Biology subjects

Cvijovic, I.

Publications and source records attributed to Cvijovic, I..

6 recordsLinked to original sources

bioRxiv2025

Dynamics of local B cell migration during affinity maturation in the human tonsil

Affinity maturation enhances B cell binding within germinal centers, where spatial structure preserves sequence diversity by restricting cell movement. While recent studies show that some B cell lineages span multiple germinal centers, the sources, rates and consequences of this spreading process remain unknown. Here, we show that the spatial arrangement of B cells in the human tonsil is driven by local migration during affinity maturation. Through an evolutionary re-analysis of spatial transcriptomics data, we demonstrate that these local migrations follow a clock-like process, in which cells migrate at an average rate of [~]1/50 cell divisions that is consistent across lineages and time. Migrating cells continue to evolve and diversify in their new germinal centers at similar rates, such that the largest lineages in each germinal center often originate from another. These results suggest that affinity maturation operates in a regime of pervasive but intermediate migration, balancing diversity and selection.

immunology↗

bioRxiv2025

Beyond polyA: scalable single-cell total RNA-seq unifies coding and non-coding transcriptomics

Non-coding RNAs represent a widespread and diverse layer of post-transcriptional regulation across cell types and states, yet much of their diversity remains uncharted at single-cell resolution. This gap stems from the limitations of widely used single-cell RNA-sequencing protocols, which focus on polyadenylated transcripts and miss many short or non-polyadenylated RNAs. Here, we adapted single-cell RNA-sequencing on the 10x Genomics platform to capture a broad complement of coding and non-coding RNAs--including miRNAs, tRNAs, lncRNAs, histone RNAs, and non-adenylated viral transcripts. This approach enabled the discovery of rich, dynamic non-coding RNA programs across immune cells, virally infected hepatocytes, and the developing human brain. In dengue virus-infected hepatocytes, we detect non-adenylated viral transcripts and distinguish active from transcriptionally quiescent infected states, each with distinct host regulatory signatures. In brain tissue, we identify biotype-specific, cell-type- restricted non-coding RNAs, including miRNAs whose expression anticorrelates with predicted targets, consistent with post-transcriptional regulatory relationships. We show that MIR137, one of the strongest GWAS loci associated with schizophrenia and intellectual disability, is expressed specifically in Cajal-Retzius cells, an early-born but transient population that guides subsequent cortical neuron migration. These findings demonstrate the importance of non-coding RNAs in defining cell identity and state, and show how expanded transcriptome coverage can reveal additional layers of gene control--now accessible through practical and scalable single-cell profiling.

genomics↗

bioRxiv2023

Long-term B cell memory emerges at uniform relative rates in the human immune response

B cells generate pathogen-specific antibodies and play an essential role in providing adaptive protection against infection. Antibody genes are modified in evolutionary processes acting on the B cell populations within an individual. These populations proliferate, differentiate, and migrate to long-term niches in the body. However, the dynamics of these processes in the human immune system are primarily inferred from mouse studies. We addressed this gap by sequencing the antibody repertoire and transcriptomes from single B cells in four immune-rich tissues from six individuals. We find that B cells descended from the same pre-B cell ("lineages") often co-localize within the same tissue, with the bone marrow harboring the largest excess of lineages without representation in other tissues. Within lineages, cells with different levels of somatic hypermutation are uniformly distributed among tissues and functional states. This suggests that the relative probabilities of localization and differentiation outcomes change negligibly during affinity maturation, and quantitatively agrees with a simple dynamical model of B cell differentiation. While lineages strongly co-localize, we find individual B cells nevertheless make independent differentiation decisions. Proliferative antibody secreting cells, however, deviate from these global patterns. These cells are often clonally expanded, their clones appear universally distributed among all sampled organs, and form lineages with an excess of cells of the same type. Collectively, our findings show the limits of peripheral blood monitoring of the immune repertoire, and provide a probabilistic model of the dynamics of antibody memory formation in humans.

immunology↗

bioRxiv2023

Reference-Free Germline Immunoglobulin Allele Discovery from B CellReceptor Sequencing Data

Antibodies, or immunoglobulins, are a diverse set of molecules that play a critical role in adaptive immunity. They are generated in a process which begins with the recombination of germline V, D, and J gene segment alleles, and refined by hypermutation of these germline sequences upon antigen exposure. Antibody repertoire analysis often requires the knowledge of the germline V, D, and J alleles to detect hypermutations and understand the phylogenetic relationships of related B cells. However, germline immunoglobulin alleles are remarkably diverse and incompletely annotated, making it necessary to construct personalized databases for every individual. Though several approaches for the detection of germline immunoglobulin variants exist, they often rely on refining existing databases using simplifying assumptions about the relationships of germline alleles in a given organism, or about the form of evolutionary process that shapes antibody repertoires. Here, we present grmlin, an alternative computational approach to detecting germline alleles. Our approach exploits two empirical properties of B cell repertoires: the abundance of germline sequences in antibody repertoires and the enormous diversity of antibody sequence space, to detect germline alleles from B cell receptor sequencing data without reliance on a reference database. As such, it is in principle applicable to non-model organisms. We validate this approach by detecting the germline alleles of 11 pairs of twins and show that it achieves equivalent sensitivity and better specificity than previous methods.

immunology↗

bioRxiv2021

Binding affinity landscapes constrain the evolution of broadly neutralizing anti-influenza antibodies

Over the past two decades, several broadly neutralizing antibodies (bnAbs) that confer protection against diverse influenza strains have been isolated1,2. Structural and biochemical characterization of these bnAbs has provided molecular insight into how they bind distinct antigens1. However, our understanding of the evolutionary pathways leading to bnAbs, and thus how best to elicit them, remains limited. Here, we measure equilibrium dissociation constants of combinatorially complete mutational libraries for two naturally isolated influenza bnAbs3-5 (CR-9114, 16 mutations; CR-6261, 11 mutations), reconstructing all possible intermediates back to the unmutated germline sequences. We find that these two libraries exhibit strikingly different patterns of breadth: while many variants of CR-6261 display moderate affinity to diverse antigens, those of CR-9114 display appreciable affinity only in specific, nested combinations. By examining the extensive pairwise and higher-order epistasis between mutations, we find key sites with strong synergistic interactions that are highly similar across antigens for CR-6261 and different for CR-9114. Together, these features of the binding affinity landscapes strongly favor sequential acquisition of affinity to diverse antigens for CR-9114, while the acquisition of breadth to more similar antigens for CR-6261 is less constrained. These results, if generalizable to other bnAbs, may explain the molecular basis for the widespread observation that sequential exposure favors greater breadth6-8, and such mechanistic insight will be essential for predicting and eliciting broadly protective immune responses.

evolutionary biology↗

bioRxiv2017

The effect of strong purifying selection on genetic diversity

Purifying selection reduces genetic diversity, both at sites under direct selection and at linked neutral sites. This process, known as background selection, is thought to play an important role in shaping genomic diversity in natural populations. Yet despite its importance, the effects of background selection are not fully understood. Previous theoretical analyses of this process have taken a backwards-time approach based on the structured coalescent. While they provide some insight, these methods are either limited to very small samples or are computationally prohibitive. Here, we present a new forward-time analysis of the trajectories of both neutral and deleterious mutations at a nonrecombining locus. We find that strong purifying selection leads to remarkably rich dynamics: neutral mutations can exhibit sweep-like behavior, and deleterious mutations can reach substantial frequencies even when they are guaranteed to eventually go extinct. Our analysis of these dynamics allows us to calculate analytical expressions for the full site frequency spectrum. We find that whenever background selection is strong enough to lead to a reduction in genetic diversity, it also results in substantial distortions to the site frequency spectrum, which can mimic the effects of population expansions or positive selection. Because these distortions are most pronounced in the low and high frequency ends of the spectrum, they become particularly important in larger samples, but may have small effects in smaller samples. We also apply our forward-time framework to calculate other quantities, such as the ultimate fates of polymorphisms or the fitnesses of their ancestral backgrounds.

evolutionary biology↗