Genomic characterization of thymic epithelial tumors in a real-world dataset.

BACKGROUND: Thymic epithelial tumors (TETs) are rare neoplasms arising in the mediastinum, including thymic carcinomas and thymomas. Due to their rarity, little is known about the genomic profiles of TETs. Herein, we investigated the genomic characteristics of TETs evaluated in a large comprehensive genomic profiling database in a real-world setting. METHODS: We included data from two different cohorts: Foundation Medicine Inc. (FMI) in the United States and the Center for Cancer Genomics and Advanced Therapeutics (C-CAT) in Japan. Samples profiled were examined for all classes of alterations in 253 genes targeted across all assays. Tumor mutational burden (TMB) and microsatellite instability (MSI) were also evaluated. RESULTS: A total of 794 patients were collected in our study, including 722 cases from FMI and 72 cases from C-CAT. In the FMI data, CDKN2A (39.9%), TP53 (30.2%) and CDKN2B (24.6%) were frequently altered in thymic carcinoma, versus TP53 (7.8%), DNMT3A (6.8%), and CDKN2A (5.8%) in thymoma. TMB-high (≥10 mutations/Mb) and MSI were present in 7.0% and 2.3% of thymic carcinomas, and 1.6% and 0.3% of thymomas, respectively. Within C-CAT data, CDKN2A (38.5%), TP53 (36.5%) and CDKN2B (30.8%) were also frequently altered in thymic carcinoma, while alterations of TSC1, SETD2 and LTK (20.0% each) were found in thymoma. CONCLUSIONS: To the best of our knowledge, this is the largest cohort in which genomic alterations, TMB and MSI status of TETs were investigated. Potential targets for treatment previously unbeknownst in TETs are identified in this study, entailing newfound opportunities to advance therapeutic development.

Local chromatin context regulates the genetic requirements of the heterochromatin spreading reaction.

Heterochromatin spreading, the expansion of repressive chromatin structure from sequence-specific nucleation sites, is critical for stable gene silencing. Spreading re-establishes gene-poor constitutive heterochromatin across cell cycles but can also invade gene-rich euchromatin de novo to steer cell fate decisions. How chromatin context (i.e. euchromatic, heterochromatic) or different nucleation pathways influence heterochromatin spreading remains poorly understood. Previously, we developed a single-cell sensor in fission yeast that can separately record heterochromatic gene silencing at nucleation sequences and distal sites. Here we couple our quantitative assay to a genetic screen to identify genes encoding nuclear factors linked to the regulation of heterochromatin nucleation and the distal spreading of gene silencing. We find that mechanisms underlying gene silencing distal to a nucleation site differ by chromatin context. For example, Clr6 histone deacetylase complexes containing the Fkh2 transcription factor are specifically required for heterochromatin spreading at constitutive sites. Fkh2 recruits Clr6 to nucleation-distal chromatin sites in such contexts. In addition, we find that a number of chromatin remodeling complexes antagonize nucleation-distal gene silencing. Our results separate the regulation of heterochromatic gene silencing at nucleation versus distal sites and show that it is controlled by context-dependent mechanisms. The results of our genetic analysis constitute a broad community resource that will support further analysis of the mechanisms underlying the spread of epigenetic silencing along chromatin.

The histone chaperone FACT facilitates heterochromatin spreading by regulating histone turnover and H3K9 methylation states.

Heterochromatin formation requires three distinct steps: nucleation, self-propagation (spreading) along the chromosome, and faithful maintenance after each replication cycle. Impeding any of those steps induces heterochromatin defects and improper gene expression. The essential histone chaperone FACT (facilitates chromatin transcription) has been implicated in heterochromatin silencing, but the mechanisms by which FACT engages in this process remain opaque. Here, we pinpoint its function to the heterochromatin spreading process in fission yeast. FACT impairment reduces nucleation-distal H3K9me3 and HP1/Swi6 accumulation at subtelomeres and derepresses genes in the vicinity of heterochromatin boundaries. FACT promotes spreading by repressing heterochromatic histone turnover, which is crucial for the H3K9me2 to me3 transition that enables spreading. FACT mutant spreading defects are suppressed by removal of the H3K9 methylation antagonist Epe1. Together, our study identifies FACT as a histone chaperone that promotes heterochromatin spreading and lends support to the model that regulated histone turnover controls the propagation of repressive methylation marks.

Optogenetic Control Reveals Differential Promoter Interpretation of Transcription Factor Nuclear Translocation Dynamics.

Gene expression is thought to be affected not only by the concentration of transcription factors (TFs) but also the dynamics of their nuclear translocation. Testing this hypothesis requires direct control of TF dynamics. Here, we engineer CLASP, an optogenetic tool for rapid and tunable translocation of a TF of interest. Using CLASP fused to Crz1, we observe that, for the same integrated concentration of nuclear TF over time, changing input dynamics changes target gene expression: pulsatile inputs yield higher expression than continuous inputs, or vice versa, depending on the target gene. Computational modeling reveals that a dose-response saturating at low TF input can yield higher gene expression for pulsatile versus continuous input, and that multi-state promoter activation can yield the opposite behavior. Our integrated tool development and modeling approach characterize promoter responses to Crz1 nuclear translocation dynamics, extracting quantitative features that may help explain the differential expression of target genes.

Set1/COMPASS repels heterochromatin invasion at euchromatic sites by disrupting Suv39/Clr4 activity and nucleosome stability.

Protection of euchromatin from invasion by gene-repressive heterochromatin is critical for cellular health and viability. In addition to constitutive loci such as pericentromeres and subtelomeres, heterochromatin can be found interspersed in gene-rich euchromatin, where it regulates gene expression pertinent to cell fate. While heterochromatin and euchromatin are globally poised for mutual antagonism, the mechanisms underlying precise spatial encoding of heterochromatin containment within euchromatic sites remain opaque. We investigated ectopic heterochromatin invasion by manipulating the fission yeast mating type locus boundary using a single-cell spreading reporter system. We found that heterochromatin repulsion is locally encoded by Set1/COMPASS on certain actively transcribed genes and that this protective role is most prominent at heterochromatin islands, small domains interspersed in euchromatin that regulate cell fate specifiers. Sensitivity to invasion by heterochromatin, surprisingly, is not dependent on Set1 altering overall gene expression levels. Rather, the gene-protective effect is strictly dependent on Set1's catalytic activity. H3K4 methylation, the Set1 product, antagonizes spreading in two ways: directly inhibiting catalysis by Suv39/Clr4 and locally disrupting nucleosome stability. Taken together, these results describe a mechanism for spatial encoding of euchromatic signals that repel heterochromatin invasion.

Epigenetic fates of gene silencing established by heterochromatin spreading in cell identity and genome stability.

Heterochromatin spreading, the propagation of repressive chromatin along the chromosome, is a reaction critical to genome stability and defense, as well as maintenance of unique cell fates. Here, we discuss the intrinsic properties of the spreading reaction and circumstances under which its products, formed distal to DNA-encoded nucleation sites, can be epigenetically maintained. Finally, we speculate that the epigenetic properties of heterochromatin evolved together with the need to stabilize cellular identity.

Noncoding RNA-nucleated heterochromatin spreading is intrinsically labile and requires accessory elements for epigenetic stability.

The heterochromatin spreading reaction is a central contributor to the formation of gene-repressive structures, which are re-established with high positional precision, or fidelity, following replication. How the spreading reaction contributes to this fidelity is not clear. To resolve the origins of stable inheritance of repression, we probed the intrinsic character of spreading events in fission yeast using a system that quantitatively describes the spreading reaction in live single cells. We show that spreading triggered by noncoding RNA-nucleated elements is stochastic, multimodal, and fluctuates dynamically across time. This lack of stability correlates with high histone turnover. At the mating type locus, this unstable behavior is restrained by an accessory cis-acting element REIII, which represses histone turnover. Further, REIII safeguards epigenetic memory against environmental perturbations. Our results suggest that the most prevalent type of spreading, driven by noncoding RNA-nucleators, is epigenetically unstable and requires collaboration with accessory elements to achieve high fidelity.

Sertraline and relapse prevention training following treatment by very-low-calorie diet: a controlled clinical trial.

This study examined the combination of sertraline, a selective serotonin reuptake inhibitor, and relapse prevention training in the maintenance of weight loss following treatment by a very-low-calorie diet. A total of 53 women who had lost a mean (+/- SD) of 22.9 +/- 7.1 kg from a pretreatment weight of 103.1 +/- 17.8 kg were randomly assigned to a 54-week weight maintenance program that was combined with either: 1) 200 mg/d of sertraline; or 2) placebo. During the first 6 weeks, sertraline subjects lost significantly more weight and reported significantly greater reductions in hunger and preoccupation with food than did subjects on placebo. After this time, however, women in both conditions regained weight steadily. The 13 sertraline subjects who completed the 54-week study regained 17.7 +/- 10.6 kg of their original 26.3 +/- 7.6 kg loss, equal to a regain of 70.9 +/- 41.7%. The 17 placebo completers regained 11.8 +/- 9.0 kg of their 23.4 +/- 7.8 kg loss, equal to a 46.5 +/- 34.6% regain. End-of-treatment differences between groups in weight change were not statistically significant. Nor were there significant differences between the two conditions at any time in changes in fat-free mass, resting metabolic rate or dysphoria, all of which tended to increase with weight regain. The results are discussed in relation to findings from other long-term studies that combined diet and medication.

Psychiatric emergencies in the elderly.

Psychiatric disorders are best managed by interdisciplinary teams of psychiatrists, psychiatric nurses, social workers, and psychologists. Some Emergency Departments have access to such psychiatric services either in the hospital or in associated clinics or community mental health centers. Unfortunately, many are not staffed with mental health professionals or such expertise is available only on a limited basis, particularly on evenings and weekends. Therefore, one or more members of the Emergency Department staff should have specialized psychiatric training and experience. We have reviewed the format for conducting a psychiatric history and mental status examination and have discussed the most common emergency psychiatric disorders of the elderly and their management in the Emergency Department. In order to assess and treat elderly psychiatric patients properly, emergency personnel must be aware of the medical disorders associated with psychiatric illness and must be prepared to initiate treatment quickly and appropriately. For most patients, emergency intervention is the first step in ensuring that a correct diagnosis is made and that ongoing psychiatric treatment is arranged through timely consultation and referral.

Chronic Vietnam PTSD and acute civilian PTSD. A comparison of treatment experiences.

Many types of external trauma have been linked to the genesis of posttraumatic stress disorder (PTSD) and yet recent reports have focused almost exclusively on PTSD occurring in the Vietnam veteran (PTSD/veteran). The extent to which treatment experiences with PTSD/veteran can be generalized to other traumatized patients, for example, acute civilian populations, has not been investigated. Clinical observations comparing PTSD precipitated by a motor vehicle accident with PTSD/veteran suggested there were major differences between these two groups on the following variables: source of referral, age, sex, socioeconomic level, nature of stressor, timing of the stressor, character of the intrusive and avoidance symptoms, and treatment noncompliance behavior. These differences were of sufficient magnitude to call into question the feasibility, at this time, of constructing generalizations regarding PTSD utilizing only the PTSD/veteran population.

Methadone and naltrexone in the treatment of heroin dependence.

Over the past 20 years, methadone maintenance has been shown to be a safe, effective treatment for large numbers of heroin addicts. The majority of patients derive major benefits while in treatment, most measurably in the areas of decreased use of illicit opiates, diminished criminality, increased levels of employment and more stable interpersonal relationships. An advantage of methadone maintenance over other treatments is that it attracts and retains a relatively large segment of the addict population and is reasonably cost-effective. Naltrexone is well suited as a transitional treatment for individuals who have progressed using methadone maintenance. Patients completing a course of methadone maintenance should be encouraged to use naltrexone during the postmethadone period, when symptoms of protracted abstinence often lead them to reinitiate use of heroin. Those with stable family relationships, good jobs, minimal antisocial behavior, and low drug-craving before beginning a course of naltrexone appear to benefit most from the treatment. Rates of retention improve when naltrexone is used within a comprehensive rehabilitation program. Although addicted individuals are often stereotyped, they are, in fact, a heterogeneous group representing a range of psychopathologies and life situations. Thus, within any one facility, a variety of modalities should be available to allow treatment to be tailored to the individual. No single treatment is best for all patients, and, moreover, the preferred modality for any one individual may change over time as a result of progress in treatment or varying life circumstances. Multimodality programs that include methadone and naltrexone enable the maximal number of individuals to benefit from treatment.

Naltrexone: a clinical perspective.

The narcotic antagonist naltrexone was studied in over 300 opiate addicts. Patient selection was a major factor in determining retention and treatment outcome. Treatment time ranged from 1 week to over a year (mean = 2 months). A quarter of the study patients had multiple treatment episodes. Stabilized patients had few side effects, except for occasional nausea and abdominal cramps. Almost half the subjects tested naltrexone by using opiates at least once; all reported satisfactory narcotic blockade. Very few subjects switched to nonopiates to get high, although several did increase their alcohol consumption during the first weeks of therapy. One-third of subjects contacted in a follow-up study were opiate-free 6 months after stopping naltrexone, indicating a successful short-term treatment modality.