High expression of CD38 and MHC class II on CD8+ T cells during severe influenza disease reflects bystander activation and trogocytosis

IL-15-Activated CD38+HLA-DR+CD8+ T cells induce liver injury in cirrhosis via JAK/STAT5 and PI3K/mTOR pathways

The development and progression of liver cirrhosis are considerably influenced by immune processes, with CD8 + T cells playing a key role. Notably, cytokines can activate bystander CD38 + HLA-DR + CD8 + T cells without the need for T cell receptor (TCR) stimulation. However, their role in liver fibrosis remains controversial. This study aimed to investigate the pathological role of CD38 + HLA-DR + CD8 + T cells in cirrhosis progression and explore the mechanisms that regulate their functions. Peripheral blood mononuclear cells (PBMCs) were extracted from patients with cirrhosis and healthy donors, and the ratio of CD38+HLA-DR+CD8+ T cells was assessed through flow cytometry. The relationship between the prevalence of these cells and certain clinical indicators was investigated. Additionally, CD8+ T cells from healthy donors were used to examine the impact of cytokine IL-15 on CD38+HLA-DR+CD8+ T cells, utilizing flow cytometry and in vitro cytotoxicity assays. Finally, the signaling pathways involved in IL-15 activation of CD38+HLA-DR+CD8+ T cells were examined in vitro. The proportion of CD38+HLA-DR+CD8+ T cells was significantly increased in patients with cirrhosis compared to healthy donors and exhibited a strong correlation with disease severity, hepatic damage, and inflammation in cirrhosis. IL-15-stimulated CD38+HLA-DR+CD8+ T cells from healthy donors demonstrated proliferation and overexpression of cytotoxic molecules, exhibiting NKG2D- and FasL-dependent innate-like cytotoxicity without TCR activation. Notably, IL-15 did not alter the mitochondrial function of these cells. The JAK/STAT5 and PI3K/mTOR pathways were found to play a critical role in IL-15-induced innate-like cytotoxicity. These findings suggested that CD38+HLA-DR+CD8+ T cells from patients with cirrhosis contribute to immune-mediated liver injury. Furthermore, the JAK/STAT5 and PI3K/mTOR pathways were essential for IL-15-induced activation of CD38+HLA-DR+CD8+ T cells, which expressed NKG2D and FasL, demonstrating innate cytotoxicity independent of TCR engagement.

Simultaneous coinfection with influenza virus and an arbovirus impedes influenza-specific but not Semliki Forest virus-specific responses

Outbreaks of respiratory virus infections and arbovirus infections both pose a substantial threat to global public health. Clinically, both types of infection range from mild to severe and coinfections may occur more commonly than supposed. Our previous experimental coinfection study in mice demonstrated that prior infection with the arbovirus Semliki Forest virus (SFV) negatively impacted immune responses to influenza A virus (IAV). Here, we investigate whether simultaneous coinfection impacts the outcome of immune responses or disease. Simultaneous SFV and IAV infection did not lead to exacerbated or attenuated disease compared with the single virus infection control groups. SFV brain virus titers and brain pathology, including inflammation and immune responses, were comparable in the coinfection and single infection groups. By contrast, there was enhanced IAV replication, but no exacerbated lung pathology in coinfected mice. The magnitude of IAV-specific CD8+ T-cell responses in the lungs was lower compared with IAV-only infection. Considered along with our previous study, this study provides evidence that the timing of viral coinfection is pivotal in determining effects on immune responses, pathological changes and disease outcome.

Single-cell immune profiling of third trimester pregnancies defines importance of chemokine receptors and prevalence of CMV-induced NK cells in the periphery and decidua

Human pregnancy presents a unique physiological state that allows for growth of an antigenically dissimilar foetus and requires specific adaptations of the immune system. The immune system plays an important role in establishing and maintaining successful pregnancy, yet deep understanding of immunological responses in pregnancy is lacking. To provide in-depth understanding of the immunological landscape of pregnancy, with a focus on NK cells, we used high-throughput cell surface proteome screening of >350 markers and scRNAseq with 130 CITE-seq antibodies to identify key differentially expressed molecules and investigated their potential roles in altered immunity. We identified skewing in NK cell subsets towards higher frequencies of CD56bright cells caused by a reduced number of CD56dim cells in the peripheral blood during pregnancy and provide evidence for a role of chemokine receptor, CX3CR1, in NK cell activation. In addition, we defined a new cytomegalovirus (CMV)-induced decidual NK cell population in CMV+ pregnancies with tissue-residency markers. Overall, our data provide fundamental knowledge into how NK cell immunity is altered in pregnancy, and key knowledge needed to inform vaccine and therapeutic strategies to manage infections or pregnancy complications.

Prior influenza virus infection alleviates an arbovirus encephalitis by reducing viral titer, inflammation, and cellular infiltrates in the central nervous system

Respiratory and encephalitic virus infections represent a significant risk to public health globally. Detailed investigations of immunological responses and disease outcomes during sequential virus infections are rare. Here, we define the impact of influenza virus infection on a subsequent virus encephalitis. We used a model system in which mice were given influenza A virus (IAV) infection 8 days prior to Semliki Forest virus (SFV) infection (IAV→SFV). IAV infection clearly attenuated the subsequent SFV infection with reduced titers of infectious SFV and lower levels of cytokines and chemokines in the central nervous system (CNS). In contrast, the SFV viremia in both IAV→SFV and SFV-only mice was comparable. Increased type I interferon (IFN) levels in the CNS after IAV infection might have contributed to some level of protection towards SFV infection in the CNS, suggesting that early control of SFV replication in the CNS during IAV→SFV infection led to reduced adaptive response, given the lower number of CD8+ T cells recruited to the brain in IAV→SFV infection. In lungs, however, prior IAV infection elicited effector CD8+ T cells with highly activated CD38 and/or CD25 phenotypes, while SFV-only infection elicited distinct effector CD8+ T cells with increased frequencies of KLRG1 expression, a hallmark of short-lived effector T cells. Taken together, our findings demonstrate that prior IAV infection can confer protective immunity toward secondary SFV infection, confirmed by reduced disease severity and inflammatory immune responses in the brain. Our work provides important insights into therapies and vaccine regimens directed against unrelated pathogens.

IMPORTANCE

Influenza viruses are medically important human pathogens that caused epidemics and pandemics throughout history. Conversely, encephalitic arthropod-borne virus (arboviral) diseases affect both humans and domestic animals, creating massive public health issues. Influenza viruses circulate globally while arboviruses dominate tropical regions. Given both influenza virus and encephalitic arboviruses, such as alphaviruses, circulate in many regions globally, co-infections are likely to occur. In addition, arthropod-borne neurotropic infections are generally mild or asymptomatic, hence are likely to be unnoticed as a risk factor during influenza infection. However, the consequences of such co-infections are unclear. Our recent study showed that alphavirus infection preceding Influenza A virus (IAV) infection negatively impacted immune responses to the influenza virus in mice. Here, we aim to investigate the immune responses when the order of sequential infection with IAV and alphavirus are swapped. Altogether, our findings will provide key insights to improved diagnostics, preventative vaccines, and antiviral therapies.

Molecular determinants of cross-strain influenza A virus recognition by αβ T cell receptors

Cross-reactive αβ T cell receptors (TCRs) recognizing multiple peptide variants can provide effective control of rapidly evolving viruses yet remain understudied. By screening 12 naturally occurring influenza-derived HLA-B*35:01-restricted nucleoprotein (NP)418-426 epitopes (B*35:01-NP418) that emerged since 1918 within influenza A viruses, including 2024 A/H5N1 viruses, we identified functional broadly cross-reactive T cells universally recognizing NP418 variants. Binding studies demonstrated that TCR cross-reactivity was concomitant with diminished antigen sensitivity. Primary human B*35:01/NP418+CD8+ T cell lines displayed reduced cross-reactivity in the absence of CD8 coreceptor binding, validating the low avidity of cross-reactive B*35:01-NP418+CD8+ T cell responses. Six TCR-HLA-B*35:01/NP418 crystal structures showed how cross-reactive TCRs recognized multiple B*35:01/NP418 epitope variants. Specific TCR interactions were formed with invariant and conserved peptide-HLA features, thus remaining distal from highly varied positions of the NP418 epitope. Our study defines molecular mechanisms associated with extensive TCR cross-reactivity toward naturally occurring viral variants highly relevant to universal protective immunity against influenza.

IL-15-induced CD38+HLA-DR+CD8+ T cells correlate with liver injury via NKG2D in chronic hepatitis B cirrhosis

Objectives

CD8+ T cells play a critical role in the immune dysfunction associated with liver cirrhosis. CD38+HLA-DR+CD8+ T cells, or bystander-activated CD8+ T cells, are involved in tissue injury but their specific contribution to liver cirrhosis remains unclear. This study sought to identify the mechanism for CD38+HLA-DR+CD8+ T cell-mediated pathogenesis during liver cirrhosis.

Methods

The immunophenotype, antigen specificity, cytokine secretion and cytotoxicity-related indicators of CD38+HLA-DR+CD8+ T cells were determined using flow cytometry. The functional properties of these cells were assessed using transcriptome analysis. CD38+HLA-DR+CD8+ T-cell killing was detected using cytotoxicity and antibody-blocking assays.

Results

The proportion of CD38+HLA-DR+CD8+ T cells was significantly elevated in liver cirrhosis patients and correlated with tissue damage. Transcriptome analysis revealed that these cells had innate-like functional characteristics. This CD8+ T-cell population primarily consisted of effector memory T cells and produced a high level of cytotoxicity-related cytokines, granzyme B and perforin. IL-15 promoted CD38+HLA-DR+CD8+ T-cell activation and proliferation, inducing significant TCR-independent cytotoxicity mediated through NKG2D.

Conclusions

CD38+HLA-DR+CD8+ T cells correlated with cirrhosis-related liver injury and contributed to liver damage by signalling through NKG2D in a TCR-independent manner.

Defining the balance between optimal immunity and immunopathology in influenza virus infection

Influenza A viruses remain a global threat to human health, with continued pandemic potential. In this Review, we discuss our current understanding of the optimal immune responses that drive recovery from influenza virus infection, highlighting the fine balance between protective immune mechanisms and detrimental immunopathology. We describe the contribution of innate and adaptive immune cells, inflammatory modulators and antibodies to influenza virus-specific immunity, inflammation and immunopathology. We highlight recent human influenza virus challenge studies that advance our understanding of susceptibility to influenza and determinants of symptomatic disease. We also describe studies of influenza virus-specific immunity in high-risk groups following infection and vaccination that inform the design of future vaccines to promote optimal antiviral immunity, particularly in vulnerable populations. Finally, we draw on lessons from the COVID-19 pandemic to refocus our attention to the ever-changing, highly mutable influenza A virus, predicted to cause future global pandemics.

Physiological and therapeutic relevance of T cell receptor-mediated antigen trogocytosis

Trogocytosis is an active process whereby fragments of plasma membrane proteins and cytoplasm are transferred from one cell to another in a cell-cell contact-dependent manner. T cells trogocytose pieces of the cells presenting antigen to them at the site of the immunological synapse. Fragments of the antigen-presenting cell membrane rich in antigen/major histocompatibility (MHC) complexes are internalized by the T cell. Those complexes are redirected to the plasma membrane of the T cell, which subsequently becomes an antigen-presenting cell to other T cells. Removing antigen/MHC complexes from professional and tumoral cells has consequences for the intensity and duration of the immune response. However, the acquired capacity of T cells to present the trogocytosed cognate antigen/MHC complexes also affects the properties of the trogocytotic T cells. Acting as antigen-presenting cells, trogocytotic CD4 T cells influence both the differentiation of cytotoxic T cells and the differentiation of other CD4 T cells into pro-inflammatory effector T cells. Furthermore, trogocytosis of antigen/MHC complexes promotes the differentiation of the trogocytotic CD4 T cells towards regulatory T cells and Th2 effector cells. Trogoctyosis is, therefore, a parallel mechanism to signal transduction by membrane receptors, including the T cell antigen receptor, at the plane of the plasma membrane.

Twin study identifies early immunological and metabolic dysregulation of CD8+ T cells in multiple sclerosis

Multiple sclerosis (MS) is an inflammatory neurological disease of the central nervous system with a subclinical phase preceding frank neuroinflammation. CD8+ T cells are abundant within MS lesions, but their potential role in disease pathology remains unclear. Using high-throughput single-cell RNA sequencing and single-cell T cell receptor analysis, we compared CD8+ T cell clones from the blood and cerebrospinal fluid (CSF) of monozygotic twin pairs in which the cotwin had either no or subclinical neuroinflammation (SCNI). We identified peripheral MS-associated immunological and metabolic alterations indicative of an enhanced migratory, proinflammatory, and activated CD8+ T cell phenotype, which was also evident in cotwins with SCNI and in an independent validation cohort of people with MS. Together, our in-depth single-cell analysis indicates a disease-driving proinflammatory role of infiltrating CD8+ T cells and identifies potential immunological and metabolic therapeutic targets in both prodromal and definitive stages of the disease.

Association of CD8+TILs co-expressing granzyme A and interferon-γ with colon cancer cells in the tumor microenvironment

CD8+T cells secreting granzyme A (GZMA) can induce pyroptosis in tumor cells by effectively cleaving gasdermin B (GSDMB), which is stimulated by interferon-γ (IFN-γ). However, the interaction between GZMA-expressing CD8+T cells and GSDMB-expressing tumor cells in colon cancer remains poorly understood. Our research employed multi-color immunohistochemistry (mIHC) staining and integrated clinical data to explore the spatial distribution and clinical relevance of GZMA- and IFN-γ-expressing CD8+ tumor-infiltrating lymphocytes (TILs), as well as GSDMB-expressing CK+ cells, within the tumor microenvironment (TME) of human colon cancer samples. Additionally, we utilizing single-cell RNA sequencing (scRNA-seq) data to examine the functional dynamics and interactions among these cell populations. scRNA-seq analysis of colorectal cancer (CRC) tissues revealed that CD8+TILs co-expressed GZMA and IFN-γ, but not other cell types. Our mIHC staining results indicated that a significant reduction in the infiltration of GZMA+IFN-γ+CD8+TILs in colon cancer patients (P < 0.01). Functional analysis results indicated that GZMA+IFN-γ+CD8+TILs demonstrated enhanced activation and effector functions compared to other CD8+TIL subsets. Furthermore, GSDMB-expressing CK+ cells exhibited augmented immunogenicity. Correlation analysis highlighted a positive association between GSDMB+CK+ cells and GZMA+IFN-γ+CD8+TILs (r = 0.221, P = 0.033). Analysis of cell-cell interactions further showed that these interactions were mediated by IFN-γ and transforming growth factor-β (TGF-β), the co-stimulatory molecule ICOS, and immune checkpoint molecules TIGIT and TIM-3. These findings suggested that GZMA+IFN-γ+CD8+TILs modulating GSDMB-expressing tumor cells, significantly impacted the immune microenvironment and patients' prognosis in colon cancer. By elucidating these mechanisms, our present study aims to provide novel insights for the advancement of immunotherapeutic strategies in colon cancer.

Prior infection with unrelated neurotropic virus exacerbates influenza disease and impairs lung T cell responses

Immunity to infectious diseases is predominantly studied by measuring immune responses towards a single pathogen, although co-infections are common. In-depth mechanisms on how co-infections impact anti-viral immunity are lacking, but are highly relevant to treatment and prevention. We established a mouse model of co-infection with unrelated viruses, influenza A (IAV) and Semliki Forest virus (SFV), causing disease in different organ systems. SFV infection eight days before IAV infection results in prolonged IAV replication, elevated cytokine/chemokine levels and exacerbated lung pathology. This is associated with impaired lung IAV-specific CD8+ T cell responses, stemming from suboptimal CD8+ T cell activation and proliferation in draining lymph nodes, and dendritic cell paralysis. Prior SFV infection leads to increased blood brain barrier permeability and presence of IAV RNA in brain, associated with increased trafficking of IAV-specific CD8+ T cells and establishment of long-term tissue-resident memory. Relative to lung IAV-specific CD8+ T cells, brain memory IAV-specific CD8+ T cells have increased TCR repertoire diversity within immunodominant DbNP366+CD8+ and DbPA224+CD8+ responses, featuring suboptimal TCR clonotypes. Overall, our study demonstrates that infection with an unrelated neurotropic virus perturbs IAV-specific immune responses and exacerbates IAV disease. Our work provides key insights into therapy and vaccine regimens directed against unrelated pathogens.

Autoimmunity-associated allele of tyrosine phosphatase gene PTPN22 enhances anti-viral immunity

The 1858C>T allele of the tyrosine phosphatase PTPN22 is present in 5-10% of the North American population and is strongly associated with numerous autoimmune diseases. Although research has been done to define how this allele potentiates autoimmunity, the influence PTPN22 and its pro-autoimmune allele has in anti-viral immunity remains poorly defined. Here, we use single cell RNA-sequencing and functional studies to interrogate the impact of this pro-autoimmune allele on anti-viral immunity during Lymphocytic Choriomeningitis Virus clone 13 (LCMV-cl13) infection. Mice homozygous for this allele (PEP-619WW) clear the LCMV-cl13 virus whereas wildtype (PEP-WT) mice cannot. This is associated with enhanced anti-viral CD4 T cell responses and a more immunostimulatory CD8α- cDC phenotype. Adoptive transfer studies demonstrated that PEP-619WW enhanced anti-viral CD4 T cell function through virus-specific CD4 T cell intrinsic and extrinsic mechanisms. Taken together, our data show that the pro-autoimmune allele of Ptpn22 drives a beneficial anti-viral immune response thereby preventing what is normally a chronic virus infection.

Intercellular Transfer of Immune Regulatory Molecules Via Trogocytosis

Trogocytosis, an active cellular process involving the transfer of plasma membrane and attached cytosol during cell-to-cell contact, has been observed prominently in CD4 T cells interacting with antigen-presenting cells carrying antigen-loaded major histocompatibility complex (MHC) class II molecules. Despite the inherent absence of MHC class II molecules in CD4 T cells, they actively acquire these molecules from encountered antigen-presenting cells, leading to the formation of antigen-loaded MHC class II molecules-dressed CD4 T cells. Subsequently, these dressed CD4 T cells engage in antigen presentation to other CD4 T cells, revealing a dynamic mechanism of immune communication. The transferred membrane proteins through trogocytosis retain their surface localization, thereby altering cellular functions. Concurrently, the donor cells experience a loss of membrane proteins, resulting in functional changes due to the altered membrane properties. This chapter provides a focused exploration into trogocytosis-mediated transfer of immune regulatory molecules and its consequential impact on diverse immune responses.

Broad spectrum SARS-CoV-2-specific immunity in hospitalized First Nations peoples recovering from COVID-19

Indigenous peoples globally are at increased risk of COVID-19-associated morbidity and mortality. However, data that describe immune responses to SARS-CoV-2 infection in Indigenous populations are lacking. We evaluated immune responses in Australian First Nations peoples hospitalized with COVID-19. Our work comprehensively mapped out inflammatory, humoral and adaptive immune responses following SARS-CoV-2 infection. Patients were recruited early following the lifting of strict public health measures in the Northern Territory, Australia, between November 2021 and May 2022. Australian First Nations peoples recovering from COVID-19 showed increased levels of MCP-1 and IL-8 cytokines, IgG-antibodies against Delta-RBD and memory SARS-CoV-2-specific T cell responses prior to hospital discharge in comparison with hospital admission, with resolution of hyperactivated HLA-DR+ CD38+ T cells. SARS-CoV-2 infection elicited coordinated ASC, Tfh and CD8+ T cell responses in concert with CD4+ T cell responses. Delta and Omicron RBD-IgG, as well as Ancestral N-IgG antibodies, strongly correlated with Ancestral RBD-IgG antibodies and Spike-specific memory B cells. We provide evidence of broad and robust immune responses following SARS-CoV-2 infection in Indigenous peoples, resembling those of non-Indigenous COVID-19 hospitalized patients.

Severe respiratory viral infections: T-cell functions diverging from immunity to inflammation

Respiratory viral infections such as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza A virus (IAV) trigger distinct clinical outcomes defined by immunity-based viral clearance or disease associated with exaggerated and prolonged inflammation. The important role of T cells in shaping both antiviral immunity and inflammation has revived interest in understanding the host-pathogen interactions that lead to the diverse functions of T cells in respiratory viral infections. Inborn deficiencies and acquired insufficiency in immunity can prolong infection and shift the immune response towards exacerbated inflammation, which results from persistent innate immune activation and bystander T-cell activation that is nonspecific to the pathogen but is often driven by cytokines. This review discusses how virus variants, exposure doses, routes of infection, host genetics, and immune history can modulate the activation and function of T cells, thus influencing clinical outcomes. Knowledge of virus-host interaction can inform strategies to prevent immune dysfunction in respiratory viral infection and help in the treatment of associated diseases.

Trogocytosis and cross-dressing in antigen presentation

Antigen (Ag)-presenting cells capture or synthesize Ags that are processed into peptides bound and displayed on the plasma membrane by major histocompatibility complex (MHC) molecules. Here, we review a mechanism that enables cells to present Ag-loaded MHC molecules that they have not produced themselves, namely trogocytosis. During trogocytosis, a cell acquires fragments from another living cell without, in most cases, affecting the viability of the donor cell. The trogocytic cell can incorporate into its own plasma membrane (becoming cross-dressed) proteins acquired from the donor cell, including intact Ag and MHC molecules. Trogocytosis and cross-dressing expand the immunological functions that immune and nonimmune cells are able to carry out, with both beneficial and deleterious consequences.

Cell-Intrinsic CD38 Expression Sustains Exhausted CD8+ T Cells by Regulating Their Survival and Metabolism during Chronic Viral Infection

Acute and chronic viral infections result in the differentiation of effector and exhausted T cells with functional and phenotypic differences that dictate whether the infection is cleared or progresses to chronicity. High CD38 expression has been observed on CD8+ T cells across various viral infections and tumors in patients, suggesting an important regulatory function for CD38 on responding T cells. Here, we show that CD38 expression was increased and sustained on exhausted CD8+ T cells following chronic lymphocytic choriomeningitis virus (LCMV) infection, with lower levels observed on T cells from acute LCMV infection. We uncovered a cell-intrinsic role for CD38 expression in regulating the survival of effector and exhausted CD8+ T cells. We observed increased proliferation and function of Cd38-/- CD8+ progenitor exhausted T cells compared to those of wild-type (WT) cells. Furthermore, decreased oxidative phosphorylation and glycolytic potential were observed in Cd38-/- CD8+ T cells during chronic but not acute LCMV infection. Our studies reveal that CD38 has a dual cell-intrinsic function in CD8+ T cells, where it decreases proliferation and function yet supports their survival and metabolism. These findings show that CD38 is not only a marker of T cell activation but also has regulatory functions on effector and exhausted CD8+ T cells. IMPORTANCE Our study shows how CD38 expression is regulated on CD8+ T cells responding during acute and chronic viral infection. We observed higher CD38 levels on CD8+ T cells during chronic viral infection compared to levels during acute viral infection. Deleting CD38 had an important cell-intrinsic function in ensuring the survival of virus-specific CD8+ T cells throughout the course of viral infection. We found defective metabolism in Cd38-/- CD8+ T cells arising during chronic infection and changes in their progenitor T cell phenotype. Our studies revealed a dual cell-intrinsic role for CD38 in limiting proliferation and granzyme B production in virus-specific exhausted T cells while also promoting their survival. These data highlight new avenues for research into the mechanisms through which CD38 regulates the survival and metabolism of CD8+ T cell responses to viral infections.

Tracking the clonal dynamics of SARS-CoV-2-specific T cells in children and adults with mild/asymptomatic COVID-19

Children infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) develop less severe coronavirus disease 2019 (COVID-19) than adults. The mechanisms for the age-specific differences and the implications for infection-induced immunity are beginning to be uncovered. We show by longitudinal multimodal analysis that SARS-CoV-2 leaves a small footprint in the circulating T cell compartment in children with mild/asymptomatic COVID-19 compared to adult household contacts with the same disease severity who had more evidence of systemic T cell interferon activation, cytotoxicity and exhaustion. Children harbored diverse polyclonal SARS-CoV-2-specific naïve T cells whereas adults harbored clonally expanded SARS-CoV-2-specific memory T cells. A novel population of naïve interferon-activated T cells is expanded in acute COVID-19 and is recruited into the memory compartment during convalescence in adults but not children. This was associated with the development of robust CD4+ memory T cell responses in adults but not children. These data suggest that rapid clearance of SARS-CoV-2 in children may compromise their cellular immunity and ability to resist reinfection.