Applicability of Gene Expression in Saliva as an Alternative to Blood for Biodosimetry and Prediction of Radiation-induced Health Effects.

As the great majority of gene expression (GE) biodosimetry studies have been performed using blood as the preferred source of tissue, searching for simple and less-invasive sampling methods is important when considering biodosimetry approaches. Knowing that whole saliva contains an ultrafiltrate of blood and white blood cells, it is expected that the findings in blood can also be found in saliva. This human in vivo study aims to examine radiation-induced GE changes in saliva for biodosimetry purposes and to predict radiation-induced disease, which is yet poorly characterized. Furthermore, we examined whether transcriptional biomarkers in blood can also be found equivalently in saliva. Saliva and blood samples were collected in parallel from radiotherapy (RT) treated patients who suffered from head and neck cancer (n = 8) undergoing fractioned partial-body irradiations (1.8 Gy/fraction and 50-70 Gy total dose). Samples were taken 12-24 h before first irradiation and ideally 24 and 48 h, as well as 5 weeks after radiotherapy onset. Due to the low quality and quantity of isolated RNA samples from one patient, they had to be excluded from further analysis, leaving a total of 24 saliva and 24 blood samples from 7 patients eligible for analysis. Using qRT-PCR, 18S rRNA and 16S rRNA (the ratio being a surrogate for the relative human RNA/bacterial burden), four housekeeping genes and nine mRNAs previously identified as radiation responsive in blood-based studies were detected. Significant GE associations with absorbed dose were found for five genes and after the 2nd radiotherapy fraction, shown by, e.g., the increase of CDKN1A (2.0 fold, P = 0.017) and FDXR (1.9 fold increased, P = 0.002). After the 25th radiotherapy fraction, however, all four genes (FDXR, DDB2, POU2AF1, WNT3) predicting ARS (acute radiation syndrome) severity, as well as further genes (including CCNG1 [median-fold change (FC) = 0.3, P = 0.013], and GADD45A (median-FC = 0.3, P = 0.031)) appeared significantly downregulated (FC = 0.3, P = 0.01-0.03). A significant association of CCNG1, POU2AF1, HPRT1, and WNT3 (P = 0.006-0.04) with acute or late radiotoxicity could be shown before the onset of these clinical outcomes. In an established set of four genes predicting acute health effects in blood, the response in saliva samples was similar to the expected up- (FDXR, DDB2) or downregulation (POU2AF1, WNT3) in blood for up to 71% of the measurements. Comparing GE responses (PHPT1, CCNG1, CDKN1A, GADD45A, SESN1) in saliva and blood samples, there was a significant linear association between saliva and blood response of CDKN1A (R2 = 0.60, P = 0.0004). However, the GE pattern of other genes differed between saliva and blood. In summary, the current human in vivo study, (I) reveals significant radiation-induced GE associations of five transcriptional biomarkers in salivary samples, (II) suggests genes predicting diverse clinical outcomes such as acute and late radiotoxicity as well as ARS severity, and (III) supports the view that blood-based GE response can be reflected in saliva samples, indicating that saliva is a "mirror of the body" for certain but not all genes and, thus, studies for each gene of interest in blood are required for saliva.

Examining potential confounding factors in gene expression analysis of human saliva and identifying potential housekeeping genes.

Isolation of RNA from whole saliva, a non-invasive and easily accessible biofluid that is an attractive alternative to blood for high-throughput biodosimetry of radiological/nuclear victims might be of clinical significance for prediction and diagnosis of disease. In a previous analysis of 12 human samples we identified two challenges to measuring gene expression from total RNA: (1) the fraction of human RNA in whole saliva was low and (2) the bacterial contamination was overwhelming. To overcome these challenges, we performed selective cDNA synthesis for human RNA species only by employing poly(A)+-tail primers followed by qRT-PCR. In the current study, this approach was independently validated on 91 samples from 61 healthy donors. Additionally, we used the ratio of human to bacterial RNA to adjust the input RNA to include equal amounts of human RNA across all samples before cDNA synthesis, which then ensured comparable analysis using the same base human input material. Furthermore, we examined relative levels of ten known housekeeping genes, and assessed inter- and intra-individual differences in 61 salivary RNA isolates, while considering effects of demographical factors (e.g. sex, age), epidemiological factors comprising social habits (e.g. alcohol, cigarette consumption), oral hygiene (e.g. flossing, mouthwash), previous radiological diagnostic procedures (e.g. number of CT-scans) and saliva collection time (circadian periodic). Total human RNA amounts appeared significantly associated with age only (P ≤ 0.02). None of the chosen housekeeping genes showed significant circadian periodicity and either did not associate or were weakly associated with the 24 confounders examined, with one exception, 60% of genes were altered by mouthwash. ATP6, ACTB and B2M represented genes with the highest mean baseline expression (Ct-values ≤ 30) and were detected in all samples. Combining these housekeeping genes for normalization purposes did not decrease inter-individual variance, but increased the robustness. In summary, our work addresses critical confounders and provides important information for the successful examination of gene expression in human whole saliva.

Out-of-field doses for scanning proton radiotherapy of shallowly located paediatric tumours-a comparison of range shifter and 3D printed compensator.

The lowest possible energy of proton scanning beam in cyclotron proton therapy facilities is typically between 60 and 100 MeV. Treatment of superficial lesions requires a pre-absorber to deliver doses to shallower volumes. In most of the cases a range shifter (RS) is used, but as an alternative solution, a patient-specific 3D printed proton beam compensator (BC) can be applied. A BC enables further reduction of the air gap and consequently reduction of beam scattering. Such pre-absorbers are additional sources of secondary radiation. The aim of this work was the comparison of RS and BC with respect to out-of-field doses for a simulated treatment of superficial paediatric brain tumours. EURADOS WG9 performed comparative measurements of scattered radiation in the Proteus C-235 IBA facility (Cyclotron Centre Bronowice at the Institute of Nuclear Physics, CCB IFJ PAN, Kraków, Poland) using two anthropomorphic phantoms-5 and 10 yr old-for a superficial target in the brain. Both active detectors located inside the therapy room, and passive detectors placed inside the phantoms were used. Measurements were supplemented by Monte Carlo simulation of the radiation transport. For the applied 3D printed pre-absorbers, out-of-field doses from both secondary photons and neutrons were lower than for RS. Measurements with active environmental dosimeters at five positions inside the therapy room indicated that the RS/BC ratio of the out-of-field dose was also higher than one, with a maximum of 1.7. Photon dose inside phantoms leads to higher out-of-field doses for RS than BC to almost all organs with the highest RS/BC ratio 12.5 and 13.2 for breasts for 5 and 10 yr old phantoms, respectively. For organs closest to the isocentre such as the thyroid, neutron doses were lower for BC than RS due to neutrons moderation in the target volume, but for more distant organs like bladder-conversely-lower doses for RS than BC were observed. The use of 3D printed BC as the pre-absorber placed in the near vicinity of patient in the treatment of superficial tumours does not result in the increase of secondary radiation compared to the treatment with RS, placed far from the patient.

A New Standard DNA Damage (SDD) Data Format.

Our understanding of radiation-induced cellular damage has greatly improved over the past few decades. Despite this progress, there are still many obstacles to fully understand how radiation interacts with biologically relevant cellular components, such as DNA, to cause observable end points such as cell killing. Damage in DNA is identified as a major route of cell killing. One hurdle when modeling biological effects is the difficulty in directly comparing results generated by members of different research groups. Multiple Monte Carlo codes have been developed to simulate damage induction at the DNA scale, while at the same time various groups have developed models that describe DNA repair processes with varying levels of detail. These repair models are intrinsically linked to the damage model employed in their development, making it difficult to disentangle systematic effects in either part of the modeling chain. These modeling chains typically consist of track-structure Monte Carlo simulations of the physical interactions creating direct damages to DNA, followed by simulations of the production and initial reactions of chemical species causing so-called "indirect" damages. After the induction of DNA damage, DNA repair models combine the simulated damage patterns with biological models to determine the biological consequences of the damage. To date, the effect of the environment, such as molecular oxygen (normoxic vs. hypoxic), has been poorly considered. We propose a new standard DNA damage (SDD) data format to unify the interface between the simulation of damage induction in DNA and the biological modeling of DNA repair processes, and introduce the effect of the environment (molecular oxygen or other compounds) as a flexible parameter. Such a standard greatly facilitates inter-model comparisons, providing an ideal environment to tease out model assumptions and identify persistent, underlying mechanisms. Through inter-model comparisons, this unified standard has the potential to greatly advance our understanding of the underlying mechanisms of radiation-induced DNA damage and the resulting observable biological effects when radiation parameters and/or environmental conditions change.

Perturbations of radiation field caused by titanium dental implants in pencil proton beam therapy.

The aim of this study was to investigate the absorbed dose and the linear energy transfer (LET) of a scanning proton pencil beam at the Proton Therapy Center Czech, applied to phantoms containing metal implants. We investigated two different phantoms composed of commonly used metals with a known chemical composition. Two rectangular phantoms consisted of water-equivalent environment material with a 65 mm thickness surrounding the 2, 5, 10 and 15 mm inserts of grade-2 and grade-5 Titanium. Track-etched detectors (TEDs) were placed behind the phantoms to gather the data. The measured LET spectra behind the implants were compared with Monte Carlo simulations using the Geant4 toolkit, version 10.03.p01. The simulations were used to provide additional information regarding the contribution of each type of particles to the LET spectra (protons, alpha particles, deuteron, neutrons, photons, and electrons) and to estimate the LET spectra above the TED's detection threshold. We used two different beam energies to study the most pertinent irradiation scenarios, one in the Bragg curve plateau and one at the maximum. The measurement of the LET spectra behind phantoms irradiated with a proton beam in the plateau region of the Bragg curve led to the detection of numerous particles with a very high LET. Lateral dose enhancement at the border between implants and the plastic material was detected when the phantoms were exposed to a proton beam and the data were recorded in the Bragg peak maximum. In this area, the dose increased 13 times for grade-2 Ti and 12 times for grade-5 Ti. The performed experimental study highlights the effect of dental implants on the LET spectra and absorbed dose when a proton pencil beam is crossing high-density titanium.

Dose distribution of secondary radiation in a water phantom for a proton pencil beam-EURADOS WG9 intercomparison exercise.

Systematic 3D mapping of out-of-field doses induced by a therapeutic proton pencil scanning beam in a 300 × 300 × 600 mm3 water phantom was performed using a set of thermoluminescence detectors (TLDs): MTS-7 (7LiF:Mg,Ti), MTS-6 (6LiF:Mg,Ti), MTS-N (natLiF:Mg,Ti) and TLD-700 (7LiF:Mg,Ti), radiophotoluminescent (RPL) detectors GD-352M and GD-302M, and polyallyldiglycol carbonate (PADC)-based (C12H18O7) track-etched detectors. Neutron and gamma-ray doses, as well as linear energy transfer distributions, were experimentally determined at 200 points within the phantom. In parallel, the Geant4 Monte Carlo code was applied to calculate neutron and gamma radiation spectra at the position of each detector. For the cubic proton target volume of 100 × 100 × 100 mm3 (spread out Bragg peak with a modulation of 100 mm) the scattered photon doses along the main axis of the phantom perpendicular to the primary beam were approximately 0.5 mGy Gy-1 at a distance of 100 mm and 0.02 mGy Gy-1 at 300 mm from the center of the target. For the neutrons, the corresponding values of dose equivalent were found to be ~0.7 and ~0.06 mSv Gy-1, respectively. The measured neutron doses were comparable with the out-of-field neutron doses from a similar experiment with 20 MV x-rays, whereas photon doses for the scanning proton beam were up to three orders of magnitude lower.

CONTRIBUTION OF DIFFERENT PARTICLES MEASURED WITH TRACK ETCHED DETECTORS ONBOARD ISS.

Cosmic radiation consists of primary high-energy galactic and solar particles. When passing through spacecraft walls and astronauts' bodies, the spectrum becomes even more complex due to generating of secondary particles through fragmentation and nuclear interactions. Total radiation exposure is contributed by both these components. With an advantage, space research uses track etched detectors from the group of passive detectors visualizing the tracks of particles, in this case by etching. The detectors can discriminate between various components of cosmic radiation. A method is introduced for the separation of the different types of particles according to their range using track etched detectors. The method is demonstrated using detectors placed in Russian segment of the International Space Station in 2009. It is shown that the primary high-energy heavy ions with long range contribute up to 56% of the absorbed dose and up to 50% to the dose equivalent.

Track structure modeling in liquid water: A review of the Geant4-DNA very low energy extension of the Geant4 Monte Carlo simulation toolkit.

Understanding the fundamental mechanisms involved in the induction of biological damage by ionizing radiation remains a major challenge of today's radiobiology research. The Monte Carlo simulation of physical, physicochemical and chemical processes involved may provide a powerful tool for the simulation of early damage induction. The Geant4-DNA extension of the general purpose Monte Carlo Geant4 simulation toolkit aims to provide the scientific community with an open source access platform for the mechanistic simulation of such early damage. This paper presents the most recent review of the Geant4-DNA extension, as available to Geant4 users since June 2015 (release 10.2 Beta). In particular, the review includes the description of new physical models for the description of electron elastic and inelastic interactions in liquid water, as well as new examples dedicated to the simulation of physicochemical and chemical stages of water radiolysis. Several implementations of geometrical models of biological targets are presented as well, and the list of Geant4-DNA examples is described.

Dose-dependent micronuclei formation in normal human fibroblasts exposed to proton radiation.

Micronuclei are small extranuclear bodies resulting from chromosome fragments or the whole chromosomes secluded from daughter nuclei during mitosis. The number of radiation-induced micronuclei reflects the level of chromosomal damage and relates to an absorbed dose and quality of incident ionizing radiation. The aim of the present study was to determine the micronucleus formation as a specific biological marker for acute radiation-induced DNA damage in normal human fibroblasts exposed to 30-MeV protons and Co-60 gamma radiation. We found a linear increase in binuclear cells containing micronuclei for absorbed doses from 1 to 5 Gy for both radiation modalities. However, the total number of micronuclei in binuclear cells follows a linear-quadratic dose dependence. In case of human exposure to mixed radiation fields or high LET radiation, the proportion of binuclear cells containing micronuclei from all binuclear cells can thus serve as a good biomarker of radiation-induced DNA damage.

Contribution of indirect effects to clustered damage in DNA irradiated with protons.

Protons are the dominant particles both in galactic cosmic rays and in solar particle events and, furthermore, proton irradiation becomes increasingly used in tumour treatment. It is believed that complex DNA damage is the determining factor for the consequent cellular response to radiation. DNA plasmid pBR322 was irradiated at U120-M cyclotron with 30 MeV protons and treated with two Escherichia coli base excision repair enzymes. The yields of SSBs and DSBs were analysed using agarose gel electrophoresis. DNA has been irradiated in the presence of hydroxyl radical scavenger (coumarin-3-carboxylic acid) in order to distinguish between direct and indirect damage of the biological target. Pure scavenger solution was used as a probe for measurement of induced OH· radical yields. Experimental OH· radical yield kinetics was compared with predictions computed by two theoretical models-RADAMOL and Geant4-DNA. Both approaches use Geant4-DNA for description of physical stages of radiation action, and then each of them applies a distinct model for description of the pre-chemical and chemical stage.

Microdosimetry for a carbon ion beam using track-etched detectors.

Track-etched detectors (TED) have been used as linear energy transfer (LET) spectrometers in heavy ion beams for many years. LET spectra and depth-dose distribution of a carbon ion beam were measured behind polymethylmethacrylate degraders at Heavy Ion Medical Accelerator in Chiba, Japan. The measurements were performed along monoenergetic beam with energy 290 MeV u(-1) in different positions: (1) at beam extraction area, (2) at beginning, (3) maximum and (4) behind the Bragg peak region (0, 117, 147 and 151 mm of water-equivalent depth, respectively). The LET spectra inside and outside of the primary ion beam have been evaluated. TED record only heavy charged particles with LET above 8-10 keV µm(-1), while electrons and ions with lower LET are not detected. The Geant4 simulation toolkit version 4.9.6.P01 has been used to estimate the contribution of non-detected particles to absorbed dose. Presented results demonstrate the applicability of TED for microdosimetry measurements in therapeutic carbon ion beams.

Dose distribution outside the target volume for 170-MeV proton beam.

Dose delivered outside the proton field during radiotherapy can potentially lead to secondary cancer development. Measurements with a 170-MeV proton beam were performed with passive detectors (track etched detectors and thermoluminescence dosemeters) in three different depths along the Bragg curve. The measurement showed an uneven decrease of the dose outside of the beam field with local enhancements. The major contribution to the delivered dose is due to high-energy protons with linear energy transfer (LET) up to 10 keV µm(-1). However, both measurement and preliminary Monte Carlo calculation also confirmed the presence of particles with higher LET.

Radiation damage to DNA in DNA-protein complexes.

The most aggressive product of water radiolysis, the hydroxyl (OH) radical, is responsible for the indirect effect of ionizing radiations on DNA in solution and aerobic conditions. According to radiolytic footprinting experiments, the resulting strand breaks and base modifications are inhomogeneously distributed along the DNA molecule irradiated free or bound to ligands (polyamines, thiols, proteins). A Monte-Carlo based model of simulation of the reaction of OH radicals with the macromolecules, called RADACK, allows calculating the relative probability of damage of each nucleotide of DNA irradiated alone or in complexes with proteins. RADACK calculations require the knowledge of the three dimensional structure of DNA and its complexes (determined by X-ray crystallography, NMR spectroscopy or molecular modeling). The confrontation of the calculated values with the results of the radiolytic footprinting experiments together with molecular modeling calculations show that: (1) the extent and location of the lesions are strongly dependent on the structure of DNA, which in turns is modulated by the base sequence and by the binding of proteins and (2) the regions in contact with the protein can be protected against the attack by the hydroxyl radicals via masking of the binding site and by scavenging of the radicals.

Radiation-induced tetramer-to-dimer transition of Escherichia coli lactose repressor.

The wild type lactose repressor of Escherichia coli is a tetrameric protein formed by two identical dimers. They are associated via a C-terminal 4-helix bundle (called tetramerization domain) whose stability is ensured by the interaction of leucine zipper motifs. Upon in vitro gamma-irradiation the repressor losses its ability to bind the operator DNA sequence due to damage of its DNA-binding domains. Using an engineered dimeric repressor for comparison, we show here that irradiation induces also the change of repressor oligomerisation state from tetramer to dimer. The splitting of the tetramer into dimers can result from the oxidation of the leucine residues of the tetramerization domain.

Microdosimetry distributions for 40-200 MeV protons.

Theoretical calculations have been performed to obtain microdosimetrical characteristics for protons in energy range from 40 to 200 MeV. This energy range is a representative of proton energies in tissue during radiation therapy and it also represents a large portion of the proton fluency in the South Atlantic Anomaly. Distributions of deposited energy calculated using Monte Carlo track structure code TRIOL and own-made programs were compared with experimental data obtained using spherical tissue-equivalent proportional counter. A good agreement between calculated and experimentally obtained microdosimetry spectra has been found.

The comparison of calculated and experimental microdosimetric distributions for carbon ions.

The aim of this work is to present microdosimetric characteristics of 400 MeV amu(-1) and 500 MeV amu(-1) carbon ions obtained by theoretical calculations and to analyse them with respect to experimental data obtained by tissue-equivalent proportional counter in a scope of project ICCHIBAN and by etched track detector CR 39 Page irradiated by LHE nuclotron at JINR, Dubna, Russia. Track structures provided by Monte Carlo code TRIOL are used as an input data for calculations of energy distributions. The calculations of frequency f(y) and dose d(y) distributions are performed using own developed programs.