Biology subjects

Walczak, A.

Publications and source records attributed to Walczak, A..

14 recordsLinked to original sources

bioRxiv2026

Modeling Protein Evolution via Generative Inference From Monte Carlo Chains to Population Genetics

Generative models derived from large protein sequence alignments define complex fitness landscapes, but their utility for accurately modeling non-equilibrium evolutionary dynamics remains unclear. In this work, we perform a rigorous comparative analysis of three simulation schemes, designed to mimic evolution in silico by local sampling of the probability distribution defined by a generative model. We compare standard independent Markov Chain Monte Carlo, Monte Carlo on a phylogenetic tree, and a population genetics dynamics, benchmarking their outputs against deep sequencing data from four distinct in vitro evolution experiments. We find that standard Monte Carlo fails to reproduce the correct phylogenetic structure and generates unrealistic, gradual mutational sweeps. Performing Monte Carlo on a tree inferred from data improves phylogenetic fidelity and historical accuracy. The population genetics scheme successfully captures phylogenetic correlations, mutational abundances, and selective sweeps as emergent properties, without the need to infer additional information from data. However, the latter choice come at the price of not sampling the proper generative model distribution at long times. Our findings highlight the crucial role of phylogenetic correlations and finite-population effects in shaping evolutionary trajectories on fitness landscapes. These models therefore provide powerful tools for predicting complex adaptive paths and for reliably extrapolating evolutionary dynamics beyond current experimental limitations.

evolutionary biology↗

bioRxiv2026

Noradrenaline prolongs the state of motor arrest via cerebrospinal fluid signaling

Neuromodulators can mediate whole-body physiological changes, however how signaling from relatively small populations of neurons produces widespread and sustained effects remains incompletely understood. Here, we demonstrate that sustained noradrenergic activation induces prolonged motor arrest accompanied by postural collapse, bradycardia, and emetic responses. Motor suppression arises from inhibition of brainstem commands to the spinal cord rather than motoneuron silencing. Noradrenaline induces a glial calcium wave that propagates throughout the central nervous system. This wave most prominently persists at the brainstem-spinal cord boundary and ventricular midline. At this location, ependymal radial glia express Adra1a receptors on cilia contacting cerebrospinal fluid (CSF). Ventricular noradrenaline injections recapitulated the glial wave and motor arrest, while CSF administration of an Adra1 antagonist shortened motor arrest. Altogether, noradrenaline sustains motor arrest by signaling through the CSF via ciliary Adra1a receptors on ependymal radial glia showing that cerebrospinal fluid as a critical transmission route for persistence of behavioral states. HighlightsO_LINoradrenergic surges coordinate a whole-body response with motor arrest, postural disruptions, bradycardia, and emesis-like reflexes C_LIO_LIMotor arrest results from silencing of brainstem motor commands to the spinal cord C_LIO_LINoradrenaline-induced glial calcium waves last longest at the obex/ventricular midline where cilia of CSF-contacting glial cells bear Adra1 receptors C_LIO_LINoradrenergic signaling in the CSF is necessary and sufficient for motor arrest to persist C_LI

neuroscience↗

bioRxiv2025

Dynamics of memory B cells and plasmablasts in healthy individuals

Our adaptive immune system relies on the persistence over long times of a diverse set of antigen-experienced B cells to encode our memories of past infections and to protect us against future ones. While longitudinal repertoire sequencing promises to track the long-term dynamics of many B cell clones simultaneously, sampling and experimental noise make it hard to draw reliable quantitative conclusions. Leveraging statistical inference, we infer the dynamics of memory B cell clonal dynamics and conversion to plasmablasts, which includes clone creation, degradation, abundance fluctuations, and differentiation. We find that memory B cell clones degrade slowly, with a half-life of 10 years. Based on the inferred parameters, we predict that it takes about 50 years to renew 50% of the repertoire, with most observed clones surviving for a lifetime. We infer that, on average, 1 out of 100 memory B cells differentiates into a plasmablast each year, more than expected from purely antigen-stimulated differentiation, and that plasmablast clones degrade with a half-life of about one year in the absence of memory imports. Our method is general and could be applied to other longitudinal repertoire sequencing B cell subsets.

immunology↗

bioRxiv2024

Learning predictive signatures of HLA type from T-cell repertoires

T cells recognize a wide range of pathogens using surface receptors that interact directly with pep-tides presented on major histocompatibility complexes (MHC) encoded by the HLA loci in humans. Understanding the association between T cell receptors (TCR) and HLA alleles is an important step towards predicting TCR-antigen specificity from sequences. Here we analyze the TCR alpha and beta repertoires of large cohorts of HLA-typed donors to systematically infer such associations, by looking for overrepresentation of TCRs in individuals with a common allele.TCRs, associated with a specific HLA allele, exhibit sequence similarities that suggest prior antigen exposure. Immune repertoire sequencing has produced large numbers of datasets, however the HLA type of the corresponding donors is rarely available. Using our TCR-HLA associations, we trained a computational model to predict the HLA type of individuals from their TCR repertoire alone. We propose an iterative procedure to refine this model by using data from large cohorts of untyped individuals, by recursively typing them using the model itself. The resulting model shows good predictive performance, even for relatively rare HLA alleles.

immunology↗

bioRxiv2023

Variability in the local and global composition of human T-cell receptor repertoires during thymic development across cell types and individuals

The adaptive immune response relies on T cells that combine phenotypic specialization with diversity of T cell receptors (TCRs) to recognize a wide range of pathogens. TCRs are acquired and selected during T cell maturation in the thymus. Characterizing TCR repertoires across individuals and T cell maturation stages is important for better understanding adaptive immune responses and for developing new diagnostics and therapies. Analyzing a dataset of human TCR repertoires from thymocyte subsets, we find that the variability between individuals generated during the TCR V(D)J recombination is maintained through all stages of T cell maturation and differentiation. The inter-individual variability of repertoires of the same cell type is of comparable magnitude to the variability across cell types within the same individual. To zoom in on smaller scales than whole repertoires, we defined a distance measuring the relative overlap of locally similar sequences in repertoires. We find that the whole repertoire models correctly predict local similarity networks, suggesting a lack of forbidden T cell receptor sequences. The local measure correlates well with distances calculated using whole repertoire traits and carries information about cell types.

immunology↗

bioRxiv2022

DRAG in situ barcoding reveals an increased number of HSPCs contributing to myelopoiesis with age

Ageing is associated with changes in the cellular composition of the immune system. During ageing, hematopoietic stem and progenitor cells (HSPCs) that produce immune cells are thought to decline in their regenerative capacity. However, HSPC function has been mostly assessed using transplantation assays, and it remains unclear how HSPCs age in the native bone marrow niche. To address this issue, we developed a novel in situ single cell lineage tracing technology to quantify the clonal composition and cell production of single cells in their native niche. Our results demonstrate that a pool of HSPCs with unequal output maintains myelopoiesis through overlapping waves of cell production throughout adult life. During ageing, the increased frequency of myeloid cells is explained by greater numbers of HSPCs contributing to myelopoiesis, rather than increased myeloid output of individual HSPCs. Strikingly, the myeloid output of HSPCs remained constant over time despite accumulating significant transcriptomic changes throughout adulthood. Together, these results show that, unlike emergency myelopoiesis post-transplantation, aged HSPCs in their native microenvironment do not functionally decline in their regenerative capacity.

immunology↗

bioRxiv2022

Benchmarking solutions to the T-cell receptor epitope prediction problem: IMMREP22 workshop report

Many different solutions to predicting the cognate epitope target of a T-cell receptor (TCR) have been proposed. However several questions on the advantages and disadvantages of these different approaches remain unresolved, as most methods have only been evaluated within the context of their initial publications and data sets. Here, we report the findings of the first public TCR-epitope prediction benchmark performed on 23 prediction models in the context of the ImmRep 2022 TCR-epitope specificity workshop. This benchmark revealed that the use of paired-chain alpha-beta, as well as CDR1/2 or V/J information, when available, improves classification obtained with CDR3 data, independent of the underlying approach. In addition, we found that straight-forward distance-based approaches can achieve a respectable performance when compared to more complex machine-learning models. Finally, we highlight the need for a truly independent follow-up benchmark and provide recommendations for the design of such a next benchmark.

bioinformatics↗

bioRxiv2022

Determining probabilities of HIV-1 bNAb development in healthy and chronically infected individuals

HIV-1 broadly neutralizing antibodies (bNAbs) are able to suppress viremia and prevent infection. Their induction by vaccination is therefore a major goal. However, in contrast to antibodies that neutralize other pathogens, HIV-1-specific bNAbs frequently carry uncommon molecular characteristics that might prevent their induction. Here, we performed unbiased sequence analyses of B cell receptor repertoires from 57 healthy and 46 chronically HIV-1- or HCV-infected individuals and learned probabilistic models to predict the likelihood of bNAb development. We formally show that lower probabilities for bNAbs are predictive of higher HIV-1 neutralization activity. Moreover, ranking of bNAbs by their probabilities allowed to identify highly potent antibodies with superior generation probabilities as preferential targets for vaccination approaches. Importantly, we found equal bNAb probabilities across infected and healthy donors. This implies that chronic infection is not a prerequisite for the generation of bNAbs, fostering the hope that HIV-1 vaccines can induce bNAb development in healthy individuals. Significance StatementWhile HIV-1 broadly neutralizing antibodies (bNAbs) can develop in chronically HIV-1-infected individuals, they could not yet be elicited by active vaccination. Here, we computationally demonstrate that HIV-1 bNAbs carry distinct sequence features making them unlikely outcomes of the antibody evolution. However, our approach allowed us to identify bNAbs with higher probabilities of being generated. These candidates can now serve as the most promising targets to be induced by vaccination. Moreover, we show that chronic infection has no influence on the probabilities of finding typical bNAb sequence features in the memory B cell compartment. Both findings are critical to design effective vaccination strategies.

immunology↗

bioRxiv2020

An important role of the interplay between Bdnf transcription and histone acetylation in epileptogenesis

Brain-Derived Neurotrophic Factor is one of the most important trophic proteins in the brain. The role of this growth factor in neuronal plasticity, in health and disease, has been extensively studied. However, mechanisms of epigenetic regulation of Bdnf gene expression in epilepsy are still elusive. In our previous work, using a rat model of neuronal activation upon kainate-induced seizures, we observed a repositioning of Bdnf alleles from the nuclear periphery towards the nuclear center. This change of Bdnf intranuclear position was associated with transcriptional gene activity. In the present study, using the same neuronal activation model, we analyzed the relation between the percentage of the Bdnf allele at the nuclear periphery and clinical and morphological traits of epilepsy. We observed that the decrease of the percentage of the Bdnf allele at the nuclear periphery correlates with stronger mossy fiber sprouting - an aberrant form of excitatory circuits formation. Moreover, using in vitro hippocampal cultures we showed that Bdnf repositioning is a consequence of the transcriptional activity. Inhibition of RNA polymerase II activity in primary cultured neurons with Actinomycin D completely blocked Bdnf gene transcription and repositioning observed after neuronal excitation. Interestingly, we observed that histone deacetylases inhibition with Trichostatin A induced a slight increase of Bdnf gene transcription and its repositioning even in the absence of neuronal excitation. Presented results provide novel insight into the role of BDNF in epileptogenesis. Moreover, they strengthen the statement that this particular gene is a good candidate to search for a new generation of antiepileptic therapies.

neuroscience↗

bioRxiv2020

Contribution of resident and circulating precursors to tumor-infiltrating CD8+ T cell populations in non-small cell lung cancer patients

Tumor-infiltrating lymphocytes (TILs) in general, and CD8+ TILs in particular, represent a favorable prognostic factor in non-small cell lung cancer (NSCLC). The tissue origin, regenerative capacities, and differentiation pathways of TIL subpopulations, however, remain poorly understood. Using a combination of single cell RNA and T cell receptor (TCR) sequencing, we investigate the functional organization of TIL populations in primary NSCLC. We identify two CD8+ TIL subpopulations expressing memory-like gene modules: one is also present in blood (circulating precursors) and the other one in juxta-tumor tissue (tissue resident precursors). In tumors, these two precursor populations converge through a unique transitional state into terminally differentiated cells, often referred to as dysfunctional or exhausted. Differentiation is associated with TCR expansion, and transition from precursor to late differentiated states correlates with intratumor T cell cycling. These results provide a coherent working model for TIL origin, filiation and functional organization in primary NSCLC.

immunology↗

bioRxiv2020

Optimal prediction with resource constraints using the information bottleneck

Responding to stimuli requires that organisms encode information about the external world. Not all parts of the signal are important for behavior, and resource limitations demand that signals be compressed. Prediction of the future input is widely beneficial in many biological systems. We compute the trade-offs between representing the past faithfully and predicting the future for input dynamics with different levels of complexity. For motion prediction, we show that, depending on the parameters in the input dynamics, velocity or position coordinates prove more predictive. We identify the properties of global, transferrable strategies for time-varying stimuli. For non-Markovian dynamics we explore the role of long-term memory of the internal representation. Lastly, we show that prediction in evolutionary population dynamics is linked to clustering allele frequencies into non-overlapping memories, revealing a very different prediction strategy from motion prediction.

biophysics↗

bioRxiv2020

Ultrastructural Visualization of 3D Chromatin Folding Using Serial Block-Face Scanning Electron Microscopy and In Situ Hybridization (3D-EMISH)

The human genome is extensively folded into 3-dimensional organization, yet the detailed 3D chromatin folding structures have not been fully visualized due to the lack of robust and ultra- resolution imaging capability. Here, we report the development of a novel electron microscopy method that combines serial block-face scanning electron microscopy with in situ hybridization (3D-EMISH) to visualize 3D chromatin folding at targeted genomic regions with ultra-resolution (5x5x30 nm in xyz dimensions, respectively). We applied 3D-EMISH to human lymphoblastoid cells at a 1.7 Mb segment of the genome and visualized a large number of distinctive 3D chromatin folding structures in high ultra-resolution. We further quantitatively characterized the reconstituted chromatin folding structures by identifying sub-domains, and uncovered a high level of heterogeneity in chromatin folding ultrastructures, suggestive of extensive dynamic fluidity in 3D chromatin states.

genomics↗

bioRxiv2018

Precise tracking of vaccine-responding T-cell clones reveals convergent and personalized response in identical twins

T-cell receptor (TCR) repertoire data contain information about infections that could be used in disease diagnostics and vaccine development, but extracting that information remains a major challenge. Here we developed a statistical framework to detect TCR clone proliferation and contraction from longitudinal repertoire data. We applied this framework to data from three pairs of identical twins immunized with the yellow fever vaccine. We identified 500-1500 responding TCRs in each donor and validated them using three independent assays. While the responding TCRs were mostly private, albeit with higher overlap between twins, they could be well predicted using a classifier based on sequence similarity. Our method can also be applied to samples obtained post-infection, making it suitable for systematic discovery of new infection-specific TCRs in the clinic.

immunology↗

bioRxiv2016

Mouse T cell repertoires as statistical ensembles: overall characterization and age dependence

The ability of the adaptive immune system to respond to arbitrary pathogens stems from the broad diversity of immune cell surface receptors (TCRs). This diversity originates in a stochastic DNA editing process (VDJ recombination) that acts each time a new immune cell is created from a stem cell. By analyzing T cell sequence repertoires taken from the blood and thymus of mice of different ages, we quantify the significant changes in this process that occur in development from embryo to young adult. We find a rapid increase with age in the number of random insertions in the VDJ recombination process, leading to a dramatic increase in diversity. Since the blood accumulates thymic output over time, blood repertoires are mixtures of different statistical recombination processes and, by unraveling the mixture statistics, we can obtain a clear picture of the time evolution of the early immune system. Sequence repertoire analysis also allows us to detect the effect of selection on the output of the VDJ recombination process. The effects we find are nearly identical between thymus and blood, suggesting that they mainly reflect selection for proper folding of the TCR receptor protein.

immunology↗