Large intervening noncoding RNAs (lincRNAs) are pervasively transcribed in the genome1, 2, 3 yet their potential involvement in human disease is not well understood4,5. Recent studies of dosage compensation, imprinting, and homeotic gene expression suggest that individual lincRNAs can function as the interface between DNA and specific chromatin remodeling activities6,7,8. Here we show that lincRNAs in the HOX loci become systematically dysregulated during breast cancer progression. The lincRNA termed HOTAIR is increased in expression in primary breast tumors and metastases, and HOTAIR expression level in primary tumors is a powerful predictor of eventual metastasis and death. Enforced expression of HOTAIR in epithelial cancer cells induced genome-wide re-targeting of Polycomb Repressive Complex 2 (PRC2) to an occupancy pattern more resembling embryonic fibroblasts, leading to altered histone H3 lysine 27 methylation, gene expression, and increased cancer invasiveness and metastasis in a manner dependent on PRC2. Conversely, loss of HOTAIR can inhibit cancer invasiveness, particularly in cells that possess excessive PRC2 activity. These findings suggest that lincRNAs play active roles in modulating the cancer epigenome and may be important targets for cancer diagnosis and therapy.

The application of established drug compounds to novel therapeutic indications, known as drug repositioning, offers several advantages over traditional drug development, including reduced development costs and shorter paths to approval. Recent approaches to drug repositioning employ high-throughput experimental approaches to assess a compound’s potential therapeutic qualities. Here we present a systematic computational approach to predict novel therapeutic indications based on comprehensive testing of molecular signatures in drug-disease pairs. We integrated gene expression measurements from 100 diseases and gene expression measurements on 164 drug compounds yielding predicted therapeutic potentials for these drugs. We demonstrate the ability to recover many known drug and disease relationships using computationally derived therapeutic potentials, and also predict many new indications for these drugs. We experimentally validated a prediction for the anti-ulcer drug cimetidine as a candidate therapeutic in the treatment of lung adenocarcinoma, and demonstrate both in vitro and in vivo using mouse xenograft models. This novel computational method provides a novel and systematic approach to reposition established drugs to treat a wide range of human diseases.

Highlights d Unmodified circRNA adjuvant induces antigen-specific T and B cell responses d m 6 A RNA modification marks self circRNAs and abrogates circRNA immunity d Unmodified circRNA and K63-polyubiquitin activate RIG-I and innate immune signaling d YTHDF2 binding of m 6 A-circRNA additionally suppresses circRNA immunity

Noncoding mutations in cancer genomes are frequent but challenging to interpret. PVT1 encodes an oncogenic lncRNA, but recurrent translocations and deletions in human cancers suggest alternative mechanisms. Here, we show that the PVT1 promoter has a tumor-suppressor function that is independent of PVT1 lncRNA. CRISPR interference of PVT1 promoter enhances breast cancer cell competition and growth in vivo. The promoters of the PVT1 and the MYC oncogenes, located 55 kb apart on chromosome 8q24, compete for engagement with four intragenic enhancers in the PVT1 locus, thereby allowing the PVT1 promoter to regulate pause release of MYC transcription. PVT1 undergoes developmentally regulated monoallelic expression, and the PVT1 promoter inhibits MYC expression only from the same chromosome via promoter competition. Cancer genome sequencing identifies recurrent mutations encompassing the human PVT1 promoter, and genome editing verified that PVT1 promoter mutation promotes cancer cell growth. These results highlight regulatory sequences of lncRNA genes as potential disease-associated DNA elements.

We describe here a method for measuring DNA replication and, thus, cell proliferation in slow turnover cells that is suitable for use in humans. The technique is based on the incorporation of 2 H2O into the deoxyribose (dR) moiety of purine deoxyribonucleotides in dividing cells. For initial validation, rodents were administered 4% 2 H2O in drinking water. The proliferation rate of mammary epithelial cells in mice was 2.9% per day and increased 5-fold during pregnancy. Administration of estradiol pellets (0 -200 g) to ovariectomized rats increased mammary epithelial cell proliferation, according to a doseresponse relationship up to the 100 g dose. Similarly, proliferation of colon epithelial cells was stimulated in a dose-response manner by dietary cholic acid in rats. Bromodeoxyuridine labeling correlated with the 2 H2O results. Proliferation of slow turnover cells was then measured. Vascular smooth muscle cells isolated from mouse aorta divided with a half-life in the range of 270 -400 days and die-away values after 2 H2O wash-out confirmed these slow turnover rates. The proliferation rate of an adipocyte-enriched fraction from mouse adipose tissue depots was 1-1.5% new cells per day, whereas obese ad libitum-fed ob͞ob mice exhibited markedly higher fractional and absolute proliferation rates. In humans, stable long-term 2 H2O enrichments in body water were achieved by daily 2 H2O intake, without toxicities. Labeled dR from fully turned-over blood cells (monocytes or granulocytes) exhibited a consistent amplification factor relative to body 2 H2O enrichment (Ϸ3.5-fold). The fraction of newly divided naive-phenotype T cells after 9 weeks of labeling with 2 H2O was 0.056 (CD4 ؉ ) and 0.043 (CD8 ؉ ) (replacement rate <0.1% per day). In summary, 2 H2O labeling of dR in DNA allows safe, convenient, reproducible, and inexpensive measurement of cell proliferation in humans and experimental animals and is well suited for slow turnover cells. deuterated water ͉ cell proliferation ͉ DNA synthesis ͉ adipogenesis ͉ vascular smooth muscle cell proliferation