Chromatin and transcriptomic profiling uncover dysregulation of the Tip60 HAT/HDAC2 epigenomic landscape in the neurodegenerative brain

Disruption of histone acetylation-mediated gene control is a critical step in Alzheimer’s Disease (AD), yet chromatin analysis of antagonistic histone acetyltransferases (HATs) and histone deacetylases (HDACs) causing these alterations remains uncharacterized. We report the first Tip60 HAT versus HDAC2 chromatin (ChIP-seq) and transcriptional (RNA-seq) profiling study in Drosophila melanogaster brains that model early human AD. We find Tip60 and HDAC2 predominantly recruited to identical neuronal genes. Moreover, AD brains exhibit robust genome-wide early alterations that include enhanced HDAC2 and reduced Tip60 binding and transcriptional dysregulation. Orthologous human genes to co-Tip60/HDAC2 D. melanogaster neural targets exhibit conserved disruption patterns in AD patient hippocampi. Notably, we discovered distinct transcription factor binding sites close or within Tip60/HDAC2 co-peaks in neuronal genes, implicating them in coenzyme recruitment. Increased Tip60 protects against transcriptional dysregulation and enhanced HDAC2 enrichment genome-wide. We advocate Tip60 HAT/HDAC2 mediated epigenetic neuronal gene disruption as a genome-wide initial causal event in AD.

Intra-operative 3D guidance and edema detection in prostate brachytherapy using a non-isocentric C-arm

PURPOSE

Brachytherapy (radioactive seed insertion) has emerged as one of the most effective treatment options for patients with prostate cancer, with the added benefit of a convenient outpatient procedure. The main limitation in contemporary brachytherapy is faulty seed placement, predominantly due to the presence of intra-operative edema (tissue expansion). Though currently not available, the capability to intra-operatively monitor the seed distribution, can make a significant improvement in cancer control. We present such a system here.

METHODS

Intra-operative measurement of edema in prostate brachytherapy requires localization of inserted radioactive seeds relative to the prostate. Seeds were reconstructed using a typical non-isocentric C-arm, and exported to a commercial brachytherapy treatment planning system. Technical obstacles for 3D reconstruction on a non-isocentric C-arm include pose-dependent C-arm calibration; distortion correction; pose estimation of C-arm images; seed reconstruction; and C-arm to TRUS registration.

RESULTS

In precision-machined hard phantoms with 40-100 seeds and soft tissue phantoms with 45-87 seeds, we correctly reconstructed the seed implant shape with an average 3D precision of 0.35 mm and 0.24 mm, respectively. In a DoD Phase-1 clinical trial on six patients with 48-82 planned seeds, we achieved intra-operative monitoring of seed distribution and dosimetry, correcting for dose inhomogeneities by inserting an average of over four additional seeds in the six enrolled patients (minimum 1; maximum 9). Additionally, in each patient, the system automatically detected intra-operative seed migration induced due to edema (mean 3.84 mm, STD 2.13 mm, Max 16.19 mm).

CONCLUSIONS

The proposed system is the first of a kind that makes intra-operative detection of edema (and subsequent re-optimization) possible on any typical non-isocentric C-arm, at negligible additional cost to the existing clinical installation. It achieves a significantly more homogeneous seed distribution, and has the potential to affect a paradigm shift in clinical practice. Large scale studies and commercialization are currently underway.

Intra-operative 3D guidance in prostate brachytherapy using a non-isocentric C-arm

Intra-operative guidance in Transrectal Ultrasound (TRUS) guided prostate brachytherapy requires localization of inserted radioactive seeds relative to the prostate. Seeds were reconstructed using a typical C-arm, and exported to a commercial brachytherapy system for dosimetry analysis. Technical obstacles for 3D reconstruction on a non-isocentric C-arm included pose-dependent C-arm calibration; distortion correction; pose estimation of C-arm images; seed reconstruction; and C-arm to TRUS registration. In precision-machined hard phantoms with 40-100 seeds, we correctly reconstructed 99.8% seeds with a mean 3D accuracy of 0.68 mm. In soft tissue phantoms with 45-87 seeds and clinically realistic 15 degrees C-arm motion, we correctly reconstructed 100% seeds with an accuracy of 1.3 mm. The reconstructed 3D seed positions were then registered to the prostate segmented from TRUS. In a Phase-1 clinical trial, so far on 4 patients with 66-84 seeds, we achieved intra-operative monitoring of seed distribution and dosimetry. We optimized the 100% prescribed iso-dose contour by inserting an average of 3.75 additional seeds, making intra-operative dosimetry possible on a typical C-arm, at negligible additional cost to the existing clinical installation.

Sublethal damage repair times for a late-responding tissue relevant to brachytherapy (and external-beam radiotherapy): implications for new brachytherapy protocols

PURPOSE

Data were analyzed from recent experiments with the end point of late rectal obstruction in rats, involving acute and various protracted radiation exposures. Because the end point is of direct relevance both for brachytherapy as well as external beam radiotherapy, the goal was to estimate the linear-quadratic (LQ) parameters alpha/beta and T1/2, which are of importance for designing improved protraction/fractionation schemes.

METHODS AND MATERIALS

The data were fit to the LQ model, both in its standard form and in a form in which two different components of sublethal damage repair-fast and slow-are assumed. The design of the experiments was such that both slow and reasonably fast sublethal damage repair components should be separately estimated, if they were contributing to a significant degree.

RESULTS

LQ parameter estimates were alpha/beta = 4.6 Gy [4.0, 5.5] and T1/2 = 70.2 min [59.1, 91.4]. Despite the experimental design facilitating detection of a rapid component of repair, no statistically robust evidence for a very fast repair component was found.

CONCLUSIONS

The long estimated repair time for a late-responding normal-tissue end point with direct relevance to brachytherapy suggests a variety of possible brachytherapy protocols that may be more efficacious than continuous low dose rate irradiation. Just as a difference in alpha/beta ratios between early- and late-responding tissues are a central tenet in radiotherapy, so corresponding differences in T1/2 values have the potential to be exploited, particularly for brachytherapy.

Thermotolerance and radiation sensitizing effects of long duration, mild temperature hyperthermia

Clinical application of long duration hyperthermia at temperatures < 42 degrees C has traditionally been avoided because of the possibility of chronic thermotolerance development, such as is observed with rodent cells. In support of long duration hyperthermia, both rodent and human cells have been shown to be sensitized to low dose-rate irradiation by simultaneous heating at 40 or 41 degrees C. The relationship between these supposed contradictory responses to hyperthermia were investigated in rat 9L gliosarcoma cells in vitro. Thermotolerance developed during 41 degrees C heating with or without concurrent low dose-rate irradiation. Thermotolerance reached a maximum within 6 h during 41 degrees C heating and remained stable for at least 24 h. When cells were returned to 37 degrees C after heating at 41 degrees C for 6 h, thermotolerance remained stable for at least 12 h. The time course of thermotolerance development correlated with that of induction of 41 degrees C radiation sensitization. Radiation sensitization, on the other hand, was shown to be independent of thermotolerance because the protein synthesis inhibitor cycloheximide prevented thermotolerance induction but had no effect on radiation sensitization. We conclude that thermotolerance development during concurrent clinical application of long duration mild temperature hyperthermia and low dose-rate irradiation should not be a factor in altering treatment outcome.

Equivalence of continuous and pulse simulated low dose rate irradiation in 9L gliosarcoma cells at 37 degrees and 41 degrees C

The development of a brachytherapy technique that will use a scanning source to simulate continuous low dose rate irradiation holds the possibility of improving dose distributions and other clinically relevant factors as well as enhancing radiation safety. Rat 9L gliosarcoma cells growing in vitro have been used as a model to determine the role of fraction size when individual pulses of irradiation are given at appropriate intervals to result in an overall dose rate that is identical to currently applied continuous low dose rate irradiation. With an overall dose rate of 0.5 Gy/hr, cell killing was identical for fractionation schemes of 0.25 Gy every 0.5 hr, 1.00 Gy every 2.0 hr, and 3.00 Gy every 6.0 hr. The cell sensitivity of these schemes was also identical to continuous irradiation at the same overall dose rate. Increasing the fraction size to 6.0 Gy with intervals of 12 hr increased the cytotoxicity. This breaking point was above the Dq (3.9 Gy) of acutely irradiated 9L cells. These data support the hypothesis that continuous low dose rate irradiation can be simulated by fractionated high dose rate irradiation as long as the fraction size remains less than the Dq of the acute radiation response of the cells and the overall dose rate remains constant. The role of simultaneous heating at 41 degrees C during pulsed and continuous low dose rate irradiation was also investigated. Substantial sensitization was observed for both continuous low dose rate irradiation and pulse simulated low dose rate irradiation. The Do thermal enhancement ratios were 1.98 and 1.92, respectively. The above results demonstrate that modalities utilizing intermittent high dose rate irradiation can be designed such that they will be equivalent to continuous low dose rate irradiation, and that in either case simultaneous extended low temperature heating can greatly enhance the cytotoxic effects of these irradiations.