Imputation of single-cell transcriptome data enables the reconstruction of networks predictive of breast cancer metastasis

Single-cell transcriptome data provide a unique opportunity to explore the gene networks of a particular cell type. However, insufficient capture rate and high dimensionality of single-cell RNA sequencing (scRNA-seq) data challenge cell-type-specific gene network (CGN) reconstruction. Here, we demonstrated that the imputation of scRNA-seq data enables reconstruction of CGNs by effective retrieval of gene functional associations. We reconstructed CGNs for seven primary and nine metastatic breast cancer cell lines using scRNA-seq data with imputation. Key genes for primary or metastatic cell lines were prioritized based on network centrality measures and CGN hub genes that were presumed to be the major determinant of cell type characteristics. To identify novel genes in breast cancer metastasis, we used the average rank difference of centrality between the primary and metastatic cell lines. Genes predicted using CGN centrality analysis were more enriched for known breast cancer metastatic genes than those predicted using differential expression. The molecular chaperone CCT2 was identified as a novel gene for breast metastasis during knockdown assays of several candidate genes. Overall, our study demonstrated an effective CGN reconstruction technique with imputation of scRNA-seq data and the feasibility of identifying key genes for particular cell subsets using single-cell network analysis.

Temporal dynamics of HCMV gene expression in lytic and latent infections

During productive human cytomegalovirus (HCMV) infection, viral genes are expressed in a coordinated cascade that conventionally relies on the dependencies of viral genes on protein synthesis and viral DNA replication. By contrast, the transcriptional landscape of HCMV latency is poorly understood. Here, we examine viral gene expression dynamics during the establishment of both productive and latent HCMV infections. We redefine HCMV gene expression kinetics during productive infection and reveal that viral gene regulation does not represent a simple sequential cascade; many viral genes are regulated by multiple independent modules. Using our improved gene expression classification combined with transcriptome-wide measurements of the effects of a wide array of epigenetic inhibitors on viral gene expression during latency, we show that a defining feature of latency is the unique repression of immediate-early (IE) genes. Altogether, we recharacterize HCMV gene expression kinetics and reveal governing principles of lytic and latent gene expression.

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Redefining HCMV gene expression cascade during productive infection

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Many viral genes are regulated by multiple independent modules

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Diverse inhibitors induce broad viral gene expression in monocytes

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In monocytes, immediate-early (IE) genes are repressed compared to all other HCMV genes

0894 A Two Item Questionnaire Reflecting Parental Concern As An Indicator Of The Severity Of Obstructive Sleep Apnea In Children

Introduction

The currently available questionnaires based on parental reporting of OSA symptoms include large number of items and are not sufficient to the diagnosis and assessment of OSA severity. We aimed to evaluate a simple 2-item questionnaire regarding parental concern as a predictor of the severity of OSA in children as measured by polysomnography.

Methods

Prospective analysis of parental concern regarding their children referred for PSG due to suspected OSA. Parents of all study children completed the brief Parental Concern Scale (PCS) questionnaire and the validated Pediatric Sleep Questionnaire-Sleep-Related Breathing Disorder questionnaire (PSQ-SRBD). The PCS consisted of 1 question on the need for surgery and 1 question on concerns about the child’s breathing.

Results

Ninety-five children (mean age 4.2 ± 2.5 years, 52% males, mean body mass index z score 0.45 ± 1.8) were recruited. Twenty-three children (24%) had moderate-severe OSA and were referred for adenotonsillectomy. Significant correlations were found between the need for surgery score and the apnea-hypopnea index (r=0.22, P = .029), as well as the mean SpO2 levels (r=-0.24, P = .02). The likelihood for the diagnosis of moderate-severe OSA by PSG increased as parental ranking for the need for surgery increased (P = .003). The need for surgery score and the child’s age were the only predictors for moderate-severe OSA (P = .01 and P = .043, respectively).

Conclusion

Querying parents on their perception of their child’s need for surgery is a sensitive, practical, and easy-to-use tool that can help the clinician in prioritizing referral to PSG.

Support

 

Single cell analysis reveals human cytomegalovirus drives latently infected cells towards an anergic-like monocyte state

Human cytomegalovirus (HCMV) causes a lifelong infection through establishment of latency. Although reactivation from latency can cause life-threatening disease, our molecular understanding of HCMV latency is incomplete. Here we use single cell RNA-seq analysis to characterize latency in monocytes and hematopoietic stem and progenitor cells (HSPCs). In monocytes, we identify host cell surface markers that enable enrichment of latent cells harboring higher viral transcript levels, which can reactivate more efficiently, and are characterized by reduced intrinsic immune response that is important for viral gene expression. Significantly, in latent HSPCs, viral transcripts could be detected only in monocyte progenitors and were also associated with reduced immune-response. Overall, our work indicates that regardless of the developmental stage in which HCMV infects, HCMV drives hematopoietic cells towards a weaker immune-responsive monocyte state and that this anergic-like state is crucial for the virus ability to express its transcripts and to eventually reactivate.

Body louse remains found in textiles excavated at Masada, Israel

A leg of the body louse, Pediculus humanus humanus L. (Phthiraptera: Pediculidae), was found in a storeroom at Masada build during the reign of King Herod the Great. The unearthed culture material clearly indicates that the room was occupied by the rebels during the first Jewish revolt against the Romans (AD 66-73/4). The context of the textiles associated with the louse and their nature suggest a rebel origin. An exuvium of a leg of the third nymphal stage of body louse was found. The first three parts of the leg (tarsus, including the tarsal claw, tibia and femur) were preserved entirely, while the fourth segment of the leg, the trochanter, was only partially conserved. The comparison of the tarsus of this specimen with the legs of present day third instar nymphs of body and head lice revealed that the leg found within the archaeological debris belongs to a body louse.