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.

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.

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.

Effect of Aggregatibacter actinomycetemcomitans from Aggressive Periodontitis patients on Streptococcus mutans.

OBJECTIVES: To determine in vivo association between Aggregatibacter actinomycetemcomitans (Aa) and Streptococcus mutans (Sm) in aggressive periodontitis patients (AgP) and the in vitro influence on Sm of saliva and of Aa strains isolated from individual Aa-positive patients. MATERIALS AND METHODS: Clinical indices and saliva samples were taken from 30 AgP patients. Aa and mutans streptococci levels were determined. Antibacterial effect of saliva from 12 Aa-positive patients, and their individual Aa strain, was checked turbidimetrically in vitro on Sm. RESULTS: Aa salivary level was inversely correlated with levels of mutans streptococci and directly correlated with pockets of ≥7 mm. During exponential growth phase: (i) All Aa-positive and Aa-negative saliva samples showed no significant influence on Sm growth. (ii) Each individually isolated Aa strain presented significant inhibitory effect on Sm growth. During stationary growth phase, all the above demonstrated an inhibitory effect on Sm growth, with significantly greater influence of Aa individual strains. CONCLUSION: Saliva of each AgP Aa-positive subject had an inhibitory effect on Sm growth, which is most likely derived from Aa bacterial physiology. This research raises the possibility that suppression of Aa due to periodontal treatment may increase Sm levels and hence caries incidence.

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.

Pan-tumor landscape of fibroblast growth factor receptor 1-4 genomic alterations.

BACKGROUND: Selective tyrosine kinase inhibitors targeting fibroblast growth factor receptor (FGFR) 1-4 genomic alterations are in development or have been approved for FGFR-altered cancers (e.g. bladder cancer and advanced intrahepatic cholangiocarcinoma). Understanding FGFR inhibitor-resistance mechanisms is increasingly relevant; we surveyed the pan-tumor landscape of FGFR1-4 genomic alterations [short variants (SVs), gene rearrangements (REs), and copy number alterations (CNAs)], including their association with tumor mutational burden (TMB) and the genomic comutational landscape. PATIENTS AND METHODS: Comprehensive genomic profiling of 355 813 solid tumor clinical cases was performed using the FoundationOne and FoundationOne CDx assays (Foundation Medicine, Inc.) to identify genomic alterations in >300 cancer-associated genes and TMB (determined on ≤1.1 megabases of sequenced DNA). RESULTS: FGFR1-4 SVs and REs occurred in 9603/355 813 (2.7%), and CNAs in 15 078/355 813 (4.2%) samples. Most common FGFR alterations for bladder cancer, intrahepatic cholangiocarcinoma, and glioma were FGFR3 SVs (1051/7739, 13.6%), FGFR2 REs (618/6641, 9.3%), and FGFR1 SVs (239/11 550, 2.1%), respectively. We found several, potentially clinically relevant, tumor-specific associations between FGFR1-4 genomic alterations and other genomic markers. FGFR3 SV-altered bladder cancers and FGFR1 SV-altered gliomas were significantly less likely to be TMB-high versus unaltered samples. FGFR3 SVs in bladder cancer significantly co-occurred with TERT and CDKN2A/B alterations; TP53 and RB1 alterations were mutually exclusive. In intrahepatic cholangiocarcinoma, FGFR2 REs significantly co-occurred with BAP1 alterations, whereas KRAS, TP53, IDH1, and ARID1A alterations were mutually exclusive. FGFR1 SVs in gliomas significantly co-occurred with H3-3A and PTPN11 alterations, but were mutually exclusive with TERT, EGFR, TP53, and CDKN2A/B alterations. CONCLUSIONS: Overall, our hypothesis-generating findings may help to stratify patients in clinical trials and guide optimal targeted therapy in those with FGFR alterations.

Candida, mutans streptococci, oral hygiene and caries in children.

OBJECTIVE: to test the association between Candida and mutans streptococci (ms), oral hygiene and caries levels and in children. METHODS: 22 boys and 12 girls (age 6 to 14.5 years) participated in the study. Each participant received a toothbrush, and was asked to brush his/her teeth after proper instructions. Dental caries and oral hygiene were recorded. Candida and ms levels were determined in saliva samples. RESULTS: Candida colonies were observed in 70.5% of the children. No association was found between Candida and caries or plaque and gingival indices. C. albicans-positive children demonstrated significantly higher brushing scores. CONCLUSIONS: Our findings may suggest that there is no clear association between Candida in saliva, and levels of cariogenic bacteria and caries risk in children.

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.

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.

Malignant osteoporosis and defective immunoregulation.

The linkage between immune cells and the osteoclast has become partially understood in the laboratory, but the full spectrum of clinical disorders of this relationship remain to be elucidated. We report a 29-month-old girl with recurrent infections and multiple fractures. Immune evaluation showed normal quantitative serum immunoglobulins but absent antibodies to the respiratory viruses and tetanus toxoid and decreased in vitro polyclonal-induced immunoglobulin production. Further analysis in vitro with separated lymphocyte populations showed normal B cell function but markedly increased suppressor T cell activity. The bone evaluation showed diffuse osteopenia on x-ray. Serum calcium, phosphorus, PTH, 25-hydroxyvitamin D, and 1,25-dihydroxyvitamin D were normal for age. Urinary calcium excretion (24 h) was, however, two times normal. An iliac crest biopsy confirmed the presence of extreme osteopenia with normal mineralization and numerous small atypical osteoclasts resorbing the bone. No circulating plasma resorptive activity was demonstrated. Calcitonin therapy markedly diminished the patient's hypercalciuria. We speculate that this patient's increased bone resorption, decreased bone formation, and suppressor activity may be linked by a common pathway involving the abnormal function of immune cells. Since no similar constellation of findings has been previously reported, this case may represent a new congenital disorder: severe osteopenia associated with increased osteoclast activity in association with a defect in T cell immunoregulation.

Measurement of tissue lithium concentration by lithium magnetic resonance spectroscopy in patients with bipolar disorder.

Measurements of the lithium concentration in the occipital pole of the head and calf muscle of nine patients with bipolar disorder in remission were performed using in vivo lithium-7 nuclear magnetic resonance spectroscopy (7Li NMR). 7Li NMR measurements were performed on a 1-m-bore, 1.85-T, superconducting magnet supplemented with a multinuclear spectrometer, using 11.5-cm-diameter surface coils. The average lithium concentration in the occipital pole was 0.36 +/- 0.10 mEq/L, whereas in the muscle it was 0.50 +/- 0.17 mEq/L, both lower than the average serum lithium concentration (0.79 +/- 0.23 mEq/L). The average brain/serum lithium concentration ratio was 0.47 +/- 0.12 whereas the average muscle/serum lithium concentration ratio was 0.66 +/- 0.20. There was a positive correlation between the brain versus serum and brain versus muscle lithium concentrations. The hypothesis is advanced that the minimal effective concentration of brain lithium concentration for maintenance treatment of bipolar disorder is around 0.2-0.3 mEq/L.

Age, as well as cell turnover kinetics, regulates brain/gut repair.

The prototypical brain/gut peptide cholecystokinin (CCK) has been used to assess brain and gut repair kinetics following cytotoxic injury in the rat. Studies addressed the effect of repetitive injury as well as aging. Injury was induced by one of the two alkylating agents, one active in the brain, the other systematically. Consistently the responses differ between brain and intestine. Total RNA falls (as predicted) in the intestine (control 1.5 +/- 1.4 versus cytotoxic 0.21 +/- 0.06 tRNA mg/organ, P < or = 0.0001), but rises (unexpectedly) in the brain (control 0.79 +/- 0.04 versus cytotoxic 1.02 +/- 0.03 tRNA mg/organ, P < or = 0.001). CCK mRNA concentration falls in the brain (predicted) (control 27 +/- 1 versus cytotoxic 11 +/- 1 pg CCK mRNA/micrograms tRNA, P < or = 0.001), but rises in the intestine (unexpectedly) (control 0.18 +/- 0.02 versus cytotoxic 0.3 +/- 0.04 pg CCK mRNA/micrograms tRNA, P < or = 0.001). CCK peptides do not change in the brain (control 39 +/- 4 versus cytotoxic 34 +/- 4 nmol/g, P < or = NS), but rise (unexpectedly) in the intestine (control 43 +/- 4 versus cytotoxic 250 +/- 27 nmol/g, P < or = 0.001). We ascribe these observations to differing brain/gut cell turnover kinetics. These data indicate that a rebound phenomenon occurs during gut recovery from cytotoxic injury. We additionally show a differential age-related response to cytotoxic injury. Younger animals tolerated the injury better than old ones (mortality: young 27% (3/11) versus old 66% (8/12), P < or = 0.001). Additionally, intestinal recovery is more rapid in younger animals. These data suggest that with increasing age, chemotherapeutic dosages may need to be modulated. It is additionally possible that clinically applicable algorithms may be developed using our animal model.

Is aging preprogrammed? Observations from the brain/gut axis.

Age related differential gene expression occurs in the neuro-enteral axis. Brain and gut organ weight, total RNA, total protein and three peptides were quantified in 4-, 10- and 37-week-old Sprague-Dawley rats. As animals aged, total RNA decreased in the brain (0.65 +/- 0.3-0.28 +/- 0.03 mg/g), but remained stable in the gut (2.6 +/- 0.3-2.9 +/- 0.4 mg/g). Total protein concentration rose in the duodenum (612 +/- 28-734 +/- 34 mg/g), while levels remained stable in the brain (641 +/- 54-666 +/- 34 mg/g). Three peptides were studied, cholecystokinin (CCK), VIP and secretin. With increasing age, significant changes were found only in CCK a true neural-enteral peptide. The concentration of smaller molecular forms of CCK decreased in the brain (248 +/- 18-188 +/- 21 pmol/g), while they remained stable in the duodenum (33 +/- 2-36 +/- 3 pmol/g). By contrast, the concentration of the larger forms of CCK were stable in the brain (36 +/- 3-40 +/- 4 pmol/g), but rose in the gut (89 +/- 14-134 +/- 17 pmol/g). These data indicate that as rats age there is preprogrammed differential control of gene expression between brain and intestine.

Activation of the renin system in acute pancreatitis.

Activity of the renin-angiotensin system was assessed in patients with acute pancreatitis. Measurements of active plasma renin and inactive plasma renin were made in normal subjects, patients with acute pancreatitis, and patients with acute abdominal pain syndromes exclusive of pancreatitis. Active plasma renin values were significantly increased in acute pancreatitis, nearly 500 percent higher than in the other two groups. Inactive plasma renin values were similar in the three groups. In a subgroup of patients with acute pancreatitis, measurements were made on presentation and after recovery. The elevated active plasma renin values on admission fell significantly with recovery, in parallel with changes in serum amylase values. Inactive plasma renin values changed variably; there was a significant inverse regression relationship between the changes in active and inactive plasma renin values with recovery. The results indicate that the renin-angiotensin system is activated in acute pancreatitis to a significantly greater extent than in other syndromes with acute abdominal pain. The increased active plasma renin in acute pancreatitis is most likely due to renal release secondary to the reduced circulating volume and hypotensive effect of this disease. However, changes in the relationship between active and inactive plasma renin in some patients suggest that activation of inactive renin by proteolytic enzymes released in acute pancreatitis might play an additional role.

Unsuspected nutritional rickets.

Based on the presentation and clinical features of four cases of nutritional rickets, it is suggested that particular groups of children, namely vegetarians, children breast-fed for an unusually long time, and black children, are at risk to develop the nutritional deficiencies of vitamin D and calcium that lead to clinical rickets. The diagnoses in these cases were made by fortuitous radiologic examination, even though the children had been receiving regular pediatric supervision, indicating a lack of awareness of the condition. This report is intended to emphasize the reemergence of nutritional rickets and to illustrate the different modes of its clinical presentation.

New syndrome of hydrocephalus, endocardial fibroelastosis, and cataracts (HEC syndrome).

We report on two unrelated male infants with similar findings of communicating hydrocephalus, endocardial fibroelastosis (EFE) and congenital cataracts, who died at 4 months of age. Both mothers reported an upper respiratory infection during the first trimester of pregnancy which was further complicated by polyhydramnios in the third trimester. The infants were diagnosed with bilateral congenital nuclear cataracts at birth. Serologic tests for toxoplasmosis, rubella, cytomegalovirus, herpes simplex virus, syphilis, and galactosemia screens were negative. Chromosome analyses were normal. Both children developed communicating hydrocephalus between one and three months after birth. Patient 1 died suddenly at 4 months following an upper respiratory infection. Patient 2 developed congestive heart failure and also died at 4 months. At autopsy, both infants had enlarged hearts with endocardial fibroelastosis. No identifiable organism could be isolated. We discuss the association of birth defects in widely separated organ systems in these patients and suggest that this may represent a genetic syndrome; however, a viral etiology cannot entirely be excluded. We believe this is a distinct disorder and propose the acronym HEC for hydrocephalus, EFE and cataracts.

Arteriohepatic dysplasia (Alagille syndrome): extreme variability among affected family members.

We describe a three-generation family in which five individuals have arteriohepatic dysplasia (Alagille syndrome) with striking differences in the degree of severity. Two sisters presented with neonatal jaundice, peripheral pulmonic stenosis, and characteristic facial appearance including a broad forehead, deep-set eyes, prominent nose, and pointed chin. One died at 5 years of cirrhosis with portal hypertension and the other at 18 months of congestive heart failure. Their asymptomatic 32-year-old mother and 35-year-old maternal aunt have a similar facial appearance, pulmonic stenosis, skeletal anomalies, and bilateral posterior embryotoxon. Neither has evidence of clinical liver disease. The maternal grandfather, who refused evaluation, has a similar appearance, a history of liver disease, and a heart murmur. Extreme intrafamilial variability has not been reported previously and most affected individuals described in the past have followed a benign course. The pattern of severity in this family suggests the possibility of a maternal factor augmenting the clinical expression in affected offspring. The skeletal anomalies and posterior embryotoxon are valuable signs in detecting asymptomatic but affected individuals who are at risk for having offspring with this potentially lethal condition.

Unusual mosaicism of de novo structural abnormalities and ocular anomalies in a male with 13 trisomy syndrome.

A body with the 13 trisomy syndrome was found to have a unique form of mosaicism in which each of the two cell lines had different structural rearrangements. The predominant cell line was partially trisomic for the distal portion of the long arm of chromosome 13, while the minor cell line was trisomic for all of the long arm of 13. The patient is also unusual because he had congenital glaucoma and was still alive at 10 years.