Summary The Facilitates Chromatin Transcription (FACT) complex is involved in chromatin remodeling during transcription, replication, and DNA repair. FACT was previously considered to be ubiquitously expressed and not associated with any disease. However, we discovered that FACT is the target of a novel class of anti-cancer compounds and is not expressed in normal cells of adult mammalian tissues, except for undifferentiated and stem-like cells. Here, we show that FACT expression is strongly associated with poorly differentiated aggressive cancers with poor overall survival. In addition, FACT was found to be upregulated during in vitro transformation and to be necessary, but not fully sufficient, to drive transformation. FACT also promoted survival and growth of established tumor cells. Genome-wide mapping of chromatin-bound FACT indicated that FACT’s role in cancer likely involves selective chromatin remodeling of genes that stimulate proliferation, inhibit cell death and differentiation, and regulate cellular stress responses.

Despite the enormous theoretical attention given to the evolutionary consequences of sexual reproduction, the validity of the key assumptions on which the theory depends rarely has been evaluated. It is often argued that a reduced ability to purge deleterious mutations condemns asexual lineages to an early extinction. However, most well characterized asexual lineages fail to exhibit the high levels of neutral allelic divergence expected in the absence of recombination. With purely descriptive data, it is difficult to evaluate whether this pattern is a consequence of the rapid demise of asexual lineages, an unusual degree of mutational stability, or recombination. Here, we show in mutation-accumulation lines of asexual Daphnia that the rate of loss of nucleotide heterozygosity by ameiotic recombination is substantially greater than the rate of introduction of new variation by mutation. This suggests that the evolutionary potential of asexual diploid species is not only a matter of mutation accumulation and reduced efficiency of selection, but it underscores the limited utility of using neutral allelic divergence as an indicator of ancient asexuality.allelic divergence ͉ loss of heterozygosity ͉ mutation accumulation I t has long been assumed that the absence of meiosis reduces rates of homologous recombination to evolutionarily unimportant levels in asexual eukaryotes. The resultant reduction in the efficiency of natural selection is expected to magnify the rate of deleterious mutation accumulation and reduce the rate of fixation of adaptive mutations, condemning asexual species to an early extinction (1-4). Yet, despite this bleak theoretical forecast, some lineages, including the bdelloid rotifers (5), oribatid mites (6), and darwinulid ostracods (7,8), dispensed with sexual reproduction long ago, and the majority of animal phyla have some obligately asexual species (9).A substantial body of theory has been developed to account for the evolutionary persistence of asexual species (or lack thereof), but only a few large-scale empirical surveys have been undertaken to characterize the molecular genetic consequences of asexual reproduction (e.g., refs. 10 and 11). It has been suggested that the absence of meiosis in asexual lineages causes the two alleles at any given locus to become progressively more divergent given that within-individual recombination (gene conversion and/or crossing over) and chromosomal deletions occur at negligible levels (5, 12, 13). However, with the exception of the bdelloid rotifers, most closely studied asexual lineages fail to exhibit high levels of neutral allelic divergence (e.g., refs. 5 and 14-16). These observations call attention to other processes that might erode allelic divergence in real biological systems, such as recombination, unusually effective DNA repair, automixis, or clandestine sexual reproduction (e.g., refs. 12-16). Direct experimental observations on the genomic stability of asexual lineages are necessary to shed light on this issue.Although mitotic recombination h...

BackgroundImmune checkpoint inhibitors (ICIs) have changed the clinical management of melanoma. However, not all patients respond, and current biomarkers including PD-L1 and mutational burden show incomplete predictive performance. The clinical validity and utility of complex biomarkers have not been studied in melanoma.MethodsCutaneous metastatic melanoma patients at eight institutions were evaluated for PD-L1 expression, CD8+ T-cell infiltration pattern, mutational burden, and 394 immune transcript expression. PD-L1 IHC and mutational burden were assessed for association with overall survival (OS) in 94 patients treated prior to ICI approval by the FDA (historical-controls), and in 137 patients treated with ICIs. Unsupervised analysis revealed distinct immune-clusters with separate response rates. This comprehensive immune profiling data were then integrated to generate a continuous Response Score (RS) based upon response criteria (RECIST v.1.1). RS was developed using a single institution training cohort (n = 48) and subsequently tested in a separate eight institution validation cohort (n = 29) to mimic a real-world clinical scenario.ResultsPD-L1 positivity ≥1% correlated with response and OS in ICI-treated patients, but demonstrated limited predictive performance. High mutational burden was associated with response in ICI-treated patients, but not with OS. Comprehensive immune profiling using RS demonstrated higher sensitivity (72.2%) compared to PD-L1 IHC (34.25%) and tumor mutational burden (32.5%), but with similar specificity.ConclusionsIn this study, the response score derived from comprehensive immune profiling in a limited melanoma cohort showed improved predictive performance as compared to PD-L1 IHC and tumor mutational burden.Electronic supplementary materialThe online version of this article (10.1186/s40425-018-0344-8) contains supplementary material, which is available to authorized users.

We have developed a next-generation sequencing assay to quantify biomarkers of the host immune response in formalin-fixed, paraffin-embedded (FFPE) tumor specimens. This assay aims to provide clinicians with a comprehensive characterization of the immunologic tumor microenvironment as a guide for therapeutic decisions on patients with solid tumors. The assay relies on RNA-sequencing (seq) to semiquantitatively measure the levels of 43 transcripts related to anticancer immune responses and 11 transcripts that reflect the relative abundance of tumor-infiltrating lymphocytes, as well as on DNA-seq to estimate mutational burden. The assay has a clinically relevant 5-day turnaround time and can be conducted on as little as 2.5 ng of RNA and 1.8 ng of genomic DNA extracted from three to five standard FFPE sections. The standardized next-generation sequencing workflow produced sequencing reads adequate for clinical testing of matched RNA and DNA from several samples in a single run. Assay performance for gene-specific sensitivity, linearity, dynamic range, and detection threshold was estimated across a wide range of actual and artificial FFPE samples selected or generated to address preanalytical variability linked to specimen features (eg, tumor-infiltrating lymphocyte abundance, percentage of necrosis), and analytical variability linked to assay features (eg, batch size, run, day, operator). Analytical precision studies demonstrated that the assay is highly reproducible and accurate compared with established orthogonal approaches.

SUMMARY Melanoma is one of the most aggressive types of human cancers, and the mechanisms underlying melanoma invasive phenotype are not completely understood. Here, we report that expression of guanosine monophosphate reductase (GMPR), an enzyme involved in de novo biosynthesis of purine nucleotides, was down-regulated in invasive stages of human melanoma. Loss- and gain-of-function experiments revealed that GMPR down-regulates the amounts of several GTP-bound (active) RHO-GTPases, suppresses the ability of melanoma cells to form invadopodia, degrade extracellular matrix and invade in vitro and grow as tumor xenografts in vivo. Mechanistically, we demonstrated that GMPR partially depletes intracellular GTP pools. Pharmacological inhibition of de novo GTP biosynthesis suppressed, whereas addition of exogenous guanosine increased invasion of melanoma cells as well as cells from other cancer types. Our data identified GMPR as a melanoma invasion suppressor, and established a link between guanosine metabolism and RHO-GTPase-dependent melanoma cell invasion.