Biology subjects

Ozdilek, A.

Publications and source records attributed to Ozdilek, A..

4 recordsLinked to original sources

bioRxiv2026

Preexisting chronic infection skews the epigenetic landscape of subsequent memory CD8 T cell responses

Previous studies suggest that preexisting chronic disease impairs immune responses to subsequent infection and vaccination. However, the underlying epigenetic mechanisms are understudied. Here, we show that preexisting chronic infection with LCMV clone 13 (CL13) compromised the formation of central memory CD8 T cells (TCM) to subsequent Listeria monocytogenes infection, despite not profoundly impacting effector responses. This correlated with a skewed cytokine milieu. Our chromatin-accessibility profiling of Listeria-specific CD8 T cells showed significant epigenetic skewing of both TCM and effector memory (TEM) in mice with preexisting LCMV-CL13, a skewing that started in memory-precursor effector cells (MPECs) during the effector phase. Transcription-factor binding sites (TFBS) analyses highlighted the interferon regulatory factor (IRF) family as major TFs implicated in this skewing. Thus, our results suggest that preexisting persistent inflammation skews the phenotypic and epigenetic landscape of subsequent memory responses, arguing for interventions to optimize vaccine-induced memory in hosts with preexisting chronic disease.

immunology↗

bioRxiv2025

Molecular mechanisms of immune evasion by host protein glycosylation of a bacterial immunogen used in nucleic acid vaccines

Nucleic acid vaccines (DNA and mRNA) induce immunity by driving in situ antigen expression in host cells. For non-viral pathogens, however, host expression can impose post-translational modifications absent from the native microbial antigen. Tuberculosis (TB) remains a leading cause of infectious mortality, and nucleic acid vaccines targeting the Mycobacterium tuberculosis antigen 85 (Ag85) complex did not confer protective efficacy in clinical trials. We hypothesized that host-derived N-glycosylation of Ag85 immunogens expressed in mammalian cells compromises immune recognition. Here, we define structural, biochemical and immunological mechanisms by which host-imposed N-glycosylation remodels a bacterial antigen expressed in mammalian cells. We show that Ag85B expressed in human Expi293 cells is microheterogeneously N-glycosylated at four canonical sequons (N52, N224, N234, N280) with predominantly complex, highly fucosylated, and frequently sialylated glycans. Molecular dynamics simulations indicate that these glycans occupy substantial conformational space and reduce solvent and antibody-accessible surface area, occluding multiple established B-cell and T-cell epitope regions. Consistent with glycan-mediated shielding, mammalian-expressed Ag85B shows markedly reduced binding to an Ag85-complex monoclonal antibody by competitive ELISA and biolayer interferometry, and sialylated glycans enable Siglec-9 binding that is abrogated by sialidase treatment. Together, these findings define the structural and biochemical mechanisms by which host glycosylation can remodel bacterial vaccine antigens, supporting glycosylation-aware immunogen engineering as a design principle for nucleic acid vaccines targeting non-viral pathogens.

biochemistry↗

bioRxiv2024

Longitudinal proteomic analysis of T cell differentiation in vivo reveals dynamic changes of the interactome

CD8 T cell exhaustion impedes immune responses to cancer and chronic infections, and a biochemical understanding of exhaustion is essential to improving immunotherapy. Here, we present the first longitudinal protein abundance and phosphoproteomic analysis of antigen-specific CD8 T cells undergoing differentiation in vivo during acute (LCMV-Armstrong) and chronic (LCMV-Clone 13) infection. Comparing protein abundance across the two infection conditions identified over 180 known and novel exhaustion-associated proteins, including proteins missed by transcriptional analyses. Phosphoproteomic analysis identified >900 differentially regulated phosphosites on >400 proteins, including known inhibitory phosphosites on PD1, PAG1, SHP-1/PTPN6, SLAMF1/CD150. We also calculated phosphosite conservation across mammals, to direct follow-up studies towards sites with likely essential function. Lastly, our analysis uncovers exhaustion-associated kinases with clinical-stage inhibitors, underscoring the translational utility of our dataset to guide immunotherapy development. Together, our datasets define a biochemical atlas of T cell exhaustion in vivo, shedding light on the molecular mechanisms of T cell dysfunction.

immunology↗

bioRxiv2021

Modulation of immunosuppressant drug treatment to improve SARS-CoV-2 vaccine efficacy in mice

The COVID-19 pandemic dramatically demonstrated the need for improved vaccination strategies and therapeutic responses to combat infectious diseases. However, the efficacy of vaccines has not yet been demonstrated in combination with commonly used immunosuppressive drug regimens. We sought to determine how common pharmaceutical drugs used in autoimmune disorders can alter immune responses to the SARS-CoV-2 spike protein vaccination. We treated mice with five immunosuppressant drugs (cyclophosphamide, leflunomide, methotrexate, methylprednisolone, and mycophenolate mofetil), each with various mechanisms of action prior to and following immunization with SARS-CoV-2 spike protein. We assessed the functionality of antibody responses to spike protein and compared immune cell populations in mice that received no treatment with those that received continuous or temporarily suspended immune suppressive therapy. All tested immunosuppressants significantly reduced the antibody titers in serum and functional antibody response against SARS-CoV-2 spike protein in immunized mice. Temporarily halting selected immunosuppressants (methylprednisolone and methotrexate, but not cyclophosphamide) improved antibody responses significantly. Through proof-of-principle experiments utilizing a mouse model, we demonstrated that immune suppression in autoimmune disorders through pharmaceutical treatments may impair vaccine response to SARS-CoV-2, and temporary suspension of immunosuppressant treatment may be necessary to mount an effective antibody vaccine response. This work provides feasibility for future clinical assessment of the impact of immunosuppressants on vaccine efficacy in humans. Significance StatementImmunosuppressant regimens are widely used as therapies for a variety of diseases, including autoimmune, inflammatory, and cancer. However, immunosuppressants can impair critical immune responses to vaccination. The impact of standard immunosuppressant use on the critical, developing SARS-CoV-2 vaccination strategies has not been well-described. In this study, we use a mouse model to determine how different immunosuppressant drugs that act through different mechanisms can impair the antibody response to SARS-CoV-2 spike protein, and how modulating these drug regimens may restore antibody levels and function.

immunology↗