A5070372040- CAR-T cell therapy research
- Single-cell and spatial transcriptomics
- Immune Cell Function and Interaction
- T-cell and B-cell Immunology
- Cancer Immunotherapy and Biomarkers
- Genomics and Phylogenetic Studies
- Cancer Genomics and Diagnostics
- CRISPR and Genetic Engineering
- IL-33, ST2, and ILC Pathways
- Fungal and yeast genetics research
- RNA modifications and cancer
- RNA Research and Splicing
- Pluripotent Stem Cells Research
- Congenital heart defects research
- Cancer-related molecular mechanisms research
- MicroRNA in disease regulation
- Protein Structure and Dynamics
- Cancer Cells and Metastasis
- Molecular Biology Techniques and Applications
- RNA and protein synthesis mechanisms
- Epigenetics and DNA Methylation
- Eosinophilic Esophagitis
- Advanced biosensing and bioanalysis techniques
- Bioinformatics and Genomic Networks
- Microbial Metabolic Engineering and Bioproduction
Science for Life Laboratory
2016-2025
Uppsala University
2016-2025
Chalmers University of Technology
2023-2024
National Bioinformatics Infrastructure Sweden
2022-2024
Ludwig Cancer Research
2013-2018
Karolinska Institutet
2013-2018
Stockholm University
2005-2010
National Food Administration
2004-2005
Massively parallel DNA sequencing of thousands samples in a single machine-run is now possible, but the preparation individual libraries expensive and time-consuming. Tagmentation-based library construction, using Tn5 transposase, efficient for generating currently relies on undisclosed reagents, which severely limits development novel applications execution large-scale projects. Here, we present simple robust procedures transposase production optimized reaction conditions tagmentation-based...
Abstract Cancer-associated fibroblasts (CAFs) are a major constituent of the tumor microenvironment, although their origin and roles in shaping disease initiation, progression treatment response remain unclear due to significant heterogeneity. Here, following negative selection strategy combined with single-cell RNA sequencing 768 transcriptomes mesenchymal cells from genetically engineered mouse model breast cancer, we define three distinct subpopulations CAFs. Validation at transcriptional...
Abstract Background Most proteins interact with only a few other while small number of (hubs) have many interaction partners. Hub and non-hub differ in several respects; however, understanding is not complete about what properties characterize the hubs set them apart from low connectivity. Therefore, we investigated differentiates non-hubs static (party hubs) dynamic (date protein-protein network Saccharomyces cerevisiae . Results The interactions hub can partly be explained by bindings to...
Pdgfra+ oligodendrocyte precursor cells (OPCs) arise in distinct specification waves during embryogenesis the central nervous system (CNS). It is unclear whether there a correlation between these and different (OL) states at adult stages. Here, we present bulk single-cell transcriptomics resources providing insights on how transitions occur. We found that post-natal OPCs from brain spinal cord similar transcriptional signatures. Moreover, OPC progeny of E13.5 electrophysiological profiles to...
Abstract Midbrain dopamine (mDA) neurons constitute a heterogenous group of cells that have been intensely studied, not least because their degeneration causes major symptoms in Parkinson’s disease. Understanding the diversity mDA – previously well characterized anatomically requires systematic molecular classification at genome-wide gene expression level. Here, we use single cell RNA sequencing isolated mouse expressing transcription factor Pitx3 , marker for neurons. Analyses include...
The impact of the microenvironment on innate lymphoid cell (ILC)-mediated immunity in humans remains largely unknown. Here we used full-length Smart-seq2 single-cell RNA-sequencing to unravel tissue-specific transcriptional profiles and heterogeneity CD127+ ILCs across four human tissues. Correlation analysis identified gene modules characterizing migratory properties tonsil blood ILCs, signatures tissue-residency, activation modified metabolism colon lung ILCs. Trajectory revealed potential...
Many proteins, especially in eukaryotes, contain tandem repeats of several domains from the same family. These have a variety binding properties and are involved protein-protein interactions as well to other ligands such DNA RNA. The rapid expansion protein domain is assumed evolved through internal duplications. However, exact mechanisms behind these duplications not well-understood. Here, we studied evolution, function, structure, gene phylogenetic distribution repeats. For this purpose...
BackgroundGroup 2 innate lymphoid cells (ILC2s) are involved in the initial phase of type inflammation and can amplify allergic immune responses by orchestrating other cells. Prostaglandin (PG) E2 is a bioactive lipid that plays protective roles lung, particularly during inflammation.ObjectiveWe set out to investigate how PGE2 regulates human ILC2 function.MethodsThe effects on proliferation intracellular cytokine transcription factor expression were assessed means flow cytometry. Cytokine...
Highlights•NRP1+ ILC3s are present in lymphoid tissues, but not the peripheral blood or skin•NRP1+ express CD45RO and produce higher amounts of cytokines than NRP1− ILC3s•NRP1 is a marker for human with LTi phenotype vitro activity•NRP1+ lung tissues from smokers COPD patientsSummaryHere, we characterize subset that Neuropilin1 (NRP1) skin. NRP1+ group 3 innate cells (ILC3s) display tissue inducer (LTi) activity. In agreement this, mainly located proximity to high endothelial venules (HEVs)...
Abstract Cell replacement is a long-standing and realistic goal for the treatment of Parkinsonʼs disease (PD). Cells transplantation can be obtained from fetal brain tissue or stem cells. However, after transplantation, dopamine (DA) neurons are seen to minor component grafts, it has remained difficult determine identity other cell types. Here, we report analysis by single-cell RNA sequencing (scRNA-seq) combined with comprehensive histological analyses characterize intracerebral grafts...
Cell fate decisions during early B cell activation determine the outcome of responses to pathogens and vaccines. We examined response T-dependent antigen in mice by single-cell RNA sequencing. Early after immunization, a homogeneous population activated precursors (APs) gave rise transient wave plasmablasts (PBs), followed day later emergence germinal center cells (GCBCs). Most APs rapidly exited cycle, giving non-GC-derived memory (eMBCs) that retained an AP-like transcriptional profile....
Summary Stem cell-based embryo models offer unprecedented experimental tools for studying early human development. The usefulness of hinges on their molecular, cellular and structural fidelities to in vivo counterparts. To authenticate models, single-cell RNA-sequencing has been utilised unbiased transcriptional profiling. However, a well-organised integrated dataset, serving as universal reference benchmarking remains unavailable. Herein, we developed such reference, through integration six...
A wealth of specialized cell populations within the skin facilitates its hair-producing, protective, sensory, and thermoregulatory functions. How vast cell-type diversity tissue architecture develops is largely unexplored. Here, with single-cell transcriptomics, spatial assignment, cell-lineage tracing, we deconstruct early embryonic mouse during key transitions from seemingly uniform developmental precursor states to a multilayered, multilineage epithelium, complex dermal identity. We...
Stem cell-based embryo models offer unprecedented experimental tools for studying early human development. The usefulness of hinges on their molecular, cellular and structural fidelities to in vivo counterparts. To authenticate models, single-cell RNA sequencing has been utilized unbiased transcriptional profiling. However, an organized integrated RNA-sequencing dataset, serving as a universal reference benchmarking remains unavailable. Here we developed such through the integration six...
Significance Here, we discover prototypical pacemaker neurons in the ancient cnidarian Hydra and provide evidence for a direct interaction of these with commensal microbiota. We uncover remarkable gene-expression program conservation between cells Caenorhabditis elegans mammalian gut. suggest that emerged as using components innate immunity to interact microbial environment ion channels generate rhythmic contractions. The communication microbiota represents mechanistic link gut motility. Our...
Abstract The subthalamic nucleus (STN) is crucial for normal motor, limbic and associative function. STN dysregulation correlated with several brain disorders, including Parkinsonʼs disease obsessive compulsive disorder (OCD), which high-frequency stimulation of the increasing as therapy. However, clinical progress hampered by poor knowledge anatomical–functional organization STN. Today, experimental mouse genetics provides outstanding capacity functional decoding, provided selective...
Salamanders have a remarkable capacity to regenerate complex tissues, such as limbs and brain, are therefore an important comparative model system for regenerative medicine. Despite these unique properties among adult vertebrates, the genomic information amphibians in general, salamanders particular, is scarce. Here, we used massive parallel sequencing reconstruct de novo reference transcriptome of red spotted newt (Notophthalmus viridescens) containing 118,893 transcripts with N50 length...