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Natural Killer cells demonstrate distinct eQTL and transcriptome-wide disease associations, highlighting their role in autoimmunity.
Natural Killer cells are innate lymphocytes with central roles in immunosurveillance and are implicated in autoimmune pathogenesis. The degree to which regulatory variants affect Natural Killer cell gene expression is poorly understood. Here we perform expression quantitative trait locus mapping of negatively selected Natural Killer cells from a population of healthy Europeans (n = 245). We find a significant subset of genes demonstrate expression quantitative trait loci specific to Natural Killer cells and these are highly informative of human disease, in particular autoimmunity. A Natural Killer cell transcriptome-wide association study across five common autoimmune diseases identifies further novel associations at 27 genes. In addition to these cis observations, we find novel master-regulatory regions impacting expression of trans gene networks at regions including 19q13.4, the Killer cell Immunoglobulin-like Receptor region, GNLY, MC1R and UVSSA. Our findings provide new insights into the unique biology of Natural Killer cells, demonstrating markedly different expression quantitative trait loci from other immune cells, with implications for disease mechanisms.
Natural Killer cells demonstrate distinct eQTL and transcriptome-wide disease associations, highlighting their role in autoimmunity
AbstractNatural Killer (NK) cells are innate lymphocytes with central roles in immunosurveillance and are implicated in autoimmune pathogenesis. The degree to which regulatory variants affect NK gene expression is poorly understood. We performed expression quantitative trait locus (eQTL) mapping of negatively selected NK cells from a population of healthy Europeans (n=245). We find a significant subset of genes demonstrate eQTL specific to NK cells and these are highly informative of human disease, in particular autoimmunity. An NK cell transcriptome-wide association study (TWAS) across five common autoimmune diseases identified further novel associations at 27 genes. In addition to these cis observations, we find novel master-regulatory regions impacting expression of trans gene networks at regions including 19q13.4, the Killer cell Immunoglobulin-like Receptor (KIR) Region, GNLY and MC1R. Our findings provide new insights into the unique biology of NK cells, demonstrating markedly different eQTL from other immune cells, with implications for disease mechanisms.
Elevated reactive oxygen species can drive the alternative lengthening of telomeres pathway in ATRX-null cancers.
The alternative lengthening of telomeres (ALT) pathway is a telomerase-independent mechanism for immortalization in cancer cells and is commonly activated in low-grade and high-grade glioma, as well as osteosarcoma. The ALT pathway can be activated under various conditions and has often been shown to include mutational loss of ATRX. However, this is insufficient in isolation and so other cellular event must also be implicated. It has been shown that excessive accumulation of DNA:RNA hybrid structures (R-loops) and/or formation of DNA-protein crosslinks (DPCs) can be other important driving factors. The underlying cellular events leading to R-loop and DPC formation in ALT cancer cells to date remain unclear. Here, we demonstrate that excessive cellular reactive oxygen species (ROS) is an important causative factor in the evolution of ALT-telomere maintenance in ATRX-deficient glioma. We identified three sources of elevated ROS in ALT-positive gliomas: co-mutation of SETD2, downregulation of DRG2, and hypoxic tumour microenvironment. We demonstrate that elevated ROS leads to accumulation of R-loops and, crucially, resolution of R-loops by the enzyme RNase H1 prevents ALT pathway activity in cells exposed to elevated ROS. Further, we found a possible causal link between the formation of R-loops and the accumulation of DPCs, in particular, formation of TOP1 complexes covalently linked to DNA (Top1cc). We also demonstrate that elevation of ROS can trigger over-activity of the ALT pathway in osteosarcoma and glioma cell lines, resulting in excessive DNA damage and cell death. This work presents important mechanistic insights into the endogenous origin of excessive R-loops and DPCs in ALT-positive cancers, as well as highlighting potential novel therapeutic approaches in these difficult-to-treat cancer types.
A novel blood-free analytical framework for the quantification of neuroinflammatory load from TSPO PET Imaging.
Positron Emission Tomography (PET) of the 18 kDa translocator protein (TSPO) is critical for neuroinflammation studies but faces substantial methodological challenges. These include issues with arterial blood sampling for kinetic modeling, the absence of suitable reference regions, genetic polymorphisms affecting tracer affinity, altered blood-to-brain tracer delivery in inflammatory conditions, and high signal variability. This study presents a novel blood-free reference-free method for TSPO PET quantification, leveraging a logistic regression model to estimate the probability of TSPO overexpression across brain regions. Validation was performed on 323 human brain scans from five datasets and three radiotracers. The quantified TSPO topology in healthy controls showed strong concordance with the constitutive TSPO gene expression for all tracers. When using [ 11 C]PBR28 PET data, the method replicated previous findings in schizophrenia, Alzheimer's disease, chronic pain, and XBD173 blocking. However, model extension to [ 18 F]DPA-714 and [ 11 C]-(R)-PK11195 revealed small effect sizes and high variability, suggesting the need for tracer-specific model optimization. Finally, validation in a rat model of lipopolysaccharide-induced neuroinflammation confirmed previous evidence of increased brain TSPO uptake after a systemic challenge. This novel non-invasive method provides individualized TSPO PET quantification, demonstrating broad applicability across TSPO PET tracers and imaging sites, assuming sufficient training data for model development.
Effective altruism, technoscience and the making of philanthropic value
A recent philanthropic movement with advocates among high-profile tech entrepreneurs and philosophers, effective altruism (EA) has been widely disparaged for its flawed moral philosophy and conservative political implications. As philanthropic practice, however, it has been seldom studied. In this paper, we argue that claims to technoscientific expertise are central to how EA actors understand, legitimize, and take part in the production of philanthropic value. We analyze their practices of categorization, ranking and measurement as well as underlying technoscientific imaginaries and moral views through comparing three areas of EA intervention: neglected tropical diseases, cultured meat, and AI safety. We show how EA involves various and contested ambitions to direct knowledge production and redraw the boundaries of expert communities, shedding light on the centrality of technoscience in philanthropists’ worldmaking ambitions.
Activation-induced thrombospondin-4 works with thrombospondin-1 to build cytotoxic supramolecular attack particles.
Cytotoxic attack particles released by CTLs and NK cells include diverse phospholipid membrane and glycoprotein encapsulated entities that contribute to target cell killing. Supramolecular attack particles (SMAPs) are one type of particle characterized by a cytotoxic core enriched in granzymes and perforin surrounded by a proteinaceous shell including thrombospondin (TSP)-1. TSP-4 was also detected in bulk analysis of SMAPs released by CTLs; however, it has not been investigated whether TSP-4 contributes to distinct SMAP types or the same SMAP type as TSP-1 and, if in the same type of SMAP, whether TSP-4 and TSP-1 cooperate or compete. Here, we observed that TSP-4 expression increased upon CD8+ T cell activation while, surprisingly, TSP-1 was down-regulated. Correlative Light and Electron Microscopy and Stimulated Emission Depletion microscopy localized TSP-4 and TSP-1 in SMAP-containing multicore granules. Superresolution dSTORM revealed that TSP-4 and TSP-1 are usually enriched in the same SMAPs while particles with single-positive shells are rare. Retention Using Selective Hooks assays showed that TSP-4 localizes to the lytic granules faster than TSP-1 and promotes its accumulation therein. TSP-4 contributed to direct CTL-mediated killing, as previously shown for TSP-1. TSP-4 and TSP-1 were both required for latent SMAP-mediated cell killing, in which released SMAPs kill targets after removal of the CTLs. Of note, we found that chronic lymphocytic leukemia (CLL) cell culture supernatants suppressed expression of TSP-4 in CTL and latent SMAP-mediated killing. These results identify TSP-4 as a functionally important component of SMAPs and suggest that SMAPs may be targeted for immune suppression by CLL.
Elevated reactive oxygen species can drive the alternative lengthening of telomeres pathway in ATRX-null cancers.
The alternative lengthening of telomeres (ALT) pathway is a telomerase-independent mechanism for immortalization in cancer cells and is commonly activated in low-grade and high-grade glioma, as well as osteosarcoma. The ALT pathway can be activated under various conditions and has often been shown to include mutational loss of ATRX. However, this is insufficient in isolation and so other cellular event must also be implicated. It has been shown that excessive accumulation of DNA:RNA hybrid structures (R-loops) and/or formation of DNA-protein crosslinks (DPCs) can be other important driving factors. The underlying cellular events leading to R-loop and DPC formation in ALT cancer cells to date remain unclear. Here, we demonstrate that excessive cellular reactive oxygen species (ROS) is an important causative factor in the evolution of ALT-telomere maintenance in ATRX-deficient glioma. We identified three sources of elevated ROS in ALT-positive gliomas: co-mutation of SETD2, downregulation of DRG2, and hypoxic tumour microenvironment. We demonstrate that elevated ROS leads to accumulation of R-loops and, crucially, resolution of R-loops by the enzyme RNase H1 prevents ALT pathway activity in cells exposed to elevated ROS. Further, we found a possible causal link between the formation of R-loops and the accumulation of DPCs, in particular, formation of TOP1 complexes covalently linked to DNA (Top1cc). We also demonstrate that elevation of ROS can trigger over-activity of the ALT pathway in osteosarcoma and glioma cell lines, resulting in excessive DNA damage and cell death. This work presents important mechanistic insights into the endogenous origin of excessive R-loops and DPCs in ALT-positive cancers, as well as highlighting potential novel therapeutic approaches in these difficult-to-treat cancer types.
Loss of FAM111B protease mutated in hereditary fibrosing poikiloderma negatively regulates telomere length.
Hereditary fibrosing poikiloderma (HFP) is a rare human dominant negative disorder caused by mutations in the FAM111B gene that encodes a nuclear trypsin-like serine protease. HFP patients present with symptoms including skin abnormalities, tendon contractures, myopathy and lung fibrosis. We characterized the cellular roles of human FAM111B using U2OS and MCF7 cell lines and report here that the protease interacts with components of the nuclear pore complex. Loss of FAM111B expression resulted in abnormal nuclear shape and reduced telomeric DNA content suggesting that FAM111B protease is required for normal telomere length; we show that this function is independent of telomerase or recombination driven telomere extension. Even though FAM111B-deficient cells were proficient in DNA repair, they showed hallmarks of genomic instability such as increased levels of micronuclei and ultra-fine DNA bridges. When mutated as in HFP, FAM111B was more frequently localized to the nuclear envelope, suggesting that accumulation of the mutated protease at the nuclear periphery may drive the disease pathology.
Paracrine FGF21 dynamically modulates mTOR signaling to regulate thymus function across the lifespan
Consequences of age-associated thymic atrophy include declining T-cell responsiveness to pathogens and vaccines and diminished T-cell self-tolerance. Cortical thymic epithelial cells (cTECs) are primary targets of thymic aging, and recent studies suggested that their maintenance requires mTOR signaling downstream of medullary TEC (mTEC)-derived growth factors. Here, to test this hypothesis, we generated a knock-in mouse model in which FGF21 and mCherry are expressed by most mTECs. We find that mTEC-derived FGF21 promotes temporally distinct patterns of mTORC1 and mTORC2 signaling in cTECs, promotes thymus and individual cTEC growth and maintenance, increases T-cell responsiveness to viral infection, and diminishes indicators of peripheral autoimmunity in older mice. The effects of FGF21 overexpression on thymus size and mTOR signaling were abrogated by treatment with the mTOR inhibitor rapamycin. These results reveal a mechanism by which paracrine FGF21 signaling regulates thymus size and function throughout the lifespan, as well as potential therapeutic targets for improving T-cell function and tolerance in aging.
Evaluation of naturally occurring IgG anti-Vi antibody titers as predictors and correlates of typhoid fever in Dhaka, Bangladesh.
BACKGROUND: When delivered through vaccination Vi-polysaccharide antigen of Salmonella enterica serotype Typhi protects against typhoid by inducing IgG anti-Vi antibodies. We aimed to determine whether the presence of antibodies following natural infection is associated with a lower incidence of typhoid fever in endemic regions. METHODS: We analyzed data from a cohort study of typhoid fever conducted in Dhaka, Bangladesh. Plasma IgG anti-Vi antibodies were measured using a standard enzyme-linked immunosorbent assay in random serosurveys of a population that had not previously received typhoid vaccination. Participants were followed for up to 20 months for culture-confirmed typhoid fever. The receiver operating characteristic (ROC) curve and Cox proportional hazard models were used to evaluate the associations between antibody levels and typhoid risk. RESULTS: The ROC analysis revealed that IgG anti-Vi antibody titers were predictive of typhoid risk among the 8,261 serosurvey participants (area under the curve: 0·63; 95% confidence interval (CI): 0·58─0·67). Detection of any antibodies was associated with a lower risk of typhoid in crude analyses (hazard ratio (HR): 0·13; 95% CI: 0·03─0·52), though this association declined after adjustment (HR: 0·32; 95% CI: 0·07─1·40). A positive correlation was observed between IgG anti-Vi titers and age (correlation coefficient 0·35; p
Impact of a Brief Healthcare-based Intervention to Support Early Childhood Development in India: A Pilot Randomized Controlled Trial.
OBJECTIVES: To study the impact of a brief early childhood develop-ment (ECD) intervention, Sit Down and Play (SDP), integrated within routine healthcare visits on parent and child outcomes. METHODS: Between April, 2018 and March, 2019, caregivers and their infants aged 5-6 months attending a well-baby clinic were enrolled and randomized to intervention (n=26) or control (n=26) groups. Intervention families received SDP at recruitment and two subsequent immunization visits (8 months and 10 months). Control families received usual care. ECD outcomes were assessed through in-person assessments at the age of 12 months using the Stim Q subscales to assess parenting behaviors, and the Developmental Assessment Scale for Indian Infants (DASII) for neurodevelopment. RESULTS: There was a significant improvement in parent-child stimulation activities and verbal interactions in the intervention group compared with the control group [6.1(1.4) vs 4.9 (1.3); P=0.002]. Infants in the intervention group had significantly higher DASII scores in multivariable analyses [108.0 (103.0-111.3) vs 102.0 (96.8-108.0); P=0.04]. CONCLUSION: Our findings suggest a brief healthcare intervention supports opportunities for early learning among caregivers and neurodevelopmental outcomes in their infants.
Artificial intelligence for modelling infectious disease epidemics.
Infectious disease threats to individual and public health are numerous, varied and frequently unexpected. Artificial intelligence (AI) and related technologies, which are already supporting human decision making in economics, medicine and social science, have the potential to transform the scope and power of infectious disease epidemiology. Here we consider the application to infectious disease modelling of AI systems that combine machine learning, computational statistics, information retrieval and data science. We first outline how recent advances in AI can accelerate breakthroughs in answering key epidemiological questions and we discuss specific AI methods that can be applied to routinely collected infectious disease surveillance data. Second, we elaborate on the social context of AI for infectious disease epidemiology, including issues such as explainability, safety, accountability and ethics. Finally, we summarize some limitations of AI applications in this field and provide recommendations for how infectious disease epidemiology can harness most effectively current and future developments in AI.
Biological biomarkers in muscle diseases relevant for follow-up and evaluation of treatment.
Muscle diseases cover a diverse group of disorders that, in most cases, are hereditary. The rarity of the individual muscle diseases provides a challenge for researchers when wanting to establish natural history of the conditions and when trying to develop diagnostic tools, therapies, and outcome measures to evaluate disease progression. With emerging molecular therapies in many genetic muscle diseases, as well as biological therapies for the immune-mediated diseases, biological biomarkers play an important role in both drug development and evaluation. In this review, we focus on the role of biological biomarkers in muscle diseases and discuss their utility as surrogate end points in therapeutic trials. We categorize these as either (i) disease unspecific markers; (ii) markers of specific pathways that may be used for more than one disease; or (iii) disease-specific markers. We also propose that evaluation of specific therapeutic interventions benefits from biological markers that match the intervention.