Classification of breast tissue using a laboratory system for small-angle x-ray scattering (SAXS)

Metal-Based Drug-DNA Interactions and Analytical Determination Methods

DNA structure has many potential places where endogenous compounds and xenobiotics can bind. Therefore, xenobiotics bind along the sites of the nucleic acid with the aim of changing its structure, its genetic message, and, implicitly, its functions. Currently, there are several mechanisms known to be involved in DNA binding. These mechanisms are covalent and non-covalent interactions. The covalent interaction or metal base coordination is an irreversible binding and it is represented by an intra-/interstrand cross-link. The non-covalent interaction is generally a reversible binding and it is represented by intercalation between DNA base pairs, insertion, major and/or minor groove binding, and electrostatic interactions with the sugar phosphate DNA backbone. In the present review, we focus on the types of DNA-metal complex interactions (including some representative examples) and on presenting the methods currently used to study them.

Spectroscopic diagnosis and metabolite characterization of cisplatin resistance regulated by FDFT1 in bladder cancer tissue

As is the case for most solid tumours, chemotherapy remains the backbone in the management of metastatic disease. However, the occurrence of chemotherapy resistance is a cause to worry, especially in bladder cancer. Extensive evidence indicates molecular changes in bladder cancer cells to be the underlying cause of chemotherapy resistance, including the reduced expression of farnesyl-diphosphate farnesyltransferase 1 (FDFT1) - a gene involved in cholesterol biosynthesis. This can likely be a hallmark in examining the resistance and sensitivity of chemotherapy drugs. This work performs spectroscopic analysis and metabolite characterization on resistant, sensitive, stable-disease and healthy bladder tissues. Raman spectroscopy has detected peaks at around 1003 cm-1 (squalene), 1178 cm-1 (cholesterol), 1258 cm-1 (cholesteryl ester), 1343 cm-1 (collagen), 1525 cm-1 (carotenoid), 1575 cm-1 (DNA bases) and 1608 cm-1 (cytosine). The peak parameters were examined, and statistical analysis was performed on the peak features, attaining significant differences between the sample groups. Small-angle x-ray scattering (SAXS) measurements observed the triglyceride peak together with 6th, 7th and 8th - order collagen peaks; peak parameters were also determined. Neutron activation analysis (NAA) detected seven trace elements. Carbon (Ca), magnesium (Mg), chlorine (Cl) and sodium (Na) have been found to have the greatest concentration in the sample groups, suggestive of a role as a biomarker for cisplatin resistance studies. Results from the present research are suggested to provide an important insight into understanding the development of drug resistance in bladder cancer, opening up the possibility of novel avenues for treatment through personalised interventions.

Examination of intestinal ultrastructure, bowel wall apoptosis and tight junctions in the early phase of sepsis

Gut hyperpermeability can be caused by either apoptosis of the intestinal epithelium or altered status, permeability or porosity of tight junctions. This project aims to elucidate these mechanisms in the early phase of sepsis. Eighteen male wild type mice were randomized to two groups. All mice received one single gavage of fluorescein isothiocyanate (FITC) dextran 30 min before intervention. One group (n = 10) underwent cecal ligation and puncture to induce sepsis. The other group (n = 8) was sham operated. Septic animals exhibited significantly increased permeability for FITC 8 h post-operatively. Significantly increased serum interleukin-6, tumor-necrosis-factor-alpha and interleukin-1-beta confirmed sepsis. Septic animals showed significant bowel wall inflammation of ileum and colon samples. PCR revealed significantly increased expression of claudin-2 and decreased expressions of claudin-4, tight-junction-protein-1 and occludin-1 resembling increased permeability of tight junctions. However, these alterations could not be confirmed at the protein level. Light microscopy revealed significant dilatation of intercellular spaces at the basal sections of intestinal epithelial cells (IEC) in septic animals confirmed by increased intercellular spaces at the level of tight junctions and adherens junctions in electron microscopy (TEM). In small angle X-ray scattering no increase in number or size of nanopores could be shown in the bowel wall. HOECHST staining and PCR of ileum samples for apoptosis markers proofed no relevant differences in intestinal epithelial cell apoptosis between the groups. Intestinal hyperpermeability in septic animals was most likely caused by alterations of the intercellular contacts and not by apoptosis or increased size/number of nanopores of intestinal epithelial cells in this murine model of early sepsis.

Assessing lesion malignancy by scanning small-angle x-ray scattering of breast tissue with microcalcifications

Scanning small-angle x-ray scattering (SAXS) measurements were performed on 36 formalin-fixed breast tissue biopsies obtained from two patients. All samples contained microcalcifications of type II, i.e. formed by hydroxyapatite. We demonstrate the feasibility of classifying breast lesions by scanning SAXS of tissues containing microcalcifications with a resolution of 35 [Formula: see text]m [Formula: see text] 30 [Formula: see text]m. We report a characteristic Bragg peak found around q  =  1.725 nm^-1 that occurs primarily for malignant lesions. Such a clear SAXS fingerprint is potentially linked to structural changes of breast tissue and corresponds to dimensions of about 3.7 nm. This material property could be used as an early indicator of malignancy development, as it is readily assessed by SAXS. If this fingerprint is combined with other known SAXS features, which also indicate the level of malignancy, such as lipid spacing and collagen periodicity, it could complement traditional pathology-based analyses. To confirm the SAXS-based classification, a histopathological workup and a gold standard histopathological diagnosis were conducted to determine the malignancy level of the lesions. Our aim is to report this SAXS fingerprint, which is clearly related to malignant breast lesions. However, any further conclusion based on our dataset is limited by the low number of patients and samples. Running a broad study to increase the number of samples and patients is of great importance and relevance for the breast-imaging community.

Synchrotron radiation biomedical imaging and radiotherapy: from the UK to the Antipodes

Although the general public might think of 'X-rays' as they are applied to imaging (radiography) and for the treatment of disease (radiotherapy), the use of synchrotron radiation (SR) X-ray beams in these areas of science was a minor activity 50 years ago. The largest gains in science from SR were seen to be in those areas where signals were weakest in laboratory instruments, such as X-ray diffraction and spectroscopy. As the qualities of SR X-rays were explored and more areas of science adopted SR-based methods, this situation changed. About 30 years ago, the clinical advantages of using SR X-ray beams for radiography, radiotherapy and clinical diagnostics started to be investigated. In the UK, a multi-disciplinary group, consisting of clinicians, medical physicists and other scientists working mainly with the Synchrotron Radiation Source (SRS) in Cheshire, started to investigate techniques for diagnosis and potentially a cure for certain cancers. This preliminary work influenced the design of new facilities being constructed around the world, in particular the Imaging and Medical Beam Line on the Australian Synchrotron in Melbourne. Two authors moved from the UK to Australia to participate in this exciting venture. The following is a personal view of some of the highlights of the early-year SRS work, following through to the current activities on the new facility in Australia. This article is part of the theme issue 'Fifty years of synchrotron science: achievements and opportunities'.

Novel Detection Scheme for X-ray Small-Angle Scattering

X-ray imaging techniques, including x-ray radiography and computed tomography, have been in use for decades and proven effective and indispensable in diagnosis and therapy due to their fine resolution and fast acquisition speed. However, the innate disadvantage of x-ray is the poor soft tissue contrast. Small-angle scattering signals were shown to provide unique information about the abnormality of soft tissues that is complementary to the traditional attenuation image. Currently, there is no effective small-angle scattering detection system. In this paper, we propose a new "collimation" design dedicated to capture a small-angle scattering radiographic image directly, which carries critical pathological information for differentiation between normal and abnormal tissues. Our design consists of two interlaced gratings so that both the primary flux and Compton scattering photons are effectively blocked to leave the apertures mainly open to small-angle scattering photons. Theoretical analysis and Monte Carlo simulations demonstrate that small-angle scattering radiography is feasible with our proposed technology.

Model-free classification of X-ray scattering signals applied to image segmentation

This article describes a modeling framework to relate the molecular orientation of nanostructures to polarized resonant soft X-ray scattering measurements using the Born approximation and a full tensor treatment.

In most cases, the analysis of small-angle and wide-angle X-ray scattering (SAXS and WAXS, respectively) requires a theoretical model to describe the sample’s scattering, complicating the interpretation of the scattering resulting from complex heterogeneous samples. This is the reason why, in general, the analysis of a large number of scattering patterns, such as are generated by time-resolved and scanning methods, remains challenging. Here, a model-free classification method to separate SAXS/WAXS signals on the basis of their inflection points is introduced and demonstrated. This article focuses on the segmentation of scanning SAXS/WAXS maps for which each pixel corresponds to an azimuthally integrated scattering curve. In such a way, the sample composition distribution can be segmented through signal classification without applying a model or previous sample knowledge. Dimensionality reduction and clustering algorithms are employed to classify SAXS/WAXS signals according to their similarity. The number of clusters, i.e. the main sample regions detected by SAXS/WAXS signal similarity, is automatically estimated. From each cluster, a main representative SAXS/WAXS signal is extracted to uncover the spatial distribution of the mixtures of phases that form the sample. As examples of applications, a mudrock sample and two breast tissue lesions are segmented.

High pressure Raman study of type-I collagen

The high pressure response of type-I collagen from bovine Achilles tendon is investigated with micro-Raman spectroscopy. Fluorinert™ and methanol-ethanol mixtures were used as pressure transmitting media (PTM) in a diamond anvil cell. The Raman spectrum of collagen is dominated by three bands centred at approximately 1450, 1660 and 2930 cm^-1 , attributed to C-H deformation, C=O stretching of the peptide bond (amide-I band) and C-H stretching modes respectively. Upon pressure increase, using Fluorinert™ as PTM, a shift towards higher frequencies of the C-H stretching and deformation peaks is observed. Contrary, the amide-I band peaks are shifted to lower frequencies with moderate pressure slopes. On the other hand, when using the alcohol mixture as PTM, the amide-I band exhibits more pronounced C=O bond softening, deduced from the shift to lower frequencies, suggesting a strengthening of the hydrogen bonds between glycine and proline residues of different collagen chains due to the presence of the polar alcohol molecules. Furthermore, some of the peaks exhibit abrupt changes in their pressure slopes at approximately 2 GPa, implying a variation in the compressibility of the collagen fibres. This could be attributed to a pitch change from 10/3 to 7/2, sliding of the tropocollagen molecules, twisting variation at the molecular level and/or elimination of the D-gaps induced by kink compression. All spectral changes are reversible upon pressure release, which indicates that denaturation has not taken place. Finally, a minor lipid phase contamination was detected in some sample spots. Its pressure response is also monitored.

X-ray diffraction tomography with limited projection information

X-ray diffraction tomography (XDT) records the spatially-resolved X-ray diffraction profile of an extended object. Compared to conventional transmission-based tomography, XDT displays high intrinsic contrast among materials of similar electron density and improves the accuracy in material identification thanks to the molecular structural information carried by diffracted photons. However, due to the weak diffraction signal, a tomographic scan covering the entire object typically requires a synchrotron facility to make the acquisition time more manageable. Imaging applications in medical and industrial settings usually do not require the examination of the entire object. Therefore, a diffraction tomography modality covering only the region of interest (ROI) and subsequent image reconstruction techniques with truncated projections are highly desirable. Here we propose a table-top diffraction tomography system that can resolve the spatially-variant diffraction form factor from internal regions within extended samples. We demonstrate that the interior reconstruction maintains the material contrast while reducing the imaging time by 6 folds. The presented method could accelerate the acquisition of XDT and be applied in portable imaging applications with a reduced radiation dose.

Correlation of X-ray diffraction signatures of breast tissue and their histopathological classification

This pilot study examines the correlation of X-ray diffraction (XRD) measurements with the histopathological analysis of breast tissue. Eight breast cancer samples were investigated. Each sample contained a mixture of normal and cancerous tissues. In total, 522 separate XRD measurements were made at different locations across the samples (8 in total). The resulting XRD spectra were subjected to principal component analysis (PCA) in order to determine if there were any distinguishing features that could be used to identify different tissue components. 99.0% of the variation between the spectra were described by the first two principal components (PC). Comparing the location of points in PC space with the classification determined by histopathology indicated correlation between the shape/magnitude of the XRD spectra and the tissue type. These results are encouraging and suggest that XRD could be used for the intraoperative or postoperative classification of bulk tissue samples.

Coherent scatter imaging Monte Carlo simulation

Conventional mammography can suffer from poor contrast between healthy and cancerous tissues due to the small difference in attenuation properties. Coherent scatter slot scan imaging is an imaging technique which provides additional information and is compatible with conventional mammography. A Monte Carlo simulation of coherent scatter slot scan imaging was performed to assess its performance and provide system optimization. Coherent scatter could be exploited using a system similar to conventional slot scan mammography system with antiscatter grids tilted at the characteristic angle of cancerous tissues. System optimization was performed across several parameters, including source voltage, tilt angle, grid distances, grid ratio, and shielding geometry. The simulated carcinomas were detectable for tumors as small as 5 mm in diameter, so coherent scatter analysis using a wide-slot setup could be promising as an enhancement for screening mammography. Employing coherent scatter information simultaneously with conventional mammography could yield a conventional high spatial resolution image with additional coherent scatter information.

Design for a coherent-scatter imaging system compatible with screening mammography

A system using a wide-slot beam and simple antiscatter grids or slots has been designed to provide a localized map of tissue type that could be overlaid on the simultaneous conventional transmission image to provide an inexpensive, low dose adjunct to conventional screening mammography. Depth information is obtainable from the stereoscopic viewing angles. The system was demonstrated to produce observable contrast between adipose tissue and a phantom chosen to mimic carcinoma at an exposure comparable with screening mammography. Imaging data was collected over a range of system parameters to optimize contrast and to allow verification of simulation modeling.

Small-angle scatter tomography with a photon-counting detector array

Small-angle x-ray scatter imaging has a high intrinsic contrast in cancer research and other applications, and provides information on molecular composition and micro-structure of the tissue. In general, the implementations of small-angle coherent scatter imaging can be divided into two main categories: direct tomography and angular dispersive computerized tomography. Based on the recent development of energy-discriminative photon-counting detector array, here we propose a computerized tomography setup based on energy-dispersive measurement with a photon-counting detector array. To show merits of the energy-dispersive approach, we have performed numerical tests with a phantom containing various tissue types, in comparison with the existing imaging approaches. The results show that with an energy resolution of ~6 keV, the energy dispersive tomography system with a broadband tabletop x-ray would outperform the angular dispersive system, which makes the x-ray small-angle scatter tomography promising for high-specificity tissue imaging.

Design and implementation of coded aperture coherent scatter spectral imaging of cancerous and healthy breast tissue samples

A scatter imaging technique for the differentiation of cancerous and healthy breast tissue in a heterogeneous sample is introduced in this work. Such a technique has potential utility in intraoperative margin assessment during lumpectomy procedures. In this work, we investigate the feasibility of the imaging method for tumor classification using Monte Carlo simulations and physical experiments. The coded aperture coherent scatter spectral imaging technique was used to reconstruct three-dimensional (3-D) images of breast tissue samples acquired through a single-position snapshot acquisition, without rotation as is required in coherent scatter computed tomography. We perform a quantitative assessment of the accuracy of the cancerous voxel classification using Monte Carlo simulations of the imaging system; describe our experimental implementation of coded aperture scatter imaging; show the reconstructed images of the breast tissue samples; and present segmentations of the 3-D images in order to identify the cancerous and healthy tissue in the samples. From the Monte Carlo simulations, we find that coded aperture scatter imaging is able to reconstruct images of the samples and identify the distribution of cancerous and healthy tissues (i.e., fibroglandular, adipose, or a mix of the two) inside them with a cancerous voxel identification sensitivity, specificity, and accuracy of 92.4%, 91.9%, and 92.0%, respectively. From the experimental results, we find that the technique is able to identify cancerous and healthy tissue samples and reconstruct differential coherent scatter cross sections that are highly correlated with those measured by other groups using x-ray diffraction. Coded aperture scatter imaging has the potential to provide scatter images that automatically differentiate cancerous and healthy tissue inside samples within a time on the order of a minute per slice.

Small-angle X-ray scattering method to characterize molecular interactions: Proof of concept

Characterizing biomolecular interactions is crucial to the understanding of biological processes. Existing characterization methods have low spatial resolution, poor specificity, and some lack the capability for deep tissue imaging. We describe a novel technique that relies on small-angle X-ray scattering signatures from high-contrast molecular probes that correlate with the presence of biomolecular interactions. We describe a proof-of-concept study that uses a model system consisting of mixtures of monomer solutions of gold nanoparticles (GNPs) as the non-interacting species and solutions of GNP dimers linked with an organic molecule (dimethyl suberimidate) as the interacting species. We report estimates of the interaction fraction obtained with the proposed small-angle X-ray scattering characterization method exhibiting strong correlation with the known relative concentration of interacting and non-interacting species.

Constrained X-ray tensor tomography reconstruction

Quite recently, a method has been presented to reconstruct X-ray scattering tensors from projections obtained in a grating interferometry setup. The original publications present a rather specialised approach, for instance by suggesting a single SART-based solver. In this work, we propose a novel approach to solving the inverse problem, allowing the use of other algorithms than SART (like conjugate gradient), a faster tensor recovery, and an intuitive visualisation. Furthermore, we introduce constraint enforcement for X-ray tensor tomography (cXTT) and demonstrate that this yields visually smoother results in comparison to the state-of-art approach, similar to regularisation.

An optimized table-top small-angle X-ray scattering set-up for the nanoscale structural analysis of soft matter

The paper shows how a table top superbright microfocus laboratory X-ray source and an innovative restoring-data algorithm, used in combination, allow to analyze the super molecular structure of soft matter by means of Small Angle X-ray Scattering ex-situ experiments. The proposed theoretical approach is aimed to restore diffraction features from SAXS profiles collected from low scattering biomaterials or soft tissues, and therefore to deal with extremely noisy diffraction SAXS profiles/maps. As biological test cases we inspected: i) residues of exosomes' drops from healthy epithelial colon cell line and colorectal cancer cells; ii) collagen/human elastin artificial scaffolds developed for vascular tissue engineering applications; iii) apoferritin protein in solution. Our results show how this combination can provide morphological/structural nanoscale information to characterize new artificial biomaterials and/or to get insight into the transition between healthy and pathological tissues during the progression of a disease, or to morphologically characterize nanoscale proteins, based on SAXS data collected in a room-sized laboratory.

The identification and differentiation of secondary colorectal cancer in human liver tissue using X-ray fluorescence, coherent scatter spectroscopy, and multivariate analysis

Secondary colorectal liver cancer is the most widespread malignancy in patients with colorectal cancer. The aim of this study is to identify and differentiate between normal liver tissue and malignant secondary colorectal liver cancer tissue using X-ray scattering and X-ray fluorescence spectroscopy to investigate the best combination of data that can be used to enable classification of these two tissue types. X-ray fluorescence (XRF) and coherent scatter data were collected for 24 normal and 24 tumor matched pair tissue samples. The levels of 12 elements (P, S, K, Ca, Cr, Fe, Cu, Zn, As, Se, Br, and Rb) were measured in all samples. When comparisons were made between normal and tumor tissues, statistically significant differences were determined for K (p = 0.046), Ca (p = 0.040), Cr (p = 0.011), Fe, Cu, Zn, Br, and Rb (p < 0.01). However, for P, S, As, and Se, no statistically significant differences were found (p > 0.05). For the coherent scatter spectra collected, three peaks due to adipose, fibrous content, and water content of tissue were observed. The amplitude, full width half-maximum, and area under both fibrous content and water content peaks were found to be significantly higher in secondary colorectal liver tumors compared with surrounding normal liver tissue (p < 0.05). However, no significant differences were found for the adipose peak parameters (p > 0.05). Soft independent modeling of class analogy was performed using the XRF, coherent scatter, and elemental ratio data separately, and the accuracy of the classification of 20 unknown samples was found to be 50, 30, and 80%, respectively. Further analysis has shown that using a combination of the XRF and coherent scatter data in a single combined model gave improved normal and tumor liver tissue classification, with an accuracy that was found to be 85%.

X-ray dark-field imaging modeling

Dark-field images are formed from x-ray small-angle scattering signals. The small-angle scattering signals are particularly sensitive to structural variation and density fluctuation on a length scale of several tens to hundreds of nanometers, offering a unique contrast mechanism to reveal subtle structural features of an object. In this study, based on the principle of energy conservation, we develop a physical model to describe the relationship between x-ray small-angle scattering coefficients of an object and dark-field intensity images. This model can be used to reconstruct volumetric x-ray small-angle scattering images of an object using classical tomographic algorithms. We also establish a relationship between the small-angle scattering intensity and the visibility function measured with x-ray grating imaging. The numerical simulations and phantom experiments have demonstrated the accuracy and practicability of the proposed model.