SEM3De: image restoration for FIB-SEM.

Motivation: FIB-SEM (Focused Ion Beam-Scanning Electron Microscopy) is a technique to generate 3D images of samples up to several microns in depth. The principle is based on the alternate use of SEM to image the surface of the sample (a few nanometers thickness) and of FIB to mill the surface of the sample a few nanometers at the time. In this way, huge stacks of images can thus be acquired.Although this technique has proven useful in imaging biological systems, the presence of some visual artifacts (stripes due to sample milling, detector saturation, charge effects, focus or sample drift, etc.) still raises some challenges for image interpretation and analyses. Results: With the aim of meeting these challenges, we developed a freeware (SEM3De) that either corrects artifacts with state-of-the-art approaches or, when artifacts are impossible to correct, enables the replacement of artifactual slices by an in-painted image created from adjacent non-artifactual slices. Thus, SEM3De improves the overall usability of FIB-SEM acquisitions. Availability and implementation: SEM3De can be downloaded from https://sourceforge.net/projects/sem3de/ as a plugin for ImageJ.

New method for quantification of intratumoral heterogeneity: a feasibility study on Ktrans maps from preclinical DCE-MRI.

OBJECT: To develop new imaging biomarkers of therapeutic efficacy through the quantification of intratumoral microvascular heterogeneity. MATERIALS AND METHODS: The described method was a combination of non-supervised clustering and extraction of intratumoral complexity features (ICF): number of non-connected objects, volume fraction. It was applied to a set of 3D DCE-MRI Ktrans maps acquired previously on tumor bearing mice prior to and on day 4 of anti-angiogenic treatment. Evolutions of ICF were compared to conventional summary statistics (CSS) and to heterogeneity related whole tumor texture features (TF) on treated (n = 9) and control (n = 6) mice. RESULTS: Computed optimal number of clusters per tumor was 4. Several intratumoral features extracted from the clusters were able to monitor a therapy effect. Whereas no feature significantly changed for the control group, 6 features significantly changed for the treated group (4 ICF, 2 CSS). Among these, 5 also significantly differentiated the two groups (3 ICF, 2 CSS). TF failed in demonstrating differences within and between the two groups. DISCUSSION: ICF are potential imaging biomarkers for anti-angiogenic therapy assessment. The presented method may be expected to have advantages with respect to texture analysis-based methods regarding interpretability of results and setup of standardized image analysis protocols.

NRL and CRX Define Photoreceptor Identity and Reveal Subgroup-Specific Dependencies in Medulloblastoma.

Cancer cells often express differentiation programs unrelated to their tissue of origin, although the contribution of these aberrant phenotypes to malignancy is poorly understood. An aggressive subgroup of medulloblastoma, a malignant pediatric brain tumor of the cerebellum, expresses a photoreceptor differentiation program normally expressed in the retina. We establish that two photoreceptor-specific transcription factors, NRL and CRX, are master regulators of this program and are required for tumor maintenance in this subgroup. Beyond photoreceptor lineage genes, we identify BCL-XL as a key transcriptional target of NRL and provide evidence substantiating anti-BCL therapy as a rational treatment opportunity for select MB patients. Our results highlight the utility of studying aberrant differentiation programs in cancer and their potential as selective therapeutic vulnerabilities.

Quality of life, shoulder range of motion, and spinal accessory nerve status in 5-year survivors of head and neck cancer.

OBJECTIVE: To determine the association of neck dissection and radiation treatment for head and neck cancer (HNC) with subsequent shoulder range of motion (ROM) and quality of life (QOL) in 5-year survivors. DESIGN: A cross-sectional convenience sample. SETTING: Otolaryngology clinics at tertiary care hospital and Veterans Affairs medical center. PATIENTS: Five-year, disease-free survivors of HNC. METHODS: Demographic and cancer treatment information was collected, including type of neck dissection (none, spinal accessory "nerve sparing," and "nerve sacrificing") and radiation. QOL questionnaires were administered, and shoulder ROM was measured. MAIN OUTCOME MEASUREMENTS: University of Washington Quality of Life (UWQOL), Functional Assessment of Cancer Therapy (FACT) Head and Neck, and Performance Status Scale for Head and Neck. Shoulder ROM measurements included abduction, adduction, flexion, extension, internal and external rotation. RESULTS: One hundred and five survivors completed QOL surveys; 85 survivors underwent additional shoulder ROM evaluations. The nerve sacrifice group exhibited significantly poorer scores for UWQOL measures of disfigurement, level of activity, recreation and/or entertainment, speech and shoulder disability, and willingness to eat in public, FACT functional well-being, and FACT Head and Neck (P < .05). Shoulder ROM for flexion and abduction was poorest in the nerve sacrifice group (P < .05). Radiation was associated with significantly worse UWQOL swallowing (P < .05), but no other differences were found for QOL or ROM measurements. Decreased QOL scores were associated with decreased shoulder flexion and abduction (P < .05). Survivors with decreased shoulder abduction had significantly (P < .05) worse scores in disfigurement, recreation and/or entertainment, employment, shoulder disability, and FACT emotional well-being. CONCLUSIONS: Sparing the spinal accessory nerve during neck dissection is associated with significantly less long-term shoulder disability in 5-year survivors of HNC. QOL measures demonstrated the highest level of function in the no dissection group, an intermediate level of functioning with nerve sparing, and poorest function when the nerve is sacrificed. Decreased shoulder flexion and abduction is associated with reduced QOL in long-term survivors of HNC.

T2*-relaxivity contrast imaging: first results.

In this study, T2*- relaxivity contrast imaging (RCI) is proposed for new contrast generation in MRI. The method produces images of relaxivities r*2,vasc and r*2,EES caused by susceptibility gradients across the vessel walls and cell membranes, respectively. The sensitivity to noise was assessed with a simulation study, and initial results are presented for five colorectal tumor xenografts in nude mice. Simulations show that the new relaxivity parameters are at least as accurate and precise as standard parameters such as plasma volume and interstitial volume. Mean values of both relaxivities were significantly different (r*2,vasc=10.9±2.9 mM(-1) s(-1) and r*2,EES=15.6±2.6 mM(-1) s(-1)). r*2,vasc (r=0.67) and r*2,EES (r=0.52) were weakly correlated with plasma volume and interstitial volume, respectively. Images of r*2,vasc and r*2,EES reveal a different tumor structure than plasma volume and interstitial volume maps. These results suggest that relaxivity contrast imaging is practically feasible and might offer supplementary information compared to dynamic contrast-enhanced-MRI.

Radial multigradient-echo DCE-MRI for 3D K(trans) mapping with individual arterial input function measurement in mouse tumor models.

The purpose of this study was to provide proof of concept for a new three-dimensional (3D) radial dynamic contrast enhanced MRI acquisition technique, called "Radial Entire Tumor with Individual Arterial input function dynamic contrast-enhanced MRI" (RETIA dynamic contrast-enhanced MRI), which allows for the simultaneous measurement of an arterial input function in the mouse heart at 2 s temporal resolution and coverage of the whole tumor. Alternating 2D and 3D projections contribute to the 2D heart image or 3D tumor data with a 3-cm field of view. Sixty-four 2D images of the heart are obtained during acquisition of each 3D tumor dataset. In a pilot study, global K(trans) and ve values were measured in four mice, in a respiratory motion-animated subcutaneously implanted breast tumor model. This technique is expected to be most useful for the characterization of microvasculature in motion-animated orthotopic tumors.

2D and 3D radial multi-gradient-echo DCE MRI in murine tumor models with dynamic R*2-corrected R1 mapping.

Dynamic contrast-enhanced MRI is extensively studied to define and evaluate biomarkers for early assessment of vasculature-targeting therapies. In this study, two-dimensional and three-dimensional radial multi-gradient-echo techniques for dynamic R*(2)-corrected R(1) mapping based on the spoiled gradient recalled signal equation were implemented and validated at 4.7 T. The techniques were evaluated on phantoms and on a respiratory motion animated tumor model. R(1) measurements were validated with respect to a standard inversion-recovery spin-echo sequence in a four-compartment phantom covering a range of relaxation rates typically found in tumor tissue. In the range of [0.4, 3] sec(-1), R(1) differences were less than 10% for both two-dimensional and three-dimensional experiments. A dynamic contrast-enhanced MRI pilot study was performed on a colorectal tumor model subcutaneously implanted in mice at the abdominal level. Low motion sensitivity of radial acquisition allowed image recording without respiratory triggering. Three-dimensional K(trans) maps and significantly different mean K(trans) values were obtained for two contrast agents with different molecular weights. The radial multi-gradient-echo approach should be most useful for preclinical experimental conditions where the tissue of interest experiences physiologic motion, like spontaneous extracerebral tumors developed by transgenic mice, and where dynamic contrast-enhanced MRI is performed with high-relaxivity contrast agents.

Simultaneous dynamic T1 and T2* measurement for AIF assessment combined with DCE MRI in a mouse tumor model.

A double-delay SR-MGE-SNAP sequence allowing simultaneous T1 and T2* measurement was developed for integrating arterial input function (AIF) measurement into DCE MRI. Implemented on a 4.7-T animal MR system, this technique was applied to mice with colorectal tumor xenografts. AIF, measured in the mouse heart, was modeled by a bi-exponential function, whereas tumor K(trans) and v(e) parameter maps were obtained from analysis with a two- compartment model using an individually measured AIF. AIF analysis of T2*-corrected data yielded A1 = 9.2 +/- 4.3 kg/l, A(2) = 4.2 +/- 0.8 kg/l, m1 = 2.3 +/- 1.1 min(-1), and m2 = 0.05 +/- 0.02 min(-1). The mean initial plasma concentration C ( p )(t = 0) = 8.0 +/- 2.7 mM was compatible with estimated 8.6 mM. Without T2*-correction distribution phase parameters A1, m1, and C(p)(t = 0) were underestimated. In tumors, neglect of T2* effects yielded mean K(trans) values which were reduced by 14% (P < 0.05), whereas v(e) showed only a slight non-significant reduction. Simultaneous measurement of DeltaR1 and DeltaR2* studied in highly and poorly vascularized and (pre-)necrotic tumor regions revealed complementary behavior of both parameters with respect to vascular properties. In conclusion, the presented measurement technique is a promising tool for dynamic MRI applications studied in animal models at high field strengths and/or with CA of high relaxivities, as it combines classical DCE MRI integrating AIF assessment with dynamic T2* measurement.

Early effects of combretastatin A4 phosphate assessed by anatomic and carbogen-based functional magnetic resonance imaging on rat bladder tumors implanted in nude mice.

Combretastatin A4 phosphate (CA4P) causes rapid disruption of the tumor vasculature and is currently being evaluated for antivascular therapy. We describe the initial results obtained with a noninvasive multiparametric magnetic resonance imaging (MRI) approach to assess the early effects of CA4P on rat bladder tumors implanted on nude mice. MRI (4.7 T) comprised a fast spin-echo sequence for growth curve assessment; a multislice multiecho sequence for T2 measurement before, 15 minutes after, and 24 hours after CA4P (100 mg/kg); and a fast T2w* gradient-echo sequence to assess MR signal modification under carbogen breathing before, 35 minutes after, and 24 hours after CA4P. The tumor fraction with increased T2w* signal intensity under carbogen (T+) was used to quantify CA4P effect on functional vasculature. CA4P slowed tumor growth over 24 hours and accelerated necrosis development. T+ decrease was observed already at 35 minutes post-CA4P. Early T2 increase was observed in regions becoming necrotic at 24 hours post-CA4P, as confirmed by high T2 and histology. These regions exhibited, under carbogen, a switch from T2w* signal increase before CA4P to a decrease postCA4P. The combination of carbogen-based functional MRI and T2 measurement may be useful for the early follow-up of antivascular therapy without the administration of contrast agents.

Passive staining: a novel ex vivo MRI protocol to detect amyloid deposits in mouse models of Alzheimer's disease.

Amyloid plaques are one of the hallmarks of Alzheimer's disease (AD). This study evaluated a novel microMRI strategy based on "passive staining" of brain samples by gadoteric acid. The protocol was tested at 4.7 T on control animals and APP/PS1 mice modeling AD lesions. T(1) was strongly decreased in passively stained brains. On high-resolution 3D gradient echo images, the contrast between the cortex and subcortical structures was highly improved due to a T2* effect. The brains of APP/PS1 mice revealed plaques as hypo-intense spots. They appeared larger in long compared to short TE images. This suggests that, after passive staining, plaques caused a susceptibility effect. This easily performed protocol is a complementary method to classic histology to detect the 3D location of plaques. It may also be used for the validation of in vivo MRI protocols for plaque detection by facilitating registration with histology via post mortem MRI.

Morphological and carbogen-based functional MRI of a chemically induced liver tumor model in mice.

A multifocal mouse liver tumor model chemically induced with 5,9-dimethyl-7H-dibenzo[c,g]carbazole was investigated by respiratory-triggered morphological and functional MRI (fMRI) at 4.7 Tesla. The model is characterized by the presence of two tumor types: hypovascular cholangioma and vascularized hepatocellular carcinoma (HCC). Growth curves measured by 3D-MRI showed limited growth of cholangiomas and rapid growth of HCCs after a latency of about 25 weeks. Functional imaging based on T(2) (*)-weighted fast gradient-echo MRI and carbogen breathing was optimized for liver imaging in mice. A response to carbogen was observed in HCCs but not in cholangiomas. Transversal analysis (50 HCCs) of signal change upon carbogen revealed four different types of response patterns: 1) signal increase upon carbogen administration (74%); 2) small or insignificant signal change (10%), 3) transient signal decrease and delayed increase (8%), and 4) signal decrease (8%). Longitudinal follow-up of a subgroup (N = 17) showed that an initially observed type 1 response, attesting to the presence of a functional vasculature, remained stable for at least 3 weeks in 14 HCCs. A switch from a type 1 response to another response type may be useful for demonstrating, in a noninvasive manner, a disturbance of tumor vasculature induced by anti-vascular or anti-angiogenic therapy.