Summary There is substantial heterogeneity among primary prostate cancers, evident in the spectrum of molecular abnormalities and its variable clinical course. As part of The Cancer Genome Atlas (TCGA), we present a comprehensive molecular analysis of 333 primary prostate carcinomas. Our results revealed a molecular taxonomy in which 74% of these tumors fell into one of seven subtypes defined by specific gene fusions (ERG, ETV1/4, FLI1) or mutations (SPOP, FOXA1, IDH1). Epigenetic profiles showed substantial heterogeneity, including an IDH1-mutant subset with a methylator phenotype. Androgen receptor (AR) activity varied widely and in a subtype-specific manner with SPOP and FOXA1 mutant tumors having the highest levels of AR-induced transcripts. 25% of the prostate cancers had a presumed actionable lesion in the PI3K or MAPK signaling pathways, and DNA repair genes were inactivated in 19%. Our analysis reveals molecular heterogeneity among primary prostate cancers, as well as potentially actionable molecular defects.

HIV-1 replication can be inhibited by type-I interferon (IFN), and the expression of a number of gene products with anti HIV-1 activity is induced by type-I IFN1,2. However, none of the known antiretroviral proteins can account for the ability of type-I IFN to inhibit early, preintegration, phases of the HIV-1 replication cycle in human cells3,4. By comparing gene expression profiles in cell lines that differ in their ability to support the inhibitory action of IFNα on early steps of the HIV-1 replication cycle, we identified Myxovirus resistance-2 (Mx2) as an interferon-induced inhibitor of HIV-1 infection. Expression of Mx2 reduced permissiveness to a variety of lentiviruses, while depletion of Mx2 using RNA interference reduced the anti-HIV-1 potency of IFNα. HIV-1 reverse transcription proceeded normally in Mx2-expressing cells, but 2-LTR circular forms of HIV-1 DNA were less abundant, suggesting that Mx2 inhibits HIV-1 nuclear import, or destabilizes nuclear HIV-1 DNA. Consistent with this notion, mutations in the HIV-1 capsid protein that are known, or suspected to alter the nuclear import pathways used by HIV-1 conferred resistance to Mx2, while preventing cell division increased Mx2 potency. Overall, these findings indicate that Mx2 is an effector of the anti-HIV-1 activity of type-I IFN, and suggest that Mx2 inhibits HIV-1 infection by inhibiting capsid-dependent nuclear import of subviral complexes.