Biology subjects

Dulovic, A.

Publications and source records attributed to Dulovic, A..

4 recordsLinked to original sources

bioRxiv2026

Dual-Layer Serological Encoding: Integrating Pathogen-Derived and Host-Reactive Peptide Signatures Reveals Complementary Dimensions of HIV Immune Response

Serological diagnostics traditionally rely on pathogen-derived antigens to detect infection-specific antibody responses. Chronic infections also induce systemic immune remodeling that may be reflected in global antibody reactivity patterns beyond antigen specificity. Here we evaluate a dual-layer serological framework combining HIV-derived peptides with a host-derived peptide library designed to capture distributed antibody reactivity patterns. Using strict nested cross-validation in a cohort of 105 individuals, pathogen-derived 12-mer peptides achieved high classification performance with an AUC of 0.891, whereas the 10-mer host-based peptide library alone yielded moderate but statistically significant discrimination with an AUC of 0.805. Integration via regularized stacking resulted in only a modest additive improvement, reaching an AUC of 0.897, indicating partial redundancy in diagnostic ranking. In contrast, entropy and inequality analyses revealed substantial immune repertoire restructuring in HIV-positive individuals, characterized by reduced Shannon entropy and significant correlations between classifier probability and repertoire concentration. These findings support a dual-layer model of serology in which the integration of pathogen-derived and host-derived peptides into a meta model encode antigen specificity, whereas host-reactive signatures reflect systemic immune topology. Distinguishing diagnostic ranking from immune-state encoding provides a conceptual framework for multi-layer serological diagnostics.

immunology↗

bioRxiv2026

High-density peptide arrays detect tuberculosis through immune remodeling, not only antigen recognition alone

Serological diagnostics for tuberculosis rely on pathogen-derived antigens to detect infection-specific antibodies. Whether chronic TB infection also reshapes the global topology of the antibody repertoire remains largely unexplored. Here we profile serum antibody binding across 6,936 peptides in 105 individuals from three countries using two complementary libraries: Mycobacterium tuberculosis peptides (TBC) and a resemblance-ranking library representing the human self-proteome (RRL). We construct a five-dimensional immune state vector from distributional binding properties and map individual sera into an immune phase space. A remodeling classifier achieves virtually identical performance on pathogen-derived and host-derived peptides (AUC 0.63-0.73), demonstrating that the diagnostic signal arises from global repertoire restructuring rather than antigen-specific recognition. HIV co-infection partially masks this signal; restricting analysis to HIV-negative individuals increases AUC to 0.73 (permutation p = 0.005) and enables detection of smear-negative TB (AUC = 0.83, specificity 0.95 with three peptides). Phase-space projections reveal that TB severity maps onto a continuous remodeling gradient, with smear-negative patients occupying intermediate positions between healthy controls and smear-positive cases. These findings position high-density peptide arrays as sensors of antibody repertoire topology, enabling detection of chronic immune states beyond antigen-specific recognition.

immunology↗

bioRxiv2025

Lymphoid-tissue-on-chip recapitulates human antibody responses in vitro

In the past decades, vaccine development has made great strides. Nevertheless, more often than not, vaccine candidates fail in advanced stages of development and clinical trials. A key reason is the poor predictive value of non-clinical in vivo and in vitro models, due to either species-specific differences in the immune response or insufficient reflection of physiological vaccine mechanisms. Reliable modeling of human adaptive immune responses is a prerequisite to understand processes leading to vaccine-induced protective immunization and to drive informed decisions in vaccine development pipelines. Here, we present a centrifugal microfluidics based organ-on-chip approach to generate an organotypic high density lymphoid tissue on-chip. The model enables long-term culture of lymphoid tissue and raised antigen-specific antibody responses against influenza vaccines even after four weeks on-chip. Antibody response of different magnitude and quality could be induced both by direct antigen exposure as well as by recruitment of antigen-presenting cells from the periphery. The model represents an attractive approach to evaluate the impact of the mode of antigen delivery on adaptive immune responses. Beyond applications in vaccine development, the lymphoid-tissue-on-chip provides a platform to study cellular interactions during homeostasis, immune responses and long-term impact of immunomodulators over several weeks.

bioengineering↗

bioRxiv2023

Development and validation of a respiratory syncytial virus multiplex immunoassay

Respiratory syncytial virus (RSV) is one of the leading causes of severe respiratory disease in infants and adults. RSV exists as two subtypes A and B, which co-circulate throughout the season, although one will usually become dominant. While vaccines and monoclonal therapeutic antibodies either are or will shortly become available, correlates of protection remain unclear. For this purpose, we developed an RSV multiplex immunoassay that analyses antibody titers towards the post-F, Nucleoprotein, and a diverse mix of G proteins. Technical and clinical validation showed outstanding performance, while methodological developments enabled identification of the subtype of previous infections through use of the diverse G proteins for approximately 50% of samples. As a proof of concept to show the suitability of the assay in serosurveillance studies, we then evaluated titer decay and age- dependent antibody responses within population cohorts. Overall, the developed assay shows robust performance, is scalable, provides additional information on infection subtype, and is therefore ideally suited to be used in future population cohort studies. ImportanceAlthough respiratory syncytial virus (RSV) is endemic and re-infections are common and harmless to the majority of the population, it is a leading cause of hospitalization in young children, the elderly, or immunocompromised individuals. A better characterization of RSV immunology and spreading dynamics is thus critical for preparedness, especially when interventions aiming to mitigate other diseases (e.g., COVID-19) disturb its endemic cycles. This requires high-throughput information-dense assays. We therefore developed a bead-based multiplex immunoassay that allows measurements of antibodies against multiple RSV antigens simultaneously. We identified antibodies which were strong indicators of previous infection, while others allowed identification of the subtype of the previous infection. The assay itself was shown to be robust and scalable, making it ideal for to keep track of the temporal variation RSV immunity profiles within the population.

immunology↗