Dissecting cell identity via network inference and in silico gene perturbation

Cell identity is governed by the complex regulation of gene expression, represented as gene-regulatory network

Gene regulatory network reconfiguration in direct lineage reprogramming

In direct lineage conversion, transcription factor (TF) overexpression reconfigures gene regulatory networks (GRNs) to reprogram cell identity. We previously developed CellOracle, a computational method to infer GRNs from single-cell transcriptome and epigenome data. Using inferred GRNs, CellOracle simulates gene expression changes in response to TF perturbation, enabling in silico interrogation of network reconfiguration. Here, we combine CellOracle analysis with lineage tracing of fibroblast to induced endoderm progenitor (iEP) conversion, a prototypical direct reprogramming paradigm. By linking early network state to reprogramming outcome, we reveal distinct network configurations underlying successful and failed fate conversion. Via in silico simulation of TF perturbation, we identify new factors to coax cells into successfully converting their identity, uncovering a central role for the AP-1 subunit Fos with the Hippo signaling effector, Yap1. Together, these results demonstrate the efficacy of CellOracle to infer and interpret cell-type-specific GRN configurations, providing new mechanistic insights into lineage reprogramming

Transcriptional profiling reveals extraordinary diversity among skeletal muscle tissues

Skeletal muscle comprises a family of diverse tissues with highly specialized functions. Many acquired diseases, including HIV and COPD, affect specific muscles while sparing others. Even monogenic muscular dystrophies selectively affect certain muscle groups. These observations suggest that factors intrinsic to muscle tissues influence their resistance to disease. Nevertheless, most studies have not addressed transcriptional diversity among skeletal muscles. Here we use RNAseq to profile mRNA expression in skeletal, smooth, and cardiac muscle tissues from mice and rats. Our data set, MuscleDB, reveals extensive transcriptional diversity, with greater than 50% of transcripts differentially expressed among skeletal muscle tissues. We detect mRNA expression of hundreds of putative myokines that may underlie the endocrine functions of skeletal muscle. We identify candidate genes that may drive tissue specialization, including Smarca4, Vegfa, and Myostatin. By demonstrating the intrinsic diversity of skeletal muscles, these data provide a resource for studying the mechanisms of tissue specialization

Basal epithelial stem cells cross an alarmin checkpoint for postviral lung disease

Epithelial cells are charged with protection at barrier sites, but whether this normally beneficial response might sometimes become dysfunctional still needs definition. Here, we recognized a pattern of imbalance marked by basal epithelial cell growth and differentiation that replaced normal airspaces in a mouse model of progressive postviral lung disease due to the Sendai virus. Single-cell and lineage-tracing technologies identified a distinct subset of basal epithelial stem cells (basal ESCs) that extended into gas-exchange tissue to form long-term bronchiolar-alveolar remodeling regions. Moreover, this cell subset was selectively expanded by crossing a cell-growth and survival checkpoint linked to the nuclear-localized alarmin IL-33 that was independent of IL-33 receptor signaling and instead connected to autocrine chromatin accessibility. This mechanism creates an activated stem-progenitor cell lineage with potential for physiological or pathological function. Thus, conditional loss of Il33 gene function in basal epithelial cells disrupted the homeostasis of the epithelial barrier at skin and gut sites but also markedly attenuated postviral disease in the lung based on the downregulation of remodeling and inflammation. Thus, we define a basal ESC strategy to deploy innate immune machinery that appears to overshoot the primordial goal of self-defense. Our findings reveal new targets to stratify and correct chronic and often deadly postviral disease

Therapy interventions for children with neurodisability : a qualitative scoping study of current practice and perceived research needs.

Background: Therapy interventions emerged four times in the top 10 research priorities in a James Lind Alliance research prioritisation exercise for children with neurodisabilities (Morris C, Simkiss D, Busk M, Morris M, Allard A, Denness J, et al. Setting research priorities to improve the health of children and young people with neurodisability: a British Academy of Childhood Disability-James Lind Alliance Research Priority Setting Partnership. BMJ Open 2015;5:e006233). The National Institute for Health Research (NIHR) commissioned this study as part of an information-gathering exercise in response to this. Objectives: The objectives were to (1) describe the current practice, approaches and schools of thought in relation to physiotherapy, occupational therapy and speech and language therapy for children with neurodisability; (2) explore clinical decision-making; (3) investigate views on outcomes and their measurement, particularly participation as an outcome, that is, the child’s ability to have the opportunity to be involved in life situations and activities (e.g. communication, mobility, interpersonal interactions, self-care, learning and applying knowledge); (4) seek views on the aspects of therapy interventions that have an impact on outcomes; and (5) elicit stakeholder views on research needs and priorities. Design, setting and participants: More than 70 professionals (therapists, service leads, paediatricians and education staff) and 25 parents participated in a qualitative interview (either individually or as part of a focus group). Results: Professional thinking and models of service delivery are in a state of flux and development. There is a move towards goals-focused, family-centred approaches. Work tends to be highly individualised, with few protocols. Parents are certain of the value of therapies, although they may experience difficulties with provision and may seek (additional) private provision. Therapy interventions are conceived as three components: the therapist, the procedures/equipment, etc., and the wider therapeutic environment. They are believed to be highly complex and poorly understood. Although participation is widely endorsed as a core intervention objective of therapy interventions, its suitability, or appropriateness, as an outcome measure was questioned. Other child and/or parent outcomes were identified as more or equally important. Notions of intermediate outcomes – in terms of body structure/function, and the achievement of activities – were regarded as important and not counter to participation-focused approaches. Among therapists, research on intervention effectiveness was (cautiously) welcomed. A number of methodological challenges were identified. A portfolio of study designs – quantitative and qualitative, experimental and observational – was called for, and which included economic evaluation and clear pathways to impact. Limitations: The study was not successful in recruiting children and young people. Further work is required to elucidate the views of this key stakeholder group. Conclusions: Therapy interventions are poorly understood. There was strong support, tempered a little by concerns among some about the feasibility of demonstrating impact, for investment in research

All-particle cosmic ray energy spectrum measured with 26 IceTop stations

We report on a measurement of the cosmic ray energy spectrum with the IceTop air shower array, the surface component of the IceCube Neutrino Observatory at the South Pole. The data used in this analysis were taken between June and October, 2007, with 26 surface stations operational at that time, corresponding to about one third of the final array. The fiducial area used in this analysis was 0.122 km^2. The analysis investigated the energy spectrum from 1 to 100 PeV measured for three different zenith angle ranges between 0{\deg} and 46{\deg}. Because of the isotropy of cosmic rays in this energy range the spectra from all zenith angle intervals have to agree. The cosmic-ray energy spectrum was determined under different assumptions on the primary mass composition. Good agreement of spectra in the three zenith angle ranges was found for the assumption of pure proton and a simple two-component model. For zenith angles {\theta} < 30{\deg}, where the mass dependence is smallest, the knee in the cosmic ray energy spectrum was observed between 3.5 and 4.32 PeV, depending on composition assumption. Spectral indices above the knee range from -3.08 to -3.11 depending on primary mass composition assumption. Moreover, an indication of a flattening of the spectrum above 22 PeV were observed.Comment: 38 pages, 17 figure

An improved method for measuring muon energy using the truncated mean of dE/dx

The measurement of muon energy is critical for many analyses in large Cherenkov detectors, particularly those that involve separating extraterrestrial neutrinos from the atmospheric neutrino background. Muon energy has traditionally been determined by measuring the specific energy loss (dE/dx) along the muon's path and relating the dE/dx to the muon energy. Because high-energy muons (E_mu > 1 TeV) lose energy randomly, the spread in dE/dx values is quite large, leading to a typical energy resolution of 0.29 in log10(E_mu) for a muon observed over a 1 km path length in the IceCube detector. In this paper, we present an improved method that uses a truncated mean and other techniques to determine the muon energy. The muon track is divided into separate segments with individual dE/dx values. The elimination of segments with the highest dE/dx results in an overall dE/dx that is more closely correlated to the muon energy. This method results in an energy resolution of 0.22 in log10(E_mu), which gives a 26% improvement. This technique is applicable to any large water or ice detector and potentially to large scintillator or liquid argon detectors.Comment: 12 pages, 16 figure