Tumour heterogeneity in primary prostate cancer is a well-established phenomenon. However, how the subclonal diversity of tumours changes during metastasis and progression to lethality is poorly understood. Here we reveal the precise direction of metastatic spread across four lethal prostate cancer patients using whole-genome and ultra-deep targeted sequencing of longitudinally collected primary and metastatic tumours. We find one case of metastatic spread to the surgical bed causing local recurrence, and another case of cross-metastatic site seeding combining with dynamic remoulding of subclonal mixtures in response to therapy. By ultra-deep sequencing end-stage blood, we detect both metastatic and primary tumour clones, even years after removal of the prostate. Analysis of mutations associated with metastasis reveals an enrichment of TP53 mutations, and additional sequencing of metastases from 19 patients demonstrates that acquisition of TP53 mutations is linked with the expansion of subclones with metastatic potential which we can detect in the blood.

Age-associated decreases in primary CD8 T cell responses occur, in part, due to direct effects on naive CD8 T cells to reduce intrinsic functionality, but the precise nature of this defect remains undefined. Aging also causes accumulation of antigen-naive but semi-differentiated "virtual memory" (T) cells, but their contribution to age-related functional decline is unclear. Here, we show that T cells are poorly proliferative in aged mice and humans, despite being highly proliferative in young individuals, while conventional naive T cells (T cells) retain proliferative capacity in both aged mice and humans. Adoptive transfer experiments in mice illustrated that naive CD8 T cells can acquire a proliferative defect imposed by the aged environment but age-related proliferative dysfunction could not be rescued by a young environment. Molecular analyses demonstrate that aged T cells exhibit a profile consistent with senescence, marking an observation of senescence in an antigenically naive T cell population.

Polycomb repressive complex 2 (PRC2) is a histone methyltransferase that trimethylates H3K27, a mark of repressed chromatin. Mammalian PRC2 binds RNA promiscuously, with thousands of target transcripts in vivo. But what does PRC2 recognize in these RNAs? Here we show that purified human PRC2 recognizes G > C,U ≫ A in single-stranded RNA and has a high affinity for folded guanine quadruplex (G4) structures but little binding to duplex RNAs. Importantly, G-tract motifs are significantly enriched among PRC2-binding transcripts in vivo. DNA sequences coding for PRC2-binding RNA motifs are enriched at PRC2-binding sites on chromatin and H3K27me3-modified nucleosomes. Collectively, the abundance of PRC2-binding RNA motifs rationalizes the promiscuous RNA binding of PRC2, and their enrichment at Polycomb target genes provides a means for RNA-mediated regulation.

Reprogramming human somatic cells to primed or naive induced pluripotent stem cells (iPSC) recapitulates the different stages of early human embryonic development [1][2][3][4][5][6] . The molecular mechanism underpinning the reprogramming of human somatic cells to primed or naive induced pluripotency remains largely unexplored, impeding our understanding and limiting rational improvements to reprogramming protocols. To address this, we reconstructed molecular reprogramming trajectories using single-cell transcriptomics. This revealed that reprogramming into primed and naive human pluripotency follows diverging and distinct trajectories. Moreover, genome-wide accessible chromatin analyses showed key changes in regulatory elements of core pluripotency genes, and orchestrated global changes in chromatin accessibility over time. Integrated analysis of these datasets unveiled an unexpected role of trophectoderm (TE) lineage-associated transcription factors and the existence of a subpopulation of cells that enter a TE-like state during reprogramming. Furthermore, this TE-like state could be captured, allowing the derivation of induced Trophoblast Stem Cells (iTSCs). iTSCs are molecularly and functionally similar to TSCs derived from human blastocysts or first-trimester placental trophoblasts 7 . Altogether, these results provide a high-resolution roadmap for transcription factor-mediated human 3 reprogramming, revealing an unanticipated role of the TE-lineage specific regulatory program during this process and facilitating the direct reprogramming of somatic cells into iTSCs.