Defining and benchmarking open problems in single-cell analysis

With the growing number of single-cell analysis tools, benchmarks are increasingly important to guide analysis and method development. However, a lack of standardisation and extensibility in current benchmarks limits their usability, longevity, and relevance to the community. We present Open Problems, a living, extensible, community-guided benchmarking platform including 10 current single-cell tasks that we envision will raise standards for the selection, evaluation, and development of methods in single-cell analysis.

Spatial landmark detection and tissue registration with deep learning

Spatial landmarks are crucial in describing histological features between samples or sites, tracking regions of interest in microscopy, and registering tissue samples within a common coordinate framework. Although other studies have explored unsupervised landmark detection, existing methods are not well-suited for histological image data as they often require a large number of images to converge, are unable to handle nonlinear deformations between tissue sections and are ineffective for z-stack alignment, other modalities beyond image data or multimodal data. We address these challenges by introducing effortless landmark detection, a new unsupervised landmark detection and registration method using neural-network-guided thin-plate splines. Our proposed method is evaluated on a diverse range of datasets including histology and spatially resolved transcriptomics, demonstrating superior performance in both accuracy and stability compared to existing approaches.

Spatial transcriptomics of B cell and T cell receptors reveals lymphocyte clonal dynamics

The spatial distribution of lymphocyte clones within tissues is critical to their development, selection, and expansion. We have developed spatial transcriptomics of variable, diversity, and joining (VDJ) sequences (Spatial VDJ), a method that maps B cell and T cell receptor sequences in human tissue sections. Spatial VDJ captures lymphocyte clones that match canonical B and T cell distributions and amplifies clonal sequences confirmed by orthogonal methods. We found spatial congruency between paired receptor chains, developed a computational framework to predict receptor pairs, and linked the expansion of distinct B cell clones to different tumor-associated gene expression programs. Spatial VDJ delineates B cell clonal diversity and lineage trajectories within their anatomical niche. Thus, Spatial VDJ captures lymphocyte spatial clonal architecture across tissues, providing a platform to harness clonal sequences for therapy.

Single-Cell and Spatial Transcriptomic Analysis of Human Skin Delineates Intercellular Communication and Pathogenic Cells

Epidermal homeostasis is governed by a balance between keratinocyte proliferation and differentiation with contributions from cell-cell interactions, but conserved or divergent mechanisms governing this equilibrium across species and how an imbalance contributes to skin disease are largely undefined. To address these questions, human skin single-cell RNA sequencing and spatial transcriptomics data were integrated and compared with mouse skin data. Human skin cell-type annotation was improved using matched spatial transcriptomics data, highlighting the importance of spatial context in cell-type identity, and spatial transcriptomics refined cellular communication inference. In cross-species analyses, we identified a human spinous keratinocyte subpopulation that exhibited proliferative capacity and a heavy metal processing signature, which was absent in mouse and may account for species differences in epidermal thickness. This human subpopulation was expanded in psoriasis and zinc-deficiency dermatitis, attesting to disease relevance and suggesting a paradigm of subpopulation dysfunction as a hallmark of the disease. To assess additional potential subpopulation drivers of skin diseases, we performed cell-of-origin enrichment analysis within genodermatoses, nominating pathogenic cell subpopulations and their communication pathways, which highlighted multiple potential therapeutic targets. This integrated dataset is encompassed in a publicly available web resource to aid mechanistic and translational studies of normal and diseased skin.

Profiling spatiotemporal gene expression of the developing human spinal cord and implications for ependymoma origin

The spatiotemporal regulation of cell fate specification in the human developing spinal cord remains largely unknown. In this study, by performing integrated analysis of single-cell and spatial multi-omics data, we used 16 prenatal human samples to create a comprehensive developmental cell atlas of the spinal cord during post-conceptional weeks 5-12. This revealed how the cell fate commitment of neural progenitor cells and their spatial positioning are spatiotemporally regulated by specific gene sets. We identified unique events in human spinal cord development relative to rodents, including earlier quiescence of active neural stem cells, differential regulation of cell differentiation and distinct spatiotemporal genetic regulation of cell fate choices. In addition, by integrating our atlas with pediatric ependymomas data, we identified specific molecular signatures and lineage-specific genes of cancer stem cells during progression. Thus, we delineate spatiotemporal genetic regulation of human spinal cord development and leverage these data to gain disease insight.

Dose-dependent relationship between nocturnal gastroesophageal reflux and chronic rhinosinusitis in a middle-aged population: results from the SCAPIS pilot

BACKGROUND

Gastroesophageal reflux (GER) has been associated with several upper- and lower-airway diseases. It would be plausible if nightly occurring reflux via laryngopharyngeal reflux (LPR) might affect the upper airways. Still, the role of nocturnal gastroesophageal reflux (nGER) in chronic rhinosinusitis (CRS) is not fully established. The aim of this population-based study was to investigate the association between nGER and CRS.

METHODOLOGY

This cross-sectional population-based study comprises 1,111 randomly selected subjects from Gothenburg, Sweden, aged 50-64 years. The study is based on self-reported validated questionnaires. CRS was defined according to EPOS criteria. nGER was reported in relation to frequency.

RESULTS

CRS was more common among subjects with nGER than in those without (13 vs. 4.8%). There was a dose-response association between the frequency of nGER episodes and the risk of having CRS. In the logistic regression adjusted for (age, sex, BMI, educational level, smoking, and asthma). CRS was associated with nGER, OR 1.43 and the odds ratio increased if episodes were reported "almost every night", OR 4.6.

CONCLUSIONS

The study shows an association between nocturnal GER and CRS in a middle-aged population. The revealed dose dependency supports, though does not prove causality.

Markov state modelling reveals heterogeneous drug-inhibition mechanism of Calmodulin

Calmodulin (CaM) is a calcium sensor which binds and regulates a wide range of target-proteins. This implicitly enables the concentration of calcium to influence many downstream physiological responses, including muscle contraction, learning and depression. The antipsychotic drug trifluoperazine (TFP) is a known CaM inhibitor. By binding to various sites, TFP prevents CaM from associating to target-proteins. However, the molecular and state-dependent mechanisms behind CaM inhibition by drugs such as TFP are largely unknown. Here, we build a Markov state model (MSM) from adaptively sampled molecular dynamics simulations and reveal the structural and dynamical features behind the inhibitory mechanism of TFP-binding to the C-terminal domain of CaM. We specifically identify three major TFP binding-modes from the MSM macrostates, and distinguish their effect on CaM conformation by using a systematic analysis protocol based on biophysical descriptors and tools from machine learning. The results show that depending on the binding orientation, TFP effectively stabilizes features of the calcium-unbound CaM, either affecting the CaM hydrophobic binding pocket, the calcium binding sites or the secondary structure content in the bound domain. The conclusions drawn from this work may in the future serve to formulate a complete model of pharmacological modulation of CaM, which furthers our understanding of how these drugs affect signaling pathways as well as associated diseases.

Calmodulin (CaM) is a calcium-sensing protein which makes other proteins dependent on the surrounding calcium concentration by binding to these proteins. Such protein-protein interactions with CaM are vital for calcium to control many physiological pathways within the cell. The antipsychotic drug trifluoperazine (TFP) inhibits CaM’s ability to bind and regulate other proteins. Here, we use molecular dynamics simulations together with Markov state modeling and machine learning to understand the structural and dynamical features by which TFP bound to the one domain of CaM prevents association to other proteins. We find that TFP encourages CaM to adopt a conformation that is like the one stabilized in absence of calcium: depending on the binding orientation of TFP, the drug indeed either affects the CaM hydrophobic binding pocket, the calcium binding sites or the secondary structure content in the domain. Understanding TFP binding is a first step towards designing better drugs targeting CaM.

Spatially resolved clonal copy number alterations in benign and malignant tissue

Defining the transition from benign to malignant tissue is fundamental to improving early diagnosis of cancer1. Here we use a systematic approach to study spatial genome integrity in situ and describe previously unidentified clonal relationships. We used spatially resolved transcriptomics2 to infer spatial copy number variations in >120,000 regions across multiple organs, in benign and malignant tissues. We demonstrate that genome-wide copy number variation reveals distinct clonal patterns within tumours and in nearby benign tissue using an organ-wide approach focused on the prostate. Our results suggest a model for how genomic instability arises in histologically benign tissue that may represent early events in cancer evolution. We highlight the power of capturing the molecular and spatial continuums in a tissue context and challenge the rationale for treatment paradigms, including focal therapy.

Abstract 2171: The spatial landscape of clonal somatic mutations in benign and malignant tissue

Introduction: Defining the transition from benign to malignant tissue is fundamental to improve early diagnosis of cancer. In order to obtain spatial information of clonal genetic events, prior studies have used methods such as laser capture microdissection, which results in assessment of small regions or even single cells. These studies have an inherent bias as a limited number of regions per tissue section can be retrieved and examined. Furthermore, because investigators have selected such regions based on morphology, previous studies have limited their analyses to histologically defined tumour areas while excluding regions populated by benign cells. The possibility to perform unsupervised genome and tissue-wide analysis would therefore provide an important contribution to delineate clonal events. We sought study spatial genome integrity in situ to gain molecular insight into clonal relationships.

Materials and Methods: We employed spatially resolved transcriptomics (Visium, 10x Genomics) to infer spatial copy number variations in >120 000 spatial regions across multiple organs, including three whole axial prostates and additional tissues from skin, breast and brain tumors. We used this information to deduce clonal relationships between regions harboring 5-20 cells.

Results: We demonstrate that genome-wide copy number variation reveals distinct clonal patterns within tumours and in nearby benign tissue. We perform an in-depth spatial analysis of cancers that includes an unprecedented interrogation of up to 50,000 tissue domains in a single patient, and 120,000 tissue domains across 10 patients. In a prostate section, we observed that many CNVs occurred in histologically benign luminal epithelial cells, most notably in chromosomes 8 and 10. This clone constituted a region of exclusively benign acinar cells branching off a duct lined by largely copy neutral cells. The changes in these cells were shared with the nearby intermediate risk prostate cancer cells in the same tissue section. We observed similar findings in another patient’s cutaneous squamous cell carcinoma (cSCC), wherein benign squamous epithelial had alterations in chromosomes 1 and 12 that were shared with nearby cSCC. Our results suggest a model for how genomic instability arises in histo-pathologically benign tissue that may represent early events in cancer evolution. Furthermore the spatial information allowed us to identify small clonal units not evident from morphology and hence would be overlooked by pathologists.

Conclusions: We present the first large-scale, comprehensive atlas of genomic evolution at high spatial resolution in prostate cancer. Our study adds an important new approach to the armamentarium of cancer molecular pathology. We highlight the power of an unsupervised approach to capture the molecular and spatial continuums in a tissue context and challenge the rationale for focal therapy in prostate cancer.

Citation Format: Andrew Erickson, Emelie Berglund, Mengxiao He, Maja Marklund, Reza Mirzazadeh, Niklas Schultz, Linda Kvastad, Alma Andersson, Ludvig Bergenstråhle, Joseph Bergenstråhle, Ludvig Larsson, Alia Shamikh, Elisa Basmaci, Teresita Diaz De Ståhl, Timothy Rajakumar, Kim Thrane, Andrew L. Ji, Paul A. Khavari, Firaz Tarish, Anna Tanoglidi, Jonas Maaskola, Richard Colling, Tuomas Mirtti, Freddie Hamdy, Dan J. Woodcock, Thomas Helleday, Ian G. Mills, Alastair D. Lamb, Joakim Lundenberg. The spatial landscape of clonal somatic mutations in benign and malignant tissue [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2171.

Abstract PR016: The spatial landscape of clonal somatic mutations in benign and malignant tissue

Introduction: Defining the transition from benign to malignant tissue is fundamental to improve early diagnosis of cancer. In order to obtain spatial information of clonal genetic events, prior studies have used methods such as laser capture microdissection, which results in assessment of small regions or even single cells. These studies have an inherent bias as a limited number of regions per tissue section can be retrieved and examined. Furthermore, because investigators have selected such regions based on morphology, previous studies have limited their analyses to histologically defined tumor areas while excluding regions populated by benign cells. The possibility to perform unsupervised genome and tissue-wide analysis would therefore provide an important contribution to delineate clonal events. We sought study spatial genome integrity in situ to gain molecular insight into clonal relationships. Materials and Methods: We employed spatially resolved transcriptomics (Visium, 10x Genomics) to infer spatial copy number variations in >120 000 spatial regions across multiple organs, including three whole axial prostates and additional tissues from skin, breast and brain tumors. We additionally performed in silico assessment of spatial copy number inference. We used this information to deduce clonal relationships between regions harboring 5-20 cells. Results: We demonstrate that genome-wide copy number variation reveals distinct clonal patterns within tumors and in nearby benign tissue. We perform an in-depth spatial analysis of cancers that includes an unprecedented interrogation of up to 50,000 tissue domains in a single patient, and 120,000 tissue domains across 10 patients. In a prostate section, we observed that many CNVs occurred in histologically benign luminal epithelial cells, most notably in chromosomes 8 and 10. This clone constituted a region of exclusively benign acinar cells branching off a duct lined by largely copy neutral cells. The changes in these cells were shared with the nearby intermediate risk prostate cancer cells in the same tissue section. We observed similar findings in another patient’s cutaneous squamous cell carcinoma (cSCC), wherein benign squamous epithelial had alterations in chromosomes 1 and 12 that were shared with nearby cSCC. Our results suggest a model for how genomic instability arises in histo-pathologically benign tissue that may represent early events in cancer evolution. Furthermore the spatial information allowed us to identify small clonal units not evident from morphology and hence would be overlooked by pathologists. Conclusions: We present the first large-scale, comprehensive atlas of genomic evolution at high spatial resolution in prostate cancer. Our study adds an important new approach to the armamentarium of cancer molecular pathology. We highlight the power of an unsupervised approach to capture the molecular and spatial continuums in a tissue context and challenge the rationale for focal therapy in prostate cancer

Citation Format: Andrew Erickson, Emelie Berglund, Mengxiao He, Maja Marklund, Reza Mirzazadeh, Niklas Schultz, Ludvig Bergenstråhle, Linda Kvastad, Alma Andersson, Joseph Bergenstråhle, Ludvig Larsson, Alia Shamikh, Elisa Basmaci, Teresita Diaz De Ståhl, Timothy Rajakumar, Kim Thrane, Andrew L. Ji, Paul A. Khavari, Firaz Tarish, Anna Tanoglidi, Jonas Maaskola, Richard Colling, Tuomas Mirtti, Freddie C. Hamdy, Dan J. Woodcock, Thomas Helleday, Ian G. Mills, Alastair D. Lamb, Joakim Lundeberg. The spatial landscape of clonal somatic mutations in benign and malignant tissue [abstract]. In: Proceedings of the AACR Special Conference on the Evolutionary Dynamics in Carcinogenesis and Response to Therapy; 2022 Mar 14-17. Philadelphia (PA): AACR; Cancer Res 2022;82(10 Suppl):Abstract nr PR016.

Super-resolved spatial transcriptomics by deep data fusion

Current methods for spatial transcriptomics are limited by low spatial resolution. Here we introduce a method that integrates spatial gene expression data with histological image data from the same tissue section to infer higher-resolution expression maps. Using a deep generative model, our method characterizes the transcriptome of micrometer-scale anatomical features and can predict spatial gene expression from histology images alone.

Spatial Transcriptomics to define transcriptional patterns of zonation and structural components in the mouse liver

Reconstruction of heterogeneity through single cell transcriptional profiling has greatly advanced our understanding of the spatial liver transcriptome in recent years. However, global transcriptional differences across lobular units remain elusive in physical space. Here, we apply Spatial Transcriptomics to perform transcriptomic analysis across sectioned liver tissue. We confirm that the heterogeneity in this complex tissue is predominantly determined by lobular zonation. By introducing novel computational approaches, we enable transcriptional gradient measurements between tissue structures, including several lobules in a variety of orientations. Further, our data suggests the presence of previously transcriptionally uncharacterized structures within liver tissue, contributing to the overall spatial heterogeneity of the organ. This study demonstrates how comprehensive spatial transcriptomic technologies can be used to delineate extensive spatial gene expression patterns in the liver, indicating its future impact for studies of liver function, development and regeneration as well as its potential in pre-clinical and clinical pathology.

Spatial deconvolution of HER2-positive breast cancer delineates tumor-associated cell type interactions

In the past decades, transcriptomic studies have revolutionized cancer treatment and diagnosis. However, tumor sequencing strategies typically result in loss of spatial information, critical to understand cell interactions and their functional relevance. To address this, we investigate spatial gene expression in HER2-positive breast tumors using Spatial Transcriptomics technology. We show that expression-based clustering enables data-driven tumor annotation and assessment of intra- and interpatient heterogeneity; from which we discover shared gene signatures for immune and tumor processes. By integration with single cell data, we spatially map tumor-associated cell types to find tertiary lymphoid-like structures, and a type I interferon response overlapping with regions of T-cell and macrophage subset colocalization. We construct a predictive model to infer presence of tertiary lymphoid-like structures, applicable across tissue types and technical platforms. Taken together, we combine different data modalities to define a high resolution map of cellular interactions in tumors and provide tools generalizing across tissues and diseases.

Spatial mapping reveals human adipocyte subpopulations with distinct sensitivities to insulin

The contribution of cellular heterogeneity and architecture to white adipose tissue (WAT) function is poorly understood. Herein, we combined spatially resolved transcriptional profiling with single-cell RNA sequencing and image analyses to map human WAT composition and structure. This identified 18 cell classes with unique propensities to form spatially organized homo- and heterotypic clusters. Of these, three constituted mature adipocytes that were similar in size, but distinct in their spatial arrangements and transcriptional profiles. Based on marker genes, we termed these Adipo^LEP, Adipo^PLIN, and Adipo^SAA. We confirmed, in independent datasets, that their respective gene profiles associated differently with both adipocyte and whole-body insulin sensitivity. Corroborating our observations, insulin stimulation in vivo by hyperinsulinemic-euglycemic clamp showed that only Adipo^PLIN displayed a transcriptional response to insulin. Altogether, by mining this multimodal resource we identify that human WAT is composed of three classes of mature adipocytes, only one of which is insulin responsive.

Abstract 129: An integrated multi-omic cellular atlas of human breast cancers

Breast cancers are complex cellular ecosystems where heterotypic interactions play central roles in disease progression and response to therapy. However, our knowledge of the cellular composition and organization of breast cancer remains limited. We present a comprehensive single cell and spatially resolved transcriptomic atlas of human breast cancers.

The 10X Genomics Chromium platform was used to generate single cell transcriptomic data (scRNA-Seq) from more than 120,000 cells sampled from 26 breast cancers. CITE-Seq was employed to simultaneously generate protein measurements using a panel of 157 antibodies against immune, stromal and epithelial cell surface markers and analysed using Seurat. Using single cell signatures, we estimated the cellular composition of more than 2000 breast cancers in the Metabric cohort using deconvolution methods. Spatial transcriptomics was conducted on 12 frozen tissues (Luminal, Her2+ and triple negative breast cancer (TNBC)) using the 10X genomics Visium solution. We also used a novel Spatial Whole Transcriptome Panel, targeting 18,000+ genes on the Nanostring GeoMX platform, to profile T cells and malignant cells across multiple tissue niches from 16 TNBC FFPE cases.

Integrative scRNA-Seq analysis identifies recurrent gene modules driving neoplastic cell heterogeneity, including interferon signaling, estrogen receptor function and mutually exclusive patterns of proliferation versus EMT. We also develop a single cell classifier of intrinsic subtype (scSubtype) to reveal frequent intra-tumoral heterogeneity for breast cancer intrinsic subtypes.

CITE-Seq revealed immune profiles at high resolution, leading to the identification of novel macrophage populations with high expression of PD-L1 and PD-L2 immune checkpoint ligands and associations with clinical outcome. We also observe enrichment of exhausted and proliferative CD8 T cells in TNBC, with unique patterns of cell-surface checkpoint protein expression when compared to other subtypes. Targeted analysis using the GeoMX revealed spatial segregation of T cell phenotypes, with exhausted and proliferative CD8 T cells forming small clusters adjacent to tumor cells with high interferon pathway activity.

Analysis of scRNA-Seq data revealed that stromal cells generate diverse functions and cell surface protein expression through differentiation within 3 major lineages: fibroblast, endothelial and perivascular-like. Subsets of stromal cells had features associated with immune regulation and Visium data revealed that stromal-immune niches were spatially organized in tumors, offering insights into anti-tumor immune suppression by stromal cells.

Finally, deconvolution stratified >2000 breast cancer cases in Metabric into nine clusters, termed ‘ecotypes', with distinct cellular compositions and clinical outcomes. This study provides a comprehensive atlas of the cellular architecture of breast cancer.

Citation Format: Sunny Z. Wu, Daniel Roden, Ghamdan Al Eryani, Simon Junankar, Elgene Lim, Aatish Thennavan, Alma Andersson, Stephen Williams, Jingjing Gong, Robin Fropf, Kit Fuhrman, Joakim Lundeberg, Chuck Perou, Alexander Swarbrick. An integrated multi-omic cellular atlas of human breast cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 129.

Integrating spatial gene expression and breast tumour morphology via deep learning

Spatial transcriptomics allows for the measurement of RNA abundance at a high spatial resolution, making it possible to systematically link the morphology of cellular neighbourhoods and spatially localized gene expression. Here, we report the development of a deep learning algorithm for the prediction of local gene expression from haematoxylin-and-eosin-stained histopathology images using a new dataset of 30,612 spatially resolved gene expression data matched to histopathology images from 23 patients with breast cancer. We identified over 100 genes, including known breast cancer biomarkers of intratumoral heterogeneity and the co-localization of tumour growth and immune activation, the expression of which can be predicted from the histopathology images at a resolution of 100 µm. We also show that the algorithm generalizes well to The Cancer Genome Atlas and to other breast cancer gene expression datasets without the need for re-training. Predicting the spatially resolved transcriptome of a tissue directly from tissue images may enable image-based screening for molecular biomarkers with spatial variation.

Modeling vitamin B1 transfer to consumers in the aquatic food web

Vitamin B1 is an essential exogenous micronutrient for animals. Mass death and reproductive failure in top aquatic consumers caused by vitamin B1 deficiency is an emerging conservation issue in Northern hemisphere aquatic ecosystems. We present for the first time a model that identifies conditions responsible for the constrained flow of vitamin B1 from unicellular organisms to planktivorous fishes. The flow of vitamin B1 through the food web is constrained under anthropogenic pressures of increased nutrient input and, driven by climatic change, increased light attenuation by dissolved substances transported to marine coastal systems. Fishing pressure on piscivorous fish, through increased abundance of planktivorous fish that overexploit mesozooplankton, may further constrain vitamin B1 flow from producers to consumers. We also found that key ecological contributors to the constrained flow of vitamin B1 are a low mesozooplankton biomass, picoalgae prevailing among primary producers and low fluctuations of population numbers of planktonic organisms.

Source apportionment of circum-Arctic atmospheric black carbon from isotopes and modeling

Black carbon (BC) contributes to Arctic climate warming, yet source attributions are inaccurate due to lacking observational constraints and uncertainties in emission inventories. Year-round, isotope-constrained observations reveal strong seasonal variations in BC sources with a consistent and synchronous pattern at all Arctic sites. These sources were dominated by emissions from fossil fuel combustion in the winter and by biomass burning in the summer. The annual mean source of BC to the circum-Arctic was 39 ± 10% from biomass burning. Comparison of transport-model predictions with the observations showed good agreement for BC concentrations, with larger discrepancies for (fossil/biomass burning) sources. The accuracy of simulated BC concentration, but not of origin, points to misallocations of emissions in the emission inventories. The consistency in seasonal source contributions of BC throughout the Arctic provides strong justification for targeted emission reductions to limit the impact of BC on climate warming in the Arctic and beyond.

ERα expression in T lymphocytes is dispensable for estrogenic effects in bone

Estrogen treatment has positive effects on the skeleton, and we have shown that estrogen receptor alpha (ERα) expression in cells of hematopoietic origin contributes to a normal estrogen treatment response in bone tissue. T lymphocytes are implicated in the estrogenic regulation of bone mass, but it is not known whether T lymphocytes are direct estrogen target cells. Therefore, the aim of this study was to determine the importance of ERα expression in T lymphocytes for the estrogenic regulation of the skeleton using female mice lacking ERα expression specifically in T lymphocytes (Lck-ERα^-/-) and ERα^flox/flox littermate (control) mice. Deletion of ERα expression in T lymphocytes did not affect bone mineral density (BMD) in sham-operated Lck-ERα^-/- compared to control mice, and ovariectomy (ovx) resulted in a similar decrease in BMD in control and Lck-ERα^-/- mice compared to sham-operated mice. Furthermore, estrogen treatment of ovx Lck-ERα^-/- led to an increased BMD that was indistinguishable from the increase seen after estrogen treatment of ovx control mice. Detailed analysis of both the appendicular (femur) and axial (vertebrae) skeleton showed that both trabecular and cortical bone parameters responded to a similar extent regardless of the presence of ERα in T lymphocytes. In conclusion, ERα expression in T lymphocytes is dispensable for normal estrogenic regulation of bone mass in female mice.

Interleukin 4 induces apoptosis of acute myeloid leukemia cells in a Stat6-dependent manner

Cytokines provide signals that regulate immature normal and acute myeloid leukemia (AML) cells in the bone marrow microenvironment. We here identify interleukin 4 (IL4) as a selective inhibitor of AML cell growth and survival in a cytokine screen using fluorescently labeled AML cells. RNA-sequencing of the AML cells revealed an IL4-induced upregulation of Stat6 target genes and enrichment of apoptosis-related gene expression signatures. Consistent with these findings, we found that IL4 stimulation of AML cells induced Stat6 phosphorylation and that disruption of Stat6 using CRISPR/Cas9-genetic engineering rendered cells partially resistant to IL4-induced apoptosis. To evaluate whether IL4 inhibits AML cells in vivo, we expressed IL4 ectopically in AML cells transplanted into mice and also injected IL4 into leukemic mice; both strategies resulted in the suppression of the leukemia cell burden and increased survival. Notably, IL4 exposure caused reduced growth and survival of primary AML CD34⁺CD38^- patient cells from several genetic subtypes of AML, whereas normal stem and progenitor cells were less affected. The IL4-induced apoptosis of AML cells was linked to Caspase-3 activation. Our results demonstrate that IL4 selectively induces apoptosis of AML cells in a Stat6-dependent manner-findings that may translate into new therapeutic opportunities in AML.

Using accelerometry to quantify prey attack and handling behaviours in piscivorous pike Esox lucius

Accelerometer technology was used to evaluate behaviours in the teleost ambush predator pike Esox lucius foraging on crucian carp Carassius carassius. Automated rule-based estimates of prey-size determined handling time were obtained and are compared with video-recorded behaviours. Solutions to tag attachment and the limitations imposed by battery-time and data-logging capacities are evaluated.

Allochthonous matter: an important factor shaping the phytoplankton community in the Baltic Sea

It is well-known that nutrients shape phytoplankton communities in marine systems, but in coastal waters allochthonous dissolved organic matter (ADOM) may also be of central importance. We studied how humic substances (proxy of ADOM) and other variables influenced the nutritional strategies, size structure and pigment content of the phytoplankton community along a south-north gradient in the Baltic Sea. During the summer, the proportion of mixotrophs increased gradually from the phosphorus-rich south to the ADOM-rich north, probably due to ADOM-fueled microbes. The opposite trend was observed for autotrophs. The chlorophyll a (Chl a): carbon (C) ratio increased while the levels of photoprotective pigments decreased from south to north, indicating adaptation to the darker humic-rich water in the north. Picocyanobacteria dominated in phosphorus-rich areas while nanoplankton increased in ADOM-rich areas. During the winter-spring the phytoplankton biomass and concentrations of photoprotective pigments were low, and no trends with respect to autotrophs and mixotrophs were observed. Microplankton was the dominant size group in the entire study area. We conclude that changes in the size structure of the phytoplankton community, the Chl a:C ratio and the concentrations of photoprotective pigments are indicative of changes in ADOM, a factor of particular importance in a changing climate.

The sources of atmospheric black carbon at a European gateway to the Arctic

Black carbon (BC) aerosols from incomplete combustion of biomass and fossil fuel contribute to Arctic climate warming. Models-seeking to advise mitigation policy-are challenged in reproducing observations of seasonally varying BC concentrations in the Arctic air. Here we compare year-round observations of BC and its δ(13)C/Δ(14)C-diagnosed sources in Arctic Scandinavia, with tailored simulations from an atmospheric transport model. The model predictions for this European gateway to the Arctic are greatly improved when the emission inventory of anthropogenic sources is amended by satellite-derived estimates of BC emissions from fires. Both BC concentrations (R(2)=0.89, P<0.05) and source contributions (R(2)=0.77, P<0.05) are accurately mimicked and linked to predominantly European emissions. This improved model skill allows for more accurate assessment of sources and effects of BC in the Arctic, and a more credible scientific underpinning of policy efforts aimed at efficiently reducing BC emissions reaching the European Arctic.

Structural circular birefringence and dichroism quantified by differential decomposition of spectroscopic transmission Mueller matrices from Cetonia aurata

Transmission Mueller-matrix spectroscopic ellipsometry is applied to the cuticle of the beetle Cetonia aurata in the spectral range 300-1000 nm. The cuticle is optically reciprocal and exhibits circular Bragg filter features for green light. By using differential decomposition of the Mueller matrix, the circular and linear birefringence as well as dichroism of the beetle cuticle are quantified. A maximum value of structural optical activity of 560°/mm is found.

Allochthonous Carbon--a Major Driver of Bacterioplankton Production in the Subarctic Northern Baltic Sea

Heterotrophic bacteria are, in many aquatic systems, reliant on autochthonous organic carbon as their energy source. One exception is low-productive humic lakes, where allochthonous dissolved organic matter (ADOM) is the major driver. We hypothesized that bacterial production (BP) is similarly regulated in subarctic estuaries that receive large amounts of riverine material. BP and potential explanatory factors were measured during May-August 2011 in the subarctic Råne Estuary, northern Sweden. The highest BP was observed in spring, concomitant with the spring river-flush and the lowest rates occurred during summer when primary production (PP) peaked. PLS correlations showed that ∼60% of the BP variation was explained by different ADOM components, measured as humic substances, dissolved organic carbon (DOC) and coloured dissolved organic matter (CDOM). On average, BP was threefold higher than PP. The bioavailability of allochthonous dissolved organic carbon (ADOC) exhibited large spatial and temporal variation; however, the average value was low, ∼2%. Bioassay analysis showed that BP in the near-shore area was potentially carbon limited early in the season, while BP at seaward stations was more commonly limited by nitrogen-phosphorus. Nevertheless, the bioassay indicated that ADOC could contribute significantly to the in situ BP, ∼60%. We conclude that ADOM is a regulator of BP in the studied estuary. Thus, projected climate-induced increases in river discharge suggest that BP will increase in subarctic coastal areas during the coming century.

Effects of predicted climatic changes on distribution of organic contaminants in brackish water mesocosms

Predicted consequences of future climate change in the northern Baltic Sea include increases in sea surface temperatures and terrestrial dissolved organic carbon (DOC) runoff. These changes are expected to alter environmental distribution of anthropogenic organic contaminants (OCs). To assess likely shifts in their distributions, outdoor mesocosms were employed to mimic pelagic ecosystems at two temperatures and two DOC concentrations, current: 15°C and 4 mg DOCL(-1) and, within ranges of predicted increases, 18°C and 6 mg DOCL(-1), respectively. Selected organic contaminants were added to the mesocosms to monitor changes in their distribution induced by the treatments. OC partitioning to particulate matter and sedimentation were enhanced at the higher DOC concentration, at both temperatures, while higher losses and lower partitioning of OCs to DOC were observed at the higher temperature. No combined effects of higher temperature and DOC on partitioning were observed, possibly because of the balancing nature of these processes. Therefore, changes in OCs' fates may largely depend on whether they are most sensitive to temperature or DOC concentration rises. Bromoanilines, phenanthrene, biphenyl and naphthalene were sensitive to the rise in DOC concentration, whereas organophosphates, chlorobenzenes (PCBz) and polychlorinated biphenyls (PCBs) were more sensitive to temperature. Mitotane and diflufenican were sensitive to both temperature and DOC concentration rises individually, but not in combination.

Circulating prolactin and breast cancer risk among pre- and postmenopausal women in the EPIC cohort

BACKGROUND

Experimental and epidemiological evidence suggests that prolactin might play a role in the etiology of breast cancer. We analyzed the relationship of prediagnostic circulating prolactin levels with the risk of breast cancer by menopausal status, use of postmenopausal hormone replacement therapy (HRT) at blood donation, and by estrogen and progesterone receptor status of the breast tumors.

PATIENTS AND METHODS

Conditional logistic regression was used to analyze the data from a case-control study nested within the prospective European EPIC cohort, including 2250 invasive breast cancer and their matched control subjects.

RESULTS

Statistically significant heterogeneity in the association of prolactin levels with breast cancer risk between women who were either pre- or postmenopausal at the time of blood donation was observed (Phet = 0.04). Higher serum levels of prolactin were associated with significant increase in the risk of breast cancer among postmenopausal women [odds ratio (OR)Q4-Q1 = 1.29 (95% confidence interval, CI, 1.05-1.58), Ptrend = 0.09]; however, this increase in risk seemed to be confined to women who used postmenopausal HRT at blood donation [ORQ4-Q1 = 1.45 (95% CI 1.08-1.95), Ptrend = 0.01], whereas no statistically significant association was found for the non-users of HRT [ORQ4-Q1 = 1.11 (95%CI 0.83-1.49), Ptrend = 0.80] (Phet = 0.08). Among premenopausal women, a statistically non-significant inverse association was observed [ORQ4-Q1 = 0.70 (95% CI 0.48-1.03), Ptrend = 0.16]. There was no heterogeneity in the prolactin-breast cancer association by hormone receptor status of the tumor.

CONCLUSION

Our study indicates that higher circulating levels of prolactin among the postmenopausal HRT users at baseline may be associated with increased breast cancer risk.

Francisella tularensis subspecies holarctica occurs in Swedish mosquitoes, persists through the developmental stages of laboratory-infected mosquitoes and is transmissible during blood feeding

In Sweden, mosquitoes are considered the major vectors of the bacterium Francisella tularensis subsp. holarctica, which causes tularaemia. The aim of this study was to investigate whether mosquitoes acquire the bacterium as aquatic larvae and transmit the disease as adults. Mosquitoes sampled in a Swedish area where tularaemia is endemic (Örebro) were positive for the presence of F. tularensis deoxyribonucleic acid throughout the summer. Presence of the clinically relevant F. tularensis subsp. holarctica was confirmed in 11 out of the 14 mosquito species sampled. Experiments performed using laboratory-reared Aedes aegypti confirmed that F. tularensis subsp. holarctica was transstadially maintained from orally infected larvae to adult mosquitoes and that 25% of the adults exposed as larvae were positive for the presence of F. tularensis-specific sequences for at least 2 weeks. In addition, we found that F. tularensis subsp. holarctica was transmitted to 58% of the adult mosquitoes feeding on diseased mice. In a small-scale in vivo transmission experiment with F. tularensis subsp. holarctica-positive adult mosquitoes and susceptible mice, none of the animals developed tularaemia. However, we confirmed that there was transmission of the bacterium to blood vials by mosquitoes that had been exposed to the bacterium in the larval stage. Taken together, these results provide evidence that mosquitoes play a role in disease transmission in part of Sweden where tularaemia recurs.

Impacts of elevated terrestrial nutrient loads and temperature on pelagic food-web efficiency and fish production

Both temperature and terrestrial organic matter have strong impacts on aquatic food-web dynamics and production. Temperature affects vital rates of all organisms, and terrestrial organic matter can act both as an energy source for lower trophic levels, while simultaneously reducing light availability for autotrophic production. As climate change predictions for the Baltic Sea and elsewhere suggest increases in both terrestrial matter runoff and increases in temperature, we studied the effects on pelagic food-web dynamics and food-web efficiency in a plausible future scenario with respect to these abiotic variables in a large-scale mesocosm experiment. Total basal (phytoplankton plus bacterial) production was slightly reduced when only increasing temperatures, but was otherwise similar across all other treatments. Separate increases in nutrient loads and temperature decreased the ratio of autotrophic:heterotrophic production, but the combined treatment of elevated temperature and terrestrial nutrient loads increased both fish production and food-web efficiency. CDOM: Chl a ratios strongly indicated that terrestrial and not autotrophic carbon was the main energy source in these food webs and our results also showed that zooplankton biomass was positively correlated with increased bacterial production. Concomitantly, biomass of the dominant calanoid copepod Acartia sp. increased as an effect of increased temperature. As the combined effects of increased temperature and terrestrial organic nutrient loads were required to increase zooplankton abundance and fish production, conclusions about effects of climate change on food-web dynamics and fish production must be based on realistic combinations of several abiotic factors. Moreover, our results question established notions on the net inefficiency of heterotrophic carbon transfer to the top of the food web.

Fast determination of antibiotics in whole blood

There is a need for analytical methods capable of monitoring blood antibiotic levels in real time. Here we present a method for quantifying antibiotic levels in whole blood that does not require any sample pretreatment. The tests employ the enzyme penicillinase to assay for penicillin G, penicillin V and ampicillin using a flow-injected biosensor, the Enzyme Thermistor. Optimal flow rates, sample volumes and pH were determined to be 0.5 mL/min, 100 μL and 7.0, respectively. Analysis of the antibiotics diluted in buffer gave a linear range of 0.17-5.0 mM. Calibration curves prepared using blood spiked with the antibiotics gave a linear range of 0.17-2.0 mM. Linear regression values for all of the calibration curves were 0.998 or higher. Assay cycle time was 5 min. The relative standard deviation value for 100 determinations of a mock blood sample spiked with penicillin G was 6.71%. Despite the elimination of sample pretreatment, no detectable clogging or signal drift was observed. The assay provides a fast, simple, reliable analytical method for determining antibiotic concentrations in blood without the need for any sample pretreatment. This is an important first step towards developing a device capable of real-time monitoring of antibiotic levels in whole blood. The technology has the potential to significantly improve the outcomes of patients undergoing critical care.

Nutritional status and health care costs for the elderly living in municipal residential homes--an intervention study

OBJECTIVE

The aim was to study the effect of individualised meals on nutritional status among older people living in municipal residential homes and to compare the results with a control group. An additional aim was to estimate direct health care costs for both groups.

SETTING

Six different municipal residential homes in the south-east of Sweden.

PARTICIPANTS

Older people living in three residential homes constituted the intervention group n=42 and the rest constituted the control group n=67.

INTERVENTION

A multifaceted intervention design was used. Based on an interview with staff a tailored education programme about nutritional care, including both theoretical and practical issues, was carried through to staff in the intervention group. Nutritional status among the elderly was measured by Mini Nutritional Assessment (MNA), individualised meals were offered to the residents based on the results of the MNA. Staff in the control group only received education on how to measure MNA and the residents followed the usual meal routines.

MEASUREMENTS

Nutritional status was measured by MNA at baseline and after 3 months. Cost data on health care visits during 2007 were collected from the Cost Per Patient database.

RESULTS

Nutritional status improved and body weight increased after 3 months in the intervention group. Thus, primary health care costs constituted about 80% of the total median cost in the intervention group and about 55% in the control group.

CONCLUSION

With improved knowledge the staff could offer the elderly more individualised meals. One of their future challenges is to recognise and assess nutritional status among this group. If malnutrition could be prevented health care costs should be reduced.