Biology subjects

Johansson, E.

Publications and source records attributed to Johansson, E..

15 recordsLinked to original sources

bioRxiv2026

COMBO-RATE: An experimentally validated bioinformatic tool to identify promiscuous HLA restrictions

Defining HLA restriction of T cell epitopes is essential for understanding immune responses in infectious disease, autoimmunity, and vaccine design. Current bioinformatic programs, including the IEDB RATE tool, enable inference of single-HLA restrictions from immune response data of HLA-typed donors. However, T cell epitopes are frequently presented by multiple HLA alleles, a phenomenon termed promiscuous restriction, limiting the utility of single-allele approaches. To address this limitation, we developed COMBO-RATE, an extension of RATE that systematically evaluates combinations of HLA alleles to identify multi-allelic restriction patterns. Analysis of three independent datasets spanning distinct antigen systems and different epitope discovery strategies revealed that promiscuous restriction is a near-universal feature of immunodominant epitopes. Focusing on the 43 immunodominant CD4 T cell epitopes identified in a B. pertussis genome-wide screen, COMBO-RATE outperformed conventional RATE, identifying restrictions for 35 of 43 epitopes, compared to 24 by RATE alone, and uncovered 64 additional allele restrictions, including 29 unique alleles. Experimental validation using single-HLA transfected cell lines and antigen presentation assays confirmed COMBO-RATE-inferred restrictions, demonstrating that a single epitope can be independently presented by distinct HLA alleles. Overall, COMBO-RATE provides a robust and scalable framework for defining complete HLA restriction profiles from existing population response data, with important implications for the design of vaccines requiring broad HLA coverage across genetically diverse populations. This pipeline is available as both a Python package and a user-friendly web application.

immunology↗

bioRxiv2026

Resolving thyroid lineage cell trajectories merging into a dual endocrine gland in mammals

The thyroid has a remarkable evolution, first appearing in invertebrate chordates as an integral exocrine constituent of the pharyngeal endostyle that is transformed into an endocrine gland during metamorphosis in basal vertebrates. In mammals, the thyroid acquires a second endocrine cell type, calcitonin-producing C-cells, which for long were inferred a neural crest origin, shuttled to the embryonic thyroid by the ultimobranchial bodies. However, recent lineage tracing experiments firmly establish these neuroendocrine cells also derive from foregut endoderm. Key questions remaining unanswered are how thyroid primordia independently develop and, unlike in all non-mammalian vertebrates, merge into a dual endocrine organ. Here, by leveraging a single-cell transcriptome atlas derived from mouse pharyngeal endoderm and its subsequent cell fates, we characterize the global gene expression profile of thyroid- and ultimobranchial-derived progenitor cells and identify comprehensive gene regulatory networks of lineage-specific transcription factors and novel target genes predicted to differentially regulate cell proliferation, plasticity and differentiation during development. Spatiotemporal analyses reveal C-cell precursors are triggered to undergo epithelial-mesenchymal transition (EMT) and cell-autonomously down-regulate collagen IV and degrade laminin that delineates the ultimobranchial body epithelium. However, the EMT program is not fully deployed until both cell lineages are mixed and propagate conjointly thus forming the typical thyroid histoarchitecture of follicles and parafollicular C-cells, every follicle/C-cell unit being enveloped by a renewed basement membrane. Mixed-type thyroid carcinoma recapitulates a synchronous lineage growth pattern but only the neuroendocrine tumor cells are able to escape the compound follicle boundaries and become invasive adopting a C-cell precursor-like migratory phenotype.

developmental biology↗

bioRxiv2025

Coevolution of neoplastic and non-neoplastic reactive astrocyte states converges on mesenchymal-like and injury-response programs during murine glioblastoma progression and post-radiotherapy recurrence

Glioblastomas initially respond to radiotherapy but invariably recur, often within high-dose radiation treatment fields. Although stromal radiation responses are incompletely understood, evidence suggests that the tumor microenvironment becomes tumor-supportive after therapy. Using a genetically engineered glioblastoma mouse model, we profiled healthy brain, primary tumors, and post-radiotherapy recurrences with single-cell and spatial transcriptomics and immunohistochemistry. Across 13 non-neoplastic cell types and 10 tumor cell states, we mapped transcriptional adaptations accompanying progression from healthy brain to primary and recurrent glioblastoma. We identified distinct astrocyte states linked to disease stage, including reactive non-neoplastic astrocytes and tumor cells adopting reactive astrocyte-like phenotypes. Reactive astrocyte-like tumor cells with mesenchymal and injury-response signatures were enriched after radiotherapy and persisted in recurrent tumors. Receptor-ligand interactions between reactive astrocytes and tumor cells included known and putative drivers of aggressiveness. These findings highlight convergent reactive astrocyte programs in astrocytes and tumor cells as potential mediators of glioblastoma radioresistance.

cancer biology↗

bioRxiv2025

Comparative Metagenomics of Soda Lakes and the Rumen Reveals Novel Microbial Lineages and Carbohydrate-active Enzyme Diversity

Microbial communities have evolved diverse strategies to metabolize similar substrates, shaped by environmental pressures and interspecies interactions. Comparative analyses across extreme and host-associated ecosystems are essential for uncovering novel microbial diversity, functional adaptations, and enzymes with industrial relevance. Here, we present a comparative metagenomic analysis of two ecologically distinct environments, highly alkaline-saline soda lakes, and the host-associated rumen to investigate microbial diversity, metabolic potential, and carbohydrate-active enzyme (CAZyme) repertoires. Taxonomic profiling revealed distinct microbial signatures: soda lake microbiomes were dominated by Proteobacteria, particularly Halomonas, and Nitrincola, while the rumen was enriched in Bacteroidota, Fibrobacteres, and Firmicutes, with Prevotella and Fibrobacter as key taxa. The soda lake MAGs exhibit greater evolutionary divergence, suggesting the presence of novel microbial lineages. Codon usage profiling revealed distinct patterns of GC3 bias, suggesting divergent translational optimization strategies shaped by environmental constraints. CAZyme profiling uncovered ecosystem-specific glycoside hydrolase repertoires, with the rumen enriched in plant fiber-degrading enzymes and soda lakes exhibiting broader GH diversity adapted to high salinity and alkalinity. These findings highlight distinct microbial and enzymatic strategies for carbon cycling and position soda lakes as promising reservoirs of extremophile-adapted enzymes for biotechnological applications.

microbiology↗

bioRxiv2025

Differential memory enrichment of cytotoxic CD4 T cells in Parkinson's disease patients reactive to α-synuclein

Parkinsons disease (PD) is a complex neurodegenerative disease with a largely unknown etiology. Although the loss of dopaminergic neurons in the substantia nigra pars compacta is the pathological hallmark of PD, neuroinflammation also plays a fundamental role in PD pathology. We have previously reported that PD patients have increased frequencies of T cell reactive to peptides from -synuclein (-syn). However, not all PD participants respond to -syn. Furthermore, we have previously found that CD4 T cells from PD participants responding to -syn (PD_R) are transcriptionally distinct from PD participants not responding to -syn (PD_NR). To gain further insight into the pathology of PD_R participants, we investigated surface protein expression of 11 proteins whose genes had previously been found to be differentially expressed when comparing PD_R and healthy control participants not responding to -syn (HC_NR). We found that Cadherin EGF LAG seven-pass G-type receptor 2 (CELSR2) was expressed on a significantly higher proportion of CD4 effector memory T cells (TEM) in PD_R compared to HC_NR. Single-cell RNA sequencing analysis of cells expressing or not expressing CELSR2 revealed that PD_R participants have elevated frequencies of activated TEM subsets and an almost complete loss of cytotoxic TEM cells. Flow cytometry analyses confirmed that Granulysin+ CD4 cytotoxic TEM cells are reduced in PD_R. Taken together, these results provide further insight into the perturbation of T cell subsets in PD_R, and highlights the need for further investigation into the role of Granulysin+ CD4 cytotoxic TEM in PD pathology.

neuroscience↗

bioRxiv2025

T cell responses towards PINK1 and α-synuclein are elevated in prodromal Parkinson's disease

A role of the immune system in Parkinsons disease (PD) progression has long been suspected due to the increased frequency of activated glial cells and infiltrating T cells into the substantia nigra. It was previously reported that PD donors have increased T cell responses towards PINK1 and -synuclein (-syn), two Lewy body-associated proteins. Further, T cell reactivity towards -syn was highest closer to disease onset, highlighting that autoreactive T cells might play a role in PD pathogenesis. However, whether T cell autoreactivity is present during prodromal PD is unknown. Here, we investigated T cell responses towards PINK1 and -syn in donors at high risk of developing PD (i.e. prodromal PD: genetic risk, hyposmia, and or REM sleep behavior disorder), in comparison to PD and healthy control donors. T cell reactivity to these two autoantigens was detected in prodromal PD at levels comparable to those detected in individuals with clinically diagnosed PD. Aligned with the increased incidence of PD in males, we found that males with PD, but not females, had elevated T cell reactivity compared to healthy controls. However, among prodromal PD donors, males and females had elevated T cell responses. These differing trends in reactivity highlights the need for further studies of the impact of biological sex on neuroinflammation and PD progression.

neuroscience↗

bioRxiv2025

Evolution of SARS-CoV-2 T cell responses as a function of multiple COVID-19 boosters

The long-term effects of repeated COVID-19 vaccinations on adaptive immunity remain incompletely understood. Here, we conducted a comprehensive three-year longitudinal study examining T cell and antibody responses in 78 vaccinated individuals without reported symptomatic infections. We observed distinct dynamics in Spike-specific humoral and cellular immune responses across multiple vaccine doses. While antibody titers incrementally increased and stabilized with each booster, T cell responses rapidly plateaued, maintaining remarkable stability across CD4+ and CD8+ subsets. Notably, approximately 30% of participants showed CD4+ T cell reactivity to non-Spike antigens, consistent with asymptomatic infections. Single-cell RNA sequencing revealed a diverse landscape of Spike-specific T cell phenotypes, with no evidence of increased exhaustion or significant functional impairment. However, qualitative changes were observed in individuals with evidence of asymptomatic infection, exhibiting unique immunological characteristics, including increased frequencies of Th17-like CD4+ T cells and GZMKhi/IFNR CD8+ T cell subsets. Remarkably, repeated vaccinations in this group were associated with a progressive increase in regulatory T cells, potentially indicating a balanced immune response that may mitigate immunopathology. By regularly stimulating T cell memory, boosters contribute to a stable and enhanced immune response, which may provide better protection against symptomatic infections.

immunology↗

bioRxiv2024

Pericytes orchestrate a tumor-restraining microenvironment in glioblastoma

Glioblastoma (GBM) is characterized by fast progression, an infiltrative growth pattern, and a high rate of relapse. A defining feature of GBM is the existence of spatially and functionally distinct cellular niches, i.e. a hypoxic niche, a leading-edge niche, and a perivascular niche, in which malignant cells engage in paracrine crosstalk with cell types comprising the tumor microenvironment. Here, by analysis of single-cell transcriptomic data of human GBM and transgenic mouse models of GBM, we unexpectedly identified pericytes, mural cells intimately associated with the endothelium, as the most active paracrine signaling hub within the tumor parenchyma. Exclusive signaling axes emanating from pericytes were received by endothelial cells, malignant cells, astrocytes, and immune cells. Depletion of pericytes through genetic engineering in several different transgenic and orthotopic mouse models of GBM demonstrated accelerated tumor progression, a disrupted blood-brain-barrier, and premature death of pericyte-poor mice. Mechanistic studies revealed that pericyte deficiency altered the cellular composition of GBM, remodeled the endothelium, and impacted on the immune cell landscape, exacerbating tumor cell invasion and immune suppression. Specifically, endothelial cells deprived of pericyte association altered their signaling programs, which in turn attracted perivascular, tumor-associated macrophages polarized towards an immune-suppressive phenotype. The recruited macrophages expressed Hepatocyte Growth Factor (HGF), which reinforced activation of its receptor tyrosine kinase MET on GBM cells harboring an extreme mesenchymal subtype driven by the key phenotypic regulator Fosl1 within hypoxic regions. Indeed, orthotopic implantation of isolated, MET-expressing GBM cells corroborated their superior tumor-initiating capability and invasive phenotype. In patients, low expression of a pericyte core gene signature was reduced in recurrent GBM, compared to primary tumors. Consistently, gene signatures for transcriptional programs of Fosl1+Met+ GBM cells were indicative of poor survival in human tumors, and spatial transcriptomics corroborated their superior invasive capacity. Taken together, we infer that the pericyte represents a critical modulator of GBM development by orchestrating a tumor-suppressive microenvironment; our findings thus highlight the importance of pericyte preservation in the face of current and future GBM therapies. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/609765v1_ufig1.gif" ALT="Figure 1"> View larger version (102K): org.highwire.dtl.DTLVardef@803a8eorg.highwire.dtl.DTLVardef@8441eaorg.highwire.dtl.DTLVardef@1038288org.highwire.dtl.DTLVardef@16eccfc_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2024

Hypoxia-induced Complement Component 3 Promotes Aggressive Tumor Growth in the Glioblastoma Microenvironment

Glioblastoma (GBM) is the most aggressive form of glioma with a high rate of relapse despite intensive treatment. Tumor recurrence is tightly linked to radio-resistance, which in turn is associated with hypoxia. Here, we discovered a strong link between hypoxia and local complement signaling using publicly available bulk, single cell, and spatially resolved transcriptomic data from human GBM patients. Complement component 3 (C3) and the receptor C3AR1 were both associated with aggressive disease and shorter survival in human glioma. In a genetically engineered mouse model of GBM, we found C3 specifically in hypoxic tumor areas. In vitro, we found an oxygen level-dependent increase in C3 and C3AR1 expression in response to hypoxia in several GBM and stromal cell types. Presence of C3 increased proliferation of GBM cells under hypoxic conditions, as well as clonal survival of GBM cells following radiation. Targeting C3aR using the antagonist SB290157 decreased GBM cell self-renewal in vitro, and prolonged survival of glioma bearing mice both alone and in combination with radiotherapy while reducing the number of M2-polarized macrophages. Our findings establish a strong link between hypoxia and complement pathways in GBM, and support a role of hypoxia-induced C3a-C3aR signaling as a contributor to glioma aggressiveness.

cancer biology↗

bioRxiv2023

A sensor complements the steric gate when DNA polymerase ϵ discriminates ribonucleotides.

The cellular imbalance between high concentrations of ribonucleotides (NTPs) and low concentrations of deoxyribonucleotides (dNTPs), is challenging for DNA polymerases when building DNA from dNTPs. It is currently believed that DNA polymerases discriminate against NTPs through a steric gate model involving a clash between a tyrosine and the 2-hydroxyl of the ribonucleotide in the polymerase active site in B-family DNA polymerases. With the help of crystal structures of a B-family polymerase with a UTP or CTP in the active site, molecular dynamics simulations, biochemical assays and yeast genetics, we have identified a mechanism by which the finger domain of the polymerase sense NTPs in the polymerase active site. In contrast to the previously proposed polar filter, our experiments suggest that the amino acid residue in the finger domain senses ribonucleotides by steric hindrance. Furthermore, our results demonstrate that the steric gate in the palm domain and the sensor in the finger domain are both important when discriminating NTPs. Structural comparisons reveal that the sensor residue is conserved among B-family polymerases and we hypothesize that a sensor in the finger domain should be considered in all types of DNA polymerases.

biochemistry↗

bioRxiv2023

Computational design of N-linked glycans for high throughput epitope profiling

Efficient identification of epitopes is crucial for drug discovery and design as it enables the selection of optimal epitopes, expansion of lead antibody diversity, and verification of binding interface. Although high resolution low throughput methods like X-ray crystallography can determine epitopes or protein-protein interactions accurately, they are time-consuming and can only be applied to a limited number of complexes. To overcome these limitations, we have developed a rapid computational method that incorporates N-linked glycans to mask epitopes or protein interaction surfaces, thereby providing an atomistic mapping of these regions. Using human coagulation factor IXa (fIXa) as a model system, we could rapidly and reliably delineate epitopes through the insertion of N-linked glycans that efficiently disrupt binding in a site-selective manner. To validate the efficacy of our method, we conducted ELISA experiments and high-throughput yeast surface display assays. Furthermore, X-ray crystallography was employed to verify the results, thereby recapitulating through the method of N-linked glycans an atomistic resolution mapping of the epitope.

bioengineering↗

bioRxiv2020

Can a nick promote partial genome re-replication?

Single-stranded DNA breaks, including simple nicks, are amongst the most common forms of DNA damage in cells. They can be readily repaired by ligation; however, if a nick occurs just ahead of an approaching replisome, the outcome is a collapsed replication fork in which the nick is converted into a single-ended double-strand DNA break. Attention has largely focused on the processes by which this broken end is used to prime replication restart. We realized that in eukaryotic cells, where replication initiates from multiple replication origins, a second fork converging on the collapsed fork offers additional opportunities for repair, but also generates a substrate that can promote localized re-replication. We have modelled this with purified proteins in vitro and have found that there is, indeed, an additional hazard that eukaryotic replisomes face. We discuss how this problem might be mitigated.

biochemistry↗

bioRxiv2020

A whole-genome sequenced control population in northern Sweden reveals subregional genetic differences.

The number of national reference populations that are whole-genome sequenced are rapidly increasing. Partly driving this development is the fact that genetic disease studies benefit from knowing the genetic variation typical for the geographical area of interest. A whole-genome sequenced Swedish national reference population (n=1000) has been recently published but with few samples from northern Sweden. In the present study we have whole-genome sequenced a control population (n=300) (ACpop) from Vasterbotten County, a sparsely populated region in northern Sweden previously shown to be genetically different from southern Sweden. The aggregated variant frequencies within ACpop are publicly available (DOI 10.17044/NBIS/G000005) to function as a basic resource in clinical genetics and for genetic studies. Our analysis of ACpop, representing approximately 0.11% of the population in Vasterbotten, indicates the presence of a genetic substructure within the county. Furthermore, a demographic analysis showed that the population from which samples were drawn was to a large extent geographically stationary, a finding that was corroborated in the genetic analysis down to the level of municipalities. Including ACpop in the reference population when imputing unknown variants in a Vasterbotten cohort resulted in a strong increase in the number of high-confidence imputed variants (up to 81% for variants with minor allele frequency < 5%). ACpop was initially designed for cancer disease studies, but the genetic structure within the cohort will be of general interest for all genetic disease studies in northern Sweden.

genetics↗

bioRxiv2020

The irradiated brain microenvironment supports glioma stemness and survival via astrocyte-derived Transglutaminase 2

The tumor microenvironment plays an essential role in supporting glioma stemness and radioresistance, and following radiotherapy, recurrent gliomas form in an irradiated microenvironment. Here, we found that astrocytes, when pre-irradiated, increased stemness and survival of co-cultured glioma cells. Tumor-naive brains increased reactive astrocytes in response to radiation, and mice subjected to radiation prior to implantation of glioma cells developed more aggressive tumors. We identified extracellular matrix derived from irradiated astrocytes as a major driver of this phenotype, and astrocyte-derived transglutaminase 2 (TGM2) as a promoter of glioma stemness and radioresistance. TGM2 levels were increased after radiation in vivo and in recurrent human glioma, and TGM2 inhibitors abrogated glioma stemness and survival. These data suggest that irradiation of the brain results in the formation of a tumor-supportive microenvironment. Therapeutic targeting of radiation-induced, astrocyte-derived extracellular matrix proteins may enhance the efficacy of standard of care radiotherapy by reducing stemness in glioma.

cancer biology↗

bioRxiv2019

Dynamics, cariogenicity, and geographic distribution of Streptococcus mutans adhesin types suggest adaptation to individual hosts

Dental caries, the most common chronic infectious disease, involve Streptococcus mutans SpaP A/B/C and Cnm/Cbm adhesin types of different virulence. We have explored their stability and dynamics over 5 years, their geographic distribution, as well as the potentially increased cariogenicity of specific SpaP B subtypes. We performed qPCR and TaqMan typing using whole saliva and isolates from 452 Swedish adolescents followed from 12 to 17 years of age. Approximately 50% of the children were infected at baseline with a single dominant (44%) or mixed (6%) SpaP A, B, or C type, some of which were also Cnm (6%) or Cbm (1%) positive. Stability (+, +) was high for S. mutans infection (85%) and dominant SpaP A or C (80% and 67%) and Cnm or Cbm (85% and 100%) types, but low for SpaP B (51%) and mixed SpaP A/B/C types (26%). Only five children switched from one SpaP type to another, and none between Cnm and Cbm types. Mixed SpaP A/B/C types were typically lost or changed into dominant types. Moreover, children infected with Cnm (n=26) types were more frequent in the northern (Skellefte[a]) region (p = 0.0041), and those with Cbm types (n=7) in the southern (Ume[a]) region. Children infected with SpaP B-2 subtypes had a doubled caries experience (p = 0.009) and 5-year caries increment (p = 0.02) compared to those infected with SpaP A. In conclusion, the stable dominant but instable mixed adhesin types and geographic differentiation of Cnm and Cbm types suggest adaptation of low and high cariogenicity types to specific individuals.

microbiology↗