid, or on-chip cultures, tissue explants preserve the whole complexity of the original tissue in vivo, its structure, extracellular matrix, and the diverse cell populations, including resident immune cells. The explant culture method can be applied to human tissue specimens obtained from biopsies or autopsies, provided that proper ethical protocols are followed. This avoids the difficulties that may arise in translating results obtained on animal models into biomedical research for humans. This advantage makes histocultures especially desirable for studying human pathogenesis in the course of infectious diseases. The disadvantage of the method is the limited lifespan of the cultured tissues; however, a number of approaches allow extending tissue viability to a period sufficient for observing the infection onset and development. Here, we provide a protocol for lung explant maintenance that allows tracing the local effects of infection with SARS-CoV-2 in humans. Further applications of the lung tissues cultured according to this protocol include, but are not limited to, histochemical and immunohistochemical studies and microscopy, FACS, qPCR, and ELISA-based analysis of the conditioned culture media.

Detecting the proliferation of cells with copper(I)-catalyzed azide-alkyne cycloaddition (click chemistry) and the thymidine analogue, 5-ethynyl-2’-deoxyuridine (EdU), is a simpler and more versatile method than traditional antibody-based approaches. Instead of the harsh series of steps typically used for 5-bromo-2’-deoxyuridine (BrdU) detection, detecting EdU does not require DNA denaturation and is suitable for use with other applications. This approach was implemented in an animal model of ischemic stroke. The following protocol details how to use EdU to label, track, and visualize leukocyte recruitment for flow cytometry and fluorescence microscopy, including the processes for EdU injection and blood and tissue sample preparation. Considerations for timing, dosing, and cell viability are also outlined to tailor the protocol to experimental needs. This method could be applied to various models that require extended tracking periods, as the signal from EdU can last several cell divisions, depending on cell type and condition.

Protein phosphorylation is a dynamic post-translational modification that regulates fundamental processes, including signal transduction, cell proliferation, differentiation, and effector function of immune cells. The Janus Kinase/Signal Transducer and Activator of Transcription (JAK/STAT) pathway is a key mediator of cytokine responses, essential for maintaining immune cell homeostasis and determining cell fate across diverse immune subsets. Dysregulation of JAK/STAT signaling has been linked to a broad spectrum of pathologies, including monogenic immune disorders, autoimmunity, and cancer. Platforms facilitating single-cell analysis of protein phosphorylation offer the ability to reveal subtle signaling defects and dissect the pleiotropy in cellular composition and phosphorylation status, providing insights into immune phenotype and function, while identifying potential therapeutic targets. While an application of cytometry-by-time-of-flight, termed phospho-CyTOF, has proven invaluable for studying protein phosphorylation in cryopreserved peripheral blood mononuclear cells (cPBMCs), its application is limited by cell loss and signaling artifacts stemming from isolation and cryopreservation. Conversely, whole blood (WB) approaches, preserving the native immune cell composition and signaling context, offer a more physiological representation but necessitate robust and consistent protocols for broad application. Herein, we present optimized dual phospho-CyTOF workflows tailored for both cPBMCs and whole blood, building upon established protocols for cytokine stimulation of both samples. These workflows facilitate comprehensive, high-dimensional profiling of JAK/STAT signaling in response to pleiotropic cytokines such as Type I interferons (IFN-α), Type II interferons (IFN-γ), and Interleukin-21 (IL-21). By leveraging CyTOF's capacity for high-dimensional profiling using pure heavy metal–labeled antibodies, these protocols aim to identify pathway-specific alterations in STAT phosphorylation across major immune subsets that may be overlooked by traditional flow cytometry. Together, these optimized dual workflows provide scalable, translationally relevant tools for dissecting the subtle and differential JAK/STAT-driven immune responses in both clinical and research settings, while also being compatible with the simultaneous assessment of crosstalk with alternative immune cell signaling pathways.

Immunopeptidomics enables the identification of peptides presented by major histocompatibility complex (MHC) molecules, offering insights into antigen presentation and immune recognition. Understanding these mechanisms in hypoxic conditions is crucial for deciphering immune responses within the tumor microenvironment. Current immunopeptidomics approaches do not capture hypoxia-induced changes in the repertoire of MHC-presented peptides. This protocol describes the isolation of MHC class I-bound peptides from in vitro hypoxia-treated cells, followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. It describes optimized steps for cell lysis, immunoaffinity purification, peptide elution, and MS-compatible preparation under controlled low-oxygen conditions. The method is compatible with various quantitative mass spectrometry approaches and can be adapted to different cell types. This workflow provides a reliable and reproducible approach to studying antigen presentation under hypoxic conditions, thereby enhancing physiological relevance and facilitating deeper immunological insights.

Adipose tissue macrophages (ATMs) critically influence obesity-induced inflammation and metabolic dysfunction. Recent studies identified distinct ATM subsets characterized by markers such as CD11c, CD9, and Trem2, associated with pro-inflammatory and metabolically activated states. This protocol outlines a detailed, reproducible methodology for isolating, characterizing, and sorting these ATM subsets from murine epididymal white adipose tissue (eWAT) using multicolor flow cytometry. Key steps include stromal vascular fraction (SVF) isolation, immunophenotyping, sequential gating strategies, and fluorescence-activated cell sorting (FACS) for downstream gene expression analysis. The protocol was validated in diet-induced obese (DIO) mice treated with the IRE1 RNase inhibitor STF-083010, demonstrating its utility for studying ATMs in the context of obesity and metabolic disease.