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Abstract The hematopoietic stem cell (HSC) niche has been extensively studied in bone marrow, yet a more systematic investigation into the microenvironment regulation of hematopoiesis in fetal liver is necessary. Here we investigate the spatial organization and transcriptional profile of individual cells in both wild type (WT) and Tet2 −/− fetal livers, by multiplexed error robust fluorescence in situ hybridization. We find that specific pairs of fetal liver cell types are preferentially positioned next to each other. Ligand-receptor signaling molecule pairs such as Kitl and Kit are enriched in neighboring cell types. The majority of HSCs are in direct contact with endothelial cells (ECs) in both WT and Tet2 −/− fetal livers. Loss of Tet2 increases the number of HSCs, and upregulates Wnt and Notch signaling genes in the HSC niche. Two subtypes of ECs, arterial ECs and sinusoidal ECs, and other cell types contribute distinct signaling molecules to the HSC niche. Collectively, this study provides a comprehensive picture and bioinformatic foundation for HSC spatial regulation in fetal liver.

Chronic myeloid leukemia (CML) is a myeloproliferative disease characterized by a unique BCR-ABL fusion gene. Tyrosine kinase inhibitors (TKIs) were developed to target the BCR-ABL oncoprotein, inhibiting its abnormal kinase activity. TKI treatments have significantly improved CML patient outcomes. However, the patients can develop drug resistance and relapse after therapy discontinues largely due to intratumor heterogeneity. It is critical to understand the differences in therapeutic responses among subpopulations of cells. Single-cell RNA sequencing measures the transcriptome of individual cells, allowing us to differentiate and analyze individual cell populations. Here, we integrated a single-cell RNA sequencing profile of CML stem cells and network analysis to decipher the mechanisms of distinct TKI responses. Compared to normal hematopoietic stem cells, a set of genes that were concordantly differentially expressed in various types of stem cells of CML patients was revealed. Further transcription regulatory network analysis found that most of these genes were directly controlled by one or more transcript factors and the genes have more regulators in the cells of the patients who responded to the treatment. The molecular markers including a known drug-resistance gene and novel gene signatures for treatment response were also identified. Moreover, we combined protein–protein interaction network construction with a cancer drug database and uncovered the drugs that target the marker genes directly or indirectly via the protein interactions. The gene signatures and their interacted proteins identified by this work can be used for treatment response prediction and lead to new strategies for drug resistance monitoring and prevention. Our single-cell-based findings offered novel insights into the mechanisms underlying the therapeutic response of CML.

Telomere length maintenance is essential for cell proliferation, which is particularly prominent in cancer. We validate that the primary colorectal tumors exhibit heterogeneous telomere lengths but mostly (90%) short telomeres relative to normal tissues. Intriguingly, relatively short telomeres are associated with tumor malignancy as indicated by poorly differentiated state, and these tumors contain more cancer stem-like cells (CSLCs) identified by several commonly used markers CD44, EPHB2 or LGR5. Moreover, promyelocytic leukemia (PML) and ALT-associated PML nuclear bodies (APBs) are frequently found in tumors with short telomeres and high proliferation. In contrast, distant normal tissues rarely or only minimally express PML. Inhibition of PML and APBs by an ATR inhibitor decreases proliferation of CSLCs and organoids, suggesting a potential therapeutic target to progressive colorectal tumors. Together, telomere maintenance underling tumor progression is connected with CSLCs.

Copy number variants in the human genome (CNVs) are associated with neurodevelopmental and psychiatric disorders such as schizophrenia and autism. Here the authors investigate how the large deletion CNV on chromosome 22q11.2 alters chromatin organization.

Abstract Cancer stem cells (CSCs) presumably contribute to tumor progression and drug resistance, yet their definitive features have remained elusive. Here, simultaneous measurement of telomere length and transcriptome in the same cells enables systematic assessment of CSCs in primary colorectal cancer (CRC). The in‐depth transcriptome profiled by SMART‐seq2 is independently validated by high‐throughput scRNA‐seq using 10 × Genomics. It is found that rare CSCs exist in dormant state and display plasticity toward cancer epithelial cells (EPCs) that essentially are presumptive tumor‐initiating cells (TICs), while both retaining the prominent signaling pathways including WNT, TGF‐β, and HIPPO/YAP. Moreover, CSCs exhibit chromosome copy number variation (CNV) pattern resembling cancer EPCs but distinct from normal stem cells, suggesting the phylogenetic relationship between CSCs and cancer EPCs. Notably, CSCs maintain shorter telomeres and possess minimal telomerase activity consistent with their nonproliferative nature, unlike cancer EPCs. Additionally, the specific signature of CSCs particularly NOTUM, SMOC2, BAMBI, PHLDA1, and TNFRSF19 correlates with the prognosis of CRC. These findings characterize the heterogeneity of CSCs and their linkage to cancer EPCs/TICs, some of which are conventionally regarded as CSCs.

A key aspect of achieving acceptable indoor air quality is source control. Cooking has been recognized as a significant source of pollutants for health impacts (e.g., PM2.5 and NO2) as well as moisture and odour. A common method of controlling this pollutant source is by using a range (or cooker) hood that vents to outside. However, field and laboratory experiments have shown highly variable performance for these devices. We use the capture efficiency metric (the fraction of the pollutants that are exhausted to outside at steady state) to characterize the range hood performance. To address this issue and provide useful information for builders, contractors, designers and home occupants, a laboratory rating method for range hood capture efficiency has recently been developed by LBNL and ASTM. The test method uses standardized emitters to create a heated plume and seed it with tracer gas. The tracer gas measurements in the room, the range hood exhaust and in the ambient air are used to estimate capture efficiency. However, this test method only applies to wall-mounted range hoods. Some range hoods are not wall-mounted: island range hoods are designed to operate over a cooktop in the middle of a room rather than against a wall and downdraft hoods draw air from near the cooktop rather than overhead. This paper discusses the development of a new test apparatus for island and downdraft hoods and presents measured capture efficiency data from example hoods. The results of this work will be used in future revisions to the ASTM standard.

Reprogramming to pluripotency after overexpression of OCT4, SOX2, KLF4, and MYC is accompanied by global genomic and epigenomic changes. Histone modification and DNA methylation states in induced pluripotent stem cells (iPSCs) have been shown to be highly similar to embryonic stem cells (ESCs). However, epigenetic differences still exist between iPSCs and ESCs. In particular, aberrant DNA methylation states found in iPSCs are a major concern when using iPSCs in a clinical setting. Thus, it is critical to find factors that regulate DNA methylation states in reprogramming. Here, we found that the miR-29 family is an important epigenetic regulator during human somatic cell reprogramming. Our global DNA methylation and hydroxymethylation analysis shows that DNA demethylation is a major event mediated by miR-29a depletion during early reprogramming, and that iPSCs derived from miR-29a depletion are epigenetically closer to ESCs. Our findings uncover an important miRNA-based approach to generate clinically robust iPSCs.

The interrogation of noncoding regions of the genome with CRISPR strategies requires dense and, ideally, inexpensive libraries to ensure coverage and customisation. Here the authors present 'Molecular Chipper' that uses fragmentation to generate guide RNAs from input DNA.

Single-cell RNA-Sequencing (scRNA-Seq) is a fast-evolving technology that enables the understanding of biological processes at an unprecedentedly high resolution. However, well-suited bioinformatics tools to analyze the data generated from this new technology are still lacking. Here we investigate the performance of non-negative matrix factorization (NMF) method to analyze a wide variety of scRNA-Seq datasets, ranging from mouse hematopoietic stem cells to human glioblastoma data. In comparison to other unsupervised clustering methods including K-means and hierarchical clustering, NMF has higher accuracy in separating similar groups in various datasets. We ranked genes by their importance scores (D-scores) in separating these groups, and discovered that NMF uniquely identifies genes expressed at intermediate levels as top-ranked genes. Finally, we show that in conjugation with the modularity detection method FEM, NMF reveals meaningful protein-protein interaction modules. In summary, we propose that NMF is a desirable method to analyze heterogeneous single-cell RNA-Seq data. The NMF based subpopulation detection package is available at: https://github.com/lanagarmire/NMFEM.

The sterol regulatory element-binding protein (SREBP) family member SREBP1 is a critical transcriptional regulator of cholesterol and fatty acid metabolism and has been implicated in insulin resistance, diabetes, and other diet-related diseases. We globally identified the promoters occupied by SREBP1 and its binding partners NFY and SP1 in a human hepatocyte cell line using chromatin immunoprecipitation combined with genome tiling arrays (ChIP-chip). We find that SREBP1 occupies the promoters of 1,141 target genes involved in diverse biological pathways, including novel targets with roles in lipid metabolism and insulin signaling. We also identify a conserved SREBP1 DNA-binding motif in SREBP1 target promoters, and we demonstrate that many SREBP1 target genes are transcriptionally activated by treatment with insulin and glucose using gene expression microarrays. Finally, we show that SREBP1 cooperates extensively with NFY and SP1 throughout the genome and that unique combinations of these factors target distinct functional pathways. Our results provide insight into the regulatory circuitry in which SREBP1 and its network partners coordinate a complex transcriptional response in the liver with cues from the diet.

A key aspect of achieving acceptable indoor air quality is source control. Cooking has been recognized as a significant source of pollutants for health impacts (e.g., PM2.5 and NO2) as well as moisture and odour. A common method of controlling this pollutant source is by using a range (or cooker) hood that vents to outside. However, field and laboratory experiments have shown highly variable performance for these devices. We use the capture efficiency metric (the fraction of the pollutants that are exhausted to outside at steady state) to characterize the range hood performance. To address this issue and provide useful information for builders, contractors, designers and home occupants, a laboratory rating method for range hood capture efficiency has recently been developed by LBNL and ASTM. The test method uses standardized emitters to create a heated plume and seed it with tracer gas. The tracer gas measurements in the room, the range hood exhaust and in the ambient air are used to estimate capture efficiency. However, this test method only applies to wall-mounted range hoods. Some range hoods are not wall-mounted: island range hoods are designed to operate over a cooktop in the middle of a room rather than against a wall and downdraft hoods draw air from near the cooktop rather than overhead. This paper discusses the development of a new test apparatus for island and downdraft hoods and presents measured capture efficiency data from example hoods. The results of this work will be used in future revisions to the ASTM standard.

ImportanceSexual dysfunction, an important determinant of women's health and quality of life, is commonly associated with declining estrogen levels around the menopausal transition.ObjectiveTo determine the effects of oral or transdermal estrogen therapy vs placebo on sexual function in postmenopausal women.Design, setting, and participantsAncillary study of the Kronos Early Estrogen Prevention Study (KEEPS), a 4-year prospective, randomized, double-blinded, placebo-controlled trial of menopausal hormone therapy in healthy, recently menopausal women. Of 727 KEEPS enrollees, 670 agreed to participate in this multicenter ancillary study. Women were 42 to 58 years old, within 36 months from last menstrual period. Data were collected from July 2005 through June 2008 and analyzed from July 2010 through June 2017.InterventionsWomen were randomized to either 0.45 mg/d oral conjugated equine estrogens (o-CEE), 50 µg/d transdermal 17β-estradiol (t-E2), or placebo. Participants also received 200 mg oral micronized progesterone (if randomized to o-CEE or t-E2) or placebo (if randomized to placebo estrogens) for 12 days each month.Main outcomes and measuresAspects of sexual function and experience (desire, arousal, lubrication, orgasm, satisfaction, and pain) were assessed using the Female Sexual Function Inventory (FSFI; range, 0-36 points; higher scores indicate better sexual function). Low sexual function (LSF) was defined as an FSFI overall score of less than 26.55. Distress related to low FSFI score (required for the diagnosis of sexual dysfunction) was not evaluated.ResultsThe 670 participants had a mean (SD) age of 52.7 (2.6) years. The t-E2 treatment was associated with a significant yet moderate improvement in the FSFI overall score across all time points compared with placebo (average efficacy, 2.6; 95% CI, 1.11-4.10; adjusted P = .002). With o-CEE treatment, there was no significant difference in FSFI overall score compared with placebo (mean efficacy, 1.4; 95% CI, -0.1 to 2.8; adjusted P = .13). There was no difference in FSFI overall score between the t-E2 and o-CEE groups on average across 48 months (adjusted P = .22). In the individual domains of sexual function, t-E2 treatment was associated with a significant increase in mean lubrication (0.61; 95% CI, 0.25-0.97; P = .001) and decreased pain (0.67; 95% CI, 0.25-1.09; P = .002) compared with placebo. Overall, the proportion of women with LSF was significantly lower after t-E2 treatment compared with placebo (67%; 95% CI, 55%-77% vs 76%; 95% CI, 67%-83%; P = .04). For o-CEE there was no significant reduction in the odds of LSF.Conclusions and relevanceTreatment with t-E2 modestly improved sexual function in early postmenopausal women, but whether it relieved symptoms of distress is not known.Trial registrationclinicaltrials.gov Identifier: NCT00154180.

In determining ventilation rates, it is often necessary to combine naturally-driven ventilation, such as infiltration, with mechanical systems. Modern calculation methods are sufficiently powerful that this can be done from first principles with time varying flows, but for some purposes simplified methods of combining the mechanical and natural ventilation are required—we call this “superposition”. An example of superposition would be ventilation standards that may pre-calculate some quantities within the body of the standard. When there are balanced mechanical systems, the solution is simple additivity, because a balanced system does not impact the internal pressure of the space. Unbalanced systems, however, change internal pressures and therefore can impact natural ventilation in such a way as to make it sub-additive. Several sub-additive superposition models are found in the literature. This paper presents the results of millions of hours of simulations of the physically correct solution, which span a broad range of climates, air leakage and structural conditions. This wide range of data allows for the comparison of three superposition models from the literature and eight new ones. The results show that by using the appropriate model(s) superposition errors can be reduced significantly, from the 20% over-prediction of simple linear addition to 1% or less.

© 2015 WCSS.Continuously growing incisors are common to all rodents, which include the Microtus genus of voles. However, unlike many rodents, voles also possess continuously growing molars. Here, we report spontaneous molar defects in a population of Prair

Aging and HIV are both risk factors for memory deficits and declines in real-world functioning. However, we know little about the profile of memory deficits driving instrumental activities of daily living (IADL) declines across the lifespan in HIV. This study examined 145 younger (

Predict (www.predict.nhs.uk) is an online, breast cancer prognostication and treatment benefit tool. The aim of this study was to incorporate the prognostic effect of HER2 status in a new version (Predict+), and to compare its performance with the original Predict and Adjuvant!. The prognostic effect of HER2 status was based on an analysis of data from 10 179 breast cancer patients from 14 studies in the Breast Cancer Association Consortium. The hazard ratio estimates were incorporated into Predict. The validation study was based on 1653 patients with early-stage invasive breast cancer identified from the British Columbia Breast Cancer Outcomes Unit. Predicted overall survival (OS) and breast cancer-specific survival (BCSS) for Predict+, Predict and Adjuvant! were compared with observed outcomes. All three models performed well for both OS and BCSS. Both Predict models provided better BCSS estimates than Adjuvant!. In the subset of patients with HER2-positive tumours, Predict+ performed substantially better than the other two models for both OS and BCSS. Predict+ is the first clinical breast cancer prognostication tool that includes tumour HER2 status. Use of the model might lead to more accurate absolute treatment benefit predictions for individual patients.

Introduction: Previous studies have demonstrated that common breast cancer susceptibility alleles are differentially associated with breast cancer risk for BRCA1 and/or BRCA2 mutation carriers. It is currently unknown how these alleles are associated with different breast cancer subtypes in BRCA1 and BRCA2 mutation carriers defined by estrogen (ER) or progesterone receptor (PR) status of the tumour.Methods: We used genotype data on up to 11,421 BRCA1 and 7,080 BRCA2 carriers, of whom 4,310 had been affected with breast cancer and had information on either ER or PR status of the tumour, to assess the associations of 12 loci with breast cancer tumour characteristics. Associations were evaluated using a retrospective cohort approach.Results: The results suggested stronger associations with ER-positive breast cancer than ER-negative for 11 loci in both BRCA1 and BRCA2 carriers. Among BRCA1 carriers, single nucleotide polymorphism (SNP) rs2981582 (FGFR2) exhibited the biggest difference based on ER status (per-allele hazard ratio (HR) for ER-positive = 1.35, 95% CI: 1.17 to 1.56 vs HR = 0.91, 95% CI: 0.85 to 0.98 for ER-negative, P-heterogeneity = 6.5 × 10-6). In contrast, SNP rs2046210 at 6q25.1 near ESR1 was primarily associated with ER-negative breast cancer risk for both BRCA1 and BRCA2 carriers. In BRCA2 carriers, SNPs in FGFR2, TOX3, LSP1, SLC4A7/NEK10, 5p12, 2q35, and 1p11.2 were significantly associated with ER-positive but not ER-negative disease. Similar results were observed when differentiating breast cancer cases by PR status.Conclusions: The associations of the 12 SNPs with risk for BRCA1 and BRCA2 carriers differ by ER-positive or ER-negative breast cancer status. The apparent differences in SNP associations between BRCA1 and BRCA2 carriers, and non-carriers, may be explicable by differences in the prevalence of tumour subtypes. As more risk modifying variants are identified, incorporating these associations into breast cancer subtype-specific risk models may improve clinical management for mutation carriers. © 2011 Mulligan et al.; licensee BioMed Central Ltd.

UnlabelledThe precision of Hologic Apex v2.0 analysis software is significantly improved from Hologic Delphi v11.2 software and is comparable to GE Lunar Prodigy v7.5 software. Apex and Delphi precisions were, respectively, 1.0% vs. 1.2% (L1-L4 spine), 1.l % vs. 1.3% (total femur), 1.6% vs. 1.9% (femoral neck), and 0.7% vs. 0.9% (dual total femur).IntroductionPrecision of bone mineral density (BMD) measurements by dual-energy X-ray absorptiometry (DXA) is known to vary by manufacturer, model, and technologist. This study evaluated the precision of three analysis versions: Apex v2.0 and Delphi v11.2 (Hologic, Inc.), and Prodigy v7.5 (GE Healthcare, Inc.) independent of technologist skill.MethodsDuplicate spine and dual hip scans on 90 women were acquired on both Delphi and Prodigy DXA systems at three clinics. BMD measures were converted to standardized BMD (sBMD) units. Precision errors were described as a root-mean-square (RMS) standard deviations and RMS percent coefficients of variation across the population.ResultsApex and Delphi values were highly correlated (r ranged from 0.90 to 0.99). Excluding the right neck, the Apex precision error was found to be 20% to 25% lower than the Delphi (spine: 1.0% versus 1.2% (p < 0.05), total hip: 1.1% versus 1.3% (p < 0.05), right neck: 2.3% versus 2.6% (p > 0.1)). No statistically significant differences were found in the precision error of the Apex and Prodigy (p > 0.05) except for the right neck (2.3% versus 1.8% respectively, p = 0.03).ConclusionThe Apex software has significantly lower precision error compared to Delphi software with similar mean values, and similar precision to that of the Prodigy.