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The retinoblastoma tumor suppressor gene (RB1) plays a critical role in coordinating multiple pathways that impact cancer initiation, disease progression, and therapeutic responses. Here we probed molecular features associated with the RB-pathway across 31 tumor-types. While the RB-pathway has been purported to exhibit multiple mutually exclusive genetic events, only RB1 alteration is mutually exclusive with deregulation of CDK4/6 activity. An ER+ breast cancer model with targeted RB1 deletion was used to identify signatures of CDK4/6 activity and RB-dependency (CDK4/6-RB integrated signature). This signature was prognostic in tumor-types with gene expression features indicative of slower growth. Single copy loss on chromosome 13q encompassing the RB1 locus is prevalent in many cancers, yielding reduced expression of multiple genes in cis, and is inversely related to the CDK4/6-RB integrated signature supporting a cause-effect relationship. Genes that are positively and inversely correlated with the CDK4/6-RB integrated signature define new tumor-specific pathways associated with RB-pathway activity., Erik Knudsen et al. present a pan-cancer analysis of the RB tumor suppressor protein pathway in 31 tumor types. They find that pathway deregulation is multi-faceted with context dependent association with survival. However, gene expression features are surprisingly invariant and support new therapeutic targets.

Intrinsic or acquired resistance to clinically approved CDK4/6 inhibitors has emerged as a major obstacle that hinders their utility beyond ER+ breast cancer. In this study, CDK4/6-dependent and -resistant models were employed to identify functional determinants of response to pharmacologic CDK4/6 inhibitors. In all models tested, the activation of RB and inhibition of CDK2 activity emerged as determinants of sensitivity. While depleting CDK4 and 6 was sufficient to limit proliferation in specific resistance settings, RB loss rendered cells completely independent of these kinases. The main downstream target in this context was the activation status of CDK2, which was suppressed with CDK4/6 inhibition in an RB-dependent fashion. Protein levels of p27 were associated with plasticity/rigidity of the cell cycle and correlated with sensitivity to CDK4/6 inhibition. Exogenous overexpression and pharmacologic induction of p27 via inhibition of SKP2 and targeting the MEK/ERK pathway enhanced the cytostatic effect of CDK4/6 inhibitors. Mice bearing ER+ xenografts displayed a durable antitumor response to palbociclib; however, over the course of treatment, few cells retained RB phosphorylation, which was associated with limited p27 protein levels as determined by multispectral imaging. Similarly, combination treatment of palbociclib with a MEK inhibitor in pancreatic cancer PDX models upregulated p27 and further enhanced the in vivo tumor response to palbociclib. Collectively, these results suggest that the cell cycle plasticity, which enables tumor models to evade palbociclib-mediated activation of RB, could be targeted using a clinically applicable CDK2 inhibitor. Significance: This work provides a mechanistic insight toward understanding the functional roles of multiple cell cycle regulators that drive plasticity and sensitivity to CDK4/6 inhibition.

PolyA_DB is a database cataloging cleavage and polyadenylation sites (PASs) in several genomes. Previous versions were based mainly on expressed sequence tags (ESTs), which had a limited amount and could lead to inaccurate PAS identification due to the presence of internal A-rich sequences in transcripts. Here, we present an updated version of the database based solely on deep sequencing data. First, PASs are mapped by the 3′ region extraction and deep sequencing (3′READS) method, ensuring unequivocal PAS identification. Second, a large volume of data based on diverse biological samples increases PAS coverage by 3.5-fold over the EST-based version and provides PAS usage information. Third, strand-specific RNA-seq data are used to extend annotated 3′ ends of genes to obtain more thorough annotations of alternative polyadenylation (APA) sites. Fourth, conservation information of PAS across mammals sheds light on significance of APA sites. The database (URL: http://www.polya-db.org/v3) currently holds PASs in human, mouse, rat and chicken, and has links to the UCSC genome browser for further visualization and for integration with other genomic data.

We investigated a small outbreak of varicella in a long-term-care facility after a case of herpes zoster. Clinical specimens and environmental samples were collected from all case patients and from surfaces in the case patients' rooms and other common-use areas. Wild-type varicella-zoster virus (VZV) DNA was identified in all 3 varicella case patients, and high concentrations of VZV DNA were detected in environmental samples from the room of the herpes zoster case patient. Genotypic analysis showed that the identical VZV strain was present in all samples; moreover, the strain was a unique Mosaic genotype isolate that included a stable Oka vaccine marker that had hitherto never been observed in a wild-type strain of VZV. This study provides evidence for the value of including environmental sampling during the investigation of varicella outbreaks and illustrates the importance of evaluating multiple vaccine-associated markers for the discrimination of vaccine virus from wild-type VZV.

In a limited area of sympatry in New York State, hybridization occurs between Prosimulium multidentatum (Twinn) and “forms” 2 and 3 of P. magnum Dyar and Shannon. Salivary gland chromosomes of the interspecific hybrids are the composite of those of the parental species with respect to fixed inversion differences, sex chromosomes and chromocenter attachment of centromeres. Backcross hybrids with P. multidentatum occur in the same area. The preferred direction of cross (P. multidentatum ♀ x P. magnum ♂) is rationalized by the earlier emergence of P. multidentatum, and the earlier emergence of males and greater longevity of females of both species. Chromosome pairing, both in F1 and backcross, is loose in hybrid segments and tight in species homozygous parts. Likewise chiasma frequency is low in hybrid as compared to parentally homozygous chromosomes. In the face of locally recurrent hybridization species integrity is maintained by meiotic irregularities in the hybrids and especially by disturbances in the sex chromosome balance of backcross hybrids, the sex chromosomes of P. multidentatum and P. magnum being non-homologous.