SEARCH · bioRxiv Science

Results for “immunology”

Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 289 records · Page 16Linked to original sources

bioRxiv2026

Radiation synergizes with BET inhibition to stimulate durable, systemic anti-tumor immunity in murine cancer models

Most patients with breast cancer (BC) and soft tissue sarcoma (STS) harbor immunologically cold tumors and do not respond to existing immunotherapies such as immune checkpoint inhibitors (ICIs) as a monotherapy. Consequently, prolonged treatment with highly toxic multiagent chemotherapy, with or without ICIs, remains the mainstay of systemic therapy in such patients. Therefore, there is an acute clinical need for novel chemotherapy-free immunotherapy regimens with high efficacy and minimal toxicity. Here, employing an in vivo drug screen, we identify that a short course of radiation therapy (RT) synergizes with pharmacological bromodomain and extraterminal (BET) inhibition to elicit a strong systemic anti-tumor immunity and long-term immunological memory in a CD8+ T cell-dependent manner in murine models of both BC and STS. Mechanistic studies reveal that RT + BET inhibition accentuates RT-induced DNA damage and micronuclei formation, increases Major Histocompatibility Complex class I and II expression on macrophages, enhances translocation of calreticulin to the plasma membrane, and blocks RT-induced Programmed Death-Ligand 1 (PD-L1) overexpression on tumor cells, thereby promoting immunogenic cell death. Our data suggest that a combination of RT + BET inhibition promotes robust anti-tumor immunity and immunological memory in immunologically cold tumors, thereby opening potential avenues for clinical translation.

immunology↗

bioRxiv2022

Host transcriptomic profiling of CD-1 outbred mice with severe clinical outcomes following infection with Orientia tsutsugamushi

Orientia tsutsugamushi is an obligately intracellular bacterium with endothelial tropism and can cause mild to lethal scrub typhus in humans. No vaccine is available for this reemerging and severely neglected infection. Previous scrub typhus studies have utilized inbred mice, yet such models have intrinsic limitations. Thus, the development of suitable mouse models that better mimic human diseases is in great need for immunologic investigation and future vaccine studies. This study is aimed at establishing scrub typhus in outbred CD-1 mice and defining immune biomarkers related to disease severity. CD-1 mice received O. tsutsugamushi Karp strain via the i.v. route; major organs were harvested at 2-12 days post-infection for kinetic analyses. We found that for our given infection doses, CD-1 mice were significantly more susceptible (90-100% lethal) than were inbred C57BL/6 mice (0-10% lethal). Gross pathology of infected CD-1 mouse organs revealed features that mimicked human scrub typhus, including pulmonary edema, interstitial pneumonia, perivascular lymphocytic infiltrates, and vasculitis. Alteration in angiopoietin/receptor expression in inflamed lungs implied endothelial dysfunction. Lung immune gene profiling using NanoString analysis displayed a Th1/CD8-skewed, but Th2 repressed profile, including novel biomarkers not previously investigated in other scrub typhus models. Bio-plex analysis revealed a robust inflammatory response in CD-1 mice as evidenced by increased serum cytokine and chemokine levels, correlating with immune cell recruitment during the severe stages of the disease. This study provides an important framework indicating a value of CD-1 mice for delineating host susceptibility to O. tsutsugamushi, immune dysregulation, and disease pathogenesis. This preclinical model is particularly useful for future translational and vaccine studies for severe scrub typhus. Author SummaryScrub typhus is a severely neglected and potentially fatal disease caused by Orientia tsutsugamushi, a genetically intractable, obligately intracellular bacterium that annually infects at least one million people worldwide. There is no vaccine available, and our current understanding of the host immunological response and mechanisms remains very limited. Appropriate animal models of infection that recapitulate the disease are essential to the development of effective therapeutics and vaccines. In this study, we characterized the immunologic responses by transcriptomics and Bio-plex assays in outbred CD-1 mice with lethal O. tsutsugamushi infection. We found that CD-1 mice were highly susceptible to infection and that the high mortality correlated with a Th1/CD8-skewed, but Th2 repressed, immune profile during the acute phase of disease. This proinflammatory state was further confirmed by elevated cytokine and chemokine levels in the sera. Collectively, this study established CD-1 mice as a practical, preclinical model to define pathogenic mechanisms underlying severe scrub typhus and for future immunologic and translational studies during O. tsutsugamushi infection.

microbiology↗

bioRxiv2023

Cardiopulmonary structural, functional and immune-alterations in a Down syndrome mouse model and upon modulation of EGCG

In individuals with Down syndrome (DS), cardiovascular and pulmonary diseases are the most common health problem and result in increased mortality and morbidity. Although these clinical comorbidities are well described, no preclinical models for DS are fully characterized for cardiopulmonary alterations, preventing research to understanding the development and pharmacological modulation of lungs, heart and immune system. Our objective is to characterize the cardiopulmonary and immunological phenotype in Ts65Dn mice and investigate the modulatory effects green tea extract enriched in epigallocatechin 3 gallate (GTE-EGCG). GTE-EGCG administration started at embryonic day 9 and was discontinued at postnatal day (PD) 180. Newborns were longitudinally monitored until PD210 using micro-computed tomography. At endpoint, we characterized the structural, functional and immunological alterations and persistent effects of GTE-EGCG administration. This study revealed normal lung development in the Ts65Dn mice and highlighted RV hypertrophy and immunological alterations. GTE-EGCG administration resulted in genotype-specific and genotype-independent alterations resulting in lung immaturation and airway hyperreactivity. Our results highlight the cardiovascular and immunological phenotype of Ts65Dn mice and potential use for safety studies of therapeutic agents in a DS-specific context. Summary statementThis study longitudinally follows respiratory and cardiac alterations in the Ts65Dn mouse model and describes the impact of prenatal EGCG modulation on the euploid and trisomic phenotype

systems biology↗

bioRxiv2023

Comprehensive genome editing confers "off-the-shelf" CAR-T cells superior efficacy against solid tumors

Biochemical and immunological negative regulators converge to inhibit tumor-reactive Chimeric Antigen Receptor T (CAR-T) cells, which may explain clinical failures of CAR-T cell therapies against solid tumors. Here, we developed a multifaceted approach to genetically engineer allogeneic ( off -the-shelf) CAR-T cells resistant to both biochemical (adenosine) and immunological (PD-L1 and TGF-{beta}) inhibitory signaling. We multiplexed an adenine base editor with a CRISPR-Cas12b nuclease to manufacture a CAR-T cell product comprising six gene edits to evade allorejection (B2M, CIITA), prevent graft-versus-host disease (CD3E) and resist major biochemical (ADORA2A) and immunological (PDCD1, TGFBR2) immunosuppressive barriers in solid tumors. Combinatorial genetic disruption in CAR-T cells enabled superior anti-tumor efficacy leading to improved tumor elimination and survival in humanized mouse models that recapitulated the suppressive features of a human tumor microenvironment (TME). This novel engineering strategy conferred CAR-T cells resistance to a diverse TME, which may unlock the therapeutic potential of CAR-T cells against solid tumors. One Sentence SummaryMultiplex genome engineered CAR-T cells resistant to allorejection and the convergence of biochemical and immunological negative regulators within the tumor microenvironment exhibit superior efficacy against solid tumors.

cell biology↗

bioRxiv2024

Unraveling factors responsible for pathogenic differences in Lassa virus strains

Lassa virus (LASV) is the etiological agent of Lassa fever (LF), a severe hemorrhagic disease with potential for lethal outcomes. Apart from acute symptoms, LF survivors often endure long-term complications, notably hearing loss, which significantly impacts their quality of life and socioeconomic status in endemic regions of West Africa. Classified as a Risk Group 4 agent, LASV poses a substantial public health threat in affected areas. Our laboratory previously developed a novel lethal guinea pig model of LF utilizing the clinical isolate LASV strain LF2384. However, the specific pathogenic factors underlying LF2384 infection in guinea pigs remained elusive. In this study, we aimed to elucidate the differences in the immunological response induced by LF2384 and LF2350, another LASV isolate from a non-lethal LF case within the same outbreak. Through comprehensive immunological gene profiling, we compared the expression kinetics of key genes in guinea pigs infected with LASV LF2384 and LF2350. Our analysis revealed differential expression patterns for several immunological genes, including CD94, CD19-2, CD23, IL-7, and CIITA, during LF2384 and LF2350 infection. Moreover, through the generation of recombinant LASVs, we sought to identify the specific viral genes responsible for the observed pathogenic differences between LF2384 and LF2350. Our investigations pinpointed the L protein as a crucial determinant of pathogenicity in guinea pigs infected with LASV LF2384. Author summaryLassa virus (LASV) is known to cause lethal hemorrhagic fever, Lassa fever, and is classified as a Risk Group-4 agent, which need to be handled in the highest biocontainment laboratories, biosafety level-4 (BSL-4), due to its high pathogenicity and the lack of preventive or treatment methods. LASV infection has a huge impact on public health and socioeconomics in endemic areas, however, its pathogenic mechanism is still largely unknown. In order to unveil the mechanisms of LASV pathogenesis, we compared the pathogenicity of two LASV isolates, which have opposite phenotypes in guinea pigs. Additionally, we determined the viral factor responsible for pathogenic differences between LASV isolates using reverse genetics. In summary, our study provides valuable insights into the immunological and virological factors underlying the pathogenic differences between LASV strains associated with lethal and non-lethal LF cases. Understanding these distinctions is essential for informing strategies for the diagnosis, treatment, and prevention of LF.

microbiology↗

bioRxiv2019

Using multiple infection history to infer contact network structure

Interactions within a population shape the spread of infectious diseases but contact patterns between individuals are difficult to access. We hypothesised that key properties of these patterns can be inferred from multiple infection data in longitudinal follow-ups. We developed a simulator for epidemics with multiple infections on networks and analysed the resulting individual infection time series by introducing the concept of infection barcodes. We find that, depending on infection multiplicity and network sampling, infection barcode summary statistics can recover network properties such as degree distribution. Furthermore, we show that by mining infection barcodes for multiple infection patterns, one can detect immunological interference between pathogens (i.e. the fact that past infections in a host condition future probability of infection). The combination of individual-based simulations and barcode analysis of infection histories opens promising perspectives to infer and validate transmission networks and immunological interference for infectious diseases from longitudinal cohort data. Author summaryInfectious disease dynamics are constrained both by between-host contacts and pathogen interactions within a host. Furthermore, multiple parasites circulate such that hosts are infected (sometimes simultaneously) by a variety of strains or species. We hypothesise that multiple infection history can inform us about the networks on which parasites are transmitted, but also on within-host interactions such as immunological interference. We developed a simulator for multiple infections on networks. By combining intuitive novel metrics for multiple infection events and established tools from computational data analysis, we show that similarity in infection history between two hosts correlates with their proximity in the contact network. By analysing pathogens co-occurrence patterns within hosts, we also recover immunological interference at the population level. The demonstrated robustness of our results in terms of observability, network clustering, and pathogen diversity opens new perspectives to extract host contact and between-pathogen immunity information from longitudinal cohort data.

ecology↗

bioRxiv2019

Plasma-derived HIV Nef+ exosomes persist in ACTG384 study participants despite successful virological suppression.

Human Immunodeficiency Virus (HIV) accessory protein Negative factor (Nef) is detected in the plasma of HIV+ individuals associated with exosomes. The role of Nef+ exosomes (exNef) in HIV pathogenesis is unknown. We perform a retrospective longitudinal analysis to determine correlative clinical associations of exNef plasma levels in ARV-treated HIV+ patients with or without immune recovery. exNef concentration in a subset of AIDS Clinical Trial Group (ACTG) 384 participants with successful virological suppression and with either high ({Delta} >100 CD4 cell recovery/High Immunological Responders (High-IR) or low ({Delta} [≤]100 CD4 cell recovery/ Low Immunologic Responders (Low-IR) immunologic recovery was measured and compared for study weeks 48, 96, and 144. CD4 recovery showed a negative correlation with exNef at study week 144 (r = -0.3573, *p=.0366). Plasma exNef concentration in high IRs negatively correlated with naive CD4 count and recovery (r = -0.3249, *p = 0. 0348 (High-IR); r =0.2981, *p= #0.0513 (Low-IR)). However, recovery of CD4 memory cells positively correlated with exNef (r =.4534, *p=.0358) in Low-IRs but not in High-IRs. Regimen A (Didanosine, Stavudine, Efavirenz) lowered exNef levels in IRs by 2-fold compared to other regimens. Nef+ exosomes persist in ART-treated HIV+ individuals despite undetectable viral loads, negatively correlates with naive and memory CD4 T cell restoration and may be associated with reduced immunological recovery. Taken together, these data suggest that exNef may represent a novel mechanism utilized by HIV to promote immune dysregulation.

microbiology↗

bioRxiv2026

Understanding cognitive function in post-COVID-19 condition with fatigue: an interdisciplinary multimodal investigation

Lingering cognitive symptoms of post-COVID-19 condition (PCC) continue to challenge our understanding, highlighting the need for interdisciplinary research. We investigated whether individuals with PCC and fatigue differ from matched controls across neurocognitive, neuroimaging, and immunological measures, integrating these findings with qualitative phenomenological analyses through multimodal cross-analysis. Individuals with PCC and clinically significant fatigue (n=34), and age-, sex-, and education-matched controls recovered from COVID-19 without PCC (n=37) were included. Assessments encompassed physician evaluation, neuropsychological and functional tests, structural and functional MRI, immunological tests, and qualitative phenomenological analysis of interviews. Data were analyzed using established methods and an interdisciplinary cross-analysis to examine persistent cognitive symptoms in PCC. Group comparisons revealed subtle differences between individuals with PCC and controls, while neurocognitive performance and immunological markers remained within normative ranges. Modest differences in white matter, myelin related, and global brain measures were observed, alongside differences in associations between network connectivity and neurocognitive performance across groups, suggesting reduced network resilience rather than domain specific deficits. This pattern resonated with qualitative phenomenological findings: altered experiences of concentrating and difficulties to execute decisions and actions, despite preserved performance on standard neurocognitive tests. These findings suggest that cognitive symptoms in post-COVID-19 fatigue are associated with subtle neurobiological alterations not captured by standard cognitive assessments. In this highly fatigued sample, converging neuroimaging, neurocognitive and immunological findings point toward reduced network efficiency rather than overt cognitive impairment. Qualitative phenomenological analysis further highlighted altered modes of being in the world characterized by increased cognitive effort and difficulties executing decisions and actions.

neuroscience↗

bioRxiv2020

Marmoset monkeys (Callithrix jacchus) develop eosinophilic airway inflammation after house dust mite exposure

BackgroundExtensive analysis of eosinophilic airway inflammation in human-relevant animal models is required to test novel, human-specific pharmaceuticals. This requires species, which show high genetic homology to humans such as non-human primates. Efficacy assessment of novel human-specific biologicals in eosinophilic airway inflammation is currently performed in the cost-intensive macaque asthma model. ObjectiveThe present study investigated whether marmoset monkeys (Callithrix jacchus), a small-bodied non-human primate species from the New World, develop eosinophilic airway inflammation in response to house dust mite allergen exposure (HDM, Dermatophagoides pteronyssinus). MethodsMarmoset monkeys were sensitized against HDM by subcutaneous (s.c.) injection and subsequent intratracheal (i.t.) HDM aerosol challenges. Airway and systemic immunologic reactions were monitored and sensitivity towards glucocorticoid therapy was assessed. The pulmonary immunologic response was analyzed by repetitive bronchoalveolar lavage (BAL). ResultsBronchoalveolar lavage fluid (BALF) exhibited increased levels of eosinophils, mast cells, and lymphocytes, as well as interleukin (IL)-13 after HDM challenges, compared to negative controls. The systemic immunologic response was assessed in peripheral blood mononuclear cells derived from sensitized animals, which secreted increased IL-13 and IFN-{gamma} upon allergen stimulation in contrast to non-sensitized negative control animals. Although IgE was not detectable, HDM-specific serum IgG was elevated in sensitized animals. Both airway and systemic responses were reduced by treatment with glucocorticoids. However, lung function and pathological analyses did not reveal significant differences between groups. ConclusionIn conclusion, marmoset monkeys developed a mild HDM-induced eosinophilic airway inflammation useful for efficacy testing of novel human-specific biologicals.

immunology↗

bioRxiv2020

Interactions of SARS-CoV-2 infection with chronic obesity inflammation: a complex network phenomenon

Obesity is one of the biggest public health problems in the world, and its pathophysiological characteristics include chronic inflammation with an increase in various circulating inflammatory markers, such as acute inflammatory cytokines. Complications in the respiratory tract are related to bodily problems, which lead to a restriction of lung function due to reduced volume, inducing an increase in respiratory work. SARS-CoV-2 has a high potential for contamination by respiratory secretions and, therefore, obesity is one of the main risk factors for complications due to the association established between obesity, chronic inflammation and respiratory infection. The objective was to analyze the complex relationships between obesity and COVID-19 in a meta-analysis study using complex network modeling and the theoretical knockouts technique. Here, we identify and justify through a mathematical analysis the relationships between all the immunological agents added to the proposed immunological networks, considered as a simple evident interaction, relationship, influence, response, activation, based on our quantifiers. They performed the knockouts of all 52 vertices in the COVID-19 network and obesity - regardless of the environment, which would result in nonsense - and the COVID-19 infection network without considering obesity. The stationary flow vector (flow profile), for some knockouts of immunological interest in COVID-19 infections, was chosen IFN, IL-6, IL-10, IL-17 and TNF. This initial study pointed out the importance of chronic inflammation in the obese individual as an important factor in potentiating the disease caused by covid-19 and, in particular, the importance on IL-17.

immunology↗

bioRxiv2020

Plasma mass spectrometry fingerprints induced by bacterial endotoxins in murine models as markers of pathophysiological evolution in sepsis

Sepsis has been called "the graveyard of pharmaceutical companies" due to the numerous failed clinical trials. The lack of tools to monitor the immunological status in sepsis constrains the development of immunomodulatory therapies. Here, we evaluated a test based on whole plasma peptidome acquired in a MALDI-TOF-mass spectrometer used for bacterial biotyping and machine-learning algorithms to discriminate the different immunological phases of sepsis. In this proof of concept study, two discrete lipopolysaccharide-(LPS) induced murine models emulating the pro- and anti-inflammatory phases that occur during sepsis were evaluated. The LPS group was inoculated with a single high dose of LPS, recalling the proinflammatory phase, and the IS groups was subjected to increasing doses of LPS to induce the anti-inflammatory/immunosuppression phase. Unstimulated mice served as controls. Both experimental groups showed the hallmarks of pro- and anti- inflammatory phases respectively; the LPS group showed leukopenia and higher levels of cytokines and tissue damage markers, and the IS group showed neutrophilia, lymphopenia and significantly lower antibody titers upon immunization. Principal component analysis of the plasma peptidomes formed three discrete clusters that mostly coincided with the experimental groups. In addition, machine-learning algorithms discriminated the different experimental groups with a sensitivity and specificity of up to 95.7% and 90.9% respectively. Our data reveal the potential of plasma peptidome analysis by MALDI-TOF-mass spectrometry as a simple, speedy and readily transferrable method for sepsis patient stratification that would contribute to therapeutic decision-making based on their immunological status.

immunology↗

bioRxiv2021

Cytotoxic lymphocytes target HIV-1 Gag through granzyme M-mediated cleavage

HIV-1 leads to progression to immunodeficiency and death of individuals who do not receive successful antiretroviral therapy. Initially, the hosts immune response controls the infection, but cannot eliminate the HIV-1 from the host. Cytotoxic lymphocytes are the key effector cells in this response and can mediate crucial antiviral responses through the release of a set of proteases called granzymes towards HIV-1-infected cells. However, little is known about the immunological molecular mechanisms by which granzymes could control HIV-1. Since we noted that HIV-1 subtype C (HIV-1C) Gag with the tetrapeptide insertion PYKE contains a putative granzyme M (GrM) cleavage site (KEPL) that overlaps with the PYKE insertion, we analyzed the proteolytic activity of GrM towards Gag. Immunoblot analysis showed that GrM could cleave Gag proteins from HIV-1B and variants from HIV-1C of which the Gag-PYKE variant was cleaved with extremely high efficiency. The main cleavage site was directly after the insertion after leucine residue 483. GrM-mediated cleavage of Gag was also observed in co-cultures using cytotoxic lymphocytes as effector cells and this cleavage could be inhibited by a GrM inhibitor peptide. Altogether, our data indicate towards a noncytotoxic immunological mechanism by which GrM-positive cytotoxic lymphocytes target the HIV-1 Gag protein within infected cells to potentially control HIV-1 infection. This mechanism could be exploited in new therapeutic strategies to treat HIV-1-infected patients to improve immunological control of the infection.

immunology↗

bioRxiv2021

SARS-CoV-2 receptor ACE2 identifies immuno-hot tumors in breast cancer

Angiotensin-converting enzyme 2 (ACE2) is known as a host cell receptor for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), which is identified to be dysregulated in multiple tumors. Although the characterization of abnormal ACE2 expression in malignancies has been preliminarily explored, in-depth analysis of ACE2 in breast cancer (BRCA) has not been elucidated. A systematic pan-cancer analysis was conducted to assess the expression pattern and immunological role of ACE2 based on RNA-sequencing (RNA-seq) data downloaded from The Cancer Genome Atlas (TCGA). Next, correlations between ACE2 expression immunological characteristics in the BRCA tumor microenvironment (TME) were evaluated. Also, the role of ACE2 in predicting the clinical features and the response to therapeutic options in BRCA was estimated. These findings were subsequently validated in another public transcriptomic cohort as well as a recruited cohort. ACE2 was lowly expressed in most cancers compared with adjacent tissues. ACE2 was positively correlated with immunomodulators, tumor-infiltrating immune cells (TIICs), cancer immunity cycles, immune checkpoints, and tumor mutation burden (TMB). Besides, high ACE2 levels indicated the triple-negative breast cancer (TNBC) subtype of BRCA, lower response to endocrine therapy and higher response to chemotherapy, anti-ERBB therapy, antiangiogenic therapy and immunotherapy. To sum up, ACE2 correlates with an inflamed TME and identifies immuno-hot tumors, which may be used as an auxiliary biomarker for the identification of immunological characteristics in BRCA.

immunology↗

bioRxiv2021

Determinants of precocious B-cell aging in European adolescences living with perinatally acquired HIV-1 after over 10 years of suppressive therapy

HIV infection results in a state of chronic immune activation leading to premature immune aging, B-cells dysfunction, that persists despite prolonged virological suppression. In this scenario, adolescence living with perinatally acquired HIV (PHIV), deserve a peculiar attention since potentially exposed for their entire life to chronic immune activation. Here we identified determinants of precocious aging B cells in 40 PHIV undergoing suppressive antiretroviral therapy (ART) for median 13.5 years. All individuals started ART by 2nd year of life and achieved virus suppression within the 1st year of ART, with majority of patient maintaining suppression until analysis and 5/40 experiencing viral Spike (transient elevation of HIV-1 VL, 50-999 copies/ml). We employed a multiomics approach including deep immunological B and T cell phenotype in PBMC, with aging B cells defined by the expression of T-bet and CD11c; plasma proteomics analysis by mass spectrometry and serum level of anti-measles antibodies as correlates of humoral response. We found that individuals with expansion of aging B cell, defined by the expression of T-bet+CD11c+, were those starting treatment later, presenting detectable levels of cell-associated HIV-1 RNA, history of Spikes, and a higher frequency of exhausted T-cells, including those expressing PD-1, LAG3, TIGIT. Accordingly, the proteomic analysis revealed that subjects with expansion of aging B cells and exhausted T cells had enrichment of proteins involved in immune inflammation and complement activation pathways, such as CLU and APCS which are also involved in tumor progression. Signs of precocious aging were associated with a reduced capacity to maintain virological memory against measles vaccination. To our knowledge, this is the first study focusing on precocious B-cell aging and dysfunctionality in PHIV with long-term virological suppression. Our experimental strategy enabled identification of clinical, viral, cellular and plasma soluble markers associated with B-cells aging. Our results pave the way to further define risk of disease progression or lymphoproliferative disorders in PHIV. Author summaryDespite a successful antiretroviral therapy (ART), adolescence living with perinatally acquired HIV (PHIV) experience B-cells dysfunction, including loss of vaccine-induced immunological memory and higher risk of developing B-cells associated tumors. It is thus paramount to define novel and precise correlates of precious aging B cell for the definition of novel therapeutic strategies. Here, we studied 40 PHIV who started treatment by 2nd year of life and maintain virological suppression for 13.5 years, with 5/40 patients experiencing transient elevation of the HIV-1 load in the plasma (Spike). We applied a multi-omics approach including immunological B and T cell phenotype, plasma proteomics analysis and serum level of anti-measles antibodies as functional correlates of vaccine-induced immunity. We found that levels of aging B cells were positively associated with age at ART start, cell associated HIV-1 RNA (caHIV-1 RNA) and the presence of Spikes. Individuals with increased proportions of aging B cells had concomitant expansion of exhausted T cells and were unable to maintain vaccine-induced immunity over time. B-cell aging, and T-cell exhaustion were also associated with proteins involved in immune inflammation. The factors found here to be associated with aging B-cell could inform further therapeutic studies.

immunology↗

bioRxiv2022

Functional, transcriptional, and microbial shifts associated with healthy pulmonary aging: insights from rhesus macaques

Older individuals are at increased risk of developing severe respiratory infections due to age-related changes in the immunological, microbial, and functional landscape of the lung. However, our understanding of the impact of age on the respiratory tract remains limited as samples from healthy humans are challenging to obtain and confounding variables such as smoking and environmental pollutant exposure make it difficult to assess the true impact of aging. On the other hand, studies in rodent models are biased by their specific pathogen free status. In this study, we utilize a rhesus macaque model of healthy aging to examine the functional, immunological, and microbial consequences of aging in the lung. Pulmonary function testing in this large (n=34 adult, n=49 aged) cross-sectional study established age and sex differences similar to humans supporting the translational accuracy of this model. Additionally, an increased abundance of myeloid cells (alveolar and infiltrating macrophages) and a concomitant decrease in T-cells were also observed in aged animals. Single cell RNA sequencing indicated a transcriptional shift in the pulmonary CD8+ T-cell population from GRZMB expressing cells to IFN expressing cells, while frequency of IL-1B expressing alveolar macrophages was significantly reduced. Interestingly, the lung microbiome of many animals was dominated by a single microbe, Tropheryma spp., the prevalence of which decreased with age. These data provide a comprehensive picture of the functional, microbial and immunological changes of the lung in healthy macaque aging and provide insight into the increased prevalence and severity of respiratory disease in the elderly.

immunology↗

bioRxiv2022

A conserved immune trajectory of recovery in hospitalized COVID-19 patients

Many studies have provided insights into the immune response to COVID-19; however, little is known about the immunological changes and immune signaling occurring during COVID-19 resolution. Individual heterogeneity and variable disease resolution timelines obscure unifying immune characteristics. Here, we collected and profiled >200 longitudinal peripheral blood samples from patients hospitalized with COVID-19, with other respiratory infections, and healthy individuals, using mass cytometry to measure immune cells and signaling states at single cell resolution. COVID-19 patients showed a unique immune composition and an early, coordinated and elevated immune cell signaling profile, which correlated with early hospital discharge. Intra-patient time course analysis tied to clinically relevant events of recovery revealed a conserved set of immunological processes that accompany, and are unique to, disease resolution and discharge. This immunological process, together with additional changes in CD4 regulatory T cells and basophils, accompanies recovery from respiratory failure and is associated with better clinical outcomes at the time of admission. Our work elucidates the biological timeline of immune recovery from COVID-19 and provides insights into the fundamental processes of COVID-19 resolution in hospitalized patients.

immunology↗

bioRxiv2022

Induction of a CD8 T cell intrinsic DNA damage and repair response is associated with clinical response to PD-1 blockade in uterine cancer.

Despite the success of immune checkpoint blockade (ICB), many patients fail to achieve durable clinical benefit, and the underlying immunological mechanisms remain poorly understood. Here, we investigated immune reinvigoration by ICB in advanced or recurrent hypermutated or microsatellite instability-high, mismatch repair deficient (MSI-H/MMRd) uterine cancer patients treated with anti-PD-1 (nivolumab). CD8 T cells underwent rapid pharmacodynamic proliferation 2-4 weeks after initiating PD-1 blockade. This immunological response, however, did not correlate with clinical response. We hypothesized that the T cell-intrinsic response to proliferative and genotoxic stress might contribute to the disparity between immunological and clinical response. We developed a high-dimensional single cell cytometric platform to simultaneously analyze T cell differentiation with changes in DNA damage and repair (DDR) pathways. This DDR-Immune platform revealed T cell subset-specific patterns of DDR, and distinct DDR pathways induced by different types of DNA damage. Applying this platform to MSI-H/MMRd or hypermutated uterine cancer patients revealed a signature of DDR exemplified by rapid increase in phosphorylated-ATM (pATM) intrinsic to CD8 T cells proliferating in response to PD-1 blockade that distinguished clinical responders and non-responders. ATM regulated transcriptional circuits in T cells were associated with better clinical response to PD-1 blockade. These findings highlight a previously unrecognized role for CD8 T cell-intrinsic DDR as a potential determinant of immune fitness and clinical outcome of PD-1 blockade therapy. STATEMENT OF SIGNIFICANCEUsing high-dimensional immune and DNA damage response (DDR) profiling in T cell subsets we identified distinct signatures in anti-PD-1 treated MSI-H/hypermutated uterine cancer patients associated with clinical response versus non-response. Thus, T cell-intrinsic DDR is a potential determinant of immune responsiveness and clinical outcome to PD-1 blockade therapy in cancer.

immunology↗

bioRxiv2022

Engineering non-cytotoxic delivery of proteins by T cells via fusion to NPC2

Engineering cellular therapeutics by programming T cells has great potential in immunology. The primary mechanism employed by T cells for the specific transfer of proteins at the immunological synapse is via the lysosomal perforin pathway that facilitates the transfer of cytotoxic granzymes leading to apoptosis in target cells. Facilitating the delivery of non-cytotoxic proteins through perforin oligomers will dramatically expand the range of protein cargos that T cells can traffic to the target cells. Here, we have identified the intralysosomal protein, NPC2, as a chaperone that can facilitate the delivery of T-cell derived reporter proteins through perforin pores at the immunological synapse. Structural and biophysical considerations suggested that NPC2 could traverse through perforin pores and in vitro experiments confirmed the transport of purified NPC2 through perforin pores on cell membranes. To characterize the ability of NPC2 to facilitate the transfer of payloads in T cells, we constructed NPC2-mCherry fusion proteins in T cells. Using confocal microscopy and flow cytometry, we confirmed the colocalization of the NPC2 fused protein with lytic granules and the transfer of the fluorescent protein payload from T cells to target cells in co-culture experiments. The NPC2 fusion enabled the localization of mCherry to secretory lysosomes in mouse TCR CD8+ T cells and human CD4+ and CD8+ chimeric antigen receptor (CAR) T cells. These results illustrate that by using NPC2 as a molecular chaperone, the NPC2-perforin pathway can be exploited as a programmable molecular delivery system for cell-based therapies.

immunology↗