Umeå University's logo

Transcriptome analysis has become an increasingly reliable method to assess the response of microorganisms to the environment inside the host cell. However, to maximize the reading depth of the pathogen and host transcriptomes, physical separation of the RNA pools is preferred, particularly to determine intracellular gene expression of the pathogen. Here, we set out to determine the intracellular gene expression of two important pathogens, the Gram-positive bacterium Staphylococcus aureus and the Gram-negative bacterium Shigella flexneri. For accurate determination, we developed a rapid method to physically separate bacterial from eukaryotic RNA with a high level of purity. Analysis by RT-qPCR demonstrated that bacterial and eukaryotic RNA could be separated efficiently, enriching the bacterial RNA pool >20-fold. Comparing gene expression of RNA extracted from different purification fractions by RNAseq showed an upregulation of different S. aureus genes. Among these was vraX, which encodes a secreted peptide that binds the C1q protein in the classical complement pathway. IMPORTANCE Infectious diseases are one of the largest causes of deaths world-wide despite access to antimicrobials and vaccines. To develop new strategies to defeat microbial infections, a greater understanding of the infection process is needed such as analyzing the microbial and host responses during different stages of infection. Several microbes can invade host cells and being able to accurately monitor their and the host cells' gene expression is critical. Here, we have developed an easy and inexpensive method to reliably enrich for and separate bacterial and eukaryotic RNA after an intracellular infection. Our method is applicable to both Gram-negative and Gram-positive bacteria. Using this method, we have identified several genes to be upregulated during S. aureus infection of macrophage cells. Our data could prove useful to obtain new strategies for developing antimicrobial drugs.

Rift Valley fever virus (RVFV) is a mosquito-borne Phlebovirus and zoonotic pathogen affecting maternal-fetal health. Vertical transmission is linked to miscarriage and severe fetal outcomes, but mechanisms of placental pathogenesis remain unclear. We used first-trimester human trophoblast stem cells (hTSCs) to model infection at the maternal-fetal interface. Immunofluorescence, qRT-PCR, western blotting, and single-cell transcriptomics showed that hTSCs are highly susceptible to RVFV. Strand-specific viral transcriptomics confirmed the ambisense S segment and revealed preferential transcription of the M and S segments over L. RVFV induced G1 arrest, impairing trophoblast proliferation and differentiation, and drove widespread transcriptional reprogramming, including strong interferon lambda 1 (IFNL1) but modest type I interferon responses, and dysregulation of inflammatory and preeclampsia-associated genes such as RUNX1 and TGFBRAP1. Recombinant IFN-λ pretreatment reduced RVFV protein expression, highlighting hTSCs as a robust model and IFN-λ as a promising antiviral strategy.

The placental intervillous space is a unique immunological niche where circulating maternal immune cells come into direct contact with the fetal syncytiotrophoblast. While adaptations in immune cell composition are known to occur in the maternal decidua throughout pregnancy, it remains unclear whether similar changes take place in the intervillous space. Here, we demonstrate that the intervillous immune cell composition undergoes dynamic changes during pregnancy, with a decreased proportion of NK cells and an increased proportion of T cells from second trimester to term pregnancy. Interestingly, second-trimester intervillous NK cells were predominantly CD56brightCD16- with high expression of CD49a, CD103, and CD69. This phenotype more closely resembled tissue-resident decidual NK (dNK) cells than peripheral NK cells. Conditioned medium from fetal villous tissue did not induce changes in peripheral NK cell phenotype, suggesting that the observed phenotypic alterations are not driven by soluble factors from the villous microenvironment. Analysis of predicted ligand-receptor complexes suggested that NK cells may provide important growth signals to the syncytiotrophoblast. In conclusion, immunological adaptations occur in the intervillous space throughout pregnancy and the presence of dNK-like cells in the intervillous space underscores a potential role for these cells in maintaining a balanced immune environment at the maternal-fetal interface.

Genetic modification is essential for understanding parasite biology, yet it remains challenging in Plasmodium. This is partially due to the parasite’s low genetic tractability and reliance on homologous recombination, since the parasites lack the canonical non-homologous end-joining pathway. Existing approaches, such as the PlasmoGEM project, enable genome-wide knockouts but remain limited in coverage and flexibility. Here, we present the Plasmodium berghei high-throughput (PbHiT) system, a scalable CRISPR-Cas9 protocol for efficient genome editing in rodent malaria parasites. The PbHiT method uses a single cloning step to generate vectors in which a guide RNA (gRNA) is physically linked to short (100 bp) homology arms, enabling precise integration at the target locus upon transfection. The gRNA also serves as a unique barcode, allowing pooled vector transfections and identification of mutants by downstream gRNA sequencing. The PbHiT system reliably recapitulates known mutant growth phenotypes and supports both knockout and tagging strategies. This protocol provides a reproducible and scalable tool for genome editing in P. berghei, enabling both targeted functional studies and high-throughput genetic screens. Additionally, we provide an online resource covering the entire P. berghei protein-coding genome and describe a step-by-step pooled ligation approach for large-scale vector production.

Here, we present a protocol for total internal reflection fluorescence (TIRF) microscopy image preprocessing and radial analysis of lymphocyte function-associated antigen-1 (LFA-1) in T cell immune synapses. We describe steps for combining customizable Fiji/ImageJ macros for image background subtraction and segmentation with flexible R-based scripts for peripheral supramolecular activation cluster (pSMAC) center identification, center-based cropping, and radial analysis of synaptic LFA-1 in T cells. This workflow supports established analyses, including radial averaging/spinning and fluorescence intensity measurements across the synapse.

Many Plasmodium genes remain uncharacterized due to low genetic tractability. Previous large-scale knockout screens have only been able to target about half of the genome in the more genetically tractable rodent malaria parasite Plasmodium berghei. To overcome this limitation, we have developed a scalable CRISPR system called P. berghei high-throughput (PbHiT), which uses a single cloning step to generate targeting vectors with 100-bp homology arms physically linked to a guide RNA (gRNA) that effectively integrate into the target locus. We show that PbHiT coupled with gRNA sequencing robustly recapitulates known knockout mutant phenotypes in pooled transfections. Furthermore, we provide an online resource of knockout and tagging designs to target the entire P. berghei genome and scale-up vector production using a pooled ligation approach. This work presents for the first time a tool for high-throughput CRISPR screens in Plasmodium for studying the parasite’s biology at scale.

Hydrogen sulfide (H₂S) acts as an energy source, a toxin, and a gasotransmitter across diverse biological contexts. We use the robust locomotory responses of Caenorhabditis elegans to high levels of H₂S to elucidate the molecular mechanisms underlying its acute and adaptive responses. We find that the H₂S-evoked behavioral response is shaped by multiple environmental factors including oxygen (O₂) levels and nutritional state and is modulated by various pathways such as insulin, TGF-β, and HIF-1 signaling, as well as by input from O₂-sensing neurons. Prolonged exposure to H₂S activates HIF-1 signaling, leading to the upregulation of stress-responsive genes, including those involved in H₂S detoxification. This promotes an adaptive state in which locomotory speed is reduced in H₂S, while responsiveness to other stimuli is preserved. In mutants deficient in HIF-1 signaling, iron storage, and detoxification mechanisms, animals display a robust initial response but rapidly enter a sleep-like behavior characterized by reduced mobility and diminished responsiveness to subsequent sensory stimuli. Furthermore, while acute production of mitochondria-derived reactive O₂ species (ROS) appears to initiate the avoidance response to H₂S, persistently high ROS promotes an adaptive state, likely by activating various stress-response pathways, without substantially compromising cellular H₂S detoxification capacity. Taken together, our study provides comprehensive molecular insights into the mechanisms through which C. elegans modulates and adapts its response to H₂S exposure.

Introduction: Chronic lymphocytic leukemia (CLL) has proven difficult to treat with chimeric antigen receptor (CAR) T cell therapy. CLL cells can negatively alter T cell fitness and induce a pseudohypoxic state. We hypothesized that production of CAR T cells under restricted oxygen conditions resembling physiological oxygen levels that can be encountered in tissues (i.e. 2% O2) could promote outgrowth of hypoxia-tolerant CAR T cells.

Methods: We performed in vitro phenotypic and functional assessments of CD19-directed CAR T cells produced in either 21% (NorCAR) or 2% (HypCAR) O2 derived from healthy donors (HDs) or patients with CLL.

Results: Production of HD-derived CAR T cells in 2% O2 promoted the enrichment of a naïve-like subset. HypCAR and NorCAR cells were functionally distinct; CD4+ HypCAR cells produced more IL-2 and tumor necrosis factor than CD4+ NorCAR cells. Production in 2% O2 was not detrimental to viability or proliferation upon cognate antigen-stimulation and led to increased activation. After chronic stimulation in hypoxia, HypCAR-product remained enriched in naïve-like cells, and demonstrated cytotoxic and cytokine production capacity. In CAR T cells derived from patients with CLL, NorCAR and HypCAR subsets were functionally and phenotypically comparable, but displayed different mitochondrial metabolism.

Discussion: We demonstrated that production in 2% O2 is not detrimental, confers subtle but lasting functional and phenotypic changes in CAR T cells warranting further research on the impact of hypoxic production on CAR T cell functionality in hypoxic tumor microenvironments.

The Shaker/Kv1 subfamily of voltage-gated potassium (K+) channels is essential for modulating membrane excitability. Their loss results in prolonged depolarization and excessive calcium influx. These channels have also been implicated in a variety of other cellular processes, but the underlying mechanisms remain poorly understood. Through comprehensive screening of K+ channel mutants in C. elegans, we discovered that shk-1 mutants are highly susceptible to bacterial pathogen infection and oxidative stress. This vulnerability is associated with reduced glycogen levels and substantial mitochondrial dysfunction, including decreased ATP production and dysregulated mitochondrial membrane potential under stress conditions. SHK-1 is predominantly expressed and functions in body wall muscle to maintain glycogen storage and mitochondrial homeostasis. RNA-sequencing data reveal that shk-1 mutants have decreased expression of a set of cation-transporting ATPases (CATP), which are crucial for maintaining electrochemical gradients. Intriguingly, overexpressing catp-3, but not other catp genes, restores the depolarization of mitochondrial membrane potential under stress and enhances stress tolerance in shk-1 mutants. This finding suggests that increased catp-3 levels may help restore electrochemical gradients disrupted by shk-1 deficiency, thereby rescuing the phenotypes observed in shk-1 mutants. Overall, our findings highlight a critical role for SHK-1 in maintaining stress tolerance by regulating glycogen storage, mitochondrial homeostasis, and gene expression. They also provide insights into how Shaker/Kv1 channels participate in a broad range of cellular processes.

Lung pathogenic T helper type 2 (pTh2) cells are important in mediating allergic asthma, but fundamental questions remain regarding their heterogeneity and epigenetic regulation. Here we investigate immune regulation in allergic asthma by single-cell RNA sequencing in mice challenged with house dust mite, in the presence and absence of histone deacetylase 1 (HDAC1) function. Our analyses indicate two distinct highly proinflammatory subsets of lung pTh2 cells and pinpoint thymic stromal lymphopoietin (TSLP) and Tumour Necrosis Factor Receptor Superfamily (TNFRSF) members as important drivers to generate pTh2 cells in vitro. Using our in vitro model, we uncover how signalling via TSLP and a TNFRSF member shapes chromatin accessibility at the type 2 cytokine gene loci by modulating HDAC1 repressive function. In summary, we have generated insights into pTh2 cell biology and establish an in vitro model for investigating pTh2 cells that proves useful for discovering molecular mechanisms involved in pTh2-mediated allergic asthma.