Phylogenetic modeling of enhancer shifts in African mole-rats reveals regulatory changes associated with tissue-specific traits.

Changes in gene regulation are thought to underlie most phenotypic differences between species. For subterranean rodents such as the naked mole-rat, proposed phenotypic adaptations include hypoxia tolerance, metabolic changes, and cancer resistance. However, it is largely unknown what regulatory changes may associate with these phenotypic traits, and whether these are unique to the naked mole-rat, the mole-rat clade, or are also present in other mammals. Here, we investigate regulatory evolution in the heart and liver from two African mole-rat species and two rodent outgroups using genome-wide epigenomic profiling. First, we adapted and applied a phylogenetic modeling approach to quantitatively compare epigenomic signals at orthologous regulatory elements and identified thousands of promoter and enhancer regions with differential epigenomic activity in mole-rats. These elements associate with known mole-rat adaptations in metabolic and functional pathways and suggest candidate genetic loci that may underlie mole-rat innovations. Second, we evaluated ancestral and species-specific regulatory changes in the study phylogeny and report several candidate pathways experiencing stepwise remodeling during the evolution of mole-rats, such as the insulin and hypoxia response pathways. Third, we report nonorthologous regulatory elements overlap with lineage-specific repetitive elements and appear to modify metabolic pathways by rewiring of HNF4 and RAR/RXR transcription factor binding sites in mole-rats. These comparative analyses reveal how mole-rat regulatory evolution informs previously reported phenotypic adaptations. Moreover, the phylogenetic modeling framework we propose here improves upon the state of the art by addressing known limitations of inter-species comparisons of epigenomic profiles and has broad implications in the field of comparative functional genomics.

Propranolol's effects on the sleep of infants with hemangiomas: A prospective pilot study.

OBJECTIVE: To assess propranolol's impact on sleep when used in infants and toddlers with infantile hemangioma (80% under 6 months old). METHODS: Parents and caregivers of infants and toddlers with infantile hemangioma presenting to a tertiary pediatric hospital's dermatology clinic and assessed by their dermatologist as requiring propranolol treatment were invited to participate. All participants completed an extended version of the Brief Infant Sleep Questionnaire (BISQ) prior to propranolol treatment initiation, which acted as the control, and 5 weeks after treatment commencement. Objective data were gathered through actigraphy, which utilizes a small wristwatch-like device that measures sleep-wake patterns, for 1 week prior to initiation and again 5 weeks after commencement. BISQ responses and actigraphy values from the two time points were compared. RESULTS: 55 infants and toddlers (aged 0-2.8 years, 80% under 6 months) were included. Sleep was reported as only a minor problem by most parents 5 weeks after starting propranolol (P = .049). Subgroup analysis of 45 infants <6 months old showed no significant difference in sleep while taking propranolol. Whole cohort BISQ data analysis showed a statistically significant increase in night-time sleep (P = .024), and a decrease in the number (P = .003) and duration of daytime naps (P = .025) following commencement of propranolol. Actigraphy data completed in 10 infants showed no significant difference in sleep quality before and 5 weeks after commencing propranolol. CONCLUSION: Propranolol did not significantly impair sleep quality and pattern in our cohort of infants and toddlers with infantile hemangioma. Most parents considered the impact on sleep to be only a minor problem.

The role of Gamma Knife Radiosurgery in the management of unresectable gross disease or gross residual disease after surgery in ependymoma.

PURPOSE/OBJECTIVE: To evaluate the efficacy and the toxicity of Gamma Knife (GK)-based stereotactic radiosurgery (SRS) in the management of gross disease in ependymoma. MATERIALS AND METHODS: Eight patients with 13 ependymomas were treated with GK-based SRS in our institution for gross disease. Five patients were treated for recurrent disease that developed after surgery and external beam radiotherapy (EBRT), two received SRS to the gross disease after surgery and EBRT, and one received SRS alone (in a 1.3 year old child). Median EBRT dose was 54.4 Gy (range 50-55.8 Gy). Median SRS dose was 14 Gy (range 12-20 Gy). Seven of eight (87.5%) patients had SRS to a single lesion and one of eight (12.5%) patients had treatment to six tumors in three different sessions. RESULTS: The median follow up was 30.2 months (range 8-65.4 months). Out of the eight patients treated with SRS, six (75%) were alive, four (50%) were alive with no recurrence, two (25%) were alive with recurrence, and two (25%) died of recurrent disease. Both patients treated with SRS as a boost were alive and without recurrence. Out of the five patients who received SRS as salvage treatment, three (60%) were alive, two (40%) were alive without recurrence, two (40%) developed distant failure, and three (60%) had in-field control. Two patients who received SRS to their brainstem lesions developed symptoms related to radionecrosis and were successfully treated with steroid with good control of symptoms. CONCLUSIONS: GK-based SRS appears to be a feasible and safe treatment modality for patients with ependymoma with unresectable gross disease or gross residual disease after surgery. SRS provides reasonable local control but out-of-field tumor progression remains an issue. For patients who receive SRS as a boost, the local control appears to be excellent.

Extracranial stereotactic radioablation: results of a phase I study in medically inoperable stage I non-small cell lung cancer.

INTRODUCTION: Surgical resection is standard therapy for patients with stage I non-small cell lung cancer (NSCLC), however, many patients are medically inoperable. We set out to investigate a new therapy akin to brain radiosurgery called extracranial stereotactic radioablation (ESR) in a phase I trial. PATIENTS AND METHODS: Eligible patients included those with clinically staged T1 or T2 (tumor size, < or = 7 cm) N0M0 biopsy confirmed NSCLC. All patients had comorbid medical problems that precluded thoracotomy. The median age was 75 years, and the median Karnofsky performance status was 80. ESR was administered in three separate fractions over 2 weeks. Three to five patients were treated within each dose cohort starting at 800 cGy per fraction (total, 2,400 cGy) followed by successive dose escalations of 200 cGy per fraction (total increase per cohort, 600 cGy). Waiting periods occurred between dose cohorts to observe toxicity. Patients with T1 vs T2 tumors underwent separate independent dose escalations. RESULTS: A total of 37 patients were enrolled since February 2000. One patient experienced grade 3 pneumonitis, and another patient had grade 3 hypoxia. For the entire population, there was no appreciable decline in cardiopulmonary function as measured by symptoms, physical examination, need for oxygen supplementation, pulmonary function testing, arterial blood gas determinations, or regular chest imaging. Both T-stage groups ultimately reached and tolerated 2,000 cGy per fraction for three fractions (total, 6,000 cGy). The maximum tolerated dose for this therapy in either T-stage group has yet to be reached. Tumors responded to treatment in 87% of patients (complete response, 27%). After a median follow-up period of 15.2 months, six patients experienced local failure, all of whom had received doses of < 1,800 cGy per fraction. CONCLUSIONS: Very high radiation dose treatments were tolerated in this population of medically inoperable patients with stage I NSCLC using ESR techniques.