Gene selection for optimal prediction of cell position in tissues from single-cell transcriptomics data.

Single-cell RNA-sequencing (scRNAseq) technologies are rapidly evolving. Although very informative, in standard scRNAseq experiments, the spatial organization of the cells in the tissue of origin is lost. Conversely, spatial RNA-seq technologies designed to maintain cell localization have limited throughput and gene coverage. Mapping scRNAseq to genes with spatial information increases coverage while providing spatial location. However, methods to perform such mapping have not yet been benchmarked. To fill this gap, we organized the DREAM Single-Cell Transcriptomics challenge focused on the spatial reconstruction of cells from the Drosophila embryo from scRNAseq data, leveraging as silver standard, genes with in situ hybridization data from the Berkeley Drosophila Transcription Network Project reference atlas. The 34 participating teams used diverse algorithms for gene selection and location prediction, while being able to correctly localize clusters of cells. Selection of predictor genes was essential for this task. Predictor genes showed a relatively high expression entropy, high spatial clustering and included prominent developmental genes such as gap and pair-rule genes and tissue markers. Application of the top 10 methods to a zebra fish embryo dataset yielded similar performance and statistical properties of the selected genes than in the Drosophila data. This suggests that methods developed in this challenge are able to extract generalizable properties of genes that are useful to accurately reconstruct the spatial arrangement of cells in tissues

Informal caregiver burden in middle-income countries Results from Memory Centers in Lima - Peru

Objective: The aim of this study was to evaluate caregiver burden based on Zarit Burden Interview (ZBI) and depression in caregivers on the Beck Depression Inventory-II (BDI-II). Methods: Literate individuals, 18 years or older, who spoke Spanish as their native language were included. Demographic characteristics: Age, sex, education, relationship to person with dementia, length of time caregiving, other sources of help for caring, impact on the household economy, family support, and perception of impaired health; and Clinical data on care-recipients: type of dementia, time since diagnosis, treatment, and Global Deterioration Scale (GDS); the ZBI and BDI-II. Descriptive and analytical statistics were employed to assess caregiver burden and predictors of higher burden in caregivers. Results: A total of 92 informal caregivers were evaluated. Regarding care-recipients, 75% were 69 years old or over, 75% had at least one year since diagnosis, 73.9% had Alzheimer’s disease, 84.8% received treatment, 75% scored 5 or over on the GDS. For caregivers, 75% were 55.5 years old or over, predominantly female (81.5%), married (83.7%), the spouse of care-recipients (60.87%), had at least 10 years of education (75.0%) and one year of caregiving (75%), reduced entertainment time (90.2%) and self-perception of impaired health (83.7%). Median score on the ZBI was 37.5 (minimum value = 3; and maximum value = 74). The coefficient of BDI was 1.38 (p-value <0.001). Conclusion: This sample of Peruvian informal caregivers showed elevated ZBI values. Self-perception of worsened health, repercussion on the family economy and time caregiving were the main determinants of ZBI, although only BDI was a consistent predictor of ZBI

Morphogenetic defects underlie Superior Coloboma, a newly identified closure disorder of the dorsal eye

<div><p>The eye primordium arises as a lateral outgrowth of the forebrain, with a transient fissure on the inferior side of the optic cup providing an entry point for developing blood vessels. Incomplete closure of the inferior ocular fissure results in coloboma, a disease characterized by gaps in the inferior eye and recognized as a significant cause of pediatric blindness. Here, we identify eight patients with defects in tissues of the superior eye, a congenital disorder that we term <i>superior coloboma</i>. The embryonic origin of superior coloboma could not be explained by conventional models of eye development, leading us to reanalyze morphogenesis of the dorsal eye. Our studies revealed the presence of the <i>superior ocular sulcus</i> (SOS), a transient division of the dorsal eye conserved across fish, chick, and mouse. Exome sequencing of superior coloboma patients identified rare variants in a Bone Morphogenetic Protein (Bmp) receptor (<i>BMPR1A</i>) and T-box transcription factor (<i>TBX2</i>). Consistent with this, we find sulcus closure defects in zebrafish lacking Bmp signaling or Tbx2b. In addition, loss of dorsal ocular Bmp is rescued by concomitant suppression of the ventral-specific Hedgehog pathway, arguing that sulcus closure is dependent on dorsal-ventral eye patterning cues. The superior ocular sulcus acts as a conduit for blood vessels, with altered sulcus closure resulting in inappropriate connections between the hyaloid and superficial vascular systems. Together, our findings explain the existence of superior coloboma, a congenital ocular anomaly resulting from aberrant morphogenesis of a developmental structure.</p></div

clonealign: statistical integration of independent single-cell RNA and DNA sequencing data from human cancers

Measuring gene expression of tumor clones at single-cell resolution links functional consequences to somatic alterations. Without scalable methods to simultaneously assay DNA and RNA from the same single cell, parallel single-cell DNA and RNA measurements from independent cell populations must be mapped for genome-transcriptome association. We present clonealign, which assigns gene expression states to cancer clones using single-cell RNA and DNA sequencing independently sampled from a heterogeneous population. We apply clonealign to triple-negative breast cancer patient-derived xenografts and high-grade serous ovarian cancer cell lines and discover clone-specific dysregulated biological pathways not visible using either sequencing method alone.Graduate and Postdoctoral StudiesMedicine, Faculty ofScience, Faculty ofOther UBCNon UBCPathology and Laboratory Medicine, Department ofStatistics, Department ofReviewedFacult

Additional file 1 of clonealign: statistical integration of independent single-cell RNA and DNA sequencing data from human cancers

Supplementary text. (PDF 108 kb

Additional file 2 of clonealign: statistical integration of independent single-cell RNA and DNA sequencing data from human cancers

Supplementary figures. (PDF 6381 kb

Diabetes management mediating effects between diabetes symptoms and health-related quality of life in adolescents and young adults with type 1 diabetes

The primary objective was to investigate the mediating effects of diabetes management in the relationship between diabetes symptoms and generic health-related quality of life (HRQOL) in adolescents and young adults (AYAs) with type 1 diabetes. The secondary objective explored patient health communication and perceived treatment adherence barriers as mediators in a serial multiple mediator model. The PedsQL 3.2 Diabetes Module 15-item diabetes symptoms summary score, 18-item diabetes management summary score, and PedsQL 4.0 generic core scales were completed in a 10-site national field test study by 418 AYA aged 13 to 25 years with type 1 diabetes. Diabetes symptoms and diabetes management were tested for bivariate and multivariate linear associations with overall generic HRQOL. Mediational analyses were conducted to test the hypothesized mediating effects of diabetes management as an intervening variable between diabetes symptoms and generic HRQOL. The predictive effects of diabetes symptoms on HRQOL were mediated in part by diabetes management. In predictive analytics models utilizing multiple regression analyses, demographic and clinical covariates, diabetes symptoms, and diabetes management significantly accounted for 53% of the variance in generic HRQOL (P < 0.001), demonstrating a large effect size. Patient health communication and perceived treatment adherence barriers were significant mediators in an exploratory serial multiple mediator model. Diabetes management explains in part the effects of diabetes symptoms on HRQOL in AYA with type 1 diabetes. Patient health communication to healthcare providers and perceived treatment adherence barriers further explain the mechanism in the relationship between diabetes symptoms and overall HRQOL

Diabetes management mediating effects between diabetes symptoms and health‐related quality of life in adolescents and young adults with type 1 diabetes

ObjectivesThe primary objective was to investigate the mediating effects of diabetes management in the relationship between diabetes symptoms and generic health-related quality of life (HRQOL) in adolescents and young adults (AYAs) with type 1 diabetes. The secondary objective explored patient health communication and perceived treatment adherence barriers as mediators in a serial multiple mediator model.MethodsThe PedsQL 3.2 Diabetes Module 15-item diabetes symptoms summary score, 18-item diabetes management summary score, and PedsQL 4.0 generic core scales were completed in a 10-site national field test study by 418 AYA aged 13 to 25 years with type 1 diabetes. Diabetes symptoms and diabetes management were tested for bivariate and multivariate linear associations with overall generic HRQOL. Mediational analyses were conducted to test the hypothesized mediating effects of diabetes management as an intervening variable between diabetes symptoms and generic HRQOL.ResultsThe predictive effects of diabetes symptoms on HRQOL were mediated in part by diabetes management. In predictive analytics models utilizing multiple regression analyses, demographic and clinical covariates, diabetes symptoms, and diabetes management significantly accounted for 53% of the variance in generic HRQOL (P &lt; 0.001), demonstrating a large effect size. Patient health communication and perceived treatment adherence barriers were significant mediators in an exploratory serial multiple mediator model.ConclusionsDiabetes management explains in part the effects of diabetes symptoms on HRQOL in AYA with type 1 diabetes. Patient health communication to healthcare providers and perceived treatment adherence barriers further explain the mechanism in the relationship between diabetes symptoms and overall HRQOL