Integration of copy number and transcriptomics provides risk stratification in prostate cancer: A discovery and validation cohort study

BACKGROUND

Understanding the heterogeneous genotypes and phenotypes of prostate cancer is fundamental to improving the way we treat this disease. As yet, there are no validated descriptions of prostate cancer subgroups derived from integrated genomics linked with clinical outcome.

METHODS

In a study of 482 tumour, benign and germline samples from 259 men with primary prostate cancer, we used integrative analysis of copy number alterations (CNA) and array transcriptomics to identify genomic loci that affect expression levels of mRNA in an expression quantitative trait loci (eQTL) approach, to stratify patients into subgroups that we then associated with future clinical behaviour, and compared with either CNA or transcriptomics alone.

FINDINGS

We identified five separate patient subgroups with distinct genomic alterations and expression profiles based on 100 discriminating genes in our separate discovery and validation sets of 125 and 103 men. These subgroups were able to consistently predict biochemical relapse (p = 0.0017 and p = 0.016 respectively) and were further validated in a third cohort with long-term follow-up (p = 0.027). We show the relative contributions of gene expression and copy number data on phenotype, and demonstrate the improved power gained from integrative analyses. We confirm alterations in six genes previously associated with prostate cancer (MAP3K7, MELK, RCBTB2, ELAC2, TPD52, ZBTB4), and also identify 94 genes not previously linked to prostate cancer progression that would not have been detected using either transcript or copy number data alone. We confirm a number of previously published molecular changes associated with high risk disease, including MYC amplification, and NKX3-1, RB1 and PTEN deletions, as well as over-expression of PCA3 and AMACR, and loss of MSMB in tumour tissue. A subset of the 100 genes outperforms established clinical predictors of poor prognosis (PSA, Gleason score), as well as previously published gene signatures (p = 0.0001). We further show how our molecular profiles can be used for the early detection of aggressive cases in a clinical setting, and inform treatment decisions.

INTERPRETATION

For the first time in prostate cancer this study demonstrates the importance of integrated genomic analyses incorporating both benign and tumour tissue data in identifying molecular alterations leading to the generation of robust gene sets that are predictive of clinical outcome in independent patient cohorts.

Use of routinely collected data on trihalomethane in drinking water for epidemiological purposes

OBJECTIVES

To explore the use of routinely collected trihalomethane (THM) measurements for epidemiological studies. Recently there has been interest in the relation between byproducts of disinfection of public drinking water and certain adverse reproductive outcomes, including stillbirth, congenital malformations, and low birth weight.

METHOD

Five years of THM readings (1992--6), collected for compliance with statutory limits, were analysed. One water company in the north west of England, divided into 288 water zones, provided 15,984 observations for statistical analysis. On average each zone was sampled 11.1 times a year. Five year, annual, monthly, and seasonal variation in THMs were examined as well as the variability within and between zones.

RESULTS

Between 1992 and 1996 the total THM (TTHM) annual zone means were less than half the statutory concentration, at approximately 46 microg/l. Differences in annual water zone means were within 7%. Over the study period, the maximum water zone mean fell from 142.2 to 88.1 microg/l. Mean annual concentrations for individual THMs (microg/l) were 36.6, 8.0, and 2.8 for chloroform, bromodichloromethane (BDCM), and dibromochloromethane (DBCM) respectively. Bromoform data were not analysed, because a high proportion of the data were below the detection limit. The correlation between chloroform and TTHM was 0.98, between BDCM and TTHM 0.62, and between DBCM and TTHM -0.09. Between zone variation was larger than within zone variation for chloroform and BDCM, but not for DBCM. There was only little seasonal variation (<3%). Monthly variation was found although there were no consistent trends within years.

CONCLUSION

In an area where the TTHM concentrations were less than half the statutory limit (48 microg/l) chloroform formed a high proportion of TTHM. The results of the correlation analysis suggest that TTHM concentrations provided a good indication of chloroform concentrations, a reasonable indication of BDCM concentrations, but no indication of DBCM. Zone means were similar over the years, but the maximum concentrations reduced considerably, which suggests that successful improvements in treatment have been made to reduce high TTHM concentrations in the area. For chloroform and BDCM, the main THMs, the component between water zones was greater than variation within water zones and explained most of the overall exposure variation. Variation between months and seasons was low and showed no clear trends within years. The results indicate that routinely collected data can be used to obtain exposure estimates for epidemiological studies at a small area level.

Jean-Baptiste Bouillaud, Claude-François Lallemand, and the role of the frontal lobe: location and mislocation of language in the early 19th century

In 1825, Jean-Baptiste Bouillaud read a paper at the Royal Academy of Medicine in Paris supporting Franz Gall's theory of a relation between speech and the frontal lobes. Bouillaud argued that if the frontal lobes are crucial to speech, 2 conditions must be satisfied: when the frontal lobes are affected, speech must also be affected; conversely, when the frontal lobes are spared, speech is also spared. Following these principles, he tested and argued in support of Gall's theory by analyzing the data from 2 neuropathological casebooks (Lallemand, 1820-1823; Rostan, 1820 and 1823). We now know that Bouillaud was wrong, since the crucial dichotomy is between the left and right hemispheres and not between the anterior and posterior areas. What is interesting is that the actual data refute Bouillaud's conclusion. We replicated his experiment by reanalyzing the 147 clinical cases described by Lallemand. There were, of course, some cases with frontal lesions and speech disorders; other cases, however, had speech disorders with lesions outside the frontal lobes, and still others had frontal lesions without speech disorders. Although Bouillaud did not notice it, as we expected, almost all patients with speech disorders had a left hemisphere lesion.

From theory to practice: the unconventional contribution of Gottlieb Burckhardt to psychosurgery

Gottlieb Burckhardt, a Swiss psychiatrist who practiced in the late 19th century, was the founder of modern psychosurgery. In 1891 he reported the results of cortical extirpations on six patients who evidently suffered from intractable psychiatric disease; two of these cases are discussed here to illustrate how Burckhardt employed contemporary brain models of language and cognition as the basis for removing specific areas of the cerebral cortex with the intention of ameliorating his patients' disturbed behavior.

Disturbed nights and 3-4 month old infants: the effects of feeding and thermal environment

Parents completed a prospective diary of a night's sleep for 87, 3-4 month old infants at home whose body temperatures were continuously recorded. We found that about half of the babies disturbed their parents in the night. Breast fed babies were more likely to wake parents in the middle of the night. The babies who disturbed their parents in the middle of the night were significantly more heavily wrapped in significantly warmer rooms. We suggest that discomfort from efforts at active thermoregulation in warm environments may lead some babies to disturb their parents at 'unsocial hours'.

Pure word deafness (acquired verbal auditory agnosia) in an Arabic speaking patient

A 38-year-old, right-handed Arabic-speaking male developed pure word deafness three days after myocardial infarction. He could recognize Arabic music and instruments but not words of songs; a radio broadcast from the Koran, but not the individual words; a male as opposed to female voice; Arabic and non-Arabic languages; and whether sentences were questions, exclamations, or imperatives. He discerned whether the speaker was emotionally neutral, happy, angry or sad. Contextual cues and reducing the rate of speaking aided verbal comprehension. Pure tone threshhold audiometry revealed mild bilateral sensorineural loss up to 2000 Hz and a moderate high frequency loss. Brainstem auditory evoked potentials were normal, cortical auditory evoked potentials abnormal. CT scan revealed bilateral infarcts subcortically just posterior to the left superior temporal gyrus and the right posterior superior and midtemporal regions. Neurolinguistic tests indicated that the deficit is prephonemic and not due to impairment of linguistic discrimination.

Intravenous metoclopramide: prevention of chemotherapy-induced nausea and vomiting. A preliminary evaluation

The authors tested the safety and efficacy of intravenous metoclopramide in the prevention of chemotherapy-induced nausea and vomiting. Those studied included hospitalized patients receiving their initial treatment with potent, emetogenic non-cisplatin-containing regimens, and outpatients receiving both their initial and maintenance non-cisplatin-containing chemotherapy. Fifty patients received metoclopramide with one or more of three intravenous metoclopramide dosage schedules, based on whether they received their chemotherapy on an inpatient or outpatient basis. Of the 50 patients treated, 39 (78%) achieved total protection (no emesis), and 9 (18%) attained major antiemetic protection (one or two emeses) when all dosage schedules of metoclopramide were combined. Therefore, total or major antiemetic protection was observed in 48 of 50 patients (96%) receiving a broad range of potentially emetogenic chemotherapy. Antiemetic protection was shown not to depend on the schedule of metoclopramide dosing used, but rather on the emetic potential of the chemotherapeutic agents or combinations employed. In addition, previously treated patients in whom chemotherapy-related nausea or vomiting had posed a significant problem in the past, were shown to have an overall lower incidence of total antiemetic and antinausea protection as compared with patients who were previously untreated or did not experience emesis with prior chemotherapy. Thirty patients experienced no nausea or vomiting with intravenous metoclopramide; in the 20 patients who experienced nausea, its incidence was shown to be directly proportional to the emetic potential of the chemotherapy agents employed. Side effects were dose-related, however none were serious enough to warrant drug withdrawal. It is concluded that intravenous metoclopramide possesses significant antiemetic activity in patients receiving potent, non-cisplatin-containing chemotherapy. The dosage and scheduling required to provide total protection against nausea and vomiting appears to be dependent on the inherent emetic potency of the chemotherapy used. Further studies involving large numbers of patients are required to determine the optimal dosage and scheduling of this agent.