Biology subjects

Belkina, A.

Publications and source records attributed to Belkina, A..

8 recordsLinked to original sources

bioRxiv2026

Male and female mice achieve equivalent protection against heterologous SARS-CoV-2 infection through divergent immune mechanisms

Biological sex is a major determinant of antiviral immunity, yet how it shapes lung-resident antiviral immunity remains poorly understood. We report that prior mild SARS-CoV-2 BA.1 infection protects mice from lethal heterologous Delta challenge through distinct sex-biased immune mechanisms. Although heterologous protection is clinically equivalent between sexes, T- and B-cell depletions before BA.1 exposure abrogate protection only in males. Depletion with anti-CD4, but not anti-CD8, abolishes protection in both sexes, but co-depletion with anti-CD4/anti-CD8 partially restores protection in females only. Further, females exhibit enhanced IFN-gamma-associated myeloid inflammation upon secondary Delta infection. Using lymphoid-deficient mice that display female-biased resistance to Delta infection, IFN-gamma treatment provides partial protection to naive males against Delta. Female resistance is lost after previous BA.1 exposure, highlighting the importance of lymphoid-mediated inflammatory regulation. Together, equivalent antiviral protection against heterologous respiratory viral infection is governed by sexually dimorphic mechanisms, with significant implications for designing mucosal vaccines and immunotherapies.

immunology↗

bioRxiv2026

A 50-marker mass cytometry panel to expand analysis of the functional breadth of human immune cells

Human immune single-cell proteomic functional profiling has historically been performed with a limited number of inflammatory and/or cytotoxic readouts, capturing only a fraction of the complex orchestra of factors that comprise immune responses. Given the rising global crisis of chronic inflammation and the lack of clinically available treatment options, there is an urgent need to gain insight into the cell subsets that exhibit anti-inflammatory functional profiles and elucidate the mechanisms regulating these effector capacities. To address this, we developed a 50-marker CyTOF panel that enables unprecedented functional fingerprinting of human T cells, NK cells, monocytes, and B cells, detecting 24 intracellular targets. Healthy donor PBMCs were stimulated ex vivo and stained with this panel; from T cells, cytokines associated with the hallmark Type 1 (IFN-{gamma}, TNF-), Type 2 (IL-4, IL-5, and IL-13), and Type 17 (IL-17A, IL-17F) functional lineages were detected, as well as the chemokines MIP-1-, MIP1-{beta}, and IL-8 and the cell repair factor amphiregulin; from monocytes, IL-1{beta}, IL-35, and IL-8 were detected. To ascertain if some of the cytokines less commonly included in Intracellular Cytokine Staining (ICS) panels were produced in response to physiological TCR stimulation via viral peptides, we measured the T cell response to a CMV-EBV-Flu (CEF) pool; in addition to TNF-, IFN-{gamma}, and IL-2, we also found that individual T cells produced additional cytokines with IFN-{gamma} and TNF-, such as amphiregulin, MIP-1, IL-13, and IL-4. This mass cytometry panel provides an exceptionally broad and deeply resolved view of the functional diversity of human immune cells, surpassing, to our knowledge, the capabilities of previously reported approaches. Due to minimal signal overlap, CyTOF enables flexible panel customization, allowing markers and metal tags to be readily expanded or modified. Based on its resolution and adaptability, we anticipate that this panel and its derivatives will enable the discovery of novel immunomodulatory mechanisms for therapeutic intervention.

immunology↗

bioRxiv2025

A Mouse Model of SARS-CoV-2-Driven Acute Maladaptive Responses and Chronic Systemic Diseases

Our understanding of SARS-CoV-2 acute and post-acute pathogenesis is hindered by the lack of adequate small animal models. We present RAB/6N, a mouse model prone to severe disease after exposure to SARS-CoV-2 clinical isolates, with lethal cases showing no widespread brain infection typical of the widely used K18-hACE2 mouse model. Lung viral replication in RAB/6N mice remains steady for several days before a decline in viral titers. Delayed initiation of infection clearance is marked by increased lung T-cell extravasation and type-2 immune responses, leading to maladaptive lung consolidation. While systemic antiviral cytokine responses only correlate with SARS-CoV-2 brain infection in K18-hACE2 mice, they are concomitant with pulmonary immune dynamics in infected RAB/6N mice. Convalescent RAB/6N mice display systemic inflammation and decreased antibody titers against SARS-CoV-2 spike RBD, persistent viral RNA and prolonged lymphoid infiltration in the lungs. These animals also exhibit signatures of multi-organ dysfunction, cognitive impairment, cardiac inflammation, hyper- immunoglobulin production, and various autoimmune disorders, illuminating the molecular correlates of various pathologies associated with post-acute sequelae of COVID-19 (PASC). RAB/6N mice pave the way for dissecting the molecular drivers underlying SARS-CoV-2-induced acute maladaptive responses and subsequent post-acute systemic diseases. This preclinical platform also opens opportunities for the exploration of therapeutic interventions against systemic PASC and for anticipating the emergence of PASC-associated comorbidities. One-sentence summaryWe generated a hACE2-transgenic mouse model that develops maladaptive lung immune responses upon acute SARS-CoV-2 infection, leading to fatal outcomes or post-acute systemic disease syndromes in convalescent animals.

microbiology↗

bioRxiv2025

Superior intracellular detection of cytokines, transcription factors, and phosphoproteins by CyTOF compared with fluorescent cytometry

Unraveling biological complexity, whether it be immune subset distribution in infectious disease(s), autoimmunity or tumor heterogeneity, requires technologies capable of single-cell proteomic analysis, such as flow cytometry. Surface immunophenotyping alone is often insufficient, as interrogating functional capacity is required to determine cellular mechanisms and effectively inform diagnostic biomarker discovery, therapeutics and vaccine development. However, large panels with intracellular markers are subject to numerous challenges, including spectral overlap and background cellular autofluorescence, reducing resolving power for rare subsets or populations defined by low-abundance expression. We posited that mass cytometry may overcome such limitations; to address this, three small (11-12-plex) clone-matched antibody panels were evaluated by spectral flow and mass cytometry. Panels were comprised of surface and intracellular targets (phospho-epitopes, transcription factors or cytokines) and designed to minimize fluorescence spectral overlap. CyTOF technology offered superior signal resolution across the range of intracellular targets. Improved signal-to-noise provided better resolution of phospho-events and transcription factor expression, in particular TOX and T-bet. Most strikingly, stimulation-specific IL-10+ and IL-13+ cells were only detected by CyTOF. Superior resolution of these cytokines enabled accurate population clustering, permitting more unique immune cell signatures to be found, including Tr1 and Tc2 populations, thus providing a more comprehensive picture of the immuno-diversity present. Our findings indicate that CyTOF technology could catalyze seminal discoveries in functional immune profiling, driving therapeutic design and diagnostics.

immunology↗

bioRxiv2025

Neutrophils respond with pathogen-specific defenses during bacterial pneumonia

Neutrophils have historically been envisioned as a homogenous population of short-lived innate immune cells that migrate to sites of infection, kill pathogens, and die. Recent work, including studies in pneumonia models, has shown that neutrophil transcriptomes reflect the environment from which they were isolated. We used high-parameter spectral flow cytometry to compare and contrast a wide array of surface proteins on neutrophils from different tissues, infections, host age, pathogen virulence, and across multiple time-points of pneumonia. Circulating and airspace neutrophils consistently differed, and surface protein phenotypes unique to each infection setting were identified, revealing tissue-specific and microbe-specific neutrophil plasticity. Phenotypic differences in circulating neutrophils from mice infected with different pathogens (E. coli, S. pneumoniae, S. aureus, and P. aeruginosa) identified, even in the absence of bacteremia. Neutrophil activation state was diminished with less virulent pathogens and host age. In the airspace, VISTA, CD200R, and PD-L1 were selectively high on BAL neutrophils (BALN) during S. pneumoniae infection, and we identified pro-degranulation-like (CD88High VISTAHigh PD-L1+ CD101-) neutrophils in S. pneumoniae and pro-phagocytosis-like (CD101+ CD18Low PD-L1-) neutrophils in E. coli infections. Stimulation of VISTA with its ligand VISG-3 enhanced the neutrophil respiratory burst, degranulation, and killing of S. pneumoniae but not E. coli. We conclude that neutrophil cell surface protein expression depends on anatomic location and infection type, resulting in pathogen-specific neutrophil-mediated immune defense in discreet areas of the pneumonic lung. Graphical AbstractIn brief, Pihl et al. have found that neutrophil cell surface phenotype varies drastically based on tissue, time post-infection, and infection. BALN from early infections have higher activation and maturation statuses, while blood neutrophils are more migration primed, and late infections have more immune-suppressive and altered pathogen killing statuses. Neutrophil phenotype is skewed towards pro-phagocytosis associated marker expression on BALN from E. coli-infected mice while S. pneumoniae results in a pro-degranulation phenotype. In vitro BMN stimulation of VISTA with VSIG-3 results in degranulation, respiratory burst, and pathogen specific killing of S. pneumoniae but not E. coli. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=186 SRC="FIGDIR/small/649365v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@4e4829org.highwire.dtl.DTLVardef@1638108org.highwire.dtl.DTLVardef@1ac413dorg.highwire.dtl.DTLVardef@1ef36b5_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2024

Nuclear Histone H3 Post-translational Modification Profiling in Whole Cells using Spectral Flow Cytometry

Histone modifications play essential roles in regulating chromatin accessibility and downstream transcription, serving as critical determinants of cell identity and function. However, the diversity of histone post-translational modifications (PTMs) and their tendency to be studied in isolation limits our understanding of their coordinated roles in shaping cellular states. Conventional flow cytometry methods for histone PTM assessment suffer from low multiplexing capacity and typically require nuclear isolation, resulting in significant sample loss and an incomplete picture of the overall cell state. Here, we present EpiFlow, a spectral flow cytometry protocol designed for multiparametric analysis of histone PTMs within whole cells. By utilizing a 96-well plate format and preserving the cell entirely, EpiFlow improves throughput and efficiency while retaining sample integrity. This method resolves subtle variations in histone PTMs within neural progenitor cells, capturing distinct chromatin states across the cell cycle and correlating them with several markers. Furthermore, we provide an open-access GitHub repository containing detailed protocols and analysis workflows, ensuring reproducibility and accessibility of this approach. EpiFlow offers a robust framework for exploring chromatin dynamics, with broad implications for advancing fundamental research and therapeutic research.

developmental biology↗

bioRxiv2020

Single cell atlas of beige remodeling of white adipose tissue reveals a myeloid to lymphoid shift during cold exposure compared to beta 3 adrenergic stimulation

White adipose tissue (WAT) is a dynamic tissue, which responds to environmental stimuli and dietary cues by changing its morphology and metabolic capacity. The ability of WAT to undergo a beige remodeling has become an appealing strategy to combat obesity and its related metabolic complications. Within the cell mixture that constitutes the stromal vascular fraction (SVF), WAT beiging is initiated through expansion and differentiation of adipocytes progenitor cells, however, the extent of the SVF cellular changes is still poorly understood. Additionally, direct beta 3 adrenergic receptor (Adrb3) stimulation has been extensively used to mimic physiological cold- induced beiging, yet it is still unknown whether Adrb3 activation induces the same WAT remodeling as cold exposure. Here, by using single cell RNA sequencing, we provide a comprehensive atlas of the cellular dynamics during beige remodeling within white adipose tissue. We reveal drastic changes both in the overall cellular composition and transcriptional states of individual cell subtypes between Adrb3- and cold-induced beiging. Moreover, we demonstrate that cold exposure induces a myeloid to lymphoid shift of the immune compartment compared to Adrb3 activation. Further analysis, showed that Adrb3 stimulation leads to activation of the interferon/Stat1 pathways favoring infiltration of myeloid immune cells, while repression of this pathway by cold promotes lymphoid immune cells recruitment. These findings provide new insight into the cellular dynamics during WAT beige remodeling and could ultimately lead to novel strategies to identify translationally-relevant drug targets to counteract obesity and T2D.

cell biology↗

bioRxiv2018

Multivariate Computational Analysis of Gamma Delta T cell Inhibitory Receptor Signatures Reveals the Divergence of Healthy and ART-Suppressed HIV+ Aging

Even with effective viral control, HIV-infected individuals are at a higher risk for morbidities associated with older age than the general population, and these serious non-AIDS events (SNAEs) track with plasma inflammatory and coagulation markers. The cell subsets driving inflammation in aviremic HIV infection are not yet elucidated. Also, whether ART-suppressed HIV infection causes premature induction of the inflammatory events found in uninfected elderly or if a novel inflammatory network ensues when HIV and older age co-exist is unclear. In this study we measured combinational expression of five inhibitory receptors (IRs) on seven immune cell subsets and 16 plasma markers from peripheral blood mononuclear cells (PBMC) and plasma samples, respectively, from a HIV and Aging cohort comprised of ART-suppressed HIV-infected and uninfected controls stratified by age ([≤]35 or [≥]50 years old). For data analysis, multiple multivariate computational algorithms (cluster identification, characterization, and regression (CITRUS), partial least squares regression (PLSR), and partial least squares-discriminant analysis (PLS-DA)) were used to determine if immune parameter disparities can distinguish the subject groups and to investigate if there is a cross-impact of aviremic HIV and age on immune signatures. IR expression on gamma delta ({gamma}{delta}) T cells exclusively separated HIV+ subjects from controls in CITRUS analyses and secretion of inflammatory cytokines and cytotoxic mediators from {gamma}{delta} T cells tracked with TIGIT expression among HIV+ subjects. Also, plasma markers predicted the percentages of TIGIT+ {gamma}{delta} T cells in subjects with and without HIV in PSLR models, and a PLS-DA model of {gamma}{delta} T cell IR signatures and plasma markers significantly stratified all four of the subject groups (uninfected younger, uninfected older, HIV+ younger, and HIV+ older). These data implicate {gamma}{delta} T cells as an inflammatory driver in ART-suppressed HIV infection and provide evidence of distinct inflamm-aging processes with and without ART-suppressed HIV infection.

immunology↗