Grating-based x-ray dark-field CT for lung cancer diagnosis in mice.

BACKGROUND: The low absorption of x-rays in lung tissue and the poor resolution of conventional computed tomography (CT) limits its use to detect lung disease. However, x-ray dark-field imaging can sense the scattered x-rays deflected by the structures being imaged. This technique can facilitate the detection of small alveolar lesions that would be difficult to detect with conventional CT. Therefore, it may provide an alternative imaging modality to diagnose lung disease at an early stage. METHODS: Eight mice were inoculated with lung cancers simultaneously. Each time two mice were scanned using a grating-based dark-field CT on days 4, 8, 12, and 16 after the introduction of the cancer cells. The detectability index was calculated between nodules and healthy parenchyma for both attenuation and dark-field modalities. High-resolution micro-CT and pathological examinations were used to crosscheck and validate our results. Paired t-test was used for comparing the ability of dark-field and attenuation modalities in pulmonary nodule detection. RESULTS: The nodules were shown as a signal decrease in the dark-field modality and a signal increase in the attenuation modality. The number of nodules increased from day 8 to day 16, indicating disease progression. The detectability indices of dark-field modality were higher than those of attenuation modality (p = 0.025). CONCLUSIONS: Compared with the standard attenuation CT, the dark-field CT improved the detection of lung nodules. RELEVANCE STATEMENT: Dark-field CT has a higher detectability index than conventional attenuation CT in lung nodule detection. This technique could improve the early diagnosis of lung cancer. KEY POINTS: • Lung cancer progression was observed using x-ray dark-field CT. • Dark-field modality complements with attenuation modality in lung nodule detection. • Dark-field modality showed a detectability index higher than that attenuation in nodule detection.

Epigenetic balance ensures mechanistic control of MLL amplification and rearrangement.

MLL/KMT2A amplifications and translocations are prevalent in infant, adult, and therapy-induced leukemia. However, the molecular contributor(s) to these alterations are unclear. Here, we demonstrate that histone H3 lysine 9 mono- and di-methylation (H3K9me1/2) balance at the MLL/KMT2A locus regulates these amplifications and rearrangements. This balance is controlled by the crosstalk between lysine demethylase KDM3B and methyltransferase G9a/EHMT2. KDM3B depletion increases H3K9me1/2 levels and reduces CTCF occupancy at the MLL/KMT2A locus, in turn promoting amplification and rearrangements. Depleting CTCF is also sufficient to generate these focal alterations. Furthermore, the chemotherapy doxorubicin (Dox), which associates with therapy-induced leukemia and promotes MLL/KMT2A amplifications and rearrangements, suppresses KDM3B and CTCF protein levels. KDM3B and CTCF overexpression rescues Dox-induced MLL/KMT2A alterations. G9a inhibition in human cells or mice also suppresses MLL/KMT2A events accompanying Dox treatment. Therefore, MLL/KMT2A amplifications and rearrangements are controlled by epigenetic regulators that are tractable drug targets, which has clinical implications.

Unannotated microprotein EMBOW regulates the interactome and chromatin and mitotic functions of WDR5.

The conserved WD40-repeat protein WDR5 interacts with multiple proteins both inside and outside the nucleus. However, it is currently unclear whether and how the distribution of WDR5 between complexes is regulated. Here, we show that an unannotated microprotein EMBOW (endogenous microprotein binder of WDR5) dually encoded in the human SCRIB gene interacts with WDR5 and regulates its binding to multiple interaction partners, including KMT2A and KIF2A. EMBOW is cell cycle regulated, with two expression maxima at late G1 phase and G2/M phase. Loss of EMBOW decreases WDR5 interaction with KIF2A, aberrantly shortens mitotic spindle length, prolongs G2/M phase, and delays cell proliferation. In contrast, loss of EMBOW increases WDR5 interaction with KMT2A, leading to WDR5 binding to off-target genes, erroneously increasing H3K4me3 levels, and activating transcription of these genes. Together, these results implicate EMBOW as a regulator of WDR5 that regulates its interactions and prevents its off-target binding in multiple contexts.

The choice of an autocorrelation length in dark-field lung imaging.

Respiratory diseases are one of the most common causes of death, and their early detection is crucial for prompt treatment. X-ray dark-field radiography (XDFR) is a promising tool to image objects with unresolved micro-structures such as lungs. Using Talbot-Lau XDFR, we imaged inflated porcine lungs together with Polymethylmethacrylat (PMMA) microspheres (in air) of diameter sizes between 20 and 500 [Formula: see text] over an autocorrelation range of 0.8-5.2 [Formula: see text]. The results indicate that the dark-field extinction coefficient of porcine lungs is similar to that of densely-packed PMMA spheres with diameter of [Formula: see text], which is approximately the mean alveolar structure size. We evaluated that, in our case, the autocorrelation length would have to be limited to [Formula: see text] in order to image [Formula: see text]-thick lung tissue without critical visibility reduction (signal saturation). We identify the autocorrelation length to be the critical parameter of an interferometer that allows to avoid signal saturation in clinical lung dark-field imaging.

B-lymphoid tyrosine kinase-mediated FAM83A phosphorylation elevates pancreatic tumorigenesis through interacting with ß-catenin.

Abnormal activation of Wnt/ß-catenin-mediated transcription is closely associated with the malignancy of pancreatic cancer. Family with sequence similarity 83 member A (FAM83A) was shown recently to have oncogenic effects in a variety of cancer types, but the biological roles and molecular mechanisms of FAM83A in pancreatic cancer need further investigation. Here, we newly discovered that FAM83A binds directly to ß-catenin and inhibits the assembly of the cytoplasmic destruction complex thus inhibiting the subsequent phosphorylation and degradation. FAM83A is mainly phosphorylated by the SRC non-receptor kinase family member BLK (B-lymphoid tyrosine kinase) at tyrosine 138 residue within the DUF1669 domain that mediates the FAM83A-ß-catenin interaction. Moreover, FAM83A tyrosine 138 phosphorylation enhances oncogenic Wnt/ß-catenin-mediated transcription through promoting ß-catenin-TCF4 interaction and showed an elevated nucleus translocation, which inhibits the recruitment of histone deacetylases by TCF4. We also showed that FAM83A is a direct downstream target of Wnt/ß-catenin signaling and correlates with the levels of Wnt target genes in human clinical pancreatic cancer tissues. Notably, the inhibitory peptides that target the FAM83A-ß-catenin interaction significantly suppressed pancreatic cancer growth and metastasis in vitro and in vivo. Our results revealed that blocking the FAM83A cascade signaling defines a therapeutic target in human pancreatic cancer.

Iterative phase contrast CT reconstruction with novel tomographic operator and data-driven prior.

Breast cancer remains the most prevalent malignancy in women in many countries around the world, thus calling for better imaging technologies to improve screening and diagnosis. Grating interferometry (GI)-based phase contrast X-ray CT is a promising technique which could make the transition to clinical practice and improve breast cancer diagnosis by combining the high three-dimensional resolution of conventional CT with higher soft-tissue contrast. Unfortunately though, obtaining high-quality images is challenging. Grating fabrication defects and photon starvation lead to high noise amplitudes in the measured data. Moreover, the highly ill-conditioned differential nature of the GI-CT forward operator renders the inversion from corrupted data even more cumbersome. In this paper, we propose a novel regularized iterative reconstruction algorithm with an improved tomographic operator and a powerful data-driven regularizer to tackle this challenging inverse problem. Our algorithm combines the L-BFGS optimization scheme with a data-driven prior parameterized by a deep neural network. Importantly, we propose a novel regularization strategy to ensure that the trained network is non-expansive, which is critical for the convergence and stability analysis we provide. We empirically show that the proposed method achieves high quality images, both on simulated data as well as on real measurements.

Iterative signal retrieval for X-ray grating interferometry with dual-shot.

BACKGROUND: X-ray grating interferometry normally requires multiple steps and exposures, causing a prolonged imaging time. There is motivation to use fewer steps to reduce scanning time and complexity, while keeping fidelity of the retrieved signals. OBJECTIVE: We propose an iterative signal retrieval method, extracting attenuation, dark field contrast (DFC), and differential phase contrast (DPC) signals from two X-ray exposures. METHODS: Two shots were captured at G2 grating positions with difference of 1/4 grating period. The algorithm consists of two stages. At the first stage, amplitude of sample phase stepping curve retrieved by virtual phase stepping (VPS) method, visibility and local phase of background phase stepping curve are used to limit the results to the proximity of the ground truth. After the second stage, three high-quality parameters, amplitude, visibility, and local phase, are retrieved through finetuning, and three signals are calculated. Simulated and real-sample experiments were conducted to validate this method. RESULTS: We used standard phase stepping result as benchmark and calculated structural similarity (SSIM) and peak signal-to-noise ratio (PSNR) between benchmark and parameters retrieved by our dual-shot method and virtual phase stepping (VPS) method. For both simulated and real-sample experiments, the SSIM and PSNR value of dual-shot method are higher than those of VPS method. For real-sample method, we also conducted a three-step PS, and the SSIM and PSNR value of dual-shot method are slightly lower than those of three-step PS. CONCLUSION: Using our dual-shot method demonstrates higher performance than other single-shot method in retrieving high-quality signals, and it also reduces radiation dose and time.

Intensity-based iterative reconstruction for helical grating interferometry breast CT with static grating configuration.

Grating interferometry breast computed tomography (GI-BCT) has the potential to provide enhanced soft tissue contrast and to improve visualization of cancerous lesions for breast imaging. However, with a conventional scanning protocol, a GI-BCT scan requires longer scanning time and higher operation complexity compared to conventional attenuation-based CT. This is mainly due to multiple grating movements at every projection angle, so-called phase stepping, which is used to retrieve attenuation, phase, and scattering (dark-field) signals. To reduce the measurement time and complexity and extend the field of view, we have adopted a helical GI-CT setup and present here the corresponding tomographic reconstruction algorithm. This method allows simultaneous reconstruction of attenuation, phase contrast, and scattering images while avoiding grating movements. Experiments on simulated phantom and real initial intensity, visibility and phase maps are provided to validate our method.

INSIDEnet: Interpretable NonexpanSIve Data-Efficient network for denoising in grating interferometry breast CT.

PURPOSE: Breast cancer is the most common malignancy in women. Unfortunately, current breast imaging techniques all suffer from certain limitations: they are either not fully three dimensional, have an insufficient resolution or low soft-tissue contrast. Grating interferometry breast computed tomography (GI-BCT) is a promising X-ray phase contrast modality that could overcome these limitations by offering high soft-tissue contrast and excellent three-dimensional resolution. To enable the transition of this technology to clinical practice, dedicated data-processing algorithms must be developed in order to effectively retrieve the signals of interest from the measured raw data. METHODS: This article proposes a novel denoising algorithm that can cope with the high-noise amplitudes and heteroscedasticity which arise in GI-BCT when operated in a low-dose regime to effectively regularize the ill-conditioned GI-BCT inverse problem. We present a data-driven algorithm called INSIDEnet, which combines different ideas such as multiscale image processing, transform-domain filtering, transform learning, and explicit orthogonality to build an Interpretable NonexpanSIve Data-Efficient network (INSIDEnet). RESULTS: We apply the method to simulated breast phantom datasets and to real data acquired on a GI-BCT prototype and show that the proposed algorithm outperforms traditional state-of-the-art filters and is competitive with deep neural networks. The strong inductive bias given by the proposed model's architecture allows to reliably train the algorithm with very limited data while providing high model interpretability, thus offering a great advantage over classical convolutional neural networks (CNNs). CONCLUSIONS: The proposed INSIDEnet is highly data-efficient, interpretable, and outperforms state-of-the-art CNNs when trained on very limited training data. We expect the proposed method to become an important tool as part of a dedicated plug-and-play GI-BCT reconstruction framework, needed to translate this promising technology to the clinics.

The classification of renal stones by gratings-based dark-field radiography.

INTRODUCTION: Occurrence of urinary calculi is a common medical condition. Since treatment and prevention measures depend on the type of stone found, reliable diagnostic tools are required. Dual energy computed tomography (CT) allows for rough classification of the stones found. After extraction, stone composition can be confirmed by laboratory analysis.We investigated to which degree gratings-based X-ray interferometry, which can measure attenuation, refraction and scattering (dark-field) properties of samples, allows for the discrimination of urinary stone type by calculating the ratio (R) of attenuation and scattering signals. MATERIAL AND METHODS: In an experimental setup we investigated 322 renal stone fragments from 96 patients which were extracted during routine clinical practice. Laboratory analysis showed the chemical composition of the urinary stones.These were correlated with dark field analysis of the stone samples. Measurements were performed on a X-rays gratings interferometer prototype. The attenuation, refraction and scattering signals were measured and the R-value calculated. RESULTS: The spread of R-values of a given type of calculi is large, reducing the specificity of the method. Only uric acid stones can reliably be distinguished (sensitivity of 0.86 at a specificity of 0.9) from the other stones. CONCLUSIONS: Gratings-based dark-field imaging is a non-destructive and potentially non-invasive technique that allows to discriminate between uric acid and non-uric acid stones, which from a clinical point of view represents by far the most important question for stone treatment.

UHRF1 regulates alternative splicing by interacting with splicing factors and U snRNAs in a H3R2me involved manner.

The well-established functions of UHRF1 converge to DNA biological processes, as exemplified by DNA methylation maintenance and DNA damage repair during cell cycles. However, the potential effect of UHRF1 on RNA metabolism is largely unexplored. Here, we revealed that UHRF1 serves as a novel alternative RNA splicing regulator. The protein interactome of UHRF1 identified various splicing factors. Among them, SF3B3 could interact with UHRF1 directly and participate in UHRF1-regulated alternative splicing events. Furthermore, we interrogated the RNA interactome of UHRF1, and surprisingly, we identified U snRNAs, the canonical spliceosome components, in the purified UHRF1 complex. Unexpectedly, we found H3R2 methylation status determines the binding preference of U snRNAs, especially U2 snRNAs. The involvement of U snRNAs in UHRF1-containing complex and their binding preference to specific chromatin configuration imply a finely orchestrated mechanism at play. Our results provided the resources and pinpointed the molecular basis of UHRF1-mediated alternative RNA splicing, which will help us better our understanding of the physiological and pathological roles of UHRF1 in disease development.

Fabrication of X-ray Gratings for Interferometric Imaging by Conformal Seedless Gold Electroplating.

We present a method to produce small pitch gratings for X-ray interferometric imaging applications, allowing the phase sensitivity to be increased and/or the length of the laboratory setup to be minimized. The method is based on fabrication of high aspect ratio silicon microstructures using deep reactive ion etching (Bosch technique) of dense grating arrays and followed by conformal electroplating of Au. We demonstrated that low resistivity Si substrates (<0.01 Ohm·cm) enable the metal seeding layer deposition step to be avoided, which is normally required to initiate the electroplating process. Etching conditions were optimized to realize Si recess structures with a slight bottom tapering, which ensured the void-free Au filling of the trenches. Vapor HF was used to remove the native oxide layer from the Si grating surface prior to electroplating in the cyanide-based Au electrolyte. Fabrication of Au gratings with pitch in the range 1.2-3.0 µm was successfully realized. A substantial improved aspect ratio of 45:1 for a pitch size of 1.2 µm was achieved with respect to the prior art on 4-inch wafer-based technology. The fabricated Au gratings were tested with X-ray interferometers in Talbot-Laue configuration with measured visibility of 13% at an X-ray design energy of 26 keV.

High sensitivity X-ray phase contrast imaging by laboratory grating-based interferometry at high Talbot order geometry.

X-ray phase contrast imaging is a powerful analysis technique for materials science and biomedicine. Here, we report on laboratory grating-based X-ray interferometry employing a microfocus X-ray source and a high Talbot order (35th) asymmetric geometry to achieve high angular sensitivity and high spatial resolution X-ray phase contrast imaging in a compact system (total length <1 m). The detection of very small refractive angles (∼50 nrad) at an interferometer design energy of 19 keV was enabled by combining small period X-ray gratings (1.0, 1.5 and 3.0 µm) and a single-photon counting X-ray detector (75 µm pixel size). The performance of the X-ray interferometer was fully characterized in terms of angular sensitivity and spatial resolution. Finally, the potential of laboratory X-ray phase contrast for biomedical imaging is demonstrated by obtaining high resolution X-ray phase tomographies of a mouse embryo embedded in solid paraffin and a formalin-fixed full-thickness sample of human left ventricle in water with a spatial resolution of 21.5 µm.

Modeling of beam hardening effects in a dual-phase X-ray grating interferometer for quantitative dark-field imaging.

X-ray grating interferometry (XGI) can provide access to unresolved sub-pixel information by utilizing the so-called dark-field or visibility reduction contrast. A recently developed variant of conventional XGI named dual-phase grating interferometer, based only on phase-shifting structures, has allowed for straightforward micro-structural investigations over multiple length scales with conventional X-ray sources. Nonetheless, the theoretical framework of the image formation for the dark-field signal has not been fully developed yet, thus hindering the quantification of unresolved micro-structures. In this work, we expand the current theoretical formulation of dual-phase grating interferometers taking into account polychromatic sources and beam hardening effects. We propose a model that considers the contribution of beam hardening to the visibility reduction and accounts for it. Finally, the method is applied to previously acquired and new experimental data showing that discrimination between actual micro-structures and beam hardening effects can be achieved.

SETD5-Coordinated Chromatin Reprogramming Regulates Adaptive Resistance to Targeted Pancreatic Cancer Therapy.

Molecular mechanisms underlying adaptive targeted therapy resistance in pancreatic ductal adenocarcinoma (PDAC) are poorly understood. Here, we identify SETD5 as a major driver of PDAC resistance to MEK1/2 inhibition (MEKi). SETD5 is induced by MEKi resistance and its deletion restores refractory PDAC vulnerability to MEKi therapy in mouse models and patient-derived xenografts. SETD5 lacks histone methyltransferase activity but scaffolds a co-repressor complex, including HDAC3 and G9a. Gene silencing by the SETD5 complex regulates known drug resistance pathways to reprogram cellular responses to MEKi. Pharmacological co-targeting of MEK1/2, HDAC3, and G9a sustains PDAC tumor growth inhibition in vivo. Our work uncovers SETD5 as a key mediator of acquired MEKi therapy resistance in PDAC and suggests a context for advancing MEKi use in the clinic.

Can grating interferometry-based mammography discriminate benign from malignant microcalcifications in fresh biopsy samples?

PURPOSE: In addition to absorption imaging, grating interferometry-based mammography (GIM) is capable of detecting differential-phase and scattering signals. In particular, the scattering signal can enable a quantifiable characterization of breast lesions. The purpose of this study was to determine if suspicious microcalcifications associated with benign or malignant lesions can be discriminated based on their absorption and scattering properties. MATERIALS AND METHODS: In this prospective, ethically approved study, 62 patients (mean age 60 y, range 39-89) with suspicious microcalcifications, who underwent stereotactic biopsies, were included. Biopsies were measured with an experimental GIM device and the ratios of the scattering and absorption signal (R-value) for microcalcifications were calculated. The mean R-values for benign and malignant lesions associated with microcalcifications were compared with the final histopathological diagnosis using a t-test. RESULTS: Twenty of the 62 participants had microcalcifications associated with malignancy. Comparing the two largest histopathological sub-groups of fibrosis (n = 23) vs. ductal carcinoma in situ (n = 15) resulted in an average R-value of 4.08 for benign and 2.80 for malignant lesions; p = 0.07. All microcalcifications associated with malignancy had an R-value below 4.71. Excluding microcalcifications with an R-value above this threshold would result in an 11 % reduction of false positives. CONCLUSION: The novel GIM modality has the potential to non-invasively characterize microcalcifications and might aid in the discrimination of benign from malignant lesions in fresh biopsy samples.

Correction to: Towards clinical grating-interferometry mammography.

The article Towards clinical grating-interferometry mammography, written by Carolina Arboleda, Zhentian Wang, Konstantins Jefimovs, Thomas Koehler, Udo Van Stevendaal, Norbert Kuhn, Bernd David, Sven Prevrhal, Kristina Lång, Serafino Forte, Rahel Antonia Kubik-Huch, Cornelia Leo.

Towards clinical grating-interferometry mammography.

OBJECTIVES: Grating-interferometry-based mammography (GIM) might facilitate breast cancer detection, as several research works have demonstrated in a pre-clinical setting, since it is able to provide attenuation, differential phase contrast, and scattering images simultaneously. In order to translate this technique to the clinics, it has to be adapted to cover a large field-of-view within a clinically acceptable exposure time and radiation dose. METHODS: We set up a grating interferometer that fits into a standard mammography system and fulfilled the aforementioned conditions. Here, we present the first mastectomy images acquired with this experimental device. RESULTS AND CONCLUSION: Our system performs at a mean glandular dose of 1.6 mGy for a 5-cm-thick, 18%-dense breast, and a field-of-view of 26 × 21 cm2. It seems to be well-suited as basis for a clinical-environment device. Further, dark-field signals seem to support an improved lesion visualization. Evidently, the effective impact of such indications must be evaluated and quantified within the context of a proper reader study. KEY POINTS: • Grating-interferometry-based mammography (GIM) might facilitate breast cancer detection, since it is sensitive to refraction and scattering and thus provides additional tissue information. • The most straightforward way to do grating-interferometry in the clinics is to modify a standard mammography device. • In a first approximation, the doses given with this technique seem to be similar to those of conventional mammography.

The trigonometric orthogonality of phase-stepping curves in grating-based x-ray phase-contrast imaging: Integral property and its implications for noise optimization.

PURPOSE: Grating-based x-ray phase-contrast imaging (GPCI) is a promising technique for clinical applications as it can provide two newly emerging imaging modalities (differential phase-contrast and dark-field contrast) in addition to the conventional absorption contrast. As far, phase-stepping strategy is the most commonly used approach in GPCI to indirectly acquire differential phase-contrast and dark-field contrast. It is known that the obtained phase-stepping curves (PSCs) have the cosine property and the convolution property, leading to two types of information retrieval approaches in literature: the Fourier component analysis and the multi-order moment analysis. The purpose of this paper is to derive a new property of PSCs and apply the property to noise optimization for information retrieval. METHODS: Based on the cosine expression of the flat PSC without the sample and the well-established convolution relationship between the flat PSC and the sample PSC, we reveal an important integral property of PSCs: the inner product of PSCs and an arbitrary function contains only zero-order and first-order components in the Fourier series. Furthermore, we apply the property to the direct multi-order moment analysis and propose a set of generalized forms including an optimal one in the presence of noise. RESULTS: To validate the effectiveness of our analysis, we compared the simulated and real experiment results retrieved by the original direct multi-order moment analysis with the ones retrieved by our proposed noise-optimal form. A significant improvement of noise performance by our method is observed and the improvement ratio in differential phase-contrast is consistent with our theoretical calculation (39.2%). CONCLUSIONS: In this paper, we reveal a new integral property of the acquired PSCs with and without samples in GPCI, which can be applied to information retrieval approaches like the direct multi-order moment analysis. Then we optimize these approaches to improve the noise performance, offering great potentials of dose reduction in practical applications.

Diffractive small angle X-ray scattering imaging for anisotropic structures.

Insights into the micro- and nano-architecture of materials is crucial for understanding and predicting their macroscopic behaviour. In particular, for emerging applications such as meta-materials, the micrometer scale becomes highly relevant. The micro-architecture of such materials can be tailored to exhibit specific mechanical, optical or electromagnetic behaviours. Consequently, quality control at micrometer scale must be guaranteed over extended areas. Mesoscale investigations over millimetre sized areas can be performed by scanning small angle X-ray scattering methods (SAXS). However, due to their long measurement times, real time or operando investigations are hindered. Here we present a method based on X-ray diffractive optics that enables the acquisition of SAXS signals in a single shot (few milliseconds) over extended areas. This method is applicable to a wide range of X-ray sources with varying levels of spatial coherence and monochromaticity, as demonstrated from the experimental results. This enables a scalable solution of spatially resolved SAXS.