Sequencing of prostate cancers identifies new cancer genes, routes of progression and drug targets

Prostate cancer represents a substantial clinical challenge because it is difficult to predict outcome and advanced disease is often fatal. We sequenced the whole genomes of 112 primary and metastatic prostate cancer samples. From joint analysis of these cancers with those from previous studies (930 cancers in total), we found evidence for 22 previously unidentified putative driver genes harboring coding mutations, as well as evidence for NEAT1 and FOXA1 acting as drivers through noncoding mutations. Through the temporal dissection of aberrations, we identified driver mutations specifically associated with steps in the progression of prostate cancer, establishing, for example, loss of CHD1 and BRCA2 as early events in cancer development of ETS fusion-negative cancers. Computational chemogenomic (canSAR) analysis of prostate cancer mutations identified 11 targets of approved drugs, 7 targets of investigational drugs, and 62 targets of compounds that may be active and should be considered candidates for future clinical trials

A series of repetitive DNA sequences are associated with human core and H1 histone genes

Repetitive DNA sequences, derived from the human beta-globin gene cluster, were mapped within a series of human genomic DNA segments containing core (H2A, H2B, H3 and H4) and H1 histone genes. Cloned recombinant lambda CH4A phage with human histone gene inserts were analyzed by Southern blot analysis using the following 32P-labeled (nick translated) repetitive sequences as probes: Alu I, Kpn I and LTR-like. A cloned DNA designated RS002-5\u27C6 containing (i) a (TG)16 simple repeat, (ii) an (ATTTT)n repeat and (iii) a 52 base pair alternating purine and pyrimidine sequence was also used as a radiolabelled hybridization probe. Analysis of 12 recombinant phage, containing 6 arrangements of core histone genes, indicated the presence of Alu I, Kpn and RS002-5\u27C6 repetitive sequences. In contrast, analysis of 4 human genomic DNA segments, containing both core and H1 histone genes, indicated the presence of only Alu I family sequences. LTR-like sequences were not detected in association with any of the core or H1 histone genes examined. These results suggest that human histone and beta-globin genes share certain aspects of sequence organization in flanking regions despite marked differences in their overall structure and pattern of expression

Downregulation of cell growth and cell cycle regulated genes during chick osteoblast differentiation with the reciprocal expression of histone gene variants

Expression of cell cycle (core and H1 histone) and cell growth (c-myc and c-fos) regulated genes was examined in primary cultures of chick calvarial osteoblasts during a developmental sequence associated with the progressive maturation of the osteoblast in a bonelike mineralized extracellular matrix. We have identified a transition point early in the developmental sequence which occurs when proliferation ceases and expression of genes related to the differentiated phenotype of osteoblasts is initiated. During this transition period, cellular levels of RNA transcripts from core and H1 histone genes and the c-myc and c-fos protooncogenes decrease in a parallel and coordinate manner. The decline in histone gene transcription that accompanies the loss of accumulated histone mRNA indicates that the downregulation of histone gene expression is at least, in part, transcriptionally mediated. In contrast, persistence of c-myc and c-fos transcription following completion of the proliferation period, when the mRNAs are no longer present at detectable levels, suggests that the initial downregulation of protooncogene expression is controlled at the level of messenger RNA stability. Thus, two types of signaling mechanisms are operative in the down-regulation of cell proliferation genes during osteoblast differentiation--one that impinges on regulatory sequences that influence the interactions of transcription factors with cis-acting promoter elements and a second that modulates messenger RNA turnover. Of significance, downregulation of the cell cycle regulated histone genes is accompanied by a reciprocal increase in the expression of a structurally distinct subset of the histone genes that are not coupled with DNA replication during the period of expression of osteoblast phenotype markers.(ABSTRACT TRUNCATED AT 250 WORDS

In situ plasma remediation of buried nuclear, chemical and biological wastes

Issued as final reportThis item was temporarily removed from SMARTech at the request of the Georgia Tech Research Institute on May 8, 2009

The human H1 histone gene FNC16 is functionally expressed in proliferating HeLa S3 cells and is down-regulated during terminal differentiation in HL60 cells

The human H1 histone gene FNC16 resides in a 2.7-kb EcoRI fragment present in a histone gene cluster that also contains one copy of each of the core (H2A, H2B, H3, and H4) histone genes. The cap site for FNC16 H1 mRNA is located 58 nucleotides upstream of the ATG translational start codon, and S1 nuclease protection analysis clearly distinguishes between correctly initiated FNC16 transcripts and transcripts from other nonidentical H1 histone genes. We have observed, using S1 analysis, that the FNC16 H1 histone gene is expressed in a replication-dependent manner in HeLa cells and is expressed in proliferating, but down-regulated in differentiated, HL60 cells. Similar results were found in HeLa S3 and HL60 cells for the cell cycle-dependent human H4 histone gene FO108. Nuclear extracts derived from HeLa S3 cells are capable of directing FNC16 H1 histone gene transcription in vitro. This finding is consistent with previous work that established at least two sites for protein-DNA interaction in vitro in the proximal promoter region of this gene. We have observed a difference in the extent to which the FNC16 H1 histone gene is expressed in HeLa S3 and proliferating HL60 cells, which suggests that this H1 gene is differentially regulated in various cell types. Although results reported for a potentially identical human H1 histone gene designated Hh8C (LaBella, F., Zhong, R., and Heintz, N. (1988) J. Biol. Chem. 263, 2115-2118) support differential regulation of human H1 genes in various cell types, their observations that the Hh8C gene is not expressed in HeLa cells and that the restriction patterns differ indicate that FNC16 and Hh8C are different H1 genes

A human histone H2B.1 variant gene, located on chromosome 1, utilizes alternative 3\u27 end processing

A variant human H2B histone gene (GL105), previously shown to encode a 2300 nt replication independent mRNA, has been cloned. We demonstrate this gene expresses alternative mRNAs regulated differentially during the HeLa S3 cell cycle. The H2B-Gl105 gene encodes both a 500 nt cell cycle dependent mRNA and a 2300 nt constitutively expressed mRNA. The 3\u27 end of the cell cycle regulated mRNA terminates immediately following the region of hyphenated dyad symmetry typical of most histone mRNAs, whereas the constitutively expressed mRNA has a 1798 nt non-translated trailer that contains the same region of hyphenated dyad symmetry but is polyadenylated. The cap site for the H2B-GL105 mRNAs is located 42 nt upstream of the protein coding region. The H2B-GL105 histone gene was localized to chromosome region 1q21-1q23 by chromosomal in situ hybridization and by analysis of rodent-human somatic cell hybrids using an H2B-GL105 specific probe. The H2B-GL105 gene is paired with a functional H2A histone gene and this H2A/H2B gene pair is separated by a bidirectionally transcribed intergenic promoter region containing consensus TATA and CCAAT boxes and an OTF-1 element. These results demonstrate that cell cycle regulated and constitutively expressed histone mRNAs can be encoded by the same gene, and indicate that alternative 3\u27 end processing may be an important mechanism for regulation of histone mRNA. Such control further increases the versatility by which cells can modulate the synthesis of replication-dependent as well as variant histone proteins during the cell cycle and at the onset of differentiation

Level of renal function in patients starting dialysis: an ERA-EDTA Registry study

Methods. Renal registries participating in the European Renal Association-European Dialysis and Transplant Association Registry provided data on serum creatinine 0-4 weeks before the start of dialysis in incident dialysis patients in 1999 and 2003. Data were available in 11 472 patients from nine renal registries. Glomerular filtration rate (GFR) was estimated by the four-variable Modification of Diet in Renal Disease equation. Results. The unadjusted median eGFR at the start of dialysis was 7.0 mL/min/1.73 m(2) in the 1999 data (median serum creatinine 7.5 mg/dL) and 7.7 mL/min/1.73 m(2) in the 2003 data (serum creatinine 7.0 mg/dL). Using linear regression with adjustment for the other covariates, older patients, males, patients with diabetes mellitus, hypertension/renal vascular disease (HT/RVD) as primary renal disease (vs glomerulonephritis), ischaemic heart disease or peripheral vascular disease and patients starting on peritoneal dialysis (PD) initiated dialysis at higher levels of eGFR (range delta eGFR: 0.1-1.2 mL/min/1.73 m(2)). Using the same analyses, eGFR differed between countries (range: 6.5-8.6 mL/min/1.73 m(2)). Conclusions. During 2003, patients started dialysis at somewhat higher eGFR levels than those starting during 1999. There were also international differences in eGFR. Such differences may, at least in part, be explained by differences in creatinine measurement methods between countries and time periods. Finally, older patients, males, patients with HT/RVD or comorbidity and those starting on PD had slightly higher eGFR levels than younger patients, females, those with glomerulonephritis, without comorbidity and those starting on haemodialysis. Further research is needed into other, more clinically related factors affecting the decision to start dialysi

Cardiovascular and noncardiovascular mortality among patients starting dialysis

CONTEXT: Cardiovascular mortality is considered the main cause of death in patients receiving dialysis and is 10 to 20 times higher in such patients than in the general population. OBJECTIVE: To evaluate if high overall mortality in patients starting dialysis is a consequence of increased cardiovascular mortality risk only or whether noncardiovascular mortality is equally increased. DESIGN, SETTING, AND PATIENTS: Using data from between January 1, 1994, and January 1, 2007, age-stratified mortality in a European cohort of adults starting dialysis and receiving follow-up for a mean of 1.8 (SD, 1.1) years (European Renal Association-European Dialysis and Transplant Association [ERA-EDTA] Registry [N = 123,407]) was compared with the European general population (Eurostat). MAIN OUTCOME MEASURES: Cause of death was recorded by ERA-EDTA codes in patients and matching International Statistical Classification of Diseases, 10th Revision codes in the general population. Standardized cardiovascular and noncardiovascular mortality rates, their ratio, difference, and relative excess of cardiovascular over noncardiovascular mortality were calculated. RESULTS: Overall all-cause mortality rates in patients and the general population were 192 per 1000 person-years (95% confidence interval [CI], 190-193) and 12.055 per 1000 person-years (95% CI, 12.05-12.06), respectively. Cause of death was known for 90% of the patients and 99% of the general population. In patients, 16,654 deaths (39%) were cardiovascular and 21,654 (51%) were noncardiovascular. In the general population, 7,041,747 deaths (40%) were cardiovascular and 10,183,322 (58%) were noncardiovascular. Cardiovascular and noncardiovascular mortality rates in patients were respectively 38.1 per 1000 person-years (95% CI, 37.2-39.0) and 50.1 per 1000 person-years (95% CI, 48.9-51.2) higher than in the general population. On a relative scale, standardized cardiovascular and noncardiovascular mortality were respectively 8.8 (95% CI, 8.6-9.0) and 8.1 (95% CI, 7.9-8.3) times higher than in the general population. The ratio of these rates, ie, relative excess of cardiovascular over noncardiovascular mortality in patients starting dialysis compared with the general population, was 1.09 (95% CI, 1.06-1.12). Relative excess in a sensitivity analysis in which unknown/missing causes of death were regarded either as noncardiovascular or cardiovascular varied between 0.90 (95% CI, 0.88-0.93) and 1.39 (95% CI, 1.35-1.43). CONCLUSION: Patients starting dialysis have a generally increased risk of death that is not specifically caused by excess cardiovascular mortality

The transcription factor ERG recruits CCR4-NOT to control mRNA decay and mitotic progression.

Control of mRNA levels, a fundamental aspect in the regulation of gene expression, is achieved through a balance between mRNA synthesis and decay. E26-related gene (Erg) proteins are canonical transcription factors whose previously described functions are confined to the control of mRNA synthesis. Here, we report that ERG also regulates gene expression by affecting mRNA stability and identify the molecular mechanisms underlying this function in human cells. ERG is recruited to mRNAs via interaction with the RNA-binding protein RBPMS, and it promotes mRNA decay by binding CNOT2, a component of the CCR4-NOT deadenylation complex. Transcriptome-wide mRNA stability analysis revealed that ERG controls the degradation of a subset of mRNAs highly connected to Aurora signaling, whose decay during S phase is necessary for mitotic progression. Our data indicate that control of gene expression by mammalian transcription factors may follow a more complex scheme than previously anticipated, integrating mRNA synthesis and degradation