Laboratory cryo soft X-ray microscopy

Lens-based water-window X-ray microscopy allows two- and three-dimensional (2D and 3D) imaging of intact unstained cells in their near-native state with unprecedented contrast and resolution. Cryofixation is essential to avoid radiation damage to the sample. Present cryo X-ray microscopes rely on synchrotron radiation sources, thereby limiting the accessibility for a wider community of biologists. In the present paper we demonstrate water-window cryo X-ray microscopy with a laboratory-source-based arrangement. The microscope relies on a λ=2.48-nm liquid-jet high-brightness laser-plasma source, normal-incidence multilayer condenser optics, 30-nm zone-plate optics, and a cryo sample chamber. We demonstrate 2D imaging of test patterns, and intact unstained yeast, protozoan parasites and mammalian cells. Overview 3D information is obtained by stereo imaging while complete 3D microscopy is provided by full tomographic reconstruction. The laboratory microscope image quality approaches that of the synchrotron microscopes, but with longer exposure times. The experimental image quality is analyzed from a numerical wave-propagation model of the imaging system and a path to reach synchrotron-like exposure times in laboratory microscopy is outlined.

Laboratory soft-x-ray microscope for cryotomography of biological specimens

Soft-x-ray cryotomography allows quantitative and high-resolution three-dimensional imaging of intact unstained cells. To date, the method relies on synchrotron-radiation sources, which limits accessibility for researchers. Here we present a laboratory water-window microscope for cryotomography. It is based on a λ=2.48 nm liquid-jet laser-plasma source, a normal-incidence multilayer condenser, a 30 nm zone-plate objective, and a cryotilt sample holder. We demonstrate high-resolution imaging, as well as quantitative tomographic imaging, of frozen intact cells. The reconstructed tomogram of the intracellular local absorption coefficient shows details down to ∼100 nm.

Numerical model for tomographic image formation in transmission x-ray microscopy

We present a numerical image-formation model for investigating the influence of partial coherence, sample thickness and depth-of-focus on the accuracy of tomographic reconstructions in transmission x-ray microscopes. The model combines wave propagation through the object by finite difference techniques with Fourier methods. We include a ray-tracing model to analyse the origin of detrimental stray light in zone plate-based x-ray microscopes. These models allow optimization of x-ray microscopy systems for quantitative tomographic imaging of thick objects. Results show that both the depth-of-focus and the reconstructed local absorption coefficient are highly dependent on the degree of coherence of the optical system.

Prediction of Metastasis in Node-Negative, Hormone Receptor Positive, Tamoxifen Adjuvant Treated Primary Breast Cancer Patients Using Ki-67 (IHC) and RT-PCR Based 14-Gene Prognostic Signature

Background: Risk estimation based on the recommendations of St. Gallen Consensus commonly decides for additional cytostatic therapy in node-negative (N-), hormone receptor positive (HR+) primary breast cancer patients. High proliferative activity in the HR+ subtype confers a 19-fold relative risk of relapse compared with HR+ tumors of low proliferative activity. Furthermore immunohistochemically determined Ki-67 is characterized as a Luminal B marker that identifies a high risk subgroup in HR+, N- breast cancer patients.Aim of this investigation was to compare risk estimation using Ki-67 (%) with the results of a RT-PCR based multi-gene prognostic signature. Methods: Tumor tissues of totally 321 unselected primary breast cancer patients were formalin fixed and routinely processed for immunohistochemical determination and scored for protein expression of ER, PgR and Ki-67. HER2 was determined using dd-PCR. Content of both hormone receptors and proliferation activity were evaluated counting positively coloured nuclei from at least 100 tumor cells. The median follow up was 61 months. To calculate the cut off for high proliferation Ki-67 values were subjected to a log rank CART analysis. High proliferation was defined by Ki-67 of 19% and more. With this cut off it was possible to distinguish significantly various patient cohorts (N-, pT1, postmenopausal) into two different risk groups regarding metastasis free survival. The definition of low risk was low proliferation and HER2 negativity, of high risk high proliferation or HER2 positivity. The risk for metastasis of 16 new primary breast cancer patients was estimated based on two surrogate risk groups and the multi-gene prognostic signature. Results: Tamoxifen adjuvant treated HR+, HER2-, low proliferating (Ki-67 <19%), N- low risk patients (N= 68) and HR+, HER2-, high proliferating/HR+, HER2+, N- high risk patients (N= 84) showed a recurrence rate of 2.94% and 27.4%, respectively (P< .000). In the ongoing observation study all 5 low proliferating HER2- tumors had a low risk gene prognostic signature. From 11 high proliferating HER2- patients one patient had a low risk gene signature (9%), 3 patients a moderate risk gene signature (27%) and 7 patients a high risk gene signature (64%). Conclusion: Despite the small number of patients investigated up to now (N= 16) the preliminary results appear to show that low proliferative activity is associated with a low risk gene prognostic signature, whereas high proliferation means only in part a high risk gene prognostic signature.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 6025.

Gene Expression Profiling for Therapy Prediction in a Breast Cancer Neoadjuvant Therapy Study Applying Docetaxel/Epirubicin/Cyclophosphamide

Background: Gene expression profiling is a powerful tool to identify markers associated with clinical and therapy outcome of cancer patients. Prediction of the response to neoadjuvant regimens remains a persistent challenge. Aim of this ongoing study is the development of a gene set predicting the response of the tumor to a taxane- anthracycline based neoadjuvant chemotherapy.Material and Methods: Microarray expression profiling was performed on biopsy samples from patients before treatment using Human Genome Survey microarrays (HGSM). The protocol for a phase II study was elaborated for the treatment of breast cancer patients suffering from a primary tumor 1.5 cm or inflammatory breast cancer with Docetaxel/Epirubicin/Cyclophosphamide (TEC) prior to surgical treatment. The study was approved by the local ethical committee and all patients signed an informed consent.Results: Overall 80 patients have been enrolled in the presented study. High quality gene expression data were available from 58 patients. Of these patients 21 responded to the TEC regimen (pCR or MIB1 expressing cells in the residual tumor <= 5% and decrease of Mib1-expression >= 20%). Based on the gene-expression profile we were able to identify a preliminary gene set of 150 genes which allows us to separate responding tumors from the non responding ones based on their gene expression profile. A comparable separation of the groups could not achieved by established tumor markers, e.g. ER, PgR, HER2, uPA etc. which are measured simultaneously on the HGSM. Among the genes distinguishing the two groups several genes normally expressed in mononuclear blood cells were identified, pointing to the presence of tumor infiltrating leukocytes, predominantly in the tumors responding the TEC regimen. The presence of these cells has already been verified in a subset of the samples.Conclusion: We identified a gene set which allows to select patients who will benefit from neoadjuvant chemotherapy. Furthermore at least in the so far investigated samples tumor infiltrating leukocytes are significantly more often found in tumors which respond to a taxane- anthracycline based neoadjuvant chemotherapy.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 2039.

Sub-25-nm laboratory x-ray microscopy using a compound Fresnel zone plate

Improving the resolution in x-ray microscopes is of high priority to enable future applications in nanoscience. However, high-resolution zone-plate optics often have low efficiency, which makes implementation in laboratory microscopes difficult. We present a laboratory x-ray microscope based on a compound zone plate. The compound zone plate utilizes multiple diffraction orders to achieve high resolution while maintaining reasonable efficiency. We analyze the illumination conditions necessary for this type of optics in order to suppress stray light and demonstrate microscopic imaging resolving 25 nm features.

High-resolution computed tomography with a compact soft x-ray microscope

Computed tomography based on high-resolution soft x-ray microscopy utilizes the natural contrast for biological specimens provided by the water window (lambda = 2.4 - 4.4 nm) and the high resolving power of zone plate objectives. It is capable of revealing the 3D structure of biological specimens at sub-visible-microscopic resolution. To date, the technique has only been available at synchrotron-based microscopes, which limits the researchers access. In the present paper we demonstrate high-resolution soft x-ray tomography with a laboratory zone-plate-based soft x-ray microscope. The specimen, a diatom mounted on a glass capillary, was reconstructed from a tilt series of 53 images covering 180 degrees using a filtered back projection algorithm. The resolution of the tomogram was estimated to a half period of 140 nm using a differential-phase-residual method. Cryo-fixation, increased source brightness and extended-depth-of-focus objectives are important for pushing the resolution of compact systems for biological samples.

Compact Zernike phase contrast x-ray microscopy using a single-element optic

We demonstrate Zernike phase contrast in a compact soft x-ray microscope using a single-element optic. The optic is a combined imaging zone plate and a Zernike phase plate and does not require any additional alignment or components. Contrast is increased and inversed in an image of a test object using the Zernike zone plate. This type of optic may be implemented into any existing x-ray microscope where phase contrast is of interest.

Theoretical development of a high-resolution differential-interference-contrast optic for x-ray microscopy

In this paper, the theoretical background and development of a differential-interference contrast (DIC) x-ray optic is presented. The single-element optic is capable of high-resolution phase contrast imaging and is compatible with compact sources. It is shown that an understanding of the coherence requirements in this type of imaging is imperative and is explained in detail. The optic is capable of a wavefront separation equal to the resolution of the optic which places only minor constraints on the object illumination.

A 9 keV electron-impact liquid-gallium-jet x-ray source

We demonstrate a high-brightness compact 9 keV electron-impact microfocus x-ray source based on a liquid-gallium-jet anode. A approximately 30 W, 50 kV electron gun is focused onto the approximately 20 ms, 30 mum diameter liquid-gallium-jet anode to produce an approximately 10 microm full width at half maximum x-ray spot. The peak spectral brightness is >2 x 10(10) photons(s mm(2) mrad(2)x0.1% BW). Calculation and experiments show potential for increasing this brightness by approximately three orders of magnitude, making the source suitable for laboratory-scale x-ray crystallography and hard x-ray microscopy.

Simulation of partially coherent image formation in a compact soft X-ray microscope

In this paper, we describe a numerical method of simulating two-dimensional images in a compact soft X-ray microscope using partially coherent illumination considerations. The work was motivated by recent test object images obtained by the latest generation in-house compact soft X-ray microscope, which showed diffraction-like artifacts not observed previously. The numerical model approximates the condenser zone plate as a secondary incoherent source represented by individually coherent but mutually incoherent source points, each giving rise to a separate image. A final image is obtained by adding up all the individual source point contributions. The results are compared with the microscope images and show qualitative agreement, indicating that the observed effects are caused by partially coherent illumination.

Semi-quantitative gene expression profiling for therapy prediction in a breast cancer neoadjuvant therapy study applying docetaxel/epirubicin/cyclophosphamide

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Background: More than 28000 curated human genes can be analyzed semi-quantitatively using a chemiluminescent detection technology and 60mer oligonucleotides on a Human Genome Survey Microarray (HGSM, Applied Biosytems). Methods: HGSM expression profiling was performed on biopsy samplesfrom a setting of patients under neoadjuvant treatment. The protocol for a phase II study was elaborated for the treatment of breast cancer patients suffering from a primary tumor > 1,5 cm or inflammatory breast cancer with Docetaxel / Epirubicin/Cyclophosphamide (TEC) prior to surgical treatment. The study was approved by the local ethical committee and 80 patients will be included into the study after written informed consent. 40 patients have been already included in the ongoing study. In this prospective study a biopsy from the tumor is taken before chemotherapy. Therefore, success of treatment is detectable directly at the operated residual tumor. Our results demonstrate a low rate of false-positives (1.2%), a high specificity and quantification accuracy of HGSM system. Comparison of data from HGSM and RT-PCR obtained on mRNA from fresh frozen tissue resulted a Pearson-correlation of 0.92 to 0.63 for the breast cancer genes. Results: Tumour response (pCR, pPR) of more than 70 % can be achieved using neoadjuvant TEC- regimen. 25 % of pCR in this study is comparable with data of other published neoadjuvant trails. First expression profiling results are obtainable showing that a subset of 148 genes indicates patients with complete remission (pCR, no detectable tumor at end of chemotherapy), partial remission (pPR) and progressive disease (pPD). Remarkable, that the expression profile clearly separated pCR and pPD tumors whereas pPR tumors presented with a closer relationship to pPD tumors than to pCR tumors but displayed small specific subprofiles. A comparable separation of the groups could not achieved by established tumor markers, e.g. ER, PgR, HER2, uPA etc. which are measured simultaneously on the HGSM. Conclusions: HGSM expression profiling is promising to have the potential to figure out genes that are related to cancer progression and chemotherapy resistance, especially in PST.

No significant financial relationships to disclose.

Laboratory arrangement for soft x-ray zone plate efficiency measurements

We demonstrate a laboratory-scale arrangement for rapid and accurate measurements of the absolute and local efficiency of soft x-ray micro zone plates in the water window. This in-house instrument is based on a single-line lambda = 2.88 nm liquid-jet laser-plasma source. Measurements are performed by a simultaneous comparison of first diffraction-order photon flux with the flux in a calibrated reference signal. This arrangement eliminates existing source emission fluctuations. The performance of the method is demonstrated by the result from measurements of two approximately 55 microm diameter nickel micro zone plates, showing a groove efficiency of 12.9% +/- 1.1% and 11.7% +/- 1.0%. Furthermore, we show that spatially resolved efficiency mapping is an effective tool for a detailed characterization of local zone plate properties. Thus, this laboratory-scale instrument allows rapid feedback to the fabrication process which is important for future improvements.

Whole genome expression analysis for biologic rational pathway modeling: application in cancer prognosis and therapy prediction

Using semi-quantitative microarray technology, almost every one of the approximately 30 000 human genes can be analyzed simultaneously with a low rate of false-positives, a high specificity, and a high quantification accuracy. This is supported by data from comparative studies of microarrays and reverse-transcription PCR for established cancer genes including those for epidermal growth factor receptor (EGFR), human epidermal growth factor receptor-2 (HER2/ERBB2), estrogen receptor (ESR1), progesterone receptor (PGR), urokinase-type plasminogen activator (PLAU), and plasminogen activator inhibitor-1 (SERPINE1). As such, semi-quantitative expression data provide an almost completely comprehensive background of biological knowledge that can be applied to cancer diagnostics. In clinical terms, expression profiling may be able to provide significant information regarding (i) the identification of high-risk patients requiring aggressive chemotherapy; (ii) the pathway control of therapy predictive parameters (e.g. ESR1 and HER2); (iii) the discovery of targets for biologically rational therapeutics (e.g. capecitabine and trastuzumab); (iv) additional support for decisions about switching therapy; (v) target discovery; and (vi) the prediction of the course of new therapies in clinical trials. In conclusion, whole genome expression analysis might be able to determine important genes related to cancer progression and adjuvant chemotherapy resistance, especially in the context of new approaches involving primary systemic chemotherapy. In this review, we will survey the current progress in whole genome expression analyses for cancer prognosis and prediction. Special emphasis is given to the approach of combining biostatistical analysis of expression data with knowledge of biochemical and genetic pathways.

Medical Uses of Cosmetic Colored Contact Lenses

PURPOSE

To explore the clinical issues surrounding the use of hand-painted contact lenses for medical indications and to assess patient satisfaction with the use of these lenses for an unsightly eye.

METHODS

A questionnaire was sent to all patients visiting the contact lens department of Western Eye Hospital for a colored contact lens fitting during a 1-year period. The questionnaire related to patient satisfaction with the lenses and aspects of wear.

RESULTS

Replies were received from 25 of a total of 33 patients. The average wearing time was 11.3 hours per day. Most (88%) patients wore lenses for cosmetic reasons, and 12% wore lenses for cosmetic and refractive purposes. Satisfaction was 76% regarding lens comfort and 88% regarding lens color.

CONCLUSIONS

Provided lens care is satisfactory and the patient does not have unreasonable expectations, a tinted contact lens can be a useful device. In view of the cost implication, this is a valuable service provided by the hospital.

Therapy prediction in a breast cancer primary systemic chemotherapy (PST) study applying docetaxel/epirubicin/cyclophosphamide (TEC) by gene expression profiling

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Background: Currently there are no tests to assist in selecting the optimal PST regimen for breast cancer patients. Primary study goals of this prospective, single-armed multicentric investigation are pathologically confirmed tumor response and the rate of breast conserving therapy (BCT). Secondary goals are to find histopathologic and gene profiling patterns best correlating with tumor remission in a taxane- anthracycline based neoadjuvant setting as well as to evaluate cytostatic toxicity and quality of life. Methods: In this phase II study of totally 40 eligible patients with invasive breast cancer Human Genome Survey Microarray (HGSM) expression profiling is performed on jet-biopsy sample basis. The protocol was elaborated for the treatment of patients suffering from a primary tumor with 6 cycles of TEC (3-weekly) prior to the surgical treatment. The selection of predictor genes was done with BRB-ArrayTools Version 3.3 using a model based on the Compound Covariate Predictor, Diagonal Linear Discriminant Analysis, Nearest Neighbor Classification, and Support Vector Machines with linear kernel.We estimated the prediction error of each model using leave-one-out cross-validation (LOOCV) as described by Simon R. 2000 random permutations were used. Clustering was done using Cluster 3.0 and Java TreeView 1.0.12. Results: Tumor response (pCR, pPR) of more than 70% can be achieved using neoadjuvant TEC-regimen. 22% pCR (ypT0; ypN0) and 90% BCT in this study are comparable with data of other published PST trials. Preliminary expression profiling results reveal a subset of 148 genes that classifies all patients with a complete remission (pCR), in one cluster with a very closely related gene expression pattern (n=5; PPV = 100%). Furthermore 10 patients defined as responders due to selected MIB1-expression based criteria (expressing cells in the residual tumor ≤ 5% and a Δ MIB1-expression ≥ 20%) can be correctly classified in 9 of 10 cases. Comparable separation of the groups could not be achieved by established tumor factors. Conclusions: HGSM expression profiling is promising to have the potential to figure out genes that are related to chemotherapy response, especially in PST.

No significant financial relationships to disclose.