MetaGate: Interactive analysis of high-dimensional cytometry data with metadata integration.

Flow cytometry is a powerful technology for high-throughput protein quantification at the single-cell level. Technical advances have substantially increased data complexity, but novel bioinformatical tools often show limitations in statistical testing, data sharing, cross-experiment comparability, or clinical data integration. We developed MetaGate as a platform for interactive statistical analysis and visualization of manually gated high-dimensional cytometry data with integration of metadata.

MetaGate: Interactive Analysis of High-Dimensional Cytometry Data with Meta Data Integration.

Flow cytometry is a powerful technology for high-throughput protein quantification at the single-cell level, widely used in basic research and routine clinical diagnostics. Traditionally, data analysis is carried out using manual gating, in which cut-offs are defined manually for each marker. Recent technical advances, including the introduction of mass cytometry, have increased the number of proteins that can be simultaneously assessed in each cell.

Effect of mTOR Inhibition with Sirolimus on Natural Killer Cell Reconstitution in Allogeneic Stem Cell Transplantation.

Sirolimus is an inhibitor of the mammalian target of rapamycin (mTOR) and is emerging as a promising component of graft-versus-host disease (GVHD) prophylaxis regimens in the context of allogeneic hematopoietic stem cell transplantation (HSCT). Multiple studies have explored the clinical benefits of adding sirolimus to GVHD prophylaxis; however, detailed immunologic studies have not yet been carried out in this context. Mechanistically, mTOR is at the center of metabolic regulation in T cells and natural killer (NK) cells and is critical for their differentiation to mature effector cells.

The Karolinska KI/K COVID-19 Immune Atlas: An open resource for immunological research and educational purposes.

The Karolinska KI/K COVID-19 Immune Atlas project was conceptualized in March 2020 as a part of the academic research response to the developing SARS-CoV-2 pandemic. The aim was to rapidly provide a curated dataset covering the acute immune response towards SARS-CoV-2 infection in humans, as it occurred during the first wave. The Immune Atlas was built as an open resource for broad research and educational purposes.

An optimized platform for efficient siRNA delivery into human NK cells.

The molecular networks that regulate natural killer (NK) cell functions are not completely understood. Here, we present a workflow for efficient delivery of siRNA into human NK cells without compromising viability. This methodology represents a promising approach for rapidly interrogating gene functions in primary human NK cells.

A Systemic Protein Deviation Score Linked to PD-1 CD8 T Cell Expansion That Predicts Overall Survival in Diffuse Large B Cell Lymphoma.

Background: Current prognostic variables can only partly explain the large outcome heterogeneity in diffuse large B cell lymphoma (DLBCL). We aimed to investigate the utility of systems-level protein and immune repertoire profiling for outcome prognostication in DLBCL.

Methods: In this retrospective study, we used proximity extension assay technology to quantify 81 immune-related proteins in serum or plasma in 2 independent cohorts in a total 111 DLBCL patients.

Umbilical Cord Blood and iPSC-Derived Natural Killer Cells Demonstrate Key Differences in Cytotoxic Activity and KIR Profiles.

Natural killer (NK) cells derived or isolated from different sources have been gaining in importance for cancer therapies. In this study, we evaluate and compare key characteristics between NK cells derived or isolated from umbilical cord blood, umbilical cord blood hematopoietic stem/progenitor cells, peripheral blood, and induced pluripotent stem cells (iPSCs). Specifically, we find CD56 NK cells isolated and expanded directly from umbilical cord blood (UCB56) and NK cells derived from CD34 hematopoietic stem/progenitors in umbilical cord blood (UCB34) differ in their expression of markers associated with differentiation including CD16, CD2, and killer Ig-like receptors (KIRs).

Natural killer cell immunotypes related to COVID-19 disease severity.

Understanding innate immune responses in COVID-19 is important to decipher mechanisms of host responses and interpret disease pathogenesis. Natural killer (NK) cells are innate effector lymphocytes that respond to acute viral infections but might also contribute to immunopathology. Using 28-color flow cytometry, we here reveal strong NK cell activation across distinct subsets in peripheral blood of COVID-19 patients.

Metabolic Reprograming via Deletion of CISH in Human iPSC-Derived NK Cells Promotes In Vivo Persistence and Enhances Anti-tumor Activity.

Cytokine-inducible SH2-containing protein (CIS; encoded by the gene CISH) is a key negative regulator of interleukin-15 (IL-15) signaling in natural killer (NK) cells. Here, we develop human CISH-knockout (CISH) NK cells using an induced pluripotent stem cell-derived NK cell (iPSC-NK cell) platform. CISH iPSC-NK cells demonstrate increased IL-15-mediated JAK-STAT signaling activity.

Intra-lineage Plasticity and Functional Reprogramming Maintain Natural Killer Cell Repertoire Diversity.

Natural killer (NK) cell repertoires are made up of phenotypically distinct subsets with different functional properties. The molecular programs involved in maintaining NK cell repertoire diversity under homeostatic conditions remain elusive. Here, we show that subset-specific NK cell proliferation kinetics correlate with mTOR activation, and global repertoire diversity is maintained through a high degree of intra-lineage subset plasticity during interleukin (IL)-15-driven homeostatic proliferation in vitro.

Critical Role of CD2 Co-stimulation in Adaptive Natural Killer Cell Responses Revealed in NKG2C-Deficient Humans.

Infection by human cytomegalovirus (HCMV) leads to NKG2C-driven expansion of adaptive natural killer (NK) cells, contributing to host defense. However, approximately 4% of all humans carry a homozygous deletion of the gene that encodes NKG2C (NKG2C(-/-)). Assessment of NK cell repertoires in 60 NKG2C(-/-) donors revealed a broad range of NK cell populations displaying characteristic footprints of adaptive NK cells, including a terminally differentiated phenotype, functional reprogramming, and epigenetic remodeling of the interferon (IFN)-γ promoter.

Coordinated expression of DNAM-1 and LFA-1 in educated NK cells.

The functional capacity of NK cells is dynamically tuned by integrated signals from inhibitory and activating cell surface receptors in a process termed NK cell education. However, the understanding of the cellular and molecular mechanisms behind this functional tuning is limited. In this study, we show that the expression of the adhesion molecule and activation receptor DNAX accessory molecule 1 (DNAM-1) correlates with the quantity and quality of the inhibitory input by HLA class I-specific killer cell Ig-like receptors and CD94/NKG2A as well as with the magnitude of functional responses.

A longitudinal study of posttraumatic stress symptoms and their predictors in rescue workers after a firework factory disaster.

Introduction: This is a follow up study on rescue workers participating in the primary rescue during and immediately after the explosion of a firework factory. We aimed to estimate the possible PTSD prevalence at five and 18 months post disaster, determining if the level of PTSD symptoms at 18 months could be predicted from factors measured at five months.

Methods: We included measures of posttraumatic symptoms, social support, locus of control and demographic questions.

Detection of Legionella by cultivation and quantitative real-time polymerase chain reaction in biological waste water treatment plants in Norway.

Cases of Legionnaires' disease associated with biological treatment plants (BTPs) have been reported in six countries between 1997 and 2010. However, knowledge about the occurrence of Legionella in BTPs is scarce. Hence, we undertook a qualitative and quantitative screening for Legionella in BTPs treating waste water from municipalities and industries in Norway, to assess the transmission potential of Legionella from these installations.

Prevention of Legionnaires' disease in hospitals.

Background: The first instance of Legionella infection in a Norwegian hospital was confirmed in 2005. We describe the best-known methods of eradicating Legionella in hospitals.

Materials And Method: The article is based on the authors' experience of measures to prevent Legionnaires' disease in hospitals and on a non-systematic search in PubMed.

Alternative routes for dissemination of Legionella pneumophila causing three outbreaks in Norway.

Three outbreaks of Legionnaires' disease were reported in the Fredrikstad/Sarpsborg community, Norway, in 2005 and 2008 caused by the L. pneumophila ST15 and ST462 strains determined by sequence based typing. In this retrospective study, we suggest that the aeration ponds, a part of the biological treatment plant at Borregaard Ind.

Tracking airborne Legionella and Legionella pneumophila at a biological treatment plant.

Biological treatment plants are frequently used to degrade organic substances in wastewater from wood refinement processes. Aeration ponds in such plants provide an optimal growth environment for many microorganisms, including Legionella species. To investigate whether legionellae could be dispersed as aerosols from the ponds and transported by the wind, the wetted-wall cyclone SASS 2000(PLUS) and the impactors MAS-100 and STA-204 were used to collect air samples directly above, upwind, and downwind of aeration ponds during a 4-month period.

An outbreak of legionnaires disease caused by long-distance spread from an industrial air scrubber in Sarpsborg, Norway.

Background: On 21 May 2005, the Norwegian health authorities were alerted by officials from a local hospital that several recent patients had received the diagnosis of legionnaires disease; all patients resided in 2 neighboring municipalities. We investigated the outbreak to identify the source and to implement control measures.

Methods: We interviewed all surviving case patients and investigated and harvested samples from 23 businesses with cooling towers and other potential infection sources.

Human papillomavirus infection in cervical biopsies from Norwegian gynecological in-patients.

Polymerase chain reaction (PCR) and Southern blotting were used to assess the prevalence of HPV in cervical biopsies of 100 women who were treated at the gynecology department of Telemark Central Hospital for non-cancerous conditions. Nine (9%) of the biopsies were HPV positive. Four (4%) were of HPV type 18, one (1%) was HPV11 positive, and four contained different unrecognized HPV types (HPVX).

PCR amplicon restriction endonuclease analysis of the chromosomal dhps gene of Neisseria meningitidis: a method for studying spread of the disease-causing strain in contacts of patients with meningococcal disease.

We tested two sets of primers derived from the dhps gene of Neisseria meningitidis for the amplification of meningococcal DNA by PCR. Both the NM1-NM6 primers and the NM3-NM6 primers amplified dhps DNA from all of the meningococci included in the study, resulting, in most cases, in amplicons of 0.70 and 0.

Genetic homogeneity of Taylorella equigenitalis from Norwegian trotting horses revealed by chromosomal DNA fingerprinting.

Chromosomal DNA fingerprinting indicated that Norwegian Taylorella equigenitalis strains are genetically homogeneous and similar to some Swedish isolates but different from other European strains. As contagious equine metritis is rarely a serious disease in Norwegian horses, we conclude that the dominant T. equigenitalis strain in Norway is a genetically homogeneous clone of low virulence.

Human papillomavirus infection in Norwegian women with cervical cancer.

The objective of the present study was to determine the prevalence of human papillomavirus (HPV) infections in Norwegian women with cervical cancer. We used the polymerase chain reaction (PCR) and Southern blot techniques to assess the prevalence of HPV in cervical biopsies of 133 women admitted to the Norwegian Radium Hospital for treatment of cervical cancer. At the time of sampling (from February 1988 to April 1989) about 85% of Norwegian women with cervical cancer were treated at the Norwegian Radium Hospital.

[Meningococcal project Telemark. Experiences after 5 years with contact tracing and eradication of the pathogenic bacteria in near contacts of the patients with meningococcal disease].

Since 1987 we have analysed throat samples from 1,086 healthy contacts of 32 patients with meningococcal disease. The disease-causing strain was found in contacts of 17 out of the 32 patients. 161 (18%) of the contacts carried meningococci, and 30 (3%) of them were carriers of the disease-causing strain as determined by DNA fingerprinting.