Triple-negative breast cancer (TNBC) is an aggressive subtype that frequently develops resistance to chemotherapy. An unresolved question is whether resistance is caused by the selection of rare ...pre-existing clones or alternatively through the acquisition of new genomic aberrations. To investigate this question, we applied single-cell DNA and RNA sequencing in addition to bulk exome sequencing to profile longitudinal samples from 20 TNBC patients during neoadjuvant chemotherapy (NAC). Deep-exome sequencing identified 10 patients in which NAC led to clonal extinction and 10 patients in which clones persisted after treatment. In 8 patients, we performed a more detailed study using single-cell DNA sequencing to analyze 900 cells and single-cell RNA sequencing to analyze 6,862 cells. Our data showed that resistant genotypes were pre-existing and adaptively selected by NAC, while transcriptional profiles were acquired by reprogramming in response to chemotherapy in TNBC patients.
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•Single-cell sequencing of breast cancer patients treated with chemotherapy•Patients showed clonal persistence or extinction in response to therapy•Resistance occurred through adaptive selection of pre-existing genomic aberrations•Chemotherapy induced transcriptional reprogramming of resistant signatures
Combination of single-cell DNA and RNA sequencing depicts the evolutionary trajectories of chemoresistance in human triple-negative breast cancer at the genomic and transcriptomic level, highlighting the presence of pre-existing genomic alterations and transcriptional reprogramming of resistant signatures.
Aneuploidy is a hallmark of breast cancer; however, knowledge of how these complex genomic rearrangements evolve during tumorigenesis is limited. In this study, we developed a highly multiplexed ...single-nucleus sequencing method to investigate copy number evolution in patients with triple-negative breast cancer. We sequenced 1,000 single cells from tumors in 12 patients and identified 1-3 major clonal subpopulations in each tumor that shared a common evolutionary lineage. For each tumor, we also identified a minor subpopulation of non-clonal cells that were classified as metastable, pseudodiploid or chromazemic. Phylogenetic analysis and mathematical modeling suggest that these data are unlikely to be explained by the gradual accumulation of copy number events over time. In contrast, our data challenge the paradigm of gradual evolution, showing that the majority of copy number aberrations are acquired at the earliest stages of tumor evolution, in short punctuated bursts, followed by stable clonal expansions that form the tumor mass.
The mitochondrial protein, translocator protein (TSPO), is a widely used biomarker of neuroinflammation, but its non-selective cellular expression pattern implies roles beyond inflammatory processes. ...In the present study, we investigated whether neuronal activity modifies TSPO levels in the adult central nervous system. First, we used single-cell RNA sequencing to generate a cellular landscape of basal TSPO gene expression in the hippocampus of adult (12 weeks old) C57BL6/N mice, followed by confocal laser scanning microscopy to verify TSPO protein in neuronal and non-neuronal cell populations. We then quantified TSPO mRNA and protein levels after stimulating neuronal activity with distinct stimuli, including designer receptors exclusively activated by designer drugs (DREADDs), exposure to a novel environment and acute treatment with the psychostimulant drug, amphetamine. Single-cell RNA sequencing demonstrated a non-selective and multi-cellular gene expression pattern of TSPO at basal conditions in the adult mouse hippocampus. Confocal laser scanning microscopy confirmed that TSPO protein is present in neuronal and non-neuronal (astrocytes, microglia, vascular endothelial cells) cells of cortical (medial prefrontal cortex) and subcortical (hippocampus) brain regions. Stimulating neuronal activity through chemogenetic (DREADDs), physiological (novel environment exposure) or psychopharmacological (amphetamine treatment) approaches led to consistent increases in TSPO gene and protein levels in neurons, but not in microglia or astrocytes. Taken together, our findings show that neuronal activity has the potential to modify TSPO levels in the adult central nervous system. These findings challenge the general assumption that altered TSPO expression or binding unequivocally mirrors ongoing neuroinflammation and emphasize the need to consider non-inflammatory interpretations in some physiological or pathological contexts.
Objective
Connectivity atypicalities in autism spectrum disorders (ASD) have been extensively proposed. The default mode network (DMN) is critical in this study, given the insight it provides for ...long‐distance connectivity, and the importance of regions in this network for introspection and social emotion processing, areas affected in ASD. However, study of this network has largely been limited to adults; research earlier in development is lacking. The objective of this study was to examine DMN connectivity in children/adolescents with ASD.
Methods
A total of 115 children/adolescents, aged 6 to 17 years (71 males with ASD and 44 group age‐matched TD males) were included in these analyses. We examined group differences in (1) functional connectivity between the posterior cingulate cortex and regions across the brain, (2) connectivity within the DMN as a function of age and intelligence quotient (IQ), and (3) the association between DMN connectivity and empathic accuracy.
Results
Individuals with ASD, relative to controls, showed either stronger or weaker connectivity between the posterior cingulate cortex (PCC) and DMN regions, depending on the region, but also showed stronger connectivity with non‐DMN regions. A significant group‐by‐age interaction was observed in functional connectivity between the PCC and medial prefrontal cortex; connectivity increased with age in controls, but decreased in individuals with ASD. No effects of IQ were found. There was a significant group difference in the relation between DMN connectivity and empathic accuracy.
Interpretation
Differences in functional connectivity may suggest the presence of neural atypicalities that impact the development of typical connectivity in ASD. In addition to affecting DMN dynamics, these atypicalities may also impact social–cognitive abilities. Ann Neurol 2015;77:866–876
We present an update of the ‘key points’ from the Antarctic Climate Change and the Environment (ACCE) report that was published by the Scientific Committee on Antarctic Research (SCAR) in 2009. We ...summarise subsequent advances in knowledge concerning how the climates of the Antarctic and Southern Ocean have changed in the past, how they might change in the future, and examine the associated impacts on the marine and terrestrial biota. We also incorporate relevant material presented by SCAR to the Antarctic Treaty Consultative Meetings, and make use of emerging results that will form part of the Intergovernmental Panel on Climate Change (IPCC) Fifth Assessment Report.
Surface mining for coal has taken place in the Central Appalachian region of the United States for well over a century, with a notable increase since the 1970s. Researchers have quantified the ...ecosystem and health impacts stemming from mining, relying in part on a geospatial dataset defining surface mining's extent at a decadal interval. This dataset, however, does not deliver the temporal resolution necessary to support research that could establish causal links between mining activity and environmental or public health and safety outcomes, nor has it been updated since 2005. Here we use Google Earth Engine and Landsat imagery to map the yearly extent of surface coal mining in Central Appalachia from 1985 through 2015, making our processing models and output data publicly available. We find that 2,900 km2 of land has been newly mined over this 31-year period. Adding this more-recent mining to surface mines constructed prior to 1985, we calculate a cumulative mining footprint of 5,900 km2. Over the study period, correlating active mine area with historical surface mine coal production shows that each metric ton of coal is associated with 12 m2 of actively mined land. Our automated, open-source model can be regularly updated as new surface mining occurs in the region and can be refined to capture mining reclamation activity into the future. We freely and openly offer the data for use in a range of environmental, health, and economic studies; moreover, we demonstrate the capability of using tools like Earth Engine to analyze years of remotely sensed imagery over spatially large areas to quantify land use change.
The ~70 km-diameter Yarrabubba impact structure in Western Australia is regarded as among Earth’s oldest, but has hitherto lacked precise age constraints. Here we present U-Pb ages for impact21 ...driven shock recrystallised accessory minerals. Shock-recrystallised monazite yields a precise impact age of 2229 ± 5 Ma, coeval with shock-reset zircon. This result establishes Yarrabubba as the oldest recognized meteorite impact structure on Earth, extending the terrestrial cratering record back >200 million years. The age of Yarrabubba coincides, within uncertainty, with temporal constraint for the youngest Palaeoproterozoic glacial deposits, the Rietfontein diamictite in South Africa. Numerical impact simulations indicate that a 70 km-diameter crater into a continental glacier could release between 8.7x1013 to 5.0x1015 kg of H2O vapour instantaneously into the atmosphere. These results provide new estimates of impact-produced H2O vapour abundances for models investigating termination of the Paleoproterozoic glaciations, and highlight the possible role of impact cratering in modifying Earth’s climate.
Aim
The introduction of aquatic non‐indigenous species (ANS) has become a major driver for global changes in species biogeography. We examined spatial patterns and temporal trends of ANS detections ...since 1965 to inform conservation policy and management.
Location
Global.
Methods
We assembled an extensive dataset of first records of detection of ANS (1965–2015) across 49 aquatic ecosystems, including the (a) year of first collection, (b) population status and (c) potential pathway(s) of introduction. Data were analysed at global and regional levels to assess patterns of detection rate, richness and transport pathways.
Results
An annual mean of 43 (±16 SD) primary detections of ANS occurred—one new detection every 8.4 days for 50 years. The global rate of detections was relatively stable during 1965–1995, but increased rapidly after this time, peaking at roughly 66 primary detections per year during 2005–2010 and then declining marginally. Detection rates were variable within and across regions through time. Arthropods, molluscs and fishes were the most frequently reported ANS. Most ANS were likely introduced as stowaways in ships’ ballast water or biofouling, although direct evidence is typically absent.
Main conclusions
This synthesis highlights the magnitude of recent ANS detections, yet almost certainly represents an underestimate as many ANS go unreported due to limited search effort and diminishing taxonomic expertise. Temporal rates of detection are also confounded by reporting lags, likely contributing to the lower detection rate observed in recent years. There is a critical need to implement standardized, repeated methods across regions and taxa to improve the quality of global‐scale comparisons and sustain core measures over longer time‐scales. It will be fundamental to fill in knowledge gaps given that invasion data representing broad regions of the world's oceans are not yet readily available and to maintain knowledge pipelines for adaptive management.
Type 2 diabetes and obesity, as states of chronic inflammation, are risk factors for severe COVID-19. Metformin has cytokine-reducing and sex-specific immunomodulatory effects. Our aim was to ...identify whether metformin reduced COVID-19-related mortality and whether sex-specific interactions exist.
In this retrospective cohort analysis, we assessed de-identified claims data from UnitedHealth Group (UHG)'s Clinical Discovery Claims Database. Patient data were eligible for inclusion if they were aged 18 years or older; had type 2 diabetes or obesity (defined based on claims); at least 6 months of continuous enrolment in 2019; and admission to hospital for COVID-19 confirmed by PCR, manual chart review by UHG, or reported from the hospital to UHG. The primary outcome was in-hospital mortality from COVID-19. The independent variable of interest was home metformin use, defined as more than 90 days of claims during the year before admission to hospital. Covariates were comorbidities, medications, demographics, and state. Heterogeneity of effect was assessed by sex. For the Cox proportional hazards, censoring was done on the basis of claims made after admission to hospital up to June 7, 2020, with a best outcome approach. Propensity-matched mixed-effects logistic regression was done, stratified by metformin use.
6256 of the 15 380 individuals with pharmacy claims data from Jan 1 to June 7, 2020 were eligible for inclusion. 3302 (52·8%) of 6256 were women. Metformin use was not associated with significantly decreased mortality in the overall sample of men and women by either Cox proportional hazards stratified model (hazard ratio HR 0·887 95% CI 0·782–1·008) or propensity matching (odds ratio OR 0·912 95% CI 0·777–1·071, p=0·15). Metformin was associated with decreased mortality in women by Cox proportional hazards (HR 0·785, 95% CI 0·650–0·951) and propensity matching (OR 0·759, 95% CI 0·601–0·960, p=0·021). There was no significant reduction in mortality among men (HR 0·957, 95% CI 0·82–1·14; p=0·689 by Cox proportional hazards).
Metformin was significantly associated with reduced mortality in women with obesity or type 2 diabetes who were admitted to hospital for COVID-19. Prospective studies are needed to understand mechanism and causality. If findings are reproducible, metformin could be widely distributed for prevention of COVID-19 mortality, because it is safe and inexpensive.
National Heart, Lung, and Blood Institute; Agency for Healthcare Research and Quality; Patient-Centered Outcomes Research Institute; Minnesota Learning Health System Mentored Training Program, M Health Fairview Institutional Funds; National Center for Advancing Translational Sciences; and National Cancer Institute.
RATIONALE:Autologous bone marrow–derived or cardiac-derived stem cell therapy for heart disease has demonstrated safety and efficacy in clinical trials, but functional improvements have been limited. ...Finding the optimal stem cell type best suited for cardiac regeneration is the key toward improving clinical outcomes.
OBJECTIVE:To determine the mechanism by which novel bone-derived stem cells support the injured heart.
METHODS AND RESULTS:Cortical bone–derived stem cells (CBSCs) and cardiac-derived stem cells were isolated from enhanced green fluorescent protein (EGFP+) transgenic mice and were shown to express c-kit and Sca-1 as well as 8 paracrine factors involved in cardioprotection, angiogenesis, and stem cell function. Wild-type C57BL/6 mice underwent sham operation (n=21) or myocardial infarction with injection of CBSCs (n=67), cardiac-derived stem cells (n=36), or saline (n=60). Cardiac function was monitored using echocardiography. Only 2/8 paracrine factors were detected in EGFP+ CBSCs in vivo (basic fibroblast growth factor and vascular endothelial growth factor), and this expression was associated with increased neovascularization of the infarct border zone. CBSC therapy improved survival, cardiac function, regional strain, attenuated remodeling, and decreased infarct size relative to cardiac-derived stem cells– or saline-treated myocardial infarction controls. By 6 weeks, EGFP+ cardiomyocytes, vascular smooth muscle, and endothelial cells could be identified in CBSC-treated, but not in cardiac-derived stem cells–treated, animals. EGFP+ CBSC-derived isolated myocytes were smaller and more frequently mononucleated, but were functionally indistinguishable from EGFP− myocytes.
CONCLUSIONS:CBSCs improve survival, cardiac function, and attenuate remodeling through the following 2 mechanisms(1) secretion of proangiogenic factors that stimulate endogenous neovascularization, and (2) differentiation into functional adult myocytes and vascular cells.
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