Analysis of structural variation among inbred mouse strains.

BACKGROUND: 'Long read' sequencing methods have been used to identify previously uncharacterized structural variants that cause human genetic diseases. Therefore, we investigated whether long read sequencing could facilitate genetic analysis of murine models for human diseases. RESULTS: The genomes of six inbred strains (BTBR T + Itpr3tf/J, 129Sv1/J, C57BL/6/J, Balb/c/J, A/J, SJL/J) were analyzed using long read sequencing. Our results revealed that (i) Structural variants are very abundant within the genome of inbred strains (4.8 per gene) and (ii) that we cannot accurately infer whether structural variants are present using conventional short read genomic sequence data, even when nearby SNP alleles are known. The advantage of having a more complete map was demonstrated by analyzing the genomic sequence of BTBR mice. Based upon this analysis, knockin mice were generated and used to characterize a BTBR-unique 8-bp deletion within Draxin that contributes to the BTBR neuroanatomic abnormalities, which resemble human autism spectrum disorder. CONCLUSION: A more complete map of the pattern of genetic variation among inbred strains, which is produced by long read genomic sequencing of the genomes of additional inbred strains, could facilitate genetic discovery when murine models of human diseases are analyzed.

Transcription factor expression defines subclasses of developing projection neurons highly similar to single-cell RNA-seq subtypes.

We are only just beginning to catalog the vast diversity of cell types in the cerebral cortex. Such categorization is a first step toward understanding how diversification relates to function. All cortical projection neurons arise from a uniform pool of progenitor cells that lines the ventricles of the forebrain. It is still unclear how these progenitor cells generate the more than 50 unique types of mature cortical projection neurons defined by their distinct gene-expression profiles. Moreover, exactly how and when neurons diversify their function during development is unknown. Here we relate gene expression and chromatin accessibility of two subclasses of projection neurons with divergent morphological and functional features as they develop in the mouse brain between embryonic day 13 and postnatal day 5 in order to identify transcriptional networks that diversify neuron cell fate. We compare these gene-expression profiles with published profiles of single cells isolated from similar populations and establish that layer-defined cell classes encompass cell subtypes and developmental trajectories identified using single-cell sequencing. Given the depth of our sequencing, we identify groups of transcription factors with particularly dense subclass-specific regulation and subclass-enriched transcription factor binding motifs. We also describe transcription factor-adjacent long noncoding RNAs that define each subclass and validate the function of Myt1l in balancing the ratio of the two subclasses in vitro. Our multidimensional approach supports an evolving model of progressive restriction of cell fate competence through inherited transcriptional identities.

InpherNet accelerates monogenic disease diagnosis using patients' candidate genes' neighbors.

PURPOSE: Roughly 70% of suspected Mendelian disease patients remain undiagnosed after genome sequencing, partly because knowledge about pathogenic genes is incomplete and constantly growing. Generating a novel pathogenic gene hypothesis from patient data can be time-consuming especially where cohort-based analysis is not available. METHODS: Each patient genome contains dozens to hundreds of candidate variants. Many sources of indirect evidence about each candidate may be considered. We introduce InpherNet, a network-based machine learning approach leveraging Monarch Initiative data to accelerate this process. RESULTS: InpherNet ranks candidate genes based on orthologs, paralogs, functional pathway members, and colocalized interaction partner gene neighbors. It can propose novel pathogenic genes and reveal known pathogenic genes whose diagnosed patient-based annotation is missing or partial. InpherNet is applied to patient cases where the causative gene is incorrectly ranked low by clinical gene-ranking methods that use only patient-derived evidence. InpherNet correctly ranks the causative gene top 1 or top 1-5 in roughly twice as many cases as seven comparable tools, including in cases where no clinical evidence for the diagnostic gene is in our knowledgebase. CONCLUSION: InpherNet improves the state of the art in considering candidate gene neighbors to accelerate monogenic diagnosis.

Genome-wide profiling of 24 hr diel rhythmicity in the water flea, Daphnia pulex: network analysis reveals rhythmic gene expression and enhances functional gene annotation.

BACKGROUND: Marine and freshwater zooplankton exhibit daily rhythmic patterns of behavior and physiology which may be regulated directly by the light:dark (LD) cycle and/or a molecular circadian clock. One of the best-studied zooplankton taxa, the freshwater crustacean Daphnia, has a 24 h diel vertical migration (DVM) behavior whereby the organism travels up and down through the water column daily. DVM plays a critical role in resource tracking and the behavioral avoidance of predators and damaging ultraviolet radiation. However, there is little information at the transcriptional level linking the expression patterns of genes to the rhythmic physiology/behavior of Daphnia. RESULTS: Here we analyzed genome-wide temporal transcriptional patterns from Daphnia pulex collected over a 44 h time period under a 12:12 LD cycle (diel) conditions using a cosine-fitting algorithm. We used a comprehensive network modeling and analysis approach to identify novel co-regulated rhythmic genes that have similar network topological properties and functional annotations as rhythmic genes identified by the cosine-fitting analyses. Furthermore, we used the network approach to predict with high accuracy novel gene-function associations, thus enhancing current functional annotations available for genes in this ecologically relevant model species. Our results reveal that genes in many functional groupings exhibit 24 h rhythms in their expression patterns under diel conditions. We highlight the rhythmic expression of immunity, oxidative detoxification, and sensory process genes. We discuss differences in the chronobiology of D. pulex from other well-characterized terrestrial arthropods. CONCLUSIONS: This research adds to a growing body of literature suggesting the genetic mechanisms governing rhythmicity in crustaceans may be divergent from other arthropod lineages including insects. Lastly, these results highlight the power of using a network analysis approach to identify differential gene expression and provide novel functional annotation.

Five-Year Community Management Rate for Dementia Patients: A Proposed Indicator for Dementia Policies.

BACKGROUND AND PURPOSE: There is no specific indicator for monitoring dementia management. We propose an auxiliary indicator called the community management rate, defined as the proportion of dementia patients who receive informal care from close caregivers or themselves within their community population. The 5-year community management rate is the percentage of dementia patients who are receiving community management at 5 years after they were diagnosed. The aim of this study was to identify how the community management rate has changed over time and how the 5-year community management rate differs according to age, sex, income, residence area, and comorbidities. METHODS: We analyzed customized research database of the Korean National Health Insurance Services from 2003 to 2018. The 5-year community management rate was calculated annually with newly diagnosed dementia patients, and compared among subgroups according to age, sex, income, residence area, and comorbidities. RESULTS: This study analyzed 549,297 patients. Among those newly diagnosed with dementia in 2003, the mean duration of community management during the 15-year follow-up was 5.98 years. The community management rate decreased rapidly from 2003 to 2006, after which it increased. A low 5-year community management rate was associated with older age, higher comorbidity burden, nonmetropolitan residence, and low income. CONCLUSIONS: The community management rate seems to reflect diverse patient factors. Efforts are needed to reduce the comorbidity burden and differences in the 5-year community management rate according to residence area and income. This study indicates the need for further investigations into the use of this indicator to monitor the management of dementia patients.

The Effect of Population Structure on Murine Genome-Wide Association Studies.

The ability to use genome-wide association studies (GWAS) for genetic discovery depends upon our ability to distinguish true causative from false positive association signals. Population structure (PS) has been shown to cause false positive signals in GWAS. PS correction is routinely used for analysis of human GWAS results, and it has been assumed that it also should be utilized for murine GWAS using inbred strains. Nevertheless, there are fundamental differences between murine and human GWAS, and the impact of PS on murine GWAS results has not been carefully investigated. To assess the impact of PS on murine GWAS, we examined 8223 datasets that characterized biomedical responses in panels of inbred mouse strains. Rather than treat PS as a confounding variable, we examined it as a response variable. Surprisingly, we found that PS had a minimal impact on datasets measuring responses in ≤20 strains; and had surprisingly little impact on most datasets characterizing 21 - 40 inbred strains. Moreover, we show that true positive association signals arising from haplotype blocks, SNPs or indels, which were experimentally demonstrated to be causative for trait differences, would be rejected if PS correction were applied to them. Our results indicate because of the special conditions created by GWAS (the use of inbred strains, small sample sizes) PS assessment results should be carefully evaluated in conjunction with other criteria, when murine GWAS results are evaluated.

Wound-healing effects of human dermal components with gelatin dressing.

There have been numerous investigations regarding various types of dressings and artificial dermis of solid form, yet limited research and development on paste types, such as hydrogels with dermal powder, have ensued. In this study, we compared the in vivo wound healing effects of gelatin paste containing dermal powder to a collagen type I/chondroitin 6-sulfate (coll/chondroitin) sponge and gelatin alone, after 48 days post grafting, in a skin wound rat model. In the dermis powder/gelatin paste-treated group, wound area contraction was minimized 50%, while in the gelatin and coll/chondroitin sponge groups, the initial area contracted 83-85% and 79-85%, respectively. Histological analysis revealed the wounds treated with dermal powder/gelatin were associated with many fibroblasts, which infiltrated the wound bed, as well as thick collagen bundles that were arranged in dendritic arrays, resembling normal skin. Furthermore, in contrast to the gelatin- and coll/chondroitin sponge-treated groups, the powder/gelatin paste-treated wounds exhibited an abundance of elastic fibers (Victoria blue staining) and extensive formation of blood vessels around the dermis (CD31 staining). Therefore, the dermis powder/gelatin paste not only renders convenience to users but also has prominent wound-healing effects on full-thickness wounds.

Improving Identification of Key Players in Aging via Network De-Noising and Core Inference.

Current "ground truth" knowledge about human aging has been obtained by transferring aging-related knowledge from well-studied model species via sequence homology or by studying human gene expression data. Since proteins function by interacting with each other, analyzing protein-protein interaction (PPI) networks in the context of aging is promising. Unlike existing static network research of aging, since cellular functioning is dynamic, we recently integrated the static human PPI network with aging-related gene expression data to form dynamic, age-specific networks. Then, we predicted as key players in aging those proteins whose network topologies significantly changed with age. Since current networks are noisy , here, we use link prediction to de-noise the human network and predict improved key players in aging from the de-noised data. Indeed, de-noising gives more significant overlap between the predicted data and the "ground truth" aging-related data. Yet, we obtain novel predictions, which we validate in the literature. Also, we improve the predictions by an alternative strategy: removing "redundant" edges from the age-specific networks and using the resulting age-specific network "cores" to study aging. We produce new knowledge from dynamic networks encompassing multiple data types, via network de-noising or core inference, complementing the existing knowledge obtained from sequence or expression data.

Application of mesenchymal stem cells derived from bone marrow and umbilical cord in human hair multiplication.

BACKGROUND: The methods currently used for treating alopecia have some limitations. The drug treatment is so temporary that medication discontinuance may progress depilation immediately. The number of hair transplantation restricts because total transplantable hair number is no increase. To overcome these problems, researchers have attempted the in vitro culturing of hair follicle cells and implanting these cells in the treatment area. OBJECTIVES: In the present study, culture-expanded mesenchymal stem cells (MSCs) that do not possess aggregative activity were used to produce self-aggregated cell-aggregated spheroidal dermal papilla like tissues (DPLTs) with the aid of a special culture condition in vitro, and hair bulb structure inductive capacity pertinent to the aggregative activity was then evaluated. Then hair inducing activity of self-aggregated DPLTs employing MSCs was tested in athymic mice. METHODS: We isolated and cultivated MSCs from bone marrow and umbilical cord in vitro. After propagated MSCs underwent preconditioning in dermal papilla forming medium (DPFM), then subcultured MSCs formed self-aggregated DPLTs. We compared real human scalp dermal papilla cells (hDPCs) with DPLTs employing DPCs, DPLTs employing hBM-MSCs and DPLTs employing hUC-MSCs. RESULTS: Light microscopy and immunohistochemical staining were used to confirm that reconstructed DPLTs generated by this procedure had the size, shape, and expression of protein similar to actual DP. CONCLUSIONS: The DPLTs have the same hair bulb structure inductive ability as natural DPLTs in vitro. Transplanted DPLTs can induce new hair follicle in athymic mice. As a result, UC-MSCs and BM-MSCs may be an applicable and novel cell source for the generation of human hair cell therapy.