Biology subjects

Brodin, P.

Publications and source records attributed to Brodin, P..

At least 19 recordsLinked to original sources

bioRxiv2026

Galectin-3 recruitment at the Mycobacterium tuberculosis-containing phagosome is critical in macrophage but dispensable in epithelial cells

Mycobacterium tuberculosis (Mtb) virulence relies in part on its ability to induce phagosomal membrane rupture, enabling bacterial access to the host cell cytosol. This process is largely mediated by the ESX-1 secretion system, which is present in Mtb but absent from the vaccine strain BCG. Galectin-3 (Gal3), a {beta}-galactoside-binding lectin, is recruited to damaged endomembranes and functions as a cytosolic sensor of membrane disruption. However, the kinetics and quantitative features of Gal3 recruitment to Mtb-containing vacuoles have remained poorly characterized. Here, we performed a longitudinal quantitative imaging study of Gal3 recruitment in human macrophages over a five-day infection period. Gal3 was recruited to mycobacteria-containing vacuoles shortly after infection with both live and heat-killed Mtb. Differences between the two conditions emerged from day 1 post-infection and persisted until macrophage death. A similar kinetic profile was observed with recombinant BCG::ESX-1, whereas parental BCG failed to induce Gal3 recruitment, confirming the requirement for ESX-1-dependent membrane damage. Cytoplasmic Gal3 levels were higher in bystander macrophages than in infected cells and were comparable to non-infected controls, suggesting that diffuse cytoplasmic Gal3 is associated with cells lacking intracellular mycobacteria. Functional studies revealed that Gal3 silencing enhanced long-term intracellular Mtb replication, demonstrating a role for Gal3 in restricting bacterial growth. Importantly, Gal3 recruitment was not observed in alveolar epithelial cells. This cell-type specificity was confirmed in a microfluidic alveolus-on-chip model. Together, these findings identify sustained Gal3 recruitment to the mycobacteria-containing vacuole as a robust quantitative marker of ESX-1-dependent phagosomal rupture and Mtb virulence.

microbiology↗

bioRxiv2026

Culsma: A Formal Language for Laboratory Protocols

Laboratory protocols are commonly communicated in natural language, leaving room for variation in how experimental commitments are understood and carried out. We present Culsma, an executable specification language in which protocols are written as programs. The same program is legible to bench scientists and directly machine-readable by software that checks and runs it. It serves as the protocol's operational specification, making experimental commitments explicit for checking before execution and retaining them in results. Culsma addresses how experimental procedures are modeled: it defines operations by the experimental changes and relationships they establish, giving a fine-grained, compositional basis whose technique- and device-specific realizations remain extensible. We examine this boundary in workflows spanning molecular and cell biology, protein biochemistry, and immunoassays, which combine material handling, separation, and measurement differently, asking which distinctions the operation interface preserves. A maintained, source-linked benchmark broadens this evaluation with versioned checks of source-step correspondence and software execution.

bioinformatics↗

bioRxiv2026

Genetic, intrinsic, and environmental determinants of innate immune cytokine responses in healthy four-year-old children

Abstract/SummaryInnate immune responses are crucial for host defence but vary markedly between individuals. Although determinants of this variation are well characterised in adults, data from healthy children remain scarce. We therefore profiled whole-blood cytokine responses to innate immune stimulation in 286 children aged approximately four years and examined genetic, host-intrinsic, and environmental correlates of response. Cytokine responses showed marked inter-individual heterogeneity and stimulus-specific patterns. The top 50 genetic variants explained a substantial proportion ([~]20-45%) of this variance across many stimulus conditions, including a biologically coherent association of the STING locus with cGAMP-induced cytokine production. In contrast, sex, age, adiposity, and perinatal variables showed limited or modest associations. Systemic inflammatory biomarkers of systemic inflammation (hsCRP, glycoprotein acetyls, granulocyte-to-lymphocyte ratio) were strongly positively associated with cytokine responses. Finally, seasonal population-level viral infection burden was positively associated with antiviral and inflammatory cytokine responses. Collectively, these findings advance our understanding of variation in early-life whole-blood cytokine responses, underscoring this developmental period as a critical window for understanding immune development trajectories relevant to long-term health.

immunology↗

bioRxiv2026

Development of a cost-effective Alveolus-on-Chip for studying Mycobacterium tuberculosis infection.

We developed a cost-effective human alveolus-on-chip based on 3D printing molds (3DP-Lung) to study early events of Mycobacterium tuberculosis (Mtb) infection in a physiologically human relevant microenvironment. This organ-on-chip platform is compatible with advanced imaging and recreates the alveolar-capillary interface by co-culturing primary human alveolar epithelial cells, endothelial cells and macrophages. We show that epithelial-only models display limited susceptibility to Mtb infection, whereas the integration of macrophages significantly enhances infection levels of the alveolar barrier and supports intracellular bacterial replication. Quantitative imaging reveals that macrophages act as a permissive niche, promoting Mtb infection of both epithelial and endothelial compartments. This accessible organ-on-chip platform enables robust modeling of early events of host-respiratory pathogen interactions and provides a valuable tool for studying tuberculosis pathogenesis in human-relevant conditions. More broadly, it lowers technical and economic barriers to accelerate the adoption of organ-on-chip technologies for studying human specific infection. SummaryA cost-effective human alveolus-on-chip enables physiologically relevant modeling of early host pathogen interaction and revealing a key role of macrophages in Mycobacterium tuberculosis infection

microbiology↗

bioRxiv2026

Systems-level longitudinal immune profiling reveals individualized immunotypes and genetic associations

The human immune system exhibits substantial inter-individual variation, yet how this variability is coordinated across the system and persists over time remains incompletely defined. Here, we integrated whole-genome sequencing with longitudinal multi-omics immune profiling in 101 healthy individuals followed over two years, combining mass cytometry-based immune cell profiling, PBMC transcriptomics, plasma proteomics, and clinical measurements. Coordinated variation across cellular composition, gene expression, and circulating proteins revealed reproducible immune patterns within individuals across visits. Integrative analyses identified three major immunotypes: adaptive lymphoid (CD4 T cell and B cell enriched), myeloid-inflammation (monocyte and dendritic cell-driven), and cytotoxic (CD8 T cell-dominated), each associated with distinct metabolic and inflammatory profiles. Genome-wide association analyses identified cell-type-specific quantitative trait loci primarily affecting memory lymphocytes, and a polygenic score for memory B cells correlated with both cellular abundance and transcriptional activity. Together, these findings provide a systems-level view for understanding baseline immune heterogeneity in human populations. TeaserLongitudinally stable immune individuality reflects coordinated modules shaped by systemic physiology and genetics

systems biology↗

bioRxiv2025

Cis-aconitate therapy protects against influenza mortality by dual targeting of viral polymerase and ERK/AKT/NF-κB signaling

Influenza virus poses a significant global health challenge, causing approximately 500,000 deaths annually. Its ability to evade antiviral treatments and vaccine-induced immunity underscores the need for novel therapeutic approaches. Our study identifies cis-aconitate (cis-aco), a mitochondria-derived metabolite, as a potent dual-action agent against influenza, independently of its metabolic derivative, itaconate. Cis-aco impairs viral polymerase activity, suppressing viral mRNA expression and protein synthesis to inhibit replication across a range of influenza subtypes. This antiviral efficacy is confirmed in ex vivo human airway and lung organotypic models. Beyond its antiviral properties, cis-aco exhibits potent anti-inflammatory effects, disrupting key inflammatory cascades and reducing the secretion of inflammatory mediators. In a mouse model of influenza pneumonia, cis-aco mitigates viral replication, inflammation, and immune cell activation, significantly improving survival. Notably, its efficacy persists even when administered at later stages of infection, when oseltamivir/Tamiflu(R) is no longer effective. These findings position cis-aco as a promising influenza treatment, combining antiviral and anti-inflammatory benefits within a clinically relevant timeframe.

immunology↗

bioRxiv2025

Single-Cell Protein Interactomes by the Proximity Network Assay

Cellular functions depend on dynamic interactions of proteins and their spatial organisation. While transcriptomic and proteomic methods of molecular parts-lists have enabled single-cell profiling based on abundance, scalable technologies allowing high-resolution measurements of protein organization and interactions at scale are lacking. Here we present the Proximity Network Assay (PNA), a DNA-based method for constructing three-dimensional nanoscale maps of 155 plasma membrane proteins in single cells without the use of optics. PNA employs barcoded antibodies and in situ rolling circle amplification to generate >40,000 spatial nodes per cell, which are linked through proximity-dependent gap-fill ligation and decoded by DNA sequencing forming single cell Proximity Networks. PNA captures abundance, self-clustering, and [~]12,000 pairwise colocalization relationships per single-cell, validating established protein interactions. This new modality provides a framework to uncover novel spatial biomarkers, reveal functional mechanisms, and advance translational studies in immunology, oncology, and cell therapy.

bioengineering↗

bioRxiv2025

Mycobacterium tuberculosis-infected macrophages accumulate more nanoparticles

In response to the escalating threat of infectious diseases and the widespread emergence of antimicrobial-resistant strains, novel therapeutic strategies are being actively developed. Nanoparticle-based delivery systems have emerged as promising tools to improve the targeted administration of antimicrobials directly to sites of infection. In the context of pulmonary infections, aerosolized nanocarriers can enhance local biodistribution while minimizing systemic exposure and associated side effects. In this study, we demonstrate that following pulmonary administration in Mycobacterium tuberculosis-infected mice, poly(lactic-co-glycolic acid) (PLGA) nanoparticles are broadly distributed throughout the lungs and preferentially interact with alveolar macrophages--the primary host cells of the pathogen. Remarkably, infected macrophages internalize significantly more nanoparticles than uninfected cells independently of the virulence and viability of the bacteria. Using transcriptomic analysis, we uncovered a list of 21 commonly modulated genes that may be responsible for this phenotype. Collectively, our findings reveal a striking feature of nanoparticles: their capacity to selectively accumulate in infected cells, offering a powerful mechanism to enhance antimicrobial delivery precisely where it is most needed.

cell biology↗

bioRxiv2024

Antibody-mediated cellular responses are dysregulated in Multisystem Inflammatory Syndrome in Children (MIS-C)

Multisystem Inflammatory Syndrome in Children (MIS-C) is a severe complication of SARS-CoV-2 infection characterized by multi-organ involvement and inflammation. Testing of cellular function ex vivo to understand the aberrant immune response in MIS-C is limited. Despite strong antibody production in MIS-C, SARS-CoV-2 nucleic acid testing can remain positive for 4-6 weeks after infection. Therefore, we hypothesized that dysfunctional cell-mediated antibody responses downstream of antibody production may be responsible for delayed clearance of viral products in MIS-C. In MIS-C, monocytes were hyperfunctional for phagocytosis and cytokine production, while natural killer (NK) cells were hypofunctional for both killing and cytokine production. The decreased NK cell cytotoxicity correlated with an NK exhaustion marker signature and systemic IL-6 levels. Potentially providing a therapeutic option, cellular engagers of CD16 and SARS-CoV-2 proteins were found to rescue NK cell function in vitro. Together, our results reveal dysregulation in antibody-mediated cellular responses unique to MIS-C that likely contribute to the immune pathology of this disease. SummaryMIS-C is a severe complication of SARS-CoV-2 infection characterized by multi-organ involvement and inflammation. Limited studies tested cellular function ex vivo to understand the aberrant immune response in MIS-C. We found dysregulation in antibody-mediated cellular responses unique to MIS-C that likely contribute to the immune pathology of this disease O_FIG O_LINKSMALLFIG WIDTH=138 HEIGHT=200 SRC="FIGDIR/small/589585v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@16d9e0dorg.highwire.dtl.DTLVardef@1a37693org.highwire.dtl.DTLVardef@bdb0cforg.highwire.dtl.DTLVardef@1a32604_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical abstractC_FLOATNO C_FIG

immunology↗

bioRxiv2024

Cluster-free annotation of single cells using Earth mover's distance-based classification

Grouping individual cells in clusters and annotating these based on feature expression is a common procedure in single-cell analysis pipelines. Multiple methods have been reported for single-cell mRNA sequencing and cytometry datasets where the vast majority rely on sequential 2-step procedures involving I) cell clustering based on notions of similarity and II) cluster annotation via manual or semi-automated methods. However, as arbitrary borders are drawn between more or less similar groups of cells, one cannot guarantee that all cells within a cluster are of the same type. Further, dimensionality reduction has been shown to cause considerable distortion in high-dimensional datasets and is prone to variable annotations of the same cell when relative changes occur in data composition. Another limitation of existing methods is that simultaneous analyses of large sets of cells are computationally expensive and difficult to scale for growing datasets or metanalyses across multiple datasets. Here we present an alternative method based on calculation of Earth Movers Distance and a Bayesian classifier coupled to Random Forest, which annotates one cell at a time removing the need for prior clustering and resulting in improved accuracy, better scaling with increasing cell numbers and less computational resources needed.

bioinformatics↗

bioRxiv2024

High-throughput analysis of membrane fluidity unveils a hidden dimension in immune cell states

Cell membranes undergo biophysical remodelling as an adaptation to the surroundings and to perform specific biological functions. However, the extent and relevance of such changes in human immune cells remain unknown, largely due to the lack of single-cell and multidimensional methodologies. Here, we apply a cytometry-based method to fill this gap by combining biophysical profiling with simultaneous analysis of immune cell markers. This platform reveals notable cell type-dependent plasma membrane order heterogeneity in immune cells. By sorting immune cells according to their membrane order and performing transcriptome and spatial surface proteome analyses together with functional tests, we show that plasma membrane order can be used to identify subsets of immune cells with distinct phenotypes and functional behaviours. Our findings demonstrate a broad heterogeneity of plasma membrane order in immune cells that will provide a more precise definition of immune cell states based on their biophysical properties in health and disease.

biophysics↗

bioRxiv2023

An oxadiazole-based compound potentiates anti- tuberculosis treatment by increasing host resistance via zinc poisoning

Anti-tuberculosis drugs, mostly developed over 60 years ago, combined with a poorly effective vaccine, have failed to eradicate tuberculosis. More worryingly, multi-resistant strains of Mycobacterium tuberculosis are constantly emerging. Innovative strategies are thus urgently needed to improve tuberculosis treatment. Recently, host-directed therapy has emerged as a promising strategy to be used in adjunct with existing or future antibiotics, by improving innate immunity or limiting immunopathology. Here, using high content imaging, we identified novel 1,2,4-oxadiazole-based compounds, that allow human macrophages to control MTB replication. Genome-wide gene expression analysis revealed that these molecules induced zinc remobilization inside cells, resulting in bacterial zinc intoxication. More importantly, we also demonstrated that, upon treatment with these novel compounds, M. tuberculosis became even more sensitive to anti-tuberculosis drugs, in vitro and in vivo, in a mouse model of tuberculosis. Manipulation of heavy metal homeostasis holds thus great promise to be exploited to develop host-directed therapeutic interventions.

microbiology↗

bioRxiv2023

Scalable in-vitro immunostimulation of human blood for in-depth profiling of acute immune response effects

In-vitro immune stimulation of whole blood has great analytic potential for exploring the immune system function. However, logistical and biological constraints might limit the extent to which such investigations can be performed. Flexible and often even low-tech mobile applicability can increase the diversity of conditions that can be investigated. To this end, we developed and optimized a medium that enables prolonged in-vitro stimulation and enables highly functional immune responses within 24 hours of incubation. In addition, we also developed and optimized a low-tech water-based mobile incubator to enable logistical flexibility. Finally, we describe the implementation of both systems using a practical example of sample collection at a sampling site with no access to laboratory equipment outside of a research lab.

immunology↗

bioRxiv2023

Molecular Pixelation: Single cell spatial proteomics by sequencing

The spatial distribution of cell surface proteins govern vital processes of the immune system such as inter-cell communication and mobility. However, tools for studying these at high multiplexing scale, resolution, and throughput needed to drive novel discoveries are lacking. We present Molecular Pixelation, a DNA-sequencing based method for single cell analysis to quantify protein abundance, spatial distribution, and colocalization of targeted proteins using Antibody Oligonucleotide Conjugates (AOCs). Relative locations of AOCs are inferred by sequentially associating these into local neighborhoods using DNA-pixels containing unique pixel identifier (UPI) sequences, forming >1,000 connected spatial zones per single cell in three dimensions. DNA-sequencing reads are computationally arranged into spatial single cell maps for 76 proteins without cell compartmentalization. By studying immune cell dynamics and using spatial statistics on graph representations of the data, previously known and novel patterns of protein spatial polarization and co-localization were found in chemokine-stimulated T-cells.

immunology↗

bioRxiv2022

Data availability of open T-cell receptor repertoire data, a systematic assessment

The improvement of next-generation sequencing technologies has promoted the field of immunogenetics and produced numerous immunogenomics data. Modern data-driven research has the power to promote novel biomedical discoveries through secondary analysis of such data. Therefore, it is important to ensure data-driven research with great reproducibility and robustness for promoting a precise and accurate secondary analysis of the immunogenomics data. In scientific research, rigorous conduct in designing and conducting experiments is needed, specifically in scientific and articulate writing, reporting and interpreting results. It is also crucial to make raw data available, discoverable, and well described or annotated in order to promote future re-analysis of the data. In order to assess the data availability of published T cell receptor (TCR) repertoire data, we examined 11,918 TCR-Seq samples corresponding to 134 TCR-Seq studies ranging from 2006 to 2022. Among the 134 studies, only 38.1% had publicly available raw TCR-Seq data shared in public repositories. We also found a statistically significant association between the presence of data availability statements and the increase in raw data availability (p=0.014). Yet, 46.8% of studies with data availability statements failed to share the raw TCR-Seq data. There is a pressing need for the biomedical community to increase awareness of the importance of promoting raw data availability in scientific research and take immediate action to improve its raw data availability enabling cost-effective secondary analysis of existing immunogenomics data by the larger scientific community.

scientific communication and education↗

bioRxiv2022

Graph deep learning reveals multiple signal pathways activated in anti-citrullinated protein antibodies stimulated synoviocytes

AO_SCPLOWBSTRACTC_SCPLOWWe present a study of anti-citrullinated protein antibodies stimulated fibroblast-like synoviocytes from patients with rheumatoid arthritis, which is powered by a novel graph deep learning framework applied to single-cell mRNA expression data. This new analytical framework discovered dominant pathways that suggest IL1-IL1R mediated signaling, a novel signal transduction response to ACPA-stimulation, and comfirmed our previous finding of PI3K/AKT activation in response of ACPA-stimulation as well. The study demonstrated the capability of graph deep learning framework on signaling pathway analysis. The findings suggest that ACPAs contribute to distinct pathogenic events through activating multiple signaling pathways.

molecular biology↗

bioRxiv2021

A screening pipeline identifies a broad-spectrum inhibitor of bacterial AB toxins with cross protection against influenza A virus H1N1 and SARS-CoV-2

A challenge for the development of host-targeted anti-infectives against a large spectrum of AB-like toxin-producing bacteria encompasses the identification of chemical compounds corrupting toxin transport through both endolysosomal and retrograde pathways. Here, we performed a high-throughput screening of small chemical compounds blocking active Rac1 proteasomal degradation triggered by the Cytotoxic Necrotizing Factor-1 (CNF1) toxin, followed by orthogonal screens against two AB toxins hijacking defined endolysosomal (Diphtheria toxin) or retrograde (Shiga-like toxin 1) pathways to intoxicate cells. This led to the identification of the molecule N-(3,3-diphenylpropyl)-1-propyl-4-piperidinamine, referred to as C910. This compound induces the swelling of EEA1-positive early endosomes, in absence of PIKfyve kinase inhibition, and disturbs the trafficking of CNF1 and the B-subunit of Shiga toxin along the endolysosomal or retrograde pathways, respectively. Together, we show that C910 protects cells against 8 bacterial AB toxins including large clostridial glucosylating toxins from Clostridium difficile. Of interest, C910 also reduced viral infection in vitro including influenza A virus subtype H1N1 and SARS-CoV-2. Moreover, parenteral administration of C910 to the mice resulted in its accumulation in lung tissues and reduced lethal influenza infection.

microbiology↗

bioRxiv2021

Large scale screening discovers clofoctol as an inhibitor of SARS-CoV-2 replication that reduces COVID-19-like pathology

Drug repurposing has the advantage of shortening regulatory preclinical development steps. Here, we screened a library of drug compounds, already registered in one or several geographical areas, to identify those exhibiting antiviral activity against SARS-CoV-2 with relevant potency. Of the 1,942 compounds tested, 21 exhibited a substantial antiviral activity in Vero-81 cells. Among them, clofoctol, an antibacterial drug used for the treatment of bacterial respiratory tract infections, was further investigated due to favorable safety profile and pharmacokinetic properties. Notably, the peak concentration of clofoctol that can be achieved in human lungs is more than 20 times higher than its IC50 measured against SARS-CoV-2 in human pulmonary cells. This compound inhibits SARS-CoV-2 at a post-entry step. Lastly, therapeutic treatment of human ACE2 receptor transgenic mice decreased viral load, reduced inflammatory gene expression and lowered pulmonary pathology. Altogether, these data strongly support clofoctol as a therapeutic candidate for the treatment of COVID-19 patients. SummaryAntivirals targeting SARS-CoV-2 are sorely needed. In this study, we screened a library of drug compounds and identified clofoctol as an antiviral against SARS-CoV-2. We further demonstrated that, in vivo, this compound reduces inflammatory gene expression and lowers pulmonary pathology.

microbiology↗