Ancient genomes reveal over two thousand years of dingo population structure.

Dingoes are culturally and ecologically important free-living canids whose ancestors arrived in Australia over 3,000 B.P., likely transported by seafaring people. However, the early history of dingoes in Australia-including the number of founding populations and their routes of introduction-remains uncertain. This uncertainty arises partly from the complex and poorly understood relationship between modern dingoes and New Guinea singing dogs, and suspicions that post-Colonial hybridization has introduced recent domestic dog ancestry into the genomes of many wild dingo populations. In this study, we analyzed genome-wide data from nine ancient dingo specimens ranging in age from 400 to 2,746 y old, predating the introduction of domestic dogs to Australia by European colonists. We uncovered evidence that the continent-wide population structure observed in modern dingo populations had already emerged several thousand years ago. We also detected excess allele sharing between New Guinea singing dogs and ancient dingoes from coastal New South Wales (NSW) compared to ancient dingoes from southern Australia, irrespective of any post-Colonial hybrid ancestry in the genomes of modern individuals. Our results are consistent with several demographic scenarios, including a scenario where the ancestry of dingoes from the east coast of Australia results from at least two waves of migration from source populations with varying affinities to New Guinea singing dogs. We also contribute to the growing body of evidence that modern dingoes derive little genomic ancestry from post-Colonial hybridization with other domestic dog lineages, instead descending primarily from ancient canids introduced to Sahul thousands of years ago.

Testing Times: Disentangling Admixture Histories in Recent and Complex Demographies using ancient DNA.

Our knowledge of human evolutionary history has been greatly advanced by paleogenomics. Since the 2020s, the study of ancient DNA has increasingly focused on reconstructing the recent past. However, the accuracy of paleogenomic methods in resolving questions of historical and archaeological importance amidst the increased demographic complexity and decreased genetic differentiation remains an open question. We evaluated the performance and behavior of two commonly used methods, qpAdm and the f3-statistic, on admixture inference under a diversity of demographic models and data conditions. We performed two complementary simulation approaches - firstly exploring a wide demographic parameter space under four simple demographic models of varying complexities and configurations using branch-length data from two chromosomes - and secondly, we analyzed a model of Eurasian history composed of 59 populations using whole-genome data modified with ancient DNA conditions such as SNP ascertainment, data missingness, and pseudo-haploidization. We observe population differentiation is the primary factor driving qpAdm performance. Notably, whilst complex gene-flow histories influence which models are classified as plausible, they do not reduce overall performance. Under conditions reflective of the historical period, qpAdm most frequently identifies the true model as plausible amongst a small candidate set of closely related populations. To increase the utility for resolving fine-scaled hypotheses, we provide a heuristic for further distinguishing between candidate models that incorporates qpAdm model P-values and f3-statistics. Finally, we demonstrate a significant performance increase for qpAdm using whole-genome branch-length f2-statistics, highlighting the potential for improved demographic inference that could be achieved with future advancements in f-statistic estimations.

Patient and Clinician Preferences for Biologic Treatments for Severe Uncontrolled Asthma: A Discrete Choice Experiment (DCE).

OBJECTIVES: To estimate the preferences of patients with asthma and asthma-treating clinicians for attributes of biologic treatments, to compare patients' and clinicians' preferences, and to better understand the reasons for their preferences. METHODS: Adults with moderate-to-severe asthma and clinicians who treat asthma in the US completed a cross-sectional, online survey including a discrete choice experiment (DCE) that consisted of seven attributes spanning treatment efficacy, risk and convenience. Marginal utilities were estimated using a mixed logit model, and relative attribute importance scores calculated. Clinicians were also asked about the value of biomarker agnostic biologic treatments. The survey was followed by qualitative interviews targeting a sub-sample of survey participants, in which the rationale behind their survey responses was discussed. RESULTS: In the DCE, both patients and clinicians placed the most importance on exacerbation and hospitalization rate reduction, and risk of injection site reaction. Patients valued location of administration more than clinicians. Rationale for individual-level preferences varied, with patients and clinicians reporting their preference depended on event frequency and anticipated quality of life impacts. Clinicians mentioned compliance and financial impacts, while patients mentioned personal experience, particularly around site reactions. Most patients and clinicians would value a biomarker agnostic asthma treatment. CONCLUSIONS: Asthma treatment preferences are largely driven by treatment efficacy and minimizing the risk of site reactions, although preferences differ between patients and clinicians across other attributes, highlighting the need for shared decision-making and individualized care.

Depression at the intersection of race/ethnicity, sex/gender, and sexual orientation in a nationally representative sample of US adults: A design-weighted intersectional MAIHDA.

This study examined how race/ethnicity, sex/gender, and sexual orientation intersect under interlocking systems of oppression to socially pattern depression among US adults. With cross-sectional data from the 2015-2020 National Survey on Drug Use and Health (NSDUH; n=234,722), we conducted design-weighted multilevel analysis of individual heterogeneity and discriminatory accuracy (MAIHDA) under an intersectional framework to predict past-year and lifetime major depressive episode (MDE). With 42 intersectional groups constructed from seven race/ethnicity, two sex/gender, and three sexual orientation categories, we estimated age-standardized prevalence and excess/reduced prevalence attributable to two-way or higher interaction effects. Models revealed heterogeneity across groups, with prevalence ranging from 1.9-19.7% (past-year) and 4.5-36.5% (lifetime). Approximately 12.7% (past-year) and 12.5% (lifetime) of total individual variance were attributable to between-group differences, indicating key relevance of intersectional groups in describing the population distribution of depression. Main effects indicated, on average, people who were White, women, gay/lesbian, or bisexual had greater odds of MDE. Main effects explained most between-group variance. Interaction effects (past-year: 10.1%; lifetime: 16.5%) indicated a further source of heterogeneity around averages with groups experiencing excess/reduced prevalence compared to main effects expectations. We extend the MAIHDA framework to calculate nationally representative estimates from complex sample survey data using design-weighted, Bayesian methods.

Association of neighborhood socioeconomic status with echocardiographic parameters and re-admission following transcatheter aortic valve replacement.

BACKGROUND: Data on predictors of poor hemodynamic presentation and rehospitalizations following transcatheter aortic valve replacement (TAVR) are limited. We evaluate the association between neighborhood socioeconomic status (NSES) on echocardiographic presentation and post-TAVR readmission at a high-volume institution. METHODS: All patients undergoing TAVR at a single institution between 2012 and 2022 were included. Patient addresses, baseline variables including Society of Thoracic Surgeons (STS) preoperative risk of mortality and frailty, and post-procedural outcomes were extracted from electronic health records. Using a validated US Census Bureau Index, the NSES of each patient (1-100) was tabulated, with lower values correlating to increased social deprivation. Patients were separated into four ranked groups based on NSES (rank 1: 1-25, rank 4: 76-100). Multivariable regression was performed to determine variables associated with number of days hospitalized in one-year following index TAVR procedure. RESULTS: A total of 2031 patients were included. The median NSES was 68 (IQR: 53-80). There was a total of 232 (11.4%) readmissions. The median number of days hospitalized in one year following TAVR was 4 (interquartile range [IQR]: 2-7) After adjusting for baseline variables including STS risk score and patient frailty, compared to patients in the lowest ranked socioeconomic group, patients of higher NSES were associated with lower aortic valve gradients at baselines (Exp[ß]=0.997, 95% CI: 0.993-0.999, P=0.049). Additionally, compared to patients in the lowest ranked socioeconomic group, patients of NSES were associated with shorter duration of readmission after risk-factor adjustments (Exp[ß]=0.996, 95% CI: 0.992-0.999, P=0.032). CONCLUSIONS: Patients of lower socioeconomic status are associated with higher aortic valve gradient at baseline and more days hospitalized in the first year after their index TAVR procedure after adjusting for other risk factors. As TAVR volume continues to expand, physicians and health systems must consider this independent factor when determining patient prognosis and readmission policies.

Adaptation to ex vivo culture reduces human hematopoietic stem cell activity independently of cell cycle.

Loss of long-term hematopoietic stem cell (LT-HSC) function ex vivo hampers the success of clinical protocols reliant on culture. However, the kinetics and mechanisms by which this occurs remain incompletely characterized. Here, through time-resolved scRNA-Seq, matched in vivo functional analysis and the use of a reversible in vitro system of early G1 arrest, we define the sequence of transcriptional and functional events occurring during the first ex vivo division of human LT-HSCs. We demonstrate that the sharpest loss of LT-HSC repopulation capacity happens early on, between 6 and 24 hours of culture, before LT-HSCs commit to cell cycle progression. During this time window, LT-HSCs adapt to the culture environment, limiting global variability in gene expression and transiently upregulating gene networks involved in signaling and stress responses. From 24 hours, LT-HSC progression past early G1 contributes to the establishment of differentiation programmes in culture. However, contrary to current assumptions, we demonstrate that loss of HSC function ex vivo is independent of cell cycle progression. Finally, we show that targeting LT-HSC adaptation to culture by inhibiting early activation of JAK/STAT signaling improves HSC long-term repopulating function ex vivo. Collectively, our study demonstrates that controlling early LT-HSC adaptation to ex vivo culture, for example via JAK inhibition, is of critical importance to improve HSC gene therapy and expansion protocols.

Novel dosimetric validation of a commercial CT scanner based deep learning automated contour solution for prostate radiotherapy.

PURPOSE: OAR delineation accuracy influences: (i) a patient's optimised dose distribution (PD), (ii) the reported doses (RD) presented at approval, which represent plan quality. This study utilised a novel dosimetric validation methodology, comprehensively evaluating a new CT-scanner-based AI contouring solution in terms of PD and RD within an automated planning workflow. METHODS: 20 prostate patients were selected to evaluate AI contouring for rectum, bladder, and proximal femurs. Five planning 'pipelines' were considered; three using AI contours with differing levels of manual editing (nominally none (AIStd), minor editing in specific regions (AIMinEd), and fully corrected (AIFullEd)). Remaining pipelines were manual delineations from two observers (MDOb1, MDOb2). Automated radiotherapy plans were generated for each pipeline. Geometric and dosimetric agreement of contour sets AIStd, AIMinEd, AIFullEd and MDOb2 were evaluated against the reference set MDOb1. Non-inferiority of AI pipelines was assessed, hypothesising that compared to MDOb1, absolute deviations in metrics for AI contouring were no greater than that from MDOb2. RESULTS: Compared to MDOb1, organ delineation time was reduced by 24.9 min (96 %), 21.4 min (79 %) and 12.2 min (45 %) for AIStd, AIMinEd and AIFullEd respectively. All pipelines exhibited generally good dosimetric agreement with MDOb1. For RD, median deviations were within ± 1.8 cm3, ± 1.7 % and ± 0.6 Gy for absolute volume, relative volume and mean dose metrics respectively. For PD, respective values were within ± 0.4 cm3, ± 0.5 % and ± 0.2 Gy. Statistically (p < 0.05), AIMinEd and AIFullEd were dosimetrically non-inferior to MDOb2. CONCLUSIONS: This novel dosimetric validation demonstrated that following targeted minor editing (AIMinEd), AI contours were dosimetrically non-inferior to manual delineations, reducing delineation time by 79 %.

Ultraviolet light and riboflavin accelerates red blood cell dysfunction in vitro and in a guinea pig transfusion model.

BACKGROUND: Quality assessment of modified or processed red blood cell (RBC) components, such as pathogen-reduced RBCs, using only in vitro testing may not always be predictive of in vivo performance. Mouse or rat in vivo models are limited by a lack of applicability to certain aspects of human RBC biology. Here, we used a guinea pig model to study the effects of riboflavin combined with UV light on the integrity of RBCs in vitro and following transfusion in vivo. MATERIALS AND METHODS: Guinea pig RBCs were collected from whole blood (WB) treated with varying UV doses (10, 20, 40 or 80 J/mL) in the presence of riboflavin (UVR-RBCs). In vitro tests for UVR-RBCs included hemolysis, osmotic fragility, and cellular morphology by scanning electron microscopy. Guinea pigs transfused with one-day post-treatment UVR-RBCs were evaluated for plasma hemoglobin (Hb), non-transferrin bound iron (NTBI), total iron and Perls-detectable hemosiderin deposition in the spleen and kidney, and renal uptake of Hb. RESULTS: Acute RBC injury was dose dependently accelerated after treatment with UV light in the presence of riboflavin. Aberrant RBC morphology was evident at 20, 40, and 80 J/mL, and membrane lysis with Hb release was prominent at 80 J/mL. Guinea pigs transfused with 40 and 80 J/mL UVR-RBCs showed increased plasma Hb levels, and plasma NTBI was elevated in all UVR-RBC groups (10-80 J/mL). Total iron levels and Perls-hemosiderin staining in spleen and kidney as well as Hb uptake in renal proximal tubules were increased 8 hours post-transfusion with 40 and 80 J/mL UVR-RBCs. DISCUSSION: UVR-RBCs administered to guinea pigs increased markers of intravascular and extravascular hemolysis in a UV dose-dependent manner. This model may allow for the discrimination of RBC injury during testing of extensively processed RBCs intended for transfusion.

Correction: Quantifying spatial variability in shell midden formation in the Farasan Islands, Saudi Arabia.

[This corrects the article DOI: 10.1371/journal.pone.0217596.].

An Undergraduate Health Care Experience Course Increases Confidence and Improves Student Understanding of Health Care Careers.

Increasing the health care work force is critical to underserved communities. Unfortunately, students in these areas lack accessibility to the clinical experiences needed to get an introductory understanding of careers in health care. Therefore, a health care experience (HCE) course was created for undergraduate students that included didactic training, active learning exercises, and coordinated shadowing experiences. To evaluate the effect of the HCE on student interest in science, health care, and rural health a study was performed on HCE participants. This study assessed student background, interest in health care, and plans for future careers in underserved settings. Students who enrolled in the HCE demonstrated high interest in science, health care, and rural health. Evaluation of student reflections indicated students attained novel learning, gained insights, and recognized the importance of communication. The HCE course students exhibited amplified confidence in HCEs and had a significant increase in understanding of health care compared with a control group of students who had not completed the HCE. Undergraduate institutions can include courses like the HCE into curricula to increase accessibility to career experiences for students interested in health care careers.

Synthesis, Characterization, and the Effect of Lewis Bases on the Nuclearity of Iron Alkoxide Complexes.

Inspired by the potential of alkoxides as weak-field ligands and their ability to bridge, we report herein a series of high-spin iron complexes supported by a bis-alkoxide framework PhDbf. A diiron complex [Fe2(PhDbf)2] (1a) is obtained upon metalation of the ligand, whereas addition of substituted pyridines affords five-coordinate mononuclear iron complexes [(R-Py)2Fe(PhDbf)] (2a-4a, R = H, p-tBu, p-CF3). The potential for nuclearity control of the metal complexes via auxiliary ligands is highlighted by the formation of asymmetric diiron species [(p-CF3-Py)Fe2(PhDbf)2] (5a) and [(m-CF3-Py)Fe2(PhDbf)2] (6a) with trifluoromethyl substituted pyridines, while electron-rich pyridines only produced monomeric species. Electronic properties analysis via UV-vis, electron paramagnetic resonance, 57Fe Mössbauer spectroscopy, and time-dependent density functional theory, along with redox capabilities of these complexes are reported to illustrate the effect of nuclearity on reactivity and the potential of these complexes to access higher oxidation states relevant in oxidative chemistry. Species 1a-5a, [(THF)2Fe(PhDbf)][PF6] (7), [PyFe(PhDbf)Cl] (2b), and [Py2Fe(PhDbf)][PF6] (2c) were characterized via SCXRD. Indirect evidence for the formation of dimeric Fe(III) species (1b, 5b, and 6b) is discussed.

What might make nurses stay? A protocol for discrete choice experiments to understand NHS nurses' preferences at early-career and late-career stages.

INTRODUCTION: Like many countries, England has a national shortage of registered nurses. Employers strive to retain existing staff, to ease supply pressures. Disproportionate numbers of nurses leave the National Health Services (NHS) both early in their careers, and later, as they near retirement age. Research is needed to understand the job preferences of early-career and late-career nurses working in the NHS, so tailored policies can be developed to better retain these two groups. METHODS AND ANALYSIS: We will collect job preference data for early-career and late-career NHS nurses, respectively using two separate discrete choice experiments (DCEs). Findings from the literature, focus groups, academic experts and stakeholder discussions will be used to identify and select the DCE attributes (ie, job features) and levels. We will generate an orthogonal, fractional factorial design using the experimental software Ngene. The DCEs will be administered through online surveys distributed by the regulator Nursing and Midwifery Council. For each group, we expect to achieve a final sample of 2500 registered NHS nurses working in England. For early-career nurses, eligible participants will be registered nurses who graduated in the preceding 5 years (ie, 2019-2023). Eligible participants for the late-career survey will be registered nurses aged 55 years and above. We will use conditional and mixed logit models to analyse the data. Specifically, study 1 will estimate the job preferences of early-career nurses and the possible trade-offs. Study 2 will estimate the retirement preferences of late-career NHS nurses and the potential trade-offs. ETHICS AND DISSEMINATION: The research protocol was reviewed and approved by the host research organisation Ethics Committees Research Governance (University of Southampton, number 80610) (https://www.southampton.ac.uk/about/governance/regulations-policies/policies/ethics). The results will be disseminated via conference presentations, publications in peer-reviewed journals and annual reports to key stakeholders, the Department of Health and Social Care, and NHS England/Improvement retention leaders. REGISTRATION DETAILS: Registration on OSF http://doi.org/10.17605/OSF.IO/RDN9G.

OCA-B/Pou2af1 is sufficient to promote CD4+ T cell memory and prospectively identifies memory precursors.

The molecular mechanisms leading to the establishment of immunological memory are inadequately understood, limiting the development of effective vaccines and durable antitumor immune therapies. Here, we show that ectopic OCA-B expression is sufficient to improve antiviral memory recall responses, while having minimal effects on primary effector responses. At peak viral response, short-lived effector T cell populations are expanded but show increased Gadd45b and Socs2 expression, while memory precursor effector cells show increased expression of Bcl2, Il7r, and Tcf7 on a per-cell basis. Using an OCA-B mCherry reporter mouse line, we observe high OCA-B expression in CD4+ central memory T cells. We show that early in viral infection, endogenously elevated OCA-B expression prospectively identifies memory precursor cells with increased survival capability and memory recall potential. Cumulatively, the results demonstrate that OCA-B is both necessary and sufficient to promote CD4 T cell memory in vivo and can be used to prospectively identify memory precursor cells.

Living in disadvantaged neighborhoods linked to less intervention for severe aortic stenosis.

To investigate the association between area deprivation index (ADI) and aortic valve replacement (AVR) in patients with severe aortic stenosis (AS). Patients aged 40-95 years with severe AS confirmed by echocardiography were included. The 9-digit zip code of patient residence address was used to identify the ADI ranking, based on which patients were divided into 5 groups (with Group E being most deprived). The rates of AV intervention were compared among 5 groups using competing risks analysis, with death as a competing event. We included 1751 patients with severe AS from 2013 to 2018 followed for a median 2.8 (interquartile range, 1.5-4.8) years. The more distressed ADI groups tended to be younger (P = 0.002), female (P < 0.001), and of African American race (P < 0.001), have higher presentation of sepsis (P = 0.031), arrhythmia (P = 0.022), less likely to have previous diagnosis of AS (P < 0.001); and were less likely to undergo AVR (52.5% vs 46.9% vs 46.1% vs 48.9% vs 39.7%, P = 0.023). Using competing risk analysis, the highest ADI group (E) were the least and the lowest ADI group (A) the most likely to undergo AVR (Gray's test, P = 0.025). The association between ADI ranking and AVR rates was influenced by sex and race. Within group analysis, there was significant association between race and AVR (Gray's test, P < 0.001), and between sex and AVR (Gray's test, P < 0.001). Patients with severe AS living in more deprived neighborhoods were less likely to undergo aortic valve interventions, which was influenced by female gender, and African American race.

In chronic kidney disease altered cardiac metabolism precedes cardiac hypertrophy.

Conduit arterial disease in chronic kidney disease (CKD) is an important cause of cardiac complications. Cardiac function in CKD has not been studied in the absence of arterial disease. In an Alport syndrome model bred not to have conduit arterial disease, mice at 225 days of life (dol) had CKD equivalent to humans with CKD stage 4-5. Parathyroid hormone (PTH) and FGF23 levels were one log order elevated, circulating sclerostin was elevated, and renal activin A was strongly induced. Aortic Ca levels were not increased, and vascular smooth muscle cell (VSMC) transdifferentiation was absent. The CKD mice were not hypertensive, and cardiac hypertrophy was absent. Freshly excised cardiac tissue respirometry (Oroboros) showed that ADP-stimulated O2 flux was diminished from 52 to 22 pmol/mg (P = 0.022). RNA-Seq of cardiac tissue from CKD mice revealed significantly decreased levels of cardiac mitochondrial oxidative phosphorylation genes. To examine the effect of activin A signaling, some Alport mice were treated with a monoclonal Ab to activin A or an isotype-matched IgG beginning at 75 days of life until euthanasia. Treatment with the activin A antibody (Ab) did not affect cardiac oxidative phosphorylation. However, the activin A antibody was active in the skeleton, disrupting the effect of CKD to stimulate osteoclast number, eroded surfaces, and the stimulation of osteoclast-driven remodeling. The data reported here show that cardiac mitochondrial respiration is impaired in CKD in the absence of conduit arterial disease. This is the first report of the direct effect of CKD on cardiac respiration.NEW & NOTEWORTHY Heart disease is an important morbidity of chronic kidney disease (CKD). Hypertension, vascular stiffness, and vascular calcification all contribute to cardiac pathophysiology. However, cardiac function in CKD devoid of vascular disease has not been studied. Here, in an animal model of human CKD without conduit arterial disease, we analyze cardiac respiration and discover that CKD directly impairs cardiac mitochondrial function by decreasing oxidative phosphorylation. Protection of cardiac oxidative phosphorylation may be a therapeutic target in CKD.

Examining household effects on individual Twitter adoption: A multilevel analysis based on U.K. household survey data.

Previous studies mainly focused on individual-level factors that influence the adoption and usage of mobile technology and social networking sites, with little emphasis paid to the influences of household situations. Using multilevel modelling approach, this study merges household- (n1 = 1,455) and individual-level (n2 = 2,570) data in the U.K. context to investigate (a) whether a household economic capital (HEC) can affect its members' Twitter adoption, (b) whether the influences are mediated by the member's activity variety and self-reported efficacy with mobile technology, and (c) whether the members' traits, including educational level, gross income and residential area, moderate the relationship between HEC and Twitter adoption. Significant direct and indirect associations were discovered between HEC and its members' Twitter adoption. The educational level and gross income of household members moderated the influence of HEC on individuals' Twitter adoption.

Glioblastoma and radiotherapy: A multicenter AI study for Survival Predictions from MRI (GRASP study).

BACKGROUND: The aim was to predict survival of glioblastoma at 8 months after radiotherapy (a period allowing for completing a typical course of adjuvant temozolomide), by applying deep learning to the first brain MRI after radiotherapy completion. METHODS: Retrospective and prospective data were collected from 206 consecutive glioblastoma, isocitrate dehydrogenase -wildtype patients diagnosed between March 2014 and February 2022 across 11 UK centers. Models were trained on 158 retrospective patients from 3 centers. Holdout test sets were retrospective (n = 19; internal validation), and prospective (n = 29; external validation from 8 distinct centers). Neural network branches for T2-weighted and contrast-enhanced T1-weighted inputs were concatenated to predict survival. A nonimaging branch (demographics/MGMT/treatment data) was also combined with the imaging model. We investigated the influence of individual MR sequences; nonimaging features; and weighted dense blocks pretrained for abnormality detection. RESULTS: The imaging model outperformed the nonimaging model in all test sets (area under the receiver-operating characteristic curve, AUC P = .038) and performed similarly to a combined imaging/nonimaging model (P > .05). Imaging, nonimaging, and combined models applied to amalgamated test sets gave AUCs of 0.93, 0.79, and 0.91. Initializing the imaging model with pretrained weights from 10 000s of brain MRIs improved performance considerably (amalgamated test sets without pretraining 0.64; P = .003). CONCLUSIONS: A deep learning model using MRI images after radiotherapy reliably and accurately determined survival of glioblastoma. The model serves as a prognostic biomarker identifying patients who will not survive beyond a typical course of adjuvant temozolomide, thereby stratifying patients into those who might require early second-line or clinical trial treatment.

Effector-Phase IL-2 Signals Drive Th1 Effector and Memory Responses Dependently and Independently of TCF-1.

Following viral infection, CD4+ T cell differentiation is tightly regulated by cytokines and TCR signals. Although most activated CD4+ T cells express IL-2Rα after lymphocytic choriomeningtis virus infection, by day 3 postinfection, only half of activated T cells maintain expression. IL-2Rα at this time point distinguishes precursors for terminally differentiated Th1 cells (IL-2Rαhi) from precursors for Tfh cells and memory T cells (IL-2Rαlo) and is linked to strong TCR signals. In this study, we test whether TCR-dependent IL-2 links the TCR to CD4+ T cell differentiation. We employ a mixture of anti-IL-2 Abs to neutralize IL-2 throughout the primary CD4+ T cell response to lymphocytic choriomeningitis virus infection in mice or only after the establishment of lineage-committed effector cells (day 3 postinfection). We report that IL-2 signals drive the formation of Th1 precursor cells in the early stages of the immune response and sustain Th1 responses during its later stages (after day 3). Effector-stage IL-2 also shapes the composition and function of resulting CD4+ memory T cells. Although IL-2 has been shown previously to drive Th1 differentiation by reducing the activity of the transcriptional repressor TCF-1, we found that sustained IL-2 signals were still required to drive optimal Th1 differentiation even in the absence of TCF-1. Therefore, we concluded that IL-2 plays a central role throughout the effector phase in regulating the balance between Th1 and Tfh effector and memory cells via mechanisms that are both dependent and independent of its role in modulating TCF-1 activity.

Preleukemic single-cell landscapes reveal mutation-specific mechanisms and gene programs predictive of AML patient outcomes.

Acute myeloid leukemia (AML) and myeloid neoplasms develop through acquisition of somatic mutations that confer mutation-specific fitness advantages to hematopoietic stem and progenitor cells. However, our understanding of mutational effects remains limited to the resolution attainable within immunophenotypically and clinically accessible bulk cell populations. To decipher heterogeneous cellular fitness to preleukemic mutational perturbations, we performed single-cell RNA sequencing of eight different mouse models with driver mutations of myeloid malignancies, generating 269,048 single-cell profiles. Our analysis infers mutation-driven perturbations in cell abundance, cellular lineage fate, cellular metabolism, and gene expression at the continuous resolution, pinpointing cell populations with transcriptional alterations associated with differentiation bias. We further develop an 11-gene scoring system (Stem11) on the basis of preleukemic transcriptional signatures that predicts AML patient outcomes. Our results demonstrate that a single-cell-resolution deep characterization of preleukemic biology has the potential to enhance our understanding of AML heterogeneity and inform more effective risk stratification strategies.